Selected Publications
Kirk AM, Crawford JC, Chou CH, Guy C, Pandey K, Kozlik T, Shah RK, Chung S, Nguyen P, Zhang X, Wang J, Bell M, Mettelman RC, Allen EK, Pogorelyy MV, Kim H, Minervina AA, Awad W, Bajracharya R, White T, Long D Jr, Gordon B, Morrison M, Glazer ES, Murphy AJ, Jiang Y, Fitzpatrick EA, Yarchoan M, Sethupathy P, Croft NP, Purcell AW, Federico SM, Stewart E, Gottschalk S, Zamora AE, DeRenzo C, Strome SE, Thomas PG. DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma. Cell Rep Med Mar 19;5(3):101469, 2024. doi: 10.1016/j.xcrm.2024.101469. PMID: 38508137; PMCID: PMC10983114.
Mettelman RC, Souquette A, Van de Velde LA, Vegesana K, Allen EK, Kackos CM, Trifkovic S, DeBeauchamp J, Wilson TL, St James DG, Menon SS, Wood T, Jelley L, Webby RJ, Huang QS, Thomas PG; SHIVERS-II Investigation Team. Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology. Nat Immunol. Sep;24(9):1511-1526, 2023. doi: 10.1038/s41590-023-01590-2. Epub Aug 17, 2023. PMID: 37592015; PMCID: PMC10566627
Wilson TL, Kim H, Chou CH, Langfitt D, Mettelman RC, Minervina AA, Allen EK, Métais JY, Pogorelyy MV, Riberdy JM, Velasquez MP, Kottapalli P, Trivedi S, Olsen SR, Lockey T, Willis C, Meagher MM, Triplett BM, Talleur AC, Gottschalk S, Crawford JC, Thomas PG. Common Trajectories of Highly Effective CD19-Specific CAR T Cells Identified by Endogenous T-cell Receptor Lineages. Cancer Discov. Sep 2;12(9):2098-2119, 2022. doi: 10.1158/2159-8290.CD-21-1508. PMID: 35792801; PMCID: PMC9437573
Pogorelyy MV, Rosati E, Minervina AA, Mettelman RC, Scheffold A, Franke A, Bacher P, Thomas PG. Resolving SARS-CoV-2 CD4+ T cell specificity via reverse epitope discovery. Cell Rep Med. Aug 16, 2022;3(8):100697. doi: 10.1016/j.xcrm.2022.100697. Epub 2022 Jul 1. PMID: 35841887; PMCID: PMC9247234.
Minervina AA, Pogorelyy MV, Kirk AM, Crawford JC, Allen EK, Chou CH, Mettelman RC, Allison KJ, Lin CY, Brice DC, Zhu X, Vegesana K, Wu G, Trivedi S, Kottapalli P, Darnell D, McNeely S, Olsen SR, Schultz-Cherry S, Estepp JH; SJTRC Study Team; McGargill MA, Wolf J, Thomas PG. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells. Nat Immunol May 2022;23(5):781-790. doi: 10.1038/s41590-022-01184-4. Epub 2022 Apr 5. PMID: 35383307; PMCID: PMC9106845
Mudd P, Minervina AA, Pogorelyy MV, Turner JS, Kim W, Kalaidina E, Petersen J, Schmitz AJ, Lei T, Haile A, Kirk AM, Mettelman RC, Crawford JC, Nguyen THO, Rowntree LC, Rosati E, Richards KA, Sant AJ, Klebert MK, Suessen T, Middleton WD, Wolf J, Teefey SA, O'Halloran JA, Presti RM, Kedzierska K, Rossjohn J, Thomas PG, Ellebedy AH. SARS-CoV-2 mRNA vaccination elicits a robust and persistent T follicular helper cell response in humans. Cell 185(4):603-613, 2022. doi: 10.1016/j.cell.2021.12.026
Schattgen SA, Guion K, Crawford JC, Souquette A, Barrio AM, Stubbington MJT, Thomas PG, Bradley P. Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA). Nat Biotechnol 40(1):54-63, 2022. doi: 10.1038/s41587-021-00989-2
Van de Velde LA, Allen EK, Crawford JC, Wilson TL, Guy CS, Russier M, Zeitler L, Bahrami A, Finkelstein D, Pelletier S, Schultz-Cherry S, Thomas PG, Murray PJ. Neuroblastoma formation requires unconventional CD4 T cells and arginase-1-dependent myeloid cells. Cancer Res 81(19):5047-5059, 2021. doi: 10.1158/0008-5472.CAN-21-0691
Mudd PA, Crawford JC, Turner JS, Souquette A, Reynolds D, Bender D, Bosanquet JP, Anand NJ, Striker DA, Martin RS, Boon ACM, House SL, Remy KE, Hotchkiss RS, Presti RM, O'Halloran JA, Powderly WG, Thomas PG, Ellebedy AH. Distinct inflammatory profiles distinguish COVID-19 from influenza with limited contributions from cytokine storm. Sci Adv Dec 9;6(50):eabe3024, 2020. doi: 10.1126/sciadv.abe3024. Print Dec 2020.
