Laura A. Pace

All Publications

• Large-scale mutational analysis identifies UNC93B1 variants that drive TLR-mediated autoimmunity in mice and humans. The Journal of experimental medicine Rael, V. E., Yano, J. A., Huizar, J. P., Slayden, L. C., Weiss, M. A., Turcotte, E. A., Terry, J. M., Zuo, W., Thiffault, I., Pastinen, T., Farrow, E. G., Jenkins, J. L., Becker, M. L., Wong, S. C., Stevens, A. M., Otten, C., Allenspach, E. J., Bonner, D. E., Bernstein, J. A., Wheeler, M. T., Saxton, R. A., Undiagnosed Diseases Network, Liu, B., Majer, O., Barton, G. M., Acosta, M. T., Adams, D. R., Alvarez, R. L., Alvey, J., Allworth, A., Andrews, A., Ashley, E. A., Afzali, B., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Cassini, T., Chanprasert, S., Chao, H., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Delgado, M., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Fu, J., Gahl, W. A., Glass, I., Goddard, P. C., Godfrey, R. A., Gropman, A., Halley, M. C., Hamid, R., Hanchard, N., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Hutchison, S., Introne, W., Izumi, K., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Kaitryn, E., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Lewis, R. A., Liu, P., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A., Mahoney, R., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McConkie-Rosell, A., McCray, A. T., McGee, E., Might, M., Mikati, M., Miller, D., Mirzaa, G., Morava, E., Moretti, P., Morimoto, M., Mulvihill, J. J., Nakano-Okuno, M., Nelson, S. F., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Papp, J. C., Parker, N. H., Petcharet, L., Phillips, J. A., Posey, J. E., Potocki, L., Pusey Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenthal, E., Rossignol, F., Ruzhnikov, M., Sabaii, M., Sampson, J. B., Schedl, T., Schoch, K., Scott, D. A., Seto, E., Sharma, P., Shashi, V., Shelkowitz, E., Sheppeard, S., Shin, J., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, K. S., Solnica-Krezel, L., Solomon, B., Spillmann, R. C., Stergachis, A., Stoler, J. M., Sullivan, K., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, Q. K., Tan, A. L., Tarakad, A., Taylor, H., Tekin, M., Thorson, W., Tifft, C. J., Toro, C., Tran, A. A., Ungar, R. A., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Walley, N. M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Hubshman, M. W., Wener, M., Wenger, T., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Worley, K., Yamamoto, S., Zhang, Z., Zuchner, S. 2024; 221 (8)

  Abstract

  Nucleic acid-sensing Toll-like receptors (TLR) 3, 7/8, and 9 are key innate immune sensors whose activities must be tightly regulated to prevent systemic autoimmune or autoinflammatory disease or virus-associated immunopathology. Here, we report a systematic scanning-alanine mutagenesis screen of all cytosolic and luminal residues of the TLR chaperone protein UNC93B1, which identified both negative and positive regulatory regions affecting TLR3, TLR7, and TLR9 responses. We subsequently identified two families harboring heterozygous coding mutations in UNC93B1, UNC93B1+/T93I and UNC93B1+/R336C, both in key negative regulatory regions identified in our screen. These patients presented with cutaneous tumid lupus and juvenile idiopathic arthritis plus neuroinflammatory disease, respectively. Disruption of UNC93B1-mediated regulation by these mutations led to enhanced TLR7/8 responses, and both variants resulted in systemic autoimmune or inflammatory disease when introduced into mice via genome editing. Altogether, our results implicate the UNC93B1-TLR7/8 axis in human monogenic autoimmune diseases and provide a functional resource to assess the impact of yet-to-be-reported UNC93B1 mutations.

  View details for DOI 10.1084/jem.20232005

  View details for PubMedID 38780621

• Loss-of-function in RBBP5 results in a syndromic neurodevelopmental disorder associated with microcephaly. Genetics in medicine : official journal of the American College of Medical Genetics Huang, Y., Jay, K. L., Huang, A. Y., Wan, J., Jangam, S. V., Chorin, O., Rothschild, A., Barel, O., Mariani, M., Iascone, M., Xue, H., Huang, J., Mignot, C., Keren, B., Saillour, V., Mah-Som, A. Y., Sacharow, S., Rajabi, F., Costin, C., Yamamoto, S., Kanca, O., Bellen, H. J., Rosenfeld, J. A., Palmer, C. G., Nelson, S. F., Wangler, M. F., Martinez-Agosto, J. A. 2024: 101218

  Abstract

  Epigenetic dysregulation has been associated with many inherited disorders. RBBP5 (HGNC:9888) encodes a core member of the protein complex that methylates histone 3 lysine-4 (H3K4) and has not been implicated in human disease.We identify five unrelated individuals with de novo heterozygous variants in RBBP5. Three nonsense/frameshift and two missense variants were identified in probands with neurodevelopmental symptoms including global developmental delay, intellectual disability, microcephaly, and short stature. Here, we investigate the pathogenicity of the variants through protein structural analysis and transgenic Drosophila models.Both missense p.(T232I) and p.(E296D) variants affect evolutionarily conserved amino acids located at the interface between RBBP5 and the nucleosome. In Drosophila, overexpression analysis identifies partial loss-of-function mechanisms when the variants are expressed using the fly Rbbp5 or human RBBP5 cDNA. Loss of Rbbp5 leads to a reduction in brain size. The human reference or variant transgenes fail to rescue this loss and expression of either missense variant in an Rbbp5 null background results in a less severe microcephaly phenotype than the human reference, indicating both missense variants are partial loss-of-function alleles.Haploinsufficiency of RBBP5 observed through de novo null and hypomorphic loss-of-function variants is associated with a syndromic neurodevelopmental disorder.

  View details for DOI 10.1016/j.gim.2024.101218

  View details for PubMedID 39036895

• The Undiagnosed Diseases Network: Characteristics of solvable applicants and diagnostic suggestions for non-accepted ones. Genetics in medicine : official journal of the American College of Medical Genetics Mulvihill, J. J., Findley, L., Ni, W., Sinsheimer, J. S., Cole, F. S., Esteves, C., Bernstein, J. A., Newman, J. H., Wheeler, M. T., Mokry, J. R. 2024: 101203

  Abstract

  Can certain characteristics identify as solvable some undiagnosed patients who seek extensive evaluation and thorough record review, like by the Undiagnosed Diseases Network (UDN)?The UDN is a national research resource to solve medical mysteries through team science. Applicants provide informed consent to access to their medical records. After review, expert panels assess if applicants meet inclusion and exclusion criteria to select participants. When not accepting applicants, UDN experts may offer suggestions for diagnostic efforts. Using minimal information from initial applications, we compare features in applicants not accepted with those accepted and either solved or still not solved by the UDN. The diagnostic suggestions offered to non-accepted applicants and their clinicians were tallied.Non-accepted applicants were more often female, older at first symptoms and application, and longer in review than accepted applicants. The accepted and successfully diagnosed applicants were younger in ages, shorter in review time, more often non-white, of Hispanic ethnicity, and presenting with nervous system features. Half of non-accepted applicants were given suggestions for further local diagnostic evaluation. A few seemed to have two major diagnoses or a provocative environmental exposure history.Comprehensive UDN record review generates possibly helpful advice.

  View details for DOI 10.1016/j.gim.2024.101203

  View details for PubMedID 38967101

• Undiagnosed Disease Network collaborative approach in diagnosing rare disease in a patient with a mosaic CACNA1D variant. American journal of medical genetics. Part A Ezell, K. M., Tinker, R. J., Furuta, Y., Gulsevin, A., Bastarache, L., Hamid, R., Cogan, J. D., Rives, L., Neumann, S., Corner, B., Kozuria, M., Phillips, J. A. 2024; 194 (7): e63597

  Abstract

  The Undiagnosed Disease Network (UDN) is comprised of clinical and research experts collaborating to diagnose rare disease. The UDN is funded by the National Institutes of Health and includes 12 different clinical sites (About Us, 2022). Here we highlight the success of collaborative efforts within the UDN Clinical Site at Vanderbilt University Medical Center (VUMC) in utilizing a cohort of experts in bioinformatics, structural biology, and genetics specialists in diagnosing rare disease. Our UDN team identified a de novo mosaic CACNA1D variant c.2299T>C in a 5-year-old female with a history of global developmental delay, dystonia, dyskinesis, and seizures. Using a collaborative multidisciplinary approach, our VUMC UDN team diagnosed the participant with Primary Aldosteronism, Seizures, and Neurologic abnormalities (PASNA) OMIM: 615474 due to a rare mosaic CACNA1D variant (O'Neill, 2013). Interestingly, this patient was mosaic, a phenotypic trait previously unreported in PASNA cases. This report highlights the importance of a multidisciplinary approach in diagnosing rare disease.

  View details for DOI 10.1002/ajmg.a.63597

  View details for PubMedID 38511854

  View details for PubMedCentralID PMC11161305

• Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proceedings of the National Academy of Sciences of the United States of America Murali, R., Pace, L. A., Sanford, R. A., Ward, L. M., Lynes, M. M., Hatzenpichler, R., Lingappa, U. F., Fischer, W. W., Gennis, R. B., Hemp, J. 2024; 121 (26): e2316422121

  Abstract

  Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.

  View details for DOI 10.1073/pnas.2316422121

  View details for PubMedID 38900790

  View details for PubMedCentralID PMC11214002

• Reanalysis of RNA sequencing data ends diagnostic odyssey and expands the phenotypic spectrum of congenital titinopathy. American journal of medical genetics. Part A McNamee, L., Schoch, K., Huang, A., Lee, H., Wang, L. K., Smith, E. C., Lark, R. K., Buckley, A. F., Jobanputra, V., Nelson, S. F., Shashi, V. 2024: e63798

  Abstract

  Although next-generation sequencing has enabled diagnoses for many patients with Mendelian disorders, the majority remain undiagnosed. Here, we present a sibling pair who were clinically diagnosed with Escobar syndrome, however targeted gene testing was negative. Exome sequencing (ES), and later genome sequencing (GS), revealed compound heterozygous TTN variants in both siblings, a maternally inherited frameshift variant [(NM_133378.4):c.36812del; p.(Asp12271Valfs*10)], and a paternally inherited missense variant [(NM_133378.4):c.12322G > A; p.(Asp4108Asn)]. This result was considered nondiagnostic due to poor clinical fit and limited pathogenicity evidence for the missense variant of uncertain significance (VUS). Following initial nondiagnostic RNA sequencing (RNAseq) on muscle and further pursuit of other variants detected on the ES/GS, a reanalysis of noncanonical splice sites in the muscle transcriptome identified an out-of-frame exon retraction in TTN, near the known VUS. Interim literature included reports of patients with similar TTN variants who had phenotypic concordance with the siblings, and a diagnosis of a congenital titinopathy was given 4 years after the TTN variants had been initially reported. This report highlights the value of reanalysis of RNAseq with a different approach, expands the phenotypic spectrum of congenital titinopathy and also illustrates how a perceived phenotypic mismatch, and failure to consider known variants, can result in a prolongation of the diagnostic journey.

  View details for DOI 10.1002/ajmg.a.63798

  View details for PubMedID 38924341

• Dominant missense variants in SREBF2 are associated with complex dermatological, neurological, and skeletal abnormalities. Genetics in medicine : official journal of the American College of Medical Genetics Moulton, M. J., Atala, K., Zheng, Y., Dutta, D., Grange, D. K., Lin, W. W., Wegner, D. J., Wambach, J. A., Duker, A. L., Bober, M. B., Kratz, L., Wise, C. A., Oxendine, I., Khanshour, A., Wangler, M. F., Yamamoto, S., Cole, F. S., Rios, J., Bellen, H. J. 2024; 26 (9): 101174

  Abstract

  We identified 2 individuals with de novo variants in SREBF2 that disrupt a conserved site 1 protease (S1P) cleavage motif required for processing SREBP2 into its mature transcription factor. These individuals exhibit complex phenotypic manifestations that partially overlap with sterol regulatory element binding proteins (SREBP) pathway-related disease phenotypes, but SREBF2-related disease has not been previously reported. Thus, we set out to assess the effects of SREBF2 variants on SREBP pathway activation.We undertook ultrastructure and gene expression analyses using fibroblasts from an affected individual and utilized a fly model of lipid droplet (LD) formation to investigate the consequences of SREBF2 variants on SREBP pathway function.We observed reduced LD formation, endoplasmic reticulum expansion, accumulation of aberrant lysosomes, and deficits in SREBP2 target gene expression in fibroblasts from an affected individual, indicating that the SREBF2 variant inhibits SREBP pathway activation. Using our fly model, we discovered that SREBF2 variants fail to induce LD production and act in a dominant-negative manner, which can be rescued by overexpression of S1P.Taken together, these data reveal a mechanism by which SREBF2 pathogenic variants that disrupt the S1P cleavage motif cause disease via dominant-negative antagonism of S1P, limiting the cleavage of S1P targets, including SREBP1 and SREBP2.

  View details for DOI 10.1016/j.gim.2024.101174

  View details for PubMedID 38847193

• EFEMP1 haploinsufficiency causes a Marfan-like hereditary connective tissue disorder. American journal of medical genetics. Part A Forghani, I., Lang, S. H., Rodier, M. J., Bivona, S. A., Morales, A. A., Zuchner, S., Bademci, G., Tekin, M. 2024; 194 (6): e63556

  Abstract

  Phenotypic features of a hereditary connective tissue disorder, including craniofacial characteristics, hyperextensible skin, joint laxity, kyphoscoliosis, arachnodactyly, inguinal hernia, and diverticulosis associated with biallelic pathogenic variants in EFEMP1 have been previously described in four patients. Genome sequencing on a proband and her mother with comparable phenotypic features revealed that both patients were heterozygous for a stop-gain variant c.1084C>T (p.Arg362*). Complementary RNA-seq on fibroblasts revealed significantly reduced levels of mutant EFEMP1 transcript. Considering the absence of other molecular explanations, we extrapolated that EFEMP1 could be the cause of the patient's phenotypes. Furthermore, nonsense-mediated decay was demonstrated for the mutant allele as the principal mechanism for decreased levels of EFEMP1 mRNA. We provide strong clinical and genetic evidence for the haploinsufficiency of EFEMP1 due to nonsense-medicated decay to cause severe kyphoscoliosis, generalized hypermobility of joints, high and narrow arched palate, and potentially severe diverticulosis. To the best of our knowledge, this is the first report of an autosomal dominant EFEMP1-associated hereditary connective tissue disorder and therefore expands the phenotypic spectrum of EFEMP1 related disorders.

  View details for DOI 10.1002/ajmg.a.63556

  View details for PubMedID 38348595

  View details for PubMedCentralID PMC11060917

• Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder. Genetics in medicine : official journal of the American College of Medical Genetics Kohler, J. N., Legro, N. R., Baldridge, D., Shin, J., Bowman, A., Ugur, B., Jackstadt, M. M., Shriver, L. P., Patti, G. J., Zhang, B., Feng, W., McAdow, A. R., Goddard, P., Ungar, R. A., Jensen, T., Smith, K. S., Fresard, L., Alvarez, R., Bonner, D., Reuter, C. M., McCormack, C., Kravets, E., Marwaha, S., Holt, J. M., Worthey, E., Ashley, E. A., Montgomery, S. B., Fisher, P., Postlethwait, J., De Camilli, P., Solnica-Krezel, L., Bernstein, J. A., Wheeler, M. T. 2024: 101166

  Abstract

  The function of FAM177A1 and its relationship to human disease is largely unknown. Recent studies have demonstrated FAM177A1 to be a critical immune-associated gene. One previous case study has linked FAM177A1 to a neurodevelopmental disorder in four siblings.We identified five individuals from three unrelated families with biallelic variants in FAM177A1. The physiological function of FAM177A1 was studied in a zebrafish model organism and human cell lines with loss-of-function variants similar to the affected cohort.These individuals share a characteristic phenotype defined by macrocephaly, global developmental delay, intellectual disability, seizures, behavioral abnormalities, hypotonia, and gait disturbance. We show that FAM177A1 localizes to the Golgi complex in mammalian and zebrafish cells. Intersection of the RNA-seq and metabolomic datasets from FAM177A1-deficient human fibroblasts and whole zebrafish larvae demonstrated dysregulation of pathways associated with apoptosis, inflammation, and negative regulation of cell proliferation.Our data sheds light on the emerging function of FAM177A1 and defines FAM177A1-related neurodevelopmental disorder as a new clinical entity.

  View details for DOI 10.1016/j.gim.2024.101166

  View details for PubMedID 38767059

• Immunological and hematological findings as major features in a patient with a new germline pathogenic CBL variant. American journal of medical genetics. Part A Stellacci, E., Carter, J. N., Pannone, L., Stevenson, D., Moslehi, D., Venanzi, S., Bernstein, J. A., Tartaglia, M., Martinelli, S. 2024: e63627

  Abstract

  Casitas B-lineage lymphoma (CBL) encodes an adaptor protein with E3-ligase activity negatively controlling intracellular signaling downstream of receptor tyrosine kinases. Somatic CBL mutations play a driver role in a variety of cancers, particularly myeloid malignancies, whereas germline defects in the same gene underlie a RASopathy having clinical overlap with Noonan syndrome (NS) and predisposing to juvenile myelomonocytic leukemia and vasculitis. Other features of the disorder include cardiac defects, postnatal growth delay, cryptorchidism, facial dysmorphisms, and predisposition to develop autoimmune disorders. Here we report a novel CBL variant (c.1202G>T; p.Cys401Phe) occurring de novo in a subject with café-au-lait macules, feeding difficulties, mild dysmorphic features, psychomotor delay, autism spectrum disorder, thrombocytopenia, hepatosplenomegaly, and recurrent hypertransaminasemia. The identified variant affects an evolutionarily conserved residue located in the RING finger domain, a known mutational hot spot of both germline and somatic mutations. Functional studies documented enhanced EGF-induced ERK phosphorylation in transiently transfected COS1 cells. The present findings further support the association of pathogenic CBL variants with immunological and hematological manifestations in the context of a presentation with only minor findings reminiscent of NS or a clinically related RASopathy.

  View details for DOI 10.1002/ajmg.a.63627

  View details for PubMedID 38613168

• Recurrent ATP1A1 variant Gly903Arg causes developmental delay, intellectual disability, and autism. Annals of clinical and translational neurology Dohrn, M. F., Bademci, G., Rebelo, A. P., Jeanne, M., Borja, N. A., Beijer, D., Danzi, M. C., Bivona, S. A., Gueguen, P., Zafeer, M. F., Tekin, M., Züchner, S. 2024; 11 (4): 1075-1079

  Abstract

  ATP1A1 encodes a sodium-potassium ATPase that has been linked to several neurological diseases. Using exome and genome sequencing, we identified the heterozygous ATP1A1 variant NM_000701.8: c.2707G>A;p.(Gly903Arg) in two unrelated children presenting with delayed motor and speech development and autism. While absent in controls, the variant occurred de novo in one proband and co-segregated in two affected half-siblings, with mosaicism in the healthy mother. Using a specific ouabain resistance assay in mutant transfected HEK cells, we found significantly reduced cell viability. Demonstrating loss of ATPase function, we conclude that this novel variant is pathogenic, expanding the phenotype spectrum of ATP1A1.

  View details for DOI 10.1002/acn3.51963

  View details for PubMedID 38504481

  View details for PubMedCentralID PMC11021672

• De novo variants in DENND5B cause a neurodevelopmental disorder. American journal of human genetics Scala, M., Tomati, V., Ferla, M., Lena, M., Cohen, J. S., Fatemi, A., Brokamp, E., Bican, A., Phillips, J. A., Koziura, M. E., Nicouleau, M., Rio, M., Siquier, K., Boddaert, N., Musante, I., Tamburro, S., Baldassari, S., Iacomino, M., Scudieri, P., Rosenfeld, J. A., Bellus, G., Reed, S., Al Saif, H., Russo, R. S., Walsh, M. B., Cantagrel, V., Crunk, A., Gustincich, S., Ruggiero, S. M., Fitzgerald, M. P., Helbig, I., Striano, P., Severino, M., Salpietro, V., Pedemonte, N., Zara, F. 2024; 111 (3): 529-543

  Abstract

  The Rab family of guanosine triphosphatases (GTPases) includes key regulators of intracellular transport and membrane trafficking targeting specific steps in exocytic, endocytic, and recycling pathways. DENND5B (Rab6-interacting Protein 1B-like protein, R6IP1B) is the longest isoform of DENND5, an evolutionarily conserved DENN domain-containing guanine nucleotide exchange factor (GEF) that is highly expressed in the brain. Through exome sequencing and international matchmaking platforms, we identified five de novo variants in DENND5B in a cohort of five unrelated individuals with neurodevelopmental phenotypes featuring cognitive impairment, dysmorphism, abnormal behavior, variable epilepsy, white matter abnormalities, and cortical gyration defects. We used biochemical assays and confocal microscopy to assess the impact of DENND5B variants on protein accumulation and distribution. Then, exploiting fluorescent lipid cargoes coupled to high-content imaging and analysis in living cells, we investigated whether DENND5B variants affected the dynamics of vesicle-mediated intracellular transport of specific cargoes. We further generated an in silico model to investigate the consequences of DENND5B variants on the DENND5B-RAB39A interaction. Biochemical analysis showed decreased protein levels of DENND5B mutants in various cell types. Functional investigation of DENND5B variants revealed defective intracellular vesicle trafficking, with significant impairment of lipid uptake and distribution. Although none of the variants affected the DENND5B-RAB39A interface, all were predicted to disrupt protein folding. Overall, our findings indicate that DENND5B variants perturb intracellular membrane trafficking pathways and cause a complex neurodevelopmental syndrome with variable epilepsy and white matter involvement.

  View details for DOI 10.1016/j.ajhg.2024.02.001

  View details for PubMedID 38387458

  View details for PubMedCentralID PMC10940048

• Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis. Genetics in medicine : official journal of the American College of Medical Genetics Pucel, J., Briere, L. C., Reuter, C., Gochyyev, P., LeBlanc, K. 2024: 101115

  Abstract

  Exome (ES) and genome sequencing (GS) are increasingly being utilized for individuals with rare and undiagnosed diseases; however, guidelines on their use remain limited. This study aimed to identify factors associated with diagnosis by ES and/or GS in a heterogeneous population of patients with rare and undiagnosed diseases.In this case control study, we reviewed data from 400 diagnosed and 400 undiagnosed randomly selected participants in the Undiagnosed Diseases Network (UDN), all of whom had undergone ES and/or GS. We analyzed factors associated with receiving a diagnosis by ES and/or GS.Factors associated with a decreased odds of being diagnosed included adult symptom onset, singleton sequencing, and having undergone ES and/or GS prior to acceptance to the UDN (48%, 51%, and 32% lower odds, respectively). Factors that increased the odds of being diagnosed by ES and/or GS included having primarily neurological symptoms and having undergone prior chromosomal microarray testing (44% and 59% higher odds, respectively).We identified several factors that were associated with receiving a diagnosis by ES and/or GS. This will ideally inform the utilization of ES and/or GS and help manage expectations of individuals and families undergoing these tests.

  View details for DOI 10.1016/j.gim.2024.101115

  View details for PubMedID 38436216

• Recurring homozygous ACTN2 variant (p.Arg506Gly) causes a recessive myopathy. Annals of clinical and translational neurology Donkervoort, S., Mohassel, P., O'Leary, M., Bonner, D. E., Hartley, T., Acquaye, N., Brull, A., Mozaffar, T., Saporta, M. A., Dyment, D. A., Sampson, J. B., Pajusalu, S., Austin-Tse, C., Hurth, K., Cohen, J. S., McWalter, K., Warman-Chardon, J., Crunk, A., Foley, A. R., Mammen, A. L., Wheeler, M. T., O'Donnell-Luria, A., Bönnemann, C. G. 2024

  Abstract

  ACTN2, encoding alpha-actinin-2, is essential for cardiac and skeletal muscle sarcomeric function. ACTN2 variants are a known cause of cardiomyopathy without skeletal muscle involvement. Recently, specific dominant monoallelic variants were reported as a rare cause of core myopathy of variable clinical onset, although the pathomechanism remains to be elucidated. The possibility of a recessively inherited ACTN2-myopathy has also been proposed in a single series.We provide clinical, imaging, and histological characterization of a series of patients with a novel biallelic ACTN2 variant.We report seven patients from five families with a recurring biallelic variant in ACTN2: c.1516A>G (p.Arg506Gly), all manifesting with a consistent phenotype of asymmetric, progressive, proximal, and distal lower extremity predominant muscle weakness. None of the patients have cardiomyopathy or respiratory insufficiency. Notably, all patients report Palestinian ethnicity, suggesting a possible founder ACTN2 variant, which was confirmed through haplotype analysis in two families. Muscle biopsies reveal an underlying myopathic process with disruption of the intermyofibrillar architecture, Type I fiber predominance and atrophy. MRI of the lower extremities demonstrate a distinct pattern of asymmetric muscle involvement with selective involvement of the hamstrings and adductors in the thigh, and anterior tibial group and soleus in the lower leg. Using an in vitro splicing assay, we show that c.1516A>G ACTN2 does not impair normal splicing.This series further establishes ACTN2 as a muscle disease gene, now also including variants with a recessive inheritance mode, and expands the clinical spectrum of actinopathies to adult-onset progressive muscle disease.

  View details for DOI 10.1002/acn3.51983

  View details for PubMedID 38311799

• Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections. Genetics in medicine : official journal of the American College of Medical Genetics Jeffries, L., Mis, E. K., McWalter, K., Donkervoort, S., Brodsky, N. N., Carpier, J. M., Ji, W., Ionita, C., Roy, B., Morrow, J. S., Darbinyan, A., Iyer, K., Aul, R. B., Banka, S., Chao, K. R., Cobbold, L., Cohen, S., Custodio, H. M., Drummond-Borg, M., Elmslie, F., Finanger, E., Hainline, B. E., Helbig, I., Hewson, S., Hu, Y., Jackson, A., Josifova, D., Konstantino, M., Leach, M. E., Mak, B., McCormick, D., McGee, E., Nelson, S., Nguyen, J., Nugent, K., Ortega, L., Goodkin, H. P., Roeder, E., Roy, S., Sapp, K., Saade, D., Sisodiya, S. M., Stals, K., Towner, S., Wilson, W., Khokha, M. K., Bönnemann, C. G., Lucas, C. L., Lakhani, S. A. 2024; 26 (2): 101023

  Abstract

  We sought to delineate a multisystem disorder caused by recessive cysteine-rich with epidermal growth factor-like domains 1 (CRELD1) gene variants.The impact of CRELD1 variants was characterized through an international collaboration utilizing next-generation DNA sequencing, gene knockdown, and protein overexpression in Xenopus tropicalis, and in vitro analysis of patient immune cells.Biallelic variants in CRELD1 were found in 18 participants from 14 families. Affected individuals displayed an array of phenotypes involving developmental delay, early-onset epilepsy, and hypotonia, with about half demonstrating cardiac arrhythmias and some experiencing recurrent infections. Most harbored a frameshift in trans with a missense allele, with 1 recurrent variant, p.(Cys192Tyr), identified in 10 families. X tropicalis tadpoles with creld1 knockdown displayed developmental defects along with increased susceptibility to induced seizures compared with controls. Additionally, human CRELD1 harboring missense variants from affected individuals had reduced protein function, indicated by a diminished ability to induce craniofacial defects when overexpressed in X tropicalis. Finally, baseline analyses of peripheral blood mononuclear cells showed similar proportions of immune cell subtypes in patients compared with healthy donors.This patient cohort, combined with experimental data, provide evidence of a multisystem clinical syndrome mediated by recessive variants in CRELD1.

  View details for DOI 10.1016/j.gim.2023.101023

  View details for PubMedID 37947183

  View details for PubMedCentralID PMC10932913

• LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants. BMC genomics Lu, J., Toro, C., Adams, D. R., Moreno, C. A., Lee, W. P., Leung, Y. Y., Harms, M. B., Vardarajan, B., Heinzen, E. L. 2024; 25 (1): 115

  Abstract

  Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class.Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases.LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.

  View details for DOI 10.1186/s12864-023-09935-9

  View details for PubMedID 38279154

  View details for PubMedCentralID PMC10811831

• A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3. American journal of human genetics Paul, M. S., Michener, S. L., Pan, H., Chan, H., Pfliger, J. M., Rosenfeld, J. A., Lerma, V. C., Tran, A., Longley, M. A., Lewis, R. A., Weisz-Hubshman, M., Bekheirnia, M. R., Bekheirnia, N., Massingham, L., Zech, M., Wagner, M., Engels, H., Cremer, K., Mangold, E., Peters, S., Trautmann, J., Mester, J. L., Guillen Sacoto, M. J., Person, R., McDonnell, P. P., Cohen, S. R., Lusk, L., Cohen, A. S., Le Pichon, J. B., Pastinen, T., Zhou, D., Engleman, K., Racine, C., Faivre, L., Moutton, S., Denommé-Pichon, A. S., Koh, H. Y., Poduri, A., Bolton, J., Knopp, C., Julia Suh, D. S., Maier, A., Toosi, M. B., Karimiani, E. G., Maroofian, R., Schaefer, G. B., Ramakumaran, V., Vasudevan, P., Prasad, C., Osmond, M., Schuhmann, S., Vasileiou, G., Russ-Hall, S., Scheffer, I. E., Carvill, G. L., Mefford, H., Bacino, C. A., Lee, B. H., Chao, H. T. 2024; 111 (1): 96-118

  Abstract

  PPFIA3 encodes the protein-tyrosine phosphatase, receptor-type, F-polypeptide-interacting-protein-alpha-3 (PPFIA3), which is a member of the LAR-protein-tyrosine phosphatase-interacting-protein (liprin) family involved in synapse formation and function, synaptic vesicle transport, and presynaptic active zone assembly. The protein structure and function are evolutionarily well conserved, but human diseases related to PPFIA3 dysfunction are not yet reported in OMIM. Here, we report 20 individuals with rare PPFIA3 variants (19 heterozygous and 1 compound heterozygous) presenting with developmental delay, intellectual disability, hypotonia, dysmorphisms, microcephaly or macrocephaly, autistic features, and epilepsy with reduced penetrance. Seventeen unique PPFIA3 variants were detected in 18 families. To determine the pathogenicity of PPFIA3 variants in vivo, we generated transgenic fruit flies producing either human wild-type (WT) PPFIA3 or five missense variants using GAL4-UAS targeted gene expression systems. In the fly overexpression assays, we found that the PPFIA3 variants in the region encoding the N-terminal coiled-coil domain exhibited stronger phenotypes compared to those affecting the C-terminal region. In the loss-of-function fly assay, we show that the homozygous loss of fly Liprin-α leads to embryonic lethality. This lethality is partially rescued by the expression of human PPFIA3 WT, suggesting human PPFIA3 function is partially conserved in the fly. However, two of the tested variants failed to rescue the lethality at the larval stage and one variant failed to rescue lethality at the adult stage. Altogether, the human and fruit fly data reveal that the rare PPFIA3 variants are dominant-negative loss-of-function alleles that perturb multiple developmental processes and synapse formation.

  View details for DOI 10.1016/j.ajhg.2023.12.004

  View details for PubMedID 38181735

  View details for PubMedCentralID PMC10806447

• De novo missense variants in ZBTB47 are associated with developmental delays, hypotonia, seizures, gait abnormalities, and variable movement abnormalities. American journal of medical genetics. Part A Ward, S. K., Wadley, A., Tsai, C. A., Benke, P. J., Emrick, L., Fisher, K., Houck, K. M., Dai, H., Guillen Sacoto, M. J., Craigen, W., Glaser, K., Murdock, D. R., Rohena, L., Diderich, K. E., Bruggenwirth, H. T., Lee, B., Bacino, C., Burrage, L. C., Rosenfeld, J. A. 2024; 194 (1): 17-30

  Abstract

  The collection of known genetic etiologies of neurodevelopmental disorders continues to increase, including several syndromes associated with defects in zinc finger protein transcription factors (ZNFs) that vary in clinical severity from mild learning disabilities and developmental delay to refractory seizures and severe autism spectrum disorder. Here we describe a new neurodevelopmental disorder associated with variants in ZBTB47 (also known as ZNF651), which encodes zinc finger and BTB domain-containing protein 47. Exome sequencing (ES) was performed for five unrelated patients with neurodevelopmental disorders. All five patients are heterozygous for a de novo missense variant in ZBTB47, with p.(Glu680Gly) (c.2039A>G) detected in one patient and p.(Glu477Lys) (c.1429G>A) identified in the other four patients. Both variants impact conserved amino acid residues. Bioinformatic analysis of each variant is consistent with pathogenicity. We present five unrelated patients with de novo missense variants in ZBTB47 and a phenotype characterized by developmental delay with intellectual disability, seizures, hypotonia, gait abnormalities, and variable movement abnormalities. We propose that these variants in ZBTB47 are the basis of a new neurodevelopmental disorder.

  View details for DOI 10.1002/ajmg.a.63399

  View details for PubMedID 37743782

  View details for PubMedCentralID PMC11221546

• A medical odyssey of a 72-year-old man with Charcot-Marie-Tooth disease type 2 newly diagnosed with biallelic variants in SORD gene causing sorbitol dehydrogenase deficiency. American journal of medical genetics. Part A Furuta, Y., Nelson, E. T., Neumann, S. M., Phillips, J. A., Hamid, R., Tinker, R. J., Cogan, J. D., Rives, L., Newman, J. H. 2023; 191 (12): 2873-2877

  Abstract

  A 72-year-old man was referred to the Undiagnosed Diseases Network (UDN) because of gradual progressive weakness in both lower extremities for the past 45 years. He was initially diagnosed as having Charcot-Marie-Tooth disease type 2 (CMT2) without a defined molecular genetic cause. Exome sequencing (ES) failed to detect deleterious neuromuscular variants. Very recently, biallelic variants in sorbitol dehydrogenase (SORD) were discovered to be a novel cause of inherited neuropathies including CMT2 or distal hereditary motor neuropathy (dHMN) referred to as Sorbitol Dehydrogenase Deficiency with Peripheral Neuropathy (SORDD, OMIM 618912). The most common variant identified was c.757delG; p.A253Qfs*27. Through the Vanderbilt UDN clinical site, this patient was formally diagnosed with SORDD after the identification of homozygosity for the above SORD frameshift through UDN Genome Sequencing (GS). His medical odyssey was solved by GS and detection of extremely high levels of sorbitol. The diagnosis provided him the opportunity to receive potential treatment with an investigational drug in a clinical trial for SORDD. We suggest that similar studies be considered in other individuals thought to possibly have CMT2 or dHMN.

  View details for DOI 10.1002/ajmg.a.63383

  View details for PubMedID 37622199

• Assessment of comorbid symptoms in pediatric autonomic dysfunction. Clinical autonomic research : official journal of the Clinical Autonomic Research Society Tarbell, S. E., Olufs, E. L., Fischer, P. R., Chelimsky, G., Numan, M. T., Medow, M., Abdallah, H., Ahrens, S., Boris, J. R., Butler, I. J., Chelimsky, T. C., Coleby, C., Fortunato, J. E., Gavin, R., Gilden, J., Gonik, R., Klaas, K., Marsillio, L., Marriott, E., Pace, L. A., Pianosi, P., Simpson, P., Stewart, J., Van Waning, N., Weese-Mayer, D. E. 2023; 33 (6): 843-858

  Abstract

  Pediatric patients with autonomic dysfunction and orthostatic intolerance (OI) often present with co-existing symptoms and signs that might or might not directly relate to the autonomic nervous system. Our objective was to identify validated screening instruments to characterize these comorbidities and their impact on youth functioning.The Pediatric Assembly of the American Autonomic Society reviewed the current state of practice for identifying symptom comorbidities in youth with OI. The assembly includes physicians, physician-scientists, scientists, advanced practice providers, psychologists, and a statistician with expertise in pediatric disorders of OI. A total of 26 representatives from the various specialties engaged in iterative meetings to: (1) identify and then develop consensus on the symptoms to be assessed, (2) establish committees to review the literature for screening measures by member expertise, and (3) delineate the specific criteria for systematically evaluating the measures and for making measure recommendations by symptom domains.We review the measures evaluated and recommend one measure per system/concern so that assessment results from unrelated clinical centers are comparable. We have created a repository to apprise investigators of validated, vetted assessment tools to enhance comparisons across cohorts of youth with autonomic dysfunction and OI.This effort can facilitate collaboration among clinical settings to advance the science and clinical treatment of these youth. This effort is essential to improving management of these vulnerable patients as well as to comparing research findings from different centers.

