Arjun Rustagi, MD, PhD

Assistant Professor

Dr. Arjun Rustagi is dedicated to understanding the early immune responses to infections, and the methods pathogens use to persist despite these responses, in order to inform new prevention and treatment strategies. His research has focused on viral pathogenesis and immunity. He set up the respiratory viral biosafety level 3 (BSL3) program at Stanford in early 2020 in order to study SARS-CoV-2, contributing to several projects in SARS-CoV-2 virology including a study of intact in vitro lung tissue infection. He also protocoled the first peripheral immune profiling study of severe COVID-19. His ongoing interest is in the full spectrum of in vitro respiratory pathogen models, particularly those that recapitulate lung epithelium and mucosal immunity.

Education
Fellowship, 2021 - Infectious Diseases, Stanford University
Internship & Residency, 2018 - Internal Medicine, Stanford University
MD with Honors, 2015 - , University of Washington
PhD, 2013 - Pathobiology, University of Washington
BS, 2005 - Biological Sciences, Stanford University
Honors and Awards
  • ReCAP (Research Career Accelerator Program) Scholar, Stanford University School of Medicine, 2023
  • Chief Fellow, Infectious Diseases Fellowship, Stanford University, 2019
  • Alpha Omega Alpha, University of Washington School of Medicine, 2014
  • Poncin Fellowship for Graduate Training, University of Washington, 2013-2014
  • Service Award, University of Washington School of Medicine, 2013
  • Travel Award, Keystone Symposia X7: HIV Evolution, Genomics and Pathogenesis, Office of AIDS Research Scholarship, 2011
  • Travel Award, American Society for Virology, 2010
  • Turner Society Endowed Fellowship, University of Washington, 2008
Websites
Publications

  1. Carroll TD, Wong T, Morris MK, Di Germanio C, Ma ZM, Stone M, Ball E, Fritts L, Rustagi A, Simmons G, Busch M, Miller CJ. Vaccine-Boosted CCP Decreases Virus Replication and Hastens Resolution of Infection Despite Transiently Enhancing Disease in SARS-CoV-2-Infected Hamsters. Volume 229 of Issue 6. The Journal of infectious diseases 2024. PMID: 38213276


  2. Wu TT, Travaglini KJ, Rustagi A, Xu D, Zhang Y, Andronov L, Jang S, Gillich A, Dehghannasiri R, Martínez-Colón GJ, Beck A, Liu DD, Wilk AJ, Morri M, Trope WL, Bierman R, Weissman IL, Shrager JB, Quake SR, Kuo CS, Salzman J, Moerner WE, Kim PS, Blish CA, Krasnow MA. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. Volume 221 of Issue 6. The Journal of experimental medicine 2024. PMID: 38597954


  3. Westberg M, Su Y, Zou X, Huang P, Rustagi A, Garhyan J, Patel PB, Fernandez D, Wu Y, Hao C, Lo CW, Karim M, Ning L, Beck A, Saenkham-Huntsinger P, Tat V, Drelich A, Peng BH, Einav S, Tseng CK, Blish C, Lin MZ. An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Volume 16 of Issue 738. Science translational medicine 2024. PMID: 38478629


  4. Choi SS, van Unen V, Zhang H, Rustagi A, Alwahabi SA, Santos AJM, Chan JE, Lam B, Solis D, Mah J, Röltgen K, Trope W, Guh-Siesel A, Lin Z, Beck A, Edwards C, Mallajosyula V, Martin BA, Dunn JCY, Shrager J, Baric RA, Pinsky B, Boyd SD, Blish CA, Davis MM, Kuo CJ. Organoid modeling of lung-resident immune responses to SARS-CoV-2 infection. Research square 2023. PMID: 37205380


  5. Cable J, Balachandran S, Daley-Bauer LP, Rustagi A, Antony F, Frere JJ, Strampe J, Kedzierska K, Cannon JL, McGargill MA, Weiskopf D, Mettelman RC, Niessl J, Thomas PG, Briney B, Valkenburg SA, Bloom JD, Bjorkman PJ, Iketani S, Rappazzo CG, Crooks CM, Crofts KF, Pöhlmann S, Krammer F, Sant AJ, Nabel GJ, Schultz-Cherry S. Viral immunity: Basic mechanisms and therapeutic applications-a Keystone Symposia report. Volume 1521 of Issue 1. Annals of the New York Academy of Sciences 2023. PMID: 36718537


