Selected Publications

All Publications

Transcriptomic profiling after B-cell depletion reveals central and peripheral immune cell changes in multiple sclerosis.Wei J, Moon J, Yasumizu Y, Zhang L, Raddassi K, Buitrago-Pocasangre NC, Deerhake ME, Strauli N, Chen CW, Herman A, Pedotti R, Raposo C, Yim I, Pappalardo JL, Longbrake EE, Sumida TS, Axisa PP, Hafler DA. J Clin Invest. 2025 Mar 11; 2025 Mar 11. PMID: 40067358.
Alterations in Gut Microbiome-Host Relationships After Immune Perturbation in Patients With Multiple Sclerosis.Gupta VK, Janda GS, Pump HK, Lele N, Cruz I, Cohen I, Ruff WE, Hafler DA, Sung J, Longbrake EE. Neurol Neuroimmunol Neuroinflamm. 2025 Mar; 2025 Jan 16. PMID: 39819054.
Identification of a multi-omics factor predictive of long COVID in the IMPACC study.Gabernet G, Maciuch J, Gygi JP, Moore JF, Hoch A, Syphurs C, Chu T, Jayavelu ND, Corry DB, Kheradmand F, Baden LR, Sekaly RP, McComsey GA, Haddad EK, Cairns CB, Rouphael N, Fernandez-Sesma A, Simon V, Metcalf JP, Agudelo Higuita NI, Hough CL, Messer WB, Davis MM, Nadeau KC, Pulendran B, Kraft M, Bime C, Reed EF, Schaenman J, Erle DJ, Calfee CS, Atkinson MA, Brackenridge SC, Melamed E, Shaw AC, Hafler DA, Ozonoff A, Bosinger SE, Eckalbar W, Maecker HT, Kim-Schulze S, Steen H, Krammer F, Westendorf K, Peters B, Fourati S, Altman MC, Levy O, Smolen KK, Montgomery RR, Diray-Arce J, Kleinstein SH, Guan L, Ehrlich LIR. bioRxiv. 2025 Feb 14; 2025 Feb 14. PMID: 39990442.
Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors.Jayavelu ND, Samaha H, Wimalasena ST, Hoch A, Gygi JP, Gabernet G, Ozonoff A, Liu S, Milliren CE, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Schaenman J, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Sesma AF, Simon V, Krammer F, Kraft M, Bime C, Calfee CS, Erle DJ, Langelier CR, Guan L, Maecker HT, Peters B, Kleinstein SH, Reed EF, Diray-Arce J, Rouphael N, Altman MC. medRxiv. 2025 Feb 13; 2025 Feb 13. PMID: 39990570.
Elucidating the role of autoreactive T cells and B cells in autoimmune hepatitis.Yasumizu Y, Hafler DA. J Clin Invest. 2025 Jan 16; 2025 Jan 16. PMID: 39817449.
Author Correction: Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain.Marsh SE, Walker AJ, Kamath T, Dissing-Olesen L, Hammond TR, de Soysa TY, Young AMH, Murphy S, Abdulraouf A, Nadaf N, Dufort C, Walker AC, Lucca LE, Kozareva V, Vanderburg C, Hong S, Bulstrode H, Hutchinson PJ, Gaffney DJ, Hafler DA, Franklin RJM, Macosko EZ, Stevens B. Nat Neurosci. 2025 Jan. PMID: 39672966.
Circulating tumor-reactive KIR(+)CD8(+) T cells suppress anti-tumor immunity in patients with melanoma.Lu BY, Lucca LE, Lewis W, Wang J, Nogueira CV, Heer S, Rayon-Estrada V, Axisa PP, Reeves SM, Buitrago-Pocasangre NC, Pham GH, Kojima ML, Wei W, Aizenbud L, Bacchiocchi A, Zhang L, Walewski JJ, Chiang V, Olino K, Clune J, Halaban R, Kluger Y, Coyle AJ, Kisielow J, Obermair FJ, Kluger HM, Hafler DA. Nat Immunol. 2025 Jan; 2024 Nov 28. PMID: 39609626.
Cholesterol promotes IFNG mRNA expression in CD4(+) effector/memory cells by SGK1 activation.Hanin A, Comi M, Sumida TS, Hafler DA. Life Sci Alliance. 2024 Dec; 2024 Oct 4. PMID: 39366761.
Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping.Wang K, Nie Y, Maguire C, Syphurs C, Sheen H, Karoly M, Lapp L, Gygi JP, Jayavelu ND, Patel RK, Hoch A, Corry D, Kheradmand F, McComsey GA, Fernandez-Sesma A, Simon V, Metcalf JP, Higuita NIA, Messer WB, Davis MM, Nadeau KC, Kraft M, Bime C, Schaenman J, Erle D, Calfee CS, Atkinson MA, Brackenridge SC, Hafler DA, Shaw A, Rahman A, Hough CL, Geng LN, Ozonoff A, Haddad EK, Reed EF, van Bakel H, Kim-Schultz S, Krammer F, Wilson M, Eckalbar W, Bosinger S, Langelier CR, Sekaly RP, Montgomery RR, Maecker HT, Krumholz H, Melamed E, Steen H, Pulendran B, Augustine AD, Cairns CB, Rouphael N, Becker PM, Fourati S, Shannon CP, Smolen KK, Peters B, Kleinstein SH, Levy O, Altman MC, Iwasaki A, Diray-Arce J, Ehrlich LIR, Guan L. bioRxiv. 2024 Nov 25; 2024 Nov 25. PMID: 39651165.
Chronic Viral Reactivation and Associated Host Immune Response and Clinical Outcomes in Acute COVID-19 and Post-Acute Sequelae of COVID-19.Maguire C, Chen J, Rouphael N, Pickering H, Phan HV, Glascock A, Chu V, Dandekar R, Corry D, Kheradmand F, Baden LR, Selaky R, McComsey GA, Haddad EK, Cairns CB, Pulendran B, Fernandez-Sesma A, Simon V, Metcalf JP, Higuita NIA, Messer WB, David MM, Nadeau KC, Kraft M, Bime C, Schaenman J, Erle D, Calfee CS, Atkinson MA, Brackenridge SC, Ehrlich LIR, Montgomery RR, Shaw AC, Hough CL, Geng LN, Hafler DA, Augustine AD, Becker PM, Peters B, Ozonoff A, Kim-Schulze SH, Krammer F, Bosinger S, Eckalbar W, Altman MC, Wilson M, Guan L, Kleinstein SH, Smolen KK, Reed EF, Levy O, Maecker H, Hunt P, Steen H, Diray-Arce J, Langelier CR, Melamed E. bioRxiv. 2024 Nov 16; 2024 Nov 16. PMID: 39605478.