  View details for DOI 10.1007/s10286-023-00984-4

  View details for PubMedID 37733160

  View details for PubMedCentralID 3904426

• Dominant negative variants in IKZF2 cause ICHAD syndrome, a new disorder characterised by immunodysregulation, craniofacial anomalies, hearing impairment, athelia and developmental delay. Journal of medical genetics Mohajeri, A., Vaseghi-Shanjani, M., Rosenfeld, J. A., Yang, G. X., Lu, H., Sharma, M., Lin, S., Salman, A., Waqas, M., Sababi Azamian, M., Worley, K. C., Del Bel, K. L., Kozak, F. K., Rahmanian, R., Biggs, C. M., Hildebrand, K. J., Lalani, S. R., Nicholas, S. K., Scott, D. A., Mostafavi, S., van Karnebeek, C., Henkelman, E., Halparin, J., Yang, C. L., Armstrong, L., Turvey, S. E., Lehman, A. 2023; 60 (11): 1092-1104

  Abstract

  Helios (encoded by IKZF2), a member of the Ikaros family of transcription factors, is a zinc finger protein involved in embryogenesis and immune function. Although predominantly recognised for its role in the development and function of T lymphocytes, particularly the CD4+ regulatory T cells (Tregs), the expression and function of Helios extends beyond the immune system. During embryogenesis, Helios is expressed in a wide range of tissues, making genetic variants that disrupt the function of Helios strong candidates for causing widespread immune-related and developmental abnormalities in humans.We performed detailed phenotypic, genomic and functional investigations on two unrelated individuals with a phenotype of immune dysregulation combined with syndromic features including craniofacial differences, sensorineural hearing loss and congenital abnormalities.Genome sequencing revealed de novo heterozygous variants that alter the critical DNA-binding zinc fingers (ZFs) of Helios. Proband 1 had a tandem duplication of ZFs 2 and 3 in the DNA-binding domain of Helios (p.Gly136_Ser191dup) and Proband 2 had a missense variant impacting one of the key residues for specific base recognition and DNA interaction in ZF2 of Helios (p.Gly153Arg). Functional studies confirmed that both these variant proteins are expressed and that they interfere with the ability of the wild-type Helios protein to perform its canonical function-repressing IL2 transcription activity-in a dominant negative manner.This study is the first to describe dominant negative IKZF2 variants. These variants cause a novel genetic syndrome characterised by immunodysregulation, craniofacial anomalies, hearing impairment, athelia and developmental delay.

  View details for DOI 10.1136/jmg-2022-109127

  View details for PubMedID 37316189

  View details for PubMedCentralID PMC11206234

• Genomics Research with Undiagnosed Children: Ethical Challenges at the Boundaries of Research and Clinical Care JOURNAL OF PEDIATRICS Halley, M. C., Young, J. L., Tang, C., Mintz, K. T., Lucas-Griffin, S., Maghiro, A., Ashley, E. A., Tabor, H. K., Undiagnosed Diseases Network 2023; 261

  View details for DOI 10.1018/j.jpeds.2023.113537

  View details for Web of Science ID 001029333600001

• Unraveling non-participation in genomic research: A complex interplay of barriers, facilitators, and sociocultural factors. Journal of genetic counseling McConkie-Rosell, A., Spillmann, R. C., Schoch, K., Sullivan, J. A., Walley, N., McDonald, M., Hooper, S. R., Shashi, V. 2023; 32 (5): 993-1008

  Abstract

  Although genomic research offering next-generation sequencing (NGS) has increased the diagnoses of rare/ultra-rare disorders, populations experiencing health disparities infrequently participate in these studies. The factors underlying non-participation would most reliably be ascertained from individuals who have had the opportunity to participate, but decline. We thus enrolled parents of children and adult probands with undiagnosed disorders who had declined genomic research offering NGS with return of results with undiagnosed disorders (Decliners, n = 21) and compared their data to those who participated (Participants, n = 31). We assessed: (1) practical barriers and facilitators, (2) sociocultural factors-genomic knowledge and distrust, and (3) the value placed upon a diagnosis by those who declined participation. The primary findings were that residence in rural and medically underserved areas (MUA) and higher number of barriers were significantly associated with declining participation in the study. Exploratory analyses revealed multiple co-occurring practical barriers, greater emotional exhaustion and research hesitancy in the parents in the Decliner group compared to the Participants, with both groups identifying a similar number of facilitators. The parents in the Decliner group also had lower genomic knowledge, but distrust of clinical research was not different between the groups. Importantly, despite their non-participation, those in the Decliner group indicated an interest in obtaining a diagnosis and expressed confidence in being able to emotionally manage the ensuing results. Study findings support the concept that some families who decline participation in diagnostic genomic research may be experiencing pile-up with exhaustion of family resources - making participation in the genomic research difficult. This study highlights the complexity of the factors that underlie non-participation in clinically relevant NGS research. Thus, approaches to mitigating barriers to NGS research participation by populations experiencing health disparities need to be multi-pronged and tailored so that they can benefit from state-of -the art genomic technologies.

  View details for DOI 10.1002/jgc4.1707

  View details for PubMedID 37005744

  View details for PubMedCentralID PMC10542653

• Full-length Isoform Sequencing for Resolving the Molecular Basis of Charcot-Marie-Tooth 2A. Neurology. Genetics Stergachis, A. B., Blue, E. E., Gillentine, M. A., Wang, L. K., Schwarze, U., Cortés, A. S., Ranchalis, J., Allworth, A., Bland, A. E., Chanprasert, S., Chen, J., Doherty, D., Folta, A. B., Glass, I., Horike-Pyne, M., Huang, A. Y., Khan, A. T., Leppig, K. A., Miller, D. E., Mirzaa, G., Parhin, A., Raskind, W. H., Rosenthal, E. A., Sheppeard, S., Strohbehn, S., Sybert, V. P., Tran, T. T., Wener, M. H., Byers, P. H., Nelson, S. F., Bamshad, M. J., Dipple, K. M., Jarvik, G. P., Hoppins, S., Hisama, F. M. 2023; 9 (5): e200090

  Abstract

  Transcript sequencing of patient-derived samples has been shown to improve the diagnostic yield for solving cases of suspected Mendelian conditions, yet the added benefit of full-length long-read transcript sequencing is largely unexplored.We applied short-read and full-length transcript sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis.We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts the branch point critical for intron 6 splicing. Full-length long-read isoform complementary DNA (cDNA) sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates 5 distinct altered splicing transcripts. All 5 altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A).This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.

  View details for DOI 10.1212/NXG.0000000000200090

  View details for PubMedID 37560121

  View details for PubMedCentralID PMC10409571

• Heterozygous rare variants in NR2F2 cause a recognizable multiple congenital anomaly syndrome with developmental delays. European journal of human genetics : EJHG Ganapathi, M., Matsuoka, L. S., March, M., Li, D., Brokamp, E., Benito-Sanz, S., White, S. M., Lachlan, K., Ahimaz, P., Sewda, A., Bastarache, L., Thomas-Wilson, A., Stoler, J. M., Bramswig, N. C., Baptista, J., Stals, K., Demurger, F., Cogne, B., Isidor, B., Bedeschi, M. F., Peron, A., Amiel, J., Zackai, E., Schacht, J. P., Iglesias, A. D., Morton, J., Schmetz, A., Seidel, V., Lucia, S., Baskin, S. M., Thiffault, I., Cogan, J. D., Gordon, C. T., Chung, W. K., Bowdin, S., Bhoj, E. 2023; 31 (10): 1117-1124

  Abstract

  Nuclear receptor subfamily 2 group F member 2 (NR2F2 or COUP-TF2) encodes a transcription factor which is expressed at high levels during mammalian development. Rare heterozygous Mendelian variants in NR2F2 were initially identified in individuals with congenital heart disease (CHD), then subsequently in cohorts of congenital diaphragmatic hernia (CDH) and 46,XX ovotesticular disorders/differences of sexual development (DSD); however, the phenotypic spectrum associated with pathogenic variants in NR2F2 remains poorly characterized. Currently, less than 40 individuals with heterozygous pathogenic variants in NR2F2 have been reported. Here, we review the clinical and molecular details of 17 previously unreported individuals with rare heterozygous NR2F2 variants, the majority of which were de novo. Clinical features were variable, including intrauterine growth restriction (IUGR), CHD, CDH, genital anomalies, DSD, developmental delays, hypotonia, feeding difficulties, failure to thrive, congenital and acquired microcephaly, dysmorphic facial features, renal failure, hearing loss, strabismus, asplenia, and vascular malformations, thus expanding the phenotypic spectrum associated with NR2F2 variants. The variants seen were predicted loss of function, including a nonsense variant inherited from a mildly affected mosaic mother, missense and a large deletion including the NR2F2 gene. Our study presents evidence for rare, heterozygous NR2F2 variants causing a highly variable syndrome of congenital anomalies, commonly associated with heart defects, developmental delays/intellectual disability, dysmorphic features, feeding difficulties, hypotonia, and genital anomalies. Based on the new and previous cases, we provide clinical recommendations for evaluating individuals diagnosed with an NR2F2-associated disorder.

  View details for DOI 10.1038/s41431-023-01434-5

  View details for PubMedID 37500725

  View details for PubMedCentralID PMC10545729

• The contribution of mosaicism to genetic diseases and de novo pathogenic variants. American journal of medical genetics. Part A Tinker, R. J., Bastarache, L., Ezell, K., Kobren, S. N., Esteves, C., Rosenfeld, J. A., Macnamara, E. F., Hamid, R., Cogan, J. D., Rinker, D., Mukharjee, S., Glass, I., Dipple, K., Phillips, J. A. 2023; 191 (10): 2482-2492

  Abstract

  The contribution of mosaicism to diagnosed genetic disease and presumed de novo variants (DNV) is under investigated. We determined the contribution of mosaic genetic disease (MGD) and diagnosed parental mosaicism (PM) in parents of offspring with reported DNV (in the same variant) in the (1) Undiagnosed Diseases Network (UDN) (N = 1946) and (2) in 12,472 individuals electronic health records (EHR) who underwent genetic testing at an academic medical center. In the UDN, we found 4.51% of diagnosed probands had MGD, and 2.86% of parents of those with DNV exhibited PM. In the EHR, we found 6.03% and 2.99% and (of diagnosed probands) had MGD detected on chromosomal microarray and exome/genome sequencing, respectively. We found 2.34% (of those with a presumed pathogenic DNV) had a parent with PM for the variant. We detected mosaicism (regardless of pathogenicity) in 4.49% of genetic tests performed. We found a broad phenotypic spectrum of MGD with previously unknown phenotypic phenomena. MGD is highly heterogeneous and provides a significant contribution to genetic diseases. Further work is required to improve the diagnosis of MGD and investigate how PM contributes to DNV risk.

  View details for DOI 10.1002/ajmg.a.63309

  View details for PubMedID 37246601

  View details for PubMedCentralID PMC11167532

• Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. bioRxiv : the preprint server for biology Vollger, M. R., Korlach, J., Eldred, K. C., Swanson, E., Underwood, J. G., Cheng, Y. H., Ranchalis, J., Mao, Y., Blue, E. E., Schwarze, U., Munson, K. M., Saunders, C. T., Wenger, A. M., Allworth, A., Chanprasert, S., Duerden, B. L., Glass, I., Horike-Pyne, M., Kim, M., Leppig, K. A., McLaughlin, I. J., Ogawa, J., Rosenthal, E. A., Sheppeard, S., Sherman, S. M., Strohbehn, S., Yuen, A. L., Reh, T. A., Byers, P. H., Bamshad, M. J., Hisama, F. M., Jarvik, G. P., Sancak, Y., Dipple, K. M., Stergachis, A. B. 2023

  Abstract

  Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA, PDK3, MAB21L1, and RB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four 'omes' to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.

  View details for DOI 10.1101/2023.09.26.559521

  View details for PubMedID 37808736

  View details for PubMedCentralID PMC10557686

• Parental perspectives of episodic irritability in an ultra-rare genetic disorder associated with NACC1. Orphanet journal of rare diseases Schoch, K., McConkie-Rosell, A., Walley, N., Bhambhani, V., Feyma, T., Pizoli, C. E., Smith, E. C., Tan, Q. K., Shashi, V. 2023; 18 (1): 269

  Abstract

  A recurrent de novo variant (c.892C>T) in NACC1 causes a neurodevelopmental disorder with epilepsy, cataracts, feeding difficulties, and delayed brain myelination (NECFM). An unusual and consistently reported feature is episodic extreme irritability and inconsolability. We now characterize these episodes, their impact on the family, and ascertain treatments that may be effective. Parents of 14 affected individuals provided narratives describing the irritability episodes, including triggers, behavioral and physiological changes, and treatments. Simultaneously, parents of 15 children completed the Non-communicating Children's Pain Checklist-Revised (NCCPC-R), a measure to assess pain in non-verbal children.The episodes of extreme irritability include a prodromal, peak, and resolving phase, with normal periods in between. The children were rated to have extreme pain-related behaviors on the NCCPC-R scale, although it is unknown whether the physiologic changes described by parents are caused by pain. Attempted treatments included various classes of medications, with psychotropic and sedative medications being most effective (7/15). Nearly all families (13/14) describe how the episodes have a profound impact on their lives.NECFM caused by the recurrent variant c.892C>T is associated with a universal feature of incapacitating episodic irritability of unclear etiology. Further understanding of the pathophysiology can lead to more effective therapeutic strategies.

  View details for DOI 10.1186/s13023-023-02891-3

  View details for PubMedID 37667351

  View details for PubMedCentralID PMC10476425

• Biallelic variants in ribonuclease inhibitor (RNH1), an inflammasome modulator, are associated with a distinctive subtype of acute, necrotizing encephalopathy. Genetics in medicine : official journal of the American College of Medical Genetics Shashi, V., Schoch, K., Ganetzky, R., Kranz, P. G., Sondheimer, N., Markert, M. L., Cope, H., Sadeghpour, A., Roehrs, P., Arbogast, T., Muraresku, C., Tyndall, A. V., Esser, M. J., Woodward, K. E., Ping-Yee Au, B., Parboosingh, J. S., Lamont, R. E., Bernier, F. P., Wright, N. A., Benseler, S. M., Parsons, S. J., El-Dairi, M., Smith, E. C., Valdez, P., Tennison, M., Innes, A. M., Davis, E. E. 2023; 25 (9): 100897

  Abstract

  Mendelian etiologies for acute encephalopathies in previously healthy children are poorly understood, with the exception of RAN binding protein 2 (RANBP2)-associated acute necrotizing encephalopathy subtype 1 (ANE1). We provide clinical, genetic, and neuroradiological evidence that biallelic variants in ribonuclease inhibitor (RNH1) confer susceptibility to a distinctive ANE subtype.This study aimed to evaluate clinical data, neuroradiological studies, genomic sequencing, and protein immunoblotting results in 8 children from 4 families who experienced acute febrile encephalopathy.All 8 healthy children became acutely encephalopathic during a viral/febrile illness and received a variety of immune modulation treatments. Long-term outcomes varied from death to severe neurologic deficits to normal outcomes. The neuroradiological findings overlapped with ANE but had distinguishing features. All affected children had biallelic predicted damaging variants in RNH1: a subset that was studied had undetectable RNH1 protein. Incomplete penetrance of the RNH1 variants was evident in 1 family.Biallelic variants in RNH1 confer susceptibility to a subtype of ANE (ANE2) in previously healthy children. Intensive immunological treatments may alter outcomes. Genomic sequencing in children with unexplained acute febrile encephalopathy can detect underlying genetic etiologies, such as RNH1, and improve outcomes in the probands and at-risk siblings.

  View details for DOI 10.1016/j.gim.2023.100897

  View details for PubMedID 37191094

  View details for PubMedCentralID PMC10506156

• A de novo missense variant in EZH1 associated with developmental delay exhibits functional deficits in Drosophila melanogaster. Genetics Jangam, S. V., Briere, L. C., Jay, K. L., Andrews, J. C., Walker, M. A., Rodan, L. H., High, F. A., Yamamoto, S., Sweetser, D. A., Wangler, M. F. 2023; 224 (4)

  Abstract

  EZH1, a polycomb repressive complex-2 component, is involved in a myriad of cellular processes. EZH1 represses transcription of downstream target genes through histone 3 lysine27 (H3K27) trimethylation (H3K27me3). Genetic variants in histone modifiers have been associated with developmental disorders, while EZH1 has not yet been linked to any human disease. However, the paralog EZH2 is associated with Weaver syndrome. Here we report a previously undiagnosed individual with a novel neurodevelopmental phenotype identified to have a de novo missense variant in EZH1 through exome sequencing. The individual presented in infancy with neurodevelopmental delay and hypotonia and was later noted to have proximal muscle weakness. The variant, p.A678G, is in the SET domain, known for its methyltransferase activity, and an analogous somatic or germline mutation in EZH2 has been reported in patients with B-cell lymphoma or Weaver syndrome, respectively. Human EZH1/2 are homologous to fly Enhancer of zeste (E(z)), an essential gene in Drosophila, and the affected residue (p.A678 in humans, p.A691 in flies) is conserved. To further study this variant, we obtained null alleles and generated transgenic flies expressing wildtype [E(z)WT] and the variant [E(z)A691G]. When expressed ubiquitously the variant rescues null-lethality similar to the wildtype. Overexpression of E(z)WT induces homeotic patterning defects but notably the E(z)A691G variant leads to dramatically stronger morphological phenotypes. We also note a dramatic loss of H3K27me2 and a corresponding increase in H3K27me3 in flies expressing E(z)A691G, suggesting this acts as a gain-of-function allele. In conclusion, here we present a novel EZH1 de novo variant associated with a neurodevelopmental disorder. Furthermore, we found that this variant has a functional impact in Drosophila.

  View details for DOI 10.1093/genetics/iyad110

  View details for PubMedID 37314226

  View details for PubMedCentralID PMC10411565

• Macrocephaly and developmental delay caused by missense variants in RAB5C HUMAN MOLECULAR GENETICS Koop, K., Yuan, W., Tessadori, F., Rodriguez-Polanco, W. R., Grubbs, J., Zhang, B., Osmond, M., Graham, G., Sawyer, S., Conboy, E., Vetrini, F., Treat, K., Ploski, R., Pienkowski, V., Klosowska, A., Fieg, E., Krier, J., Mallebranche, C., Alban, Z., Aldinger, K. A., Ritter, D., Macnamara, E., Sullivan, B., Herriges, J., Alaimo, J. T., Helbig, C., Ellis, C. A., van Eyk, C., Gecz, J., Farrugia, D., Osei-Owusu, I., Ades, L., van den Boogaard, M., Fuchs, S., Bakker, J., Duran, K., Dawson, Z. D., Lindsey, A., Huang, H., Baldridge, D., Silverman, G. A., Grant, B. D., Raizen, D., van Haaften, G., Pak, S. C., Rehmann, H., Schedl, T., van Hasselt, P., Undiagnosed Dis Network 2023: 3063-3077

  Abstract

  Rab GTPases are important regulators of intracellular vesicular trafficking. RAB5C is a member of the Rab GTPase family that plays an important role in the endocytic pathway, membrane protein recycling and signaling. Here we report on 12 individuals with nine different heterozygous de novo variants in RAB5C. All but one patient with missense variants (n = 9) exhibited macrocephaly, combined with mild-to-moderate developmental delay. Patients with loss of function variants (n = 2) had an apparently more severe clinical phenotype with refractory epilepsy and intellectual disability but a normal head circumference. Four missense variants were investigated experimentally. In vitro biochemical studies revealed that all four variants were damaging, resulting in increased nucleotide exchange rate, attenuated responsivity to guanine exchange factors and heterogeneous effects on interactions with effector proteins. Studies in C. elegans confirmed that all four variants were damaging in vivo and showed defects in endocytic pathway function. The variant heterozygotes displayed phenotypes that were not observed in null heterozygotes, with two shown to be through a dominant negative mechanism. Expression of the human RAB5C variants in zebrafish embryos resulted in defective development, further underscoring the damaging effects of the RAB5C variants. Our combined bioinformatic, in vitro and in vivo experimental studies and clinical data support the association of RAB5C missense variants with a neurodevelopmental disorder characterized by macrocephaly and mild-to-moderate developmental delay through disruption of the endocytic pathway.

  View details for DOI 10.1093/hmg/ddad130

  View details for Web of Science ID 001056475000001

  View details for PubMedID 37552066

  View details for PubMedCentralID PMC10586195

• De novo missense variants in phosphatidylinositol kinase PIP5KIγ underlie a neurodevelopmental syndrome associated with altered phosphoinositide signaling. American journal of human genetics Morleo, M., Venditti, R., Theodorou, E., Briere, L. C., Rosello, M., Tirozzi, A., Tammaro, R., Al-Badri, N., High, F. A., Shi, J., Putti, E., Ferrante, L., Cetrangolo, V., Torella, A., Walker, M. A., Tenconi, R., Iascone, M., Mei, D., Guerrini, R., van der Smagt, J., Kroes, H. Y., van Gassen, K. L., Bilal, M., Umair, M., Pingault, V., Attie-Bitach, T., Amiel, J., Ejaz, R., Rodan, L., Zollino, M., Agrawal, P. B., Del Bene, F., Nigro, V., Sweetser, D. A., Franco, B. 2023; 110 (8): 1377-1393

  Abstract

  Phosphoinositides (PIs) are membrane phospholipids produced through the local activity of PI kinases and phosphatases that selectively add or remove phosphate groups from the inositol head group. PIs control membrane composition and play key roles in many cellular processes including actin dynamics, endosomal trafficking, autophagy, and nuclear functions. Mutations in phosphatidylinositol 4,5 bisphosphate [PI(4,5)P2] phosphatases cause a broad spectrum of neurodevelopmental disorders such as Lowe and Joubert syndromes and congenital muscular dystrophy with cataracts and intellectual disability, which are thus associated with increased levels of PI(4,5)P2. Here, we describe a neurodevelopmental disorder associated with an increase in the production of PI(4,5)P2 and with PI-signaling dysfunction. We identified three de novo heterozygous missense variants in PIP5K1C, which encodes an isoform of the phosphatidylinositol 4-phosphate 5-kinase (PIP5KIγ), in nine unrelated children exhibiting intellectual disability, developmental delay, acquired microcephaly, seizures, visual abnormalities, and dysmorphic features. We provide evidence that the PIP5K1C variants result in an increase of the endosomal PI(4,5)P2 pool, giving rise to ectopic recruitment of filamentous actin at early endosomes (EEs) that in turn causes dysfunction in EE trafficking. In addition, we generated an in vivo zebrafish model that recapitulates the disorder we describe with developmental defects affecting the forebrain, including the eyes, as well as craniofacial abnormalities, further demonstrating the pathogenic effect of the PIP5K1C variants.

  View details for DOI 10.1016/j.ajhg.2023.06.012

  View details for PubMedID 37451268

  View details for PubMedCentralID PMC10432144

• Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. American journal of human genetics Calame, D. G., Guo, T., Wang, C., Garrett, L., Jolly, A., Dawood, M., Kurolap, A., Henig, N. Z., Fatih, J. M., Herman, I., Du, H., Mitani, T., Becker, L., Rathkolb, B., Gerlini, R., Seisenberger, C., Marschall, S., Hunter, J. V., Gerard, A., Heidlebaugh, A., Challman, T., Spillmann, R. C., Jhangiani, S. N., Coban-Akdemir, Z., Lalani, S., Liu, L., Revah-Politi, A., Iglesias, A., Guzman, E., Baugh, E., Boddaert, N., Rondeau, S., Ormieres, C., Barcia, G., Tan, Q. K., Thiffault, I., Pastinen, T., Sheikh, K., Biliciler, S., Mei, D., Melani, F., Shashi, V., Yaron, Y., Steele, M., Wakeling, E., Østergaard, E., Nazaryan-Petersen, L., Millan, F., Santiago-Sim, T., Thevenon, J., Bruel, A. L., Thauvin-Robinet, C., Popp, D., Platzer, K., Gawlinski, P., Wiszniewski, W., Marafi, D., Pehlivan, D., Posey, J. E., Gibbs, R. A., Gailus-Durner, V., Guerrini, R., Fuchs, H., Hrabě de Angelis, M., Hölter, S. M., Cheung, H. H., Gu, S., Lupski, J. R. 2023; 110 (8): 1394-1413

  Abstract

  DExD/H-box RNA helicases (DDX/DHX) are encoded by a large paralogous gene family; in a subset of these human helicase genes, pathogenic variation causes neurodevelopmental disorder (NDD) traits and cancer. DHX9 encodes a BRCA1-interacting nuclear helicase regulating transcription, R-loops, and homologous recombination and exhibits the highest mutational constraint of all DDX/DHX paralogs but remains unassociated with disease traits in OMIM. Using exome sequencing and family-based rare-variant analyses, we identified 20 individuals with de novo, ultra-rare, heterozygous missense or loss-of-function (LoF) DHX9 variant alleles. Phenotypes ranged from NDDs to the distal symmetric polyneuropathy axonal Charcot-Marie-Tooth disease (CMT2). Quantitative Human Phenotype Ontology (HPO) analysis demonstrated genotype-phenotype correlations with LoF variants causing mild NDD phenotypes and nuclear localization signal (NLS) missense variants causing severe NDD. We investigated DHX9 variant-associated cellular phenotypes in human cell lines. Whereas wild-type DHX9 was restricted to the nucleus, NLS missense variants abnormally accumulated in the cytoplasm. Fibroblasts from an individual with an NLS variant also showed abnormal cytoplasmic DHX9 accumulation. CMT2-associated missense variants caused aberrant nucleolar DHX9 accumulation, a phenomenon previously associated with cellular stress. Two NDD-associated variants, p.Gly411Glu and p.Arg761Gln, altered DHX9 ATPase activity. The severe NDD-associated variant p.Arg141Gln did not affect DHX9 localization but instead increased R-loop levels and double-stranded DNA breaks. Dhx9-/- mice exhibited hypoactivity in novel environments, tremor, and sensorineural hearing loss. All together, these results establish DHX9 as a critical regulator of mammalian neurodevelopment and neuronal homeostasis.

  View details for DOI 10.1016/j.ajhg.2023.06.013

  View details for PubMedID 37467750

  View details for PubMedCentralID PMC10432148

• HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder. American journal of human genetics Niggl, E., Bouman, A., Briere, L. C., Hoogenboezem, R. M., Wallaard, I., Park, J., Admard, J., Wilke, M., Harris-Mostert, E. D., Elgersma, M., Bain, J., Balasubramanian, M., Banka, S., Benke, P. J., Bertrand, M., Blesson, A. E., Clayton-Smith, J., Ellingford, J. M., Gillentine, M. A., Goodloe, D. H., Haack, T. B., Jain, M., Krantz, I., Luu, S. M., McPheron, M., Muss, C. L., Raible, S. E., Robin, N. H., Spiller, M., Starling, S., Sweetser, D. A., Thiffault, I., Vetrini, F., Witt, D., Woods, E., Zhou, D., Genomics England Research Consortium, Undiagnosed Diseases Network, Elgersma, Y., van Esbroeck, A. C., Ambrose, J. C., Arumugam, P., Bevers, R., Bleda, M., Boardman-Pretty, F., Boustred, C. R., Brittain, H., Brown, M. A., Caulfield, M. J., Chan, G. C., Giess, A., Griffin, J. N., Hamblin, A., Henderson, S., Hubbard, T. J., Jackson, R., Jones, L. J., Kasperaviciute, D., Kayikci, M., Kousathanas, A., Lahnstein, L., Lakey, A., Leigh, S. E., Leong, I. U., Lopez, F. J., Maleady-Crowe, F., McEntagart, M., Minneci, F., Mitchell, J., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A. C., O'Donovan, P., Odhams, C. A., Patch, C., Perez-Gil, D., Pereira, M. B., Pullinger, J., Rahim, T., Rendon, A., Rogers, T., Savage, K., Sawant, K., Scott, R. H., Siddiq, A., Sieghart, A., Smith, S. C., Sosinsky, A., Stuckey, A., Tanguy, M., Taylor Tavares, A. L., Thomas, E. R., Thompson, S. R., Tucci, A., Welland, M. J., Williams, E., Witkowska, K., Wood, S. M., Zarowiecki, M., Acosta, M. T., Adams, D. R., Alvarez, R. L., Alvey, J., Allworth, A., Andrews, A., Ashley, E. A., Afzali, B., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennet, J., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Chang, T. C., Chanprasert, S., Chao, H., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Delgado, M., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Fu, J., Gahl, W. A., Glass, I., Goddard, P. C., Godfrey, R. A., Grajewski, A., Halley, M. C., Hamid, R., Hanchard, N., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Kaitryn, E., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Levitt, R., Lewis, R. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A., Mahoney, R., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCray, A. T., McGee, E., Might, M., Miller, D., Mirzaa, G., Morava, E., Moretti, P., Morimoto, M., Mulvihill, J. J., Nakano-Okuno, M., Nelson, S. F., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Papp, J. C., Parker, N. H., Petcharet, L., Phillips, J. A., Posey, J. E., Potocki, L., Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenthal, E., Rossignol, F., Ruzhnikov, M., Sabaii, M., Sacco, R., Sampson, J. B., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, D. A., Seto, E., Sharma, P., Shashi, V., Shelkowitz, E., Sheppeard, S., Shin, J., Silverman, E., Sinsheimer, J., Sisco, K., Smith, E., Smith, K., Solnica-Krezel, L., Solomon, B., Spillmann, R., Stergachis, A., Stoler, J., Sullivan, K., Sullivan, J., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, Q. K., Tan, A. L., Tarakad, A., Tekin, M., Telischi, F., Thorson, W., Tifft, C., Toro, C., Tran, A. A., Ungar, R. A., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Walley, N. M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Weisz, M., Wener, M., Wenger, T., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Yamamoto, S., Zhang, Z., Zuchner, S. 2023; 110 (8): 1414-1435

  Abstract

  Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.

  View details for DOI 10.1016/j.ajhg.2023.07.005

  View details for PubMedID 37541189

• A humanized Caenorhabditis elegans model of hereditary spastic paraplegia-associated variants in KLC4. Disease models & mechanisms Gümüşderelioğlu, S., Resch, L., Brock, T., Luxton, G. W., Cope, H., Tan, Q. K., Hopkins, C., Starr, D. A. 2023; 16 (8)

  Abstract

  Hereditary spastic paraplegia (HSP) is a group of degenerative neurological disorders. We identified a variant in human kinesin light chain 4 (KLC4) that is suspected to be associated with autosomal-dominant HSP. How this and other variants relate to pathologies is unknown. We created a humanized Caenorhabditis elegans model in which klc-2 was replaced by human KLC4 (referred to as hKLC4) and assessed the extent to which hKLC4 retained function in the worm. We observed a slight decrease in motility but no nuclear migration defects in the humanized worms, suggesting that hKLC4 retains much of the function of klc-2. Five hKLC4 variants were introduced into the humanized model. The clinical variant led to early lethality, with significant defects in nuclear migration when homozygous and a weak nuclear migration defect when heterozygous, possibly correlating with the clinical finding of late-onset HSP when the proband was heterozygous. Thus, we were able to establish humanized C. elegans as an animal model for HSP and to use it to test the significance of five variants of uncertain significance in the human gene KLC4.

  View details for DOI 10.1242/dmm.050076

  View details for PubMedID 37565267

  View details for PubMedCentralID PMC10481945

• H4C5 missense variant leads to a neurodevelopmental phenotype overlapping with Angelman syndrome. American journal of medical genetics. Part A Borja, N., Borjas-Mendoza, P., Bivona, S., Peart, L., Gonzalez, J., Johnson, B. K., Guo, S., Yusupov, R., Bademci, G., Tekin, M. 2023; 191 (7): 1911-1916

  Abstract

  Recurrent de novo missense variants in H4 histone genes have recently been associated with a novel neurodevelopmental syndrome that is characterized by intellectual disability and developmental delay as well as more variable findings that include short stature, microcephaly, and facial dysmorphisms. A 4-year-old male with autism, developmental delay, microcephaly, and a happy demeanor underwent evaluation through the Undiagnosed Disease Network. He was clinically suspected to have Angelman syndrome; however, molecular testing was negative. Genome sequencing identified the H4 histone gene variant H4C5 NM_003545.4: c.295T>C, p.Tyr99His, which parental testing confirmed to be de novo. The variant met criteria for a likely pathogenic classification and is one of the seven known disease-causing missense variants in H4C5. A comparison of our proband's findings to the initial description of the H4-associated neurodevelopmental syndrome demonstrates that his phenotype closely matches the spectrum of those reported among the 29 affected individuals. As such, this report corroborates the delineation of neurodevelopmental syndrome caused by de novo missense H4 gene variants. Moreover, it suggests that cases of clinically suspected Angelman syndrome without molecular confirmation should undergo exome or genome sequencing, as novel neurodevelopmental syndromes with phenotypes overlapping with Angelman continue to be discovered.

  View details for DOI 10.1002/ajmg.a.63193

  View details for PubMedID 36987712

  View details for PubMedCentralID PMC10286100

• Neurologic involvement in seronegative primary Sjögren's syndrome with positive minor salivary gland biopsy: a single-center experience. Frontiers in neurology Hoshina, Y., Wong, K. H., Galli, J., Bacharach, R., Klein, J., Lebiedz-Odrobina, D., Rose, J. W., Trump, B., Hull, C., Greenlee, J. E., Clardy, S. L. 2023; 14: 1174116

  Abstract

  To assess the demographics, neurologic manifestations, comorbidities, and treatment of patients with seronegative primary Sjögren's syndrome (pSS).We conducted a retrospective chart review on patients with seronegative pSS evaluated by a neurologist at the University of Utah Health between January 2010 and October 2018. The diagnosis was based on characteristic symptoms, positive minor salivary gland biopsy according to the American-European Consensus Group 2002 criteria, and seronegative antibody status.Of 45 patients who met the study criteria, 42 (93.3%) were Caucasian, and 38 (84.4%) were female. The patients' mean age at diagnosis was 47.8 ± 12.6 (range 13-71) years. Paresthesia, numbness and dizziness, and headache were noted in 40 (88.9%), 39 (86.7%), and 36 patients (80.0%), respectively. Thirty-four patients underwent brain magnetic resonance imaging. Of these, 18 (52.9%) showed scattered nonspecific periventricular and subcortical cerebral white matter T2/fluid-attenuated inversion recovery hyperintense foci. Twenty-nine patients (64.4%) presented to the neurology clinic prior to pSS diagnosis, and the median delay in diagnosis from the first neurology clinic visit was 5 (interquartile ranges 2.0-20.5) months. Migraine and depression were the most common comorbidities in 31 patients (68.9%). Thirty-six patients received at least one immunotherapy, and 39 were on at least one medication for neuropathic pain.Patients often display various nonspecific neurological symptoms. Clinicians should express a high degree of skepticism regarding seronegative pSS and consider minor salivary gland biopsy to avoid delaying diagnosis, as undertreatment can affect patients' quality of life.