  6. Lee MJ, Leong MW, Rustagi A, Beck A, Zeng L, Holmes S, Qi LS, Blish CA. SARS-CoV-2 escapes direct NK cell killing through Nsp1-mediated downregulation of ligands for NKG2D. Volume 41 of Issue 13. Cell reports 2022. PMID: 36543165


  7. Martínez-Colón GJ, Ratnasiri K, Chen H, Jiang S, Zanley E, Rustagi A, Verma R, Chen H, Andrews JR, Mertz KD, Tzankov A, Azagury D, Boyd J, Nolan GP, Schürch CM, Matter MS, Blish CA, McLaughlin TL. SARS-CoV-2 infection drives an inflammatory response in human adipose tissue through infection of adipocytes and macrophages. Volume 14 of Issue 674. Science translational medicine 2022. PMID: 36137009


  8. Ram-Mohan N, Rogers AJ, Blish CA, Nadeau KC, Zudock EJ, Kim D, Quinn JV, Sun L, Liesenfeld O, Stanford COVID-19 Biobank Study Group, Yang S. Using a 29-mRNA Host Response Classifier To Detect Bacterial Coinfections and Predict Outcomes in COVID-19 Patients Presenting to the Emergency Department. Volume 10 of Issue 6. Microbiology spectrum 2022. PMID: 36250865


  9. Richards CM, Jabs S, Qiao W, Varanese LD, Schweizer M, Mosen PR, Riley NM, Klüssendorf M, Zengel JR, Flynn RA, Rustagi A, Widen JC, Peters CE, Ooi YS, Xie X, Shi PY, Bartenschlager R, Puschnik AS, Bogyo M, Bertozzi CR, Blish CA, Winter D, Nagamine CM, Braulke T, Carette JE. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Volume 378 of Issue 6615. Science (New York, N.Y.) 2022. PMID: 36074821


  10. Hagey RJ, Elazar M, Pham EA, Tian S, Ben-Avi L, Bernardin-Souibgui C, Yee MF, Moreira FR, Rabinovitch MV, Meganck RM, Fram B, Beck A, Gibson SA, Lam G, Devera J, Kladwang W, Nguyen K, Xiong A, Schaffert S, Avisar T, Liu P, Rustagi A, Fichtenbaum CJ, Pang PS, Khatri P, Tseng CT, Taubenberger JK, Blish CA, Hurst BL, Sheahan TP, Das R, Glenn JS. Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2. Volume 28 of Issue 9. Nature medicine 2022. PMID: 35982307


  11. Zhu C, Lee JY, Woo JZ, Xu L, Nguyenla X, Yamashiro LH, Ji F, Biering SB, Van Dis E, Gonzalez F, Fox D, Wehri E, Rustagi A, Pinsky BA, Schaletzky J, Blish CA, Chiu C, Harris E, Sadreyev RI, Stanley S, Kauppinen S, Rouskin S, N??r AM. An intranasal ASO therapeutic targeting SARS-CoV-2. Nature communications 2022. PMID: 35922434


  12. Biering SB, Sarnik SA, Wang E, Zengel JR, Leist SR, Schäfer A, Sathyan V, Hawkins P, Okuda K, Tau C, Jangid AR, Duffy CV, Wei J, Gilmore RC, Alfajaro MM, Strine MS, Nguyenla X, Van Dis E, Catamura C, Yamashiro LH, Belk JA, Begeman A, Stark JC, Shon DJ, Fox DM, Ezzatpour S, Huang E, Olegario N, Rustagi A, Volmer AS, Livraghi-Butrico A, Wehri E, Behringer RR, Cheon DJ, Schaletzky J, Aguilar HC, Puschnik AS, Button B, Pinsky BA, Blish CA, Baric RS, O'Neal WK, Bertozzi CR, Wilen CB, Boucher RC, Carette JE, Stanley SA, Harris E, Konermann S, Hsu PD. Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection. Volume 54 of Issue 8. Nature genetics 2022. PMID: 35879412


  13. Jia X, Cao S, Lee AS, Manohar M, Sindher SB, Ahuja N, Artandi M, Blish CA, Blomkalns AL, Chang I, Collins WJ, Desai M, Din HN, Do E, Fernandes A, Geng LN, Rosenberg-Hasson Y, Mahoney MR, Glascock AL, Chan LY, Fong SY, CLIAHUB Consortium, Chan Zuckerberg Biohub, Phelps M, Raeber O, Stanford COVID-19 Biobank Study Group, Purington N, Röltgen K, Rogers AJ, Snow T, Wang TT, Solis D, Vaughan L, Verghese M, Maecker H, Wittman R, Puri R, Kistler A, Yang S, Boyd SD, Pinsky BA, Chinthrajah S, Nadeau KC. Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome. Volume 7 of Issue 13. JCI insight 2022. PMID: 35801588


