Chris Cotsapas, PhD

Associate Professor of Neurology; Associate Professor of Genetics

Research Interests

Arthritis, Rheumatoid; Autoimmune Diseases; Diabetes Mellitus, Type 1; Genetics; Genetics, Medical; Genetics, Population; Graves Disease; Immune System Diseases; Lupus Erythematosus, Systemic; Multiple Sclerosis; Thyroiditis, Autoimmune; Inflammatory Bowel Diseases; Human Genome Project; Computational Biology; Autoimmune Diseases of the Nervous System; Demyelinating Autoimmune Diseases, CNS; Genomics; Genetic Research; Systems Biology

Research Organizations

Neurology: Nowak Lab

Faculty Research

HTI

Office of Cooperative Research

Research Summary

We look for genetic factors that predispose to disease and try to understand the biology they perturb. We ask what genes are perturbed, what processes they participate in and whether these perturbations are sufficient to induce differences at the molecular and cellular levels.This gives us novel targets for biomarkers, diagnosis and treatment.

Our approach encompasses statistical and computational tools, genetics and molecular biology. We are a hybrid lab with strong quantitative and experimental skills and we cycle between hypotheses generated by rigorous analysis and confirmation and discovery in experimental systems.

Selected Publications

Full List of PubMed Publications

  • Roden C, Gaillard J, Kanoria S, Rennie W, Barish S, Cheng J, Pan W, Liu J, Cotsapas C, Ding Y, Lu J: Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. Genome Res. 2017 Jan 13; 2017 Jan 13. PMID: 28087842
  • Garyu JW, Meffre E, Cotsapas C, Herold KC: Progress and challenges for treating Type 1 diabetes. J Autoimmun. 2016 Jul; 2016 May 17. PMID: 27210268
  • Choi J, Shooshtari P, Samocha KE, Daly MJ, Cotsapas C: Network Analysis of Genome-Wide Selective Constraint Reveals a Gene Network Active in Early Fetal Brain Intolerant of Mutation. PLoS Genet. 2016 Jun 15; 2016 Jun 15. PMID: 27305007
  • Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML: Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science. 2016 Mar 25; 2016 Mar 24. PMID: 27013732
  • Raj P, Rai E, Song R, Khan S, Wakeland BE, Viswanathan K, Arana C, Liang C, Zhang B, Dozmorov I, Carr-Johnson F, Mitrovic M, Wiley GB, Kelly JA, Lauwerys BR, Olsen NJ, Cotsapas C, Garcia CK, Wise CA, Harley JB, Nath SK, James JA, Jacob CO, Tsao BP, Pasare C, Karp DR, Li QZ, Gaffney PM, Wakeland EK: Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity. Elife. 2016 Feb 15; 2016 Feb 15. PMID: 26880555
  • Tooley JE, Vudattu N, Choi J, Cotsapas C, Devine L, Raddassi K, Ehlers MR, McNamara JG, Harris KM, Kanaparthi S, Phippard D, Herold KC: Changes in T-cell subsets identify responders to FcR-nonbinding anti-CD3 mAb (teplizumab) in patients with type 1 diabetes. Eur J Immunol. 2016 Jan; 2015 Dec 14. PMID: 26518356
  • Moutsianas L, Jostins L, Beecham AH, Dilthey AT, Xifara DK, Ban M, Shah TS, Patsopoulos NA, Alfredsson L, Anderson CA, Attfield KE, Baranzini SE, Barrett J, Binder TM, Booth D, Buck D, Celius EG, Cotsapas C, D'Alfonso S, Dendrou CA, Donnelly P, Dubois B, Fontaine B, Lar Fugger L, Goris A, Gourraud PA, Graetz C, Hemmer B, Hillert J, International IBD Genetics Consortium (IIBDGC)., Kockum I, Leslie S, Lill CM, Martinelli-Boneschi F, Oksenberg JR, Olsson T, Oturai A, Saarela J, Søndergaard HB, Spurkland A, Taylor B, Winkelmann J, Zipp F, Haines JL, Pericak-Vance MA, Spencer CC, Stewart G, Hafler DA, Ivinson AJ, Harbo HF, Hauser SL, De Jager PL, Compston A, McCauley JL, Sawcer S, McVean G, International Multiple Sclerosis Genetics Consortium.: Class II HLA interactions modulate genetic risk for multiple sclerosis. Nat Genet. 2015 Oct; 2015 Sep 7. PMID: 26343388
