Publications

A selection of recent and significant publications can be viewed below.

Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark.

Wang L, Pattnaik A, Sahoo SS, Stone EG, Zhuang Y, Benton A, Tajmul M, Chakravorty S, Dhawan D, Nguyen MA, Sirit I, Mundy K, Ricketts CJ, Hadisurya M, Baral G, Tinsley SL, Anderson NL, Hoda S, Briggs SD, Kaimakliotis HZ, Allen-Petersen BL, Tao WA, Linehan WM, Knapp DW, Hanna JA, Olson MR, Afzali B, Kazemian M.

Nat Commun (2024 Aug 24) 15:7288. Abstract/Full Text

The Role of Interferon-γ in Autoimmune Polyendocrine Syndrome Type 1.

Oikonomou V, Smith G, Constantine GM, Schmitt MM, Ferré EMN, Alejo JC, Riley D, Kumar D, Dos Santos Dias L, Pechacek J, Hadjiyannis Y, Webb T, Seifert BA, Ghosh R, Walkiewicz M, Martin D, Besnard M, Snarr BD, Deljookorani S, Lee CR, DiMaggio T, Barber P, Rosen LB, Cheng A, Rastegar A, de Jesus AA, Stoddard J, Kuehn HS, Break TJ, Kong HH, Castelo-Soccio L, Colton B, Warner BM, Kleiner DE, Quezado MM, Davis JL, Fennelly KP, Olivier KN, Rosenzweig SD, Suffredini AF, Anderson MS, Swidergall M, Guillonneau C, Notarangelo LD, Goldbach-Mansky R, Neth O, Monserrat-Garcia MT, Valverde-Fernandez J, Lucena JM, Gomez-Gila AL, Garcia Rojas A, Seppänen MRJ, Lohi J, Hero M, Laakso S, Klemetti P, Lundberg V, Ekwall O, Olbrich P, Winer KK, Afzali B, Moutsopoulos NM, Holland SM, Heller T, Pittaluga S, Lionakis MS.

N Engl J Med (2024 May 30) 390:1873-1884. Abstract/Full Text

The role of transcription factors in shaping regulatory T cell identity.

Trujillo-Ochoa JL, Kazemian M, Afzali B.

Nat Rev Immunol (2023 Dec) 23:842-856. Abstract/Full Text

Predictors and significance of kidney dysfunction in patients with chronic graft-versus-host disease.

Beshensky D, Pirsl F, Holtzman NG, Steinberg SM, Mays JW, Cowen EW, Comis LE, Joe GO, Magone MT, Schulz E, Waldman MA, Pavletic SZ.

Bone Marrow Transplant (2023 Oct) 58:1112-1120. Abstract/Full Text

Preexisting Autoimmunity Is Associated With Increased Severity of Coronavirus Disease 2019: A Retrospective Cohort Study Using Data From the National COVID Cohort Collaborative (N3C).

Yadaw AS, Sahner DK, Sidky H, Afzali B, Hotaling N, Pfaff ER, Mathé EA.

Clin Infect Dis (2023 Sep 18) 77:816-826. Abstract/Full Text

Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

West EE, Merle NS, Kamiński MM, Palacios G, Kumar D, Wang L, Bibby JA, Overdahl K, Jarmusch AK, Freeley S, Lee DY, Thompson JW, Yu ZX, Taylor N, Sitbon M, Green DR, Bohrer A, Mayer-Barber KD, Afzali B, Kazemian M, Scholl-Buergi S, Karall D, Huemer M, Kemper C.

Immunity (2023 Sep 12) 56:2036-2053.e12. Abstract/Full Text

In vivo Polycystin-1 interactome using a novel Pkd1 knock-in mouse model.

Lin CC, Menezes LF, Qiu J, Pearson E, Zhou F, Ishimoto Y, Anderson DE, Germino GG.

PLoS One (2023) 18:e0289778. Abstract/Full Text

Transcription factor EGR2 controls homing and pathogenicity of T(H)17 cells in the central nervous system.

