Honors & Awards

  • Postdoctoral Fellowship in Aging Research Program, Ellison Medical Foundation/AFAR (2011-2012)

Education & Certifications

  • PhD, Université Bordeaux II, France, Genetics (2008)

All Publications

  • Age-related loss of neural stem cell O-GlcNAc promotes a glial fate switch through STAT3 activation. Proceedings of the National Academy of Sciences of the United States of America White, C. W., Fan, X., Maynard, J. C., Wheatley, E. G., Bieri, G., Couthouis, J., Burlingame, A. L., Villeda, S. A. 2020


    Increased neural stem cell (NSC) quiescence is a major determinant of age-related regenerative decline in the adult hippocampus. However, a coextensive model has been proposed in which division-coupled conversion of NSCs into differentiated astrocytes restrict the stem cell pool with age. Here we report that age-related loss of the posttranslational modification, O-linked beta-N-acetylglucosamine (O-GlcNAc), in NSCs promotes a glial fate switch. We detect an age-dependent decrease in NSC O-GlcNAc levels coincident with decreased neurogenesis and increased gliogenesis in the mature hippocampus. Mimicking an age-related loss of NSC O-GlcNAcylation in young mice reduces neurogenesis, increases astrocyte differentiation, and impairs associated cognitive function. Using RNA-sequencing of primary NSCs following decreased O-GlcNAcylation, we detected changes in the STAT3 signaling pathway indicative of glial differentiation. Moreover, using O-GlcNAc-specific mass spectrometry analysis of the aging hippocampus, together with an in vitro site-directed mutagenesis approach, we identify loss of STAT3 O-GlcNAc at Threonine 717 as a driver of astrocyte differentiation. Our data identify the posttranslational modification, O-GlcNAc, as a key molecular regulator of regenerative decline underlying an age-related NSC fate switch.

    View details for DOI 10.1073/pnas.2007439117

    View details for PubMedID 32848054

  • A memory of eS25 loss drives resistance phenotypes. Nucleic acids research Johnson, A. G., Flynn, R. A., Lapointe, C. P., Ooi, Y. S., Zhao, M. L., Richards, C. M., Qiao, W., Yamada, S. B., Couthouis, J., Gitler, A. D., Carette, J. E., Puglisi, J. D. 2020


    In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. Yet the direct and indirect consequences from these lesions are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation and suggests caution in the interpretation of ribosomal protein gene mutation data.

    View details for DOI 10.1093/nar/gkaa444

    View details for PubMedID 32463448

  • Evolution of a Human-Specific Tandem Repeat Associated with ALS. American journal of human genetics Course, M. M., Gudsnuk, K., Smukowski, S. N., Winston, K., Desai, N., Ross, J. P., Sulovari, A., Bourassa, C. V., Spiegelman, D., Couthouis, J., Yu, C. E., Tsuang, D. W., Jayadev, S., Kay, M. A., Gitler, A. D., Dupre, N., Eichler, E. E., Dion, P. A., Rouleau, G. A., Valdmanis, P. N. 2020


    Tandem repeats are proposed to contribute to human-specific traits, and more than 40 tandem repeat expansions are known to cause neurological disease. Here, we characterize a human-specific 69 bp variable number tandem repeat (VNTR) in the last intron of WDR7, which exhibits striking variability in both copy number and nucleotide composition, as revealed by long-read sequencing. In addition, greater repeat copy number is significantly enriched in three independent cohorts of individuals with sporadic amyotrophic lateral sclerosis (ALS). Each unit of the repeat forms a stem-loop structure with the potential to produce microRNAs, and the repeat RNA can aggregate when expressed in cells. We leveraged its remarkable sequence variability to align the repeat in 288 samples and uncover its mechanism of expansion. We found that the repeat expands in the 3'-5' direction, in groups of repeat units divisible by two. The expansion patterns we observed were consistent with duplication events, and a replication error called template switching. We also observed that the VNTR is expanded in both Denisovan and Neanderthal genomes but is fixed at one copy or fewer in non-human primates. Evaluating the repeat in 1000 Genomes Project samples reveals that some repeat segments are solely present or absent in certain geographic populations. The large size of the repeat unit in this VNTR, along with our multiplexed sequencing strategy, provides an unprecedented opportunity to study mechanisms of repeat expansion, and a framework for evaluating the roles of VNTRs in human evolution and disease.

