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. Nature Immunology. 2022 March 17. Pubmed (* equal contribution, + corresponding author)

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Shared transcriptional profiles of atypical B cells suggest common drivers of expansion and function in malaria, HIV, and autoimmunity


Holla P, Dizon B, Ambegaonkar AA, Rogel N, Goldschmidt E, Boddapati AK, 

Sohn H, Sturdevant D, Austin JW, Kardava L, Yuesheng L, Liu P, Moir S, Pierce SK* and Madi A*Science Adv. 2021: Vol. 7, no. 22, eabg8384 doi: 10.1126/sciadv.abg8384. Pubmed

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An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets.


Zhang H, Madi A*, Yosef N, Chihara N, Awasthi A, Pot C, Lambden C, Srivastava A, Burkett PR, Nyman J, Christian E, Etminan Y, Lee A, Stroh H, Xia J, Karwacz K, Thakore PI, Acharya N, Schnell A, Wang C, Apetoh L, Rozenblatt-Rosen O, Anderson AC, Regev A*, Kuchroo VK*. Cell Rep. 2020 Nov 24;33(8):108433. doi: 10.1016/j.celrep.2020.108433. (* corresponding author) Pubmed


Endogenous Glucocorticoid Signaling Regulates CD8+ T Cell Differentiation and Development of Dysfunction in the Tumor Microenvironment

Acharya N*, Madi A*, Zhang H, Klapholz M, Escobar G, Dulberg S, Christian H,Ferreira M, Dixon KO, Fell G, Tooley K, Mangani D, Xia J, Singer M, Bosenberg M, Neuberg D, Rozenblatt-Rosen O, Regev A, Kuchroo VK and Anderson AC: Immunity 2020 (* equal contribution)


The yin and yang of co-inhibitory receptors: toward anti-tumor immunity without autoimmunity.

Schnell A*, Bod L*, Madi A, Kuchroo VK: Cell Res. 2020 (* equal contribution) doi:

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Challenges in the implementation of MIRIBEL criteria on nanobiomed manuscripts.

Florindo H.F., Madi A & Satchi-Fainaro R: Nature Nanotechnology 2019 Jul;14(7):627-628  doi: 10.1038/s41565-019-0498-7 Nature


Checkpoint blockade immunotherapy induces dynamic changes in novel subsets of PD-1-CD8+ tumor-infiltrating T cells.

Kurtulus S*, Madi A*, Escobar J, Klapholz M, Nyman J, Pawlak M, Dionne D, Xia J, Rozenblatt-Rosen O, Kuchroo VK, Regev A, Anderson AC: Immunity 2019 Jan 15;50(1):181-194.e6. (* equal contribution) Pubmed


Acute microglia ablation induces neurodegeneration in the somatosensory system.

Rubino SJ, Mayo L, Wimmer I, Siedler V, Brunner F, Hametner S, Madi A, Lanser A, Moreira T, Donnelly D, Cox L, Rezende RM, Butovsky O, Lassmann H, Weiner HL: Nat Commun. 2018 Nov 1;9(1):4578. doi: 10.1038/s41467-018-05929-4. Pubmed

Induction and transcriptional regulation of a “co-inhibitory” gene module in T cells.

Chihara N*, Madi A*, Kondo T, Singer M, Marjanovic ND, Kowalczyk MS, Wang C, Kurtulus S, Zhang H, Nyman J, Nevin J, Burkett PR, Rozenblatt-Rosen O, Anderson AC, Regev A, Kuchroo VK: Nature 2018, 558(7710):454-459. DOI: 10.1038/s41586-018-0206-z. (* equal contribution) Pubmed


 SGK1 Governs the Reciprocal Development of Th17 and Regulatory T Cells.

Wu C, Chen Z, Xiao S, Thalhamer T, Madi A, Han T, Kuchroo VK: Cell Rep. 2018, 16;22(3):653-665. doi: 10.1016/j.celrep.2017.12.068. 


The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

Krasemann S, Madore C, Cialic R, Baufeld C, Calcagno N, El Fatimy R, Beckers L, O'Loughlin E, Xu Y, Fanek Z, Greco DJ, Smith ST, Tweet G, Humulock Z, Zrzavy T, Conde-Sanroman P, Gacias M, Weng Z, Chen H, Tjon E, Mazaheri F, Hartmann K, Madi A, Ulrich JD, Glatzel M, Worthmann A, Heeren J, Budnik B, Lemere C, Ikezu T, Heppner FL, Litvak V, Holtzman DM, Lassmann H, Weiner HL, Ochando J, Haass C, Butovsky O: Immunity 2017 Sep 19;47(3):566-581.e9. doi: 10.1016/j.immuni.2017.08.008. Pubmed

T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences.

