Steven Yukl, MD
Professor
Medicine
School of Medicine

After the start of the COVID-19 pandemic, we also became interested in the transcriptional regulation of SARS-CoV-2, another RNA virus. We are currently investigating how SARS-CoV-2 subgenomic transcription (which is analogous to RNA splicing) allows for variation in the expression of different coronavirus genes over time, and how these SARS-CoV-2 subgenomic RNAs interact with human cells to govern the pathogenesis of COVID-19.

• ABX464 Decreases the Total Human Immunodeficiency Virus (HIV) Reservoir and HIV Transcription Initiation in CD4+ T Cells From Antiretroviral Therapy-Suppressed Individuals Living With HIV.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 Moron-Lopez S, Bernal S, Wong JK, Martinez-Picado J, Yukl SA
• Novel assays to investigate the mechanisms of latent infection with HIV-2.
  PloS one 2022 Lu MD, Telwatte S, Kumar N, Ferreira F, Martin HA, Kadiyala GN, Wedrychowski A, Moron-Lopez S, Chen TH, Goecker EA, Coombs RW, Lu CM, Wong JK, Tsibris A, Yukl 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) 2022 Xie G, Moron-Lopez S, Siegel DA, Yin K, Polos A, Cohen J, Greenblatt RM, Tien PC, Lee SA, Yukl SA, Roan NR
• Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses.
  Cell 2022 Einkauf KB, Osborn MR, Gao C, Sun W, Sun X, Lian X, Parsons EM, Gladkov GT, Seiger KW, Blackmer JE, Jiang C, Yukl SA, Rosenberg ES, Yu XG, Lichterfeld M
• Gag p24 Is a Marker of Human Immunodeficiency Virus Expression in Tissues and Correlates With Immune Response.
  The Journal of infectious diseases 2021 Wu G, Zuck P, Goh SL, Milush JM, Vohra P, Wong JK, Somsouk M, Yukl SA, Shacklett BL, Chomont N, Haase AT, Hatano H, Schacker TW, Deeks SG, Hazuda DJ, Hunt PW, Howell BJ
• 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 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
• Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts.
  Methods (San Diego, Calif.) 2021 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 simultaneous quantification of multiple noncoding and coding regions of SARS-CoV-2 RNA.
  Journal of virological methods 2021 Telwatte S, Kumar N, Vallejo-Gracia A, Kumar GR, Lu CM, Ott M, Wong JK, Yukl SA
• Relationship between CD4 T cell turnover, cellular differentiation and HIV persistence during ART.
  PLoS pathogens 2021 Bacchus-Souffan C, Fitch M, Symons J, Abdel-Mohsen M, Reeves DB, Hoh R, Stone M, Hiatt J, Kim P, Chopra A, Ahn H, York VA, Cameron DL, Hecht FM, Martin JN, Yukl SA, Mallal S, Cameron PU, Deeks SG, …
• Novel RT-ddPCR Assays for determining the transcriptional profile of SARS-CoV-2.
  bioRxiv : the preprint server for biology 2021 Telwatte S, Kumar N, Vallejo-Gracia A, Kumar GR, Lu CM, Ott M, Wong JK, Yukl SA
• Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103+ and Gut CD4+ T Cells.
  Journal of virology 2020 Yukl SA, Khan S, Chen TH, Trapecar M, Wu F, Xie G, Telwatte S, Fulop D, Pico AR, Laird GM, Ritter KD, Jones NG, Lu CM, Siliciano RF, Roan NR, Milush JM, Somsouk M, Deeks SG, Hunt PW, Sanjabi S
• Human splice factors contribute to latent HIV infection in primary cell models and blood CD4+ T cells from ART-treated individuals.
  PLoS pathogens 2020 Moron-Lopez S, Telwatte S, Sarabia I, Battivelli E, Montano M, Macedo AB, Aran D, Butte AJ, Jones RB, Bosque A, Verdin E, Greene WC, Wong JK, Yukl SA
• Mechanistic differences underlying HIV latency in the gut and blood contribute to differential responses to latency-reversing agents.
  AIDS (London, England) 2020 Telwatte S, Kim P, Chen TH, Milush JM, Somsouk M, Deeks SG, Hunt PW, Wong JK, Yukl SA
• Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir.
  eLife 2020 Neidleman J, Luo X, Frouard J, Xie G, Hsiao F, Ma T, Morcilla V, Lee A, Telwatte S, Thomas R, Tamaki W, Wheeler B, Hoh R, Somsouk M, Vohra P, Milush J, James KS, Archin NM, Hunt PW, Deeks SG, Yukl SA,…
• HSF1 inhibition attenuates HIV-1 latency reversal mediated by several candidate LRAs In Vitro and Ex Vivo.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Timmons A, Fray E, Kumar M, Wu F, Dai W, Bullen CK, Kim P, Hetzel C, Yang C, Beg S, Lai J, Pomerantz JL, Yukl SA, Siliciano JD, Siliciano RF
• Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127) preferentially support latent HIV-1 infection.
