All Publications

  • Enrichment of Rare Variants of Hemophagocytic Lymphohistiocytosis Genes in Systemic Juvenile Idiopathic Arthritis. medRxiv : the preprint server for health sciences Marques, M. C., Rubin, D., Shuldiner, E., Datta, M., Schmitz, E., Cruz, G. G., Patt, A., Bennett, E., Grom, A., Foell, D., Gattorno, M., Bohnsack, J., Yeung, R. S., Prahalad, S., Mellins, E., Anton, J., Len, C. A., Oliveira, S., Woo, P., Ozen, S., Deng, Z., Ombrello, M. J. 2024


    To evaluate whether there is an enrichment of rare variants in familial hemophagocytic lymphohistiocytosis (HLH) genes and systemic juvenile idiopathic arthritis (sJIA) with or without macrophage activation syndrome (MAS).Targeted sequencing of HLH genes (LYST, PRF1, RAB27A, STX11, STXBP2, UNC13D) was performed in sJIA subjects from an established cohort. Sequence data from control subjects were obtained in silico (dbGaP:phs000280.v8.p2). Rare variant association testing (RVT) was performed with sequence kernel association test (SKAT) package. Significance was defined as p<0.05 after 100,000 permutations.Sequencing data from 524 sJIA cases were jointly called and harmonized with exome-derived target data from 3000 controls. Quality control operations produced a set of 481 cases and 2924 ancestrally-matched control subjects. RVT of sJIA cases and controls revealed a significant association with rare protein-altering variants (minor allele frequency [MAF]<0.01) of STXBP2 (p=0.020), and ultra-rare variants (MAF<0.001) of STXBP2 (p=0.007) and UNC13D (p=0.045). A subanalysis of 32 cases with known MAS and 90 without revealed significant association of rare UNC13D variants (p=0.0047). Additionally, sJIA patients more often carried ≥2 HLH variants than did controls (p=0.007), driven largely by digenic combinations involving LYST.We identified an enrichment of rare HLH variants in sJIA patients compared with healthy controls, driven by STXBP2 and UNC13D. Biallelic variation in HLH genes was associated with sJIA, driven by LYST. Only UNC13D displayed enrichment in patients with MAS. This suggests that HLH variants may contribute to the pathophysiology of sJIA, even without MAS.

    View details for DOI 10.1101/2024.03.13.24304215

    View details for PubMedID 38529491

    View details for PubMedCentralID PMC10962746

  • Enrichment of Rare Variants of Hemophagocytic Lymphohistiocytosis Genes in Systemic Juvenile Idiopathic Arthritis Marques, M., Rubin, D., Shuldiner, E., Datta, M., Schmitz, E., Grom, A., Foell, D., Gattorno, M., Bohnsack, J., Yeung, R., Prahalad, S., Mellins, E., Lopez, J., Len, C., Oliveira, S., Woo, P., Ozen, S., Deng, Z., Ombrello, M., Incharge Consortium WILEY. 2023: 65-67
  • High-Throughput Identification, Modeling, and Analysis of Cancer Driver Genes In Vivo. Cold Spring Harbor perspectives in medicine Tang, Y. J., Shuldiner, E. G., Karmakar, S., Winslow, M. M. 2023


    The vast number of genomic and molecular alterations in cancer pose a substantial challenge to uncovering the mechanisms of tumorigenesis and identifying therapeutic targets. High-throughput functional genomic methods in genetically engineered mouse models allow for rapid and systematic investigation of cancer driver genes. In this review, we discuss the basic concepts and tools for multiplexed investigation of functionally important cancer genes in vivo using autochthonous cancer models. Furthermore, we highlight emerging technical advances in the field, potential opportunities for future investigation, and outline a vision for integrating multiplexed genetic perturbations with detailed molecular analyses to advance our understanding of the genetic and molecular basis of cancer.