Gao Y, Wang Y, Chauss D, Villarino AV, Link VM, Nagashima H, Spinner CA, Koparde VN, Bouladoux N, Abers MS, Break TJ, Chopp LB, Park JH, Zhu J, Wiest DL, Leonard WJ, Lionakis MS, O'Shea JJ, Afzali B, Belkaid Y, Lazarevic V.

Nat Immunol (2023 Aug) 24:1331-1344. Abstract/Full Text

C5a-licensed phagocytes drive sterilizing immunity during systemic fungal infection.

Desai JV, Kumar D, Freiwald T, Chauss D, Johnson MD, Abers MS, Steinbrink JM, Perfect JR, Alexander B, Matzaraki V, Snarr BD, Zarakas MA, Oikonomou V, Silva LM, Shivarathri R, Beltran E, Demontel LN, Wang L, Lim JK, Launder D, Conti HR, Swamydas M, McClain MT, Moutsopoulos NM, Kazemian M, Netea MG, Kumar V, Köhl J, Kemper C, Afzali B, Lionakis MS.

Cell (2023 Jun 22) 186:2802-2822.e22. Abstract/Full Text

Mechanisms of Cyst Development in Polycystic Kidney Disease.

Qiu J, Germino GG, Menezes LF.

Adv Kidney Dis Health (2023 May) 30:209-219. Abstract/Full Text

Prediagnostic Appearance of Thrombospondin Type-1 Domain 7A Autoantibodies in Membranous Nephropathy.

Burbelo PD, Olson SW, Keller JM, Joshi M, Schwartz DM, Chuang YJ, Lambeau G, Beck LH Jr, Waldman M.

Kidney360 (2023 Feb 1) 4:217-225. Abstract/Full Text

Pregnancy History and Kidney Disease Progression Among Women Enrolled in Cure Glomerulonephropathy.

Reynolds ML, Oliverio AL, Zee J, Hendren EM, O'Shaughnessy MM, Ayoub I, Almaani S, Vasylyeva TL, Twombley KE, Wadhwani S, Steinke JM, Rizk DV, Waldman M, Helmuth ME, Avila-Casado C, Alachkar N, Nester CM, Derebail VK, Hladunewich MA, Mariani LH.

Kidney Int Rep (2023 Apr) 8:805-817. Abstract/Full Text

A comprehensive single cell data analysis of lymphoblastoid cells reveals the role of super-enhancers in maintaining EBV latency.

Yan B, Wang C, Chakravorty S, Zhang Z, Kadadi SD, Zhuang Y, Sirit I, Hu Y, Jung M, Sahoo SS, Wang L, Shao K, Anderson NL, Trujillo-Ochoa JL, Briggs SD, Liu X, Olson MR, Afzali B, Zhao B, Kazemian M.

J Med Virol (2023 Jan) 95:e28362. Abstract/Full Text

Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations.

Kumar D, Sahoo SS, Chauss D, Kazemian M, Afzali B.

J Autoimmun (2023 Jan) 134:102982. Abstract/Full Text

A central role for STAT5 in the transcriptional programing of T helper cell metabolism.

Villarino AV, Laurence AD, Davis FP, Nivelo L, Brooks SR, Sun HW, Jiang K, Afzali B, Frasca D, Hennighausen L, Kanno Y, O'Shea JJ.

Sci Immunol (2022 Nov 25) 7:eabl9467. Abstract/Full Text

Systematic single-cell pathway analysis to characterize early T cell activation.

Bibby JA, Agarwal D, Freiwald T, Kunz N, Merle NS, West EE, Singh P, Larochelle A, Chinian F, Mukherjee S, Afzali B, Kemper C, Zhang NR.

Cell Rep (2022 Nov 22) 41:111697. Abstract/Full Text

EBV-associated diseases: Current therapeutics and emerging technologies.

Chakravorty S, Afzali B, Kazemian M.

Front Immunol (2022) 13:1059133. Abstract/Full Text

Potential for false decline of anti-SARS-CoV-2 spike antibody titers after COVID-19 vaccination.

Waldman M, Sacks DB, Howard L, Cole J.

Lancet Rheumatol (2022 Sep) 4:e586-e587. Abstract/Full Text

1,25-Dihydroxyvitamin D3 suppresses CD4(+) T-cell effector functionality by inhibition of glycolysis.