Single-cell transcriptomic and proteomic analysis of Parkinson's disease brains.Zhu B, Park JM, Coffey SR, Russo A, Hsu IU, Wang J, Su C, Chang R, Lam TT, Gopal PP, Ginsberg SD, Zhao H, Hafler DA, Chandra SS, Zhang L. Sci Transl Med. 2024 Oct 30; 2024 Oct 30. PMID: 39475571.
An autoimmune transcriptional circuit drives FOXP3(+) regulatory T cell dysfunction.Sumida TS, Lincoln MR, He L, Park Y, Ota M, Oguchi A, Son R, Yi A, Stillwell HA, Leissa GA, Fujio K, Murakawa Y, Kulminski AM, Epstein CB, Bernstein BE, Kellis M, Hafler DA. Sci Transl Med. 2024 Aug 28; 2024 Aug 28. PMID: 39196959.
Meta-analysis identifies common gut microbiota associated with multiple sclerosis.Lin Q, Dorsett Y, Mirza A, Tremlett H, Piccio L, Longbrake EE, Choileain SN, Hafler DA, Cox LM, Weiner HL, Yamamura T, Chen K, Wu Y, Zhou Y. Genome Med. 2024 Jul 31; 2024 Jul 31. PMID: 39085949.
Single-Cell Transcriptomic Analyses of Brain Parenchyma in Patients With New-Onset Refractory Status Epilepticus (NORSE).Hanin A, Zhang L, Huttner AJ, Plu I, Mathon B, Bielle F, Navarro V, Hirsch LJ, Hafler DA. Neurol Neuroimmunol Neuroinflamm. 2024 Jul; 2024 May 29. PMID: 38810181.
The regulation and differentiation of regulatory T cells and their dysfunction in autoimmune diseases.Sumida TS, Cheru NT, Hafler DA. Nat Rev Immunol. 2024 Jul; 2024 Feb 19. PMID: 38374298.
Neutrophils insert elastase into hepatocytes to regulate calcium signaling in alcohol-associated hepatitis.Ogino N, Leite MF, Guerra MT, Kruglov E, Asashima H, Hafler DA, Ito T, Pereira JP, Peiffer BJ, Sun Z, Ehrlich BE, Nathanson MH. J Clin Invest. 2024 Jun 25; 2024 Jun 25. PMID: 38916955.
Genetic mapping across autoimmune diseases reveals shared associations and mechanisms.Lincoln MR, Connally N, Axisa PP, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers IH, Padyukov L, Rich SS, Graham RR, Gaffney PM, Langefeld CD, Vyse TJ, Hafler DA, Chun S, Sunyaev SR, Cotsapas C. Nat Genet. 2024 May; 2024 May 13. PMID: 38741015.
Emerging Cerebrospinal Fluid Biomarkers of Disease Activity and Progression in Multiple Sclerosis.Cross AH, Gelfand JM, Thebault S, Bennett JL, von Büdingen HC, Cameron B, Carruthers R, Edwards K, Fallis R, Gerstein R, Giacomini PS, Greenberg B, Hafler DA, Ionete C, Kaunzner UW, Kodama L, Lock C, Longbrake EE, Musch B, Pardo G, Piehl F, Weber MS, Yuen S, Ziemssen T, Bose G, Freedman MS, Anania VG, Ramesh A, Winger RC, Jia X, Herman A, Harp C, Bar-Or A. JAMA Neurol. 2024 Mar 11; 2024 Mar 11. PMID: 38466277.
Systems Analysis of Immune Changes after B-cell Depletion in Autoimmune Multiple Sclerosis.Wei J, Moon J, Yasumizu Y, Zhang L, Radassi K, Buitrago-Pocasangre N, Deerhake ME, Strauli N, Chan A, Herman A, Pedotte R, Raposo C, Tackenberg B, Yim I, Pappalardo J, Longbrake EE, Sumida TS, Axisa PP, Hafler DA. bioRxiv. 2024 Feb 9; 2024 Feb 9. PMID: 38370778.
Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study.Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N. Nat Commun. 2024 Jan 3; 2024 Jan 3. PMID: 38172101.
scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles.Zhu B, Wang Y, Ku LT, van Dijk D, Zhang L, Hafler DA, Zhao H. Genome Biol. 2023 Dec 18; 2023 Dec 18. PMID: 38111007.
Early cellular and molecular signatures correlate with severity of West Nile virus infection.Lee HJ, Zhao Y, Fleming I, Mehta S, Wang X, Wyk BV, Ronca SE, Kang H, Chou CH, Fatou B, Smolen KK, Levy O, Clish CB, Xavier RJ, Steen H, Hafler DA, Love JC, Shalek AK, Guan L, Murray KO, Kleinstein SH, Montgomery RR. iScience. 2023 Dec 15; 2023 Nov 2. PMID: 38047068.
Corrigendum to "Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: results from the IMPACC study" [eBioMedicine 83 (2022) 104208].Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Agudelo Higuita NI, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LIR, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N. EBioMedicine. 2023 Dec; 2023 Nov 1. PMID: 37918220.
Microfluidic Immuno-Serolomic Assay Reveals Systems Level Association with COVID-19 Pathology and Vaccine Protection.Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, Fan R. Small Methods. 2023 Oct; 2023 Jun 13. PMID: 37312418.
Prior cycles of anti-CD20 antibodies affect antibody responses after repeated SARS-CoV-2 mRNA vaccination.Asashima H, Kim D, Wang K, Lele N, Buitrago-Pocasangre NC, Lutz R, Cruz I, Raddassi K, Ruff WE, Racke MK, Wilson JE, Givens TS, Grifoni A, Weiskopf D, Sette A, Kleinstein SH, Montgomery RR, Shaw AC, Li F, Fan R, Hafler DA, Tomayko MM, Longbrake EE. JCI Insight. 2023 Aug 22; 2023 Aug 22. PMID: 37606046.