  PLoS pathogens 2020 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) 2020 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 7.6 Tissue-specific differences in the mechanisms that govern HIV latency in blood, liver, gut and genital tract in ART-suppressed women.
  Journal of virus eradication 2019 S. Moron-Lopez, G. Xie, P. Kim, J. Wong, J. Price, N. Elnachef, R. Greenblatt, P. Tien, N. Roan, S. Yukl
• OP 8.3 Intensification of ART with ABX464 decreases the total HIV reservoir and HIV transcription initiation in CD4 T cells from HIV-infected ART-suppressed individuals.
  Journal of virus eradication 2019 S. Moron-Lopez, S. Bernal, J.M. Steens, J.K. Wong, J. Martinez-Picado, S.A. Yukl
• PP 1.3 Single cell analysis reveals molecular signatures of HIV latency in primary cell models.
  Journal of virus eradication 2019 S. Telwatte, M. Montano, R. Resop, E. Battivelli, S. Morón-López, E. Verdin, W. Greene, A. Bosque, J. Wong, S. Yukl
• Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency.
  Retrovirology 2019 Telwatte S, Morón-López S, Aran D, Kim P, Hsieh C, Joshi S, Montano M, Greene WC, Butte AJ, Wong JK, Yukl SA
• 10 Tissue-specific effects of latency-reversing agents on HIV transcriptional blocks in gut and blood.
  Journal of virus eradication 2019 S. Telwatte, P. Kim, T.-H. Chen, J. Milush, M. Somsouk, P. Hunt, S. Deeks, J. Wong, S. Yukl
• 12 In-depth transcription profile comparison of multiple primary cell HIV latency models.
  Journal of virus eradication 2019 S. Moron-Lopez, I. Sarabia, E. Battivelli, M. Montano, S. Telwatte, A. Bosque, E. Verdin, W. Greene, J.K. Wong, S.A. Yukl
• Disruption of latent HIV in vivo during the clearance of actinic keratosis by ingenol mebutate.
  JCI insight 2019 Jiang G, Maverakis E, Cheng MY, Elsheikh MM, Deleage C, Méndez-Lagares G, Shimoda M, Yukl SA, Hartigan-O'Connor DJ, Thompson GR, Estes JD, Wong JK, Dandekar S
• Characterization of the HIV-1 transcription profile after romidepsin administration in ART-suppressed individuals.
  AIDS (London, England) 2019 Moron-Lopez S, Kim P, Søgaard OS, Tolstrup M, 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 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
• HIV latency in isolated patient CD4+ T cells may be due to blocks in HIV transcriptional elongation, completion, and splicing.
  Science translational medicine 2018 Yukl SA, Kaiser P, Kim P, Telwatte S, Joshi SK, Vu M, Lampiris H, Wong JK
• HIV latency is reversed by ACSS2-driven histone crotonylation.
  The Journal of clinical investigation 2018 Jiang G, Nguyen D, Archin NM, Yukl SA, Méndez-Lagares G, Tang Y, Elsheikh MM, Thompson GR, Hartigan-O'Connor DJ, Margolis DM, Wong JK, Dandekar S
• Acetylation.
  2018 Anna Cereseto, Yuntao Wu, Jan Davidson-Moncada, Thomas S. Uldrick, Joel Palefsky, Steven A. Yukl, Joseph K. Wong, Shokouh Makvandi-Nejad, Courtney V. Fletcher, Anthony T. Podany, Andrea Calcagno, C. …
• Anatomic Compartments as a Barrier to HIV Cure.
  Encyclopedia of AIDS 2018 Steven A. Yukl, Joseph K. Wong
• OP4.6 Gut and blood differ in mechanisms governing HIV transcription/latency.
  Journal of virus eradication 2017 S. Telwatte, S. Lee, M. Somsouk, H. Hatano, C. Baker, P. Kim, T.-H. Chen, J. Milush, P. Hunt, S. Deeks, J.K. Wong, S.A. Yukl
• HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: An observational study.
  PLoS medicine 2017 Henrich TJ, Hatano H, Bacon O, Hogan LE, Rutishauser R, Hill A, Kearney MF, Anderson EM, Buchbinder SP, Cohen SE, Abdel-Mohsen M, Pohlmeyer CW, Fromentin R, Hoh R, Liu AY, McCune JM, Spindler J, …
• An Optimized and Validated Method for Isolation and Characterization of Lymphocytes from HIV+ Human Gut Biopsies.
  AIDS research and human retroviruses 2017 Trapecar M, Khan S, Roan NR, Chen TH, Telwatte S, Deswal M, Pao M, Somsouk M, Deeks SG, Hunt PW, Yukl S, Sanjabi S
• Differentiating Immune Cell Targets in Gut-Associated Lymphoid Tissue for HIV Cure.