  View details for DOI 10.3389/fneur.2023.1174116

  View details for PubMedID 37360347

  View details for PubMedCentralID PMC10289021

• Genomics Research with Undiagnosed Children: Ethical Challenges at the Boundaries of Research and Clinical Care. The Journal of pediatrics Halley, M. C., Young, J. L., Tang, C., Mintz, K. T., Lucas-Griffin, S., Maghiro, A. S., Ashley, E. A., Tabor, H. K. 2023: 113537

  Abstract

  To explore the perspectives of parents of undiagnosed children enrolled in genomic diagnosis research regarding their motivations for enrolling their children, their understanding of the potential burdens and benefits, and the extent to which their experiences ultimately aligned with or diverged from their original expectations.In-depth interviews were conducted with parents, audio-recorded and transcribed. A structured codebook was applied to each transcript, after which iterative memoing was used to identify themes.Fifty-four parents participated, including 17 (31.5%) whose child received a diagnosis through research. Themes describing parents' expectations and experiences of genomic diagnosis research included: 1) the extent to which parents' motivations for participation focused on their hope that it would directly benefit their child; 2) the ways in which parents' frustrations regarding the research process confused the dual clinical and research goals of their participation; and 3) the limited clinical benefits parents ultimately experienced for their children.Our results suggest that parents of undiagnosed children seeking enrollment in genomic diagnosis research are at risk of a form of therapeutic misconception - in this case, diagnostic misconception. These findings indicate the need to examine the processes and procedures associated with this research in order to appropriately communicate and balance the potential burdens and benefits of study participation.

  View details for DOI 10.1016/j.jpeds.2023.113537

  View details for PubMedID 37271495

• Creating a data dictionary for pediatric autonomic disorders. Clinical autonomic research : official journal of the Clinical Autonomic Research Society Boris, J. R., Abdallah, H., Ahrens, S., Chelimsky, G., Chelimsky, T. C., Fischer, P. R., Fortunato, J. E., Gavin, R., Gilden, J. L., Gonik, R., Grubb, B. P., Klaas, K. M., Marriott, E., Marsillio, L. E., Medow, M. S., Norcliffe-Kaufmann, L., Numan, M. T., Olufs, E., Pace, L. A., Pianosi, P. T., Simpson, P., Stewart, J. M., Tarbell, S., Van Waning, N. R., Weese-Mayer, D. E. 2023; 33 (3): 301-377

  Abstract

  Whether evaluating patients clinically, documenting care in the electronic health record, performing research, or communicating with administrative agencies, the use of a common set of terms and definitions is vital to ensure appropriate use of language. At a 2017 meeting of the Pediatric Section of the American Autonomic Society, it was determined that an autonomic data dictionary comprising aspects of evaluation and management of pediatric patients with autonomic disorders would be an important resource for multiple stakeholders.Our group created the list of terms for the dictionary. Definitions were prioritized to be obtained from established sources with which to harmonize. Some definitions needed mild modification from original sources. The next tier of sources included published consensus statements, followed by Internet sources. In the absence of appropriate sources, we created a definition.A total of 589 terms were listed and defined in the dictionary. Terms were organized by Signs/Symptoms, Triggers, Co-morbid Disorders, Family History, Medications, Medical Devices, Physical Examination Findings, Testing, and Diagnoses.Creation of this data dictionary becomes the foundation of future clinical care and investigative research in pediatric autonomic disorders, and can be used as a building block for a subsequent adult autonomic data dictionary.

  View details for DOI 10.1007/s10286-023-00923-3

  View details for PubMedID 36800049

  View details for PubMedCentralID PMC9936127

• De novo variants in MRTFB have gain-of-function activity in Drosophila and are associated with a novel neurodevelopmental phenotype with dysmorphic features. Genetics in medicine : official journal of the American College of Medical Genetics Andrews, J. C., Mok, J. W., Kanca, O., Jangam, S., Tifft, C., Macnamara, E. F., Russell, B. E., Wang, L. K., Nelson, S. F., Bellen, H. J., Yamamoto, S., Malicdan, M. C., Wangler, M. F. 2023; 25 (6): 100833

  Abstract

  Myocardin-related transcription factor B (MRTFB) is an important transcriptional regulator, which promotes the activity of an estimated 300 genes but is not known to underlie a Mendelian disorder.Probands were identified through the efforts of the Undiagnosed Disease Network. Because the MRTFB protein is highly conserved between vertebrate and invertebrate model organisms, we generated a humanized Drosophila model expressing the human MRTFB protein in the same spatial and temporal pattern as the fly gene. Actin binding assays were used to validate the effect of the variants on MRTFB.Here, we report 2 pediatric probands with de novo variants in MRTFB (p.R104G and p.A91P) and mild dysmorphic features, intellectual disability, global developmental delays, speech apraxia, and impulse control issues. Expression of the variants within wing tissues of a fruit fly model resulted in changes in wing morphology. The MRTFBR104G and MRTFBA91P variants also display a decreased level of actin binding within critical RPEL domains, resulting in increased transcriptional activity and changes in the organization of the actin cytoskeleton.The MRTFBR104G and MRTFBA91P variants affect the regulation of the protein and underlie a novel neurodevelopmental disorder. Overall, our data suggest that these variants act as a gain of function.

  View details for DOI 10.1016/j.gim.2023.100833

  View details for PubMedID 37013900

• Dominant-negative variant in SLC1A4 causes an autosomal dominant epilepsy syndrome. Annals of clinical and translational neurology Pujol-Gimenez, J., Mirzaa, G., Blue, E. E., Albano, G., Miller, D. E., Allworth, A., Bennett, J. T., Byers, P. H., Chanprasert, S., Chen, J., Doherty, D., Folta, A. B., Gillentine, M. A., Glass, I., Hing, A., Horike-Pyne, M., Leppig, K. A., Parhin, A., Ranchalis, J., Raskind, W. H., Rosenthal, E. A., Schwarze, U., Sheppeard, S., Strohbehn, S., Sybert, V. P., Timms, A., Wener, M., University of Washington Center for Mendelian Genomics (UW-CMG)a, U. D., Bamshad, M. J., Hisama, F. M., Jarvik, G. P., Dipple, K. M., Hediger, M. A., Stergachis, A. B., Bamshad, M. J., Leal, S. M., Nickerson, D. A., Anderson, P., Bacus, T. J., Blue, E. E., Brower, K., Buckingham, K. J., Chong, J. X., Sanchez, D. C., Davis, C. P., Davis, C. J., Frazar, C. D., Gomeztagle-Burgess, K., Gordon, W. W., Horike-Pyne, M., Hurless, J. R., Jarvik, G. P., Johanson, E., Kolar, J. T., Marvin, C. T., McGee, S., McGoldrick, D. J., Mekonnen, B., Nielsen, P. M., Patterson, K., Radhakrishnan, A., Richardson, M. A., Roote, G. T., Ryke, E. L., Schrauwen, I., Shively, K. M., Smith, J. D., Tackett, M., Wang, G., Weiss, J. M., Wheeler, M. M., Yi, Q., Zhang, X., Acosta, M. T., Adam, M., Adams, D. R., Alvarez, R. L., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Chang, T. C., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Gahl, W. A., Glass, I., Gochuico, B., Goddard, P. C., Godfrey, R. A., Golden-Grant, K., Grajewski, A., Hadley, D., Hahn, S., Halley, M. C., Hamid, R., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Karaviti, L., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Levitt, R., Lewis, R. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A., Mahoney, R., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCray, A. T., McGee, E., Mefford, H., Merritt, J. L., Might, M., Mirzaa, G., Morava, E., Moretti, P., Mulvihill, J., Nakano-Okuno, M., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Pusey Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, D. A., Scott, C. R., Shashi, V., Shin, J., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solnica-Krezel, L., Solomon, B., Spillmann, R. C., Stoler, J. M., Sullivan, K., Sullivan, J. A., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, Q. K., Tan, A. L., Tekin, M., Telischi, F., Thorson, W., Tifft, C. J., Toro, C., Tran, A. A., Ungar, R. A., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Wallace, S., Walley, N. M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Hubshman, M. W., Wener, M., Wenger, T., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Worley, K., Xiao, C., Yamamoto, S., Yang, J., Zhang, Z., Zuchner, S. 2023

  Abstract

  SLC1A4 is a trimeric neutral amino acid transporter essential for shuttling L-serine from astrocytes into neurons. Individuals with biallelic variants in SLC1A4 are known to have spastic tetraplegia, thin corpus callosum, and progressive microcephaly (SPATCCM) syndrome, but individuals with heterozygous variants are not thought to have disease. We identify an 8-year-old patient with global developmental delay, spasticity, epilepsy, and microcephaly who has a de novo heterozygous three amino acid duplication in SLC1A4 (L86_M88dup). We demonstrate that L86_M88dup causes a dominant-negative N-glycosylation defect of SLC1A4, which in turn reduces the plasma membrane localization of SLC1A4 and the transport rate of SLC1A4 for L-serine.

  View details for DOI 10.1002/acn3.51786

  View details for PubMedID 37194416

• Bi-allelic variants in INTS11 are associated with a complex neurological disorder. American journal of human genetics Tepe, B., Macke, E. L., Niceta, M., Weisz Hubshman, M., Kanca, O., Schultz-Rogers, L., Zarate, Y. A., Schaefer, G. B., Granadillo De Luque, J. L., Wegner, D. J., Cogne, B., Gilbert-Dussardier, B., Le Guillou, X., Wagner, E. J., Pais, L. S., Neil, J. E., Mochida, G. H., Walsh, C. A., Magal, N., Drasinover, V., Shohat, M., Schwab, T., Schmitz, C., Clark, K., Fine, A., Lanpher, B., Gavrilova, R., Blanc, P., Burglen, L., Afenjar, A., Steel, D., Kurian, M. A., Prabhakar, P., Gößwein, S., Di Donato, N., Bertini, E. S., Wangler, M. F., Yamamoto, S., Tartaglia, M., Klee, E. W., Bellen, H. J. 2023; 110 (5): 774-789

  Abstract

  The Integrator complex is a multi-subunit protein complex that regulates the processing of nascent RNAs transcribed by RNA polymerase II (RNAPII), including small nuclear RNAs, enhancer RNAs, telomeric RNAs, viral RNAs, and protein-coding mRNAs. Integrator subunit 11 (INTS11) is the catalytic subunit that cleaves nascent RNAs, but, to date, mutations in this subunit have not been linked to human disease. Here, we describe 15 individuals from 10 unrelated families with bi-allelic variants in INTS11 who present with global developmental and language delay, intellectual disability, impaired motor development, and brain atrophy. Consistent with human observations, we find that the fly ortholog of INTS11, dIntS11, is essential and expressed in the central nervous systems in a subset of neurons and most glia in larval and adult stages. Using Drosophila as a model, we investigated the effect of seven variants. We found that two (p.Arg17Leu and p.His414Tyr) fail to rescue the lethality of null mutants, indicating that they are strong loss-of-function variants. Furthermore, we found that five variants (p.Gly55Ser, p.Leu138Phe, p.Lys396Glu, p.Val517Met, and p.Ile553Glu) rescue lethality but cause a shortened lifespan and bang sensitivity and affect locomotor activity, indicating that they are partial loss-of-function variants. Altogether, our results provide compelling evidence that integrity of the Integrator RNA endonuclease is critical for brain development.

  View details for DOI 10.1016/j.ajhg.2023.03.012

  View details for PubMedID 37054711

  View details for PubMedCentralID PMC10183469

• Loss-of-function variants in MYCBP2 cause neurobehavioural phenotypes and corpus callosum defects. Brain : a journal of neurology AlAbdi, L., Desbois, M., Rusnac, D. V., Sulaiman, R. A., Rosenfeld, J. A., Lalani, S., Murdock, D. R., Burrage, L. C., Billie Au, P. Y., Towner, S., Wilson, W. G., Wong, L., Brunet, T., Strobl-Wildemann, G., Burton, J. E., Hoganson, G., McWalter, K., Begtrup, A., Zarate, Y. A., Christensen, E. L., Opperman, K. J., Giles, A. C., Helaby, R., Kania, A., Zheng, N., Grill, B., Alkuraya, F. S. 2023; 146 (4): 1373-1387

  Abstract

  The corpus callosum is a bundle of axon fibres that connects the two hemispheres of the brain. Neurodevelopmental disorders that feature dysgenesis of the corpus callosum as a core phenotype offer a valuable window into pathology derived from abnormal axon development. Here, we describe a cohort of eight patients with a neurodevelopmental disorder characterized by a range of deficits including corpus callosum abnormalities, developmental delay, intellectual disability, epilepsy and autistic features. Each patient harboured a distinct de novo variant in MYCBP2, a gene encoding an atypical really interesting new gene (RING) ubiquitin ligase and signalling hub with evolutionarily conserved functions in axon development. We used CRISPR/Cas9 gene editing to introduce disease-associated variants into conserved residues in the Caenorhabditis elegans MYCBP2 orthologue, RPM-1, and evaluated functional outcomes in vivo. Consistent with variable phenotypes in patients with MYCBP2 variants, C. elegans carrying the corresponding human mutations in rpm-1 displayed axonal and behavioural abnormalities including altered habituation. Furthermore, abnormal axonal accumulation of the autophagy marker LGG-1/LC3 occurred in variants that affect RPM-1 ubiquitin ligase activity. Functional genetic outcomes from anatomical, cell biological and behavioural readouts indicate that MYCBP2 variants are likely to result in loss of function. Collectively, our results from multiple human patients and CRISPR gene editing with an in vivo animal model support a direct link between MYCBP2 and a human neurodevelopmental spectrum disorder that we term, MYCBP2-related developmental delay with corpus callosum defects (MDCD).

  View details for DOI 10.1093/brain/awac364

  View details for PubMedID 36200388

  View details for PubMedCentralID PMC10319777

• Participation in a national diagnostic research study: assessing the patient experience. Orphanet journal of rare diseases Rosenfeld, L. E., LeBlanc, K., Nagy, A., Ego, B. K., Undiagnosed Diseases Network, McCray, A. T., Acosta, M. T., Adam, M., Adams, D. R., Alvarez, R. L., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Chang, T. C., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cooper, C. M., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Gahl, W. A., Glass, I., Gochuico, B., Goddard, P. C., Godfrey, R. A., Golden-Grant, K., Grajewski, A., Hadley, D., Hahn, S., Halley, M. C., Hamid, R., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Karaviti, L., Kennedy, J., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., Lee, B. H., Levitt, R., Lewis, R. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Mahoney, R., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McGee, E., Mefford, H., Merritt, J. L., Might, M., Mirzaa, G., Morava, E., Moretti, P., Mulvihill, J., Nakano-Okuno, M., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, D. A., Scott, C. R., Shashi, V., Shin, J., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solem, E., Solnica-Krezel, L., Solomon, B., Spillmann, R. C., Stoler, J. M., Sullivan, K., Sullivan, J. A., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, Q. K., Tan, A. L., Tekin, M., Telischi, F., Thorson, W., Tifft, C. J., Toro, C., Tran, A. A., Ungar, R. A., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Wallace, S., Walley, N. M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Hubshman, M. W., Wener, M., Wenger, T., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Worley, K., Xiao, C., Yamamoto, S., Yang, J., Zhang, Z., Zuchner, S. 2023; 18 (1): 73

  Abstract

  INTRODUCTION: The Undiagnosed Diseases Network (UDN), a clinical research study funded by the National Institutes of Health, aims to provide answers for patients with undiagnosed conditions and generate knowledge about underlying disease mechanisms. UDN evaluations involve collaboration between clinicians and researchers and go beyond what is possible in clinical settings. While medical and research outcomes of UDN evaluations have been explored, this is the first formal assessment of the patient and caregiver experience.METHODS: We invited UDN participants and caregivers to participate in focus groups via email, newsletter, and a private participant Facebook group. We developed focus group questions based on research team expertise, literature focused on patients with rare and undiagnosed conditions, and UDN participant and family member feedback. In March 2021, we conducted, recorded, and transcribed four 60-min focus groups via Zoom. Transcripts were evaluated using a thematic analysis approach.RESULTS: The adult undiagnosed focus group described the UDN evaluation as validating and an avenue for access to medical providers. They also noted that the experience impacted professional choices and helped them rely on others for support. The adult diagnosed focus group described the healthcare system as not set up for rare disease. In the pediatric undiagnosed focus group, caregivers discussed a continued desire for information and gratitude for the UDN evaluation. They also described an ability to rule out information and coming to terms with not having answers. The pediatric diagnosed focus group discussed how the experience helped them focus on management and improved communication. Across focus groups, adults (undiagnosed/diagnosed) noted the comprehensiveness of the evaluation. Undiagnosed focus groups (adult/pediatric) discussed a desire for ongoing communication and care with the UDN. Diagnosed focus groups (adult/pediatric) highlighted the importance of the diagnosis they received in the UDN. The majority of the focus groups noted a positive future orientation after participation.CONCLUSION: Our findings are consistent with prior literature focused on the patient experience of rare and undiagnosed conditions and highlight benefits from comprehensive evaluations, regardless of whether a diagnosis is obtained. Focus group themes also suggest areas for improvement and future research related to the diagnostic odyssey.

  View details for DOI 10.1186/s13023-023-02695-5

  View details for PubMedID 37032333

• Loss of Neuron Navigator 2 Impairs Brain and Cerebellar Development. Cerebellum (London, England) Accogli, A., Lu, S., Musante, I., Scudieri, P., Rosenfeld, J. A., Severino, M., Baldassari, S., Iacomino, M., Riva, A., Balagura, G., Piccolo, G., Minetti, C., Roberto, D., Xia, F., Razak, R., Lawrence, E., Hussein, M., Chang, E. Y., Holick, M., Calì, E., Aliberto, E., De-Sarro, R., Gambardella, A., Network, U. D., Group, S. S., Emrick, L., McCaffery, P. J., Clagett-Dame, M., Marcogliese, P. C., Bellen, H. J., Lalani, S. R., Zara, F., Striano, P., Salpietro, V. 2023; 22 (2): 206-222

  Abstract

  Cerebellar hypoplasia and dysplasia encompass a group of clinically and genetically heterogeneous disorders frequently associated with neurodevelopmental impairment. The Neuron Navigator 2 (NAV2) gene (MIM: 607,026) encodes a member of the Neuron Navigator protein family, widely expressed within the central nervous system (CNS), and particularly abundant in the developing cerebellum. Evidence across different species supports a pivotal function of NAV2 in cytoskeletal dynamics and neurite outgrowth. Specifically, deficiency of Nav2 in mice leads to cerebellar hypoplasia with abnormal foliation due to impaired axonal outgrowth. However, little is known about the involvement of the NAV2 gene in human disease phenotypes. In this study, we identified a female affected with neurodevelopmental impairment and a complex brain and cardiac malformations in which clinical exome sequencing led to the identification of NAV2 biallelic truncating variants. Through protein expression analysis and cell migration assay in patient-derived fibroblasts, we provide evidence linking NAV2 deficiency to cellular migration deficits. In model organisms, the overall CNS histopathology of the Nav2 hypomorphic mouse revealed developmental anomalies including cerebellar hypoplasia and dysplasia, corpus callosum hypo-dysgenesis, and agenesis of the olfactory bulbs. Lastly, we show that the NAV2 ortholog in Drosophila, sickie (sick) is widely expressed in the fly brain, and sick mutants are mostly lethal with surviving escapers showing neurobehavioral phenotypes. In summary, our results unveil a novel human neurodevelopmental disorder due to genetic loss of NAV2, highlighting a critical conserved role of the NAV2 gene in brain and cerebellar development across species.

  View details for DOI 10.1007/s12311-022-01379-3

  View details for PubMedID 35218524

  View details for PubMedCentralID PMC9985553

• Rare variants in PPFIA3 cause delayed development, intellectual disability, autism, and epilepsy. medRxiv : the preprint server for health sciences Paul, M. S., Michener, S. L., Pan, H., Pfliger, J. M., Rosenfeld, J. A., Lerma, V. C., Tran, A., Longley, M. A., Lewis, R. A., Weisz-Hubshman, M., Bekheirnia, M. R., Bekheirnia, N., Massingham, L., Zech, M., Wagner, M., Engels, H., Cremer, K., Mangold, E., Peters, S., Trautmann, J., Mester, J. L., Guillen Sacoto, M. J., Person, R., McDonnell, P. P., Cohen, S. R., Lusk, L., Cohen, A. S., Pichon, J. L., Pastinen, T., Zhou, D., Engleman, K., Racine, C., Faivre, L., Moutton, S., Pichon, A. D., Schuhmann, S., Vasileiou, G., Russ-Hall, S., Scheffer, I. E., Carvill, G. L., Mefford, H., Network, U. D., Bacino, C. A., Lee, B. H., Chao, H. T. 2023

  Abstract

  PPFIA3 encodes the Protein-Tyrosine Phosphatase, Receptor-Type, F Polypeptide-Interacting Protein Alpha-3 (PPFIA3), which is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family involved in synaptic vesicle transport and presynaptic active zone assembly. The protein structure and function are well conserved in both invertebrates and vertebrates, but human diseases related to PPFIA3 dysfunction are not yet known. Here, we report 14 individuals with rare mono-allelic PPFIA3 variants presenting with features including developmental delay, intellectual disability, hypotonia, autism, and epilepsy. To determine the pathogenicity of PPFIA3 variants in vivo , we generated transgenic fruit flies expressing either human PPFIA3 wildtype (WT) or variant protein using GAL4-UAS targeted gene expression systems. Ubiquitous expression with Actin-GAL4 showed that the PPFIA3 variants had variable penetrance of pupal lethality, eclosion defects, and anatomical leg defects. Neuronal expression with elav-GAL4 showed that the PPFIA3 variants had seizure-like behaviors, motor defects, and bouton loss at the 3 rd instar larval neuromuscular junction (NMJ). Altogether, in the fly overexpression assays, we found that the PPFIA3 variants in the N-terminal coiled coil domain exhibited stronger phenotypes compared to those in the C-terminal region. In the loss-of-function fly assay, we show that the homozygous loss of fly Liprin- α leads to embryonic lethality. This lethality is partially rescued by the expression of human PPFIA3 WT, suggesting human PPFIA3 protein function is partially conserved in the fly. However, the PPFIA3 variants failed to rescue lethality. Altogether, the human and fruit fly data reveal that the rare PPFIA3 variants are dominant negative loss-of-function alleles that perturb multiple developmental processes and synapse formation.

  View details for DOI 10.1101/2023.03.27.23287689

  View details for PubMedID 37034625

  View details for PubMedCentralID PMC10081396

• A Case Study of Dysfunctional Nicotinamide Metabolism in a 20-Year-Old Male. Metabolites DeBalsi, K. L., Newman, J. H., Sommerville, L. J., Phillips, J. A., Hamid, R., Cogan, J., Fessel, J. P., Evans, A. M., Kennedy, A. D. 2023; 13 (3)

  Abstract

  We present a case study of a 20-year-old male with an unknown neurodegenerative disease who was referred to the Undiagnosed Diseases Network Vanderbilt Medical Center site. A previous metabolic panel showed that the patient had a critical deficiency in nicotinamide intermediates that are generated during the biosynthesis of NAD(H). We followed up on these findings by evaluating the patient's ability to metabolize nicotinamide. We performed a global metabolic profiling analysis of plasma samples that were collected: (1) under normal fed conditions (baseline), (2) after the patient had fasted, and (3) after he was challenged with a 500 mg nasogastric tube bolus of nicotinamide following the fast. Our findings showed that the patient's nicotinamide N-methyltransferase (NNMT), a key enzyme in NAD(H) biosynthesis and methionine metabolism, was not functional under normal fed or fasting conditions but was restored in response to the nicotinamide challenge. Altered levels of metabolites situated downstream of NNMT and in neighboring biochemical pathways provided further evidence of a baseline defect in NNMT activity. To date, this is the only report of a critical defect in NNMT activity manifesting in adulthood and leading to neurodegenerative disease. Altogether, this study serves as an important reference in the rare disease literature and also demonstrates the utility of metabolomics as a diagnostic tool for uncharacterized metabolic diseases.

  View details for DOI 10.3390/metabo13030399

  View details for PubMedID 36984839

  View details for PubMedCentralID PMC10055858

• MYH2-associated myopathy caused by a novel splice-site variant. Neuromuscular disorders : NMD Cassini, T. A., Malicdan, M. C., Macnamara, E. F., Lehky, T., Horkayne-Szakaly, I., Huang, Y., Jones, R., Godfrey, R., Wolfe, L., Gahl, W. A., Toro, C. 2023; 33 (3): 257-262

  Abstract

  MYH2 encodes MyHCIIa, a myosin heavy chain found in fast type 2A fibers. Pathogenic variants in this gene have previously been implicated in dominant and recessive forms of myopathy. Three individuals reported here are part of a family in which four generations of individuals are affected by a slowly progressive, predominantly proximal myopathy in an autosomal dominant inheritance pattern. Affected individuals in this family lacked classic features of an MYH2-associated myopathy such as congenital contractures and ophthalmoplegia. A novel variant, MYH2 c.5673+1G>C, was detected in the proband and subsequently found to segregate with disease in five additional family members. Further studies demonstrated that this variant affects splicing, resulting in novel transcripts. These data and muscle biopsy findings in the proband, indicate that this family's MYH2 variant is causative of their myopathy, adding to our understanding of the clinical and molecular characteristics of the disease.

  View details for DOI 10.1016/j.nmd.2022.12.014

  View details for PubMedID 36774715

  View details for PubMedCentralID PMC10023425

• Expansion of the clinical and molecular spectrum of WWOX-related epileptic encephalopathy. American journal of medical genetics. Part A Chong, S. C., Cao, Y., Fung, E. L., Kleppe, S., Gripp, K. W., Hertecant, J., El-Hattab, A. W., Suleiman, J., Clark, G., von Allmen, G., Rodziyevska, O., Lewis, R. A., Rosenfeld, J. A., Dong, J., Wang, X., Miller, M. J., Bi, W., Liu, P., Scaglia, F. 2023; 191 (3): 776-785

  Abstract

  WWOX biallelic loss-of-function pathogenic single nucleotide variants (SNVs) and copy number variants (CNVs) including exonic deletions and duplications cause WWOX-related epileptic encephalopathy (WOREE) syndrome. This disorder is characterized by refractory epilepsy, axial hypotonia, peripheral hypertonia, progressive microcephaly, and premature death. Here we report five patients with WWOX biallelic predicted null variants identified by exome sequencing (ES), genome sequencing (GS), and/or chromosomal microarray analysis (CMA). SNVs and intragenic deletions of one or more exons were commonly reported in WOREE syndrome patients which made the genetic diagnosis challenging and required a combination of different diagnostic technologies. These patients presented with severe, developmental and epileptic encephalopathy (DEE), and other cardinal features consistent with WOREE syndrome. This report expands the clinical phenotype associated with this condition, including failure to thrive in most patients and epilepsy that responded to a ketogenic diet in three patients. Dysmorphic features and abnormal prenatal findings were not commonly observed. Additionally, recurrent pancreatitis and sensorineural hearing loss each were observed in single patients. In summary, these phenotypic features broaden the clinical spectrum of WOREE syndrome.

  View details for DOI 10.1002/ajmg.a.63074

  View details for PubMedID 36537114

• Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ genomic medicine Morimoto, M., Bhambhani, V., Gazzaz, N., Davids, M., Sathiyaseelan, P., Macnamara, E. F., Lange, J., Lehman, A., Zerfas, P. M., Murphy, J. L., Acosta, M. T., Wang, C., Alderman, E., Reichert, S., Thurm, A., Adams, D. R., Introne, W. J., Gorski, S. M., Boerkoel, C. F., Gahl, W. A., Tifft, C. J., Malicdan, M. C. 2023; 8 (1): 4

  Abstract

  Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.

  View details for DOI 10.1038/s41525-022-00343-8

  View details for PubMedID 36765070

  View details for PubMedCentralID PMC9918471

• TMEM161B regulates cerebral cortical gyration, Sonic Hedgehog signaling, and ciliary structure in the developing central nervous system. Proceedings of the National Academy of Sciences of the United States of America Akula, S. K., Marciano, J. H., Lim, Y., Exposito-Alonso, D., Hylton, N. K., Hwang, G. H., Neil, J. E., Dominado, N., Bunton-Stasyshyn, R. K., Song, J. H., Talukdar, M., Schmid, A., Teboul, L., Mo, A., Shin, T., Finander, B., Beck, S. G., Yeh, R. C., Otani, A., Qian, X., DeGennaro, E. M., Alkuraya, F. S., Maddirevula, S., Cascino, G. D., Giannini, C., Burrage, L. C., Rosenfield, J. A., Ketkar, S., Clark, G. D., Bacino, C., Lewis, R. A., Segal, R. A., Bazan, J. F., Smith, K. A., Golden, J. A., Cho, G., Walsh, C. A. 2023; 120 (4): e2209964120

  Abstract

  Sonic hedgehog signaling regulates processes of embryonic development across multiple tissues, yet factors regulating context-specific Shh signaling remain poorly understood. Exome sequencing of families with polymicrogyria (disordered cortical folding) revealed multiple individuals with biallelic deleterious variants in TMEM161B, which encodes a multi-pass transmembrane protein of unknown function. Tmem161b null mice demonstrated holoprosencephaly, craniofacial midline defects, eye defects, and spinal cord patterning changes consistent with impaired Shh signaling, but were without limb defects, suggesting a CNS-specific role of Tmem161b. Tmem161b depletion impaired the response to Smoothened activation in vitro and disrupted cortical histogenesis in vivo in both mouse and ferret models, including leading to abnormal gyration in the ferret model. Tmem161b localizes non-exclusively to the primary cilium, and scanning electron microscopy revealed shortened, dysmorphic, and ballooned ventricular zone cilia in the Tmem161b null mouse, suggesting that the Shh-related phenotypes may reflect ciliary dysfunction. Our data identify TMEM161B as a regulator of cerebral cortical gyration, as involved in primary ciliary structure, as a regulator of Shh signaling, and further implicate Shh signaling in human gyral development.

  View details for DOI 10.1073/pnas.2209964120

  View details for PubMedID 36669111

  View details for PubMedCentralID PMC9942790

• Continuing a search for a diagnosis: the impact of adolescence and family dynamics. Orphanet journal of rare diseases Miller, I. M., Yashar, B. M., Macnamara, E. F. 2023; 18 (1): 6

  Abstract

  The "diagnostic odyssey" describes the process those with undiagnosed conditions undergo to identify a diagnosis. Throughout this process, families of children with undiagnosed conditions have multiple opportunities to decide whether to continue or stop their search for a diagnosis and accept the lack of a diagnostic label. Previous studies identified factors motivating a family to begin searching, but there is limited information about the decision-making process in a prolonged search and how the affected child impacts a family's decision. This study aimed to understand how families of children with undiagnosed diseases decide whether to continue to pursue a diagnosis after standard clinical testing has failed. Parents who applied to the Undiagnosed Disease Network (UDN) at the National Institutes of Health (NIH) were recruited to participate in semi-structured interviews. The 2015 Supportive Care Needs model by Pelenstov, which defines critical needs in families with rare/undiagnosed diseases, provided a framework for interview guide development and transcript analysis (Pelentsov et al in Disabil Health J 8(4):475-491, 2015. https://doi.org/10.1016/J.DHJO.2015.03.009 ). A deductive, iterative coding approach was used to identify common unifying themes. Fourteen parents from 13 families were interviewed. The average child's age was 11 years (range 3-18) and an average 63% of their life had been spent searching for a diagnosis. Our analysis found that alignment or misalignment of parent and child needs impact the trajectory of the diagnostic search. When needs and desires align, reevaluation of a decision to pursue a diagnosis is limited. However, when there is conflict between parent and child desires, there is reevaluation, and often a pause, in the search. This tension is exacerbated when children are adolescents and attempting to balance their dependence on parents for medical care with a natural desire for independence. Our results provide novel insights into the roles of adolescents in the diagnostic odyssey. The tension between desired and realistic developmental outcomes for parents and adolescents impacts if, and how, the search for a diagnosis progresses.

  View details for DOI 10.1186/s13023-022-02598-x

  View details for PubMedID 36624503

  View details for PubMedCentralID PMC9830697

• Repeat expansions nested within tandem CNVs: a unique structural change in GLS exemplifies the diagnostic challenges of non-coding pathogenic variation. Human molecular genetics Fazal, S., Danzi, M. C., van Kuilenburg, A. B., Reich, S., Traschütz, A., Bender, B., Leen, R., Toro, C., Usdin, K., Hayward, B., Adams, D. R., van Karnebeek, C. D., Ferreira, C. R., D'Sousa, P., Network, U. D., Tekin, M., Züchner, S., Synofzik, M. 2023; 32 (1): 46-54

  Abstract

  Glutaminase deficiency has recently been associated with ataxia and developmental delay due to repeat expansions in the 5'UTR of the glutaminase (GLS) gene. Patients with the described GLS repeat expansion may indeed remain undiagnosed due to the rarity of this variant, the challenge of its detection and the recency of its discovery. In this study, we combined advanced bioinformatics screening of ~3000 genomes and ~1500 exomes with optical genome mapping and long-read sequencing for confirmation studies. We identified two GLS families, previously intensely and unsuccessfully analyzed. One family carries an unusual and complex structural change involving a homozygous repeat expansion nested within a quadruplication event in the 5'UTR of GLS. Glutaminase deficiency and its metabolic consequences were validated by in-depth biochemical analysis. The identified GLS patients showed progressive early-onset ataxia, cognitive deficits, pyramidal tract damage and optic atrophy, thus demonstrating susceptibility of several specific neuron populations to glutaminase deficiency. This large-scale screening study demonstrates the ability of bioinformatics analysis-validated by latest state-of-the-art technologies (optical genome mapping and long-read sequencing)-to effectively flag complex repeat expansions using short-read datasets and thus facilitate diagnosis of ultra-rare disorders.

  View details for DOI 10.1093/hmg/ddac173

  View details for PubMedID 35913761

  View details for PubMedCentralID PMC9837832

• Quantitative gastrointestinal function and corresponding symptom profiles in autonomic neuropathy FRONTIERS IN NEUROLOGY Langford, J. S., Tokita, E., Martindale, C., Millsap, L., Hemp, J., Pace, L. A., Cortez, M. M. 2022; 13: 1027348

  Abstract

  Peripheral neuropathies with autonomic nervous system involvement are a recognized cause of gastrointestinal dysmotility for a wide spectrum of diseases. Recent advances in wireless motility capsule testing allow improved sampling of regional and whole gut motility to aid in the diagnosis of gastrointestinal motility disorders and may provide additional insight into segment-specific enteric involvement of peripheral neuropathies affecting autonomic nervous system function.We utilized standardized autonomic nervous system (ANS) reflex assessment and wireless motility capsule testing to evaluate 20 individuals with idiopathic autonomic neuropathy and unexplained gastrointestinal symptoms. Additionally, we examined the relationship between quantifiable autonomic neuropathy and gastrointestinal dysmotility at specific neuroanatomical levels. Symptom profiles were evaluated using the 31-item Composite Autonomic Symptom Score questionnaire (COMPASS-31) and compared to wireless motility capsule data.We found that transit times were predominately abnormal (delayed) in the foregut (10 of 20; 50%), while contractility abnormalities were far more prominent in the hindgut (17 of 20; 85%), and that motility and symptom patterns, as assessed by the COMPASS-31 GI domain items, generally corresponded. Finally, we also found that there was neuroanatomical overlap in the presence of autonomic reflex abnormalities and WMC-based transit and/or contractility abnormalities.We found that transit times were predominately abnormal in the foregut and midgut, while contractility abnormalities were far more prominent in the hindgut in individuals with idiopathic autonomic neuropathy. There was a high rate of agreement in segmental wireless motility capsule data with neuroanatomically corresponding standardized ANS function measures (e.g., cardiovagal, sudomotor, adrenergic). Expanded sudomotor testing, including additional neuroanatomical segments, could provide additional indirect assessment of visceral involvement in ANS dysfunction.