    View details for DOI 10.1101/cshperspect.a041382

    View details for PubMedID 37277208

  • Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth. Nature cell biology Tang, R., Shuldiner, E. G., Kelly, M., Murray, C. W., Hebert, J. D., Andrejka, L., Tsai, M. K., Hughes, N. W., Parker, M. I., Cai, H., Li, Y. C., Wahl, G. M., Dunbrack, R. L., Jackson, P. K., Petrov, D. A., Winslow, M. M. 2023


    Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signalling is incomplete. Here to uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumour barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRASG12D-driven tumour growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogues interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signalling. Furthermore, HRAS and NRAS mutations identified in oncogenic KRAS-driven human tumours partially abolished this effect. By comparing the tumour-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogues are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role RAS paralogue imbalance in oncogenic KRAS-driven lung cancer.

    View details for DOI 10.1038/s41556-022-01049-w

    View details for PubMedID 36635501

  • Large-Scale Targeted Sequencing Study Links Systemic Juvenile Idiopathic Arthritis with Rare Variants of MEFV, LYST, STXBP2, UNC13D Marques, M., Rubin, D., Shuldiner, E., Schmitz, E., Baskin, E., Patt, A., Grom, A., Foell, D., Gattorno, M., Bohnsack, J., Yeung, R., Prahalad, S., Mellins, E., Anton, J., Foell, D., Gattorno, M., Bohnsack, J., Yeung, R., Prahalad, S., Mellins, E., Anton, J., Len, C., Oliveira, S., Woo, P., Ozen, S., Ombrello, M., INCHARGE Consortium WILEY. 2022: 1139-1140
  • Regulatory Haplotype of CXCR4 Is Associated with sJIA and Corelates with Enhanced Neutrophil and CD14+Monocyte Migration Nakano, H., Shuldiner, E., Hinks, A., Sudman, M., Remmers, E., Satorius, C., Schmitz, E., Arthur, V., Woo, P., Grom, A., Foell, D., Bohnsack, J., Gattorno, M., Ozen, S., Prahalad, S., Yeung, R., Mellins, E., Oliveira, S., Anton, J., Len, C., Lake, C., Bergeron, L., Millwood, M., de los Santos, E., Marques, M., Langefeld, C., Thompson, S., Thomson, W., Ombrello, M., Juvenile Arthrit Consortium, Genomic Ascertainment Cohort, INCHARGE Consortium WILEY. 2022: 1714-1716
  • A journey to deconvolute the multifaceted functions and context-dependency of cancer driver genes Cai, H., Chew, S., Li, C., Murray, C. W., Andrejka, L., Hebert, J. D., Tsai, M. K., Tang, R., Hughes, N. W., Shuldiner, E. G., Ashkin, E. L., Lee, S. C., Yousefi, M., Petrov, D. A., Swanton, C., Winslow, M. W. AMER ASSOC CANCER RESEARCH. 2022
  • Dense Genotyping of Immunologic Loci Identifies CXCR4 as a Novel Susceptibility Locus for Systemic Juvenile Idiopathic Arthritis Nakano, H., Shuldiner, E., Schmitz, E., Remmers, E., Ombrello, M., Int Childhood Genetics Consort, Juvenile Arthritis Immunochip SPRINGER/PLENUM PUBLISHERS. 2022: S15-S16
  • A functional taxonomy of tumor suppression in oncogenic KRAS-driven lung cancer. Cancer discovery Cai, H. n., Chew, S. K., Li, C. n., Tsai, M. K., Andrejka, L. n., Murray, C. W., Hughes, N. W., Shuldiner, E. G., Ashkin, E. L., Tang, R. n., Hung, K. L., Chen, L. C., Lee, S. Y., Yousefi, M. n., Lin, W. Y., Kunder, C. A., Cong, L. n., McFarland, C. D., Petrov, D. A., Swanton, C. n., Winslow, M. M. 2021


