1
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Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, Ott M, Eckhardt M, Hultquist JF, Marson A, Kaake RM, Krogan NJ. CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells. mBio 2024; 15:e0222223. [PMID: 38411080 PMCID: PMC11005436 DOI: 10.1128/mbio.02222-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/09/2024] [Indexed: 02/28/2024] Open
Abstract
During HIV infection of CD4+ T cells, ubiquitin pathways are essential to viral replication and host innate immune response; however, the role of specific E3 ubiquitin ligases is not well understood. Proteomics analyses identified 116 single-subunit E3 ubiquitin ligases expressed in activated primary human CD4+ T cells. Using a CRISPR-based arrayed spreading infectivity assay, we systematically knocked out 116 E3s from activated primary CD4+ T cells and infected them with NL4-3 GFP reporter HIV-1. We found 10 E3s significantly positively or negatively affected HIV infection in activated primary CD4+ T cells, including UHRF1 (pro-viral) and TRAF2 (anti-viral). Furthermore, deletion of either TRAF2 or UHRF1 in three JLat models of latency spontaneously increased HIV transcription. To verify this effect, we developed a CRISPR-compatible resting primary human CD4+ T cell model of latency. Using this system, we found that deletion of TRAF2 or UHRF1 initiated latency reactivation and increased virus production from primary human resting CD4+ T cells, suggesting these two E3s represent promising targets for future HIV latency reversal strategies. IMPORTANCE HIV, the virus that causes AIDS, heavily relies on the machinery of human cells to infect and replicate. Our study focuses on the host cell's ubiquitination system which is crucial for numerous cellular processes. Many pathogens, including HIV, exploit this system to enhance their own replication and survival. E3 proteins are part of the ubiquitination pathway that are useful drug targets for host-directed therapies. We interrogated the 116 E3s found in human immune cells known as CD4+ T cells, since these are the target cells infected by HIV. Using CRISPR, a gene-editing tool, we individually removed each of these enzymes and observed the impact on HIV infection in human CD4+ T cells isolated from healthy donors. We discovered that 10 of the E3 enzymes had a significant effect on HIV infection. Two of them, TRAF2 and UHRF1, modulated HIV activity within the cells and triggered an increased release of HIV from previously dormant or "latent" cells in a new primary T cell assay. This finding could guide strategies to perturb hidden HIV reservoirs, a major hurdle to curing HIV. Our study offers insights into HIV-host interactions, identifies new factors that influence HIV infection in immune cells, and introduces a novel methodology for studying HIV infection and latency in human immune cells.
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Affiliation(s)
- Ujjwal Rathore
- Gladstone Institutes, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Paige Haas
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Vigneshwari Easwar Kumar
- Gladstone Institutes, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Joseph Hiatt
- Gladstone Institutes, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Medical Scientist Training Program, University of California, San Francisco, California, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, USA
| | - Kelsey M. Haas
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Mehdi Bouhaddou
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Danielle L. Swaney
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Erica Stevenson
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Lorena Zuliani-Alvarez
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Michael J. McGregor
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | | | - Charles Ochieng' Olwal
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana
| | - Hannes Braberg
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Margaret Soucheray
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, USA
| | - Manon Eckhardt
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alexander Marson
- Gladstone Institutes, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Medicine, University of California, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, California, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Robyn M. Kaake
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Nevan J. Krogan
- Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
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2
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Cisneros WJ, Walter M, Soliman SH, Simons LM, Cornish D, Halle AW, Kim EY, Wolinsky SM, Shilatifard A, Hultquist JF. Release of P-TEFb from the Super Elongation Complex promotes HIV-1 latency reversal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582881. [PMID: 38464055 PMCID: PMC10925308 DOI: 10.1101/2024.03.01.582881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The persistence of HIV-1 in long-lived latent reservoirs during suppressive antiretroviral therapy (ART) remains one of the principal barriers to a functional cure. Blocks to transcriptional elongation play a central role in maintaining the latent state, and several latency reversal strategies focus on the release of positive transcription elongation factor b (P-TEFb) from sequestration by negative regulatory complexes, such as the 7SK complex and BRD4. Another major cellular reservoir of P-TEFb is in Super Elongation Complexes (SECs), which play broad regulatory roles in host gene expression. Still, it is unknown if the release of P-TEFb from SECs is a viable latency reversal strategy. Here, we demonstrate that the SEC is not required for HIV-1 replication in primary CD4+ T cells and that a small molecular inhibitor of the P-TEFb/SEC interaction (termed KL-2) increases viral transcription. KL-2 acts synergistically with other latency reversing agents (LRAs) to reactivate viral transcription in several cell line models of latency in a manner that is, at least in part, dependent on the viral Tat protein. Finally, we demonstrate that KL-2 enhances viral reactivation in peripheral blood mononuclear cells (PBMCs) from people living with HIV on suppressive ART, most notably in combination with inhibitor of apoptosis protein antagonists (IAPi). Taken together, these results suggest that the release of P-TEFb from cellular SECs may be a novel route for HIV-1 latency reactivation.