  View details for DOI 10.3389/fneur.2022.1027348

  View details for Web of Science ID 000904823300001

  View details for PubMedID 36588909

  View details for PubMedCentralID PMC9798202

• A concurrent dual analysis of genomic data augments diagnoses: experiences of two clinical sites in the Undiagnosed Diseases Network. Genetics in medicine : official journal of the American College of Medical Genetics Spillmann, R. C., Tan, Q. K., Reuter, C., Schoch, K., Kohler, J., Bonner, D., Zastrow, D., Alkelai, A., Baugh, E., Cope, H., Marwaha, S., Wheeler, M. T., Bernstein, J. A., Shashi, V. 2022

  Abstract

  Next generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultra-rare conditions. However, diagnosis rates differ between analytical pipelines. In the NIH-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice.A retrospective review was performed at two UDN clinical sites, to compare variants, and diagnoses/candidate genes identified with the dual analyses of the NGS data.Ninety-five individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, while the clinical sites prioritized more research variants/candidate genes (p <0.001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the two pipelines were more often due to variant prioritization disparities, than variant detection.The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provides a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.

  View details for DOI 10.1016/j.gim.2022.12.001

  View details for PubMedID 36481303

• Endocannabinoid dysfunction in neurological disease: neuro-ocular DAGLA-related syndrome. Brain : a journal of neurology Bainbridge, M. N., Mazumder, A., Ogasawara, D., Abou Jamra, R., Bernard, G., Bertini, E., Burglen, L., Cope, H., Crawford, A., Derksen, A., Dure, L., Gantz, E., Koch-Hogrebe, M., Hurst, A. C., Mahida, S., Marshall, P., Micalizzi, A., Novelli, A., Peng, H., Rodriguez, D., Robbins, S. L., Rutledge, S. L., Scalise, R., Schließke, S., Shashi, V., Srivastava, S., Thiffault, I., Topol, S., Qebibo, L., Wieczorek, D., Cravatt, B., Haricharan, S., Torkamani, A., Friedman, J. 2022; 145 (10): 3383-3390

  Abstract

  The endocannabinoid system is a highly conserved and ubiquitous signalling pathway with broad-ranging effects. Despite critical pathway functions, gene variants have not previously been conclusively linked to human disease. We identified nine children from eight families with heterozygous, de novo truncating variants in the last exon of DAGLA with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. All children displayed paroxysms of nystagmus or eye deviation accompanied by compensatory head posture and worsened incoordination most frequently after waking. RNA sequencing showed clear expression of the truncated transcript and no differences were found between mutant and wild-type DAGLA activity. Immunofluorescence staining of patient-derived fibroblasts and HEK cells expressing the mutant protein showed distinct perinuclear aggregation not detected in control samples. This report establishes truncating variants in the last DAGLA exon as the cause of a unique paediatric syndrome. Because enzymatic activity was preserved, the observed mislocalization of the truncated protein may account for the observed phenotype. Potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect. To our knowledge, this is the first report directly linking an endocannabinoid system component with human genetic disease and sets the stage for potential future therapeutic avenues.

  View details for DOI 10.1093/brain/awac223

  View details for PubMedID 35737950

  View details for PubMedCentralID PMC9586540

• PRUNE1 c.933G>A synonymous variant induces exon 7 skipping, disrupts the DHHA2 domain, and leads to an atypical NMIHBA syndrome presentation: Case report and review of the literature. American journal of medical genetics. Part A Magyar, C. L., Murdock, D. R., Burrage, L. C., Dai, H., Lalani, S. R., Lewis, R. A., Lin, Y., Astudillo, M. F., Rosenfeld, J. A., Tran, A. A., Gibson, J. B., Bacino, C. A., Lee, B. H., Chao, H. T. 2022; 188 (6): 1868-1874

  Abstract

  Prune exopolyphosphatase-1 (PRUNE1) encodes a member of the aspartic acid-histidine-histidine (DHH) phosphodiesterase superfamily that regulates cell migration and proliferation during brain development. In 2015, biallelic PRUNE1 loss-of-function variants were identified to cause the neurodevelopmental disorder with microcephaly, hypotonia, and variable brain abnormalities (NMIHBA, OMIM#617481). NMIHBA is characterized by the namesake features and structural brain anomalies including thinning of the corpus callosum, cerebral and cerebellar atrophy, and delayed myelination. To date, 47 individuals have been reported in the literature, but the phenotypic spectrum of PRUNE1-related disorders and their causative variants remains to be characterized fully. Here, we report a novel homozygous PRUNE1 NM_021222.2:c.933G>A synonymous variant identified in a 6-year-old boy with intellectual and developmental disabilities, hypotonia, and spastic diplegia, but with the absence of microcephaly, brain anomalies, or seizures. Fibroblast RNA sequencing revealed that the PRUNE1 NM_021222.1:c.933G>A variant resulted in an in-frame skipping of the penultimate exon 7, removing 53 amino acids from an important protein domain. This case represents the first synonymous variant and the third pathogenic variant known to date affecting the DHH-associated domain (DHHA2 domain). These findings extend the genotypic and phenotypic spectrums in PRUNE1-related disorders and highlight the importance of considering synonymous splice site variants in atypical presentations.

  View details for DOI 10.1002/ajmg.a.62704

  View details for PubMedID 35194938

  View details for PubMedCentralID PMC11149102

• Functional analysis of a novel de novo variant in PPP5C associated with microcephaly, seizures, and developmental delay. Molecular genetics and metabolism Fielder, S. M., Rosenfeld, J. A., Burrage, L. C., Emrick, L., Lalani, S., Attali, R., Bembenek, J. N., Hoang, H., Baldridge, D., Silverman, G. A., Schedl, T., Pak, S. C. 2022; 136 (1): 65-73

  Abstract

  We describe a proband evaluated through the Undiagnosed Diseases Network (UDN) who presented with microcephaly, developmental delay, and refractory epilepsy with a de novo p.Ala47Thr missense variant in the protein phosphatase gene, PPP5C. This gene has not previously been associated with a Mendelian disease, and based on the population database, gnomAD, the gene has a low tolerance for loss-of-function variants (pLI = 1, o/e = 0.07). We functionally evaluated the PPP5C variant in C. elegans by knocking the variant into the orthologous gene, pph-5, at the corresponding residue, Ala48Thr. We employed assays in three different biological processes where pph-5 was known to function through opposing the activity of genes, mec-15 and sep-1. We demonstrated that, in contrast to control animals, the pph-5 Ala48Thr variant suppresses the neurite growth phenotype and the GABA signaling defects of mec-15 mutants, and the embryonic lethality of sep-1 mutants. The Ala48Thr variant did not display dominance and behaved similarly to the reference pph-5 null, indicating that the variant is likely a strong hypomorph or complete loss-of-function. We conclude that pph-5 Ala48Thr is damaging in C. elegans. By extension in the proband, PPP5C p.Ala47Thr is likely damaging, the de novo dominant presentation is consistent with haplo-insufficiency, and the PPP5C variant is likely responsible for one or more of the proband's phenotypes.

  View details for DOI 10.1016/j.ymgme.2022.03.007

  View details for PubMedID 35361529

  View details for PubMedCentralID PMC10200280

• <i>Gene.iobio</i>: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization (vol 11, 20307, 2021) SCIENTIFIC REPORTS Di Sera, T., Velinder, M., Ward, A., Qiao, Y., Georges, S., Miller, C., Pitman, A., Richards, W., Ekawade, A., Viskochil, D., Carey, J. C., Pace, L., Bale, J., Clardy, S. L., Andrews, A., Botto, L., Marth, G. 2022; 12 (1): 5800

  View details for DOI 10.1038/s41598-022-09959-3

  View details for Web of Science ID 000780164200084

  View details for PubMedID 35388139

  View details for PubMedCentralID PMC8986806

• Genome sequencing reveals novel noncoding variants in PLA2G6 and LMNB1 causing progressive neurologic disease. Molecular genetics & genomic medicine Borja, N., Bivona, S., Peart, L. S., Johnson, B., Gonzalez, J., Barbouth, D., Moore, H., Guo, S., Bademci, G., Tekin, M. 2022; 10 (4): e1892

  Abstract

  Neurodegenerative disorders and leukodystrophies are progressive neurologic conditions that can occur following the disruption of intricately coordinated patterns of gene expression. Exome sequencing has been adopted as an effective diagnostic tool for determining the underlying genetic etiology of Mendelian neurologic disorders, however genome sequencing offer advantages in its ability to identify and characterize copy number, structural, and sequence variants in noncoding regions. Genome sequencing from peripheral leukocytes was performed on two patients with progressive neurologic disease of unknown etiology following negative genetic investigations including exome sequencing. RNA sequencing from peripheral blood was performed to determine gene expression patterns in one of the patients. Potential causative variants were matched to the patients' clinical presentation. The first proband was found to be heterozygous for a likely pathogenic missense variant in PLA2G6 (c.386T>C; p.Leu129Pro) and have an additional deep intronic variant in PLA2G6 (c.2035-926G>A). RNA sequencing indicated this latter variant created a splice acceptor site leading to the incorporation of a pseudo-exon introducing a premature termination codon. The second proband was heterozygous for a 261 kb deletion upstream of LMNB1 that included an enhancer region. Previous reports of copy number variants spanning this region of cis-acting regulatory elements corroborated its pathogenicity. When combined with clinical presentations, these findings led to a definitive diagnosis of autosomal recessive infantile neuroaxonal dystrophy and autosomal dominant adult-onset demyelinating leukodystrophy, respectively. In patients with progressive neurologic disease of unknown etiology, genome sequencing with the addition of RNA analysis where appropriate should be considered for the identification of causative noncoding pathogenic variants.

  View details for DOI 10.1002/mgg3.1892

  View details for PubMedID 35247231

  View details for PubMedCentralID PMC9000935

• Bilateral choanal stenosis in auriculocondylar syndrome caused by a PLCB4 variant. American journal of medical genetics. Part A Peart, L. S., Gonzalez, J., Bivona, S., Latchman, K., Torres, L., Tekin, M. 2022; 188 (4): 1307-1310

  Abstract

  Auriculocondylar syndrome (ARCND) is characterized by a distinguished feature of question mark ears and a variation of other minor and major malformations. Monoallelic or biallelic PLCB4 variants have been reported in a subset of affected individuals, referred to as ARCND2. We report on a 3-year-old female with ARCND who presented at birth with question mark ears, micrognathia, and bilateral choanal stenosis that was characterized by difficulty in breathing. She was found to be heterozygous for a novel PLCB4 variant, p.Glu358Gly. Respiratory distress is rare in autosomal dominant ARCND2 and choanal stenosis has not been reported. Our study expands the clinical phenotype of ARCND by adding choanal stenosis as a finding and suggests that PLCB4 play a role in the development of choanal structures.

  View details for DOI 10.1002/ajmg.a.62634

  View details for PubMedID 34995019

• Bi-allelic variants in neuronal cell adhesion molecule cause a neurodevelopmental disorder characterized by developmental delay, hypotonia, neuropathy/spasticity. American journal of human genetics Kurolap, A., Kreuder, F., Gonzaga-Jauregui, C., Duvdevani, M. P., Harel, T., Tammer, L., Xin, B., Bakhtiari, S., Rice, J., van Eyk, C. L., Gecz, J., Mah, J. K., Atkinson, D., Cope, H., Sullivan, J. A., Douek, A. M., Colquhoun, D., Henry, J., Wlodkowic, D., Parman, Y., Candayan, A., Kocasoy-Orhan, E., Ilivitzki, A., Soudry, S., Leibu, R., Glaser, F., Sency, V., Ast, G., Shashi, V., Fahey, M. C., Battaloğlu, E., Jordanova, A., Meiner, V., Innes, A. M., Wang, H., Elpeleg, O., Kruer, M. C., Kaslin, J., Baris Feldman, H. 2022; 109 (3): 518-532

  Abstract

  Cell adhesion molecules are membrane-bound proteins predominantly expressed in the central nervous system along principal axonal pathways with key roles in nervous system development, neural cell differentiation and migration, axonal growth and guidance, myelination, and synapse formation. Here, we describe ten affected individuals with bi-allelic variants in the neuronal cell adhesion molecule NRCAM that lead to a neurodevelopmental syndrome of varying severity; the individuals are from eight families. This syndrome is characterized by developmental delay/intellectual disability, hypotonia, peripheral neuropathy, and/or spasticity. Computational analyses of NRCAM variants, many of which cluster in the third fibronectin type III (Fn-III) domain, strongly suggest a deleterious effect on NRCAM structure and function, including possible disruption of its interactions with other proteins. These findings are corroborated by previous in vitro studies of murine Nrcam-deficient cells, revealing abnormal neurite outgrowth, synaptogenesis, and formation of nodes of Ranvier on myelinated axons. Our studies on zebrafish nrcamaΔ mutants lacking the third Fn-III domain revealed that mutant larvae displayed significantly altered swimming behavior compared to wild-type larvae (p < 0.03). Moreover, nrcamaΔ mutants displayed a trend toward increased amounts of α-tubulin fibers in the dorsal telencephalon, demonstrating an alteration in white matter tracts and projections. Taken together, our study provides evidence that NRCAM disruption causes a variable form of a neurodevelopmental disorder and broadens the knowledge on the growing role of the cell adhesion molecule family in the nervous system.

  View details for DOI 10.1016/j.ajhg.2022.01.004

  View details for PubMedID 35108495

  View details for PubMedCentralID PMC8948158

• PUS7 deficiency in human patients causes profound neurodevelopmental phenotype by dysregulating protein translation. Molecular genetics and metabolism Han, S. T., Kim, A. C., Garcia, K., Schimmenti, L. A., Macnamara, E., Network, U. D., Gahl, W. A., Malicdan, M. C., Tifft, C. J. 2022; 135 (3): 221-229

  Abstract

  Protein translation is a highly regulated process involving the interaction of numerous genes on every component of the protein translation machinery. Upregulated protein translation is a hallmark of cancer and is implicated in autism spectrum disorder, but the risks of developing each disease do not appear to be correlated with one another. In this study we identified two siblings from the NIH Undiagnosed Diseases Program with loss of function variants in PUS7, a gene previously implicated in the regulation of total protein translation. These patients exhibited a neurodevelopmental phenotype including autism spectrum disorder in the proband. Both patients also had features of Lesch-Nyhan syndrome, including hyperuricemia and self-injurious behavior, but without pathogenic variants in HPRT1. Patient fibroblasts demonstrated upregulation of protein synthesis, including elevated MYC protein, but did not exhibit increased rates of cell proliferation. Interestingly, the dysregulation of protein translation also resulted in mildly decreased levels of HPRT1 protein suggesting an association between dysregulated protein translation and the LNS-like phenotypic findings. These findings strengthen the correlation between neurodevelopmental disease, particularly autism spectrum disorders, and the rate of protein translation.

  View details for DOI 10.1016/j.ymgme.2022.01.103

  View details for PubMedID 35144859

  View details for PubMedCentralID PMC8958514

• Gain-of-function mutations in RPA1 cause a syndrome with short telomeres and somatic genetic rescue. Blood Sharma, R., Sahoo, S. S., Honda, M., Granger, S. L., Goodings, C., Sanchez, L., Künstner, A., Busch, H., Beier, F., Pruett-Miller, S. M., Valentine, M. B., Fernandez, A. G., Chang, T. C., Géli, V., Churikov, D., Hirschi, S., Pastor, V. B., Boerries, M., Lauten, M., Kelaidi, C., Cooper, M. A., Nicholas, S., Rosenfeld, J. A., Polychronopoulou, S., Kannengiesser, C., Saintomé, C., Niemeyer, C. M., Revy, P., Wold, M. S., Spies, M., Erlacher, M., Coulon, S., Wlodarski, M. W. 2022; 139 (7): 1039-1051

  Abstract

  Human telomere biology disorders (TBD)/short telomere syndromes (STS) are heterogeneous disorders caused by inherited loss-of-function mutations in telomere-associated genes. Here, we identify 3 germline heterozygous missense variants in the RPA1 gene in 4 unrelated probands presenting with short telomeres and varying clinical features of TBD/STS, including bone marrow failure, myelodysplastic syndrome, T- and B-cell lymphopenia, pulmonary fibrosis, or skin manifestations. All variants cluster to DNA-binding domain A of RPA1 protein. RPA1 is a single-strand DNA-binding protein required for DNA replication and repair and involved in telomere maintenance. We showed that RPA1E240K and RPA1V227A proteins exhibit increased binding to single-strand and telomeric DNA, implying a gain in DNA-binding function, whereas RPA1T270A has binding properties similar to wild-type protein. To study the mutational effect in a cellular system, CRISPR/Cas9 was used to knock-in the RPA1E240K mutation into healthy inducible pluripotent stem cells. This resulted in severe telomere shortening and impaired hematopoietic differentiation. Furthermore, in patients with RPA1E240K, we discovered somatic genetic rescue in hematopoietic cells due to an acquired truncating cis RPA1 mutation or a uniparental isodisomy 17p with loss of mutant allele, coinciding with stabilized blood counts. Using single-cell sequencing, the 2 somatic genetic rescue events were proven to be independently acquired in hematopoietic stem cells. In summary, we describe the first human disease caused by germline RPA1 variants in individuals with TBD/STS.

  View details for DOI 10.1182/blood.2021011980

  View details for PubMedID 34767620

  View details for PubMedCentralID PMC8854676

• A dominant negative variant of RAB5B disrupts maturation of surfactant protein B and surfactant protein C. Proceedings of the National Academy of Sciences of the United States of America Huang, H., Pan, J., Spielberg, D. R., Hanchard, N. A., Scott, D. A., Burrage, L. C., Dai, H., Murdock, D., Rosenfeld, J. A., Mohammad, A., Huang, T., Lindsey, A. G., Kim, H., Chen, J., Ramu, A., Morrison, S. A., Dawson, Z. D., Hu, A. Z., Tycksen, E., Silverman, G. A., Baldridge, D., Wambach, J. A., Pak, S. C., Brody, S. L., Schedl, T. 2022; 119 (6)

  Abstract

  Pathogenic variants in surfactant proteins SP-B and SP-C cause surfactant deficiency and interstitial lung disease. Surfactant proteins are synthesized as precursors (proSP-B, proSP-C), trafficked, and processed via a vesicular-regulated secretion pathway; however, control of vesicular trafficking events is not fully understood. Through the Undiagnosed Diseases Network, we evaluated a child with interstitial lung disease suggestive of surfactant deficiency. Variants in known surfactant dysfunction disorder genes were not found in trio exome sequencing. Instead, a de novo heterozygous variant in RAB5B was identified in the Ras/Rab GTPases family nucleotide binding domain, p.Asp136His. Functional studies were performed in Caenorhabditis elegans by knocking the proband variant into the conserved position (Asp135) of the ortholog, rab-5 Genetic analysis demonstrated that rab-5[Asp135His] is damaging, producing a strong dominant negative gene product. rab-5[Asp135His] heterozygotes were also defective in endocytosis and early endosome (EE) fusion. Immunostaining studies of the proband's lung biopsy revealed that RAB5B and EE marker EEA1 were significantly reduced in alveolar type II cells and that mature SP-B and SP-C were significantly reduced, while proSP-B and proSP-C were normal. Furthermore, staining normal lung showed colocalization of RAB5B and EEA1 with proSP-B and proSP-C. These findings indicate that dominant negative-acting RAB5B Asp136His and EE dysfunction cause a defect in processing/trafficking to produce mature SP-B and SP-C, resulting in interstitial lung disease, and that RAB5B and EEs normally function in the surfactant secretion pathway. Together, the data suggest a noncanonical function for RAB5B and identify RAB5B p.Asp136His as a genetic mechanism for a surfactant dysfunction disorder.

  View details for DOI 10.1073/pnas.2105228119

  View details for PubMedID 35121658

  View details for PubMedCentralID PMC8832968

• Clinical application of a scale to assess genomic healthcare empowerment (GEmS): Process and illustrative case examples. Journal of genetic counseling McConkie-Rosell, A., Schoch, K., Sullivan, J., Spillmann, R. C., Cope, H., Tan, Q. K., Palmer, C. G., Hooper, S. R., Shashi, V. 2022; 31 (1): 59-70

  Abstract

  The Genome Empowerment Scale (GEmS), developed as a research tool, assesses perspectives of parents of children with undiagnosed disorders about to undergo exome or genome sequencing related to the process of empowerment. We defined genomic healthcare empowerment as follows: perceived ability to understand and seek new information related to the genomic sequencing, manage emotions related to the diagnostic process and outcomes, and utilize genomic sequencing information to the betterment of the individual/child and family. The GEmS consists of four scales, two are primarily emotion-focused (Meaning of a Diagnosis, and Emotional Management of the Process) and two are action-oriented (Seeking Information and Support, and Implications and Planning). The purpose of this research was to provide a strategy for interpreting results from the GEmS and present illustrative cases. These illustrations should serve to facilitate use of the GEmS in the clinical and research arena, particularly with respect to guiding genetic counseling processes for parents of children with undiagnosed conditions.

  View details for DOI 10.1002/jgc4.1451

  View details for PubMedID 34115423

  View details for PubMedCentralID PMC8664895

• The clinical and molecular spectrum of QRICH1 associated neurodevelopmental disorder. Human mutation Kumble, S., Levy, A. M., Punetha, J., Gao, H., Ah Mew, N., Anyane-Yeboa, K., Benke, P. J., Berger, S. M., Bjerglund, L., Campos-Xavier, B., Ciliberto, M., Cohen, J. S., Comi, A. M., Curry, C., Damaj, L., Denommé-Pichon, A. S., Emrick, L., Faivre, L., Fasano, M. B., Fiévet, A., Finkel, R. S., García-Miñaúr, S., Gerard, A., Gomez-Puertas, P., Guillen Sacoto, M. J., Hoffman, T. L., Howard, L., Iglesias, A. D., Izumi, K., Larson, A., Leiber, A., Lozano, R., Marcos-Alcalde, I., Mintz, C. S., Mullegama, S. V., Møller, R. S., Odent, S., Oppermann, H., Ostergaard, E., Pacio-Míguez, M., Palomares-Bralo, M., Parikh, S., Paulson, A. M., Platzer, K., Posey, J. E., Potocki, L., Revah-Politi, A., Rio, M., Ritter, A. L., Robinson, S., Rosenfeld, J. A., Santos-Simarro, F., Sousa, S. B., Wéber, M., Xie, Y., Chung, W. K., Brown, N. J., Tümer, Z. 2022; 43 (2): 266-282

  Abstract

  De novo variants in QRICH1 (Glutamine-rich protein 1) has recently been reported in 11 individuals with intellectual disability (ID). The function of QRICH1 is largely unknown but it is likely to play a key role in the unfolded response of endoplasmic reticulum stress through transcriptional control of proteostasis. In this study, we present 27 additional individuals and delineate the clinical and molecular spectrum of the individuals (n = 38) with QRICH1 variants. The main clinical features were mild to moderate developmental delay/ID (71%), nonspecific facial dysmorphism (92%) and hypotonia (39%). Additional findings included poor weight gain (29%), short stature (29%), autism spectrum disorder (29%), seizures (24%) and scoliosis (18%). Minor structural brain abnormalities were reported in 52% of the individuals with brain imaging. Truncating or splice variants were found in 28 individuals and 10 had missense variants. Four variants were inherited from mildly affected parents. This study confirms that heterozygous QRICH1 variants cause a neurodevelopmental disorder including short stature and expands the phenotypic spectrum to include poor weight gain, scoliosis, hypotonia, minor structural brain anomalies, and seizures. Inherited variants from mildly affected parents are reported for the first time, suggesting variable expressivity.

  View details for DOI 10.1002/humu.24308

  View details for PubMedID 34859529

• Loss of IRF2BPL impairs neuronal maintenance through excess Wnt signaling. Science advances Marcogliese, P. C., Dutta, D., Ray, S. S., Dang, N. D., Zuo, Z., Wang, Y., Lu, D., Fazal, F., Ravenscroft, T. A., Chung, H., Kanca, O., Wan, J., Douine, E. D., Network, U. D., Pena, L. D., Yamamoto, S., Nelson, S. F., Might, M., Meyer, K. C., Yeo, N. C., Bellen, H. J. 2022; 8 (3): eabl5613

  Abstract

  De novo truncations in Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) lead to severe childhood-onset neurodegenerative disorders. To determine how loss of IRF2BPL causes neural dysfunction, we examined its function in Drosophila and zebrafish. Overexpression of either IRF2BPL or Pits, the Drosophila ortholog, represses Wnt transcription in flies. In contrast, neuronal depletion of Pits leads to increased wingless (wg) levels in the brain and is associated with axonal loss, whereas inhibition of Wg signaling is neuroprotective. Moreover, increased neuronal expression of wg in flies is sufficient to cause age-dependent axonal loss, similar to reduction of Pits. Loss of irf2bpl in zebrafish also causes neurological defects with an associated increase in wnt1 transcription and downstream signaling. WNT1 is also increased in patient-derived astrocytes, and pharmacological inhibition of Wnt suppresses the neurological phenotypes. Last, IRF2BPL and the Wnt antagonist, CKIα, physically and genetically interact, showing that IRF2BPL and CkIα antagonize Wnt transcription and signaling.

  View details for DOI 10.1126/sciadv.abl5613

  View details for PubMedID 35044823

  View details for PubMedCentralID PMC8769555

• Perceived utility and disutility of genomic sequencing for pediatric patients: Perspectives from parents with diverse sociodemographic characteristics. American journal of medical genetics. Part A Halley, M. C., Young, J. L., Fernandez, L., Kohler, J. N., Undiagnosed Diseases Network, Bernstein, J. A., Wheeler, M. T., Tabor, H. K. 1800

  Abstract

  Given the limited therapeutic options for most rare diseases diagnosed through genomic sequencing (GS) and the proportion of patients who remain undiagnosed even after GS, it is important to characterize a broader range of benefits and potential harms of GS from the perspectives of families with diverse sociodemographic characteristics. We recruited parents of children enrolled in the Undiagnosed Diseases Network. Parents completed an in-depth interview, and we conducted a comparative content analysis of the data. Parents (n=30) were demographically diverse, with 43.3% identifying as Hispanic, 33.3% primarily Spanish-speaking, and widely variable household income and education. Parents reported minimal changes in their child's health status following GS but did report a range of other forms of perceived utility, including improvements in their child's healthcare management and access, in their own psychological well-being, and in disease-specific social connections and research opportunities. Parents who received a diagnosis more frequently perceived utility across all domains; however, disutility also was reported by both those with and without a diagnosis. Impacts depended on multiple mediating factors, including parents' underlying expectations and beliefs, family sociodemographic characteristics, individual disease characteristics, and prior healthcare access. Our study suggests that the perceived utility of GS varies widely among parents and may depend on multiple individual, sociodemographic, and contextual factors that are relevant for pre- and post-GS counseling, for value assessment of GS, and for policymaking related to access to new genomic technologies.

  View details for DOI 10.1002/ajmg.a.62619

  View details for PubMedID 34981646

• Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder. American journal of human genetics Küry, S., Ebstein, F., Mollé, A., Besnard, T., Lee, M. K., Vignard, V., Hery, T., Nizon, M., Mancini, G. M., Giltay, J. C., Cogné, B., McWalter, K., Deb, W., Mor-Shaked, H., Li, H., Schnur, R. E., Wentzensen, I. M., Denommé-Pichon, A. S., Fourgeux, C., Verheijen, F. W., Faurie, E., Schot, R., Stevens, C. A., Smits, D. J., Barr, E., Sheffer, R., Bernstein, J. A., Stimach, C. L., Kovitch, E., Shashi, V., Schoch, K., Smith, W., van Jaarsveld, R. H., Hurst, A. C., Smith, K., Baugh, E. H., Bohm, S. G., Vyhnálková, E., Ryba, L., Delnatte, C., Neira, J., Bonneau, D., Toutain, A., Rosenfeld, J. A., Audebert-Bellanger, S., Gilbert-Dussardier, B., Odent, S., Laumonnier, F., Berger, S. I., Smith, A. C., Bourdeaut, F., Stern, M. H., Redon, R., Krüger, E., Margueron, R., Bézieau, S., Poschmann, J., Isidor, B. 2022

  Abstract

  Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.

  View details for DOI 10.1016/j.ajhg.2021.12.011

  View details for PubMedID 35051358

• De novo variants in CACNA1E found in patients with intellectual disability, developmental regression and social cognition deficit but no seizures. Molecular autism Royer-Bertrand, B., Jequier Gygax, M., Cisarova, K., Rosenfeld, J. A., Bassetti, J. A., Moldovan, O., O'Heir, E., Burrage, L. C., Allen, J., Emrick, L. T., Eastman, E., Kumps, C., Abbas, S., Van Winckel, G., Chabane, N., Zackai, E. H., Lebon, S., Keena, B., Bhoj, E. J., Umair, M., Li, D., Donald, K. A., Superti-Furga, A. 2021; 12 (1): 69

  Abstract

  De novo variants in the voltage-gated calcium channel subunit α1 E gene (CACNA1E) have been described as causative of epileptic encephalopathy with contractures, macrocephaly and dyskinesias.Following the observation of an index patient with developmental delay and autism spectrum disorder (ASD) without seizures who had a de novo deleterious CACNA1E variant, we screened GeneMatcher for other individuals with CACNA1E variants and neurodevelopmental phenotypes without epilepsy. The spectrum of pathogenic CACNA1E variants was compared to the mutational landscape of variants in the gnomAD control population database.We identified seven unrelated individuals with intellectual disability, developmental regression and ASD-like behavioral profile, and notably without epilepsy, who had de novo heterozygous putatively pathogenic variants in CACNA1E. Age of onset of clinical manifestation, presence or absence of regression and degree of severity were variable, and no clear-cut genotype-phenotype association could be recognized. The analysis of disease-associated variants and their comparison to benign variants from the control population allowed for the identification of regions in the CACNA1E protein that seem to be intolerant to substitutions and thus more likely to harbor pathogenic variants. As in a few reported cases with CACNA1E variants and epilepsy, one patient showed a positive clinical behavioral response to topiramate, a specific calcium channel modulator.The significance of our study is limited by the absence of functional experiments of the effect of identified variants, the small sample size and the lack of systematic ASD assessment in all participants. Moreover, topiramate was given to one patient only and for a short period of time.Our results indicate that CACNA1E variants may result in neurodevelopmental disorders without epilepsy and expand the mutational and phenotypic spectrum of this gene. CACNA1E deserves to be included in gene panels for non-specific developmental disorders, including ASD, and not limited to patients with seizures, to improve diagnostic recognition and explore the possible efficacy of topiramate.

  View details for DOI 10.1186/s13229-021-00473-3

  View details for PubMedID 34702355

  View details for PubMedCentralID PMC8547031

• Variable clinical severity in TANGO2 deficiency: Case series and literature review. American journal of medical genetics. Part A Schymick, J., Leahy, P., Cowan, T., Ruzhnikov, M. R., Gates, R., Fernandez, L., Pramanik, G., Undiagnosed Diseases Network, Yarlagadda, V., Wheeler, M., Bernstein, J. A., Enns, G. M., Lee, C. 2021

  Abstract

  Biallelic pathogenic variants in the TANGO2 (transport and Golgi organization 2 homolog) gene have been identified as causing a rare metabolic disorder characterized by susceptibility to recurrent rhabdomyolysis, lactic acidosis, encephalopathy, and life-threatening tachyarrhythmias. Recently published reports suggest variable clinical severity and phenotypes. This study details five new patients from two families with biallelic pathogenic variants in the TANGO2 gene identified by whole exome sequencing and includes the largest number of affected individuals from a single family reported to date. We document significant intrafamilial variability and highlight that milder phenotypes may be underrecognized. We present biochemical and clinical data to help highlight the features that aid in consideration of this condition in the differential with disorders of fatty acid oxidation. We also present a comprehensive literature review summarizing the molecular, clinical, and biochemical findings for 92 individuals across 13 publications. Of the 27 pathogenic variants reported to date, the recurrent exons 3-9 deletion represents the most common variant seen in 42% of individuals with TANGO2 deficiency. Common clinical features seen in >70% of all individuals include acute metabolic crisis, rhabdomyolysis, neurologic abnormalities, developmental delay, and intellectual disability. Findings such as elevated creatine kinase, hypothyroidism, ketotic hypoglycemia, QT prolongation, or abnormalities of long-chain acylcarnitines and urine dicarboxylic acids should raise clinical suspicion for this life-threatening condition.

  View details for DOI 10.1002/ajmg.a.62543

  View details for PubMedID 34668327

• <i>Gene.iobio</i>: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization SCIENTIFIC REPORTS Di Sera, T., Velinder, M., Ward, A., Qiao, Y., Georges, S., Miller, C., Pitman, A., Richards, W., Ekawade, A., Viskochil, D., Carey, J. C., Pace, L., Bale, J., Clardy, S. L., Andrews, A., Botto, L., Marth, G. 2021; 11 (1): 20307

  Abstract

  With increasing utilization of comprehensive genomic data to guide clinical care, anticipated to become the standard of care in many clinical settings, the practice of diagnostic medicine is undergoing a notable shift. However, the move from single-gene or panel-based genetic testing to exome and genome sequencing has not been matched by the development of tools to enable diagnosticians to interpret increasingly complex or uncertain genomic findings. Here, we present gene.iobio, a real-time, intuitive and interactive web application for clinically-driven variant interrogation and prioritization. We show gene.iobio is a novel and effective approach that significantly improves upon and reimagines existing methods. In a radical departure from existing methods that present variants and genomic data in text and table formats, gene.iobio provides an interactive, intuitive and visually-driven analysis environment. We demonstrate that adoption of gene.iobio in clinical and research settings empowers clinical care providers to interact directly with patient genomic data both for establishing clinical diagnoses and informing patient care, using sophisticated genomic analyses that previously were only accessible via complex command line tools.