    View details for DOI 10.1016/j.ajhg.2020.07.004

    View details for PubMedID 32750315

  • Knockout of reactive astrocyte activating factors slows disease progression in an ALS mouse model. Nature communications Guttenplan, K. A., Weigel, M. K., Adler, D. I., Couthouis, J., Liddelow, S. A., Gitler, A. D., Barres, B. A. 2020; 11 (1): 3753


    Reactive astrocytes have been implicated in the pathogenesis of neurodegenerative diseases, including a non-cell autonomous effect on motor neuron survival in ALS. We previously defined a mechanism by which microglia release three factors, IL-1α, TNFα, and C1q, to induce neurotoxic astrocytes. Here we report that knocking out these three factors markedly extends survival in the SOD1G93A ALS mouse model, providing evidence for gliosis as a potential ALS therapeutic target.

    View details for DOI 10.1038/s41467-020-17514-9

    View details for PubMedID 32719333

  • Genome-wide synthetic lethal CRISPR screen identifies FIS1 as a genetic interactor of ALS-linked C9ORF72. Brain research Chai, N., Haney, M. S., Couthouis, J., Morgens, D. W., Benjamin, A., Wu, K., Ousey, J., Fang, S., Finer, S., Bassik, M. C., Gitler, A. D. 2019: 146601


    Mutations in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis (ALS). Both toxic gain of function and loss of function pathogenic mechanisms have been proposed. Accruing evidence from mouse knockout studies point to a role for C9ORF72 as a regulator of immune function. To provide further insight into its cellular function, we performed a genome-wide synthetic lethal CRISPR screen in human myeloid cells lacking C9ORF72. We discovered a strong synthetic lethal genetic interaction between C9ORF72 and FIS1, which encodes a mitochondrial membrane protein involved in mitochondrial fission and mitophagy. Mass spectrometry experiments revealed that in C9ORF72 knockout cells, FIS1 strongly bound to a class of immune regulators that activate the receptor for advanced glycation end (RAGE) products and trigger inflammatory cascades. These findings present a novel genetic interactor for C9ORF72 and suggest a compensatory role for FIS1 in suppressing inflammatory signaling in the absence of C9ORF72.

    View details for DOI 10.1016/j.brainres.2019.146601

    View details for PubMedID 31843624

  • LRRK2 modifies alpha-syn pathology and spread in mouse models and human neurons ACTA NEUROPATHOLOGICA Bieri, G., Brahic, M., Bousset, L., Couthouis, J., Kramer, N. J., Ma, R., Nakayama, L., Monbureau, M., Defensor, E., Schuele, B., Shamloo, M., Melki, R., Gitler, A. D. 2019; 137 (6): 961–80
  • Variants in KIAA0825 underlie autosomal recessive postaxial polydactyly HUMAN GENETICS Ullah, I., Kakar, N., Schrauwen, I., Hussain, S., Chakchouk, I., Liaqat, K., Acharya, A., Wasif, N., Santos-Cortez, R. P., Khan, S., Aziz, A., Lee, K., Couthouis, J., Horn, D., Kragesteen, B. K., Spielmann, M., Thiele, H., Nickerson, D. A., Bamshad, M. J., Gitler, A. D., Ahmad, J., Ansar, M., Borck, G., Ahmad, W., Leal, S. M. 2019; 138 (6): 593–600
  • Variants in KIAA0825 underlie autosomal recessive postaxial polydactyly. Human genetics Ullah, I., Kakar, N., Schrauwen, I., Hussain, S., Chakchouk, I., Liaqat, K., Acharya, A., Wasif, N., Santos-Cortez, R. L., Khan, S., Aziz, A., Lee, K., Couthouis, J., Horn, D., Kragesteen, B. K., Spielmann, M., Thiele, H., Nickerson, D. A., Bamshad, M. J., Gitler, A. D., Ahmad, J., Ansar, M., Borck, G., Ahmad, W., Leal, S. M. 2019


    Postaxial polydactyly (PAP) is a common limb malformation that often leads to cosmetic and functional complications. Molecular evaluation of polydactyly can serve as a tool to elucidate genetic and signaling pathways that regulate limb development, specifically, the anterior-posterior specification of the limb. To date, only five genes have been identified for nonsyndromic PAP: FAM92A, GLI1, GLI3, IQCE and ZNF141. In this study, two Pakistani multiplex consanguineous families with autosomal recessive nonsyndromic PAP were clinically and molecularly evaluated. From both pedigrees, a DNA sample from an affected member underwent exome sequencing. In each family, we identified a segregating frameshift (c.591dupA [p.(Q198Tfs*21)]) and nonsense variant (c.2173A>T [p.(K725*)]) in KIAA0825 (also known as C5orf36). Although KIAA0825 encodes a protein of unknown function, it has been demonstrated that its murine ortholog is expressed during limb development. Our data contribute to the establishment of a catalog of genes important in limb patterning, which can aid in diagnosis and obtaining a better understanding of the biology of polydactyly.