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Affiliation(s)
- William J. Cisneros
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Miriam Walter
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shimaa H.A. Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Daphne Cornish
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ariel W. Halle
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven M. Wolinsky
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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3
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Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569805. [PMID: 38076945 PMCID: PMC10705567 DOI: 10.1101/2023.12.03.569805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.
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4
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Bouzidi MS, Dossani ZY, Di Benedetto C, Raymond KA, Desai S, Chavez LR, Betancur P, Pillai SK. High-resolution Inference of Multiplexed Anti-HIV Gene Editing using Single-Cell Targeted DNA Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.576921. [PMID: 38328062 PMCID: PMC10849705 DOI: 10.1101/2024.01.24.576921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Gene therapy-based HIV cure strategies typically aim to excise the HIV provirus directly, or target host dependency factors (HDFs) that support viral persistence. Cure approaches will likely require simultaneous co-targeting of multiple sites within the HIV genome to prevent evolution of resistance, and/or co-targeting of multiple HDFs to fully render host cells refractory to HIV infection. Bulk cell-based methods do not enable inference of co-editing within individual viral or target cell genomes, and do not discriminate between monoallelic and biallelic gene disruption. Here, we describe a targeted single-cell DNA sequencing (scDNA-seq) platform characterizing the near full-length HIV genome and 50 established HDF genes, designed to evaluate anti-HIV gene therapy strategies. We implemented the platform to investigate the capacity of multiplexed CRISPR-Cas9 ribonucleoprotein complexes (Cas9-RNPs) to simultaneously 1) inactivate the HIV provirus, and 2) knockout the CCR5 and CXCR4 HDF (entry co-receptor) genes in microglia and primary monocyte-derived macrophages (MDMs). Our scDNA-seq pipeline revealed that antiviral gene editing is rarely observed at multiple loci (or both alleles of a locus) within an individual cell, and editing probabilities across sites are linked. Our results demonstrate that single-cell sequencing is critical to evaluate the true efficacy and therapeutic potential of HIV gene therapy.
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Affiliation(s)
- Mohamed S. Bouzidi
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Zain Y. Dossani
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | - Kyle A. Raymond
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
| | | | - Leonard R. Chavez
- Vitalant Research Institute, San Francisco, CA, USA
- Rewrite Therapeutics, Berkeley, CA, USA
| | - Paola Betancur
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Satish K. Pillai
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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5
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Xiao H, Rosen A, Chhibbar P, Moise L, Das J. From bench to bedside via bytes: Multi-omic immunoprofiling and integration using machine learning and network approaches. Hum Vaccin Immunother 2023; 19:2282803. [PMID: 38100557 PMCID: PMC10730168 DOI: 10.1080/21645515.2023.2282803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
A significant surge in research endeavors leverages the vast potential of high-throughput omic technology platforms for broad profiling of biological responses to vaccines and cutting-edge immunotherapies and stem-cell therapies under development. These profiles capture different aspects of core regulatory and functional processes at different scales of resolution from molecular and cellular to organismal. Systems approaches capture the complex and intricate interplay between these layers and scales. Here, we summarize experimental data modalities, for characterizing the genome, epigenome, transcriptome, proteome, metabolome, and antibody-ome, that enable us to generate large-scale immune profiles. We also discuss machine learning and network approaches that are commonly used to analyze and integrate these modalities, to gain insights into correlates and mechanisms of natural and vaccine-mediated immunity as well as therapy-induced immunomodulation.