  View details for DOI 10.1038/s41598-021-99752-5

  View details for Web of Science ID 000707032500099

  View details for PubMedID 34645894

  View details for PubMedCentralID PMC8514592

• Has the time come for gastrointestinal functional testing to be included as part of autonomic nervous system testing? Pace, L., Hemp, J., Cortez, M., Goodman, B. ELSEVIER. 2021: 41

  View details for DOI 10.1016/j.jns.2021.118868

  View details for Web of Science ID 000713637302128

• Symptomatic gastrointestinal dysmotility in autonomic neuropathy Langford, J., Millsap, L., Pace, L., Hemp, J., Cortez, M. ELSEVIER. 2021: 41

  View details for DOI 10.1016/j.jns.2021.118869

  View details for Web of Science ID 000713637302129

• One is the loneliest number: genotypic matchmaking using the electronic health record. Genetics in medicine : official journal of the American College of Medical Genetics Brokamp, E., Koziura, M. E., Phillips, J. A., Tang, L. A., Cogan, J. D., Rives, L. C., Robertson, A. K., Duncan, L., Bican, A., Peterson, J. F., Newman, J. H., Hamid, R., Bastarache, L. 2021; 23 (10): 1830-1832

  View details for DOI 10.1038/s41436-021-01179-w

  View details for PubMedID 34230636

  View details for PubMedCentralID PMC11140587

• Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genetics in medicine : official journal of the American College of Medical Genetics Rodan, L. H., Spillmann, R. C., Kurata, H. T., Lamothe, S. M., Maghera, J., Jamra, R. A., Alkelai, A., Antonarakis, S. E., Atallah, I., Bar-Yosef, O., Bilan, F., Bjorgo, K., Blanc, X., Van Bogaert, P., Bolkier, Y., Burrage, L. C., Christ, B. U., Granadillo, J. L., Dickson, P., Donald, K. A., Dubourg, C., Eliyahu, A., Emrick, L., Engleman, K., Gonfiantini, M. V., Good, J. M., Kalser, J., Kloeckner, C., Lachmeijer, G., Macchiaiolo, M., Nicita, F., Odent, S., O'Heir, E., Ortiz-Gonzalez, X., Pacio-Miguez, M., Palomares-Bralo, M., Pena, L., Platzer, K., Quinodoz, M., Ranza, E., Rosenfeld, J. A., Roulet-Perez, E., Santani, A., Santos-Simarro, F., Pode-Shakked, B., Skraban, C., Slaugh, R., Superti-Furga, A., Thiffault, I., van Jaabrsveld, R. H., Vincent, M., Wang, H. G., Zacher, P., Rush, E., Pitt, G. S., Au, P. Y., Shashi, V. 2021; 23 (10): 1922-1932

  Abstract

  CACNA1C encodes the alpha-1-subunit of a voltage-dependent L-type calcium channel expressed in human heart and brain. Heterozygous variants in CACNA1C have previously been reported in association with Timothy syndrome and long QT syndrome. Several case reports have suggested that CACNA1C variation may also be associated with a primarily neurological phenotype.We describe 25 individuals from 22 families with heterozygous variants in CACNA1C, who present with predominantly neurological manifestations.Fourteen individuals have de novo, nontruncating variants and present variably with developmental delays, intellectual disability, autism, hypotonia, ataxia, and epilepsy. Functional studies of a subgroup of missense variants via patch clamp experiments demonstrated differential effects on channel function in vitro, including loss of function (p.Leu1408Val), neutral effect (p.Leu614Arg), and gain of function (p.Leu657Phe, p.Leu614Pro). The remaining 11 individuals from eight families have truncating variants in CACNA1C. The majority of these individuals have expressive language deficits, and half have autism.We expand the phenotype associated with CACNA1C variants to include neurodevelopmental abnormalities and epilepsy, in the absence of classic features of Timothy syndrome or long QT syndrome.

  View details for DOI 10.1038/s41436-021-01232-8

  View details for PubMedID 34163037

  View details for PubMedCentralID PMC8488020

• Genetic counselor roles in the undiagnosed diseases network research study: Clinical care, collaboration, and curation. Journal of genetic counseling Kohler, J. N., Kelley, E. G., Boyd, B. M., Sillari, C. H., Marwaha, S., Undiagnosed Diseases Network, Wheeler, M. T., Acosta, M. T., Adam, M., Adams, D. R., Agrawal, P. B., Alejandro, M. E., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Azamian, M. S., Bacino, C. A., Bademci, G., Baker, E., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bennet, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonnenmann, C., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Chang, T. C., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Sessions Cole, F., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Deardorff, M., Dell'Angelica, E. C., Dhar, S. U., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Draper, D. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Esteves, C., Falk, M., Fernandez, L., Ferreira, C., Fieg, E. L., Findley, L. C., Fisher, P. G., Fogel, B. L., Forghani, I., Fresard, L., Gahl, W. A., Glass, I., Gochuico, B., Godfrey, R. A., Golden-Grant, K., Goldman, A. M., Goldrich, M. P., Goldstein, D. B., Grajewski, A., Groden, C. A., Gutierrez, I., Hahn, S., Hamid, R., Hanchard, N. A., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Huryn, L., Isasi, R., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Karaviti, L., Kennedy, J., Kiley, D., Kobren, S. N., Kohane, I. S., Kohler, J. N., Krakow, D., Krasnewich, D. M., Kravets, E., Korrick, S., Koziura, M., Krier, J. B., Lalani, S. R., Lam, B., Lam, C., LaMoure, G. L., Lanpher, B. C., Lanza, I. R., Latham, L., LeBlanc, K., Lee, B. H., Lee, H., Levitt, R., Lewis, R. A., Lincoln, S. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., MacDowall, J., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Majcherska, M. M., Mak, B. C., Maclidan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Markello, T. C., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., McGee, E., Mefford, H., Lawrence Merritt, J., Might, M., Mirzaa, G., Morava, E., Moretti, P. M., Mosbrook-Davis, D., Mulvihill, J. J., Murdock, D. R., Nagy, A., Nakano-Okuno, M., Nath, A., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Carl Pallais, J., Palmer, C. G., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Power, B., Pusey, B. N., Quinlan, A., Raskind, W., Raja, A. N., Rao, D. A., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Samson, S. L., Saporta, M., Ron Scott, C., Schaechter, J., Schedl, T., Schoch, K., Scott, D. A., Shashi, V., Shin, J., Signer, R., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solem, E., Solnica-Krezel, L., Solomon, B., Spillmann, R. C., Stoler, J. M., Sullivan, J. A., Sullivan, K., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, A. L., Tan, Q. K., Tekin, M., Telischi, F., Thorson, W., Thurm, A., Tifft, C. J., Toro, C., Tran, A. A., Tucker, B. M., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Wallace, S., Walley, N. M., Walsh, C. A., Walker, M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Wener, M., Wenger, T., Perry, K. W., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Woods, J. D., Yamamoto, S., Yang, J., Yousef, M., Zastrow, D. B., Zein, W., Zhao, C., Zuchner, S. 2021

  Abstract

  Genetic counselors (GCs) are increasingly filling important positions on research study teams, but there is limited literature describing the roles of GCs in these settings. GCs on the Undiagnosed Diseases Network (UDN) study team serve in a variety of roles across the research network and provide an opportunity to better understand genetic counselor roles in research. To quantitatively characterize the tasks regularly performed and professional fulfillment derived from these tasks, two surveys were administered to UDN GCs in a stepwise fashion. Responses from the first, free-response survey elicited the scope of tasks which informed development of a second structured, multiple-select survey. In survey 2, respondents were asked to select which roles they performed. Across 19 respondents, roles in survey 2 received a total of 947 selections averaging approximately 10 selections per role. When asked to indicate what roles they performed, respondent selected a mean of 50 roles (range 22-70). Survey 2 data were analyzed via thematic coding of responses and hierarchical cluster analysis to identify patterns in responses. From the thematic analysis, 20 non-overlapping codes emerged in seven categories: clinical interaction and care, communication, curation, leadership, participant management, research, and team management. Three themes emerged from the categories that represented the roles of GCs in the UDN: clinical care, collaboration, and curation. Cluster analyses showed that responses were more similar among individuals at the same institution than between institutions. This study highlights the ways GCs apply their unique skill set in the context of a clinical translational research network. Additionally, findings from this study reinforce the wide applicability of core skills that are part of genetic counseling training. Clinical literacy, genomics expertise and analysis, interpersonal, psychosocial and counseling skills, education, professional practice skills, and an understanding of research processes make genetic counselors well suited for such roles and poised to positively impact research experiences and outcomes for participants.

  View details for DOI 10.1002/jgc4.1493

  View details for PubMedID 34374469

• Pathogenic MAST3 Variants in the STK Domain Are Associated with Epilepsy. Annals of neurology Spinelli, E., Christensen, K. R., Bryant, E., Schneider, A., Rakotomamonjy, J., Muir, A. M., Giannelli, J., Littlejohn, R. O., Roeder, E. R., Schmidt, B., Wilson, W. G., Marco, E. J., Iwama, K., Kumada, S., Pisano, T., Barba, C., Vetro, A., Brilstra, E. H., van Jaarsveld, R. H., Matsumoto, N., Goldberg-Stern, H., Carney, P. W., Andrews, P. I., El Achkar, C. M., Berkovic, S., Rodan, L. H., McWalter, K., Guerrini, R., Scheffer, I. E., Mefford, H. C., Mandelstam, S., Laux, L., Millichap, J. J., Guemez-Gamboa, A., Nairn, A. C., Carvill, G. L. 2021; 90 (2): 274-284

  Abstract

  The MAST family of microtubule-associated serine-threonine kinases (STKs) have distinct expression patterns in the developing and mature human and mouse brain. To date, only MAST1 has been conclusively associated with neurological disease, with de novo variants in individuals with a neurodevelopmental disorder, including a mega corpus callosum.Using exome sequencing, we identify MAST3 missense variants in individuals with epilepsy. We also assess the effect of these variants on the ability of MAST3 to phosphorylate the target gene product ARPP-16 in HEK293T cells.We identify de novo missense variants in the STK domain in 11 individuals, including 2 recurrent variants p.G510S (n = 5) and p.G515S (n = 3). All 11 individuals had developmental and epileptic encephalopathy, with 8 having normal development prior to seizure onset at <2 years of age. All patients developed multiple seizure types, 9 of 11 patients had seizures triggered by fever and 9 of 11 patients had drug-resistant seizures. In vitro analysis of HEK293T cells transfected with MAST3 cDNA carrying a subset of these patient-specific missense variants demonstrated variable but generally lower expression, with concomitant increased phosphorylation of the MAST3 target, ARPP-16, compared to wild-type. These findings suggest the patient-specific variants may confer MAST3 gain-of-function. Moreover, single-nuclei RNA sequencing and immunohistochemistry shows that MAST3 expression is restricted to excitatory neurons in the cortex late in prenatal development and postnatally.In summary, we describe MAST3 as a novel epilepsy-associated gene with a potential gain-of-function pathogenic mechanism that may be primarily restricted to excitatory neurons in the cortex. ANN NEUROL 2021;90:274-284.

  View details for DOI 10.1002/ana.26147

  View details for PubMedID 34185323

  View details for PubMedCentralID PMC8324566

• PPP3CA truncating variants clustered in the regulatory domain cause early-onset refractory epilepsy. Clinical genetics Panneerselvam, S., Wang, J., Zhu, W., Dai, H., Pappas, J. G., Rabin, R., Low, K. J., Rosenfeld, J. A., Emrick, L., Xiao, R., Xia, F., Yang, Y., Eng, C. M., Anderson, A., Chau, V., Soler-Alfonso, C., Streff, H., Lalani, S. R., Mercimek-Andrews, S., Bi, W. 2021; 100 (2): 227-233

  Abstract

  PPP3CA encodes the catalytic subunit of calcineurin, a calcium-calmodulin-regulated serine-threonine phosphatase. Loss-of-function (LoF) variants in the catalytic domain have been associated with epilepsy, while gain-of-function (GoF) variants in the auto-inhibitory domain cause multiple congenital abnormalities. We herein report five new patients with de novo PPP3CA variants. Interestingly, the two frameshift variants in this study and the six truncating variants reported previously are all located within a 26-amino acid region in the regulatory domain (RD). Patients with a truncating variant had more severe earlier onset seizures compared to patients with a LoF missense variant, while autism spectrum disorder was a more frequent feature in the latter. Expression studies of a truncating variant showed apparent RNA expression from the mutant allele, but no detectable mutant protein. Our data suggest that PPP3CA truncating variants clustered in the RD, causing more severe early-onset refractory epilepsy and representing a type of variants distinct from LoF or GoF missense variants.

  View details for DOI 10.1111/cge.13979

  View details for PubMedID 33963760

• Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome. Nature genetics Cousin, M. A., Creighton, B. A., Breau, K. A., Spillmann, R. C., Torti, E., Dontu, S., Tripathi, S., Ajit, D., Edwards, R. J., Afriyie, S., Bay, J. C., Harper, K. M., Beltran, A. A., Munoz, L. J., Falcon Rodriguez, L., Stankewich, M. C., Person, R. E., Si, Y., Normand, E. A., Blevins, A., May, A. S., Bier, L., Aggarwal, V., Mancini, G. M., van Slegtenhorst, M. A., Cremer, K., Becker, J., Engels, H., Aretz, S., MacKenzie, J. J., Brilstra, E., van Gassen, K. L., van Jaarsveld, R. H., Oegema, R., Parsons, G. M., Mark, P., Helbig, I., McKeown, S. E., Stratton, R., Cogne, B., Isidor, B., Cacheiro, P., Smedley, D., Firth, H. V., Bierhals, T., Kloth, K., Weiss, D., Fairley, C., Shieh, J. T., Kritzer, A., Jayakar, P., Kurtz-Nelson, E., Bernier, R. A., Wang, T., Eichler, E. E., van de Laar, I. M., McConkie-Rosell, A., McDonald, M. T., Kemppainen, J., Lanpher, B. C., Schultz-Rogers, L. E., Gunderson, L. B., Pichurin, P. N., Yoon, G., Zech, M., Jech, R., Winkelmann, J., Beltran, A. S., Zimmermann, M. T., Temple, B., Moy, S. S., Klee, E. W., Tan, Q. K., Lorenzo, D. N. 2021; 53 (7): 1006-1021

  Abstract

  SPTBN1 encodes βII-spectrin, the ubiquitously expressed β-spectrin that forms micrometer-scale networks associated with plasma membranes. Mice deficient in neuronal βII-spectrin have defects in cortical organization, developmental delay and behavioral deficiencies. These phenotypes, while less severe, are observed in haploinsufficient animals, suggesting that individuals carrying heterozygous SPTBN1 variants may also show measurable compromise of neural development and function. Here we identify heterozygous SPTBN1 variants in 29 individuals with developmental, language and motor delays; mild to severe intellectual disability; autistic features; seizures; behavioral and movement abnormalities; hypotonia; and variable dysmorphic facial features. We show that these SPTBN1 variants lead to effects that affect βII-spectrin stability, disrupt binding to key molecular partners, and disturb cytoskeleton organization and dynamics. Our studies define SPTBN1 variants as the genetic basis of a neurodevelopmental syndrome, expand the set of spectrinopathies affecting the brain and underscore the critical role of βII-spectrin in the central nervous system.

  View details for DOI 10.1038/s41588-021-00886-z

  View details for PubMedID 34211179

  View details for PubMedCentralID PMC8273149

• Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Molecular genetics & genomic medicine Cope, H., Barseghyan, H., Bhattacharya, S., Fu, Y., Hoppman, N., Marcou, C., Walley, N., Rehder, C., Deak, K., Alkelai, A., Vilain, E., Shashi, V. 2021; 9 (7): e1665

  Abstract

  Currently available structural variant (SV) detection methods do not span the complete spectrum of disease-causing SVs. Optical genome mapping (OGM), an emerging technology with the potential to resolve diagnostic dilemmas, was performed to investigate clinically-relevant SVs in a 4-year-old male with an epileptic encephalopathy of undiagnosed molecular origin.OGM was utilized to image long, megabase-size DNA molecules, fluorescently labeled at specific sequence motifs throughout the genome with high sensitivity for detection of SVs greater than 500 bp in size. OGM results were confirmed in a CLIA-certified laboratory via mate-pair sequencing.OGM identified a mosaic, de novo 90 kb deletion and inversion on the X chromosome disrupting the CDKL5 gene. Detection of the mosaic deletion, which had been previously undetected by chromosomal microarray, an infantile epilepsy panel including exon-level microarray for CDKL5, exome sequencing as well as genome sequencing, resulted in a diagnosis of X-linked dominant early infantile epileptic encephalopathy-2.OGM affords an effective technology for the detection of SVs, especially those that are mosaic, since these remain difficult to detect with current NGS technologies and with conventional chromosomal microarrays. Further research in undiagnosed populations with OGM is warranted.

  View details for DOI 10.1002/mgg3.1665

  View details for PubMedID 33955715

  View details for PubMedCentralID PMC8372083

• Missense and truncating variants in CHD5 in a dominant neurodevelopmental disorder with intellectual disability, behavioral disturbances, and epilepsy. Human genetics Parenti, I., Lehalle, D., Nava, C., Torti, E., Leitão, E., Person, R., Mizuguchi, T., Matsumoto, N., Kato, M., Nakamura, K., de Man, S. A., Cope, H., Shashi, V., Friedman, J., Joset, P., Steindl, K., Rauch, A., Muffels, I., van Hasselt, P. M., Petit, F., Smol, T., Le Guyader, G., Bilan, F., Sorlin, A., Vitobello, A., Philippe, C., van de Laar, I. M., van Slegtenhorst, M. A., Campeau, P. M., Au, P. Y., Nakashima, M., Saitsu, H., Yamamoto, T., Nomura, Y., Louie, R. J., Lyons, M. J., Dobson, A., Plomp, A. S., Motazacker, M. M., Kaiser, F. J., Timberlake, A. T., Fuchs, S. A., Depienne, C., Mignot, C. 2021; 140 (7): 1109-1120

  Abstract

  Located in the critical 1p36 microdeletion region, the chromodomain helicase DNA-binding protein 5 (CHD5) gene encodes a subunit of the nucleosome remodeling and deacetylation (NuRD) complex required for neuronal development. Pathogenic variants in six of nine chromodomain (CHD) genes cause autosomal dominant neurodevelopmental disorders, while CHD5-related disorders are still unknown. Thanks to GeneMatcher and international collaborations, we assembled a cohort of 16 unrelated individuals harboring heterozygous CHD5 variants, all identified by exome sequencing. Twelve patients had de novo CHD5 variants, including ten missense and two splice site variants. Three familial cases had nonsense or missense variants segregating with speech delay, learning disabilities, and/or craniosynostosis. One patient carried a frameshift variant of unknown inheritance due to unavailability of the father. The most common clinical features included language deficits (81%), behavioral symptoms (69%), intellectual disability (64%), epilepsy (62%), and motor delay (56%). Epilepsy types were variable, with West syndrome observed in three patients, generalized tonic-clonic seizures in two, and other subtypes observed in one individual each. Our findings suggest that, in line with other CHD-related disorders, heterozygous CHD5 variants are associated with a variable neurodevelopmental syndrome that includes intellectual disability with speech delay, epilepsy, and behavioral problems as main features.

  View details for DOI 10.1007/s00439-021-02283-2

  View details for PubMedID 33944996

  View details for PubMedCentralID PMC8197709

• Heterozygous variants in SPTBN1 cause intellectual disability and autism. American journal of medical genetics. Part A Rosenfeld, J. A., Xiao, R., Bekheirnia, M. R., Kanani, F., Parker, M. J., Koenig, M. K., van Haeringen, A., Ruivenkamp, C., Rosmaninho-Salgado, J., Almeida, P. M., Sá, J., Pinto Basto, J., Palen, E., Oetjens, K. F., Burrage, L. C., Xia, F., Liu, P., Eng, C. M., Yang, Y., Posey, J. E., Lee, B. H. 2021; 185 (7): 2037-2045

  Abstract

  Spectrins are common components of cytoskeletons, binding to cytoskeletal elements and the plasma membrane, allowing proper localization of essential membrane proteins, signal transduction, and cellular scaffolding. Spectrins are assembled from α and β subunits, encoded by SPTA1 and SPTAN1 (α) and SPTB, SPTBN1, SPTBN2, SPTBN4, and SPTBN5 (β). Pathogenic variants in various spectrin genes are associated with erythroid cell disorders (SPTA1, SPTB) and neurologic disorders (SPTAN1, SPTBN2, and SPTBN4), but no phenotypes have been definitively associated with variants in SPTBN1 or SPTBN5. Through exome sequencing and case matching, we identified seven unrelated individuals with heterozygous SPTBN1 variants: two with de novo missense variants and five with predicted loss-of-function variants (found to be de novo in two, while one was inherited from a mother with a history of learning disabilities). Common features include global developmental delays, intellectual disability, and behavioral disturbances. Autistic features (4/6) and epilepsy (2/7) or abnormal electroencephalogram without overt seizures (1/7) were present in a subset. Identification of loss-of-function variants suggests a haploinsufficiency mechanism, but additional functional studies are required to fully elucidate disease pathogenesis. Our findings support the essential roles of SPTBN1 in human neurodevelopment and expand the knowledge of human spectrinopathy disorders.

  View details for DOI 10.1002/ajmg.a.62201

  View details for PubMedID 33847457

  View details for PubMedCentralID PMC11182376

• Postural orthostatic tachycardia syndrome (POTS): Priorities for POTS care and research from a 2019 National Institutes of Health Expert Consensus Meeting - Part 2. Autonomic neuroscience : basic & clinical Raj, S. R., Bourne, K. M., Stiles, L. E., Miglis, M. G., Cortez, M. M., Miller, A. J., Freeman, R., Biaggioni, I., Rowe, P. C., Sheldon, R. S., Shibao, C. A., Diedrich, A., Systrom, D. M., Cook, G. A., Doherty, T. A., Abdallah, H. I., Grubb, B. P., Fedorowski, A., Stewart, J. M., Arnold, A. C., Pace, L. A., Axelsson, J., Boris, J. R., Moak, J. P., Goodman, B. P., Chemali, K. R., Chung, T. H., Goldstein, D. S., Darbari, A., Vernino, S. 2021: 102836

  Abstract

  The National Institutes of Health hosted a workshop in 2019 to build consensus around the current state of understanding of the pathophysiology of postural orthostatic tachycardia syndrome (POTS) and to identify knowledge gaps that must be addressed to enhance clinical care of POTS patients through research. This second (of two) articles summarizes current knowledge gaps, and outlines the clinical and research priorities for POTS. POTS is a complex, multi-system, chronic disorder of the autonomic nervous system characterized by orthostatic intolerance and orthostatic tachycardia without hypotension. Patients often experience a host of other related disabling symptoms. The functional and economic impacts of this disorder are significant. The pathophysiology remains incompletely understood. Beyond the significant gaps in understanding the disorder itself, there is a paucity of evidence to guide treatment which can contribute to suboptimal care for this patient population. The vast majority of physicians have minimal to no familiarity or training in the assessment and management of POTS. Funding for POTS research remains very low relative to the size of the patient population and impact of the syndrome. In addition to efforts to improve awareness and physician education, an investment in research infrastructure including the development of standardized disease-specific evaluation tools and outcome measures is needed to facilitate effective collaborative research. A national POTS research consortium could facilitate well-controlled multidisciplinary clinical research studies and therapeutic trials. These priorities will require a substantial increase in the number of research investigators and the amount of research funding in this area.

  View details for DOI 10.1016/j.autneu.2021.102836

  View details for PubMedID 34246578

• Postural orthostatic tachycardia syndrome (POTS): State of the science and clinical care from a 2019 National Institutes of Health Expert Consensus Meeting - Part 1. Autonomic neuroscience : basic & clinical Vernino, S., Bourne, K. M., Stiles, L. E., Grubb, B. P., Fedorowski, A., Stewart, J. M., Arnold, A. C., Pace, L. A., Axelsson, J., Boris, J. R., Moak, J. P., Goodman, B. P., Chemali, K. R., Chung, T. H., Goldstein, D. S., Diedrich, A., Miglis, M. G., Cortez, M. M., Miller, A. J., Freeman, R., Biaggioni, I., Rowe, P. C., Sheldon, R. S., Shibao, C. A., Systrom, D. M., Cook, G. A., Doherty, T. A., Abdallah, H. I., Darbari, A., Raj, S. R. 2021: 102828

  Abstract

  Postural orthostatic tachycardia syndrome (POTS) is a chronic and often disabling disorder characterized by orthostatic intolerance with excessive heart rate increase without hypotension during upright posture. Patients often experience a constellation of other typical symptoms including fatigue, exercise intolerance and gastrointestinal distress. A typical patient with POTS is a female of child-bearing age, who often first displays symptoms in adolescence. The onset of POTS may be precipitated by immunological stressors such as a viral infection. A variety of pathophysiologies are involved in the abnormal postural tachycardia response; however, the pathophysiology of the syndrome is incompletely understood and undoubtedly multifaceted. Clinicians and researchers focused on POTS convened at the National Institutes of Health in July 2019 to discuss the current state of understanding of the pathophysiology of POTS and to identify priorities for POTS research. This article, the first of two articles summarizing the information discussed at this meeting, summarizes the current understanding of this disorder and best practices for clinical care. The evaluation of a patient with suspected POTS should seek to establish the diagnosis, identify co-morbid conditions, and exclude conditions that could cause or mimic the syndrome. Once diagnosed, management typically begins with patient education and non-pharmacologic treatment options. Various medications are often used to address specific symptoms, but there are currently no FDA-approved medications for the treatment of POTS, and evidence for many of the medications used to treat POTS is not robust.

  View details for DOI 10.1016/j.autneu.2021.102828

  View details for PubMedID 34144933

• Progressive cerebellar atrophy in a patient with complex II and III deficiency and a novel deleterious variant in SDHA: A Counseling Conundrum. Molecular genetics & genomic medicine Sturrock, B. R., Macnamara, E. F., McGuire, P., Kruk, S., Yang, I., Murphy, J., Tifft, C. J., Gordon-Lipkin, E. 2021; 9 (6): e1692

  Abstract

  Complex II is an essential component of the electron transport chain, linking it with the tricarboxylic acid cycle. Its four subunits are encoded in the nuclear genome, and deleterious variants in these genes, including SDHA (OMIM 600857), are associated with a wide range of symptoms including neurological disease, cardiomyopathy, and neoplasia (paraganglioma-pheochromocytomas (PGL/PCC), and gastrointestinal stromal tumors). Deleterious variants of SDHA are most frequently associated with Leigh and Leigh-like syndromes.Here, we describe a case of a 9-year-old boy with tremor, nystagmus, hypotonia, developmental delay, significant ataxia, and progressive cerebellar atrophy. He was found to have biallelic variants in SDHA, a known pathogenic variant (c.91C>T (p.R31*)), and a variant of unknown significance (c.454G>A (p.E152K)). Deficient activity of complexes II and III was detected in fibroblasts from the patient consistent with a diagnosis of a respiratory chain disorder.We, therefore, consider whether c.454G>A (p.E152K) is, indeed, a pathogenic variant, and what implications it has for family members who carry the same variant.

  View details for DOI 10.1002/mgg3.1692

  View details for PubMedID 33960148

  View details for PubMedCentralID PMC8222855

• A description of novel variants and review of phenotypic spectrum in UBA5-related early epileptic encephalopathy. Cold Spring Harbor molecular case studies Briere, L. C., Walker, M. A., High, F. A., Cooper, C., Rogers, C. A., Callahan, C. J., Ishimura, R., Ichimura, Y., Caruso, P. A., Sharma, N., Brokamp, E., Koziura, M. E., Mohammad, S. S., Dale, R. C., Riley, L. G., Phillips, J. A., Komatsu, M., Sweetser, D. A. 2021; 7 (3)

  Abstract

  Early infantile epileptic encephalopathy-44 (EIEE44, MIM: 617132) is a previously described condition resulting from biallelic variants in UBA5, a gene involved in a ubiquitin-like post-translational modification system called UFMylation. Here we report five children from four families with biallelic pathogenic variants in UBA5 All five children presented with global developmental delay, epilepsy, axial hypotonia, appendicular hypertonia, and a movement disorder, including dystonia in four. Affected individuals in all four families have compound heterozygous pathogenic variants in UBA5 All have the recurrent mild c.1111G > A (p.Ala371Thr) variant in trans with a second UBA5 variant. One patient has the previously described c.562C > T (p. Arg188*) variant, two other unrelated patients have a novel missense variant, c.907T > C (p.Cys303Arg), and the two siblings have a novel missense variant, c.761T > C (p.Leu254Pro). Functional analyses demonstrate that both the p.Cys303Arg variant and the p.Leu254Pro variants result in a significant decrease in protein function. We also review the phenotypes and genotypes of all 15 previously reported families with biallelic UBA5 variants, of which two families have presented with distinct phenotypes, and we describe evidence for some limited genotype-phenotype correlation. The overlap of motor and developmental phenotypes noted in our cohort and literature review adds to the increasing understanding of genetic syndromes with movement disorders-epilepsy.

  View details for DOI 10.1101/mcs.a005827

  View details for PubMedID 33811063

  View details for PubMedCentralID PMC8208045

• Rare disease patient matchmaking: development and outcomes of an internet case-finding strategy in the Undiagnosed Diseases Network. Orphanet journal of rare diseases LeBlanc, K., Glanton, E., Nagy, A., Bater, J., Berro, T., McGuinness, M. A., Studwell, C., Might, M. 2021; 16 (1): 210

  Abstract

  Although clinician, researcher, and patient resources for matchmaking exist, finding similar patients remains an obstacle for rare disease diagnosis. The goals of this study were to develop and test the effectiveness of an Internet case-finding strategy and identify factors associated with increased matching within a rare disease population.Public web pages were created for consented participants. Matches made, time to each inquiry and match, and outcomes were recorded and analyzed using descriptive statistics. A Poisson regression model was run to identify characteristics associated with matches.385 participants were referred to the project and 158 had pages posted. 579 inquiries were received; 89.0% were from the general public and 24.7% resulted in a match. 81.6% of pages received at least one inquiry and 15.0% had at least one patient match. Primary symptom category of neurology, diagnosis, gene page, and photo were associated with increased matches (p ≤ 0.05).This Internet case-finding strategy was of interest to patients, families, and clinicians, and similar patients were identified using this approach. Extending matchmaking efforts to the general public resulted in matches and suggests including this population in matchmaking activities can improve identification of similar patients.

  View details for DOI 10.1186/s13023-021-01825-1

  View details for PubMedID 33971915

  View details for PubMedCentralID PMC8108446

• Model organisms contribute to diagnosis and discovery in the undiagnosed diseases network: current state and a future vision. Orphanet journal of rare diseases Baldridge, D., Wangler, M. F., Bowman, A. N., Yamamoto, S., Schedl, T., Pak, S. C., Postlethwait, J. H., Shin, J., Solnica-Krezel, L., Bellen, H. J., Westerfield, M. 2021; 16 (1): 206

  Abstract

  Decreased sequencing costs have led to an explosion of genetic and genomic data. These data have revealed thousands of candidate human disease variants. Establishing which variants cause phenotypes and diseases, however, has remained challenging. Significant progress has been made, including advances by the National Institutes of Health (NIH)-funded Undiagnosed Diseases Network (UDN). However, 6000-13,000 additional disease genes remain to be identified. The continued discovery of rare diseases and their genetic underpinnings provides benefits to affected patients, of whom there are more than 400 million worldwide, and also advances understanding the mechanisms of more common diseases. Platforms employing model organisms enable discovery of novel gene-disease relationships, help establish variant pathogenicity, and often lead to the exploration of underlying mechanisms of pathophysiology that suggest new therapies. The Model Organism Screening Center (MOSC) of the UDN is a unique resource dedicated to utilizing informatics and functional studies in model organisms, including worm (Caenorhabditis elegans), fly (Drosophila melanogaster), and zebrafish (Danio rerio), to aid in diagnosis. The MOSC has directly contributed to the diagnosis of challenging cases, including multiple patients with complex, multi-organ phenotypes. In addition, the MOSC provides a framework for how basic scientists and clinicians can collaborate to drive diagnoses. Customized experimental plans take into account patient presentations, specific genes and variant(s), and appropriateness of each model organism for analysis. The MOSC also generates bioinformatic and experimental tools and reagents for the wider scientific community. Two elements of the MOSC that have been instrumental in its success are (1) multidisciplinary teams with expertise in variant bioinformatics and in human and model organism genetics, and (2) mechanisms for ongoing communication with clinical teams. Here we provide a position statement regarding the central role of model organisms for continued discovery of disease genes, and we advocate for the continuation and expansion of MOSC-type research entities as a Model Organisms Network (MON) to be funded through grant applications submitted to the NIH, family groups focused on specific rare diseases, other philanthropic organizations, industry partnerships, and other sources of support.

  View details for DOI 10.1186/s13023-021-01839-9

  View details for PubMedID 33962631

  View details for PubMedCentralID PMC8103593

• Interoceptive attention regulation in Ehlers-Danlos syndromes: associations between pain and psychiatric symptom severity TRANSLATIONAL BEHAVIORAL MEDICINE Niermeyer, M., Ball, D., Green, M., Jensen, B., Pace, L., Shingleton, R., Fawver, B., Trapp, S. K. 2021; 11 (10): 1923-1930

  Abstract

  High rates of comorbid chronic pain, anxiety, and mood disorders among individuals with the Ehlers-Danlos syndromes (EDS+) are becoming increasingly recognized, though this complex symptomology remains poorly understood and undertreated. The current project examined whether interoceptive attention regulation is protective against depressive and anxiety symptoms in individuals with suspected EDS+. Data were collected from individuals participating in a transdisciplinary diagnostic visit within an EDS+ specialty consultation clinic. Participants were included in the current analyses (n = 49) if they had complete data on the following measures: the PHQ-8, the GAD-7, the Pain Severity subscale from the West Haven-Yale Multidimensional Pain Inventory, and the Attention Regulation subscale from the Multidimensional Assessment of Interoceptive Awareness. Consistent with expectations, the sample showed high levels of clinically significant anxiety and depressive symptoms. Pain severity ratings were significantly correlated with depressive but not anxiety severity. Moreover, higher levels of perceived interoceptive attention regulation abilities were significantly associated with less severe anxiety and depressive symptoms; however, attention regulation did not moderate the associations of pain with anxiety and depressive symptom severity.The current project replicated recent findings that pain, anxiety, and depression are common in individuals with EDS+. The ability to focus and control somatic attention appears to be protective and a potential target for interventions in EDS+.

  View details for DOI 10.1093/tbm/ibab049

  View details for Web of Science ID 000715378700015

  View details for PubMedID 33949672

  View details for PubMedCentralID PMC9034325

• Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain GENETICS IN MEDICINE Marbach, F., Stoyanov, G., Erger, F., Stratakis, C. A., Settas, N., London, E., Rosenfeld, J. A., Torti, E., Haldeman-Englert, C., Sklirou, E., Kessler, E., Ceulemans, S., Nelson, S. F., Martinez-Agosto, J. A., Palmer, C. S., Signer, R. H., Acosta, M. T., Adam, M., Adams, D. R., Agrawal, P. B., Alejandro, M. E., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Azamian, M. S., Bacino, C. A., Bademci, G., Baker, E., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonnenmann, C., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Chang, T., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Daya, J. G., Deardorff, M., Dell'Angelica, E. C., Dhar, S. U., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Draper, D. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Esteves, C., Falk, M., Fernandez, L., Ferreira, C., Fieg, E. L., Findley, L. C., Fisher, P. G., Fogel, B. L., Forghani, I., Fresard, L., Gahl, W. A., Glass, I., Gochuico, B., Godfrey, R. A., Golden-Grant, K., Goldman, A. M., Goldrich, M. P., Goldstein, D. B., Grajewski, A., Groden, C. A., Gutierrez, I., Hahn, S., Hamid, R., Hanchard, N. A., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Huryn, L., Isasi, R., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Karaviti, L., Kennedy, J., Kiley, D., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Krier, J. B., LaMoure, G. L., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., Latham, L., LeBlanc, K., Lee, B. H., Lee, H., Levitt, R., Lewis, R. A., Lincoln, S. A., Liu, P., Liu, X., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., MacDowall, J., MacRae, C. A., Macnamara, E. F., Maduro, V. V., Majcherska, M. M., Mak, B. C., Malicdan, M. V., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Markello, T. C., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., McGee, E., Mefford, H., Merritt, J., Might, M., Mirzaa, G., Morava, E., Moretti, P. M., Moretti, P., Mosbrook-Davis, D., Mulvihill, J. J., Murdock, D. R., Nagy, A., Nakano-Okuno, M., Nath, A., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J., Palmer, C. S., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Power, B., Pusey, B. N., Quinlan, A., Raja, A. N., Rao, D. A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Samson, S. L., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, C., Scott, D. A., Shashi, V., Shin, J., Signer, R. H., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solem, E., Solnica-Krezel, L., Ben Solomon, Spillmann, R. C., Stoler, J. M., Sullivan, J. A., Sullivan, K., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, A. M., Tan, Q., Tekin, M., Telischi, F., Thorson, W., Thurm, A., Tifft, C. J., Toro, C., Tran, A. A., Tucker, B. M., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Wallace, S., Walley, N. M., Walsh, C. A., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Wener, M., Wenger, T., Perry, K., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Woods, J. D., Yamamoto, S., Yang, J., Yousef, M., Zastrow, D. B., Zein, W., Zhao, C., Zuchner, S., Andrews, M. V., Grange, D. K., Willaert, R., Person, R., Telegrafi, A., Sievers, A., Laugsch, M., Theiss, S., Cheng, Y., Lichtarge, O., Katsonis, P., Stocco, A., Schaaf, C. P., Undiagnosed Diseases Network 2021

  Abstract

  We characterize the clinical and molecular phenotypes of six unrelated individuals with intellectual disability and autism spectrum disorder who carry heterozygous missense variants of the PRKAR1B gene, which encodes the R1β subunit of the cyclic AMP-dependent protein kinase A (PKA).Variants of PRKAR1B were identified by single- or trio-exome analysis. We contacted the families and physicians of the six individuals to collect phenotypic information, performed in vitro analyses of the identified PRKAR1B-variants, and investigated PRKAR1B expression during embryonic development.Recent studies of large patient cohorts with neurodevelopmental disorders found significant enrichment of de novo missense variants in PRKAR1B. In our cohort, de novo origin of the PRKAR1B variants could be confirmed in five of six individuals, and four carried the same heterozygous de novo variant c.1003C>T (p.Arg335Trp; NM_001164760). Global developmental delay, autism spectrum disorder, and apraxia/dyspraxia have been reported in all six, and reduced pain sensitivity was found in three individuals carrying the c.1003C>T variant. PRKAR1B expression in the brain was demonstrated during human embryonal development. Additionally, in vitro analyses revealed altered basal PKA activity in cells transfected with variant-harboring PRKAR1B expression constructs.Our study provides strong evidence for a PRKAR1B-related neurodevelopmental disorder.