    Cancer genotyping has identified a large number of putative tumor suppressor genes. Carcinogenesis is a multi-step process, however the importance and specific roles of many of these genes during tumor initiation, growth and progression remain unknown. Here we use a multiplexed mouse model of oncogenic KRAS-driven lung cancer to quantify the impact of forty-eight known and putative tumor suppressor genes on diverse aspects of carcinogenesis at an unprecedented scale and resolution. We uncover many previously understudied functional tumor suppressors that constrain cancer in vivo. Inactivation of some genes substantially increased growth, while the inactivation of others increases tumor initiation and/or the emergence of exceptionally large tumors. These functional in vivo analyses revealed an unexpectedly complex landscape of tumor suppression that has implications for understanding cancer evolution, interpreting clinical cancer genome sequencing data, and directing approaches to limit tumor initiation and progression.

    View details for DOI 10.1158/2159-8290.CD-20-1325

    View details for PubMedID 33608386

  • IL1RN Variation Influences Both Disease Susceptibility and Response to Recombinant Human Interleukin-1 Receptor Antagonist Therapy in Systemic Juvenile Idiopathic Arthritis ARTHRITIS & RHEUMATOLOGY Arthur, V. L., Shuldiner, E., Remmers, E. F., Hinks, A., Grom, A. A., Foell, D., Martini, A., Gattorno, M., Ozen, S., Prahalad, S., Zeft, A. S., Bohnsack, J. F., Ilowite, N. T., Mellins, E. D., Russo, R., Len, C., Oliveira, S., Yeung, R. M., Rosenberg, A. M., Wedderburn, L. R., Anton, J., Haas, J., Roesen-Wolff, A., Minden, K., Szymanski, A., Thomson, W., Kastner, D. L., Woo, P., Ombrello, M. J., INCHARGE Consortium 2018; 70 (8): 1319–30


    To determine whether systemic juvenile idiopathic arthritis (JIA) susceptibility loci that were identified by candidate gene studies demonstrate association with systemic JIA in the largest study population assembled to date.Single-nucleotide polymorphisms (SNPs) from 11 previously reported systemic JIA risk loci were examined for association in 9 populations, including 770 patients with systemic JIA and 6,947 controls. The effect of systemic JIA-associated SNPs on gene expression was evaluated in silico in paired whole genome and RNA sequencing data from the lymphoblastoid cell lines (LCLs) of 373 European subjects from the 1000 Genomes Project. Responses of systemic JIA-associated SNPs to anakinra treatment were evaluated in 38 US patients for whom treatment response data were available.We found no association between the previously reported 26 SNPs and systemic JIA. Expanded analysis of the regions containing the 26 SNPs revealed only 1 significant association: the promoter region of IL1RN (P < 1 × 10-4 ). Systemic JIA-associated SNPs correlated with IL1RN expression in LCLs, with an inverse correlation between systemic JIA risk and IL1RN expression. The presence of homozygous IL1RN high expression alleles correlated strongly with a lack of response to anakinra therapy (odds ratio 28.7 [95% confidence interval 3.2-255.8]).In our study, IL1RN was the only candidate locus associated with systemic JIA. The implicated SNPs are among the strongest known determinants of IL1RN and interleukin-1 receptor antagonist levels, linking low expression with increased systemic JIA risk. Homozygous high expression alleles predicted nonresponsiveness to anakinra therapy, making them ideal candidate biomarkers to guide systemic JIA treatment. This study is an important first step toward the personalized treatment of systemic JIA.

