FY 2024 Publications
Acute and persistent responses after H5N1 vaccination in humans.
Apps R, Biancotto A, Candia J, Kotliarov Y, Perl S, Cheung F, Farmer R, Mulè MP, Rachmaninoff N, Chen J, Martins AJ, Shi R, Zhou H, Bansal N, Schum P, Olnes MJ, Milanez-Almeida P, Han KL, Sellers B, Cortese M, Hagan T, Rouphael N, Pulendran B, King L, Manischewitz J, Khurana S, Golding H, van der Most RG, Dickler HB, Germain RN, Schwartzberg PL, Tsang JS. Cell Rep. 2024 Sep 4;43(9):114706. doi: 10.1016/j.celrep.2024.114706. Epub ahead of print. PMID: 39235945.
A unified metric of human immune health.
Sparks R, Rachmaninoff N, Lau WW, Hirsch DC, Bansal N, Martins AJ, Chen J, Liu CC, Cheung F, Failla LE, Biancotto A, Fantoni G, Sellers BA, Chawla DG, Howe KN, Mostaghimi D, Farmer R, Kotliarov Y, Calvo KR, Palmer C, Daub J, Foruraghi L, Kreuzburg S, Treat JD, Urban AK, Jones A, Romeo T, Deuitch NT, Moura NS, Weinstein B, Moir S, Ferrucci L, Barron KS, Aksentijevich I, Kleinstein SH, Townsley DM, Young NS, Frischmeyer-Guerrerio PA, Uzel G, Pinto-Patarroyo GP, Cudrici CD, Hoffmann P, Stone DL, Ombrello AK, Freeman AF, Zerbe CS, Kastner DL, Holland SM, Tsang JS. Nat Med. 2024 Jul 3. doi: 10.1038/s41591-024-03092-6. Epub ahead of print. PMID: 38961223.
Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint.
Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers BA, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Immunity. 2024 May 14;57(5):1160-1176.e7. doi: 10.1016/j.immuni.2024.04.009. Epub 2024 May 1. PMID: 38697118
Deep phenotyping of post-infectious myalgic encephalomyelitis/chronic fatigue syndrome.
Walitt B, Singh K, LaMunion SR, Hallett M, Jacobson S, Chen K, Enose-Akahata Y, Apps R, Barb JJ, Bedard P, Brychta RJ, Buckley AW, Burbelo PD, Calco B, Cathay B, Chen L, Chigurupati S, Chen J, Cheung F, Chin LMK, Coleman BW, Courville AB, Deming MS, Drinkard B, Feng LR, Ferrucci L, Gabel SA, Gavin A, Goldstein DS, Hassanzadeh S, Horan SC, Horovitz SG, Johnson KR, Govan AJ, Knutson KM, Kreskow JD, Levin M, Lyons JJ, Madian N, Malik N, Mammen AL, McCulloch JA, McGurrin PM, Milner JD, Moaddel R, Mueller GA, Mukherjee A, Muñoz-Braceras S, Norato G, Pak K, Pinal-Fernandez I, Popa T, Reoma LB, Sack MN, Safavi F, Saligan LN, Sellers BA, Sinclair S, Smith B, Snow J, Solin S, Stussman BJ, Trinchieri G, Turner SA, Vetter CS, Vial F, Vizioli C, Williams A, Yang SB; Center for Human Immunology, Autoimmunity, and Inflammation (CHI) Consortium; Nath A. Nat Commun. 2024 Feb 21;15(1):907. doi: 10.1038/s41467-024-45107-3. PMID: 38383456; PMCID: PMC10881493.
Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans. Link VM, Subramanian P, Cheung F, Han KL, Stacy A, Chi L, Sellers BA, Koroleva G, Courville AB, Mistry S, Burns A, Apps R, Hall KD, Belkaid Y. Nat Med. 2024 Jan 30. doi: 10.1038/s41591-023-02761-2. Epub ahead of print. PMID: 38291301.
FY 2023 Publications
Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19.