  14. Kratochvil MJ, Kaber G, Demirdjian S, Cai PC, Burgener EB, Nagy N, Barlow GL, Popescu M, Nicolls MR, Ozawa MG, Regula DP, Pacheco-Navarro AE, Yang S, de Jesus Perez VA, Karmouty-Quintana H, Peters AM, Zhao B, Buja ML, Johnson PY, Vernon RB, Wight TN, Stanford COVID-19 Biobank Study Group, Milla CE, Rogers AJ, Spakowitz AJ, Heilshorn SC, Bollyky PL. Biochemical, biophysical, and immunological characterization of respiratory secretions in severe SARS-CoV-2 infections. Volume 7 of Issue 12. JCI insight 2022. PMID: 35730564


  15. Zeng L, Liu Y, Nguyenla XH, Abbott TR, Han M, Zhu Y, Chemparathy A, Lin X, Chen X, Wang H, Rane DA, Spatz JM, Jain S, Rustagi A, Pinsky B, Zepeda AE, Kadina AP, Walker JA, Holden K, Temperton N, Cochran JR, Barron AE, Connolly MD, Blish CA, Lewis DB, Stanley SA, La Russa MF, Qi LS. Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro. Volume 13 of Issue 1. Nature communications 2022. PMID: 35589813


  16. Yen M, Ren J, Liu Q, Glassman CR, Sheahan TP, Picton LK, Moreira FR, Rustagi A, Jude KM, Zhao X, Blish CA, Baric RS, Su LL, Garcia KC. Facile discovery of surrogate cytokine agonists. Volume 185 of Issue 8. Cell 2022. PMID: 35325595


  17. Carroll T, Fox D, van Doremalen N, Ball E, Morris MK, Sotomayor-Gonzalez A, Servellita V, Rustagi A, Yinda CK, Fritts L, Port JR, Ma ZM, Holbrook MG, Schulz J, Blish CA, Hanson C, Chiu CY, Munster V, Stanley S, Miller CJ. The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters. 2022. PMID: 35143587


  18. Ram-Mohan N, Kim D, Zudock EJ, Hashemi MM, Tjandra KC, Rogers AJ, Blish CA, Nadeau KC, Newberry JA, Quinn JV, O'Hara R, Ashley E, Nguyen H, Jiang L, Hung P, Blomkalns AL, Yang S, Stanford COVID-19 Biobank Study Group. SARS-CoV-2 RNAemia Predicts Clinical Deterioration and Extrapulmonary Complications from COVID-19. Volume 74 of Issue 2. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022. PMID: 33949665


  19. Wilk AJ, Lee MJ, Wei B, Parks B, Pi R, Martínez-Colón GJ, Ranganath T, Zhao NQ, Taylor S, Becker W, Stanford COVID-19 Biobank, Jimenez-Morales D, Blomkalns AL, O'Hara R, Ashley EA, Nadeau KC, Yang S, Holmes S, Rabinovitch M, Rogers AJ, Greenleaf WJ, Blish CA. Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. Volume 218 of Issue 8. The Journal of experimental medicine 2021. PMID: 34128959


  20. Verma R, Kim E, Martínez-Colón GJ, Jagannathan P, Rustagi A, Parsonnet J, Bonilla H, Khosla C, Holubar M, Subramanian A, Singh U, Maldonado Y, Blish CA, Andrews JR. SARS-CoV-2 Subgenomic RNA Kinetics in Longitudinal Clinical Samples. Volume 8 of Issue 7. Open forum infectious diseases 2021. PMID: 34295944


  21. Delaveris CS, Wilk AJ, Riley NM, Stark JC, Yang SS, Rogers AJ, Ranganath T, Nadeau KC, Stanford COVID-19 Biobank, Blish CA, Bertozzi CR. Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19. Volume 7 of Issue 4. ACS central science 2021. PMID: 34056095


  22. Long DR, Gombar S, Hogan CA, Greninger AL, O'Reilly-Shah V, Bryson-Cahn C, Stevens B, Rustagi A, Jerome KR, Kong CS, Zehnder J, Shah NH, Weiss NS, Pinsky BA, Sunshine JE. Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients. Volume 72 of Issue 2. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021. PMID: 33501950