Bishop EL, Gudgeon NH, Mackie GM, Chauss D, Roberts J, Tennant DA, Maslowski KM, Afzali B, Hewison M, Dimeloe S.

Immunology (2022 Jul) 166:299-309. Abstract/Full Text

Folic acid-mediated fibrosis is driven by C5a receptor 1-mediated activation of kidney myeloid cells.

Sahu RK, Xavier S, Chauss D, Wang L, Chew C, Taylor R, Stallcup WB, Ma JZ, Kazemian M, Afzali B, Köhl J, Portilla D.

Am J Physiol Renal Physiol (2022 Jun 1) 322:F597-F610. Abstract/Full Text

Structural determinants of the dominant conformational epitopes of phospholipase A2 receptor in primary membranous nephropathy.

Tang H, Zhu R, Waldman M, Zhu Q.

J Biol Chem (2022 Mar) 298:101605. Abstract/Full Text

The state of complement in COVID-19.

Afzali B, Noris M, Lambrecht BN, Kemper C.

Nat Rev Immunol (2022 Feb) 22:77-84. Abstract/Full Text

Reply to Grigoriev et al., "Sequences of SARS-CoV-2 'Hybrids' with the Human Genome: Signs of Non-coding RNA?".

Yan B, Chakravorty S, Mirabelli C, Wang L, Trujillo-Ochoa JL, Chauss D, Kumar D, Lionakis MS, Olson MR, Wobus CE, Afzali B, Kazemian M.

J Virol (2022 Jan 26) 96:e0169021. Abstract/Full Text

A Novel Predictive Model for Hospital Survival in Patients who are Critically Ill with Dialysis-Dependent AKI: A Retrospective Single-Center Exploratory Study.

Ganguli A, Farooq S, Desai N, Adhikari S, Shah V, Sherman MJ, Veis JH, Moore J.

Kidney360 (2022 Apr 28) 3:636-646. Abstract/Full Text

Autocrine vitamin D signaling switches off pro-inflammatory programs of T(H)1 cells.

Chauss D, Freiwald T, McGregor R, Yan B, Wang L, Nova-Lamperti E, Kumar D, Zhang Z, Teague H, West EE, Vannella KM, Ramos-Benitez MJ, Bibby J, Kelly A, Malik A, Freeman AF, Schwartz DM, Portilla D, Chertow DS, John S, Lavender P, Kemper C, Lombardi G, Mehta NN, Cooper N, Lionakis MS, Laurence A, Kazemian M, Afzali B.

Nat Immunol (2022 Jan) 23:62-74. Abstract/Full Text

Mitochondrial C5aR1 activity in macrophages controls IL-1β production underlying sterile inflammation.

Niyonzima N, Rahman J, Kunz N, West EE, Freiwald T, Desai JV, Merle NS, Gidon A, Sporsheim B, Lionakis MS, Evensen K, Lindberg B, Skagen K, Skjelland M, Singh P, Haug M, Ruseva MM, Kolev M, Bibby J, Marshall O, O'Brien B, Deeks N, Afzali B, Clark RJ, Woodruff TM, Pryor M, Yang ZH, Remaley AT, Mollnes TE, Hewitt SM, Yan B, Kazemian M, Kiss MG, Binder CJ, Halvorsen B, Espevik T, Kemper C.

Sci Immunol (2021 Dec 24) 6:eabf2489. Abstract/Full Text

COVID-19 in Patients with Glomerular Disease: Follow-Up Results from the IRoc-GN International Registry.

Waldman M, Soler MJ, García-Carro C, Lightstone L, Turner-Stokes T, Griffith M, Torras J, Martinez Valenzuela L, Bestard O, Geddes C, Flossmann O, Budge KL, Cantarelli C, Fiaccadori E, Delsante M, Morales E, Gutierrez E, Niño-Cruz JA, Martinez-Rueda AJ, Comai G, Bini C, La Manna G, Slon MF, Manrique J, Avello A, Fernandez-Prado R, Ortiz A, Marinaki S, Martin Varas CR, Rabasco Ruiz C, Sierra-Carpio M, García-Agudo R, Fernández Juárez G, Hamilton AJ, Bruchfeld A, Chrysochou C, Howard L, Sinha S, Leach T, Agraz Pamplona I, Maggiore U, Cravedi P.