Sparks R, Lau WW, Liu C, Han KL, Vrindten KL, Sun G, Cox M, Andrews SF, Bansal N, Failla LE, Manischewitz J, Grubbs G, King LR, Koroleva G, Leimenstoll S, Snow L, Chen J, Tang J, Mukherjee A, Sellers BA, Apps R, McDermott AB, Martins AJ, Bloch EM, Golding H, Khurana S, Tsang JS. Nature. 2023 Jan 4;. doi: 10.1038/s41586-022-05670-5. [Epub ahead of print] PubMed PMID: 36599369.
Adaptive immune responses to SARS-CoV-2 in the oropharyngeal lymphoid tissue of children.
Xu Q, Milanez-Almeida P, Martins AJ, Radtke AJ, Hoehn KB, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker PC, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain IT, Pittaluga S, Germain RN, Apps R, Sadtler K, Moir S, Chertow DS, Kleinstein SH, Khurana S, Tsang JS, Mudd P, Schwartzberg PL, Manthiram K. Nat Immunol. 2022 Dec 19;: PMID: 35350206; PMCID: PMC8963700.
Sex and prior exposure jointly shape innate immune responses to a live herpesvirus vaccine.
Cheung F, Apps R, Dropulic L, Kotliarov Y, Chen J, Jordan T, Langweiler M, Candia J, Biancotto A, Han KL, Rachmaninoff N, Pietz H, Wang K, Tsang JS, Cohen JI. Elife. 2023 Jan 17;12:e80652. doi: 10.7554/eLife.80652. PMID: 36648132; PMCID: PMC9844983.
Inflammatory and interferon gene expression signatures in patients with mitochondrial disease.
Warren EB, Gordon-Lipkin EM, Cheung F, Chen J, Mukherjee A, Apps R, Tsang JS, Jetmore J, Schlein ML, Kruk S, Lei Y, West AP, McGuire PJ. J Transl Med. 2023 May 19;21(1):331. doi: 10.1186/s12967-023-04180-w. PMID: 37208779; PMCID: PMC10199642.
Multiscale integration of human and single-cell variations reveals unadjuvanted vaccine high responders are naturally adjuvanted.
Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers B, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. medRxiv [Preprint]. 2023 Mar 20:2023.03.20.23287474. doi: 10.1101/2023.03.20.23287474. PMID: 37090674; PMCID: PMC10120791.
Tracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine.
Lopes de Assis F, Hoehn KB, Zhang X, Kardava L, Smith CD, El Merhebi O, Buckner CM, Trihemasava K, Wang W, Seamon CA, Chen V, Schaughency P, Cheung F, Martins AJ, Chiang CI, Li Y, Tsang JS, Chun TW, Kleinstein SH, Moir S. Cell Rep. 2023 Jul 25;42(7):112780. doi: 10.1016/j.celrep.2023.112780. Epub 2023 Jul 12. PMID: 37440409.
FY 2022 Publications
Peroxisome proliferator activated receptor-γ agonist pioglitazone improvesvascular and metabolic dysfunction in systemic lupus erythematosus.
Hasni S, Temesgen-Oyelakin Y, Davis M, Chu J, Poncio E, Naqi M, Gupta S, Wang X, Oliveira C,Claybaugh D, Dey A, Lu S, Carlucci P, Purmalek M, Manna ZG, Shi Y, Ochoa-Navas I, Chen J,Mukherjee A, Han KL, Cheung F, Koroleva G, Belkaid Y, Tsang JS, Apps R, et al. [7 more authors] (2022) Ann Rheum Dis, in press(e-pub ahead of print).
HLA-B∗46 associates with rapid HIV disease progression in Asian cohorts and prominent differences in NK cell phenotype.
Li SS, Hickey A, Shangguan S, Ehrenberg PK, Geretz A, Butler L, Kundu G, Apps R, Creegan M,Clifford RJ, Pinyakorn S, Eller LA, Luechai P, Gilbert PB, Holtz TH, Chitwarakorn A, Sacdalan C,Kroon E, Phanuphak N, de Souza M, Ananworanich J, O'Connell RJ, Robb ML, Michael NL, VasanS, et al. [1 more author] (2022). Cell Host Microbe 30, 1173-1185.e8.
Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19.
