Sulggi Lee, MD, PhD

Associate Professor

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. She also serves as an attending physician at the San Francisco General Hospital inpatient infectious diseases and HIV consult service and in the Ward 86 HIV Clinic. After receiving her bachelor’s degree in human biology from Stanford University, she received her MD/PhD degree from the University of Southern California in genetic epidemiology. She completed her internal medicine residency training at Stanford Hospital and Clinics and Infectious Diseases fellowship training at UCSF.

Dr. Lee’s research focuses on identifying underlying mechanisms of host-pathogen infectious diseases pathophysiology (e.g., HIV and COVID) leveraging patient samples from observational and clinical trials and applying high throughput genetic and immunologic assays. Her research includes studying host-specific drug responses to interventions using pharmacokinetic/ pharmacodynamic modeling as well as identifying genetic and immunologic signatures that predict unique clinical phenotypes.

Dr. Lee is the PI of UCSF Treat Acute HIV cohort, which provides immediate antiretroviral therapy (ART) to newly diagnosed acute HIV individuals in the San Francisco Bay Area, PI of the Effect of Methamphetamine on Residual Latent HIV Disease (EMRLHD) cohort, Co-PI of the UCSF SCOPE HIV cohort, which includes over 2,500 HIV+ infected participants, and during the COVID-19 pandemic, she developed the acute COVID-19 Host Immune Response Pathogenesis (CHIRP) cohort. Her current funding includes an NIH NIAID R01 grant to explore the mechanisms by which interleukin-1 beta (IL-1β)/IL-6 signaling drives systemic inflammation during chronic treated HIV disease, an NIH NIDA R61/R33 award to evaluate the host immune response to methamphetamine use and how it contributes to HIV persistence, and a recent NIAID R56/R01 award to determine the host immune responses driving early viral control during acute treated HIV.
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
  • ACTG Cure Transformative Science Group Committee, AIDS Clinical Trials Group (ACTG), 2023-2024
  • Co-Director, CFAR Bioinformatics Core, UCSF Center for AIDS Research (CFAR), 2022-2024
  • Co-Founder, Executive Committee, UCSF Women Physician Scientists Supergroup (WPSS), 2020-2023
  • Co-Founder, Director, UCSF Single Cell Sequencing Group (SSIG), 2018-2024
  • Excellence in Translational Science Award, UCSF Center for AIDS Research Program (CFAR), 2018
  • Clinical Core Director, UCSF amfAR HIV Cure Institute, 2016-2020
  • Executive Committee, UCSF AIDS Research Institute (ARI), 2015-2020
Publications

  1. 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 MJ, 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. Nature communications 2024. PMID: 39557853


  2. Babcock BR, Kosters A, Eddins DJ, Donaire MSB, Sarvadhavabhatla S, Pae V, Beltran F, Murray VW, Gill G, Xie G, Dobosh BS, Giacalone VD, Tirouvanziam RM, Ramonell RP, Jenks SA, Sanz I, Lee FE, Roan NR, Lee SA, Ghosn EEB. Transient anti-interferon autoantibodies in the airways are associated with recovery from COVID-19. Science translational medicine 2024. PMID: 39504354


  3. 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


  4. 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


  5. 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


  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. Augusto DG, Murdolo LD, Chatzileontiadou DSM, Sabatino JJ, Yusufali T, Peyser ND, Butcher X, Kizer K, Guthrie K, Murray VW, Pae V, Sarvadhavabhatla S, Beltran F, Gill GS, Lynch KL, Yun C, Maguire CT, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Vierra-Green CA, Spellman SR, Langton DJ, Dewar-Oldis MJ, Smith C, Barnard PJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Maiers M, Gras S, Hollenbach JA. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature 2023. PMID: 37468623


  8. Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio 2023. PMID: 37294090


  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. Journal of immunology (Baltimore, Md. : 1950) 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. Academic Medicine 2022. PMID: 35154118


  12. McMahon JH, Evans VA, Lau JSY, Symons J, Zerbato JM, Chang J, Solomon A, Tennakoon S, Dantanarayana A, Hagenauer M, Lee S, Palmer S, Fisher K, Bumpus N, Heck CJS, Burger D, Wu G, Zuck P, Howell BJ, Zetterberg HH, Blennow K, Gisslen M, Rasmussen TA, Lewin SR. Neurotoxicity with high-dose disulfiram and vorinostat used for HIV latency reversal. AIDS (London, England) 2022. PMID: 34586085


  14. 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


  15. Moron-Lopez S, Xie G, Kim P, Siegel DA, Lee S, Wong JK, Price JC, Elnachef N, Greenblatt RM, Tien PC, Roan NR, Yukl SA. Tissue-specific differences in HIV DNA levels and mechanisms that govern HIV transcription in blood, gut, genital tract and liver in ART-treated women. Journal of the International AIDS Society 2021. PMID: 34235864


  16. 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


  17. Johnson KA, Chen MJ, Kohn R, Sachdev D, Bacon O, Lee S, Cohen SE. Acute HIV at the Time of Initiation of Pre-exposure or Post-exposure Prophylaxis: Impact on Drug Resistance and Clinical Outcomes. Journal of acquired immune deficiency syndromes (1999) 2021. PMID: 33512849


  18. Telwatte S, Martin HA, Marczak R, Fozouni P, Vallejo-Gracia A, Kumar GR, Murray V, Lee S, Ott M, Wong JK, Yukl SA. Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts. Methods (San Diego, Calif.) 2021. PMID: 33882362


  19. 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


  20. 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 Helper Function, Lack of Terminal Differentiation, and High Proliferation Potential. Cell reports. Medicine 2020. PMID: 32839763


  21. 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


  22. 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


  23. 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:


  24. 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:


  25. 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


  26. 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


  27. 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


  28. 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


  29. Chang JL, Lee SA, Tsai AC, Musinguzi N, Muzoora C, Bwana B, Boum Y, Haberer JE, 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


  30. 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


  31. 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:


  32. 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. The Journal of infectious diseases 2017. PMID: 28329310


  33. 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:


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


  36. 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. PloS one 2016. PMID: 27483366


  37. 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. AIDS (London, England) 2016. PMID: 27088321


  38. 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. The Journal of clinical investigation 2016. PMID: 27322062


  39. 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. AIDS (London, England) 2016. PMID: 26854811


  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. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015. PMID: 26400999


  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. 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. 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. 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. Treatment of the Postmenopausal Woman 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