  View details for DOI 10.1038/s41436-021-01152-7

  View details for Web of Science ID 000638059400001

  View details for PubMedID 33833410

• Expansion of NEUROD2 phenotypes to include developmental delay without seizures. American journal of medical genetics. Part A Mis, E. K., Sega, A. G., Signer, R. H., Cartwright, T., Ji, W., Martinez-Agosto, J. A., Nelson, S. F., Palmer, C. G., Lee, H., Mitzelfelt, T., Konstantino, M., Jeffries, L., Khokha, M. K., Marco, E., Martin, M. G., Lakhani, S. A. 2021; 185 (4): 1076-1080

  Abstract

  De novo heterozygous variants in the brain-specific transcription factor Neuronal Differentiation Factor 2 (NEUROD2) have been recently associated with early-onset epileptic encephalopathy and developmental delay. Here, we report an adolescent with developmental delay without seizures who was found to have a novel de novo heterozygous NEUROD2 missense variant, p.(Leu163Pro). Functional testing using an in vivo assay of neuronal differentiation in Xenopus laevis tadpoles demonstrated that the patient variant of NEUROD2 displays minimal protein activity, strongly suggesting a loss of function effect. In contrast, a second rare NEUROD2 variant, p.(Ala235Thr), identified in an adolescent with developmental delay but lacking parental studies for inheritance, showed normal in vivo NEUROD2 activity. We thus provide clinical, genetic, and functional evidence that NEUROD2 variants can lead to developmental delay without accompanying early-onset seizures, and demonstrate how functional testing can complement genetic data when determining variant pathogenicity.

  View details for DOI 10.1002/ajmg.a.62064

  View details for PubMedID 33438828

  View details for PubMedCentralID PMC8212414

• Functional and structural analysis of cytokine selective IL6ST defects that cause recessive hyper-IgE syndrome. The Journal of allergy and clinical immunology Chen, Y., Zastrow, D. B., Metcalfe, R. D., Gartner, L., Krause, F., Morton, C. J., Marwaha, S., Fresard, L., Huang, Y., Zhao, C., McCormack, C., Bick, D., Worthey, E. A., Eng, C. M., Gold, J., Undiagnosed Diseases Network, Montgomery, S. B., Fisher, P. G., Ashley, E. A., Wheeler, M. T., Parker, M. W., Shanmugasundaram, V., Putoczki, T. L., Schmidt-Arras, D., Laurence, A., Bernstein, J. A., Griffin, M. D., Uhlig, H. H. 2021

  Abstract

  BACKGROUND: Biallelic variants in IL6ST cause a recessive form of hyper-IgE syndrome (HIES) characterized by high IgE, eosinophilia, defective acute phase response, susceptibility to bacterial infections and skeletal abnormalities due to cytokine selective loss-of-function in GP130 with defective IL-6 and IL-11, variable OSM and IL-27 but sparing LIF signaling.OBJECTIVE: To understand the functional and structural impact of recessive HIES-associated IL6ST variants.METHODS: We investigated a patient with HIES using exome, genome and RNA sequencing. Functional assays assessed IL-6, IL-11, IL-27, OSM, LIF, CT-1, CLC, and CNTF signaling. Molecular dynamic simulations and structural modeling of GP130 cytokine receptor complexes were performed.RESULTS: We identify a patient with compound heterozygous novel missense variants in IL6ST (p.Ala517Pro, and exon-skipping null variant p.Gly484_Pro518delinsArg). The p.Ala517Pro variant results in a more profound IL-6 and IL-11 dominated signaling defect compared to the previously identified recessive IL6ST variants p.Asn404Tyr, and p.Pro498Leu. Molecular dynamics simulations suggest that the p.Ala517Pro and p.Asn404Tyr variants result in increased flexibility of the extracellular membrane-proximal domains of GP130. We propose a structural model that explains the cytokine selectivity of pathogenic IL6ST variants that result in recessive HIES. The variants destabilize the hexameric cytokine receptor complexes whereas the trimeric LIF-GP130-LIFR complex remains stable by an additional membrane-proximal interaction. Deletion of this membrane-proximal interaction site in GP130 consequently causes additional defective LIF signaling and Stuve-Wiedemann syndrome.CONCLUSION: Our data provide a structural basis to understand clinical phenotypes in patients with IL6ST variants.

  View details for DOI 10.1016/j.jaci.2021.02.044

  View details for PubMedID 33771552

• Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nature genetics Bonder, M. J., Smail, C., Gloudemans, M. J., Fresard, L., Jakubosky, D., D'Antonio, M., Li, X., Ferraro, N. M., Carcamo-Orive, I., Mirauta, B., Seaton, D. D., Cai, N., Vakili, D., Horta, D., Zhao, C., Zastrow, D. B., Bonner, D. E., HipSci Consortium, iPSCORE consortium, Undiagnosed Diseases Network, PhLiPS consortium, Wheeler, M. T., Kilpinen, H., Knowles, J. W., Smith, E. N., Frazer, K. A., Montgomery, S. B., Stegle, O., Jan Bonder, M., Seaton, D., Jakubosky, D. A., Brown, C. D., Park, Y. 2021

  Abstract

  Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.

  View details for DOI 10.1038/s41588-021-00800-7

  View details for PubMedID 33664507

• Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases. Genetics in medicine : official journal of the American College of Medical Genetics Kobren, S. N., Baldridge, D., Velinder, M., Krier, J. B., LeBlanc, K., Esteves, C., Pusey, B. N., Zuchner, S., Blue, E., Lee, H., Huang, A., Bastarache, L., Bican, A., Cogan, J., Marwaha, S., Alkelai, A., Murdock, D. R., Liu, P., Wegner, D. J., Paul, A. J., Undiagnosed Diseases Network, Sunyaev, S. R., Kohane, I. S., Acosta, M. T., Adam, M., Adams, D. R., Agrawal, P. B., Alejandro, M. E., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Azamian, M. S., Bacino, C. A., Bademci, G., Baker, E., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonnenmann, C., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Chang, T. C., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Daya, J. G., Deardorff, M., Dell'Angelica, E. C., Dhar, S. U., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Draper, D. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Esteves, C., Falk, M., Fernandez, L., Ferreira, C., Fieg, E. L., Findley, L. C., Fisher, P. G., Fogel, B. L., Forghani, I., Fresard, L., Gahl, W. A., Glass, I., Gochuico, B., Godfrey, R. A., Golden-Grant, K., Goldman, A. M., Goldrich, M. P., Goldstein, D. B., Grajewski, A., Groden, C. A., Gutierrez, I., Hahn, S., Hamid, R., Hanchard, N. A., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Huryn, L., Isasi, R., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Karaviti, L., Kennedy, J., Kiley, D., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Krier, J. B., LaMoure, G. L., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., Latham, L., LeBlanc, K., Lee, B. H., Lee, H., Levitt, R., Lewis, R. A., Lincoln, S. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., MacDowall, J., MacRae, C. A., Macnamara, E. F., Maduro, V. V., Majcherska, M. M., Mak, B. C., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Markello, T. C., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., McGee, E., Mefford, H., Merritt, J. L., Might, M., Mirzaa, G., Morava, E., Moretti, P. M., Moretti, P., Mosbrook-Davis, D., Mulvihill, J. J., Murdock, D. R., Nagy, A., Nakano-Okuno, M., Nath, A., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Power, B., Pusey, B. N., Quinlan, A., Raja, A. N., Rao, D. A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Samson, S. L., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, C. R., Scott, D. A., Shashi, V., Shin, J., Signer, R. H., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solem, E., Solnica-Krezel, L., Ben Solomon, S., Spillmann, R. C., Stoler, J. M., Sullivan, J. A., Sullivan, K., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, A. L., Tan, Q. K., Tekin, M., Telischi, F., Thorson, W., Thurm, A., Tifft, C. J., Toro, C., Tran, A. A., Tucker, B. M., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Wallace, S., Walley, N. M., Walsh, C. A., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Wener, M., Wenger, T., Perry, K. W., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Woods, J. D., Yamamoto, S., Yang, J., Yousef, M., Zastrow, D. B., Zein, W., Zhao, C., Zuchner, S. 2021

  Abstract

  PURPOSE: Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. Although the computational tools incorporated into diagnostic workflows for this task are continually evolving and improving, we nevertheless sought to investigate commonalities across sequencing processing workflows to reveal consensus and standard practice tools and highlight exploratory analyses where technical and theoretical method improvements would be most impactful.METHODS: We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network via meetings with bioinformaticians, online survey forms, and analyses of internal protocols.RESULTS: We found that tools for processing genomic sequencing data can be grouped into four distinct categories. Whereas well-established practices exist for initial variant calling and quality control steps, there is substantial divergence across sites in later stages for variant prioritization and multimodal data integration, demonstrating a diversity of approaches for solving the most mysterious undiagnosed cases.CONCLUSION: The largest differences across diagnostic workflows suggest that advances in structural variant detection, noncoding variant interpretation, and integration of additional biomedical data may be especially promising for solving chronically undiagnosed cases.

  View details for DOI 10.1038/s41436-020-01084-8

  View details for PubMedID 33580225

• A fish with no sex: gonadal and adrenal functions partition between zebrafish NR5A1 co-orthologs. Genetics Yan, Y. L., Titus, T., Desvignes, T., BreMiller, R., Batzel, P., Sydes, J., Farnsworth, D., Dillon, D., Wegner, J., Phillips, J. B., Peirce, J., Dowd, J., Buck, C. L., Miller, A., Westerfield, M., Postlethwait, J. H. 2021; 217 (2)

  Abstract

  People with NR5A1 mutations experience testicular dysgenesis, ovotestes, or adrenal insufficiency, but we do not completely understand the origin of this phenotypic diversity. NR5A1 is expressed in gonadal soma precursor cells before expression of the sex-determining gene SRY. Many fish have two co-orthologs of NR5A1 that likely partitioned ancestral gene subfunctions between them. To explore ancestral roles of NR5A1, we knocked out nr5a1a and nr5a1b in zebrafish. Single-cell RNA-seq identified nr5a1a-expressing cells that co-expressed genes for steroid biosynthesis and the chemokine receptor Cxcl12a in 1-day postfertilization (dpf) embryos, as does the mammalian adrenal-gonadal (interrenal-gonadal) primordium. In 2dpf embryos, nr5a1a was expressed stronger in the interrenal-gonadal primordium than in the early hypothalamus but nr5a1b showed the reverse. Adult Leydig cells expressed both ohnologs and granulosa cells expressed nr5a1a stronger than nr5a1b. Mutants for nr5a1a lacked the interrenal, formed incompletely differentiated testes, had no Leydig cells, and grew far larger than normal fish. Mutants for nr5a1b formed a disorganized interrenal and their gonads completely disappeared. All homozygous mutant genotypes lacked secondary sex characteristics, including male breeding tubercles and female sex papillae, and had exceedingly low levels of estradiol, 11-ketotestosterone, and cortisol. RNA-seq showed that at 21dpf, some animals were developing as females and others were not, independent of nr5a1 genotype. By 35dpf, all mutant genotypes greatly under-expressed ovary-biased genes. Because adult nr5a1a mutants form gonads but lack an interrenal and conversely, adult nr5a1b mutants lack a gonad but have an interrenal, the adrenal, and gonadal functions of the ancestral nr5a1 gene partitioned between ohnologs after the teleost genome duplication, likely owing to reciprocal loss of ancestral tissue-specific regulatory elements. Identifying such elements could provide hints to otherwise unexplained cases of Differences in Sex Development.

  View details for DOI 10.1093/genetics/iyaa030

  View details for PubMedID 33724412

  View details for PubMedCentralID PMC8045690

• Discovery of a novel CHD7 CHARGE syndrome variant by integrated omics analyses. American journal of medical genetics. Part A Granadillo, J. L., Wegner, D. J., Paul, A. J., Willing, M., Sisco, K., Tedder, M. L., Sadikovic, B., Wambach, J. A., Baldridge, D., Cole, F. S. 2021; 185 (2): 544-548

  Abstract

  Chromodomain helicase DNA-binding protein 7 (CHD7) pathogenic variants are identified in more than 90% of infants and children with CHARGE (Coloboma of the iris, retina, and/or optic disk; congenital Heart defects, choanal Atresia, Retardation of growth and development, Genital hypoplasia, and characteristic outer and inner Ear anomalies and deafness) syndrome. Approximately, 10% of cases have no known genetic cause identified. We report a male child with clinical features of CHARGE syndrome and nondiagnostic genetic testing that included chromosomal microarray, CHD7 sequencing and deletion/duplication analysis, SEMA3E sequencing, and trio exome and whole-genome sequencing (WGS). We used a comprehensive clinical assessment, genome-wide methylation analysis (GMA), reanalysis of WGS data, and CHD7 RNA studies to discover a novel variant that causes CHD7 haploinsufficiency. The 7-year-old Hispanic male proband has typical phenotypic features of CHARGE syndrome. GMA revealed a CHD7-associated epigenetic signature. Reanalysis of the WGS data with focused bioinformatic analysis of CHD7 detected a novel, de novo 15 base pair deletion in Intron 4 of CHD7 (c.2239-20_2239-6delGTCTTGGGTTTTTGT [NM_017780.3]). Using proband RNA, we confirmed that this novel deletion causes CHD7 haploinsufficiency by disrupting the canonical 3' splice site and introducing a premature stop codon. Integrated genomic, epigenomic, and transcriptome analyses discovered a novel CHD7 variant that causes CHARGE syndrome.

  View details for DOI 10.1002/ajmg.a.61962

  View details for PubMedID 33184947

  View details for PubMedCentralID PMC8218330

• A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome. European journal of human genetics : EJHG Ghosh, S. G., Scala, M., Beetz, C., Helman, G., Stanley, V., Yang, X., Breuss, M. W., Mazaheri, N., Selim, L., Hadipour, F., Pais, L., Stutterd, C. A., Karageorgou, V., Begtrup, A., Crunk, A., Juusola, J., Willaert, R., Flore, L. A., Kennelly, K., Spencer, C., Brown, M., Trapane, P., Hurst, A. C., Lane Rutledge, S., Goodloe, D. H., McDonald, M. T., Shashi, V., Schoch, K., Tomoum, H., Zaitoun, R., Hadipour, Z., Galehdari, H., Pagnamenta, A. T., Mojarrad, M., Sedaghat, A., Dias, P., Quintas, S., Eslahi, A., Shariati, G., Bauer, P., Simons, C., Houlden, H., Issa, M. Y., Zaki, M. S., Maroofian, R., Gleeson, J. G. 2021; 29 (2): 271-279

  Abstract

  Trafficking protein particle (TRAPP) complexes, which include the TRAPPC4 protein, regulate membrane trafficking between lipid organelles in a process termed vesicular tethering. TRAPPC4 was recently implicated in a recessive neurodevelopmental condition in four unrelated families due to a shared c.454+3A>G splice variant. Here, we report 23 patients from 17 independent families with an early-infantile-onset neurodegenerative presentation, where we also identified the homozygous variant hg38:11:119020256 A>G (NM_016146.5:c.454+3A>G) in TRAPPC4 through exome or genome sequencing. No other clinically relevant TRAPPC4 variants were identified among any of over 10,000 patients with neurodevelopmental conditions. We found the carrier frequency of TRAPPC4 c.454+3A>G was 2.4-5.4 per 10,000 healthy individuals. Affected individuals with the homozygous TRAPPC4 c.454+3A>G variant showed profound psychomotor delay, developmental regression, early-onset epilepsy, microcephaly and progressive spastic tetraplegia. Based upon RNA sequencing, the variant resulted in partial exon 3 skipping and generation of an aberrant transcript owing to use of a downstream cryptic splice donor site, predicting a premature stop codon and nonsense mediated decay. These data confirm the pathogenicity of the TRAPPC4 c.454+3A>G variant, and refine the clinical presentation of TRAPPC4-related encephalopathy.

  View details for DOI 10.1038/s41431-020-00717-5

  View details for PubMedID 32901138

  View details for PubMedCentralID PMC7868361

• Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing. The Journal of clinical investigation Murdock, D. R., Dai, H., Burrage, L. C., Rosenfeld, J. A., Ketkar, S., Müller, M. F., Yépez, V. A., Gagneur, J., Liu, P., Chen, S., Jain, M., Zapata, G., Bacino, C. A., Chao, H. T., Moretti, P., Craigen, W. J., Hanchard, N. A., Lee, B. 2021; 131 (1)

  Abstract

  BACKGROUNDTranscriptome sequencing (RNA-seq) improves diagnostic rates in individuals with suspected Mendelian conditions to varying degrees, primarily by directing the prioritization of candidate DNA variants identified on exome or genome sequencing (ES/GS). Here we implemented an RNA-seq-guided method to diagnose individuals across a wide range of ages and clinical phenotypes.METHODSOne hundred fifteen undiagnosed adult and pediatric patients with diverse phenotypes and 67 family members (182 total individuals) underwent RNA-seq from whole blood and skin fibroblasts at the Baylor College of Medicine (BCM) Undiagnosed Diseases Network clinical site from 2014 to 2020. We implemented a workflow to detect outliers in gene expression and splicing for cases that remained undiagnosed despite standard genomic and transcriptomic analysis.RESULTSThe transcriptome-directed approach resulted in a diagnostic rate of 12% across the entire cohort, or 17% after excluding cases solved on ES/GS alone. Newly diagnosed conditions included Koolen-de Vries syndrome (KANSL1), Renpenning syndrome (PQBP1), TBCK-associated encephalopathy, NSD2- and CLTC-related intellectual disability, and others, all with negative conventional genomic testing, including ES and chromosomal microarray (CMA). Skin fibroblasts exhibited higher and more consistent expression of clinically relevant genes than whole blood. In solved cases with RNA-seq from both tissues, the causative defect was missed in blood in half the cases but none from fibroblasts.CONCLUSIONSFor our cohort of undiagnosed individuals with suspected Mendelian conditions, transcriptome-directed genomic analysis facilitated diagnoses, primarily through the identification of variants missed on ES and CMA.TRIAL REGISTRATIONNot applicable.FUNDINGNIH Common Fund, BCM Intellectual and Developmental Disabilities Research Center, Eunice Kennedy Shriver National Institute of Child Health & Human Development.

  View details for DOI 10.1172/JCI141500

  View details for PubMedID 33001864

  View details for PubMedCentralID PMC7773386

• Diagnosis of mast cell activation syndrome: a global "consensus-2" DIAGNOSIS Afrin, L. B., Ackerley, M. B., Bluestein, L. S., Brewer, J. H., Brook, J. B., Buchanan, A. D., Cuni, J. R., Davey, W. P., Dempsey, T. T., Dorff, S. R., Dubravec, M. S., Guggenheim, A. G., Hindman, K. J., Hoffman, B., Kaufman, D. L., Kratzer, S. J., Lee, T. M., Marantz, M. S., Maxwell, A. J., McCann, K. K., McKee, D. L., Otto, L., Pace, L. A., Perkins, D. D., Radovsky, L., Raleigh, M. S., Rapaport, S. A., Reinhold, E. J., Renneker, M. L., Robinson, W. A., Roland, A. M., Rosenbloom, E., Rowe, P. C., Ruhoy, I. S., Saperstein, D. S., Schlosser, D. A., Schofield, J. R., Settle, J. E., Weinstock, L. B., Wengenroth, M., Westaway, M., Xi, S., Molderings, G. J. 2021; 8 (2): 137-152

  Abstract

  The concept that disease rooted principally in chronic aberrant constitutive and reactive activation of mast cells (MCs), without the gross MC neoplasia in mastocytosis, first emerged in the 1980s, but only in the last decade has recognition of "mast cell activation syndrome" (MCAS) grown significantly. Two principal proposals for diagnostic criteria have emerged. One, originally published in 2012, is labeled by its authors as a "consensus" (re-termed here as "consensus-1"). Another sizable contingent of investigators and practitioners favor a different approach (originally published in 2011, newly termed here as "consensus-2"), resembling "consensus-1" in some respects but differing in others, leading to substantial differences between these proposals in the numbers of patients qualifying for diagnosis (and thus treatment). Overdiagnosis by "consensus-2" criteria has potential to be problematic, but underdiagnosis by "consensus-1" criteria seems the far larger problem given (1) increasing appreciation that MCAS is prevalent (up to 17% of the general population), and (2) most MCAS patients, regardless of illness duration prior to diagnosis, can eventually identify treatment yielding sustained improvement. We analyze these proposals (and others) and suggest that, until careful research provides more definitive answers, diagnosis by either proposal is valid, reasonable, and helpful.

  View details for DOI 10.1515/dx-2020-0005

  View details for Web of Science ID 000648591000003

  View details for PubMedID 32324159

• Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation. Science advances Beck, D. B., Basar, M. A., Asmar, A. J., Thompson, J. J., Oda, H., Uehara, D. T., Saida, K., Pajusalu, S., Talvik, I., D'Souza, P., Bodurtha, J., Mu, W., Barañano, K. W., Miyake, N., Wang, R., Kempers, M., Tamada, T., Nishimura, Y., Okada, S., Kosho, T., Dale, R., Mitra, A., Macnamara, E., Matsumoto, N., Inazawa, J., Walkiewicz, M., Õunap, K., Tifft, C. J., Aksentijevich, I., Kastner, D. L., Rocha, P. P., Werner, A. 2021; 7 (4)

  Abstract

  Reversible modification of proteins with linkage-specific ubiquitin chains is critical for intracellular signaling. Information on physiological roles and underlying mechanisms of particular ubiquitin linkages during human development are limited. Here, relying on genomic constraint scores, we identify 10 patients with multiple congenital anomalies caused by hemizygous variants in OTUD5, encoding a K48/K63 linkage-specific deubiquitylase. By studying these mutations, we find that OTUD5 controls neuroectodermal differentiation through cleaving K48-linked ubiquitin chains to counteract degradation of select chromatin regulators (e.g., ARID1A/B, histone deacetylase 2, and HCF1), mutations of which underlie diseases that exhibit phenotypic overlap with OTUD5 patients. Loss of OTUD5 during differentiation leads to less accessible chromatin at neuroectodermal enhancers and aberrant gene expression. Our study describes a previously unidentified disorder we name LINKED (LINKage-specific deubiquitylation deficiency-induced Embryonic Defects) syndrome and reveals linkage-specific ubiquitin cleavage from chromatin remodelers as an essential signaling mode that coordinates chromatin remodeling during embryogenesis.

  View details for DOI 10.1126/sciadv.abe2116

  View details for PubMedID 33523931

  View details for PubMedCentralID PMC7817106

• Missense variants in CTNNB1 can be associated with vitreoretinopathy-Seven new cases of CTNNB1-associated neurodevelopmental disorder including a previously unreported retinal phenotype. Molecular genetics & genomic medicine Rossetti, L. Z., Bekheirnia, M. R., Lewis, A. M., Mefford, H. C., Golden-Grant, K., Tarczy-Hornoch, K., Briere, L. C., Sweetser, D. A., Walker, M. A., Kravets, E., Stevenson, D. A., Bruenner, G., Sebastian, J., Knapo, J., Rosenfeld, J. A., Marcogliese, P. C., Undiagnosed Diseases Network, Wangler, M. F. 2020: e1542

  Abstract

  BACKGROUND: CTNNB1 (MIM 116806) encodes beta-catenin, an adherens junction protein that supports the integrity between layers of epithelial tissue and mediates intercellular signaling. Recently, various heterozygous germline variants in CTNNB1 have been associated with human disease, including neurodevelopmental disorder with spastic diplegia and visual defects (MIM 615075) as well as isolated familial exudative vitreoretinopathy without developmental delays or other organ system involvement (MIM 617572). From over 40 previously reported patients with CTNNB1-related neurodevelopmental disorder, many have had ocular anomalies including strabismus, hyperopia, and astigmatism. More recently, multiple reports indicate that these abnormalities are associated with the presence of vitreoretinopathy.METHODS: We gathered a cohort of three patients with CTNNB1-related neurodevelopmental disorder, recruited from both our own clinic and referred from outside providers. We then searched for a clinical database comprised of over 12,000 exome sequencing studies to identify and recruit four additional patients.RESULTS: Here, we report seven new cases of CTNNB1-related neurodevelopmental disorder, all harboring de novo variants, six of which were previously unreported. All patients but one presented with a spectrum of ocular abnormalities and one patient, who was found to carry a missense variant in CTNNB1, had notable vitreoretinopathy.CONCLUSIONS: Our findings suggest ophthalmologic screening should be performed in all patients with CTNNB1 variants.

  View details for DOI 10.1002/mgg3.1542

  View details for PubMedID 33350591

• BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms AMERICAN JOURNAL OF HUMAN GENETICS Barish, S., Barakat, T., Michel, B. C., Mashtalir, N., Phillips, J. B., Valencia, A. M., Ugur, B., Wegner, J., Scott, T. M., Bostwick, B., Murdock, D. R., Dai, H., Perenthaler, E., Nikoncuk, A., van Slegtenhorst, M., Brooks, A. S., Keren, B., Nava, C., Mignot, C., Douglas, J., Rodan, L., Nowak, C., Ellard, S., Stals, K., Lynch, S., Faoucher, M., Lesca, G., Edery, P., Engleman, K. L., Zhou, D., Thiffault, I., Herriges, J., Gass, J., Louie, R. J., Stolerman, E., Washington, C., Vetrini, F., Otsubo, A., Pratt, V. M., Conboy, E., Treat, K., Shannon, N., Camacho, J., Wakeling, E., Yuan, B., Chen, C., Rosenfeld, J. A., Westerfield, M., Wangler, M., Yamamoto, S., Kadoch, C., Scott, D. A., Bellen, H. J., Undiagnosed Dis Network 2020; 107 (6): 1096–1112

  Abstract

  SWI/SNF-related intellectual disability disorders (SSRIDDs) are rare neurodevelopmental disorders characterized by developmental disability, coarse facial features, and fifth digit/nail hypoplasia that are caused by pathogenic variants in genes that encode for members of the SWI/SNF (or BAF) family of chromatin remodeling complexes. We have identified 12 individuals with rare variants (10 loss-of-function, 2 missense) in the BICRA (BRD4 interacting chromatin remodeling complex-associated protein) gene, also known as GLTSCR1, which encodes a subunit of the non-canonical BAF (ncBAF) complex. These individuals exhibited neurodevelopmental phenotypes that include developmental delay, intellectual disability, autism spectrum disorder, and behavioral abnormalities as well as dysmorphic features. Notably, the majority of individuals lack the fifth digit/nail hypoplasia phenotype, a hallmark of most SSRIDDs. To confirm the role of BICRA in the development of these phenotypes, we performed functional characterization of the zebrafish and Drosophila orthologs of BICRA. In zebrafish, a mutation of bicra that mimics one of the loss-of-function variants leads to craniofacial defects possibly akin to the dysmorphic facial features seen in individuals harboring putatively pathogenic BICRA variants. We further show that Bicra physically binds to other non-canonical ncBAF complex members, including the BRD9/7 ortholog, CG7154, and is the defining member of the ncBAF complex in flies. Like other SWI/SNF complex members, loss of Bicra function in flies acts as a dominant enhancer of position effect variegation but in a more context-specific manner. We conclude that haploinsufficiency of BICRA leads to a unique SSRIDD in humans whose phenotypes overlap with those previously reported.

  View details for DOI 10.1016/j.ajhg.2020.11.003

  View details for Web of Science ID 000596042000006

  View details for PubMedID 33232675

  View details for PubMedCentralID PMC7820627

• Gender Bias in Medicine Negatively Impacts Diagnosis and Clinical Care for Individuals with Complex Medical Conditions Hemp, J., Ball, D., Green, M., Jensen, B., Shingleton, R., Trapp, S. K., Pace, L. A. MARY ANN LIEBERT, INC. 2020: A21

  View details for Web of Science ID 000598344400069

• An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids GENETICS IN MEDICINE Ferdinandusse, S., McWalter, K., te Brinke, H., Ijlst, L., Mooijer, P. M., Ruiter, J. N., van Lint, A. M., Pras-Raves, M., Wever, E., Millan, F., Sacoto, M., Begtrup, A., Tarnopolsky, M., Brady, L., Ladda, R. L., Sell, S. L., Nowak, C. B., Douglas, J., Tian, C., Ulm, E., Perlman, S., Drack, A. V., Chong, K., Martin, N., Brault, J., Brokamp, E., Toro, C., Gahl, W. A., Macnamara, E. F., Wolfe, L., Waisfisz, Q., Zwijnenburg, P. G., Ziegler, A., Barth, M., Smith, R., Ellingwood, S., Gaebler-Spira, D., Bakhtiari, S., Kruer, M. C., van Kampen, A. C., Wanders, R. A., Waterham, H. R., Cassiman, D., Vaz, F. M., Undiagnosed Dis Network 2021; 23 (4): 740-750

  Abstract

  In this study we investigate the disease etiology in 12 patients with de novo variants in FAR1 all resulting in an amino acid change at position 480 (p.Arg480Cys/His/Leu).Following next-generation sequencing and clinical phenotyping, functional characterization was performed in patients' fibroblasts using FAR1 enzyme analysis, FAR1 immunoblotting/immunofluorescence, and lipidomics.All patients had spastic paraparesis and bilateral congenital/juvenile cataracts, in most combined with speech and gross motor developmental delay and truncal hypotonia. FAR1 deficiency caused by biallelic variants results in defective ether lipid synthesis and plasmalogen deficiency. In contrast, patients' fibroblasts with the de novo FAR1 variants showed elevated plasmalogen levels. Further functional studies in fibroblasts showed that these variants cause a disruption of the plasmalogen-dependent feedback regulation of FAR1 protein levels leading to uncontrolled ether lipid production.Heterozygous de novo variants affecting the Arg480 residue of FAR1 lead to an autosomal dominant disorder with a different disease mechanism than that of recessive FAR1 deficiency and a diametrically opposed biochemical phenotype. Our findings show that for patients with spastic paraparesis and bilateral cataracts, FAR1 should be considered as a candidate gene and added to gene panels for hereditary spastic paraplegia, cerebral palsy, and juvenile cataracts.

  View details for DOI 10.1038/s41436-020-01027-3

  View details for Web of Science ID 000592640700002

  View details for PubMedID 33239752

  View details for PubMedCentralID PMC8026396

• DYRK1A pathogenic variants in two patients with syndromic intellectual disability and a review of the literature MOLECULAR GENETICS & GENOMIC MEDICINE Meissner, L. E., Macnamara, E. F., D'Souza, P., Yang, J., Vezina, G., Ferreira, C. R., Zein, W. M., Tifft, C. J., Adams, D. R., Undiagnosed Diseases Network 2020; 8 (12): e1544

  Abstract

  DYRK1A-Related Intellectual Disability Syndrome is a rare autosomal dominant condition characterized by intellectual disability, speech and language delays, microcephaly, facial dysmorphism, and feeding difficulties. Affected individuals represent simplex cases that result from de novo heterozygous pathogenic variants in DYRK1A (OMIM 614104), or chromosomal structural rearrangements involving the DYRK1A locus. Due to the rarity of DYRK1A-Related Intellectual Disability Syndrome, the spectrum of symptoms associated with this disease has not been completely defined.We present two unrelated cases of DYRK1A-Related Intellectual Disability Syndrome resulting from variants in DYRK1A. Both probands presented to the National Institutes of Health (NIH) with multiple dysmorphic facial features, primary microcephaly, absent or minimal speech, feeding difficulties, and cognitive impairment; features that have been previously reported in individuals with DYRK1A. During NIH evaluation, additional features of enlarged cerebral subarachnoid spaces, retinal vascular tortuosity, and bilateral anomalous large optic discs with increased cup-to-disc ratio were identified in the first proband and multiple ophthalmologic abnormalities and sensorineural hearing loss were identified in the second proband.We recommend that the workup of future of patients include a comprehensive eye exam. Early establishment of physical, occupational, and speech therapy may help in the management of ataxia, hypertonia, and speech impairments common in these patients.

  View details for DOI 10.1002/mgg3.1544

  View details for Web of Science ID 000586993300001

  View details for PubMedID 33159716

  View details for PubMedCentralID PMC7767569

• gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. medRxiv : the preprint server for health sciences Di Sera, T., Velinder, M., Ward, A., Qiao, Y., Georges, S., Miller, C., Pitman, A., Richards, W., Ekawade, A., Viskochil, D., Carey, J. C., Pace, L., Bale, J., Clardy, S. L., Andrews, A., Botto, L., Marth, G. 2020

  Abstract

  With increasing utilization of comprehensive genomic data to guide clinical care, anticipated to become the standard of care in many clinical settings, the practice of diagnostic medicine is undergoing a notable shift. However, the move from single-gene or panel-based genetic testing to exome and genome sequencing has not been matched by the development of tools to enable diagnosticians to interpret increasingly complex genomic findings. A new paradigm has emerged, where genome-based tests are often evaluated by a large multi-disciplinary collaborative team, typically including a diagnostic pathologist, a bioinformatician, a genetic counselor, and often a subspeciality clinician. This team-based approach calls for new computational tools to allow every member of the clinical care provider team, at varying levels of genetic knowledge and diagnostic expertise, to quickly and easily analyze and interpret complex genomic data. Here, we present gene.iobio , a real-time, intuitive and interactive web application for clinically-driven variant interrogation and prioritization. We show gene.iobio is a novel and effective approach that significantly improves upon and reimagines existing methods. In a radical departure from existing methods that present variants and genomic data in text and table formats, gene.iobio provides an interactive, intuitive and visually-driven analysis environment. We demonstrate that adoption of gene.iobio in clinical and research settings empowers clinical care providers to interact directly with patient genomic data both for establishing clinical diagnoses and informing patient care, using sophisticated genomic analyses that previously were only accessible via complex command line tools.