ScRNA-seq defines dynamic T-cell subsets in longitudinal colon and peripheral blood samples in immune checkpoint inhibitor-induced colitis.Mann JE, Lucca L, Austin MR, Merkin RD, Robert ME, Al Bawardy B, Raddassi K, Aizenbud L, Joshi NS, Hafler DA, Abraham C, Herold KC, Kluger HM. J Immunother Cancer. 2023 Aug. PMID: 37586769.
Cytokines in New-Onset Refractory Status Epilepticus Predict Outcomes.Hanin A, Cespedes J, Dorgham K, Pulluru Y, Gopaul M, Gorochov G, Hafler DA, Navarro V, Gaspard N, Hirsch LJ. Ann Neurol. 2023 Jul; 2023 Mar 17. PMID: 36871188.
Common genetic factors among autoimmune diseases.Harroud A, Hafler DA. Science. 2023 May 5; 2023 May 4. PMID: 37141355.
Regulatory T cells in peripheral tissue tolerance and diseases.Cheru N, Hafler DA, Sumida TS. Front Immunol. 2023; 2023 May 1. PMID: 37197653.
Single-cell transcriptomic atlas of Alzheimer's disease middle temporal gyrus reveals region, cell type and sex specificity of gene expression with novel genetic risk for MERTK in female.Zhang L, He CH, Coffey S, Yin D, Hsu IU, Su C, Ye Y, Zhang C, Spurrier J, Nicholson L, Rothlin CV, Ghosh S, Gopal PP, Hafler DA, Zhao H, Strittmatter SM. medRxiv. 2023 Feb 23; 2023 Feb 23. PMID: 36865305.
Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs.Côrte-Real BF, Hamad I, Arroyo Hornero R, Geisberger S, Roels J, Van Zeebroeck L, Dyczko A, van Gisbergen MW, Kurniawan H, Wagner A, Yosef N, Weiss SNY, Schmetterer KG, Schröder A, Krampert L, Haase S, Bartolomaeus H, Hellings N, Saeys Y, Dubois LJ, Brenner D, Kempa S, Hafler DA, Stegbauer J, Linker RA, Jantsch J, Müller DN, Kleinewietfeld M. Cell Metab. 2023 Feb 7. PMID: 36754020.
PD-1(high)CXCR5(-)CD4(+) peripheral helper T cells promote CXCR3(+) plasmablasts in human acute viral infection.Asashima H, Mohanty S, Comi M, Ruff WE, Hoehn KB, Wong P, Klein J, Lucas C, Cohen I, Coffey S, Lele N, Greta L, Raddassi K, Chaudhary O, Unterman A, Emu B, Kleinstein SH, Montgomery RR, Iwasaki A, Dela Cruz CS, Kaminski N, Shaw AC, Hafler DA, Sumida TS. Cell Rep. 2023 Jan 31; 2023 Jan 2. PMID: 36596303.
Differential effects of anti-CD20 therapy on CD4 and CD8 T cells and implication of CD20-expressing CD8 T cells in MS disease activity.Shinoda K, Li R, Rezk A, Mexhitaj I, Patterson KR, Kakara M, Zuroff L, Bennett JL, von Büdingen HC, Carruthers R, Edwards KR, Fallis R, Giacomini PS, Greenberg BM, Hafler DA, Ionete C, Kaunzner UW, Lock CB, Longbrake EE, Pardo G, Piehl F, Weber MS, Ziemssen T, Jacobs D, Gelfand JM, Cross AH, Cameron B, Musch B, Winger RC, Jia X, Harp CT, Herman A, Bar-Or A. Proc Natl Acad Sci U S A. 2023 Jan 17; 2023 Jan 12. PMID: 36634138.
A multiple sclerosis-protective coding variant reveals an essential role for HDAC7 in regulatory T cells.Axisa PP, Yoshida TM, Lucca LE, Kasler HG, Lincoln MR, Pham GH, Del Priore D, Carpier JM, Lucas CL, Verdin E, Sumida TS, Hafler DA. Sci Transl Med. 2022 Dec 14; 2022 Dec 14. PMID: 36516268.
Longitudinal single-cell analysis of a patient receiving adoptive cell therapy reveals potential mechanisms of treatment failure.Qu R, Kluger Y, Yang J, Zhao J, Hafler DA, Krause DS, Bersenev A, Bosenberg M, Hurwitz M, Lucca L, Kluger HM. Mol Cancer. 2022 Dec 14; 2022 Dec 14. PMID: 36514045.
The CELLO trial: Protocol of a planned phase 4 study to assess the efficacy of Ocrelizumab in patients with radiologically isolated syndrome.Longbrake EE, Hua LH, Mowry EM, Gauthier SA, Alvarez E, Cross AH, Pei J, Priest J, Raposo C, Hafler DA, Winger RC. Mult Scler Relat Disord. 2022 Dec; 2022 Aug 22. PMID: 36031693.
Impaired TIGIT expression on B cells drives circulating follicular helper T cell expansion in multiple sclerosis.Asashima H, Axisa PP, Pham THG, Longbrake EE, Ruff WE, Lele N, Cohen I, Raddassi K, Sumida TS, Hafler DA. J Clin Invest. 2022 Oct 17; 2022 Oct 17. PMID: 36250467.
Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity.Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, Fan R. bioRxiv. 2022 Sep 2; 2022 Sep 2. PMID: 36093346.
Neuroimmune interactions in health and disease.Hafler DA, Sansing LH. Semin Immunopathol. 2022 Sep. PMID: 36171280.
Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study.Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LIR, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N. EBioMedicine. 2022 Sep; 2022 Aug 8. PMID: 35952496.
Basic principles of neuroimmunology.Yoshida TM, Wang A, Hafler DA. Semin Immunopathol. 2022 Sep; 2022 Jun 22. PMID: 35732977.
Fatty Acid Metabolism and T Cells in Multiple Sclerosis.Pompura SL, Hafler DA, Dominguez-Villar M. Front Immunol. 2022; 2022 May 4. PMID: 35603182.