Kidney360 (2022 Feb 24) 3:293-306. Abstract/Full Text

Parathyroid Hormone Resistance and Autoantibodies to the PTH1 Receptor.

Mandl A, Burbelo PD, Di Pasquale G, Tay YS, Welch J, Lionakis MS, Rosenzweig SD, Waldman MA, Warner BM, Walitt B, Collins MT, Balow JE, Chiorini JA, Simonds WF, Agarwal SK, Blau JE, Weinstein LS.

N Engl J Med (2021 Nov 18) 385:1974-1980. Abstract/Full Text

Combined Immunosuppressive Therapy for Severe Graves Dermopathy.

Gubbi S, Araque KA, Avadhanula S, Azam A, Merkel R, Cochran C, Burbelo PD, Waldman M, Neumann S, Gershengorn MC, Skarulis M, Klubo-Gwiezdzinska J.

Ann Intern Med (2021 Oct) 174:1478-1480. Abstract/Full Text

Response to Comments on "Aberrant type 1 immunity drives susceptibility to mucosal fungal infections".

Break TJ, Oikonomou V, Dutzan N, Desai JV, Swidergall M, Freiwald T, Chauss D, Harrison OJ, Alejo J, Williams DW, Pittaluga S, Lee CR, Bouladoux N, Swamydas M, Hoffman KW, Greenwell-Wild T, Bruno VM, Rosen LB, Lwin W, Renteria A, Pontejo SM, Shannon JP, Myles IA, Olbrich P, Ferré EMN, Schmitt M, Martin D, Genomics and Computational Biology Core16, Barber DL, Solis NV, Notarangelo LD, Serreze DV, Matsumoto M, Hickman HD, Murphy PM, Anderson MS, Lim JK, Holland SM, Filler SG, Afzali B, Belkaid Y, Moutsopoulos NM, Lionakis MS.

Science (2021 Sep 17) 373:eabi8835. Abstract/Full Text

Host-Virus Chimeric Events in SARS-CoV-2-Infected Cells Are Infrequent and Artifactual.

Yan B, Chakravorty S, Mirabelli C, Wang L, Trujillo-Ochoa JL, Chauss D, Kumar D, Lionakis MS, Olson MR, Wobus CE, Afzali B, Kazemian M.

J Virol (2021 Jul 12) 95:e0029421. Abstract/Full Text

A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis.

Disatham J, Brennan L, Chauss D, Kantorow J, Afzali B, Kantorow M.

BMC Genomics (2021 Jul 3) 22:497. Abstract/Full Text

Acute glomerulonephritis in a hematopoietic blood stem cell donor.

Chandra P, Dahiya S, Sanchez-Petitto G, Malik J, Bolanos J, Haririan A, Weir M, Drachenberg C, Rapoport A.

Clin Nephrol Case Stud (2021) 9:81-86. Abstract/Full Text

Fibroblast tissue priming-not so nice to C you!

Afzali B, Kemper C.

Immunity (2021 May 11) 54:847-850. Abstract/Full Text

COVID-19 vaccines and kidney disease.

Windpessl M, Bruchfeld A, Anders HJ, Kramer H, Waldman M, Renia L, Ng LFP, Xing Z, Kronbichler A.

Nat Rev Nephrol (2021 May) 17:291-293. Abstract/Full Text

SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation.

Yan B, Freiwald T, Chauss D, Wang L, West E, Mirabelli C, Zhang CJ, Nichols EM, Malik N, Gregory R, Bantscheff M, Ghidelli-Disse S, Kolev M, Frum T, Spence JR, Sexton JZ, Alysandratos KD, Kotton DN, Pittaluga S, Bibby J, Niyonzima N, Olson MR, Kordasti S, Portilla D, Wobus CE, Laurence A, Lionakis MS, Kemper C, Afzali B, Kazemian M.

Sci Immunol (2021 Apr 7) 6. Abstract/Full Text

Author Correction: BACH2 enforces the transcriptional and epigenetic programs of stem-like CD8(+) T cells.