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Affiliation(s)
- Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron Rosen
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Prabal Chhibbar
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
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6
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Au TY, Arudkumar J, Assavarittirong C, Benjamin S. Killing two birds with one stone: CRISPR/Cas9 CCR5 knockout hematopoietic stem cells transplantation to treat patients with HIV infection and hematological malignancies concurrently. Clin Exp Med 2023; 23:4163-4175. [PMID: 37500934 DOI: 10.1007/s10238-023-01129-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Abstract
Human immunodeficiency virus (HIV) is known to cause hematological malignancy. Hematopoietic stem cell transplantation (HPSCT) is an advanced treatment for that. Currently, there are three successful HIV-eliminated cases, and two received HPSCT from CCR5-absent donors. It is well established that the CCR5 protein on the cell surface assists human immunodeficiency virus entry. Preliminary studies have revealed that knocking out CCR5 and/or CXCR4 may inhibit the viral entry of HIV, which may prove promising in the further development of HIV treatment options. Herein, we suggest performing autologous or allogeneic HSCT with CCR5 KO hematopoietic stem cells in patients who suffer from complicated HIV conditions, particularly drug-resistant HIV or a concurrent diagnosis of HIV with lymphoma/leukemia, to achieve complete HIV remission. Nevertheless, at the clinical forefront of CRISPR-HIV technology, more efforts should be directed to advance nonhuman primate (NHP) models for studies of HIV pathogenesis and off-target assessments within this system. CRISPR-Cas9 knock out of host HSCT-expressing CCR5 or CXCR4 may confer HIV-resistance, which when applied to bedside therapeutics in an allogeneic or autologous manner can warrant a permanent and effective treatment outcome.
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Affiliation(s)
- Tsz Yuen Au
- Center for Medical Education in English, Poznan University of Medical Sciences, Poznan, Poland
| | - Jayshen Arudkumar
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
- The University of Adelaide, Adelaide, SA, Australia.
| | - Chanika Assavarittirong
- Center for Medical Education in English, Poznan University of Medical Sciences, Poznan, Poland
| | - Shamiram Benjamin
- Center for Medical Education in English, Poznan University of Medical Sciences, Poznan, Poland
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7
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Imamichi T, Chen Q, Sowrirajan B, Yang J, Laverdure S, Marquez M, Mele AR, Watkins C, Adelsberger JW, Higgins J, Sui H. Interleukin-27-induced HIV-resistant dendritic cells suppress reveres transcription following virus entry in an SPTBN1, autophagy, and YB-1 independent manner. PLoS One 2023; 18:e0287829. [PMID: 37910521 PMCID: PMC10619827 DOI: 10.1371/journal.pone.0287829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023] Open
Abstract
Interleukin (IL)-27, a member of the IL-12 family of cytokines, induces human immunodeficiency virus (HIV)-resistant monocyte-derived macrophages and T cells. This resistance is mediated via the downregulation of spectrin beta, non-erythrocytic 1 (SPTBN1), induction of autophagy, or suppression of the acetylation of Y-box binding protein-1 (YB-1); however, the role of IL-27 administration during the induction of immature monocyte-derived dendritic cells (iDC) is poorly investigated. In the current study, we investigated the function of IL-27-induced iDC (27DC) on HIV infection. 27DC inhibited HIV infection by 95 ± 3% without significant changes in the expression of CD4, CCR5, and SPTBN1 expression, autophagy induction and acetylation of YB-1 compared to iDC. An HIV proviral DNA copy number assay displayed that 27DC suppressed reverse transcriptase (RT) reaction without influencing the virus entry. A DNA microarray analysis was performed to identify the differentially expressed genes between 27DC and iDC. Compared to iDC, 51 genes were differentially expressed in 27DC, with more than 3-fold changes in four independent donors. Cross-reference analysis with the reported 2,214 HIV regulatory host genes identified nine genes as potential interests: Ankyrin repeat domain 22, Guanylate binding protein (GBP)-1, -2, -4, -5, Stabilin 1, Serpin family G member 1 (SERPING1), Interferon alpha inducible protein 6, and Interferon-induced protein with tetratricopeptide repeats 3. A knock-down study using si-RNA failed to determine a key factor associated with the anti-HIV activity due to the induction of robust amounts of off-target effects. Overexpression of each protein in cells had no impact on HIV infection. Thus, we could not define the mechanism of the anti-HIV effect in 27DC. However, our findings indicated that IL-27 differentiates monocytes into HIV-resistant DC, and the inhibitory mechanism differs from IL-27-induced HIV-resistant macrophages and T cells.
