Sulggi Lee, MD, PhD

Associate Professor
Medicine
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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.

Publications: 

HIV-SEQ REVEALS GLOBAL HOST GENE EXPRESSION DIFFERENCES BETWEEN HIV-TRANSCRIBING CELLS FROM VIREMIC AND SUPPRESSED PEOPLE WITH HIV.

bioRxiv : the preprint server for biology

Frouard J, Telwatte S, Luo X, Elphick N, Thomas R, Arneson D, Roychoudhury P, Butte AJ, Wong JK, Hoh R, Deeks SG, Lee SA, Roan NR, Yukl S

PP4.14 – 00024 HIV RNA+ cells from ART-suppressed PWH exhibit transcriptional profiles distinct from those during active viremia.

Journal of virus eradication

J. Frouard, S. Telwatte, X. Luo, N. Elphick, R. Thomas, D. Arneson, P.D. Roychoudhury, A. Butte, J. Wong, R. Hoh, S. Deeks, S. Lee, S. Yukl, N. Roan

Rapid biphasic decay of intact and defective HIV DNA reservoir during acute treated HIV disease.

Nature communications

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

Transient anti-interferon autoantibodies in the airways are associated with recovery from COVID-19.

Science translational medicine

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

Autologous neutralizing antibody responses after antiretroviral therapy in acute and early HIV-1.

The Journal of clinical investigation

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

Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2.

Nature immunology

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

A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size.

PLoS pathogens

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

Assessing the associations between known genetic variants and substance use in people with HIV in the United States.

PloS one

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

A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.

Nature

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

Mild SARS-CoV-2 infection results in long-lasting microbiota instability.

mBio

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

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)

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

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)

Xie G, Moron-Lopez S, Siegel DA, Yin K, Polos A, Cohen J, Greenblatt RM, Tien PC, Lee SA, Yukl SA, Roan NR

Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells From HIV+ Controllers and ART-Suppressed Individuals.

Frontiers in immunology

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

Neurotoxicity with high-dose disulfiram and vorinostat used for HIV latency reversal.

AIDS (London, England)

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

Protracted yet Coordinated Differentiation of Long-Lived SARS-CoV-2-Specific CD8+ T Cells during Convalescence.

Journal of immunology (Baltimore, Md. : 1950)

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

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

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

Distinctive features of SARS-CoV-2-specific T cells predict recovery from severe COVID-19.

Cell reports

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

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)

Johnson KA, Chen MJ, Kohn R, Sachdev D, Bacon O, Lee S, Cohen SE

Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts.

Methods (San Diego, Calif.)

Telwatte S, Martin HA, Marczak R, Fozouni P, Vallejo-Gracia A, Kumar GR, Murray V, Lee S, Ott M, Wong JK, Yukl SA

SARS-CoV-2-Specific T Cells Exhibit Phenotypic Features of Helper Function, Lack of Terminal Differentiation, and High Proliferation Potential.

Cell reports. Medicine

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

Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127) preferentially support latent HIV-1 infection.

PLoS pathogens

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

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)

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

OP 4.2 Characterising ‘exceptional’ control among HIV elite controllers.

Journal of virus eradication

M. Peluso, P. Burbelo, S. Kumar, S. Munter, R. Hoh, S. Lee, P. Hunt, R. Rutishauser, T. Henrich, S. Deeks

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

S. Lee, K. Kesmy, P. Bacchetti, R. Hoh, J. Lifson, D. Cary, B. Peterlin, S. Deeks, D. Hartigan-O’Connor

RAPID antiretroviral therapy: high virologic suppression rates with immediate antiretroviral therapy initiation in a vulnerable urban clinic population.

AIDS (London, England)

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

Acquisition of tenofovir-susceptible, emtricitabine-resistant HIV despite high adherence to daily pre-exposure prophylaxis: a case report.

The lancet. HIV

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

Gut and blood differ in constitutive blocks to HIV transcription, suggesting tissue-specific differences in the mechanisms that govern HIV latency.