  AIDS research and human retroviruses 2017 Khan S, Telwatte S, Trapecar M, Yukl S, Sanjabi S
• A Randomized Controlled Trial of Lisinopril to Decrease Lymphoid Fibrosis in Antiretroviral-Treated, HIV-infected Individuals.
  Pathogens & immunity 2017 Cockerham LR, Yukl SA, Harvill K, Somsouk M, Joshi SK, Sinclair E, Liegler T, Hoh R, Lyons S, Hunt PW, Rupert A, Sereti I, Morcock DR, Rhodes A, Emson C, Hellerstein MK, Estes JD, Lewin S, Deeks SG, …
• Impact of Allogeneic Hematopoietic Stem Cell Transplantation on the HIV Reservoir and Immune Response in 3 HIV-Infected Individuals.
  Journal of acquired immune deficiency syndromes (1999) 2017 Koelsch KK, Rasmussen TA, Hey-Nguyen WJ, Pearson C, Xu Y, Bailey M, Marks KH, Sasson SC, Taylor MS, Tantau R, Obeid S, Milner B, Morrissey O, Pinto AN, Suzuki K, Busch MP, Keating SM, Kaiser P, Yukl S…
• Exploring HIV latency using transcription profiling.
  Microbiology Australia 2017 Sushama Telwatte, Steven A Yukl
• Assays for precise quantification of total (including short) and elongated HIV-1 transcripts.
  Journal of virological methods 2016 Kaiser P, Joshi SK, Kim P, Li P, Liu H, Rice AP, Wong JK, Yukl SA
• Anti-HIV Antibody Responses and the HIV Reservoir Size during Antiretroviral Therapy.
  PloS one 2016 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
• Tissue reservoirs of HIV.
  Current opinion in HIV and AIDS 2016 Wong JK, Yukl SA
• Stimulating the RIG-I pathway to kill cells in the latent HIV reservoir following viral reactivation.
  Nature medicine 2016 Li P, Kaiser P, Lampiris HW, Kim P, Yukl SA, Havlir DV, Greene WC, Wong JK
• Site-specific differences in T cell frequencies and phenotypes in the blood and gut of HIV-uninfected and ART-treated HIV+ adults.
  PloS one 2015 Yukl SA, Shergill AK, Girling V, Li Q, Killian M, Epling L, Li P, Kaiser P, Haase A, Havlir DV, McQuaid K, Sinclair E, Wong JK
• Anatomic Compartments as a Barrier to HIV Cure.
  Encyclopedia of AIDS 2015 Steven A. Yukl, Joseph K. Wong
• CD4+ and CD8+ T cell activation are associated with HIV DNA in resting CD4+ T cells.
  PloS one 2014 Cockerham LR, Siliciano JD, Sinclair E, O'Doherty U, Palmer S, Yukl SA, Strain MC, Chomont N, Hecht FM, Siliciano RF, Richman DD, Deeks SG
• Exogenous and endogenous hyaluronic acid reduces HIV infection of CD4(+) T cells.
  Immunology and cell biology 2014 Li P, Fujimoto K, Bourguingnon L, Yukl S, Deeks S, Wong JK
• Decreased HIV type 1 transcription in CCR5-Δ32 heterozygotes during suppressive antiretroviral therapy.
  The Journal of infectious diseases 2014 Wang C, Abdel-Mohsen M, Strain MC, Lada SM, Yukl S, Cockerham LR, Pilcher CD, Hecht FM, Sinclair E, Liegler T, Richman DD, Deeks SG, Pillai SK
• Advantages of using the QIAshredder instead of restriction digestion to prepare DNA for droplet digital PCR.
  BioTechniques 2014 Yukl SA, Kaiser P, Kim P, Li P, Wong JK
• Discordance between peripheral and colonic markers of inflammation during suppressive ART.
  Journal of acquired immune deficiency syndromes (1999) 2014 Dunham RM, Vujkovic-Cvijin I, Yukl SA, Broadhurst MJ, Loke P, Albright RG, Wong JK, Lederman MM, Somsouk M, Hunt PW, Martin JN, Deeks SG, McCune JM
• A comparison of methods for measuring rectal HIV levels suggests that HIV DNA resides in cells other than CD4+ T cells, including myeloid cells.
  AIDS (London, England) 2014 Yukl SA, Sinclair E, Somsouk M, Hunt PW, Epling L, Killian M, Girling V, Li P, Havlir DV, Deeks SG, Wong JK, Hatano H
• Prospective antiretroviral treatment of asymptomatic, HIV-1 infected controllers.