  • Winsvold BS, Nelson CP, Malik R, Gormley P, Anttila V, Vander Heiden J, Elliott KS, Jacobsen LM, Palta P, Amin N, de Vries B, Hämäläinen E, Freilinger T, Ikram MA, Kessler T, Koiranen M, Ligthart L, McMahon G, Pedersen LM, Willenborg C, Won HH, Olesen J, Artto V, Assimes TL, Blankenberg S, Boomsma DI, Cherkas L, Davey Smith G, Epstein SE, Erdmann J, Ferrari MD, Göbel H, Hall AS, Jarvelin MR, Kallela M, Kaprio J, Kathiresan S, Lehtimäki T, McPherson R, März W, Nyholt DR, O'Donnell CJ, Quaye L, Rader DJ, Raitakari O, Roberts R, Schunkert H, Schürks M, Stewart AF, Terwindt GM, Thorsteinsdottir U, van den Maagdenberg AM, van Duijn C, Wessman M, Kurth T, Kubisch C, Dichgans M, Chasman DI, Cotsapas C, Zwart JA, Samani NJ, Palotie A, CARDIoGRAM Consortium and the International Headache Genetics Consortium.: Genetic analysis for a shared biological basis between migraine and coronary artery disease. Neurol Genet. 2015 Jul 2; 2015 Jul 2. PMID: 27066539
  • Housley WJ, Fernandez SD, Vera K, Murikinati SR, Grutzendler J, Cuerdon N, Glick L, De Jager PL, Mitrovic M, Cotsapas C, Hafler DA: Genetic variants associated with autoimmunity drive NFκB signaling and responses to inflammatory stimuli. Sci Transl Med. 2015 Jun 10. PMID: 26062845
  • Malik R, Freilinger T, Winsvold BS, Anttila V, Vander Heiden J, Traylor M, de Vries B, Holliday EG, Terwindt GM, Sturm J, Bis JC, Hopewell JC, Ferrari MD, Rannikmae K, Wessman M, Kallela M, Kubisch C, Fornage M, Meschia JF, Lehtimäki T, Sudlow C, Clarke R, Chasman DI, Mitchell BD, Maguire J, Kaprio J, Farrall M, Raitakari OT, Kurth T, Ikram MA, Reiner AP, Longstreth WT Jr, Rothwell PM, Strachan DP, Sharma P, Seshadri S, Quaye L, Cherkas L, Schürks M, Rosand J, Ligthart L, Boncoraglio GB, Davey Smith G, van Duijn CM, Stefansson K, Worrall BB, Nyholt DR, Markus HS, van den Maagdenberg AM, Cotsapas C, Zwart JA, Palotie A, International Headache Genetics Consortium., Dichgans M, METASTROKE Collaboration of the International Stroke Genetics Consortium.: Shared genetic basis for migraine and ischemic stroke: A genome-wide analysis of common variants. Neurology. 2015 May 26; 2015 May 1. PMID: 25934857
  • International Multiple Sclerosis Genetics Consortium (IMSGC)., Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Wellcome Trust Case Control Consortium 2 (WTCCC2)., International IBD Genetics Consortium (IIBDGC)., Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TM, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BA, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL: Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet. 2013 Nov; 2013 Sep 29. PMID: 24076602
  • Querol L, Clark PL, Bailey MA, Cotsapas C, Cross AH, Hafler DA, Kleinstein SH, Lee JY, Yaari G, Willis SN, O'Connor KC: Protein array-based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis. Neurology. 2013 Sep 10; 2013 Aug 6. PMID: 23921886
  • Solovieff N, Cotsapas C, Lee PH, Purcell SM, Smoller JW: Pleiotropy in complex traits: challenges and strategies. Nat Rev Genet. 2013 Jul; 2013 Jun 11. PMID: 23752797
  • Hatoum IJ, Greenawalt DM, Cotsapas C, Daly MJ, Reitman ML, Kaplan LM: Weight loss after gastric bypass is associated with a variant at 15q26.1. Am J Hum Genet. 2013 May 2. PMID: 23643386
  • Cotsapas C, Hafler DA: Immune-mediated disease genetics: the shared basis of pathogenesis. Trends Immunol. 2013 Jan; 2012 Sep 29. PMID: 23031829
  • Morris DL, Taylor KE, Fernando MM, Nititham J, Alarcón-Riquelme ME, Barcellos LF, Behrens TW, Cotsapas C, Gaffney PM, Graham RR, Pons-Estel BA, Gregersen PK, Harley JB, Hauser SL, Hom G, International MHC and Autoimmunity Genetics Network., Langefeld CD, Noble JA, Rioux JD, Seldin MF, Systemic Lupus Erythematosus Genetics Consortium., Criswell LA, Vyse TJ: Unraveling multiple MHC gene associations with systemic lupus erythematosus: model choice indicates a role for HLA alleles and non-HLA genes in Europeans. Am J Hum Genet. 2012 Nov 2; 2012 Oct 18. PMID: 23084292
  • Voight BF, Cotsapas C: Human genetics offers an emerging picture of common pathways and mechanisms in autoimmunity. Curr Opin Immunol. 2012 Oct; 2012 Oct 5. PMID: 23041452
  • Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA: Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012 Sep 7; 2012 Sep 5. PMID: 22955828
  • Hatoum IJ, Greenawalt DM, Cotsapas C, Reitman ML, Daly MJ, Kaplan LM: Heritability of the weight loss response to gastric bypass surgery. J Clin Endocrinol Metab. 2011 Oct; 2011 Aug 10. PMID: 21832118
  • Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, Wallace C, Abecasis GR, Barrett JC, Behrens T, Cho J, De Jager PL, Elder JT, Graham RR, Gregersen P, Klareskog L, Siminovitch KA, van Heel DA, Wijmenga C, Worthington J, Todd JA, Hafler DA, Rich SS, Daly MJ, FOCiS Network of Consortia.: Pervasive sharing of genetic effects in autoimmune disease. PLoS Genet. 2011 Aug; 2011 Aug 10. PMID: 21852963
  • Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, Benita Y, International Inflammatory Bowel Disease Genetics Constortium., Cotsapas C, Daly MJ: Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet. 2011 Jan 13; 2011 Jan 13. PMID: 21249183
  • Kirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA, Frazer KA, Johnson FM, Beilharz EJ, Cox DR, Eskin E, Daly MJ: Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics. 2010 Jul; 2010 May 3. PMID: 20439770
  • Cotsapas C, Speliotes EK, Hatoum IJ, Greenawalt DM, Dobrin R, Lum PY, Suver C, Chudin E, Kemp D, Reitman M, Voight BF, Neale BM, Schadt EE, Hirschhorn JN, Kaplan LM, Daly MJ, GIANT Consortium.: Common body mass index-associated variants confer risk of extreme obesity. Hum Mol Genet. 2009 Sep 15; 2009 Jun 24. PMID: 19553259
  • Cowley MJ, Cotsapas CJ, Williams RB, Chan EK, Pulvers JN, Liu MY, Luo OJ, Nott DJ, Little PF: Intra- and inter-individual genetic differences in gene expression. Mamm Genome. 2009 May; 2009 May 8. PMID: 19424753
  • Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, Rivas M, Dermitzakis ET, Cahir-McFarland E, Kieff E, Hafler D, Daly MJ, Altshuler D: Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet. 2008 Nov; 2008 Nov 28. PMID: 19043577
  • Graham RR, Cotsapas C, Davies L, Hackett R, Lessard CJ, Leon JM, Burtt NP, Guiducci C, Parkin M, Gates C, Plenge RM, Behrens TW, Wither JE, Rioux JD, Fortin PR, Graham DC, Wong AK, Vyse TJ, Daly MJ, Altshuler D, Moser KL, Gaffney PM: Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet. 2008 Sep. PMID: 19165918
  • Cotsapas C: Identifying genetic components of drug response in mice. Pharmacogenomics. 2008 Sep. PMID: 18781858
  • Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PI, Maller J, Pe'er I, Burtt NP, Blumenstiel B, DeFelice M, Parkin M, Barry R, Winslow W, Healy C, Graham RR, Neale BM, Izmailova E, Roubenoff R, Parker AN, Glass R, Karlson EW, Maher N, Hafler DA, Lee DM, Seldin MF, Remmers EF, Lee AT, Padyukov L, Alfredsson L, Coblyn J, Weinblatt ME, Gabriel SB, Purcell S, Klareskog L, Gregersen PK, Shadick NA, Daly MJ, Altshuler D: Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet. 2007 Dec; 2007 Nov 4. PMID: 17982456
  • Pomati F, Cotsapas CJ, Castiglioni S, Zuccato E, Calamari D: Gene expression profiles in zebrafish (Danio rerio) liver cells exposed to a mixture of pharmaceuticals at environmentally relevant concentrations. Chemosphere. 2007 Nov; 2007 Aug 30. PMID: 17764721
  • Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, International HapMap Consortium., Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Johnson TA, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J: Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18. PMID: 17943131
  • Williams RB, Cotsapas CJ, Cowley MJ, Chan E, Nott DJ, Little PF: Normalization procedures and detection of linkage signal in genetical-genomics experiments. Nat Genet. 2006 Aug. PMID: 16874319
  • Cotsapas CJ, Williams RB, Pulvers JN, Nott DJ, Chan EK, Cowley MJ, Little PF: Genetic dissection of gene regulation in multiple mouse tissues. Mamm Genome. 2006 Jun; 2006 Jun 12. PMID: 16783630

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