Sulggi Lee, MD, PhD

Assoc Professor in Residence

Sulggi Lee, MD PhD, is an Associate Professor of Medicine at the University of California, San Francisco (UCSF) and a faculty member in the Division of HIV, Infectious Diseases, and Global Medicine at the Zuckerberg San Francisco General Hospital. She is the PI of the UCSF Treat Acute HIV study, Co-PI of the UCSF SCOPE HIV cohort, the PI of the COVID-19 Host Immune Response Pathogenesis (CHIRP) study, Co-PI of the UCSF AIDS Cancer Specimen Resource (ACSR), and Co-Director of the UCSF Center for AIDS Research (CFAR) Bioinformatics Core. She is one of the founding executive committee members of the UCSF Women's Physician Scientist Supergroup (WPSS) and a faculty mentor for the UCSF Medical Scientist Training Program (MSTP) Community of Underrepresented Physician Scientists (CUPS) program. Her research focuses on clinical translational studies aimed at determining how natural host responses to pathogens (e.g., HIV, SARS-CoV-2) can be leveraged as future therapeutic targets using discovery-based analytic approaches. Her collaborative, interdisciplinary team includes data scientists, immunologists, virologists, and clinicians. Her work involves the application of highly advanced laboratory assays to well-characterized patient samples from observational studies and clinical trials. The goal of her research is to identify underlying host mechanisms of pathogen control to enable the identification of potential novel therapeutic targets for reducing morbidity and mortality associated with HIV and COVID-19.

Education
Fellowship, 07/2013 - Infectious Diseases, University of California San Francisco
Residency, 06/2010 - Internal Medicine, Stanford Hospital & Clinics
M.D., Ph.D., 06/2007 - Medicine, Genetic Epidemiology, University of Southern California
B.A., 06/1998 - Human Biology, Stanford University
Honors and Awards
  • Excellence in Translational Science Award, UCSF Center for AIDS Research Program (CFAR), 2018
Websites
Publications

  1. Whitehill GD, Joy J, Marino FE, Krause R, Mallick S, Courtney H, Park K, Carey J, Hoh R, Hartig H, Pae V, Sarvadhavabhatla S, Donaire S, Deeks SG, Lynch RM, Lee SA, Bar KJ. Autologous neutralizing antibody responses after antiretroviral therapy in acute and early HIV-1. The Journal of clinical investigation 2024. PMID: 38652564


  2. Barbehenn A, Shi L, Shao J, Hoh R, Hartig HM, Pae V, Sarvadhavabhatla S, Donaire S, Sheikhzadeh C, Milush J, Laird GM, Mathias M, Ritter K, Peluso M, Martin J, Hecht F, Pilcher C, Cohen SE, Buchbinder S, Havlir D, Gandhi M, Henrich TJ, Hatano H, Wang J, Deeks SG, Lee SA. Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease. medRxiv : the preprint server for health sciences 2024. PMID: 38585951


  3. Yin K, Peluso MJ, Luo X, Thomas R, Shin MG, Neidleman J, Andrew A, Young KC, Ma T, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Deveau TM, Munter SE, Ibrahim R, Ständker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, Münch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2. Nature immunology 2024. PMID: 38212464


  4. Dwivedi AK, Gornalusse GG, Siegel DA, Barbehenn A, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Reppetti J, Vo PM, Levy CN, Roychoudhury P, Jerome KR, Hladik F, Henrich TJ, Deeks SG, Lee SA. A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size. PLoS pathogens 2023. PMID: 38019897


  5. Benjamin R Babcock, Astrid Kosters, Nadia R Roan, Sulggi Lee, Eliver E.B. Ghosn. Transient Anti-Interferon Auto Antibodies in the Airway Are Associated with Recovery in Mild COVID-19. Blood 2023. PMID:


  6. Haas CB, Jordahl KM, Nance RM, Whitney BM, Wang L, Delaney JAC, Ruderman S, Jia T, Mathews WC, Saag MS, Lee SA, Napravnik S, Jacobson JM, Chander G, McCall EM, Moore RD, Mayer KH, Mukherjee S, Lee WJ, Crane PK, Crane H, Peter I, Lindström S. Assessing the associations between known genetic variants and substance use in people with HIV in the United States. PloS one 2023. PMID: 37796845