  View details for DOI 10.1101/2020.11.05.20224865

  View details for PubMedID 33173897

  View details for PubMedCentralID PMC7654889

• MPEG1/Perforin-2 Haploinsufficiency Associated Polymicrobial Skin Infections and Considerations for Interferon-gamma Therapy FRONTIERS IN IMMUNOLOGY Merselis, L. C., Jiang, S. Y., Nelson, S. F., Lee, H., Prabaker, K. K., Baker, J. L., Munson, G. P., Butte, M. J. 2020; 11: 601584

  Abstract

  Macrophage expressed gene 1 (MPEG1) is highly expressed in macrophages and other phagocytes. The gene encodes a bactericidal pore-forming protein, dubbed Perforin-2. Structural-, animal-, and cell-based studies have established that perforin-2 facilitates the destruction of phagocytosed microbes upon its activation within acidic phagosomes. Relative to wild-type controls, Mpeg1 knockout mice suffer significantly higher mortality rates when challenged with gram-negative or -positive pathogens. Only four variants of MPEG1 have been functionally characterized, each in association with pulmonary infections. Here we report a new MPEG1 non-sense variant in a patient with the a newly described association with persistent polymicrobial infections of the skin and soft tissue.A young adult female patient was evaluated for recurrent abscesses and cellulitis of the breast and demonstrated a heterozygous, rare variant in MPEG1 p.Tyr430*. Multiple courses of broad-spectrum antimicrobials and surgical incision and drainage failed to resolve the infection. Functional studies revealed that the truncation variant resulted in significantly reduced capacity of the patient's phagocytes to kill intracellular bacteria. Patient-derived macrophages responded to interferon gamma (IFN-γ) by significantly increasing the expression of MPEG1. IFN-γ treatment supported perforin-2 dependent bactericidal activity and wound healing.This case expands the phenotype of MPEG1 deficiency to include severe skin and soft tissue infection. We showed that haploinsufficiency of perforin-2 reduced the bactericidal capacity of human phagocytes. Interferon-gamma therapy increases expression of perforin-2, which may compensate for such variants. Thus, treatment with IFN-γ could help prevent infections.

  View details for DOI 10.3389/fimmu.2020.601584

  View details for Web of Science ID 000589675900001

  View details for PubMedID 33224153

  View details for PubMedCentralID PMC7670069

• Novel NUDT2 variant causes intellectual disability and polyneuropathy. Annals of clinical and translational neurology Diaz, F., Khosa, S., Niyazov, D., Lee, H., Person, R., Morrow, M. M., Signer, R., Dorrani, N., Zheng, A., Herzog, M., Freundlich, R., Birath, J. B., Cervantes-Manzo, Y., Martinez-Agosto, J. A., Palmer, C., Nelson, S. F., Fogel, B. L., Mishra, S. K. 2020; 7 (11): 2320-2325

  Abstract

  Exome or genome sequencing was performed to identify the genetic etiology for the clinical presentation of global developmental delay, intellectual disability, and sensorimotor neuropathy with associated distal weakness in two unrelated families. A homozygous frameshift variant c.186delA (p.A63Qfs*3) in the NUDT2 gene was identified in cases 1 and 2 from one family and a third case from another family. Variants in NUDT2 were previously shown to cause intellectual disability, but here we expand the phenotype by demonstrating its association with distal upper and lower extremity weakness due to a sensorimotor polyneuropathy with demyelinating and/or axonal features.

  View details for DOI 10.1002/acn3.51209

  View details for PubMedID 33058507

  View details for PubMedCentralID PMC7664258

• Early infantile epileptic encephalopathy due to biallelic pathogenic variants in PIGQ: Report of seven new subjects and review of the literature. Journal of inherited metabolic disease Johnstone, D. L., Nguyen, T. T., Zambonin, J., Kernohan, K. D., St-Denis, A., Baratang, N. V., Hartley, T., Geraghty, M. T., Richer, J., Majewski, J., Bareke, E., Guerin, A., Pendziwiat, M., Pena, L. D., Braakman, H. M., Gripp, K. W., Edmondson, A. C., He, M., Spillmann, R. C., Eklund, E. A., Bayat, A., McMillan, H. J., Boycott, K. M., Campeau, P. M. 2020; 43 (6): 1321-1332

  Abstract

  We investigated seven children from six families to expand the phenotypic spectrum associated with an early infantile epileptic encephalopathy caused by biallelic pathogenic variants in the phosphatidylinositol glycan anchor biosynthesis class Q (PIGQ) gene. The affected children were all identified by clinical or research exome sequencing. Clinical data, including EEGs and MRIs, was comprehensively reviewed and flow cytometry and transfection experiments were performed to investigate PIGQ function. Pathogenic biallelic PIGQ variants were associated with increased mortality. Epileptic seizures, axial hypotonia, developmental delay and multiple congenital anomalies were consistently observed. Seizure onset occurred between 2.5 months and 7 months of age and varied from treatable seizures to recurrent episodes of status epilepticus. Gastrointestinal issues were common and severe, two affected individuals had midgut volvulus requiring surgical correction. Cardiac anomalies including arrythmias were observed. Flow cytometry using granulocytes and fibroblasts from affected individuals showed reduced expression of glycosylphosphatidylinositol (GPI)-anchored proteins. Transfection of wildtype PIGQ cDNA into patient fibroblasts rescued this phenotype. We expand the phenotypic spectrum of PIGQ-related disease and provide the first functional evidence in human cells of defective GPI-anchoring due to pathogenic variants in PIGQ.

  View details for DOI 10.1002/jimd.12278

  View details for PubMedID 32588908

  View details for PubMedCentralID PMC7689772

• Family genetic result communication in rare and undiagnosed disease communities: Understanding the practice JOURNAL OF GENETIC COUNSELING Studwell, C. M., Kelley, E. G., Sinsheimer, J. S., Palmer, C. S., LeBlanc, K., Undiagnosed Dis Network 2021; 30 (2): 439-447

  Abstract

  Genetic results have implications not only for the individual, but also for their family members. Research on family communication of genetic results has primarily focused on families affected by adult-onset, dominant conditions as well as more common genetic conditions such as familial hypercholesterolemia, cardiomyopathies, and genetic hearing loss. This study therefore aimed to characterize genetic result communication in families with rare and undiagnosed conditions and identify factors that influence communication. One hundred and forty-two individuals who received a diagnosis from the Undiagnosed Diseases Network (UDN), a study focused on providing diagnoses to individuals with undiagnosed conditions, were eligible to complete a survey assessing genetic results communication. Survey items assessed if communication was discussed with healthcare providers, with whom participants communicated genetic testing, why they chose to communicate with these family members, and what information they communicated. All respondents (5 adult UDN participants, 38 parents/guardians of UDN participants, and 2 identifying as both) shared genetic results with at least one family member. Individuals who identified as both were considered exclusively adult participants for the purpose of these analyses. Adult participants and parents/guardians of participants reported high levels of understanding (96%), utility (96%), and comfort communicating genetic results (89%). Additionally, parents/guardians were more likely to disclose genetic results due to a general desire to share (60% of parents/guardians vs. 14% adult participants), while adult participants reported that they shared results to communicate risk to family members (86% of adult participants vs. 24% of parents/guardians). Many respondents did not recall discussing with a healthcare provider how (64%) or what (42%) to communicate about results. The results of this study provide insight into the practice of result communication by individuals with rare and previously undiagnosed conditions, which can ideally inform development of more effective counseling strategies and guidelines to aid family communication.

  View details for DOI 10.1002/jgc4.1329

  View details for Web of Science ID 000586287200001

  View details for PubMedID 33108040

  View details for PubMedCentralID PMC8207526

• Missed diagnoses: Clinically relevant lessons learned through medical mysteries solved by the Undiagnosed Diseases Network. Molecular genetics & genomic medicine Cope, H., Spillmann, R., Rosenfeld, J. A., Brokamp, E., Signer, R., Schoch, K., Glanton, E., Sullivan, J. A., Macnamara, E., Lincoln, S., Golden-Grant, K., Orengo, J. P., Clark, G., Burrage, L. C., Posey, J. E., Punetha, J., Robertson, A., Cogan, J., Phillips, J. A., Martinez-Agosto, J., Shashi, V. 2020; 8 (10): e1397

  Abstract

  Resources within the Undiagnosed Diseases Network (UDN), such as genome sequencing (GS) and model organisms aid in diagnosis and identification of new disease genes, but are currently difficult to access by clinical providers. While these resources do contribute to diagnoses in many cases, they are not always necessary to reach diagnostic resolution. The UDN experience has been that participants can also receive diagnoses through the thoughtful and customized application of approaches and resources that are readily available in clinical settings.The UDN Genetic Counseling and Testing Working Group collected case vignettes that illustrated how clinically available methods resulted in diagnoses. The case vignettes were classified into three themes; phenotypic considerations, selection of genetic testing, and evaluating exome/GS variants and data.We present 12 participants that illustrate how clinical practices such as phenotype-driven genomic investigations, consideration of variable expressivity, selecting the relevant tissue of interest for testing, utilizing updated testing platforms, and recognition of alternate transcript nomenclature resulted in diagnoses.These examples demonstrate that when a diagnosis is elusive, an iterative patient-specific approach utilizing assessment options available to clinical providers may solve a portion of cases. However, this does require increased provider time commitment, a particular challenge in the current practice of genomics.

  View details for DOI 10.1002/mgg3.1397

  View details for PubMedID 32730690

  View details for PubMedCentralID PMC7549585

• Biallelic MADD variants cause a phenotypic spectrum ranging from developmental delay to a multisystem disorder BRAIN Schneeberger, P. E., Kortum, F., Korenke, G., Alawi, M., Santer, R., Woidy, M., Buhas, D., Fox, S., Juusola, J., Alfadhel, M., Webb, B. D., Coci, E. G., Abou Jamra, R., Siekmeyer, M., Biskup, S., Heller, C., Maier, E. M., Javaher-Haghighi, P., Bedeschi, M. F., Ajmone, P. F., Iascone, M., Peeters, H., Ballon, K., Jaeken, J., Rodriguez Alonso, A., Palomares-Bralo, M., Santos-Simarro, F., Meuwissen, M. C., Beysen, D., Kooy, R., Houlden, H., Murphy, D., Doosti, M., Karimiani, E., Mojarrad, M., Maroofian, R., Noskova, L., Kmoch, S., Honzik, T., Cope, H., Sanchez-Valle, A., Gelb, B. D., Kurth, I., Hempel, M., Kutsche, K., Undiagnosed Dise Network 2020; 143 (8): 2437-2453

  Abstract

  In pleiotropic diseases, multiple organ systems are affected causing a variety of clinical manifestations. Here, we report a pleiotropic disorder with a unique constellation of neurological, endocrine, exocrine, and haematological findings that is caused by biallelic MADD variants. MADD, the mitogen-activated protein kinase (MAPK) activating death domain protein, regulates various cellular functions, such as vesicle trafficking, activity of the Rab3 and Rab27 small GTPases, tumour necrosis factor-α (TNF-α)-induced signalling and prevention of cell death. Through national collaboration and GeneMatcher, we collected 23 patients with 21 different pathogenic MADD variants identified by next-generation sequencing. We clinically evaluated the series of patients and categorized the phenotypes in two groups. Group 1 consists of 14 patients with severe developmental delay, endo- and exocrine dysfunction, impairment of the sensory and autonomic nervous system, and haematological anomalies. The clinical course during the first years of life can be potentially fatal. The nine patients in Group 2 have a predominant neurological phenotype comprising mild-to-severe developmental delay, hypotonia, speech impairment, and seizures. Analysis of mRNA revealed multiple aberrant MADD transcripts in two patient-derived fibroblast cell lines. Relative quantification of MADD mRNA and protein in fibroblasts of five affected individuals showed a drastic reduction or loss of MADD. We conducted functional tests to determine the impact of the variants on different pathways. Treatment of patient-derived fibroblasts with TNF-α resulted in reduced phosphorylation of the extracellular signal-regulated kinases 1 and 2, enhanced activation of the pro-apoptotic enzymes caspase-3 and -7 and increased apoptosis compared to control cells. We analysed internalization of epidermal growth factor in patient cells and identified a defect in endocytosis of epidermal growth factor. We conclude that MADD deficiency underlies multiple cellular defects that can be attributed to alterations of TNF-α-dependent signalling pathways and defects in vesicular trafficking. Our data highlight the multifaceted role of MADD as a signalling molecule in different organs and reveal its physiological role in regulating the function of the sensory and autonomic nervous system and endo- and exocrine glands.

  View details for DOI 10.1093/brain/awaa204

  View details for Web of Science ID 000825023900020

  View details for PubMedID 32761064

  View details for PubMedCentralID PMC7447524

• Neuroimmunogastroenterology: At the Interface of Neuroimmunology and Gastroenterology FRONTIERS IN NEUROLOGY Sanchez, J. S., McNally, J., Cortez, M. M., Hemp, J., Pace, L. A., Clardy, S. L. 2020; 11: 787

  Abstract

  The central nervous system (CNS) is an important regulator of the gastrointestinal tract, and CNS dysfunction can result in significant and disabling gastrointestinal symptom manifestation. For patients with neuroimmunologic and neuroinflammatory conditions, the recognition of gastrointestinal symptoms is under-appreciated, yet the gastrointestinal manifestations have a dramatic impact on quality of life. The current treatment strategies, often employed independently by the neurologist and gastroenterologist, raise the question of whether such patients are being treated optimally when siloed in one specialty. Neuroimmunogastroenterology lies at the borderlands of medical specialties, and there are few resources to guide neurologists in this area. Here, we provide an overview highlighting the potential mechanisms of crosstalk between immune-mediated neurological disorders and gastrointestinal dysfunction.

  View details for DOI 10.3389/fneur.2020.00787

  View details for Web of Science ID 000561662400001

  View details for PubMedID 32849234

  View details for PubMedCentralID PMC7412790

• De Novo Variants in the ATPase Module of MORC2 Cause a Neurodevelopmental Disorder with Growth Retardation and Variable Craniofacial Dysmorphism. American journal of human genetics Guillen Sacoto, M. J., Tchasovnikarova, I. A., Torti, E., Forster, C., Andrew, E. H., Anselm, I., Baranano, K. W., Briere, L. C., Cohen, J. S., Craigen, W. J., Cytrynbaum, C., Ekhilevitch, N., Elrick, M. J., Fatemi, A., Fraser, J. L., Gallagher, R. C., Guerin, A., Haynes, D., High, F. A., Inglese, C. N., Kiss, C., Koenig, M. K., Krier, J., Lindstrom, K., Marble, M., Meddaugh, H., Moran, E. S., Morel, C. F., Mu, W., Muller, E. A., Nance, J., Natowicz, M. R., Numis, A. L., Ostrem, B., Pappas, J., Stafstrom, C. E., Streff, H., Sweetser, D. A., Szybowska, M., Undiagnosed Diseases Network, Walker, M. A., Wang, W., Weiss, K., Weksberg, R., Wheeler, P. G., Yoon, G., Kingston, R. E., Juusola, J. 2020

  Abstract

  MORC2 encodes an ATPase that plays a role in chromatin remodeling, DNA repair, and transcriptional regulation. Heterozygous variants in MORC2 have been reported in individuals with autosomal-dominant Charcot-Marie-Tooth disease type 2Z and spinal muscular atrophy, and the onset of symptoms ranges from infancy to the second decade of life. Here, we present a cohort of 20 individuals referred for exome sequencing who harbor pathogenic variants in the ATPase module of MORC2. Individuals presented with a similar phenotype consisting of developmental delay, intellectual disability, growth retardation, microcephaly, and variable craniofacial dysmorphism. Weakness, hyporeflexia, and electrophysiologic abnormalities suggestive of neuropathy were frequently observed but were not the predominant feature. Five of 18 individuals for whom brain imaging was available had lesions reminiscent of those observed in Leigh syndrome, and five of six individuals who had dilated eye exams had retinal pigmentary abnormalities. Functional assays revealed that these MORC2 variants result in hyperactivation of epigenetic silencing by the HUSH complex, supporting their pathogenicity. The described set of morphological, growth, developmental, and neurological findings and medical concerns expands the spectrum of genetic disorders resulting from pathogenic variants in MORC2.

  View details for DOI 10.1016/j.ajhg.2020.06.013

  View details for PubMedID 32693025

• Alternative transcripts in variant interpretation: the potential for missed diagnoses and misdiagnoses. Genetics in medicine : official journal of the American College of Medical Genetics Schoch, K., Tan, Q. K., Stong, N., Deak, K. L., McConkie-Rosell, A., McDonald, M. T., Goldstein, D. B., Jiang, Y. H., Shashi, V. 2020; 22 (7): 1269-1275

  Abstract

  Guidelines by professional organizations for assessing variant pathogenicity include the recommendation to utilize biologically relevant transcripts; however, there is variability in transcript selection by laboratories.We describe three patients whose genomic results were incorrect, because alternative transcripts and tissue expression patterns were not considered by the commercial laboratories.In individual 1, a pathogenic coding variant in a brain-expressed isoform of CKDL5 was missed twice on sequencing, because the variant was intronic in the transcripts considered in analysis. In individual 2, a microdeletion affecting KMT2C was not reported on microarray, since deletions of proximal exons in this gene are seen in healthy individuals; however, this individual had a more distal deletion involving the brain-expressed KMT2C isoform, giving her a diagnosis of Kleefstra syndrome. Individual 3 was reported to have a pathogenic variant in exon 10 of OFD1 on exome, but had no typical features of the OFD1-related disorders. Since exon 10 is spliced from the more biologically relevant transcripts of OFD1, it was determined that he did not have an OFD1 disorder.These examples illustrate the importance of considering alternative transcripts as a potential confounder when genetic results are negative or discordant with the phenotype.

  View details for DOI 10.1038/s41436-020-0781-x

  View details for PubMedID 32366967

  View details for PubMedCentralID PMC7335342

• Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7. Genetics in medicine : official journal of the American College of Medical Genetics Castilla-Vallmanya, L., Selmer, K. K., Dimartino, C., Rabionet, R., Blanco-Sánchez, B., Yang, S., Reijnders, M. R., van Essen, A. J., Oufadem, M., Vigeland, M. D., Stadheim, B., Houge, G., Cox, H., Kingston, H., Clayton-Smith, J., Innis, J. W., Iascone, M., Cereda, A., Gabbiadini, S., Chung, W. K., Sanders, V., Charrow, J., Bryant, E., Millichap, J., Vitobello, A., Thauvin, C., Mau-Them, F. T., Faivre, L., Lesca, G., Labalme, A., Rougeot, C., Chatron, N., Sanlaville, D., Christensen, K. M., Kirby, A., Lewandowski, R., Gannaway, R., Aly, M., Lehman, A., Clarke, L., Graul-Neumann, L., Zweier, C., Lessel, D., Lozic, B., Aukrust, I., Peretz, R., Stratton, R., Smol, T., Dieux-Coëslier, A., Meira, J., Wohler, E., Sobreira, N., Beaver, E. M., Heeley, J., Briere, L. C., High, F. A., Sweetser, D. A., Walker, M. A., Keegan, C. E., Jayakar, P., Shinawi, M., Kerstjens-Frederikse, W. S., Earl, D. L., Siu, V. M., Reesor, E., Yao, T., Hegele, R. A., Vaske, O. M., Rego, S., Shapiro, K. A., Wong, B., Gambello, M. J., McDonald, M., Karlowicz, D., Colombo, R., Serretti, A., Pais, L., O'Donnell-Luria, A., Wray, A., Sadedin, S., Chong, B., Tan, T. Y., Christodoulou, J., White, S. M., Slavotinek, A., Barbouth, D., Morel Swols, D., Parisot, M., Bole-Feysot, C., Nitschké, P., Pingault, V., Munnich, A., Cho, M. T., Cormier-Daire, V., Balcells, S., Lyonnet, S., Grinberg, D., Amiel, J., Urreizti, R., Gordon, C. T. 2020; 22 (7): 1215-1226

  Abstract

  Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts.We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts.We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts.We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.

  View details for DOI 10.1038/s41436-020-0792-7

  View details for PubMedID 32376980

  View details for PubMedCentralID PMC8093014

• Dominant-negative mutations in human IL6ST underlie hyper-IgE syndrome. The Journal of experimental medicine Béziat, V., Tavernier, S. J., Chen, Y. H., Ma, C. S., Materna, M., Laurence, A., Staal, J., Aschenbrenner, D., Roels, L., Worley, L., Claes, K., Gartner, L., Kohn, L. A., De Bruyne, M., Schmitz-Abe, K., Charbonnier, L. M., Keles, S., Nammour, J., Vladikine, N., Maglorius Renkilaraj, M. R., Seeleuthner, Y., Migaud, M., Rosain, J., Jeljeli, M., Boisson, B., Van Braeckel, E., Rosenfeld, J. A., Dai, H., Burrage, L. C., Murdock, D. R., Lambrecht, B. N., Avettand-Fenoel, V., Vogel, T. P., Esther, C. R., Haskologlu, S., Dogu, F., Ciznar, P., Boutboul, D., Ouachée-Chardin, M., Amourette, J., Lebras, M. N., Gauvain, C., Tcherakian, C., Ikinciogullari, A., Beyaert, R., Abel, L., Milner, J. D., Grimbacher, B., Couderc, L. J., Butte, M. J., Freeman, A. F., Catherinot, É., Fieschi, C., Chatila, T. A., Tangye, S. G., Uhlig, H. H., Haerynck, F., Casanova, J. L., Puel, A. 2020; 217 (6)

  Abstract

  Autosomal dominant hyper-IgE syndrome (AD-HIES) is typically caused by dominant-negative (DN) STAT3 mutations. Patients suffer from cold staphylococcal lesions and mucocutaneous candidiasis, severe allergy, and skeletal abnormalities. We report 12 patients from 8 unrelated kindreds with AD-HIES due to DN IL6ST mutations. We identified seven different truncating mutations, one of which was recurrent. The mutant alleles encode GP130 receptors bearing the transmembrane domain but lacking both the recycling motif and all four STAT3-recruiting tyrosine residues. Upon overexpression, the mutant proteins accumulate at the cell surface and are loss of function and DN for cellular responses to IL-6, IL-11, LIF, and OSM. Moreover, the patients' heterozygous leukocytes and fibroblasts respond poorly to IL-6 and IL-11. Consistently, patients with STAT3 and IL6ST mutations display infectious and allergic manifestations of IL-6R deficiency, and some of the skeletal abnormalities of IL-11R deficiency. DN STAT3 and IL6ST mutations thus appear to underlie clinical phenocopies through impairment of the IL-6 and IL-11 response pathways.

  View details for DOI 10.1084/jem.20191804

  View details for PubMedID 32207811

  View details for PubMedCentralID PMC7971136

• yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development. PLoS genetics Blanco-Sánchez, B., Clément, A., Stednitz, S. J., Kyle, J., Peirce, J. L., McFadden, M., Wegner, J., Phillips, J. B., Macnamara, E., Huang, Y., Adams, D. R., Toro, C., Gahl, W. A., Malicdan, M. C., Tifft, C. J., Zink, E. M., Bloodsworth, K. J., Stratton, K. G., Koeller, D. M., Metz, T. O., Washbourne, P., Westerfield, M. 2020; 16 (6): e1008841

  Abstract

  Hypomyelination, a neurological condition characterized by decreased production of myelin sheets by glial cells, often has no known etiology. Elucidating the genetic causes of hypomyelination provides a better understanding of myelination, as well as means to diagnose, council, and treat patients. Here, we present evidence that YIPPEE LIKE 3 (YPEL3), a gene whose developmental role was previously unknown, is required for central and peripheral glial cell development. We identified a child with a constellation of clinical features including cerebral hypomyelination, abnormal peripheral nerve conduction, hypotonia, areflexia, and hypertrophic peripheral nerves. Exome and genome sequencing revealed a de novo mutation that creates a frameshift in the open reading frame of YPEL3, leading to an early stop codon. We used zebrafish as a model system to validate that YPEL3 mutations are causative of neuropathy. We found that ypel3 is expressed in the zebrafish central and peripheral nervous system. Using CRISPR/Cas9 technology, we created zebrafish mutants carrying a genomic lesion similar to that of the patient. Our analysis revealed that Ypel3 is required for development of oligodendrocyte precursor cells, timely exit of the perineurial glial precursors from the central nervous system (CNS), formation of the perineurium, and Schwann cell maturation. Consistent with these observations, zebrafish ypel3 mutants have metabolomic signatures characteristic of oligodendrocyte and Schwann cell differentiation defects, show decreased levels of Myelin basic protein in the central and peripheral nervous system, and develop defasciculated peripheral nerves. Locomotion defects were observed in adult zebrafish ypel3 mutants. These studies demonstrate that Ypel3 is a novel gene required for perineurial cell development and glial myelination.

  View details for DOI 10.1371/journal.pgen.1008841

  View details for PubMedID 32544203

  View details for PubMedCentralID PMC7319359

• Loss- or Gain-of-Function Mutations in ACOX1 Cause Axonal Loss via Different Mechanisms NEURON Chung, H., Wangler, M. F., Marcogliese, P. C., Jo, J., Ravenscroft, T. A., Zuo, Z., Duraine, L., Sadeghzadeh, S., Li-Kroeger, D., Schmidt, R. E., Pestronk, A., Rosenfeld, J. A., Burrage, L., Herndon, M. J., Chen, S., Shillington, A., Vawter-Lee, M., Hopkin, R., Rodriguez-Smith, J., Henrickson, M., Lee, B., Moser, A. B., Jones, R. O., Watkins, P., Yoo, T., Mar, S., Choi, M., Bucelli, R. C., Yamamoto, S., Lee, H., Prada, C. E., Chae, J., Vogel, T. P., Bellen, H. J., Undiagnosed Dis Network 2020; 106 (4): 589-+

  Abstract

  ACOX1 (acyl-CoA oxidase 1) encodes the first and rate-limiting enzyme of the very-long-chain fatty acid (VLCFA) β-oxidation pathway in peroxisomes and leads to H2O2 production. Unexpectedly, Drosophila (d) ACOX1 is mostly expressed and required in glia, and loss of ACOX1 leads to developmental delay, pupal death, reduced lifespan, impaired synaptic transmission, and glial and axonal loss. Patients who carry a previously unidentified, de novo, dominant variant in ACOX1 (p.N237S) also exhibit glial loss. However, this mutation causes increased levels of ACOX1 protein and function resulting in elevated levels of reactive oxygen species in glia in flies and murine Schwann cells. ACOX1 (p.N237S) patients exhibit a severe loss of Schwann cells and neurons. However, treatment of flies and primary Schwann cells with an antioxidant suppressed the p.N237S-induced neurodegeneration. In summary, both loss and gain of ACOX1 lead to glial and neuronal loss, but different mechanisms are at play and require different treatments.

  View details for DOI 10.1016/j.neuron.2020.02.021

  View details for Web of Science ID 000535696300009

  View details for PubMedID 32169171

  View details for PubMedCentralID PMC7289150

• De Novo Variants in CDK19 Are Associated with a Syndrome Involving Intellectual Disability and Epileptic Encephalopathy. American journal of human genetics Chung, H. L., Mao, X., Wang, H., Park, Y. J., Marcogliese, P. C., Rosenfeld, J. A., Burrage, L. C., Liu, P., Murdock, D. R., Yamamoto, S., Wangler, M. F., Chao, H. T., Long, H., Feng, L., Bacino, C. A., Bellen, H. J., Xiao, B. 2020; 106 (5): 717-725

  Abstract

  We identified three unrelated individuals with de novo missense variants in CDK19, encoding a cyclin-dependent kinase protein family member that predominantly regulates gene transcription. These individuals presented with hypotonia, global developmental delay, epileptic encephalopathy, and dysmorphic features. CDK19 is conserved between vertebrate and invertebrate model organisms, but currently abnormalities in CDK19 are not known to be associated with a human disorder. Loss of Cdk8, the fly homolog of CDK19, causes larval lethality, which is suppressed by expression of human CDK19 reference cDNA. In contrast, the CDK19 p.Tyr32His and p.Thr196Ala variants identified in the affected individuals fail to rescue the loss of Cdk8 and behave as null alleles. Additionally, neuronal RNAi-mediated knockdown of Cdk8 in flies results in semi-lethality. The few eclosing flies exhibit severe seizures and a reduced lifespan. Both phenotypes are fully suppressed by moderate expression of the CDK19 reference cDNA but not by expression of the two variants. Finally, loss of Cdk8 causes an obvious loss of boutons and synapses at larval neuromuscular junctions (NMJs). Together, our findings demonstrate that human CDK19 fully replaces the function of Cdk8 in the fly, the human disease-associated CDK19 variants behave as strong loss-of-function variants, and deleterious CDK19 variants underlie a syndromic neurodevelopmental disorder.

  View details for DOI 10.1016/j.ajhg.2020.04.001

  View details for PubMedID 32330417

  View details for PubMedCentralID PMC7212481

• Mast Cell Activation Syndrome: A Primer for the Gastroenterologist DIGESTIVE DISEASES AND SCIENCES Weinstock, L. B., Pace, L. A., Rezaie, A., Afrin, L. B., Molderings, G. J. 2021; 66 (4): 965-982

  Abstract

  Mast cell activation syndrome is thought to be a common, yet under-recognized, chronic multi-system disorder caused by inappropriate mast cell activation. Gastrointestinal symptoms are frequently reported by these patients and are often mistaken by physicians as functional gastrointestinal disorders. This syndrome can be diagnosed by the medical history and measurable biomarkers. Gastroenterologists manage diseases associated with active inflammatory cells including neutrophils, lymphocytes, macrophages, and eosinophils. The mast cell has only recently been recognized as a major player in our specialty. Gastrointestinal disorders from mast cell mediators often present with apparent irritable bowel syndrome, dyspepsia, chronic or cyclical nausea, and heartburn. Individuals with mast cell activation syndrome experience significant delays in diagnosis. The gastrointestinal symptoms are often refractory to symptom-targeted prescription medications. Beyond avoiding triggers, the best therapy is directed at modulating mast cell activation and the effects of the mediators. Many of these therapies are simple over-the-counter medications. In this article, we review mast cell function and dysfunction and the gastrointestinal symptoms, comorbid conditions, diagnosis, and management of mast cell activation syndrome. Gastroenterologists who become aware of this syndrome can dramatically improve the quality of life for their patients who previously have been labeled with a functional gastrointestinal disorder.

  View details for DOI 10.1007/s10620-020-06264-9

  View details for Web of Science ID 000528511200002

  View details for PubMedID 32328892

  View details for PubMedCentralID 6049091

• The undiagnosed diseases program: Approach to diagnosis. Translational science of rare diseases Macnamara, E. F., D'Souza, P., Tifft, C. J. 2020; 4 (3-4): 179-188

  Abstract

  Undiagnosed and rare conditions are collectively common and affect millions of people worldwide. The NIH Undiagnosed Diseases Program (UDP) strives to achieve both a comprehensive diagnosis and a better understanding of the mechanisms of disease for many of these individuals. Through the careful review of records, a well-orchestrated inpatient evaluation, genomic sequencing and testing, and with the use of emerging strategies such as matchmaking programs, the UDP succeeds nearly 30 percent of the time for these highly selective cases. Although the UDP process is built on a unique set of resources, case examples demonstrate steps genetic professionals can take, in both clinical and research settings, to arrive at a diagnosis for their most challenging cases.

  View details for DOI 10.3233/TRD-190045

  View details for PubMedID 32477883

  View details for PubMedCentralID PMC7250153

• Apurinic/Apyrimidinic Endonuclease 1 Restricts the Internalization of Bacteria Into Human Intestinal Epithelial Cells Through the Inhibition of Rac1. Frontiers in immunology den Hartog, G., Butcher, L. D., Ablack, A. L., Pace, L. A., Ablack, J. N., Xiong, R., Das, S., Stappenbeck, T. S., Eckmann, L., Ernst, P. B., Crowe, S. E. 2020; 11: 553994

  Abstract

  Pathogenic intestinal bacteria lead to significant disease in humans. Here we investigated the role of the multifunctional protein, Apurinic/apyrimidinic endonuclease 1 (APE1), in regulating the internalization of bacteria into the intestinal epithelium. Intestinal tumor-cell lines and primary human epithelial cells were infected with Salmonella enterica serovar Typhimurium or adherent-invasive Escherichia coli. The effects of APE1 inhibition on bacterial internalization, the regulation of Rho GTPase Rac1 as well as the epithelial cell barrier function were assessed. Increased numbers of bacteria were present in APE1-deficient colonic tumor cell lines and primary epithelial cells. Activation of Rac1 was augmented following infection but negatively regulated by APE1. Pharmacological inhibition of Rac1 reversed the increase in intracellular bacteria in APE1-deficient cells whereas overexpression of constitutively active Rac1 augmented the numbers in APE1-competent cells. Enhanced numbers of intracellular bacteria resulted in the loss of barrier function and a delay in its recovery. Our data demonstrate that APE1 inhibits the internalization of invasive bacteria into human intestinal epithelial cells through its ability to negatively regulate Rac1. This activity also protects epithelial cell barrier function.

  View details for DOI 10.3389/fimmu.2020.553994

  View details for PubMedID 33603730

  View details for PubMedCentralID PMC7884313

• Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network. Analytical chemistry Webb-Robertson, B. M., Stratton, K. G., Kyle, J. E., Kim, Y. M., Bramer, L. M., Waters, K. M., Koeller, D. M., Metz, T. O. 2020; 92 (2): 1796-1803

  Abstract

  Advancements in molecular separations coupled with mass spectrometry have enabled metabolome analyses for clinical cohorts. A population of interest for metabolome profiling is patients with rare disease for which abnormal metabolic signatures may yield clues into the genetic basis, as well as mechanistic drivers of the disease and possible treatment options. We undertook the metabolome profiling of a large cohort of patients with mysterious conditions characterized through the Undiagnosed Diseases Network (UDN). Due to the size and enrollment procedures, collection of the metabolomes for UDN patients took place over 2 years. We describe the study designed to adjust for measurements collected over a long time scale and how this enabled statistical analyses to summarize the metabolome of individual patients. We demonstrate the removal of time-based batch effects, overall statistical characteristics of the UDN population, and two case studies of interest that demonstrate the utility of metabolome profiling for rare diseases.

  View details for DOI 10.1021/acs.analchem.9b03522

  View details for PubMedID 31742994

  View details for PubMedCentralID PMC7183858

• De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. American journal of human genetics Mao, D. n., Reuter, C. M., Ruzhnikov, M. R., Beck, A. E., Farrow, E. G., Emrick, L. T., Rosenfeld, J. A., Mackenzie, K. M., Robak, L. n., Wheeler, M. T., Burrage, L. C., Jain, M. n., Liu, P. n., Calame, D. n., Küry, S. n., Sillesen, M. n., Schmitz-Abe, K. n., Tonduti, D. n., Spaccini, L. n., Iascone, M. n., Genetti, C. A., Koenig, M. K., Graf, M. n., Tran, A. n., Alejandro, M. n., Lee, B. H., Thiffault, I. n., Agrawal, P. B., Bernstein, J. A., Bellen, H. J., Chao, H. T. 2020

  Abstract

  EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.

