faculty
John Ray
jray@benaroyaresearch.org
Assistant Member
Benaroya Research Institute
Gene Expression, Cell Cycle & Chromosome Biology
Genetics, Genomics & Evolution
Microbiology, Infection & Immunity
Using genomic approaches to study autoimmune disease susceptibility
Faculty Contact Information
Building: Benaroya Research Institute
Box: Ray Lab
Phone: 206-342-6920
https://www.benaroyaresearch.org/what-is-bri/scientists-laboratories/principal-scientist-labs/ray-laboratory
Research Summary
The Ray lab studies the mechanisms that contribute to variation in human immune responses. In particular, we determine how genetic variants and non-coding regulatory regions alter immune responses and confer autoimmune disease susceptibility. With a focus on T cells, we prioritize likely disease-causal genetic variants and enhancers, and, in human and mouse systems, we dissect their mechanisms of action. Understanding the mechanisms of inherited autoimmune disease susceptibility will inform efforts for personalized therapies and disease prevention.
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Publications
The following publications were retrieved from PubMed:
Genome-wide enhancer maps link risk variants to disease genes.
Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM.
Nature. 2021 May; 7858(593)238-243
Global discovery of lupus genetic risk variant allelic enhancer activity.
Lu X, Chen X, Forney C, Donmez O, Miller D, Parameswaran S, Hong T, Huang Y, Pujato M, Cazares T, Miraldi ER, Ray JP, de Boer CG, Harley JB, Weirauch MT, Kottyan LC.
Nat Commun. 2021 Mar 12; 1(12)1611
MAUDE: inferring expression changes in sorting-based CRISPR screens.
de Boer CG, Ray JP, Hacohen N, Regev A.
Genome Biol. 2020 Jun 3; 1(21)134
Ray JP, de Boer CG, Fulco CP, Lareau CA, Kanai M, Ulirsch JC, Tewhey R, Ludwig LS, Reilly SK, Bergman DT, Engreitz JM, Issner R, Finucane HK, Lander ES, Regev A, Hacohen N.
Nat Commun. 2020 Mar 6; 1(11)1237
Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N.
Cell. 2019 Jan 10; 1-2(176)404
Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N.
Cell. 2018 Nov 1; 4(175)998-1013.e20
Positional specificity of different transcription factor classes within enhancers.
Grossman SR, Engreitz J, Ray JP, Nguyen TH, Hacohen N, Lander ES.
Proc Natl Acad Sci U S A. 2018 Jul 24; 30(115)E7222-E7230
Resistance to checkpoint blockade therapy through inactivation of antigen presentation.
Sade-Feldman M, Jiao YJ, Chen JH, Rooney MS, Barzily-Rokni M, Eliane JP, Bjorgaard SL, Hammond MR, Vitzthum H, Blackmon SM, Frederick DT, Hazar-Rethinam M, Nadres BA, Van Seventer EE, Shukla SA, Yizhak K, Ray JP, Rosebrock D, Livitz D, Adalsteinsson V, Getz G, Duncan LM, Li B, Corcoran RB, Lawrence DP, Stemmer-Rachamimov A, Boland GM, Landau DA, Flaherty KT, Sullivan RJ, Hacohen N.
Nat Commun. 2017 Oct 26; 1(8)1136
Ray JP, Staron MM, Shyer JA, Ho PC, Marshall HD, Gray SM, Laidlaw BJ, Araki K, Ahmed R, Kaech SM, Craft J.
Immunity. 2015 Oct 20; 4(43)690-702
PTENtiating autoimmunity through Treg cell deregulation.
Ray JP, Craft J.
Nat Immunol. 2015 Feb; 2(16)139-40
Marshall HD, Ray JP, Laidlaw BJ, Zhang N, Gawande D, Staron MM, Craft J, Kaech SM.
Elife. 2015 Jan 8; (4)e04851
Ray JP, Marshall HD, Laidlaw BJ, Staron MM, Kaech SM, Craft J.
Immunity. 2014 Mar 20; 3(40)367-77
Tobin DM, Roca FJ, Ray JP, Ko DC, Ramakrishnan L.
PLoS One. 2013; 7(8)e67828
Host genotype-specific therapies can optimize the inflammatory response to mycobacterial infections.
Tobin DM, Roca FJ, Oh SF, McFarland R, Vickery TW, Ray JP, Ko DC, Zou Y, Bang ND, Chau TT, Vary JC, Hawn TR, Dunstan SJ, Farrar JJ, Thwaites GE, King MC, Serhan CN, Ramakrishnan L.
Cell. 2012 Feb 3; 3(148)434-46
The lta4h locus modulates susceptibility to mycobacterial infection in zebrafish and humans.
Tobin DM, Vary JC Jr, Ray JP, Walsh GS, Dunstan SJ, Bang ND, Hagge DA, Khadge S, King MC, Hawn TR, Moens CB, Ramakrishnan L.
Cell. 2010 Mar 5; 5(140)717-30
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