  7. Yin K, Peluso MJ, Thomas R, Shin MG, Neidleman J, Luo X, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Ibrahim R, St?ndker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, M?nch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2. bioRxiv : the preprint server for biology 2023. PMID: 36798286


  8. Dwivedi AK, Siegel DA, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Levy CN, Roychoudhury P, Hladik F, Jerome KR, Henrich TJ, Deeks SG, Lee SA. Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection. bioRxiv : the preprint server for biology 2023. PMID: 36712077


  9. Siegel DA, Thanh C, Wan E, Hoh R, Hobbs K, Pan T, Gibson EA, Kroetz DL, Martin J, Hecht F, Pilcher C, Martin M, Carrington M, Pillai S, Busch MP, Stone M, Levy CN, Huang ML, Roychoudhury P, Hladik F, Jerome KR, Kiem HP, Henrich TJ, Deeks SG, Lee SA. Host variation in type I interferon signaling genes (MX1), C-C chemokine receptor type 5 gene, and major histocompatibility complex class I alleles in treated HIV+ noncontrollers predict viral reservoir size. AIDS (London, England) 2022. PMID: 36695358


  10. Xie G, Moron-Lopez S, Siegel DA, Yin K, Polos A, Cohen J, Greenblatt RM, Tien PC, Lee SA, Yukl SA, Roan NR. Common and Divergent Features of T Cells from Blood, Gut, and Genital Tract of Antiretroviral Therapy-Treated HIV+ Women. 2022. PMID: 35296537


  11. George AF, Luo X, Neidleman J, Hoh R, Vohra P, Thomas R, Shin MG, Lee MJ, Blish CA, Deeks SG, Greene WC, Lee SA, Roan NR. Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells From HIV+ Controllers and ART-Suppressed Individuals. 2022. PMID: 35154118


  12. Neidleman J, Luo X, McGregor M, Xie G, Murray V, Greene WC, Lee SA, Roan NR. mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status. 2021. PMID: 34636722


  13. Ma T, Ryu H, McGregor M, Babcock B, Neidleman J, Xie G, George AF, Frouard J, Murray V, Gill G, Ghosn E, Newell EW, Lee SA, Roan NR. Protracted yet Coordinated Differentiation of Long-Lived SARS-CoV-2-Specific CD8+ T Cells during Convalescence. Journal of immunology (Baltimore, Md. : 1950) 2021. PMID: 34389625


  14. Neidleman J, Luo X, McGregor M, Xie G, Murray V, Greene WC, Lee SA, Roan NR. mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status. bioRxiv : the preprint server for biology 2021. PMID: 34013277


  15. Neidleman J, Luo X, George AF, McGregor M, Yang J, Yun C, Murray V, Gill G, Greene WC, Vasquez J, Lee SA, Ghosn E, Lynch KL, Roan NR. Distinctive features of SARS-CoV-2-specific T cells predict recovery from severe COVID-19. Cell reports 2021. PMID: 34260965


  16. McGinnis CS, Siegel DA, Xie G, Hartoularos G, Stone M, Ye CJ, Gartner ZJ, Roan NR, Lee SA. No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells. BMC biology 2021. PMID: 33472616


  17. Neidleman J, Luo X, Frouard J, Xie G, Gill G, Stein ES, McGregor M, Ma T, George AF, Kosters A, Greene WC, Vasquez J, Ghosn E, Lee S, Roan NR. SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential. Cell reports. Medicine 2020. PMID: 32839763


  18. Hsiao F, Frouard J, Gramatica A, Xie G, Telwatte S, Lee GQ, Roychoudhury P, Schwarzer R, Luo X, Yukl SA, Lee S, Hoh R, Deeks SG, Jones RB, Cavrois M, Greene WC, Roan NR. Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127) preferentially support latent HIV-1 infection. PLoS pathogens 2020. PMID: 32353080


  19. Lee SA, Telwatte S, Hatano H, Kashuba ADM, Cottrell ML, Hoh R, Liegler TJ, Stephenson S, Somsouk M, Hunt PW, Deeks SG, Yukl S, Savic RM. Antiretroviral Therapy Concentrations Differ in Gut vs. Lymph Node Tissues and Are Associated With HIV Viral Transcription by a Novel RT-ddPCR Assay. Journal of acquired immune deficiency syndromes (1999) 2020. PMID: 32168200