Population genetics meets single-cell sequencing.Sumida TS, Hafler DA. Science. 2022 Apr 8; 2022 Apr 7. PMID: 35389792.
Type I interferon transcriptional network regulates expression of coinhibitory receptors in human T cells.Sumida TS, Dulberg S, Schupp JC, Lincoln MR, Stillwell HA, Axisa PP, Comi M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. Nat Immunol. 2022 Apr; 2022 Mar 17. PMID: 35301508.
Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain.Marsh SE, Walker AJ, Kamath T, Dissing-Olesen L, Hammond TR, de Soysa TY, Young AMH, Murphy S, Abdulraouf A, Nadaf N, Dufort C, Walker AC, Lucca LE, Kozareva V, Vanderburg C, Hong S, Bulstrode H, Hutchinson PJ, Gaffney DJ, Hafler DA, Franklin RJM, Macosko EZ, Stevens B. Nat Neurosci. 2022 Mar; 2022 Mar 8. PMID: 35260865.
TCR-sequencing in cancer and autoimmunity: barcodes and beyond.Pauken KE, Lagattuta KA, Lu BY, Lucca LE, Daud AI, Hafler DA, Kluger HM, Raychaudhuri S, Sharpe AH. Trends Immunol. 2022 Mar; 2022 Jan 25. PMID: 35090787.
Phase 2 Trial of Rituximab in Acetylcholine Receptor Antibody-Positive Generalized Myasthenia Gravis: The BeatMG Study.Nowak RJ, Coffey CS, Goldstein JM, Dimachkie MM, Benatar M, Kissel JT, Wolfe GI, Burns TM, Freimer ML, Nations S, Granit V, Smith AG, Richman DP, Ciafaloni E, Al-Lozi MT, Sams LA, Quan D, Ubogu E, Pearson B, Sharma A, Yankey JW, Uribe L, Shy M, Amato AA, Conwit R, O'Connor KC, Hafler DA, Cudkowicz ME, Barohn RJ. Neurology. 2022 Jan 25; 2022 Jan 25. PMID: 34857535.
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19.Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C Jr, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Nat Commun. 2022 Jan 21; 2022 Jan 21. PMID: 35064122.
The double-edged sword: Harnessing PD-1 blockade in tumor and autoimmunity.Kuchroo JR, Hafler DA, Sharpe AH, Lucca LE. Sci Immunol. 2021 Nov 5; 2021 Nov 5. PMID: 34739340.
(23)Na imaging: Worth its salt for understanding multiple sclerosis.Longbrake EE, Hafler DA. Proc Natl Acad Sci U S A. 2021 Aug 17. PMID: 34376559.
Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells.Jiang R, Meng H, Raddassi K, Fleming I, Hoehn KB, Dardick KR, Belperron AA, Montgomery RR, Shalek AK, Hafler DA, Kleinstein SH, Bockenstedt LK. JCI Insight. 2021 Jun 22; 2021 Jun 22. PMID: 34061047.
Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19.Hoehn KB, Ramanathan P, Unterman A, Sumida TS, Asashima H, Hafler DA, Kaminski N, Dela Cruz CS, Sealfon SC, Bukreyev A, Kleinstein SH. J Immunol. 2021 Jun 15; 2021 May 28. PMID: 34049971.
NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data.He L, Davila-Velderrain J, Sumida TS, Hafler DA, Kellis M, Kulminski AM. Commun Biol. 2021 May 26; 2021 May 26. PMID: 34040149.
Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells.Lucca LE, Axisa PP, Lu B, Harnett B, Jessel S, Zhang L, Raddassi K, Zhang L, Olino K, Clune J, Singer M, Kluger HM, Hafler DA. J Exp Med. 2021 Apr 5. PMID: 33651881.
Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity.Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. medRxiv. 2021 Apr 3; 2021 Apr 3. PMID: 33300011.
Clinical Significance of PDCD4 in Melanoma by Subcellular Expression and in Tumor-Associated Immune Cells.Tran TT, Rane CK, Zito CR, Weiss SA, Jessel S, Lucca L, Lu BY, Oria VO, Adeniran A, Chiang VL, Omay SB, Hafler DA, Kluger HM, Jilaveanu LB. Cancers (Basel). 2021 Mar 2; 2021 Mar 2. PMID: 33801444.
Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis.Pompura SL, Wagner A, Kitz A, LaPerche J, Yosef N, Dominguez-Villar M, Hafler DA. J Clin Invest. 2021 Jan 19. PMID: 33170805.
Epigenetic fine-mapping: identification of causal mechanisms for autoimmunity.Lincoln MR, Axisa PP, Hafler DA. Curr Opin Immunol. 2020 Dec; 2020 Sep 23. PMID: 32977183.
Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells.Sumida TS, Dulberg S, Schupp J, Stillwell HA, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. bioRxiv. 2020 Oct 31; 2020 Oct 31. PMID: 33140047.
Two genetic variants explain the association of European ancestry with multiple sclerosis risk in African-Americans.Nakatsuka N, Patterson N, Patsopoulos NA, Altemose N, Tandon A, Beecham AH, McCauley JL, Isobe N, Hauser S, De Jager PL, Hafler DA, Oksenberg JR, Reich D. Sci Rep. 2020 Oct 9; 2020 Oct 9. PMID: 33037294.
Transcriptomic and clonal characterization of T cells in the human central nervous system.Pappalardo JL, Zhang L, Pecsok MK, Perlman K, Zografou C, Raddassi K, Abulaban A, Krishnaswamy S, Antel J, van Dijk D, Hafler DA. Sci Immunol. 2020 Sep 18. PMID: 32948672.
Differential expression of the T-cell inhibitor TIGIT in glioblastoma and MS.Lucca LE, Lerner BA, Park C, DeBartolo D, Harnett B, Kumar VP, Ponath G, Raddassi K, Huttner A, Hafler DA, Pitt D. Neurol Neuroimmunol Neuroinflamm. 2020 May 4; 2020 Apr 8. PMID: 32269065.
CXCR3+ T cells in multiple sclerosis correlate with reduced diversity of the gut microbiome.Choileáin SN, Kleinewietfeld M, Raddassi K, Hafler DA, Ruff WE, Longbrake EE. J Transl Autoimmun. 2020; 2019 Dec 20. PMID: 32743517.