    View details for PubMedID 30982135

  • LRRK2 modifies alpha-syn pathology and spread in mouse models and human neurons. Acta neuropathologica Bieri, G., Brahic, M., Bousset, L., Couthouis, J., Kramer, N. J., Ma, R., Nakayama, L., Monbureau, M., Defensor, E., Schule, B., Shamloo, M., Melki, R., Gitler, A. D. 2019


    Progressive aggregation of the protein alpha-synuclein (alpha-syn) and loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) are key histopathological hallmarks of Parkinson's disease (PD). Accruing evidence suggests that alpha-syn pathology can propagate through neuronal circuits in the brain, contributing to the progressive nature of the disease. Thus, it is therapeutically pertinent to identify modifiers of alpha-syn transmission and aggregation as potential targets to slow down disease progression. A growing number of genetic mutations and risk factors has been identified in studies of familial and sporadic forms of PD. However, how these genes affect alpha-syn aggregation and pathological transmission, and whether they can be targeted for therapeutic interventions, remains unclear. We performed a targeted genetic screen of risk genes associated with PD and parkinsonism for modifiers of alpha-syn aggregation, using an alpha-syn preformed-fibril (PFF) induction assay. We found that decreased expression of Lrrk2 and Gba modulated alpha-syn aggregation in mouse primary neurons. Conversely, alpha-syn aggregation increased in primary neurons from mice expressing the PD-linked LRRK2 G2019S mutation. In vivo, using LRRK2 G2019S transgenic mice, we observed acceleration of alpha-syn aggregation and degeneration of dopaminergic neurons in the SNpc, exacerbated degeneration-associated neuroinflammation and behavioral deficits. To validate our findings in a human context, we established a novel human alpha-syn transmission model using induced pluripotent stem cell (iPS)-derived neurons (iNs), where human alpha-syn PFFs triggered aggregation of endogenous alpha-syn in a time-dependent manner. In PD subject-derived iNs, the G2019S mutation enhanced alpha-syn aggregation, whereas loss of LRRK2 decreased aggregation. Collectively, these findings establish a strong interaction between the PD risk gene LRRK2 and alpha-syn transmission across mouse and human models. Since clinical trials of LRRK2 inhibitors in PD are currently underway, our findings raise the possibility that these may be effective in PD broadly, beyond cases caused by LRRK2 mutations.

    View details for PubMedID 30927072

  • These violent repeats have violent extends. Neurology. Genetics Couthouis, J., Gitler, A. D. 2018; 4 (4): e247

    View details for PubMedID 30109264

  • PINK1 Phosphorylates MIC60/Mitofilin to Control Structural Plasticity of Mitochondrial Crista Junctions. Molecular cell Tsai, P. I., Lin, C. H., Hsieh, C. H., Papakyrikos, A. M., Kim, M. J., Napolioni, V., Schoor, C., Couthouis, J., Wu, R. M., Wszolek, Z. K., Winter, D., Greicius, M. D., Ross, O. A., Wang, X. 2018


    Mitochondrial crista structure partitions vital cellular reactions and is precisely regulated by diverse cellular signals. Here, we show that, in Drosophila, mitochondrial cristae undergo dynamic remodeling among distinct subcellular regions and the Parkinson's disease (PD)-linked Ser/Thr kinase PINK1 participates in their regulation. Mitochondria increase crista junctions and numbers in selective subcellular areas, and this remodeling requires PINK1 to phosphorylate the inner mitochondrial membrane protein MIC60/mitofilin, which stabilizes MIC60 oligomerization. Expression of MIC60 restores crista structure and ATP levels of PINK1-null flies and remarkably rescues their behavioral defects and dopaminergic neurodegeneration. In an extension to human relevance, we discover that the PINK1-MIC60 pathway is conserved in human neurons, and expression of several MIC60 coding variants in the mitochondrial targeting sequence found in PD patients in Drosophila impairs crista junction formation and causes locomotion deficits. These findings highlight the importance of maintenance and plasticity of crista junctions to cellular homeostasis in vivo.