  20. Gong J, Noel S, Hsu J, Bush EL, Arend LJ, Sadasivam M, Lee SA, Kurzhagen JT, Hamad ARA, Rabb H. TCR+CD4-CD8- (double negative) T cells protect from cisplatin-induced renal epithelial cell apoptosis and acute kidney injury. American journal of physiology. Renal physiology 2020. PMID: 32281417


  21. M. Peluso, P. Burbelo, S. Kumar, S. Munter, R. Hoh, S. Lee, P. Hunt, R. Rutishauser, T. Henrich, S. Deeks. OP 4.2 Characterising ‘exceptional’ control among HIV elite controllers. Journal of virus eradication 2019. PMID:


  22. S. Lee, K. Kesmy, P. Bacchetti, R. Hoh, J. Lifson, D. Cary, B. Peterlin, S. Deeks, D. Hartigan-O’Connor. 20 Kansui, an ingenol-containing herbal supplement, safely induced CD8, NK, and monocyte activation in three ART-suppressed SIVmac251-infected rhesus macaques. Journal of virus eradication 2019. PMID:


  23. Coffey S, Bacchetti P, Sachdev D, Bacon O, Jones D, Ospina-Norvell C, Torres S, Lynch E, Camp C, Mercer-Slomoff R, Lee S, Christopoulos K, Pilcher C, Hsu L, Jin C, Scheer S, Havlir D, Gandhi M. RAPID antiretroviral therapy: high virologic suppression rates with immediate antiretroviral therapy initiation in a vulnerable urban clinic population. AIDS (London, England) 2019. PMID: 30882490


  24. Sadasivam M, Noel S, Lee SA, Gong J, Allaf ME, Pierorazio P, Rabb H, Hamad ARA. Activation and Proliferation of PD-1+ Kidney Double-Negative T Cells Is Dependent on Nonclassical MHC Proteins and IL-2. Journal of the American Society of Nephrology : JASN 2019. PMID: 30622155


  25. Cohen SE, Sachdev D, Lee SA, Scheer S, Bacon O, Chen MJ, Okochi H, Anderson PL, Kearney MF, Coffey S, Scott H, Grant RM, Havlir D, Gandhi M. Acquisition of tenofovir-susceptible, emtricitabine-resistant HIV despite high adherence to daily pre-exposure prophylaxis: a case report. The lancet. HIV 2018. PMID: 30503324


  26. Telwatte S, Lee S, Somsouk M, Hatano H, Baker C, Kaiser P, Kim P, Chen TH, Milush J, Hunt PW, Deeks SG, Wong JK, Yukl SA. Gut and blood differ in constitutive blocks to HIV transcription, suggesting tissue-specific differences in the mechanisms that govern HIV latency. PLoS pathogens 2018. PMID: 30440043


  27. Lee SA, Elliott JH, McMahon J, Hartogenesis W, Bumpus NN, Lifson JD, Gorelick RJ, Bacchetti P, Deeks SG, Lewin SR, Savic RM. Population Pharmacokinetics and Pharmacodynamics of Disulfiram on Inducing Latent HIV-1 Transcription in a Phase IIb Trial. Clinical pharmacology and therapeutics 2018. PMID: 30137649


  28. Chang JL, Lee S, Tsai AC, Musinguzi N, Muzoora C, Bwana BM, Boum Y, Haberer J, Hunt PW, Martin J, Bangsberg DR, Kroetz DL, Siedner MJ. CYP2B6 genetic polymorphisms, depression, and viral suppression in adults living with HIV initiating efavirenz-containing antiretroviral therapy regimens in Uganda: pooled analysis of two prospective studies. AIDS research and human retroviruses 2018. PMID: 29973058


  29. Carrico AW, Flentje A, Kober K, Lee S, Hunt P, Riley ED, Shoptaw S, Flowers E, Dilworth SE, Pahwa S, Aouizerat BE. Recent stimulant use and leukocyte gene expression in methamphetamine users with treated HIV infection. Brain, behavior, and immunity 2018. PMID: 29679637