Siponimod Chips Away at Progressive MS.Longbrake EE, Hafler DA. Cell. 2019 Dec 12; 2019 Dec 12. PMID: 31951523.
AKT isoforms modulate Th1-like Treg generation and function in human autoimmune disease.Kitz A, de Marcken M, Gautron AS, Mitrovic M, Hafler DA, Dominguez-Villar M. EMBO Rep. 2019 Aug. PMID: 31379130.
Aedes aegypti AgBR1 antibodies modulate early Zika virus infection of mice.Uraki R, Hastings AK, Marin-Lopez A, Sumida T, Takahashi T, Grover JR, Iwasaki A, Hafler DA, Montgomery RR, Fikrig E. Nat Microbiol. 2019 Jun; 2019 Mar 11. PMID: 30858571.
Autoantibodies against Neurologic Antigens in Nonneurologic Autoimmunity.Stathopoulos P, Chastre A, Waters P, Irani S, Fichtner ML, Benotti ES, Guthridge JM, Seifert J, Nowak RJ, Buckner JH, Holers VM, James JA, Hafler DA, O'Connor KC. J Immunol. 2019 Apr 15; 2019 Mar 1. PMID: 30824481.
Latent autoimmunity across disease-specific boundaries in at-risk first-degree relatives of SLE and RA patients.James JA, Chen H, Young KA, Bemis EA, Seifert J, Bourn RL, Deane KD, Demoruelle MK, Feser M, O'Dell JR, Weisman MH, Keating RM, Gaffney PM, Kelly JA, Langefeld CD, Harley JB, Robinson W, Hafler DA, O'Connor KC, Buckner J, Guthridge JM, Norris JM, Holers VM. EBioMedicine. 2019 Apr; 2019 Apr 3. PMID: 30952617.
From Big Data to Precision Medicine.Hulsen T, Jamuar SS, Moody AR, Karnes JH, Varga O, Hedensted S, Spreafico R, Hafler DA, McKinney EF. Front Med (Lausanne). 2019; 2019 Mar 1. PMID: 30881956.
TIGIT signaling restores suppressor function of Th1 Tregs.Lucca LE, Axisa PP, Singer ER, Nolan NM, Dominguez-Villar M, Hafler DA. JCI Insight. 2019 Feb 7; 2019 Feb 7. PMID: 30728325.
Multiple sclerosis enters a grey area.Pappalardo JL, Hafler DA. Nature. 2019 Feb. PMID: 30809050.
Fingolimod modulates T cell phenotype and regulatory T cell plasticity in vivo.Dominguez-Villar M, Raddassi K, Danielsen AC, Guarnaccia J, Hafler DA. J Autoimmun. 2019 Jan; 2018 Aug 16. PMID: 30122421.
Enhanced astrocyte responses are driven by a genetic risk allele associated with multiple sclerosis.Ponath G, Lincoln MR, Levine-Ritterman M, Park C, Dahlawi S, Mubarak M, Sumida T, Airas L, Zhang S, Isitan C, Nguyen TD, Raine CS, Hafler DA, Pitt D. Nat Commun. 2018 Dec 17; 2018 Dec 17. PMID: 30559390.
Activated β-catenin in Foxp3(+) regulatory T cells links inflammatory environments to autoimmunity.Sumida T, Lincoln MR, Ukeje CM, Rodriguez DM, Akazawa H, Noda T, Naito AT, Komuro I, Dominguez-Villar M, Hafler DA. Nat Immunol. 2018 Dec; 2018 Oct 29. PMID: 30374130.
Single-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV.Farhadian SF, Mehta SS, Zografou C, Robertson K, Price RW, Pappalardo J, Chiarella J, Hafler DA, Spudich SS. JCI Insight. 2018 Sep 20; 2018 Sep 20. PMID: 30232286.
Regulatory T cells in autoimmune disease.Dominguez-Villar M, Hafler DA. Nat Immunol. 2018 Jul; 2018 Jun 20. PMID: 29925983.
Minimum Information about T Regulatory Cells: A Step toward Reproducibility and Standardization.Fuchs A, Gliwiński M, Grageda N, Spiering R, Abbas AK, Appel S, Bacchetta R, Battaglia M, Berglund D, Blazar B, Bluestone JA, Bornhäuser M, Ten Brinke A, Brusko TM, Cools N, Cuturi MC, Geissler E, Giannoukakis N, Gołab K, Hafler DA, van Ham SM, Hester J, Hippen K, Di Ianni M, Ilic N, Isaacs J, Issa F, Iwaszkiewicz-Grześ D, Jaeckel E, Joosten I, Klatzmann D, Koenen H, van Kooten C, Korsgren O, Kretschmer K, Levings M, Marek-Trzonkowska NM, Martinez-Llordella M, Miljkovic D, Mills KHG, Miranda JP, Piccirillo CA, Putnam AL, Ritter T, Roncarolo MG, Sakaguchi S, Sánchez-Ramón S, Sawitzki B, Sofronic-Milosavljevic L, Sykes M, Tang Q, Vives-Pi M, Waldmann H, Witkowski P, Wood KJ, Gregori S, Hilkens CMU, Lombardi G, Lord P, Martinez-Caceres EM, Trzonkowski P. Front Immunol. 2017; 2018 Jan 15. PMID: 29379498.
Functional differences between PD-1+ and PD-1- CD4+ effector T cells in healthy donors and patients with glioblastoma multiforme.Goods BA, Hernandez AL, Lowther DE, Lucca LE, Lerner BA, Gunel M, Raddassi K, Coric V, Hafler DA, Love JC. PLoS One. 2017; 2017 Sep 7. PMID: 28880903.
Podoplanin is a negative regulator of Th17 inflammation.Nylander AN, Ponath GD, Axisa PP, Mubarak M, Tomayko M, Kuchroo VK, Pitt D, Hafler DA. JCI Insight. 2017 Sep 7; 2017 Sep 7. PMID: 28878118.
Resisting fatal attraction: a glioma oncometabolite prevents CD8+ T cell recruitment.Lucca LE, Hafler DA. J Clin Invest. 2017 Apr 3; 2017 Mar 20. PMID: 28319049.
