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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Crain CR, Traunbauer AK, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Dorazio D, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Sieg S, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and host mediators of non-suppressible HIV-1 viremia. Nat Med 2023; 29:3212-3223. [PMID: 37957382 PMCID: PMC10719098 DOI: 10.1038/s41591-023-02611-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) is defined as persistent low-level viremia on antiretroviral therapy (ART) without evidence of ART non-adherence or significant drug resistance. Unraveling the mechanisms behind NSV would broaden our understanding of HIV-1 persistence. Here we analyzed plasma virus sequences in eight ART-treated individuals with NSV (88% male) and show that they are composed of large clones without evidence of viral evolution over time in those with longitudinal samples. We defined proviruses that match plasma HIV-1 RNA sequences as 'producer proviruses', and those that did not as 'non-producer proviruses'. Non-suppressible viremia arose from expanded clones of producer proviruses that were significantly larger than the genome-intact proviral reservoir of ART-suppressed individuals. Integration sites of producer proviruses were enriched in proximity to the activating H3K36me3 epigenetic mark. CD4+ T cells from participants with NSV demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, participants with NSV showed significantly lower HIV-specific CD8+ T cell responses compared with untreated viremic controllers with similar viral loads. We identified potential critical host and viral mediators of NSV that may represent targets to disrupt HIV-1 persistence.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Valley Health System, Las Vegas, NV, USA
| | - Behzad Etemad
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Beijing Friendship Hospital Pinggu Campus, Capital Medical University, Beijing, China
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Gregory J Bedwell
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Radwa Sharaf
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charles R Crain
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Anna K Traunbauer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Colline Wong
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Francoise Giguel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Rinki Deo
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dominic Dorazio
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Peter L Anderson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M Lederman
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D Lichterfeld
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Scott Sieg
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Athe Tsibris
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Jose R Castillo-Mancilla
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan N Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D Gaiha
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and Host Mediators of Non-Suppressible HIV-1 Viremia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.30.23287124. [PMID: 37034605 PMCID: PMC10081408 DOI: 10.1101/2023.03.30.23287124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) can occur in persons with HIV despite adherence to combination antiretroviral therapy (ART) and in the absence of significant drug resistance. Here, we show that plasma NSV sequences are comprised primarily of large clones without evidence of viral evolution over time. We defined proviruses that contribute to plasma viremia as "producer", and those that did not as "non-producer". Compared to ART-suppressed individuals, NSV participants had a significantly larger producer reservoir. Producer proviruses were enriched in chromosome 19 and in proximity to the activating H3K36me3 epigenetic mark. CD4+ cells from NSV participants demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, NSV participants showed no elevation in HIV-specific CD8+ cell responses and producer proviruses were enriched for HLA escape mutations. We identified critical host and viral mediators of NSV that represent potential targets to disrupt HIV persistence and promote viral silencing.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Behzad Etemad
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yijia Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Radwa Sharaf
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Colline Wong
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Francoise Giguel
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Rinki Deo
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter L. Anderson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M. Lederman
- Center for AIDS Research, Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D. Lichterfeld
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Athe Tsibris
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Jose R. Castillo-Mancilla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alan N. Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D. Gaiha
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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Hanson HM, Willkomm NA, Yang H, Mansky LM. Human Retrovirus Genomic RNA Packaging. Viruses 2022; 14:1094. [PMID: 35632835 PMCID: PMC9142903 DOI: 10.3390/v14051094] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 02/07/2023] Open
Abstract
Two non-covalently linked copies of the retrovirus genome are specifically recruited to the site of virus particle assembly and packaged into released particles. Retroviral RNA packaging requires RNA export of the unspliced genomic RNA from the nucleus, translocation of the genome to virus assembly sites, and specific interaction with Gag, the main viral structural protein. While some aspects of the RNA packaging process are understood, many others remain poorly understood. In this review, we provide an update on recent advancements in understanding the mechanism of RNA packaging for retroviruses that cause disease in humans, i.e., HIV-1, HIV-2, and HTLV-1, as well as advances in the understanding of the details of genomic RNA nuclear export, genome translocation to virus assembly sites, and genomic RNA dimerization.
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Affiliation(s)
- Heather M. Hanson
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA;
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
| | - Nora A. Willkomm
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- DDS-PhD Dual Degree Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- Comparative Molecular Biosciences Graduate Program, University of Minnesota—Twin Cities, St. Paul, MN 55455, USA
| | - Louis M. Mansky
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA;
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- DDS-PhD Dual Degree Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Comparative Molecular Biosciences Graduate Program, University of Minnesota—Twin Cities, St. Paul, MN 55455, USA
- Masonic Cancer Center, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
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Investigation of the Low-Populated Excited States of the HIV-1 Nucleocapsid Domain. Viruses 2022; 14:v14030632. [PMID: 35337039 PMCID: PMC8950434 DOI: 10.3390/v14030632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
The nucleocapsid domain (NCd), located at the C-terminus of the HIV-1 Gag protein, is involved in numerous stages of the replication cycle, such as the packaging of the viral genome and reverse transcription. It exists under different forms through the viral life cycle, depending on the processing of Gag by the HIV-1 protease. NCd is constituted of two adjacent zinc knuckles (ZK1 and ZK2), separated by a flexible linker and flanked by disordered regions. Here, conformational equilibria between a major and two minor states were highlighted exclusively in ZK2, by using CPMG and CEST NMR experiments. These minor states appear to be temperature dependent, and their populations are highest at physiological temperature. These minor states are present both in NCp7, the mature form of NCd, and in NCp9 and NCp15, the precursor forms of NCd, with increased populations. The role of these minor states in the targeting of NCd by drugs and its binding properties is discussed.
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