  30. S. Lee, K. Haworth, T. Henrich, S. Deeks, H.P. Kiem. PP4.10 HIV integrates in genes regulating cell cycle, DNA damage, and viral transport. Journal of virus eradication 2017. PMID:


  31. Lee S, Byakwaga H, Boum Y, Burdo TH, Williams KC, Lederman MM, Huang Y, Tracy RP, Cao H, Haberer JE, Kembabazi A, Bangsberg DR, Martin JN, Hunt PW. Immunologic Pathways That Predict Mortality in HIV-Infected Ugandans Initiating Antiretroviral Therapy. Volume 215 of Issue 8. The Journal of infectious diseases 2017. PMID: 28329310


  32. Jonathan Chang, Sulggi Lee, Peter Hunt, Deanna Kroetz, Mark Siedner. Efavirenz-metabolizing polymorphisms, viral suppression, and depression in HIV-infected individuals initiating antiretroviral therapy in southwestern Uganda. Open forum infectious diseases 2017. PMID:


  33. Hunt PW, Lee SA, Siedner MJ. Immunologic Biomarkers, Morbidity, and Mortality in Treated HIV Infection. Volume 214 Suppl 2. The Journal of infectious diseases 2016. PMID: 27625430


  34. Lee SA, Deeks SG. The Benefits of Early Antiretroviral Therapy for HIV Infection: How Early is Early Enough? EBioMedicine 2016. PMID: 27515690


  35. Lee SA, Bacchetti P, Chomont N, Fromentin R, Lewin SR, O'Doherty U, Palmer S, Richman DD, Siliciano JD, Yukl SA, Deeks SG, Burbelo PD. Anti-HIV Antibody Responses and the HIV Reservoir Size during Antiretroviral Therapy. Volume 11 of Issue 8. PloS one 2016. PMID: 27483366


  36. Lee SA, Mefford JA, Huang Y, Witte JS, Martin JN, Haas DW, Mclaren PJ, Mushiroda T, Kubo M, Byakwaga H, Hunt PW, Kroetz DL. Host genetic predictors of the kynurenine pathway of tryptophan catabolism among treated HIV-infected Ugandans. Volume 30 of Issue 11. AIDS (London, England) 2016. PMID: 27088321


  37. Younes SA, Freeman ML, Mudd JC, Shive CL, Reynaldi A, Panigrahi S, Estes JD, Deleage C, Lucero C, Anderson J, Schacker TW, Davenport MP, McCune JM, Hunt PW, Lee SA, Serrano-Villar S, Debernardo RL, Jacobson JM, Canaday DH, Sekaly RP, Rodriguez B, Sieg SF, Lederman MM. IL-15 promotes activation and expansion of CD8+ T cells in HIV-1 infection. Volume 126 of Issue 7. The Journal of clinical investigation 2016. PMID: 27322062


  38. Ramirez CM, Sinclair E, Epling L, Lee SA, Jain V, Hsue PY, Hatano H, Conn D, Hecht FM, Martin JN, McCune JM, Deeks SG, Hunt PW. Immunologic profiles distinguish aviremic HIV-infected adults. Volume 30 of Issue 10. AIDS (London, England) 2016. PMID: 26854811


  39. Freeman ML, Mudd JC, Shive CL, Younes SA, Panigrahi S, Sieg SF, Lee SA, Hunt PW, Calabrese LH, Gianella S, Rodriguez B, Lederman MM. Reply to Barrett, et al. Volume 62 of Issue 11. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016. PMID: 27001803


  40. Elliott JH, McMahon JH, Chang CC, Lee SA, Hartogensis W, Bumpus N, Savic R, Roney J, Hoh R, Solomon A, Piatak M, Gorelick RJ, Lifson J, Bacchetti P, Deeks SG, Lewin SR. Short-term administration of disulfiram for reversal of latent HIV infection: a phase 2 dose-escalation study. The lancet. HIV 2015. PMID: 26614966


  41. Freeman ML, Mudd JC, Shive CL, Younes SA, Panigrahi S, Sieg SF, Lee SA, Hunt PW, Calabrese LH, Gianella S, Rodriguez B, Lederman MM. CD8 T-Cell Expansion and Inflammation Linked to CMV Coinfection in ART-treated HIV Infection. Volume 62 of Issue 3. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015. PMID: 26400999