  View details for DOI 10.1016/j.ajhg.2020.02.016

  View details for PubMedID 32197074

• Meeting Summary: 2019 James W. Freston Conference: Food at the Intersection of Gut Health and Disease. Gastroenterology Mullin, G. n., Chey, W. n., Crowe, S. n., Ananthakrishan, A. n., Garcia-Bailo, B. n., Dellon, E. n., DiBaise, J. n., Fasano, A. n., Haller, E. n., Hamilton, M. J., Klein, S. n., Lebwohl, B. n., Leung, J. n., Lewis, J. n., Nguyen, L. n., Pandolfino, J. n., Parrish, C. R., Scarlata, K. n., Tack, J. n., Frye, J. n., Harer, K. n., Zevallos, V. n., Srinivasan, S. n., Verma, S. n., Jansson-Knodell, C. n., Dia, V. n., Rifkin, S. n., Pace, L. n. 2020

  View details for DOI 10.1053/j.gastro.2020.03.036

  View details for PubMedID 32224128

• Etiology and Clinical Presentation of Gastroparesis GASTROPARESIS: A COMPREHENSIVE APPROACH TO EVALUATION AND MANAGEMENT Pace, L. A., Ibele, A., Gould, J. 2020: 21-31

  View details for DOI 10.1007/978-3-030-28929-4_2

  View details for Web of Science ID 000566132000003

• Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science. Genetics in medicine : official journal of the American College of Medical Genetics Schoch, K. n., Esteves, C. n., Bican, A. n., Spillmann, R. n., Cope, H. n., McConkie-Rosell, A. n., Walley, N. n., Fernandez, L. n., Kohler, J. N., Bonner, D. n., Reuter, C. n., Stong, N. n., Mulvihill, J. J., Novacic, D. n., Wolfe, L. n., Abdelbaki, A. n., Toro, C. n., Tifft, C. n., Malicdan, M. n., Gahl, W. n., Liu, P. n., Newman, J. n., Goldstein, D. B., Hom, J. n., Sampson, J. n., Wheeler, M. T., Cogan, J. n., Bernstein, J. A., Adams, D. R., McCray, A. T., Shashi, V. n. 2020

  Abstract

  The NIH Undiagnosed Diseases Network (UDN) evaluates participants with disorders that have defied diagnosis, applying personalized clinical and genomic evaluations and innovative research. The clinical sites of the UDN are essential to advancing the UDN mission; this study assesses their contributions relative to standard clinical practices.We analyzed retrospective data from four UDN clinical sites, from July 2015 to September 2019, for diagnoses, new disease gene discoveries and the underlying investigative methods.Of 791 evaluated individuals, 231 received 240 diagnoses and 17 new disease-gene associations were recognized. Straightforward diagnoses on UDN exome and genome sequencing occurred in 35% (84/240). We considered these tractable in standard clinical practice, although genome sequencing is not yet widely available clinically. The majority (156/240, 65%) required additional UDN-driven investigations, including 90 diagnoses that occurred after prior nondiagnostic exome sequencing and 45 diagnoses (19%) that were nongenetic. The UDN-driven investigations included complementary/supplementary phenotyping, innovative analyses of genomic variants, and collaborative science for functional assays and animal modeling.Investigations driven by the clinical sites identified diagnostic and research paradigms that surpass standard diagnostic processes. The new diagnoses, disease gene discoveries, and delineation of novel disorders represent a model for genomic medicine and science.

  View details for DOI 10.1038/s41436-020-00984-z

  View details for PubMedID 33093671

• Familial Hypermobile Ehlers-Danlos Syndrome and Comorbid Dysautonomia May Have a Genetic Neuroimmunologic Origin Pace, L. A., Feng, B., Hemp, J., Velinder, M. MARY ANN LIEBERT, INC. 2019: 1589-1590

  View details for Web of Science ID 000496623900052

• VarSight: prioritizing clinically reported variants with binary classification algorithms. BMC bioinformatics Holt, J. M., Wilk, B., Birch, C. L., Brown, D. M., Gajapathy, M., Moss, A. C., Sosonkina, N., Wilk, M. A., Anderson, J. A., Harris, J. M., Kelly, J. M., Shaterferdosian, F., Uno-Antonison, A. E., Weborg, A., Worthey, E. A. 2019; 20 (1): 496

  Abstract

  When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance.We tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network.We treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20.We demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets.

  View details for DOI 10.1186/s12859-019-3026-8

  View details for PubMedID 31615419

  View details for PubMedCentralID PMC6792253

• De Novo Pathogenic Variants in N-cadherin Cause a Syndromic Neurodevelopmental Disorder with Corpus Collosum, Axon, Cardiac, Ocular, and Genital Defects. American journal of human genetics Accogli, A., Calabretta, S., St-Onge, J., Boudrahem-Addour, N., Dionne-Laporte, A., Joset, P., Azzarello-Burri, S., Rauch, A., Krier, J., Fieg, E., Pallais, J. C., McConkie-Rosell, A., McDonald, M., Freedman, S. F., Rivière, J. B., Lafond-Lapalme, J., Simpson, B. N., Hopkin, R. J., Trimouille, A., Van-Gils, J., Begtrup, A., McWalter, K., Delphine, H., Keren, B., Genevieve, D., Argilli, E., Sherr, E. H., Severino, M., Rouleau, G. A., Yam, P. T., Charron, F., Srour, M. 2019; 105 (4): 854-868

  Abstract

  Cadherins constitute a family of transmembrane proteins that mediate calcium-dependent cell-cell adhesion. The extracellular domain of cadherins consists of extracellular cadherin (EC) domains, separated by calcium binding sites. The EC interacts with other cadherin molecules in cis and in trans to mechanically hold apposing cell surfaces together. CDH2 encodes N-cadherin, whose essential roles in neural development include neuronal migration and axon pathfinding. However, CDH2 has not yet been linked to a Mendelian neurodevelopmental disorder. Here, we report de novo heterozygous pathogenic variants (seven missense, two frameshift) in CDH2 in nine individuals with a syndromic neurodevelopmental disorder characterized by global developmental delay and/or intellectual disability, variable axon pathfinding defects (corpus callosum agenesis or hypoplasia, mirror movements, Duane anomaly), and ocular, cardiac, and genital anomalies. All seven missense variants (c.1057G>A [p.Asp353Asn]; c.1789G>A [p.Asp597Asn]; c.1789G>T [p.Asp597Tyr]; c.1802A>C [p.Asn601Thr]; c.1839C>G [p.Cys613Trp]; c.1880A>G [p.Asp627Gly]; c.2027A>G [p.Tyr676Cys]) result in substitution of highly conserved residues, and six of seven cluster within EC domains 4 and 5. Four of the substitutions affect the calcium-binding site in the EC4-EC5 interdomain. We show that cells expressing these variants in the EC4-EC5 domains have a defect in cell-cell adhesion; this defect includes impaired binding in trans with N-cadherin-WT expressed on apposing cells. The two frameshift variants (c.2563_2564delCT [p.Leu855Valfs∗4]; c.2564_2567dupTGTT [p.Leu856Phefs∗5]) are predicted to lead to a truncated cytoplasmic domain. Our study demonstrates that de novo heterozygous variants in CDH2 impair the adhesive activity of N-cadherin, resulting in a multisystemic developmental disorder, that could be named ACOG syndrome (agenesis of corpus callosum, axon pathfinding, cardiac, ocular, and genital defects).

  View details for DOI 10.1016/j.ajhg.2019.09.005

  View details for PubMedID 31585109

  View details for PubMedCentralID PMC6817525

• De Novo Variants in WDR37 Are Associated with Epilepsy, Colobomas, Dysmorphism, Developmental Delay, Intellectual Disability, and Cerebellar Hypoplasia. American journal of human genetics Kanca, O., Andrews, J. C., Lee, P. T., Patel, C., Braddock, S. R., Slavotinek, A. M., Cohen, J. S., Gubbels, C. S., Aldinger, K. A., Williams, J., Indaram, M., Fatemi, A., Yu, T. W., Agrawal, P. B., Vezina, G., Simons, C., Crawford, J., Lau, C. C., Chung, W. K., Markello, T. C., Dobyns, W. B., Adams, D. R., Gahl, W. A., Wangler, M. F., Yamamoto, S., Bellen, H. J., Malicdan, M. C. 2019; 105 (3): 672-674

  View details for DOI 10.1016/j.ajhg.2019.07.017

  View details for PubMedID 31491411

  View details for PubMedCentralID PMC6732524

• De Novo Variants in WDR37 Are Associated with Epilepsy, Colobomas, Dysmorphism, Developmental Delay, Intellectual Disability, and Cerebellar Hypoplasia. American journal of human genetics Kanca, O., Andrews, J. C., Lee, P., Patel, C., Braddock, S. R., Slavotinek, A. M., Cohen, J. S., Gubbels, C. S., Aldinger, K. A., Williams, J., Indaram, M., Fatemi, A., Yu, T. W., Agrawal, P. B., Vezina, G., Simons, C., Crawford, J., Lau, C. C., Undiagnosed Diseases Network, Chung, W. K., Markello, T. C., Dobyns, W. B., Adams, D. R., Gahl, W. A., Wangler, M. F., Yamamoto, S., Bellen, H. J., Malicdan, M. C., Acosta, M. T., Adams, D. R., Agrawal, P., Alejandro, M. E., Allard, P., Alvey, J., Andrews, A., Ashley, E. A., Azamian, M. S., Bacino, C. A., Bademci, G., Baker, E., Balasubramanyam, A., Baldridge, D., Bale, J., Barbouth, D., Batzli, G. F., Bayrak-Toydemir, P., Beggs, A. H., Bejerano, G., Bellen, H. J., Bernstein, J. A., Berry, G. T., Bican, A., Bick, D. P., Birch, C. L., Bivona, S., Bohnsack, J., Bonnenmann, C., Bonner, D., Boone, B. E., Bostwick, B. L., Botto, L., Briere, L. C., Brokamp, E., Brown, D. M., Brush, M., Burke, E. A., Burrage, L. C., Butte, M. J., Carey, J., Carrasquillo, O., Chang, T. C., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Cole, F. S., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., D'Souza, P., Dasari, S., Davids, M., Dayal, J. G., Dell'Angelica, E. C., Dhar, S. U., Dorrani, N., Dorset, D. C., Douine, E. D., Draper, D. D., Duncan, L., Eckstein, D. J., Emrick, L. T., Eng, C. M., Esteves, C., Estwick, T., Fernandez, L., Ferreira, C., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Fresard, L., Gahl, W. A., Godfrey, R. A., Goldman, A. M., Goldstein, D. B., Gourdine, J. F., Grajewski, A., Groden, C. A., Gropman, A. L., Haendel, M., Hamid, R., Hanchard, N. A., Hayes, N., High, F., Holm, I. A., Hom, J., Huang, A., Huang, Y., Isasi, R., Jamal, F., Jiang, Y., Johnston, J. M., Jones, A. L., Karaviti, L., Kelley, E. G., Kiley, D., Koeller, D. M., Kohane, I. S., Kohler, J. N., Krakow, D., Krasnewich, D. M., Korrick, S., Koziura, M., Krier, J. B., Kyle, J. E., Lalani, S. R., Lam, B., Lanpher, B. C., Lanza, I. R., Lau, C. C., Lazar, J., LeBlanc, K., Lee, B. H., Lee, H., Levitt, R., Levy, S. E., Lewis, R. A., Lincoln, S. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Majcherska, M. M., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Markello, T. C., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., May, T., McCauley, J., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., Metz, T. O., Might, M., Morava-Kozicz, E., Moretti, P. M., Morimoto, M., Mulvihill, J. J., Murdock, D. R., Nath, A., Nelson, S. F., Newberry, J. S., Newman, J. H., Nicholas, S. K., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Postlethwait, J. H., Potocki, L., Pusey, B. N., Quinlan, A., Raja, A. N., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rowley, R. K., Ruzhnikov, M., Sacco, R., Sampson, J. B., Samson, S. L., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, D. A., Shakachite, L., Sharma, P., Shashi, V., Shields, K., Shin, J., Signer, R., Sillari, C. H., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, K. S., Solnica-Krezel, L., Spillmann, R. C., Stoler, J. M., Stong, N., Sullivan, J. A., Sutton, S., Sweetser, D. A., Tabor, H. K., Tamburro, C. P., Tan, Q. K., Tekin, M., Telischi, F., Thorson, W., Tifft, C. J., Toro, C., Tran, A. A., Urv, T. K., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walley, N. M., Walsh, C. A., Walker, M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Waters, K. M., Webb-Robertson, B. M., Wegner, D., Westerfield, M., Wheeler, M. T., Wise, A. L., Wolfe, L. A., Woods, J. D., Worthey, E. A., Yamamoto, S., Yang, J., Yoon, A. J., Yu, G., Zastrow, D. B., Zhao, C., Zuchner, S. 2019

  Abstract

  WD40 repeat-containing proteins form a large family of proteins present in all eukaryotes. Here, we identified five pediatric probands with de novo variants in WDR37, which encodes a member of the WD40 repeat protein family. Two probands shared one variant and the others have variants in nearby amino acids outside the WD40 repeats. The probands exhibited shared phenotypes of epilepsy, colobomas, facial dysmorphology reminiscent of CHARGE syndrome, developmental delay and intellectual disability, and cerebellar hypoplasia. The WDR37 protein is highly conserved in vertebrate and invertebrate model organisms and is currently not associated with a human disease. We generated a null allele of the single Drosophila ortholog to gain functional insights and replaced the coding region of the fly gene CG12333/wdr37 with GAL4. These flies are homozygous viable but display severe bang sensitivity, a phenotype associated with seizures in flies. Additionally, the mutant flies fall when climbing the walls of the vials, suggesting a defect in grip strength, and repeat the cycle of climbing and falling. Similar to wall clinging defect, mutant males often lose grip of the female abdomen during copulation. These phenotypes are rescued by using the GAL4 in the CG12333/wdr37 locus to drive the UAS-human reference WDR37 cDNA. The two variants found in three human subjects failed to rescue these phenotypes, suggesting that these alleles severely affect the function of this protein. Taken together, our data suggest that variants in WDR37 underlie a novel syndromic neurological disorder.

  View details for DOI 10.1016/j.ajhg.2019.06.014

  View details for PubMedID 31327508

• Magnetic Resonance Imaging characteristics in case of TOR1AIP1 muscular dystrophy. Clinical imaging Bhatia, A., Mobley, B. C., Cogan, J., Koziura, M. E., Brokamp, E., Phillips, J., Newman, J., Moore, S. A., Hamid, R. 2019; 58: 108-113

  Abstract

  Mutations in the torsinA-interacting protein 1 (TOR1AIP1) gene result in a severe muscular dystrophy with minimal literature in the pediatric population. We review a case of TOR1AIP1 gene mutation in a 16-year-old Caucasian female with a long history of muscle weakness. Extensive clinical workup was performed and MRI at time of initial presentation demonstrated no significant muscular atrophy with heterogenous STIR hyperintensity of the lower extremity muscles. MRI findings seven years later included extensive atrophy of the lower extremities, with severe progression, including the gluteal muscles, iliopsoas, rectus femoris, and obturator internus. There was also significant atrophy of the rectus abdominis and internal and external oblique muscles, and iliacus muscles. The MRI findings showed more proximal involvement of lower extremities and no atrophy of the tibialis anterior, making TOR1AIP1 the more likely genetic cause. Muscle biopsy findings supported TOR1AIP1 limb-girdle muscular dystrophy. Though rare, TOR1AIP1 gene mutation occurs in pediatric patients and MRI can aid in diagnosis and help differentiate from other types of muscular dystrophy. Genetic and pathology workup is also crucial to accurate diagnosis and possible treatment of these patients.

  View details for DOI 10.1016/j.clinimag.2019.06.010

  View details for PubMedID 31299614

• Lysosomal Storage and Albinism Due to Effects of a De Novo CLCN7 Variant on Lysosomal Acidification. American journal of human genetics Nicoli, E. R., Weston, M. R., Hackbarth, M., Becerril, A., Larson, A., Zein, W. M., Baker, P. R., Burke, J. D., Dorward, H., Davids, M., Huang, Y., Adams, D. R., Zerfas, P. M., Chen, D., Markello, T. C., Toro, C., Wood, T., Elliott, G., Vu, M., Zheng, W., Garrett, L. J., Tifft, C. J., Gahl, W. A., Day-Salvatore, D. L., Mindell, J. A., Malicdan, M. C. 2019; 104 (6): 1127-1138

  Abstract

  Optimal lysosome function requires maintenance of an acidic pH maintained by proton pumps in combination with a counterion transporter such as the Cl-/H+ exchanger, CLCN7 (ClC-7), encoded by CLCN7. The role of ClC-7 in maintaining lysosomal pH has been controversial. In this paper, we performed clinical and genetic evaluations of two children of different ethnicities. Both children had delayed myelination and development, organomegaly, and hypopigmentation, but neither had osteopetrosis. Whole-exome and -genome sequencing revealed a de novo c.2144A>G variant in CLCN7 in both affected children. This p.Tyr715Cys variant, located in the C-terminal domain of ClC-7, resulted in increased outward currents when it was heterologously expressed in Xenopus oocytes. Fibroblasts from probands displayed a lysosomal pH approximately 0.2 units lower than that of control cells, and treatment with chloroquine normalized the pH. Primary fibroblasts from both probands also exhibited markedly enlarged intracellular vacuoles; this finding was recapitulated by the overexpression of human p.Tyr715Cys CLCN7 in control fibroblasts, reflecting the dominant, gain-of-function nature of the variant. A mouse harboring the knock-in Clcn7 variant exhibited hypopigmentation, hepatomegaly resulting from abnormal storage, and enlarged vacuoles in cultured fibroblasts. Our results show that p.Tyr715Cys is a gain-of-function CLCN7 variant associated with developmental delay, organomegaly, and hypopigmentation resulting from lysosomal hyperacidity, abnormal storage, and enlarged intracellular vacuoles. Our data supports the hypothesis that the ClC-7 antiporter plays a critical role in maintaining lysosomal pH.

  View details for DOI 10.1016/j.ajhg.2019.04.008

  View details for PubMedID 31155284

  View details for PubMedCentralID PMC6562152

• Neurologic Involvement in Seronegative Sjogren's Syndrome with Positive Lip Biopsy: A Single Center Experience Wong, K., Galli, J., Bacharach, R., Klein, J., Esquibel, L., Pace, L., Lebiedz-Odrobina, D., Rose, J., Trump, B., Hull, C., Greenlee, J., Clardy, S. LIPPINCOTT WILLIAMS & WILKINS. 2019

  View details for Web of Science ID 000475965900082

• Draft Genome Sequence of Hydrogenibacillus schlegelii MA48, a Deep-Branching Member of the Bacilli Class of Firmicutes. Genome announcements Maker, A., Hemp, J., Pace, L. A., Ward, L. M., Fischer, W. W. 2017; 5 (3)

  Abstract

  We report here the draft genome sequence of Hydrogenibacillus schlegelii MA48, a thermophilic facultative anaerobe that can oxidize hydrogen aerobically. H. schlegelii MA48 belongs to a deep-branching clade of the Bacilli class and provides important insight into the acquisition of aerobic respiration within the Firmicutes phylum.

  View details for DOI 10.1128/genomeA.00380-16

  View details for PubMedID 28104644

  View details for PubMedCentralID PMC5255923

• Duodenal Bulb Biopsies Remain Relevant in the Diagnosis of Adult Celiac Disease CLINICAL GASTROENTEROLOGY AND HEPATOLOGY Pace, L. A., Crowe, S. E. 2016; 14 (11): 1589-1592

  View details for DOI 10.1016/j.cgh.2016.08.020

  View details for Web of Science ID 000386760200017

  View details for PubMedID 27565522

  View details for PubMedCentralID PMC5941945

• Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification. The ISME journal Hemp, J., Lücker, S., Schott, J., Pace, L. A., Johnson, J. E., Schink, B., Daims, H., Fischer, W. W. 2016; 10 (11): 2669-2678

  Abstract

  Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the water-oxidizing complex of photosystem II. Therefore, it is likely that high-potential phototrophy originally evolved to oxidize alternative electron donors that utilized simpler redox chemistry, such as nitrite or Mn. To determine whether nitrite could have had a role in the transition to high-potential phototrophy, we sequenced and analyzed the genome of Thiocapsa KS1, a Gammaproteobacteria capable of anoxygenic phototrophic nitrite oxidation. The genome revealed a high metabolic flexibility, which likely allows Thiocapsa KS1 to colonize a great variety of habitats and to persist under fluctuating environmental conditions. We demonstrate that Thiocapsa KS1 does not utilize a high-potential reaction center for phototrophic nitrite oxidation, which suggests that this type of phototrophic nitrite oxidation did not drive the evolution of high-potential phototrophy. In addition, phylogenetic and biochemical analyses of the nitrite oxidoreductase (NXR) from Thiocapsa KS1 illuminate a complex evolutionary history of nitrite oxidation. Our results indicate that the NXR in Thiocapsa originates from a different nitrate reductase clade than the NXRs in chemolithotrophic nitrite oxidizers, suggesting that multiple evolutionary trajectories led to modern nitrite-oxidizing bacteria.

  View details for DOI 10.1038/ismej.2016.56

  View details for PubMedID 27093047

  View details for PubMedCentralID PMC5113846

• Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature biotechnology Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A. V., Meehan, M. J., Liu, W., Crüsemann, M., Boudreau, P. D., Esquenazi, E., Sandoval-Calderón, M., Kersten, R. D., Pace, L. A., Quinn, R. A., Duncan, K. R., Hsu, C., Floros, D. J., Gavilan, R. G., Kleigrewe, K., Northen, T., Dutton, R. J., Parrot, D., Carlson, E. E., Aigle, B., Michelsen, C. F., Jelsbak, L., Sohlenkamp, C., Pevzner, P., Edlund, A., McLean, J., Piel, J., Murphy, B. T., Gerwick, L., Liaw, C., Yang, Y., Humpf, H., Maansson, M., Keyzers, R. A., Sims, A. C., Johnson, A. R., Sidebottom, A. M., Sedio, B. E., Klitgaard, A., Larson, C. B., Boya P, C. A., Torres-Mendoza, D., Gonzalez, D. J., Silva, D. B., Marques, L. M., Demarque, D. P., Pociute, E., O'Neill, E. C., Briand, E., Helfrich, E. J., Granatosky, E. A., Glukhov, E., Ryffel, F., Houson, H., Mohimani, H., Kharbush, J. J., Zeng, Y., Vorholt, J. A., Kurita, K. L., Charusanti, P., McPhail, K. L., Nielsen, K. F., Vuong, L., Elfeki, M., Traxler, M. F., Engene, N., Koyama, N., Vining, O. B., Baric, R., Silva, R. R., Mascuch, S. J., Tomasi, S., Jenkins, S., Macherla, V., Hoffman, T., Agarwal, V., Williams, P. G., Dai, J., Neupane, R., Gurr, J., Rodríguez, A. M., Lamsa, A., Zhang, C., Dorrestein, K., Duggan, B. M., Almaliti, J., Allard, P., Phapale, P., Nothias, L., Alexandrov, T., Litaudon, M., Wolfender, J., Kyle, J. E., Metz, T. O., Peryea, T., Nguyen, D., VanLeer, D., Shinn, P., Jadhav, A., Müller, R., Waters, K. M., Shi, W., Liu, X., Zhang, L., Knight, R., Jensen, P. R., Palsson, B. Ø., Pogliano, K., Linington, R. G., Gutiérrez, M., Lopes, N. P., Gerwick, W. H., Moore, B. S., Dorrestein, P. C., Bandeira, N. 2016; 34 (8): 828-837

  Abstract

  The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

  View details for DOI 10.1038/nbt.3597

  View details for PubMedID 27504778

• Complex Relationships Between Food, Diet, and the Microbiome. Gastroenterology clinics of North America Pace, L. A., Crowe, S. E. 2016; 45 (2): 253-65

  Abstract

  Diet is a risk factor in several medically important disease states, including obesity, celiac disease, and functional gastrointestinal disorders. Modification of diet can prevent, treat, or alleviate some of the symptoms associated with these diseases and improve general health. It is important to provide patients with simple dietary recommendations to increase the probability of successful implementation. These recommendations include increasing vegetable, fruit, and fiber intake, consuming lean protein sources to enhance satiety, avoiding or severely limiting highly processed foods, and reducing portion sizes for overweight and obese patients.

  View details for DOI 10.1016/j.gtc.2016.02.004

  View details for PubMedID 27261897

  View details for PubMedCentralID PMC5912342

• Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia. Genome announcements Hemp, J., Ward, L. M., Pace, L. A., Fischer, W. W. 2015; 3 (6)

  Abstract

  We report here the draft genome sequence of Ardenticatena maritima 110S, the first sequenced member of class Ardenticatenia of the phylum Chloroflexi. This thermophilic organism is capable of a range of physiologies, including aerobic respiration and iron reduction. It also encodes a complete denitrification pathway with a novel nitric oxide reductase.

  View details for DOI 10.1128/genomeA.01347-15

  View details for PubMedID 26586887

  View details for PubMedCentralID PMC4653789

• Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the Chloroflexi Class Anaerolineae. Genome announcements Hemp, J., Ward, L. M., Pace, L. A., Fischer, W. W. 2015; 3 (6)

  Abstract

  We report the draft genome sequence of Levilinea saccharolytica KIBI-1, a facultative anaerobic member of the Chloroflexi class Anaerolineae. While L. saccharolytica was characterized as an obligate anaerobe, genome analysis provides evidence for the presence of both aerobic respiration and partial denitrification pathways.

  View details for DOI 10.1128/genomeA.01357-15

  View details for PubMedID 26586894

  View details for PubMedCentralID PMC4653796

• Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae. Genome announcements Ward, L. M., Hemp, J., Pace, L. A., Fischer, W. W. 2015; 3 (6)

  Abstract

  We present the draft genome sequence of Leptolinea tardivitalis YMTK-2, a member of the Chloroflexi phylum. This organism was initially characterized as a strictly anaerobic nonmotile fermenter; however, genome analysis demonstrates that it encodes for a flagella and might be capable of aerobic respiration.

  View details for DOI 10.1128/genomeA.01356-15

  View details for PubMedID 26586893

  View details for PubMedCentralID PMC4653795

• Draft Genome of Thermanaerothrix daxensis GNS-1, a Thermophilic Facultative Anaerobe from the Chloroflexi Class Anaerolineae. Genome announcements Pace, L. A., Hemp, J., Ward, L. M., Fischer, W. W. 2015; 3 (6)

  Abstract

  We present the draft genome of Thermanaerothrix daxensis GNS-1, a thermophilic member of the Chloroflexi phylum. This organism was initially characterized as a nonmotile, strictly anaerobic fermenter; however, genome analysis demonstrates that it encodes genes for a flagellum and multiple pathways for aerobic and anaerobic respiration.

  View details for DOI 10.1128/genomeA.01354-15

  View details for PubMedID 26586891

  View details for PubMedCentralID PMC4653793

• Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the Chloroflexi Class Anaerolineae. Genome announcements Hemp, J., Ward, L. M., Pace, L. A., Fischer, W. W. 2015; 3 (6)

  Abstract

  We report the draft genome sequence of Ornatilinea apprima P3M-1, a strictly anaerobic member of the Chloroflexi class Anaerolineae. This genome provides insight into the diversity of metabolism within the Anaerolineae, and the evolution of respiration within the Chloroflexi.

  View details for DOI 10.1128/genomeA.01353-15

  View details for PubMedID 26586890

  View details for PubMedCentralID PMC4653792

• Draft Genome Sequence of Herpetosiphon geysericola GC-42, a Nonphototrophic Member of the Chloroflexi Class Chloroflexia. Genome announcements Ward, L. M., Hemp, J., Pace, L. A., Fischer, W. W. 2015; 3 (6)

  Abstract

  We report here the draft genome sequence of Herpetosiphon geysericola GC-42, a predatory nonphototrophic member of the class Chloroflexia in the phylum Chloroflexi. This genome provides insight into the evolution of phototrophy and aerobic respiration within the Chloroflexi.

  View details for DOI 10.1128/genomeA.01352-15

  View details for PubMedID 26586889

  View details for PubMedCentralID PMC4653791

• The heme-copper oxidoreductase superfamily: Diversity, evolution and ecology Hemp, J., Pace, L. A., Gennis, R. B. ELSEVIER SCIENCE BV. 2012: S107-S108

  View details for DOI 10.1016/j.bbabio.2012.06.290

  View details for Web of Science ID 000308525400267

• Stercoral ulcer as a cause of lower gastrointestinal (LGI) bleeding in chronic hemodialysis patients. Clinical nephrology Saeed, F., Kalra, A., Kousar, N., Pace, L. A., Holley, J. L. 2012; 77 (1): 75-8

  Abstract

  Gastrointestinal (GI) bleeding is more common in patients with chronic kidney disease and is associated with higher mortality than in the general population. Stercoral ulceration of the colon is rarely reported in the nephrology literature. We observed 2 cases of stercoral ulcer presenting as lower gastrointestinal (LGI) bleeding in patients on chronic hemodialysis. Both patients were elderly (81 and 75 years, respectively) with a history of constipation. Diagnosis of stercoral ulcer as the cause of lower GI bleeding was made using endoscopic procedures. Stercoral ulcer should be considered in cases of lower GI bleeding in chronic dialysis patients.

  View details for DOI 10.5414/cn107000

  View details for PubMedID 22185973

• Adaptation of aerobic respiration to low O2 environments. Proceedings of the National Academy of Sciences of the United States of America Han, H., Hemp, J., Pace, L. A., Ouyang, H., Ganesan, K., Roh, J. H., Daldal, F., Blanke, S. R., Gennis, R. B. 2011; 108 (34): 14109-14

  Abstract

  Aerobic respiration in bacteria, Archaea, and mitochondria is performed by oxygen reductase members of the heme-copper oxidoreductase superfamily. These enzymes are redox-driven proton pumps which conserve part of the free energy released from oxygen reduction to generate a proton motive force. The oxygen reductases can be divided into three main families based on evolutionary and structural analyses (A-, B- and C-families), with the B- and C-families evolving after the A-family. The A-family utilizes two proton input channels to transfer protons for pumping and chemistry, whereas the B- and C-families require only one. Generally, the B- and C-families also have higher apparent oxygen affinities than the A-family. Here we use whole cell proton pumping measurements to demonstrate differential proton pumping efficiencies between representatives of the A-, B-, and C-oxygen reductase families. The A-family has a coupling stoichiometry of 1 H(+)/e(-), whereas the B- and C-families have coupling stoichiometries of 0.5 H(+)/e(-). The differential proton pumping stoichiometries, along with differences in the structures of the proton-conducting channels, place critical constraints on models of the mechanism of proton pumping. Most significantly, it is proposed that the adaptation of aerobic respiration to low oxygen environments resulted in a concomitant reduction in energy conservation efficiency, with important physiological and ecological consequences.

  View details for DOI 10.1073/pnas.1018958108

  View details for PubMedID 21844375

  View details for PubMedCentralID PMC3161551

• The diheme cytochrome c(4) from Vibrio cholerae is a natural electron donor to the respiratory cbb(3) oxygen reductase. Biochemistry Chang, H. Y., Ahn, Y., Pace, L. A., Lin, M. T., Lin, Y. H., Gennis, R. B. 2010; 49 (35): 7494-503

  Abstract

  The respiratory chain of Vibrio cholerae contains three bd-type quinol oxygen reductases as well as one cbb(3) oxygen reductase. The cbb(3) oxygen reductase has been previously isolated and characterized; however, the natural mobile electron donor(s) that shuttles electrons between the bc(1) complex and the cbb(3) oxygen reductase is not known. The most likely candidates are the diheme cytochrome c(4) and monoheme cytochrome c(5), which have been previously shown to be present in the periplasm of aerobically grown cultures of V. cholerae. Both cytochromes c(4) and c(5) from V. cholerae have been cloned and expressed heterologously in Escherichia coli. It is shown that reduced cytochrome c(4) is a substrate for the purified cbb(3) oxygen reductase and can support steady state oxygen reductase activity of at least 300 e(-1)/s. In contrast, reduced cytochrome c(5) is not a good substrate for the cbb(3) oxygen reductase. Surprisingly, the dependence of the oxygen reductase activity on the concentration of cytochrome c(4) does not exhibit saturation. Global spectroscopic analysis of the time course of the oxidation of cytochrome c(4) indicates that the apparent lack of saturation is due to the strong dependence of K(M) and V(max) on the concentration of oxidized cytochrome c(4). Whether this is an artifact of the in vitro assay or has physiological significance remains unknown. Cyclic voltammetry was used to determine that the midpoint potentials of the two hemes in cytochrome c(4) are 240 and 340 mV (vs standard hydrogen electrode), similar to the electrochemical properties of other c(4)-type cytochromes. Genomic analysis shows a strong correlation between the presence of a c(4)-type cytochrome and a cbb(3) oxygen reductase within the beta- and gamma-proteobacterial clades, suggesting that cytochrome c(4) is the likely natural electron donor to the cbb(3) oxygen reductases within these organisms. These would include the beta-proteobacteria Neisseria meningitidis and Neisseria gonnorhoeae, in which the cbb(3) oxygen reductases are the only terminal oxidases in their respiratory chains, and the gamma-proteobacterium Pseudomonas stutzeri.

  View details for DOI 10.1021/bi1004574

  View details for PubMedID 20715760

  View details for PubMedCentralID PMC2932843

• Protein kinase G type II is required for night-to-day progression of the mammalian circadian clock. Neuron Tischkau, S. A., Mitchell, J. W., Pace, L. A., Barnes, J. W., Barnes, J. A., Gillette, M. U. 2004; 43 (4): 539-49

  Abstract

  Circadian clocks comprise a cyclic series of dynamic cellular states, characterized by the changing availability of substrates that alter clock time when activated. To determine whether circadian clocks, like the cell cycle, exhibit regulation by key phosphorylation events, we examined endogenous kinase regulation of timekeeping in the mammalian suprachiasmatic nucleus (SCN). Short-term inhibition of PKG-II but not PKG-Ibeta using antisense oligodeoxynucleotides delayed rhythms of electrical activity and Bmal1 mRNA. Phase resetting was rapid and dynamic; inhibition of PKG-II forced repetition of the last 3.5 hr of the cycle. Chronic inhibition of PKG-II disrupted electrical activity rhythms and tonically increased Bmal1 mRNA. PKG-II-like immunoreactivity was detected after coimmunoprecipitation with CLOCK, and CLOCK was phosphorylated in the presence of active PKG-II. PKG-II activation may define a critical control point for temporal progression into the daytime domain by acting on the positive arm of the transcriptional/translational feedback loop.

  View details for DOI 10.1016/j.neuron.2004.07.027

  View details for PubMedID 15312652

• The intergeniculate leaflet, but not the visual midbrain, mediates hamster circadian rhythm response to constant light. Journal of biological rhythms Morin, L. P., Pace, L. 2002; 17 (3): 217-26

  Abstract

  Several studies have demonstrated a variety of effects of intergeniculate leaflet (IGL) lesions on circadian rhythm regulation. Recent studies have suggested the possibility that certain rhythm functions attributed to the IGL are actually controlled by retinorecipient midbrain nuclei or other brain areas connected to the IGL. The present investigations evaluated whether midbrain lesions previously shown to block the phasic actions of benzodiazepine would also reduce or eliminate the period-lengthening effect of constant light (LL), a function that has been attributed to the IGL. Experiment 1 established that the circadian period of controls lengthened by about 0.57 h when the animals were transferred from constant dark (DD) to LL, but the magnitude of change was attenuated by about 50% in animals with IGL lesions caused by the neurotoxin N-methyl-D-aspartate (NMDA). In experiment 2, controls were compared to groups receiving either NMDA lesions of the pretectum or tectum or knife cuts designed to sever connections between the IGL and more medial retinorecipient nuclei. As in experiment 1, there were no differences between groups with respect to circadian period in DD. However, unlike experiment 1, all groups lengthened period equally in LL (overall mean increase = 0.57 h). Thus, the effect of LL on circadian period appears to be a joint result of photic information arriving at the circadian clock directly from the retinohypothalamic tract and indirectly through the IGL via the geniculohypothalamic tract, without involvement of visual midbrain. The results may have implications for the anatomical basis of Aschoff's rule.

  View details for DOI 10.1177/07430402017003005

  View details for PubMedID 12054193