Arjun Rustagi, MD, PhD
Assistant Professor
Medicine
School of Medicine

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.

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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.

Awards

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• 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

Education & Training

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• Fellowship Infectious Diseases Stanford University 2021
• Internship & Residency Internal Medicine Stanford University 2018
• MD with Honors University of Washington 2015
• PhD Pathobiology University of Washington 2013
• BS Biological Sciences Stanford University 2005

Interests

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• respiratory infections
• innate immunity
• single cell transcriptomics
• virology

Websites

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• Infectious Disease Section at the San Francisco VA Health Care System (vamedicine.ucsf.edu)

Grants and Projects

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• Modeling early SARS-CoV-2 pathogenesis in human lung organoids and slice cultures, NIH, 2022-2026

Publications (37)

Top publication keywords:
CoinfectionNK Cell Lectin-Like Receptor Subfamily KImmunization, PassiveAntibodies, ViralImmune EvasionMucolipidosesLysosomesImmunity, InnateFlow CytometryReceptors, Natural Killer CellBacterial InfectionsVirus ReplicationInterferon Regulatory Factor-3Pneumonia, ViralAntiviral Agents

• Vaccine-Boosted CCP Decreases Virus Replication and Hastens Resolution of Infection Despite Transiently Enhancing Disease in SARS-CoV-2-Infected Hamsters.
  The Journal of infectious diseases 2024 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
• Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung.
  The Journal of experimental medicine 2024 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…
• An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations.
  Science translational medicine 2024 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…
• Organoid modeling of lung-resident immune responses to SARS-CoV-2 infection.
  Research square 2023 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, …
• Viral immunity: Basic mechanisms and therapeutic applications-a Keystone Symposia report.
  Annals of the New York Academy of Sciences 2023 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 …

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• SARS-CoV-2 escapes direct NK cell killing through Nsp1-mediated downregulation of ligands for NKG2D.
  Cell reports 2022 Lee MJ, Leong MW, Rustagi A, Beck A, Zeng L, Holmes S, Qi LS, Blish CA
• SARS-CoV-2 infection drives an inflammatory response in human adipose tissue through infection of adipocytes and macrophages.
  Science translational medicine 2022 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
• Using a 29-mRNA Host Response Classifier To Detect Bacterial Coinfections and Predict Outcomes in COVID-19 Patients Presenting to the Emergency Department.
  Microbiology spectrum 2022 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
• The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection.
  Science (New York, N.Y.) 2022 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, …
• Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.
  Nature medicine 2022 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, …
• An intranasal ASO therapeutic targeting SARS-CoV-2.
  Nature communications 2022 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, …
• Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection.
  Nature genetics 2022 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, …
• Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome.
  JCI insight 2022 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, …
• Biochemical, biophysical, and immunological characterization of respiratory secretions in severe SARS-CoV-2 infections.
  JCI insight 2022 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,…
• Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro.
  Nature communications 2022 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, …
• Facile discovery of surrogate cytokine agonists.
  Cell 2022 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
• The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters.
  PLoS pathogens 2022 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, …
• SARS-CoV-2 RNAemia Predicts Clinical Deterioration and Extrapulmonary Complications from COVID-19.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 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 …
• Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19.
  The Journal of experimental medicine 2021 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, …
• SARS-CoV-2 Subgenomic RNA Kinetics in Longitudinal Clinical Samples.
  Open forum infectious diseases 2021 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
• Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19.
  ACS central science 2021 Delaveris CS, Wilk AJ, Riley NM, Stark JC, Yang SS, Rogers AJ, Ranganath T, Nadeau KC, Stanford COVID-19 Biobank, Blish CA, Bertozzi CR
• Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 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
• Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome.
  Science immunology 2020 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 …
• Progenitor identification and SARS-CoV-2 infection in human distal lung organoids.
  Nature 2020 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, …
• Profiling of the Human Natural Killer Cell Receptor-Ligand Repertoire.
  Journal of visualized experiments : JoVE 2020 Vendrame E, McKechnie JL, Ranganath T, Zhao NQ, Rustagi A, Vergara R, Ivison GT, Kronstad LM, Simpson LJ, Blish CA
• Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis.
  JCI insight 2020 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
• Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2.
  Cell host & microbe 2020 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, …
• A single-cell atlas of the peripheral immune response in patients with severe COVID-19.
  Nature medicine 2020 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
• Eremothecium coryli bloodstream infection in a patient with acute myeloid leukemia: first case report of human infection.
  Diagnostic microbiology and infectious disease 2019 Multani A, Rustagi A, Epstein DJ, Gomez CA, Budvytiene I, Banaei N, Brown JM, Liu AY
• Deltex2 represses MyoD expression and inhibits myogenic differentiation by acting as a negative regulator of Jmjd1c.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Luo D, de Morree A, Boutet S, Quach N, Natu V, Rustagi A, Rando TA
• Innate antiviral immune signaling, viral evasion and modulation by HIV-1.
  Journal of molecular biology 2013 Rustagi A, Gale M
• Two new monoclonal antibodies for biochemical and flow cytometric analyses of human interferon regulatory factor-3 activation, turnover, and depletion.
  Methods (San Diego, Calif.) 2012 Rustagi A, Doehle BP, McElrath MJ, Gale M
• Vpu mediates depletion of interferon regulatory factor 3 during HIV infection by a lysosome-dependent mechanism.
  Journal of virology 2012 Doehle BP, Chang K, Rustagi A, McNevin J, McElrath MJ, Gale M
• HIV infection of dendritic cells subverts the IFN induction pathway via IRF-1 and inhibits type 1 IFN production.
  Blood 2011 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
• Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides.
  Nucleic acids research 2009 Bertoni C, Rustagi A, Rando TA
• An inwardly rectifying potassium channel in apical membrane of Calu-3 cells.
  The Journal of biological chemistry 2004 Wu JV, Krouse ME, Rustagi A, Joo NS, Wine JJ
• Regulation of antiprotease and antimicrobial protein secretion by airway submucosal gland serous cells.
  The Journal of biological chemistry 2004 Joo NS, Lee DJ, Winges KM, Rustagi A, Wine JJ