  42. Lee SA. Highlights from the Keystone Symposium on HIV Persistence 2015: 26-30 April 2015, Boston, Massachusetts, USA. Journal of virus eradication 2015. PMID: 27482417


  43. Lee SA, Plett SK, Luetkemeyer AF, Borgo GM, Ohliger MA, Conrad MB, Cookson BT, Sengupta DJ, Koehler JE. Bartonella quintana Aortitis in a Man with AIDS, Diagnosed by Needle Biopsy and 16S rRNA Gene Amplification. Journal of clinical microbiology 2015. PMID: 26063867


  44. souheil younes, carey shive, Arnold Reynaldi, Michael Freeman, Soumya Panigrahi, Jacob Estes, Jodi Anderson, Timothy Schacker, Miles Davenport, Joseph McCune, Peter Hunt, Sulggi Lee, Sergio Serrano-Villar, David Canaday, Cheryl Cameron, Rafick-Pierre Sekaly, Benigno Rodriguez, Scott Sieg, Michael Lederman. IL-15 drives CD8 T cell cycling and differentiation in chronic HIV-1 infection (VIR6P.1162). The Journal of Immunology 2015. PMID:


  45. Serrano-Villar S, Sainz T, Lee SA, Hunt PW, Sinclair E, Shacklett BL, Ferre AL, Hayes TL, Somsouk M, Hsue PY, Van Natta ML, Meinert CL, Lederman MM, Hatano H, Jain V, Huang Y, Hecht FM, Martin JN, McCune JM, Moreno S, Deeks SG. HIV-infected individuals with low CD4/CD8 ratio despite effective antiretroviral therapy exhibit altered T cell subsets, heightened CD8+ T cell activation, and increased risk of non-AIDS morbidity and mortality. Volume 10 of Issue 5. PLoS pathogens 2014. PMID: 24831517


  46. Lee SA, Sinclair E, Jain V, Huang Y, Epling L, Van Natta M, Meinert CL, Martin JN, McCune JM, Deeks SG, Lederman MM, Hecht FM, Hunt PW. Low proportions of CD28- CD8+ T cells expressing CD57 can be reversed by early ART initiation and predict mortality in treated HIV infection. Volume 210 of Issue 3. The Journal of infectious diseases 2014. PMID: 24585893


  47. Lee SA, Sinclair E, Hatano H, Hsue PY, Epling L, Hecht FM, Bangsberg DR, Martin JN, McCune JM, Deeks SG, Hunt PW. Impact of HIV on CD8+ T cell CD57 expression is distinct from that of CMV and aging. Volume 9 of Issue 2. PloS one 2014. PMID: 24586783


  48. Lee SA, Haiman CA, Burtt NP, Pooler LC, Cheng I, Kolonel LN, Pike MC, Altshuler D, Hirschhorn JN, Henderson BE, Stram DO. A comprehensive analysis of common genetic variation in prolactin (PRL) and PRL receptor (PRLR) genes in relation to plasma prolactin levels and breast cancer risk: the multiethnic cohort. BMC medical genetics 2007. PMID: 18053149


  49. Anna H. Wu, C. Leigh Pearce, Darcy V. Spicer, Sulggi Lee, Malalcolm C. Pike. Chapter 40 Body weight, menopausal hormone therapy, and risk of breast cancer. 2007. PMID:


  50. Lee SA, Yeka A, Nsobya SL, Dokomajilar C, Rosenthal PJ, Talisuna A, Dorsey G. Complexity of Plasmodium falciparum infections and antimalarial drug efficacy at 7 sites in Uganda. Volume 193 of Issue 8. The Journal of infectious diseases 2006. PMID: 16544257


  51. Lee S, Kolonel L, Wilkens L, Wan P, Henderson B, Pike M. Postmenopausal hormone therapy and breast cancer risk: the Multiethnic Cohort. International journal of cancer 2006. PMID: 16170777


  52. Lee SA, Ross RK, Pike MC. An overview of menopausal oestrogen-progestin hormone therapy and breast cancer risk. British journal of cancer 2005. PMID: 15900297