    View details for PubMedID 29456190

  • Genome-wide Analyses Identify KIF5A as a Novel ALS Gene. Neuron Nicolas, A., Kenna, K. P., Renton, A. E., Ticozzi, N., Faghri, F., Chia, R., Dominov, J. A., Kenna, B. J., Nalls, M. A., Keagle, P., Rivera, A. M., van Rheenen, W., Murphy, N. A., van Vugt, J. J., Geiger, J. T., Van der Spek, R. A., Pliner, H. A., Smith, B. N., Marangi, G., Topp, S. D., Abramzon, Y., Gkazi, A. S., Eicher, J. D., Kenna, A., Mora, G., Calvo, A., Mazzini, L., Riva, N., Mandrioli, J., Caponnetto, C., Battistini, S., Volanti, P., La Bella, V., Conforti, F. L., Borghero, G., Messina, S., Simone, I. L., Trojsi, F., Salvi, F., Logullo, F. O., D'Alfonso, S., Corrado, L., Capasso, M., Ferrucci, L., Moreno, C. d., Kamalakaran, S., Goldstein, D. B., Gitler, A. D., Harris, T., Myers, R. M., Phatnani, H., Musunuri, R. L., Evani, U. S., Abhyankar, A., Zody, M. C., Kaye, J., Finkbeiner, S., Wyman, S. K., LeNail, A., Lima, L., Fraenkel, E., Svendsen, C. N., Thompson, L. M., Van Eyk, J. E., Berry, J. D., Miller, T. M., Kolb, S. J., Cudkowicz, M., Baxi, E., Benatar, M., Taylor, J. P., Rampersaud, E., Wu, G., Wuu, J., Lauria, G., Verde, F., Fogh, I., Tiloca, C., Comi, G. P., Sorarù, G., Cereda, C., Corcia, P., Laaksovirta, H., Myllykangas, L., Jansson, L., Valori, M., Ealing, J., Hamdalla, H., Rollinson, S., Pickering-Brown, S., Orrell, R. W., Sidle, K. C., Malaspina, A., Hardy, J., Singleton, A. B., Johnson, J. O., Arepalli, S., Sapp, P. C., McKenna-Yasek, D., Polak, M., Asress, S., Al-Sarraj, S., King, A., Troakes, C., Vance, C., de Belleroche, J., Baas, F., Ten Asbroek, A. L., Muñoz-Blanco, J. L., Hernandez, D. G., Ding, J., Gibbs, J. R., Scholz, S. W., Floeter, M. K., Campbell, R. H., Landi, F., Bowser, R., Pulst, S. M., Ravits, J. M., MacGowan, D. J., Kirby, J., Pioro, E. P., Pamphlett, R., Broach, J., Gerhard, G., Dunckley, T. L., Brady, C. B., Kowall, N. W., Troncoso, J. C., Le Ber, I., Mouzat, K., Lumbroso, S., Heiman-Patterson, T. D., Kamel, F., Van Den Bosch, L., Baloh, R. H., Strom, T. M., Meitinger, T., Shatunov, A., Van Eijk, K. R., de Carvalho, M., Kooyman, M., Middelkoop, B., Moisse, M., McLaughlin, R. L., Van Es, M. A., Weber, M., Boylan, K. B., Van Blitterswijk, M., Rademakers, R., Morrison, K. E., Basak, A. N., Mora, J. S., Drory, V. E., Shaw, P. J., Turner, M. R., Talbot, K., Hardiman, O., Williams, K. L., Fifita, J. A., Nicholson, G. A., Blair, I. P., Rouleau, G. A., Esteban-Pérez, J., García-Redondo, A., Al-Chalabi, A., Rogaeva, E., Zinman, L., Ostrow, L. W., Maragakis, N. J., Rothstein, J. D., Simmons, Z., Cooper-Knock, J., Brice, A., Goutman, S. A., Feldman, E. L., Gibson, S. B., Taroni, F., Ratti, A., Gellera, C., Van Damme, P., Robberecht, W., Fratta, P., Sabatelli, M., Lunetta, C., Ludolph, A. C., Andersen, P. M., Weishaupt, J. H., Camu, W., Trojanowski, J. Q., Van Deerlin, V. M., Brown, R. H., van den Berg, L. H., Veldink, J. H., Harms, M. B., Glass, J. D., Stone, D. J., Tienari, P., Silani, V., Chiò, A., Shaw, C. E., Traynor, B. J., Landers, J. E. 2018; 97 (6): 1268–83.e6


    To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.

    View details for PubMedID 29566793

  • CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity. Nature genetics Kramer, N. J., Haney, M. S., Morgens, D. W., Jovičić, A., Couthouis, J., Li, A., Ousey, J., Ma, R., Bieri, G., Tsui, C. K., Shi, Y., Hertz, N. T., Tessier-Lavigne, M., Ichida, J. K., Bassik, M. C., Gitler, A. D. 2018


    Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide-repeat expansions are translated into dipeptide-repeat (DPR) proteins, which are aggregation prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA-processing pathways, and chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9ORF72 DPRs in neurons and improved survival of human induced motor neurons from patients with C9ORF72 ALS. Together, our results demonstrate the promise of CRISPR-Cas9 screens in defining mechanisms of neurodegenerative diseases.