Madi A*, Poran A*, Shifrut E, Reich-Zeliger S, Zaretsky I, Arnon T, Van Laethem F, Singer A, Lu J, Sun DP, Cohen IR and Friedman N: eLife 2017, 6:e22057 DOI: 10.7554/eLife.22057. (* equal contribution) Pubmed


Critical role of IRF1 and BATF in forming the chromatin landscape during Tr1 differentiation.

Karwacz K, Miraldi E, Pokrovskii M, Madi A, Yosef N, Wortman I, Chen X, Watters A, Carriero N, Awasthi A, Regev A, Bonneau R, Littman D, Kuchroo VK: Nature Immunol. 2017 Feb 6. doi: 10.1038/ni.3683. Pubmed

Targeting latency-associated peptide promotes anti-tumor immunity.

Gabriely G, Pires da Cunha A, Rezende RM, Kenyon B, Madi A, Vandeventer T, Rubino S, Garo L, Kolypetri P, Lanser A, Moreira T, Caetano Faria AM, Lassmann H, Kuchroo V, Murugaiyan G and Weiner HL: Science Immunol. 2017, 2(11): eaaj1738 Pubmed

Musculin promotes unidirectional development of peripheral Treg by suppressing the Th2 transcriptional program.

Wu C, Chen Z, Dardalhon V,  Xiao S, Thalhamer T, Liao M, Madi A, Franca RF, Han T, Oukka M, and Kuchroo VK: Nature Immunol. 2017 Mar;18(3):344-353. Pubmed

IL-10-dependent Tr1 cells attenuate astrocyte activation and ameliorate chronic central nervous system inflammation.

Mayo L, Pires Da Cunha A, Madi A, Beynon V, Patel B, Alvarez JI, Prat A, Sobel R, Kuchroo KV, Lassmann H, Quintana FJ and Weiner HL: Brain 2016, 139(7):1939-57. Pubmed

TIM3 Mediates T Cell Exhaustion during Mycobacterium tuberculosis Infection.

Jayaraman P, Jacques MK, Zhu C, Steblenko MK, Stowell LB, Madi A, Anderson AC, Kuchroo VK, Behar SM: PLoS Pathog. 2016, 12(3): e1005490. Pubmed

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity.

Wang C, Yosef N, Gaublomme J, Wu C, Lee Y, Clish CB, Kaminski J, Xiao S, Meyer Zu Horste G, Pawlak M, Kishi Y, Joller N, Karwacz K, Zhu C, Ordovas-Montanes M, Madi A, Wortman I, Miyazaki T, Sobel RA, Park H, Regev A, Kuchroo VK: Cell 2015, 163(6):1413-27. Pubmed

Human neonatal thymectomy induces altered B cell auto-reactivity later in life.

van den Broek T, Madi A, Delemarre EM, Schadenberg AWL, Tesselaar K, Borghans JA, Redegeld FA, Otten HG, Sorek R, Prakken B, M.D., Cohen IR, Jansen NJG: European Journal of Immunol. 2017, doi: 10.1002/eji.201746971. Pubmed

Tumor-Associated and Disease-Associated Autoantibody Repertoires in Healthy Colostrum and Maternal and Newborn Cord Sera.

Madi A, Bransburg-Zabary S, Maayan-Metzger A, Dar G, Ben-Jacob E, Cohen IR: J Immunol. 2015, 194(11):5272-81. Pubmed


T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity.

Madi A*, Shifrut E*, Reich-Zeliger S, Gal H, Best K, Ndifon W, Chain B, Cohen IR, Friedman N: Genome Res. 2014, 24(10):1603-12. (* equal contribution) Pubmed


Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence.

Thomas N, Best K, Cinelli M, Reich-Zeliger S, Gal H, Shifrut E, Madi A, Friedman N, Shawe-Taylor J, Chain B: Bioinformatics. 2014, 30(22):3181-8. Pubmed

Analyses of antigen dependency networks unveil immune system reorganization between birth and adulthood.

Madi A, Kenett DY, Bransburg-Zabary S, Merbl Y, Quintana FJ, Boccaletti S, Tauber AI, Cohen IR, Ben-Jacob E: Chaos 2011, 21(1):016109. Pubmed


Network theory analysis of antibody-antigen reactivity data: the immune trees at birth and adulthood.

Madi A, Kenett DY, Bransburg-Zabary S, Merbl Y, Quintana FJ, Tauber AI, Cohen IR, Ben-Jacob E: PLoS One 2011, 6(3):e17445. Pubmed

Organization of the autoantibody repertoire in healthy newborns and adults revealed by system level informatics of antigen microarray data.

Madi A, Hecht I, Bransburg-Zabary S, Merbl Y, Pick A, Zucker-Toledano M, Quintana FJ, Tauber AI, Cohen IR, Ben-Jacob E: Proc Natl Acad Sci U S A 2009, 106(34):14484-14489. Pubmed

Genome holography: deciphering function-form motifs from gene expression data.

Madi A, Friedman Y, Roth D, Regev T, Bransburg-Zabary S, Ben Jacob E: PLoS One 2008, 3(7):e2708. Pubmed