Boyd DF, Allen EK, Randolph AG, Guo XJ, Weng Y, Sanders CJ, Bajracharya R, Lee NK, Guy CS, Vogel P, Guan W, Li Y, Liu X, Novak T, Newhams MM, Fabrizio TP, Wohlgemuth N, Mourani PM, Wight TN, Schultz-Cherry S, Cormier SA, Shaw-Saliba K, Pekosz A, Rothman RE, Chen KF, Yang Z, Webby RJ, Zhong N, Crawford JC, Thomas PG. Exuberant fibroblast activity compromises lung function via ADAMTS4. Publisher note: An amendment to this paper has been published and can be accessed via a link at the top of the paper. Nature Dec;588(7836):E5, 2020. doi: 10.1038/s41586-020-2987-0.
Zamora AE, Crawford JC, Allen EK, Guo XJ, Bakke J, Carter RA, Abdelsamed H, Moustaki A, Li Y, Chang TC, Awad W, Dallas MH, Mullighan CG, Downing JR, Geiger TL, Chen T, Green DR, Youngblood BA, Zhang J, Thomas PG. Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8(+) T cell responses. Sci Transl Med 11(498), 2019.
Koutsakos M, Illing PT, Nguyen THO, Mifsud NA, Crawford JC, Rizzetto S, Eltahla AA, Clemens EB, Sant S, Chua BY, Wong CY, Allen EK, Teng D, Dash P, Boyd DF, Grzelak L, Zeng W, Hurt AC, Barr I, Rockman S, Jackson DC, Kotsimbos TC, Cheng AC, Richards M, Westall GP, Loudovaris T, Mannering SI, Elliott M, Tangye SG, Wakim LM, Rossjohn J, Vijaykrishna D, Luciani F, Thomas PG, Gras S, Purcell AW, Kedzierska K. Human CD8+ T cell cross-reactivity across influenza A, B and C viruses. Nat Immunol 20(5):613-625, 2019.
Bradley P, Thomas PG. Using T cell receptor repertoires to understand the principles of adaptive immune recognition. Annu Rev Immunol 37:547-570, 2019.
Guo XJ, Dash P, Crawford JC, Allen EK, Zamora AE, Boyd DF, Duan S, Bajracharya R, Awad WA, Apiwattanakul N, Vogel P, Kanneganti TD, Thomas PG. Lung γδ T cells mediate protective responses during neonatal influenza infection that are associated with Type 2 immunity. Immunity August 14, 2018.
Allen EK, Randolph AG, Bhangale T, Dogra P, Ohlson M, Oshansky CM, Zamora AE, Shannon JP, Finkelstein D, Dressen A, DeVincenzo J, Caniza M, Youngblood B, Rosenberger CM, Thomas PG. SNP-mediated disruption of CTCF binding at the IFITM3 promoter is associated with risk of severe influenza in humans. Nat Med 23(8):975-983, 2017.
Dash P, Fiore-Gartland AJ, Hertz T, Wang GC, Sharma S, Souquette A, Crawford JC, Clemens EB, Nguyen THO, Kedzierska K, La Gruta NL, Bradley P, Thomas PG. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature June 21, 2017.
Ghoneim HE, Fan Y, Moustaki A, Abdelsamed HA, Dash P, Dogra P, Carter R, Awad W, Neale G, Thomas PG, Youngblood B. De novo epigenetic programs inhibit PD-1 blockade-mediated T cell rejuvenation. Cell June 21, 2017.
Smallwood HS, Duan S, Morfouace M, Rezinciuc S, Shulkin BL, Shelat A, Zink EE, Milasta S, Bajracharya R, Oluwaseum AJ, Roussel MF, Green DR, Pasa-Tolic L, Thomas PG. Targeting metabolic reprogramming by influenza infection for therapeutic intervention. Cell Rep 19(8):1640-1653, 2017.
Brown HA, Thomas PG, Lindsley CW. Targeting phospholipase D in cancer, infection and neurodegenerative disorders. Nat Rev Drug Discov 16(5):351-367, 2017.
Guo XZ, Dash P, Calverley M, Tomchuck S, Dallas MH, Thomas PG. Rapid cloning, expression, and functional characterization of paired alphabeta and gammadelta T-cell receptor chains from single-cell analysis. Mol Ther Methods Clin Dev 3:15054, 2016.
Duan S, Meliopoulos VA, McClaren JL, Guo XZ, Sanders CJ, Smallwood HS, Webby RJ, Schultz-Cherry SL, Doherty PC, Thomas PG. Diverse heterologous primary infections radically alter immunodominance hierarchies and clinical outcomes following H7N9 influenza challenge in mice. PLoS Pathog 11(2):e1004642, 2015.