    View details for PubMedID 29609200

  • Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. Science advances vonHoldt, B. M., Shuldiner, E., Koch, I. J., Kartzinel, R. Y., Hogan, A., Brubaker, L., Wanser, S., Stahler, D., Wynne, C. D., Ostrander, E. A., Sinsheimer, J. S., Udell, M. A. 2017; 3 (7): e1700398


    Although considerable progress has been made in understanding the genetic basis of morphologic traits (for example, body size and coat color) in dogs and wolves, the genetic basis of their behavioral divergence is poorly understood. An integrative approach using both behavioral and genetic data is required to understand the molecular underpinnings of the various behavioral characteristics associated with domestication. We analyze a 5-Mb genomic region on chromosome 6 previously found to be under positive selection in domestic dog breeds. Deletion of this region in humans is linked to Williams-Beuren syndrome (WBS), a multisystem congenital disorder characterized by hypersocial behavior. We associate quantitative data on behavioral phenotypes symptomatic of WBS in humans with structural changes in the WBS locus in dogs. We find that hypersociability, a central feature of WBS, is also a core element of domestication that distinguishes dogs from wolves. We provide evidence that structural variants in GTF2I and GTF2IRD1, genes previously implicated in the behavioral phenotype of patients with WBS and contained within the WBS locus, contribute to extreme sociability in dogs. This finding suggests that there are commonalities in the genetic architecture of WBS and canine tameness and that directional selection may have targeted a unique set of linked behavioral genes of large phenotypic effect, allowing for rapid behavioral divergence of dogs and wolves, facilitating coexistence with humans.

    View details for DOI 10.1126/sciadv.1700398

    View details for PubMedID 28776031

    View details for PubMedCentralID PMC5517105

  • Genetic architecture distinguishes systemic juvenile idiopathic arthritis from other forms of juvenile idiopathic arthritis: clinical and therapeutic implications ANNALS OF THE RHEUMATIC DISEASES Ombrello, M. J., Arthur, V. L., Remmers, E. F., Hinks, A., Tachmazidou, I., Grom, A. A., Foell, D., Martini, A., Gattorno, M., Ozen, S., Prahalad, S., Zeft, A. S., Bohnsack, J. F., Ilowite, N. T., Mellins, E. D., Russo, R., Len, C., Hilario, M. O., Oliveira, S., Yeung, R. S., Rosenberg, A. M., Wedderburn, L. R., Anton, J., Haas, J., Rosen-Wolff, A., Minden, K., Tenbrock, K., Demirkaya, E., Cobb, J., Baskin, E., Signa, S., Shuldiner, E., Duerr, R. H., Achkar, J., Kamboh, M. I., Kaufman, K. M., Kottyan, L. C., Pinto, D., Scherer, S. W., Alarcon-Riquelme, M. E., Docampo, E., Estivill, X., Gul, A., Langefeld, C. D., Thompson, S., Zeggini, E., Kastner, D. L., Woo, P., Thomson, W. 2017; 76 (5)


    Juvenile idiopathic arthritis (JIA) is a heterogeneous group of conditions unified by the presence of chronic childhood arthritis without an identifiable cause. Systemic JIA (sJIA) is a rare form of JIA characterised by systemic inflammation. sJIA is distinguished from other forms of JIA by unique clinical features and treatment responses that are similar to autoinflammatory diseases. However, approximately half of children with sJIA develop destructive, long-standing arthritis that appears similar to other forms of JIA. Using genomic approaches, we sought to gain novel insights into the pathophysiology of sJIA and its relationship with other forms of JIA.We performed a genome-wide association study of 770 children with sJIA collected in nine countries by the International Childhood Arthritis Genetics Consortium. Single nucleotide polymorphisms were tested for association with sJIA. Weighted genetic risk scores were used to compare the genetic architecture of sJIA with other JIA subtypes.The major histocompatibility complex locus and a locus on chromosome 1 each showed association with sJIA exceeding the threshold for genome-wide significance, while 23 other novel loci were suggestive of association with sJIA. Using a combination of genetic and statistical approaches, we found no evidence of shared genetic architecture between sJIA and other common JIA subtypes.The lack of shared genetic risk factors between sJIA and other JIA subtypes supports the hypothesis that sJIA is a unique disease process and argues for a different classification framework. Research to improve sJIA therapy should target its unique genetics and specific pathophysiological pathways.

    View details for DOI 10.1136/annrheumdis-2016-210324

    View details for Web of Science ID 000398387200021