    View details for PubMedID 29507424

  • ERAD defects and the HFE-H63D variant are associated with increased risk of liver damages in Alpha 1-Antitrypsin Deficiency. PloS one Joly, P., Vignaud, H., Di Martino, J., Ruiz, M., Garin, R., Restier, L., Belmalih, A., Marchal, C., Cullin, C., Arveiler, B., Fergelot, P., Gitler, A. D., Lachaux, A., Couthouis, J., Bouchecareilh, M. 2017; 12 (6): e0179369


    The most common and severe disease causing allele of Alpha 1-Antitrypsin Deficiency (1ATD) is Z-1AT. This protein aggregates in the endoplasmic reticulum, which is the main cause of liver disease in childhood. Based on recent evidences and on the frequency of liver disease occurrence in Z-1AT patients, it seems that liver disease progression is linked to still unknown genetic factors.We used an innovative approach combining yeast genetic screens with next generation exome sequencing to identify and functionally characterize the genes involved in 1ATD associated liver disease.Using yeast genetic screens, we identified HRD1, an Endoplasmic Reticulum Associated Degradation (ERAD) associated protein, as an inducer of Z-mediated toxicity. Whole exome sequencing of 1ATD patients resulted in the identification of two variants associated with liver damages in Z-1AT homozygous cases: HFE H63D and HERPUD1 R50H. Functional characterization in Z-1AT model cell lines demonstrated that impairment of the ERAD machinery combined with the HFE H63D variant expression decreased both cell proliferation and cell viability, while Unfolded Protein Response (UPR)-mediated cell death was hyperstimulated.This powerful experimental pipeline allowed us to identify and functionally validate two genes involved in Z-1AT-mediated severe liver toxicity. This pilot study moves forward our understanding on genetic modifiers involved in 1ATD and highlights the UPR pathway as a target for the treatment of liver diseases associated with 1ATD. Finally, these findings support a larger scale screening for HERPUD1 R50H and HFE H63D variants in the sub-group of 1ATD patients developing significant chronic hepatic injuries (hepatomegaly, chronic cholestasis, elevated liver enzymes) and at risk developing liver cirrhosis.

    View details for PubMedID 28617828

    View details for PubMedCentralID PMC5472284

  • Spt4 selectively regulates the expression of C9orf72 sense and antisense mutant transcripts. Science Kramer, N. J., Carlomagno, Y., Zhang, Y., Almeida, S., Cook, C. N., Gendron, T. F., Prudencio, M., van Blitterswijk, M., Belzil, V., Couthouis, J., Paul, J. W., Goodman, L. D., Daughrity, L., Chew, J., Garrett, A., Pregent, L., Jansen-West, K., Tabassian, L. J., Rademakers, R., Boylan, K., Graff-Radford, N. R., Josephs, K. A., Parisi, J. E., Knopman, D. S., Petersen, R. C., Boeve, B. F., Deng, N., Feng, Y., Cheng, T., Dickson, D. W., Cohen, S. N., Bonini, N. M., Link, C. D., Gao, F., Petrucelli, L., Gitler, A. D. 2016; 353 (6300): 708-712


    An expanded hexanucleotide repeat in C9orf72 causes amyotrophic lateral sclerosis and frontotemporal dementia (c9FTD/ALS). Therapeutics are being developed to target RNAs containing the expanded repeat sequence (GGGGCC); however, this approach is complicated by the presence of antisense strand transcription of expanded GGCCCC repeats. We found that targeting the transcription elongation factor Spt4 selectively decreased production of both sense and antisense expanded transcripts, as well as their translated dipeptide repeat (DPR) products, and also mitigated degeneration in animal models. Knockdown of SUPT4H1, the human Spt4 ortholog, similarly decreased production of sense and antisense RNA foci, as well as DPR proteins, in patient cells. Therapeutic targeting of a single factor to eliminate c9FTD/ALS pathological features offers advantages over approaches that require targeting sense and antisense repeats separately.