Oshansky CM, Gartland AJ, Wong SS, Jeevan T, Wang D, Roddam PL, Caniza MA, Hertz T, Devincenzo JP, Webby RJ, Thomas PG. Mucosal immune responses predict clinical outcomes during influenza infection independently of age and viral load. Am J Respir Crit Care Med189(4):449-464, 2014.
Oguin TH 3rd, Sharma S, Stuart AD, Duan S, Scott SA, Jones CK, Daniels JS, Lindsley CW, Thomas PG, Brown HA. Phospholipase d facilitates efficient entry of influenza virus, allowing escape from innate immune inhibition. J Biol Chem 289(37):25405-17, 2014.
Rutigliano JA, Sharma S, Morris MY, Oguin TH 3rd, McClaren JL, Doherty PC, Thomas PG. Highly pathological influenza A virus infection is associated with augmented expression of PD-1 by functionally compromised virus-specific CD8+ T cells. J Virol 88(3):1636-51, 2014.
Tam VC, Quehenberger O, Oshansky CM, Suen R, Armando AM, Treuting PM, Thomas PG, Dennis EA, Aderem A. Lipidomic profiling of influenza infection identifies mediators that induce and resolve inflammation. Cell 154(1):213-27, 2013.
Wang GC, Dash P, McCullers JA, Doherty PC, Thomas PG. T cell receptor alpha beta diversity inversely correlates with pathogen-specific antibody levels in human cytomegalovirus infection. Sci Transl Med 4(128):128ra42, 2012.
Doherty PC, Thomas PG. Dangerous for ferrets: lethal for humans? BMC Biol 10:10, 2012.
Oshansky CM, Thomas PG. The human side of influenza. J Leukoc Biol 2012.
Ruckwardt TJ, Malloy AMW, Gostick E, Price DA, Dash P, McClaren JL, Thomas PG, Graham BS. Neonatal CD8 T-cell hierarchy is distinct from adults and is influenced by intrinsic T cell properties in respiratory syncytial virus infected mice. PLoS Pathog 7(12):2377, 2011.
Sharma S, Sundararajan A, Suryawanshi A, Kumar N, Veiga-Parga T, Kuchroo VK, Thomas PG, Sangster MY, Rouse BT. T cell immunoglobulin and mucin protein-3 (Tim-3)/galectin-9 interaction regulates influenza A virus-specific humoral and CD8 T-cell responses. Proc Natl Acad Sci USA 108(47):19001-6, 2011.
Moon JJ, Dash P, Oguin TH, McClaren JL, Chu HH, Thomas PG, Jenkins MK. Quantitative impact of thymic selection on Foxp3(+) and Foxp3(-) subsets of self-peptide/MHC class II-specific CD4(+) T cells. Proc Natl Acad Sci USA 108(35):14602-7, 2011.
Surman SL, Rudraraju R, Woodland DL, Dash P, Thomas PG, Hurwitz JL. Clonally related CD8 T cells responsible for rapid population of both diffuse nasal-associated lymphoid tissue and lung after respiratory virus infection. J Immunol June 20, 2011.
Billam P, Bonaparte KL, Liu J, Ruckwardt TJ, Chen M, Ryder AB, Wang R, Dash P, Thomas PG, Graham BS. T cell receptor clonotype influences epitope hierarchy in the CD8 T cell response to respiratory syncytial virus infection. J Biol Chem 286(6):4829-41, 2011.
Dash P, McClaren JL, Oguin TH, Rothwell W, Todd B, Morris MY, Becksfort J, Reynolds C, Brown SA, Doherty PC, Thomas PG. Paired analysis of TCR[alpha] and TCR[beta] chains at the single-cell level in mice. J Clin Invest 121(1):288-295, 2011.
Rawlings JS, Gatzka M, Thomas PG, Ihle JN. Chromatin condensation via the condensin II complex is required for peripheral T-cell quiescence. EMBO J December 17, 2010.
Moffat JM, Handel A, Doherty PC, Turner SJ, Thomas PG, La Gruta NL. Influenza epitope-specific CD8( ) T cell avidity, but not cytokine polyfunctionality, can be determined by TCR beta clonotype. J Immunol 185(11):6850-6856, 2010.
Ellebedy AH, Fabrizio T, Kayali G, Oguin T, Brown S, Rehg J, Thomas P, Webby RJ. Contemporary seasonal A (H1N1) influenza virus infection primes for a more robust response to split inactivated pandemic A(H1N1) vaccination in ferrets. Clin Vaccine Immunol October 20, 2010.
Sanders CJ, Doherty PC, Thomas PG. Respiratory epithelial cells in innate immunity to influenza virus infection. Cell Tissue Res September 17, 2010.
Last update: April 2024