Sacco K, Castagnoli R, Vakkilainen S, Liu C, Delmonte OM, Oguz C, Kaplan IM, Alehashemi S,Burbelo PD, Bhuyan F, de Jesus AA, Dobbs K, Rosen LB, Cheng A, Shaw E, Vakkilainen MS, PalaF, Lack J, Zhang Y, Fink DL, Oikonomou V, Snow AL, Dalgard CL, Chen J, Sellers BA, NIAIDImmune Response to COVID Group, Chile MIS-C Group, Pavia Pediatric COVID-19 Group, et al.[37 more authors] (2022). Nat Med 28, 1050-1062.
FY 2021 Publications
Identification and Validation of Nutrient State-Dependent Serum Protein Mediators of Human CD4+ T Cell Responsiveness.
Han K, Singh K, Rodman MJ,et al. Nutrients. 2021 Apr 28;13(5):1492. doi: 10.3390/nu13051492. PMID: 33924911.
Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics.
Kotliar D, Lin AE, Logue J, et al. Cell. 2020 Nov 25;183(5):1383-1401.e19. doi: 10.1016/j.cell.2020.10.002. Epub 2020 Nov 6. PMID: 33159858; PMCID: PMC7707107.
Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19.
Liu C, Martins AJ, Lau WW, et al. Cell. 2021 Feb 10:S0092-8674(21)00168-9. doi: 10.1016/j.cell.2021.02.018. Epub ahead of print. PMID: 33713619; PMCID: PMC7874909.
The complement pathway is activated in people with HIV and is associated with non-AIDS comorbidities.
Vujkovic-Cvijin I, Sortino O, Verheij E, et al. J Infect Dis. 2021 Feb 19:jiab096. doi: 10.1093/infdis/jiab096. Epub ahead of print. PMID: 33606018.
Broadly effective metabolic and immune recovery with C5 inhibition in CHAPLE disease.
Ozen A, Kasap N, Vujkovic-Cvijin I, et al. Nat Immunol. 2021 Feb;22(2):128-139. doi: 10.1038/s41590-020-00830-z. Epub 2021 Jan 4. PMID: 33398182; PMCID: PMC7856263.
Fasting-induced FOXO4 blunts human CD4+ T helper cell responsiveness.
Han K, Singh K, Rodman MJ, et al. Nat Metab. 2021 Mar 15. doi: 10.1038/s42255-021-00356-0. Epub ahead of print. PMID: 33723462.
Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children.
Anjali Ramaswamy, Nina N. Brodsky, Tomokazu S. Sumida, et al. Immunity. 2021 Apr 13. doi: 10.1016/j.immuni.2021.04.003. Online ahead of print. PMID: 33891889
Phase 1 double-blind randomized safety trial of the Janus kinase inhibitor tofacitinib in systemic lupus erythematosus.
Hasni SA, Gupta S, Davis M, et al. Nat Commun. 2021 Jun 7;12(1):3391. doi: 10.1038/s41467-021-23361-z. PubMed PMID: 34099646
HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases.
Vujkovic-Cvijin I, Sortino O, Verheij E, et al. Nat Commun 11, 2448. https://doi.org/10.1038/s41467-020-16222-8
Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota.
Lima-Junior DS, Krishnamurthy SR, Bouladoux N,et al. Cell. 2021 Jul 8;184(14):3794-3811.e19. doi: 10.1016/j.cell.2021.05.020. Epub 2021 Jun 23. PMID: 34166614; PMCID: PMC8381240.
Immunopathological signatures in multisystem inflammatorysyndrome in children and pediatric COVID-19.
Sacco K, Castagnoli R, Vakkilainen S, Liu C, Delmonte OM, Oguz C, Kaplan IM, Alehashemi S,Burbelo PD, Bhuyan F, de Jesus AA, Dobbs K, Rosen LB, Cheng A, Shaw E, Vakkilainen MS, PalaF, Lack J, Zhang Y, Fink DL, Oikonomou V, Snow AL, Dalgard CL, Chen J, Sellers BA, NIAID Immune Response to COVID Group, Chile MIS-C Group, Pavia Pediatric COVID-19 Group, et al.[37 more authors] (2022). Nat Med 28, 1050-1062.