    View details for DOI 10.1126/science.aaf7791

    View details for PubMedID 27516603

  • Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways SCIENCE Cirulli, E. T., Lasseigne, B. N., Petrovski, S., Sapp, P. C., Dion, P. A., Leblond, C. S., Couthouis, J., Lu, Y., Wang, Q., Krueger, B. J., Ren, Z., Keebler, J., Han, Y., Levy, S. E., Boone, B. E., Wimbish, J. R., Waite, L. L., Jones, A. L., Carulli, J. P., Day-Williams, A. G., Staropoli, J. F., Xin, W. W., Chesi, A., Raphael, A. R., McKenna-Yasek, D., Cady, J., de Jong, J. M., Kenna, K. P., Smith, B. N., Topp, S., Miller, J., Gkazi, A., Al-Chalabi, A., Van den Berg, L. H., Veldink, J., Silani, V., Ticozzi, N., Shaw, C. E., Baloh, R. H., Appel, S., Simpson, E., Lagier-Tourenne, C., Pulst, S. M., Gibson, S., Trojanowski, J. Q., Elman, L., McCluskey, L., Grossman, M., Shneider, N. A., Chung, W. K., Ravits, J. M., Glass, J. D., Sims, K. B., Van Deerlin, V. M., Maniatis, T., Hayes, S. D., Ordureau, A., Swarup, S., Landers, J., Baas, F., Allen, A. S., Bedlack, R. S., Harper, J. W., Gitler, A. D., Rouleau, G. A., Brown, R., Harms, M. B., Cooper, G. M., Harris, T., Myers, R. M., Goldstein, D. B. 2015; 347 (6229): 1436-1441


    Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease with no effective treatment. We report the results of a moderate-scale sequencing study aimed at increasing the number of genes known to contribute to predisposition for ALS. We performed whole-exome sequencing of 2869 ALS patients and 6405 controls. Several known ALS genes were found to be associated, and TBK1 (the gene encoding TANK-binding kinase 1) was identified as an ALS gene. TBK1 is known to bind to and phosphorylate a number of proteins involved in innate immunity and autophagy, including optineurin (OPTN) and p62 (SQSTM1/sequestosome), both of which have also been implicated in ALS. These observations reveal a key role of the autophagic pathway in ALS and suggest specific targets for therapeutic intervention.

    View details for DOI 10.1126/science.aaa3650

    View details for PubMedID 25700176

  • Targeted Exon Capture and Sequencing in Sporadic Amyotrophic Lateral Sclerosis PLOS GENETICS Couthouis, J., Raphael, A. R., Daneshjou, R., Gitler, A. D. 2014; 10 (10)


    Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that results in progressive degeneration of motor neurons, ultimately leading to paralysis and death. Approximately 10% of ALS cases are familial, with the remaining 90% of cases being sporadic. Genetic studies in familial cases of ALS have been extremely informative in determining the causative mutations behind ALS, especially as the same mutations identified in familial ALS can also cause sporadic disease. However, the cause of ALS in approximately 30% of familial cases and in the majority of sporadic cases remains unknown. Sporadic ALS cases represent an underutilized resource for genetic information about ALS; therefore, we undertook a targeted sequencing approach of 169 known and candidate ALS disease genes in 242 sporadic ALS cases and 129 matched controls to try to identify novel variants linked to ALS. We found a significant enrichment in novel and rare variants in cases versus controls, indicating that we are likely identifying disease associated mutations. This study highlights the utility of next generation sequencing techniques combined with functional studies and rare variant analysis tools to provide insight into the genetic etiology of a heterogeneous sporadic disease.

    View details for DOI 10.1371/journal.pgen.1004704

    View details for Web of Science ID 000344650700067

    View details for PubMedCentralID PMC4191946

  • Congenital muscular dystrophy and generalized epilepsy caused by GMPPB mutations. Brain research Raphael, A. R., Couthouis, J., Sakamuri, S., Siskind, C., Vogel, H., Day, J. W., Gitler, A. D. 2014; 1575: 66-71


    The alpha-dystroglycanopathies are genetically heterogeneous muscular dystrophies that result from hypoglycosylation of alpha-dystroglycan (α-DG). Alpha-dystroglycan is an essential link between the extracellular matrix and the muscle fiber sarcolemma, and proper glycosylation is critical for its ability to bind to ligands in the extracellular matrix. We sought to identify the genetic basis of alpha-dystroglycanopathy in a family wherein the affected individuals presented with congenital muscular dystrophy, brain abnormalities and generalized epilepsy. We performed whole exome sequencing and identified compound heterozygous GMPPB mutations in the affected children. GMPPB is an enzyme in the glycosylation pathway, and GMPPB mutations were recently linked to eight cases of alpha-dystroglycanopathy with a range of symptoms. We identified a novel mutation in GMPPB (p.I219T) as well as a previously published mutation (p.R287Q). Thus, our work further confirms a role for GMPPB defects in alpha-dystroglycanopathy, and suggests that glycosylation may play a role in the neuronal membrane channels or networks involved in the physiology of generalized epilepsy syndromes. This article is part of a Special Issue entitled RNA Metabolism 2013.