  23. Röltgen K, Powell AE, Wirz OF, Stevens BA, Hogan CA, Najeeb J, Hunter M, Wang H, Sahoo MK, Huang C, Yamamoto F, Manohar M, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Jardetzky TS, Zehnder JL, Wang TT, Narasimhan B, Gombar S, Tibshirani R, Nadeau KC, Kim PS, Pinsky BA, Boyd SD. Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Volume 5 of Issue 54. Science immunology 2020. PMID: 33288645


  24. Salahudeen AA, Choi SS, Rustagi A, Zhu J, van Unen V, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ. Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. Volume 588 of Issue 7839. Nature 2020. PMID: 33238290


  25. Vendrame E, McKechnie JL, Ranganath T, Zhao NQ, Rustagi A, Vergara R, Ivison GT, Kronstad LM, Simpson LJ, Blish CA. Profiling of the Human Natural Killer Cell Receptor-Ligand Repertoire. of Issue 165. Journal of visualized experiments : JoVE 2020. PMID: 33283785


  26. Wilson JG, Simpson LJ, Ferreira AM, Rustagi A, Roque J, Asuni A, Ranganath T, Grant PM, Subramanian A, Rosenberg-Hasson Y, Maecker HT, Holmes SP, Levitt JE, Blish CA, Rogers AJ. Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis. Volume 5 of Issue 17. JCI insight 2020. PMID: 32706339


  27. Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K, Jean GH, Stevens BA, Lee JY, Rustagi A, Rogers AJ, Powell AE, Hunter M, Najeeb J, Otrelo-Cardoso AR, Yost KE, Daniel B, Nadeau KC, Chang HY, Satpathy AT, Jardetzky TS, Kim PS, Wang TT, Pinsky BA, Blish CA, Boyd SD. Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2. Volume 28 of Issue 4. Cell host & microbe 2020. PMID: 32941787


  28. Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T, Simpson LJ, Grant P, Subramanian A, Rogers AJ, Blish CA. A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Volume 26 of Issue 7. Nature medicine 2020. PMID: 32514174


  29. Multani A, Rustagi A, Epstein DJ, Gomez CA, Budvytiene I, Banaei N, Brown JM, Liu AY. Eremothecium coryli bloodstream infection in a patient with acute myeloid leukemia: first case report of human infection. Volume 95 of Issue 1. Diagnostic microbiology and infectious disease 2019. PMID: 31005402


  30. Luo D, de Morree A, Boutet S, Quach N, Natu V, Rustagi A, Rando TA. Deltex2 represses MyoD expression and inhibits myogenic differentiation by acting as a negative regulator of Jmjd1c. Volume 114 of Issue 15. Proceedings of the National Academy of Sciences of the United States of America 2017. PMID: 28351977


  31. Rustagi A, Gale M. Innate antiviral immune signaling, viral evasion and modulation by HIV-1. Volume 426 of Issue 6. Journal of molecular biology 2013. PMID: 24326250


  32. Rustagi A, Doehle BP, McElrath MJ, Gale M. Two new monoclonal antibodies for biochemical and flow cytometric analyses of human interferon regulatory factor-3 activation, turnover, and depletion. Volume 59 of Issue 2. Methods (San Diego, Calif.) 2012. PMID: 22705311


  33. Doehle BP, Chang K, Rustagi A, McNevin J, McElrath MJ, Gale M. Vpu mediates depletion of interferon regulatory factor 3 during HIV infection by a lysosome-dependent mechanism. Volume 86 of Issue 16. Journal of virology 2012. PMID: 22593165


  34. Harman AN, Lai J, Turville S, Samarajiwa S, Gray L, Marsden V, Mercier SK, Mercier S, Jones K, Nasr N, Rustagi A, Cumming H, Donaghy H, Mak J, Gale M, Churchill M, Hertzog P, Cunningham AL. HIV infection of dendritic cells subverts the IFN induction pathway via IRF-1 and inhibits type 1 IFN production. Volume 118 of Issue 2. Blood 2011. PMID: 21411754


  35. Bertoni C, Rustagi A, Rando TA. Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides. Volume 37 of Issue 22. Nucleic acids research 2009. PMID: 19854937


  36. Wu JV, Krouse ME, Rustagi A, Joo NS, Wine JJ. An inwardly rectifying potassium channel in apical membrane of Calu-3 cells. Volume 279 of Issue 45. The Journal of biological chemistry 2004. PMID: 15328350


  37. Joo NS, Lee DJ, Winges KM, Rustagi A, Wine JJ. Regulation of antiprotease and antimicrobial protein secretion by airway submucosal gland serous cells. Volume 279 of Issue 37. The Journal of biological chemistry 2004. PMID: 15234967