Co-inhibitory blockade while preserving tolerance: checkpoint inhibitors for glioblastoma.Lucca LE, Hafler DA. Immunol Rev. 2017 Mar. PMID: 28258696.
Solving Immunology?Vodovotz Y, Xia A, Read EL, Bassaganya-Riera J, Hafler DA, Sontag E, Wang J, Tsang JS, Day JD, Kleinstein SH, Butte AJ, Altman MC, Hammond R, Sealfon SC. Trends Immunol. 2017 Feb; 2016 Dec 13. PMID: 27986392.
TGF-β1 modulates microglial phenotype and promotes recovery after intracerebral hemorrhage.Taylor RA, Chang CF, Goods BA, Hammond MD, Mac Grory B, Ai Y, Steinschneider AF, Renfroe SC, Askenase MH, McCullough LD, Kasner SE, Mullen MT, Hafler DA, Love JC, Sansing LH. J Clin Invest. 2017 Jan 3; 2016 Nov 28. PMID: 27893460.
The Human Functional Genomics Project: Understanding Generation of Diversity.Pappalardo JL, Hafler DA. Cell. 2016 Nov 3. PMID: 27814519.
National Heart, Lung, and Blood Institute Working Group Report on Salt in Human Health and Sickness: Building on the Current Scientific Evidence.Oh YS, Appel LJ, Galis ZS, Hafler DA, He J, Hernandez AL, Joe B, Karumanchi SA, Maric-Bilkan C, Mattson D, Mehta NN, Randolph G, Ryan M, Sandberg K, Titze J, Tolunay E, Toney GM, Harrison DG. Hypertension. 2016 Aug; 2016 Jun 20. PMID: 27324228.
AKT isoforms modulate Th1-like Treg generation and function in human autoimmune disease.Kitz A, de Marcken M, Gautron AS, Mitrovic M, Hafler DA, Dominguez-Villar M. EMBO Rep. 2016 Aug; 2016 Jun 16. PMID: 27312110.
Linking Genotype to Clinical Phenotype in Multiple Sclerosis: In Search of the Holy Grail.Longbrake EE, Hafler DA. JAMA Neurol. 2016 Jul 1. PMID: 27244583.
Power estimation for non-standardized multisite studies.Keshavan A, Paul F, Beyer MK, Zhu AH, Papinutto N, Shinohara RT, Stern W, Amann M, Bakshi R, Bischof A, Carriero A, Comabella M, Crane JC, D'Alfonso S, Demaerel P, Dubois B, Filippi M, Fleischer V, Fontaine B, Gaetano L, Goris A, Graetz C, Gröger A, Groppa S, Hafler DA, Harbo HF, Hemmer B, Jordan K, Kappos L, Kirkish G, Llufriu S, Magon S, Martinelli-Boneschi F, McCauley JL, Montalban X, Mühlau M, Pelletier D, Pattany PM, Pericak-Vance M, Cournu-Rebeix I, Rocca MA, Rovira A, Schlaeger R, Saiz A, Sprenger T, Stecco A, Uitdehaag BMJ, Villoslada P, Wattjes MP, Weiner H, Wuerfel J, Zimmer C, Zipp F, Hauser SL, Oksenberg JR, Henry RG. Neuroimage. 2016 Jul 1; 2016 Apr 1. PMID: 27039700.
Multiple sclerosis: genetics, biomarkers, treatments.Axisa PP, Hafler DA. Curr Opin Neurol. 2016 Jun. PMID: 27058221.
Production of Proinflammatory Cytokines by Monocytes in Liver-Transplanted Recipients with De Novo Autoimmune Hepatitis Is Enhanced and Induces TH1-like Regulatory T Cells.Arterbery AS, Osafo-Addo A, Avitzur Y, Ciarleglio M, Deng Y, Lobritto SJ, Martinez M, Hafler DA, Kleinewietfeld M, Ekong UD. J Immunol. 2016 May 15; 2016 Apr 18. PMID: 27183637.
PD-1 marks dysfunctional regulatory T cells in malignant gliomas.Lowther DE, Goods BA, Lucca LE, Lerner BA, Raddassi K, van Dijk D, Hernandez AL, Duan X, Gunel M, Coric V, Krishnaswamy S, Love JC, Hafler DA. JCI Insight. 2016 Apr 21. PMID: 27182555.
CNS demyelination and enhanced myelin-reactive responses after ipilimumab treatment.Cao Y, Nylander A, Ramanan S, Goods BA, Ponath G, Zabad R, Chiang VL, Vortmeyer AO, Hafler DA, Pitt D. Neurology. 2016 Apr 19; 2016 Mar 16. PMID: 26984943.
Evaluation of KIR4.1 as an Immune Target in Multiple Sclerosis.Chastre A, Hafler DA, O'Connor KC. N Engl J Med. 2016 Apr 14. PMID: 27074083.
The Link Between CD6 and Autoimmunity: Genetic and Cellular Associations.Kofler DM, Farkas A, von Bergwelt-Baildon M, Hafler DA. Curr Drug Targets. 2016. PMID: 26844569.
Investigating the Antigen Specificity of Multiple Sclerosis Central Nervous System-Derived Immunoglobulins.Willis SN, Stathopoulos P, Chastre A, Compton SD, Hafler DA, O'Connor KC. Front Immunol. 2015; 2015 Nov 25. PMID: 26648933.
Sodium chloride inhibits the suppressive function of FOXP3+ regulatory T cells.Hernandez AL, Kitz A, Wu C, Lowther DE, Rodriguez DM, Vudattu N, Deng S, Herold KC, Kuchroo VK, Kleinewietfeld M, Hafler DA. J Clin Invest. 2015 Nov 2; 2015 Oct 20. PMID: 26524592.
Biomarkers in multiple sclerosis.Housley WJ, Pitt D, Hafler DA. Clin Immunol. 2015 Nov; 2015 Jul 2. PMID: 26143623.