Yao C, Lou G, Sun HW, Zhu Z, Sun Y, Chen Z, Chauss D, Moseman EA, Cheng J, D'Antonio MA, Shi W, Shi J, Kometani K, Kurosaki T, Wherry EJ, Afzali B, Gattinoni L, Zhu Y, McGavern DB, O'Shea JJ, Schwartzberg PL, Wu T.

Nat Immunol (2021 Apr) 22:530. Abstract/Full Text

MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23.

Mikami Y, Philips RL, Sciumè G, Petermann F, Meylan F, Nagashima H, Yao C, Davis FP, Brooks SR, Sun HW, Takahashi H, Poholek AC, Shih HY, Afzali B, Muljo SA, Hafner M, Kanno Y, O'Shea JJ.

Immunity (2021 Mar 9) 54:514-525.e6. Abstract/Full Text

Recurrent Hyperkalemia in Renin-Angiotensin-Aldosterone System Inhibitor (RAASi) Treatment: Stuck between a Rock and a Hard Place.

Bolaños JA, Seliger SL.

Clin J Am Soc Nephrol (2021 Mar 8) 16:345-347. Abstract/Full Text

BACH2 enforces the transcriptional and epigenetic programs of stem-like CD8(+) T cells.

Yao C, Lou G, Sun HW, Zhu Z, Sun Y, Chen Z, Chauss D, Moseman EA, Cheng J, D'Antonio MA, Shi W, Shi J, Kometani K, Kurosaki T, Wherry EJ, Afzali B, Gattinoni L, Zhu Y, McGavern DB, O'Shea JJ, Schwartzberg PL, Wu T.

Nat Immunol (2021 Mar) 22:370-380. Abstract/Full Text

Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual.

Yan B, Chakravorty S, Mirabelli C, Wang L, Trujillo-Ochoa JL, Chauss D, Kumar D, Lionakis MS, Olson MR, Wobus CE, Afzali B, Kazemian M.

bioRxiv (2021 Feb 17) Abstract/Full Text

Lupus-like autoimmunity and increased interferon response in patients with STAT3-deficient hyper-IgE syndrome.

Goel RR, Nakabo S, Dizon BLP, Urban A, Waldman M, Howard L, Darnell D, Buhaya M, Carmona-Rivera C, Hasni S, Kaplan MJ, Freeman AF, Gupta S.

J Allergy Clin Immunol (2021 Feb) 147:746-749.e9. Abstract/Full Text

Aberrant type 1 immunity drives susceptibility to mucosal fungal infections.

Break TJ, Oikonomou V, Dutzan N, Desai JV, Swidergall M, Freiwald T, Chauss D, Harrison OJ, Alejo J, Williams DW, Pittaluga S, Lee CR, Bouladoux N, Swamydas M, Hoffman KW, Greenwell-Wild T, Bruno VM, Rosen LB, Lwin W, Renteria A, Pontejo SM, Shannon JP, Myles IA, Olbrich P, Ferré EMN, Schmitt M, Martin D, Genomics and Computational Biology Core, Barber DL, Solis NV, Notarangelo LD, Serreze DV, Matsumoto M, Hickman HD, Murphy PM, Anderson MS, Lim JK, Holland SM, Filler SG, Afzali B, Belkaid Y, Moutsopoulos NM, Lionakis MS.

Science (2021 Jan 15) 371. Abstract/Full Text

Results from the IRoc-GN international registry of patients with COVID-19 and glomerular disease suggest close monitoring.

Waldman M, Soler MJ, García-Carro C, Lightstone L, Turner-Stokes T, Griffith M, Torras J, Valenzuela LM, Bestard O, Geddes C, Flossmann O, Budge KL, Cantarelli C, Fiaccadori E, Delsante M, Morales E, Gutierrez E, Niño-Cruz JA, Martinez-Rueda AJ, Comai G, Bini C, La Manna G, Slon MF, Manrique J, Agraz I, Sinaii N, Cravedi P.

Kidney Int (2021 Jan) 99:227-237. Abstract/Full Text

Renal diseases and the role of complement: Linking complement to immune effector pathways and therapeutics.

Freiwald T, Afzali B.

Adv Immunol (2021) 152:1-81. Abstract/Full Text