    View details for DOI 10.1016/j.brainres.2014.04.028

    View details for PubMedID 24780531

  • Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy. Neuromuscular disorders Couthouis, J., Raphael, A. R., Siskind, C., Findlay, A. R., Buenrostro, J. D., Greenleaf, W. J., Vogel, H., Day, J. W., Flanigan, K. M., Gitler, A. D. 2014; 24 (5): 431-435


    Limb-girdle muscular dystrophy primarily affects the muscles of the hips and shoulders (the "limb-girdle" muscles), although it is a heterogeneous disorder that can present with varying symptoms. There is currently no cure. We sought to identify the genetic basis of limb-girdle muscular dystrophy type 1 in an American family of Northern European descent using exome sequencing. Exome sequencing was performed on DNA samples from two affected siblings and one unaffected sibling and resulted in the identification of eleven candidate mutations that co-segregated with the disease. Notably, this list included a previously reported mutation in DNAJB6, p.Phe89Ile, which was recently identified as a cause of limb-girdle muscular dystrophy type 1D. Additional family members were Sanger sequenced and the mutation in DNAJB6 was only found in affected individuals. Subsequent haplotype analysis indicated that this DNAJB6 p.Phe89Ile mutation likely arose independently of the previously reported mutation. Since other published mutations are located close by in the G/F domain of DNAJB6, this suggests that the area may represent a mutational hotspot. Exome sequencing provided an unbiased and effective method for identifying the genetic etiology of limb-girdle muscular dystrophy type 1 in a previously genetically uncharacterized family. This work further confirms the causative role of DNAJB6 mutations in limb-girdle muscular dystrophy type 1D.

    View details for DOI 10.1016/j.nmd.2014.01.014

    View details for PubMedID 24594375

  • Exome sequencing to identify de novo mutations in sporadic ALS trios. Nature neuroscience Chesi, A., Staahl, B. T., Jovicic, A., Couthouis, J., Fasolino, M., Raphael, A. R., Yamazaki, T., Elias, L., Polak, M., Kelly, C., Williams, K. L., Fifita, J. A., Maragakis, N. J., Nicholson, G. A., King, O. D., Reed, R., Crabtree, G. R., Blair, I. P., Glass, J. D., Gitler, A. D. 2013; 16 (7): 851-855

    View details for DOI 10.1038/nn.3412

    View details for PubMedID 23708140

  • Evaluating the role of the FUS/TLS-related gene EWSR1 in amyotrophic lateral sclerosis HUMAN MOLECULAR GENETICS Couthouis, J., Hart, M. P., Erion, R., King, O. D., Diaz, Z., Nakaya, T., Ibrahim, F., Kim, H., Mojsilovic-Petrovic, J., Panossian, S., Kim, C. E., Frackelton, E. C., Solski, J. A., Williams, K. L., Clay-Falcone, D., Elman, L., McCluskey, L., Greene, R., Hakonarson, H., Kalb, R. G., Lee, V. M., Trojanowski, J. Q., Nicholson, G. A., Blair, I. P., Bonini, N. M., Van Deerlin, V. M., Mourelatos, Z., Shorter, J., Gitler, A. D. 2012; 21 (13): 2899-2911


    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease affecting motor neurons. Mutations in related RNA-binding proteins TDP-43, FUS/TLS and TAF15 have been connected to ALS. These three proteins share several features, including the presence of a bioinformatics-predicted prion domain, aggregation-prone nature in vitro and in vivo and toxic effects when expressed in multiple model systems. Given these commonalities, we hypothesized that a related protein, EWSR1 (Ewing sarcoma breakpoint region 1), might also exhibit similar properties and therefore could contribute to disease. Here, we report an analysis of EWSR1 in multiple functional assays, including mutational screening in ALS patients and controls. We identified three missense variants in EWSR1 in ALS patients, which were absent in a large number of healthy control individuals. We show that disease-specific variants affect EWSR1 localization in motor neurons. We also provide multiple independent lines of in vitro and in vivo evidence that EWSR1 has similar properties as TDP-43, FUS and TAF15, including aggregation-prone behavior in vitro and ability to confer neurodegeneration in Drosophila. Postmortem analysis of sporadic ALS cases also revealed cytoplasmic mislocalization of EWSR1. Together, our studies highlight a potential role for EWSR1 in ALS, provide a collection of functional assays to be used to assess roles of additional RNA-binding proteins in disease and support an emerging concept that a class of aggregation-prone RNA-binding proteins might contribute broadly to ALS and related neurodegenerative diseases.