Class II HLA interactions modulate genetic risk for multiple sclerosis.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 TMC, Booth D, Buck D, Celius EG, Cotsapas C, D'Alfonso S, Dendrou CA, Donnelly P, Dubois B, Fontaine B, Fugger L, Goris A, Gourraud PA, Graetz C, Hemmer B, Hillert J, 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 CCA, Stewart G, Hafler DA, Ivinson AJ, Harbo HF, Hauser SL, De Jager PL, Compston A, McCauley JL, Sawcer S, McVean G. Nat Genet. 2015 Oct; 2015 Sep 7. PMID: 26343388.
Prospects of immune checkpoint modulators in the treatment of glioblastoma.Preusser M, Lim M, Hafler DA, Reardon DA, Sampson JH. Nat Rev Neurol. 2015 Sep; 2015 Aug 11. PMID: 26260659.
Sodium-activated macrophages: the salt mine expands.Lucca LE, Hafler DA. Cell Res. 2015 Aug; 2015 Jul 28. PMID: 26215700.

Highlighted Publications

Single-cell transcriptomic and proteomic analysis of Parkinson's disease brains.Zhu B, Park JM, Coffey SR, Russo A, Hsu IU, Wang J, Su C, Chang R, Lam TT, Gopal PP, Ginsberg SD, Zhao H, Hafler DA, Chandra SS, Zhang L. Sci Transl Med. 2024 Oct 30; 2024 Oct 30. PMID: 39475571.
An autoimmune transcriptional circuit drives FOXP3(+) regulatory T cell dysfunction.Sumida TS, Lincoln MR, He L, Park Y, Ota M, Oguchi A, Son R, Yi A, Stillwell HA, Leissa GA, Fujio K, Murakawa Y, Kulminski AM, Epstein CB, Bernstein BE, Kellis M, Hafler DA. Sci Transl Med. 2024 Aug 28; 2024 Aug 28. PMID: 39196959.
Single-Cell Transcriptomic Analyses of Brain Parenchyma in Patients With New-Onset Refractory Status Epilepticus (NORSE).Hanin A, Zhang L, Huttner AJ, Plu I, Mathon B, Bielle F, Navarro V, Hirsch LJ, Hafler DA. Neurol Neuroimmunol Neuroinflamm. 2024 Jul; 2024 May 29. PMID: 38810181.
Locus for severity implicates CNS resilience in progression of multiple sclerosis.Nature. 2023 Jul; 2023 Jun 28. PMID: 37380766.
Common genetic factors among autoimmune diseases.Harroud A, Hafler DA. Science. 2023 May 5; 2023 May 4. PMID: 37141355.
A multiple sclerosis-protective coding variant reveals an essential role for HDAC7 in regulatory T cells.Axisa PP, Yoshida TM, Lucca LE, Kasler HG, Lincoln MR, Pham GH, Del Priore D, Carpier JM, Lucas CL, Verdin E, Sumida TS, Hafler DA. Sci Transl Med. 2022 Dec 14; 2022 Dec 14. PMID: 36516268.
Impaired TIGIT expression on B cells drives circulating follicular helper T cell expansion in multiple sclerosis.Asashima H, Axisa PP, Pham THG, Longbrake EE, Ruff WE, Lele N, Cohen I, Raddassi K, Sumida TS, Hafler DA. J Clin Invest. 2022 Oct 17; 2022 Oct 17. PMID: 36250467.
Type I interferon transcriptional network regulates expression of coinhibitory receptors in human T cells.Sumida TS, Dulberg S, Schupp JC, Lincoln MR, Stillwell HA, Axisa PP, Comi M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. Nat Immunol. 2022 Apr; 2022 Mar 17. PMID: 35301508.
Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children.Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immunity. 2021 May 11; 2021 Apr 13. PMID: 33891889.
Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells.Lucca LE, Axisa PP, Lu B, Harnett B, Jessel S, Zhang L, Raddassi K, Zhang L, Olino K, Clune J, Singer M, Kluger HM, Hafler DA. J Exp Med. 2021 Apr 5. PMID: 33651881.
Regulatory T Cells in Multiple Sclerosis.Goverman JM. N Engl J Med. 2021 Feb 11. PMID: 33567197.
Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis.Pompura SL, Wagner A, Kitz A, LaPerche J, Yosef N, Dominguez-Villar M, Hafler DA. J Clin Invest. 2021 Jan 19. PMID: 33170805.
Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells.Sumida TS, Dulberg S, Schupp J, Stillwell HA, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. bioRxiv. 2020 Oct 31; 2020 Oct 31. PMID: 33140047.
Two genetic variants explain the association of European ancestry with multiple sclerosis risk in African-Americans.Nakatsuka N, Patterson N, Patsopoulos NA, Altemose N, Tandon A, Beecham AH, McCauley JL, Isobe N, Hauser S, De Jager PL, Hafler DA, Oksenberg JR, Reich D. Sci Rep. 2020 Oct 9; 2020 Oct 9. PMID: 33037294.
Transcriptomic and clonal characterization of T cells in the human central nervous system.Pappalardo JL, Zhang L, Pecsok MK, Perlman K, Zografou C, Raddassi K, Abulaban A, Krishnaswamy S, Antel J, van Dijk D, Hafler DA. Sci Immunol. 2020 Sep 18. PMID: 32948672.
Differential expression of the T-cell inhibitor TIGIT in glioblastoma and MS.Lucca LE, Lerner BA, Park C, DeBartolo D, Harnett B, Kumar VP, Ponath G, Raddassi K, Huttner A, Hafler DA, Pitt D. Neurol Neuroimmunol Neuroinflamm. 2020 May 4; 2020 Apr 8. PMID: 32269065.
CXCR3+ T cells in multiple sclerosis correlate with reduced diversity of the gut microbiome.Choileáin SN, Kleinewietfeld M, Raddassi K, Hafler DA, Ruff WE, Longbrake EE. J Transl Autoimmun. 2020; 2019 Dec 20. PMID: 32743517.
Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility.Science. 2019 Sep 27. PMID: 31604244.
AKT isoforms modulate Th1-like Treg generation and function in human autoimmune disease.Kitz A, de Marcken M, Gautron AS, Mitrovic M, Hafler DA, Dominguez-Villar M. EMBO Rep. 2019 Aug. PMID: 31379130.