FY 2020 Publications
Multimodal immune phenotyping of maternal peripheral blood in normal human pregnancy. Apps R, Kotliarov Y, Cheung F, Han KL, Chen J, Biancotto A, Babyak A, Zhou H, Shi R, Barnhart L,Osgood SM, Belkaid Y, Holland SM, Tsang JS, Zerbe CS (2020). JCI Insight 5. https://doi.org/10.1172/jci.insight.134838
Colchicine’s effects on metabolic and inflammatory molecules in adults with obesity and metabolic syndrome: results from a pilot randomized controlled trial.
Demidowich, A.P., Levine, J.A., Apps, R. et al. Int J Obes 44, 1793–1799 (2020).
Convergent Evolution of HLA-C Downmodulation in HIV-1 and HIV-2.
Hopfensperger K, Richard J, Stürzel CM, Bibollet-Ruche F, Apps R, Leoz M, Plantier JC, Hahn BH, Finzi A, Kirchhoff F, Sauter D (2020). mBio 11.
Effects of rosuvastatin on the immune system in healthy volunteers with normal serum cholesterol.
Karmaus PW, Shi M, Perl S, Biancotto A, Candia J, Cheung F, Kotliarov Y, Young N, Fessler MB, CHI Consortium (2019). JCI Insight 4.
Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus.
Kotliarov Y, Sparks R, Martins AJ, Mulè MP, Lu Y, Goswami M, Kardava L, Banchereau R, Pascual V, Biancotto A, Chen J, Schwartzberg PL, Bansal N, Liu CC, Cheung F, Moir S, Tsang JS (2020). Nat Med 26, 618-629.
Cancer prognosis with shallow tumor RNA sequencing.
Milanez-Almeida P, Martins AJ, Germain RN, Tsang JS (2020).Nat Med 26, 188-192.
Maternal determinants of infant immunity: Implications for effective immunization and maternal-child health.
Pasetti MF, Ackerman ME, Hoen AG, Alter G, Tsang JS, Marchant A (2020). Vaccine 38, 4491-4494.
Defective glycosylation and multisystem abnormalities characterize the primary immunodeficiency XMEN disease.
Ravell JC, Matsuda-Lennikov M, Chauvin SD, Zou J, Biancalana M, Deeb SJ, Price S, Su HC, Notarangelo G, Jiang P, Morawski A, Kanellopoulou C, Binder K, Mukherjee R, Anibal JT, Sellers B, Zheng L, He T, George AB, Pittaluga S, Powers A, Kleiner DE, Kapuria D, Ghany M, Hunsberger S, et al. [29 more authors] (2019). J Clin Invest 130, 507-522.
Improving Vaccine-Induced Immunity: Can Baseline Predict Outcome?
Tsang JS, Dobaño C, VanDamme P, Moncunill G, Marchant A, Othman RB, Sadarangani M, Koff WC, Kollmann TR (2020). Trends Immunol 41, 457-465.
HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases.
Vujkovic-Cvijin I, Sortino O, Verheij E, Sklar J, Wit FW, Kootstra NA, Sellers B, Brenchley JM, Ananworanich J, Loeff MSV, Belkaid Y, Reiss P, Sereti I (2020). Nat Commun 11, 2448.
Sequencing of RNA in single cells reveals a distinct transcriptome signature of hematopoiesis in GATA2 deficiency.
Wu Z, Gao S, Diamond C, Kajigaya S, Chen J, Shi R, Palmer C, Hsu AP, Calvo KR, Hickstein DD, Holland SM, Young NS (2020). Blood Adv 4, 2656-2670.
Highly multiplexed proteomic assessment of human bone marrow in acute myeloid leukemia.
Çelik H, Lindblad KE, Popescu B, Gui G, Goswami M, Valdez J, DeStefano C, Lai C, Thompson J, Ghannam JY, Fantoni G, Biancotto A, Candia J, Cheung F, Sukumar G, Dalgard CL, Smith RH, Larochelle A, Dillon LW, Hourigan CS (2020). Blood Adv 4, 367-379.