  PLoS pathogens 2013 Hatano H, Yukl SA, Ferre AL, Graf EH, Somsouk M, Sinclair E, Abdel-Mohsen M, Liegler T, Harvill K, Hoh R, Palmer S, Bacchetti P, Hunt PW, Martin JN, McCune JM, Tracy RP, Busch MP, O'Doherty U, …
• Comparison of HIV DNA and RNA in gut-associated lymphoid tissue of HIV-infected controllers and noncontrollers.
  AIDS (London, England) 2013 Hatano H, Somsouk M, Sinclair E, Harvill K, Gilman L, Cohen M, Hoh R, Hunt PW, Martin JN, Wong JK, Deeks SG, Yukl SA
• The distribution of HIV DNA and RNA in cell subsets differs in gut and blood of HIV-positive patients on ART: implications for viral persistence.
  The Journal of infectious diseases 2013 Yukl SA, Shergill AK, Ho T, Killian M, Girling V, Epling L, Li P, Wong LK, Crouch P, Deeks SG, Havlir DV, McQuaid K, Sinclair E, Wong JK
• Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient.
  PLoS pathogens 2013 Yukl SA, Boritz E, Busch M, Bentsen C, Chun TW, Douek D, Eisele E, Haase A, Ho YC, Hütter G, Justement JS, Keating S, Lee TH, Li P, Murray D, Palmer S, Pilcher C, Pillai S, Price RW, Rothenberger M, …
• Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies.
  PLoS pathogens 2013 Eriksson S, Graf EH, Dahl V, Strain MC, Yukl SA, Lysenko ES, Bosch RJ, Lai J, Chioma S, Emad F, Abdel-Mohsen M, Hoh R, Hecht F, Hunt P, Somsouk M, Wong J, Johnston R, Siliciano RF, Richman DD, O'…
• Role of retroviral restriction factors in the interferon-α-mediated suppression of HIV-1 in vivo.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Pillai SK, Abdel-Mohsen M, Guatelli J, Skasko M, Monto A, Fujimoto K, Yukl S, Greene WC, Kovari H, Rauch A, Fellay J, Battegay M, Hirschel B, Witteck A, Bernasconi E, Ledergerber B, Günthard HF, Wong …
• Modification of the Abbott RealTime assay for detection of HIV-1 plasma RNA viral loads less than one copy per milliliter.
  Journal of virological methods 2011 Yukl SA, Li P, Fujimoto K, Lampiris H, Lu CM, Hare CB, Deeks SG, Liegler T, Pandori M, Havlir DV, Wong JK
• CD4+ T cell reconstitution, T cell activation, and memory T cell subset composition in blood and gut of HIV-negative and ART-suppressed HIV-positive patients: implications for HIV persistence in the gut.
  Journal of the International AIDS Society 2010 S Yukl, E Sinclair, L Epling, Q Li, A Shergill, K McQuaid, L Duan, B Hare, H Lampiris, A Haase, D Havlir, J Wong
• Effect of raltegravir-containing intensification on HIV burden and T-cell activation in multiple gut sites of HIV-positive adults on suppressive antiretroviral therapy.
  AIDS (London, England) 2010 Yukl SA, Shergill AK, McQuaid K, Gianella S, Lampiris H, Hare CB, Pandori M, Sinclair E, Günthard HF, Fischer M, Wong JK, Havlir DV
• Differences in HIV burden and immune activation within the gut of HIV-positive patients receiving suppressive antiretroviral therapy.
  The Journal of infectious diseases 2010 Yukl SA, Gianella S, Sinclair E, Epling L, Li Q, Duan L, Choi AL, Girling V, Ho T, Li P, Fujimoto K, Lampiris H, Hare CB, Pandori M, Haase AT, Günthard HF, Fischer M, Shergill AK, McQuaid K, Havlir DV…
• Novel application of Locked Nucleic Acid chemistry for a Taqman assay for measuring diverse human immunodeficiency virus type 1 subtypes.
  Journal of virological methods 2010 Li P, Ruel T, Fujimoto K, Hatano H, Yukl S, Eller LA, Liegler T, Kamya M, Gassasira A, Dorsey G, Rosenthal PJ, Havlir DV, Wong JK
• Latently-infected CD4+ T cells are enriched for HIV-1 Tat variants with impaired transactivation activity.
  Virology 2009 Yukl S, Pillai S, Li P, Chang K, Pasutti W, Ahlgren C, Havlir D, Strain M, Günthard H, Richman D, Rice AP, Daar E, Little S, Wong JK
• Blood and guts and HIV: preferential HIV persistence in GI mucosa.
  The Journal of infectious diseases 2008 Yukl S, Wong JK
• The W(sh), W(57), and Ph Kit expression mutations define tissue-specific control elements located between -23 and -154 kb upstream of Kit.
  Blood 1999 Berrozpe G, Timokhina I, Yukl S, Tajima Y, Ono M, Zelenetz AD, Besmer P