TIGIT signaling restores suppressor function of Th1 Tregs.Lucca LE, Axisa PP, Singer ER, Nolan NM, Dominguez-Villar M, Hafler DA. JCI Insight. 2019 Feb 7; 2019 Feb 7. PMID: 30728325.
Multiple sclerosis enters a grey area.Pappalardo JL, Hafler DA. Nature. 2019 Feb. PMID: 30809050.
Fingolimod modulates T cell phenotype and regulatory T cell plasticity in vivo.Dominguez-Villar M, Raddassi K, Danielsen AC, Guarnaccia J, Hafler DA. J Autoimmun. 2019 Jan; 2018 Aug 16. PMID: 30122421.
Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk.Cell. 2018 Nov 29; 2018 Oct 18. PMID: 30343897.
Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells.Kleinewietfeld M, Manzel A, Titze J, Kvakan H, Yosef N, Linker RA, Muller DN, Hafler DA. Nature. 2013 Apr 25; 2013 Mar 6. PMID: 23467095.
Identification of T helper type 1-like, Foxp3+ regulatory T cells in human autoimmune disease.Dominguez-Villar M, Baecher-Allan CM, Hafler DA. Nat Med. 2011 Jun; 2011 May 3. PMID: 21540856.
CD2 costimulation reveals defective activity by human CD4+CD25(hi) regulatory cells in patients with multiple sclerosis.Baecher-Allan CM, Costantino CM, Cvetanovich GL, Ashley CW, Beriou G, Dominguez-Villar M, Hafler DA. J Immunol. 2011 Mar 15; 2011 Feb 7. PMID: 21300823.
FOXP3+ regulatory T cells in the human immune system.Sakaguchi S, Miyara M, Costantino CM, Hafler DA. Nat Rev Immunol. 2010 Jul; 2010 Jun 18. PMID: 20559327.
The role of the CD58 locus in multiple sclerosis.De Jager PL, Baecher-Allan C, Maier LM, Arthur AT, Ottoboni L, Barcellos L, McCauley JL, Sawcer S, Goris A, Saarela J, Yelensky R, Price A, Leppa V, Patterson N, de Bakker PI, Tran D, Aubin C, Pobywajlo S, Rossin E, Hu X, Ashley CW, Choy E, Rioux JD, Pericak-Vance MA, Ivinson A, Booth DR, Stewart GJ, Palotie A, Peltonen L, Dubois B, Haines JL, Weiner HL, Compston A, Hauser SL, Daly MJ, Reich D, Oksenberg JR, Hafler DA. Proc Natl Acad Sci U S A. 2009 Mar 31; 2009 Feb 23. PMID: 19237575.
MHC class II expression identifies functionally distinct human regulatory T cells.Baecher-Allan C, Wolf E, Hafler DA. J Immunol. 2006 Apr 15. PMID: 16585553.
Loss of functional suppression by CD4+CD25+ regulatory T cells in patients with multiple sclerosis.Viglietta V, Baecher-Allan C, Weiner HL, Hafler DA. J Exp Med. 2004 Apr 5. PMID: 15067033.
CD4+CD25high regulatory cells in human peripheral blood.Baecher-Allan C, Brown JA, Freeman GJ, Hafler DA. J Immunol. 2001 Aug 1. PMID: 11466340.

Highlighted Reviews

The regulation and differentiation of regulatory T cells and their dysfunction in autoimmune diseases.Sumida TS, Cheru NT, Hafler DA. Nat Rev Immunol. 2024 Jul; 2024 Feb 19. PMID: 38374298.
The double-edged sword: Harnessing PD-1 blockade in tumor and autoimmunity.Kuchroo JR, Hafler DA, Sharpe AH, Lucca LE. Sci Immunol. 2021 Nov 5; 2021 Nov 5. PMID: 34739340.
(23)Na imaging: Worth its salt for understanding multiple sclerosis.Longbrake EE, Hafler DA. Proc Natl Acad Sci U S A. 2021 Aug 17. PMID: 34376559.
Epigenetic fine-mapping: identification of causal mechanisms for autoimmunity.Lincoln MR, Axisa PP, Hafler DA. Curr Opin Immunol. 2020 Dec; 2020 Sep 23. PMID: 32977183.
Siponimod Chips Away at Progressive MS.Longbrake EE, Hafler DA. Cell. 2019 Dec 12; 2019 Dec 12. PMID: 31951523.
Multiple sclerosis enters a grey area.Pappalardo JL, Hafler DA. Nature. 2019 Feb. PMID: 30809050.
Regulatory T cells in autoimmune disease.Dominguez-Villar M, Hafler DA. Nat Immunol. 2018 Jul; 2018 Jun 20. PMID: 29925983.
Resisting fatal attraction: a glioma oncometabolite prevents CD8+ T cell recruitment.Lucca LE, Hafler DA. J Clin Invest. 2017 Apr 3; 2017 Mar 20. PMID: 28319049.
Co-inhibitory blockade while preserving tolerance: checkpoint inhibitors for glioblastoma.Lucca LE, Hafler DA. Immunol Rev. 2017 Mar. PMID: 28258696.
The Human Functional Genomics Project: Understanding Generation of Diversity.Pappalardo JL, Hafler DA. Cell. 2016 Nov 3. PMID: 27814519.
Sodium-activated macrophages: the salt mine expands.Lucca LE, Hafler DA. Cell Res. 2015 Aug; 2015 Jul 28. PMID: 26215700.
Genetic basis of autoimmunity.Marson A, Housley WJ, Hafler DA. J Clin Invest. 2015 Jun; 2015 Jun 1. PMID: 26030227.
Thymic selection: to thine own self be true.Kitz A, Hafler DA. Immunity. 2015 May 19. PMID: 25992854.
Multiple sclerosis-a quiet revolution.Ransohoff RM, Hafler DA, Lucchinetti CF. Nat Rev Neurol. 2015 Mar; 2015 Feb 17. PMID: 25686758.

bioRxiv Publications

2020

Oleic acid Induces Tissue Resident FoxP3 Regulatory T cell Lineage Stability and Suppressive Functions, Saige L. Pompura, Allon Wagner, Alexandra Kitz, Jacob LaPerche, Nir Yosef, Margarita Dominguez-Villar, David A. Hafler, bioRxiv 2020.04.14.041525