    View details for DOI 10.1093/hmg/dds116

    View details for Web of Science ID 000305457700006

    View details for PubMedID 22454397

    View details for PubMedCentralID PMC3373238

  • A yeast functional screen predicts new candidate ALS disease genes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Couthouis, J., Hart, M. P., Shorter, J., DeJesus-Hernandez, M., Erion, R., Oristano, R., Liu, A. X., Ramos, D., Jethava, N., Hosangadi, D., Epstein, J., Chiang, A., Diaz, Z., Nakaya, T., Ibrahim, F., Kim, H., Solski, J. A., Williams, K. L., Mojsilovic-Petrovic, J., Ingre, C., Boylan, K., Graff-Radford, N. R., Dickson, D. W., Clay-Falcone, D., Elman, L., McCluskey, L., Greene, R., Kalb, R. G., Lee, V. M., Trojanowski, J. Q., Ludolph, A., Robberecht, W., Andersen, P. M., Nicholson, G. A., Blair, I. P., King, O. D., Bonini, N. M., Van Deerlin, V., Rademakers, R., Mourelatos, Z., Gitler, A. D. 2011; 108 (52): 20881-20890


    Amyotrophic lateral sclerosis (ALS) is a devastating and universally fatal neurodegenerative disease. Mutations in two related RNA-binding proteins, TDP-43 and FUS, that harbor prion-like domains, cause some forms of ALS. There are at least 213 human proteins harboring RNA recognition motifs, including FUS and TDP-43, raising the possibility that additional RNA-binding proteins might contribute to ALS pathogenesis. We performed a systematic survey of these proteins to find additional candidates similar to TDP-43 and FUS, followed by bioinformatics to predict prion-like domains in a subset of them. We sequenced one of these genes, TAF15, in patients with ALS and identified missense variants, which were absent in a large number of healthy controls. These disease-associated variants of TAF15 caused formation of cytoplasmic foci when expressed in primary cultures of spinal cord neurons. Very similar to TDP-43 and FUS, TAF15 aggregated in vitro and conferred neurodegeneration in Drosophila, with the ALS-linked variants having a more severe effect than wild type. Immunohistochemistry of postmortem spinal cord tissue revealed mislocalization of TAF15 in motor neurons of patients with ALS. We propose that aggregation-prone RNA-binding proteins might contribute very broadly to ALS pathogenesis and the genes identified in our yeast functional screen, coupled with prion-like domain prediction analysis, now provide a powerful resource to facilitate ALS disease gene discovery.

    View details for DOI 10.1073/pnas.1109434108

    View details for Web of Science ID 000298479900012

    View details for PubMedID 22065782

  • The toxicity of an "artificial" amyloid is related to how it interacts with membranes PRION Couthouis, J., Marchal, C., D'Angelo, F., Berthelot, K., Cullin, C. 2010; 4 (4): 283-291


    Despite intensive research into how amyloid structures can impair cellular viability, the molecular nature of these toxic species and the cellular mechanisms involved are not clearly defined and may differ from one disease to another. We systematically analyzed, in Saccharomyces cerevisiae, genes that increase the toxicity of an amyloid (M8), previously selected in yeast on the sole basis of its cellular toxicity (and consequently qualified as "artificial"). This genomic screening identified the Vps-C HOPS (homotypic vacuole fusion and protein sorting) complex as a key-player in amyloid toxicity. This finding led us to analyze further the phenotype induced by M8 expression. M8-expressing cells displayed an identical phenotype to vps mutants in terms of endocytosis, vacuolar morphology and salt sensitivity. The direct and specific interaction between M8 and lipids reinforces the role of membrane formation in toxicity due to M8. Together these findings suggest a model in which amyloid toxicity results from membrane fission.

    View details for DOI 10.4161/pri.4.4.13126

    View details for Web of Science ID 000285872900007

    View details for PubMedID 21057225

    View details for PubMedCentralID PMC3268961

  • Screening for Toxic Amyloid in Yeast Exemplifies the Role of Alternative Pathway Responsible for Cytotoxicity PLOS ONE Couthouis, J., Rebora, K., Immel, F., Berthelot, K., Castroviejo, M., Cullin, C. 2009; 4 (3)


    The relationship between amyloid and toxic species is a central problem since the discovery of amyloid structures in different diseases. Despite intensive efforts in the field, the deleterious species remains unknown at the molecular level. This may reflect the lack of any structure-toxicity study based on a genetic approach. Here we show that a structure-toxicity study without any biochemical prerequisite can be successfully achieved in yeast. A PCR mutagenesis of the amyloid domain of HET-s leads to the identification of a mutant that might impair cellular viability. Cellular and biochemical analyses demonstrate that this toxic mutant forms GFP-amyloid aggregates that differ from the wild-type aggregates in their shape, size and molecular organization. The chaperone Hsp104 that helps to disassemble protein aggregates is strictly required for the cellular toxicity. Our structure-toxicity study suggests that the smallest aggregates are the most toxic, and opens a new way to analyze the relationship between structure and toxicity of amyloid species.

    View details for DOI 10.1371/journal.pone.0004539

    View details for Web of Science ID 000265490600001

    View details for PubMedID 19262694

    View details for PubMedCentralID PMC2650408