PLoS pathogens

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

Population Pharmacokinetics and Pharmacodynamics of Disulfiram on Inducing Latent HIV-1 Transcription in a Phase IIb Trial.

Clinical pharmacology and therapeutics

Lee SA, Elliott JH, McMahon J, Hartogenesis W, Bumpus NN, Lifson JD, Gorelick RJ, Bacchetti P, Deeks SG, Lewin SR, Savic RM

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

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

Recent stimulant use and leukocyte gene expression in methamphetamine users with treated HIV infection.

Brain, behavior, and immunity

Carrico AW, Flentje A, Kober K, Lee S, Hunt P, Riley ED, Shoptaw S, Flowers E, Dilworth SE, Pahwa S, Aouizerat BE

PP4.10 HIV integrates in genes regulating cell cycle, DNA damage, and viral transport.

Journal of virus eradication

S. Lee, K. Haworth, T. Henrich, S. Deeks, H.P. Kiem

Immunologic Pathways That Predict Mortality in HIV-Infected Ugandans Initiating Antiretroviral Therapy.

The Journal of infectious diseases

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 Biomarkers, Morbidity, and Mortality in Treated HIV Infection.

The Journal of infectious diseases

Hunt PW, Lee SA, Siedner MJ

Anti-HIV Antibody Responses and the HIV Reservoir Size during Antiretroviral Therapy.

PloS one

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

Host genetic predictors of the kynurenine pathway of tryptophan catabolism among treated HIV-infected Ugandans.

AIDS (London, England)

Lee SA, Mefford JA, Huang Y, Witte JS, Martin JN, Haas DW, Mclaren PJ, Mushiroda T, Kubo M, Byakwaga H, Hunt PW, Kroetz DL

IL-15 promotes activation and expansion of CD8+ T cells in HIV-1 infection.

The Journal of clinical investigation

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

Immunologic profiles distinguish aviremic HIV-infected adults.

AIDS (London, England)

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

Short-term administration of disulfiram for reversal of latent HIV infection: a phase 2 dose-escalation study.

The lancet. HIV

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

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

Freeman ML, Mudd JC, Shive CL, Younes SA, Panigrahi S, Sieg SF, Lee SA, Hunt PW, Calabrese LH, Gianella S, Rodriguez B, Lederman MM

Bartonella quintana Aortitis in a Man with AIDS, Diagnosed by Needle Biopsy and 16S rRNA Gene Amplification.

Journal of clinical microbiology

Lee SA, Plett SK, Luetkemeyer AF, Borgo GM, Ohliger MA, Conrad MB, Cookson BT, Sengupta DJ, Koehler JE

IL-15 drives CD8 T cell cycling and differentiation in chronic HIV-1 infection (VIR6P.1162).

The Journal of Immunology

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

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

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

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

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

Impact of HIV on CD8+ T cell CD57 expression is distinct from that of CMV and aging.

PloS one

Lee SA, Sinclair E, Hatano H, Hsue PY, Epling L, Hecht FM, Bangsberg DR, Martin JN, McCune JM, Deeks SG, Hunt PW

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

Lee SA, Haiman CA, Burtt NP, Pooler LC, Cheng I, Kolonel LN, Pike MC, Altshuler D, Hirschhorn JN, Henderson BE, Stram DO

Chapter 40 Body weight, menopausal hormone therapy, and risk of breast cancer.

Treatment of the Postmenopausal Woman

Anna H. Wu, C. Leigh Pearce, Darcy V. Spicer, Sulggi Lee, Malalcolm C. Pike

Complexity of Plasmodium falciparum infections and antimalarial drug efficacy at 7 sites in Uganda.

The Journal of infectious diseases

Lee SA, Yeka A, Nsobya SL, Dokomajilar C, Rosenthal PJ, Talisuna A, Dorsey G

Postmenopausal hormone therapy and breast cancer risk: the Multiethnic Cohort.

International journal of cancer

Lee S, Kolonel L, Wilkens L, Wan P, Henderson B, Pike M