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Affiliation(s)
- Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Qian Chen
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Bharatwaj Sowrirajan
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jun Yang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Sylvain Laverdure
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mayra Marquez
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Anthony R. Mele
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Catherine Watkins
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Joseph W. Adelsberger
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jeanette Higgins
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Hongyan Sui
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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8
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Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun 2023; 14:6030. [PMID: 37758692 PMCID: PMC10533562 DOI: 10.1038/s41467-023-41442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.
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Affiliation(s)
- Kelsey M Haas
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Michael J McGregor
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Thong T Nguyen
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Heejin Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael A P Williams
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Alexandra Hardy
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Erica J Stevenson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Ellie Sukerman
- Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Tiffany Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal and IRYCIS, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Yuan Zhou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Giorgi Metreveli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bhavya Harjai
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - James E Melnyk
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Jyoti Batra
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Laura Martin-Sancho
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Infectious Disease, Imperial College London, London, SW7 2BX, UK
| | - Jared Carlson-Stevermer
- Synthego Corporation, Redwood City, CA, 94063, USA
- Serotiny Inc., South San Francisco, CA, 94080, USA
| | - Alexander S Jureka
- Molecular Virology and Vaccine Team, Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, 30333, USA
- General Dynamics Information Technology, Federal Civilian Division, Atlanta, GA, 30329, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Brian K Shoichet
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63105, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Jeffrey R Johnson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medical Biosciences, University of the Western Cape, Bellville, 7535, Western Cape, South Africa
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marco Vignuzzi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Lorena Zuliani-Alvarez
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kris M White
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judd F Hultquist
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
| | - Adolfo García-Sastre
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
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9
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Ahmed A, Dujaili JA, Chuah LH, Hashmi FK, Le LKD, Chatha ZF, Khanal S, Awaisu A, Chaiyakunapruk N. Cost-Effectiveness Analysis of Pharmacist Adherence Interventions in People Living with HIV/AIDS in Pakistan. Healthcare (Basel) 2023; 11:2453. [PMID: 37685487 PMCID: PMC10487586 DOI: 10.3390/healthcare11172453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Background: Evidence has shown the positive impact of pharmacist involvement on the adherence and health outcomes of people living with HIV/AIDS. However, whether such intervention provides value for money remains unclear. This study aims to fill this gap by assessing the cost-effectiveness of pharmacist interventions in HIV care in Pakistan. Methods: A Markov decision analytic model was constructed, considering clinical inputs, utility data, and cost data obtained from a randomized controlled trial and an HIV cohort of Pakistani origin. The analysis was conducted from a healthcare perspective, and the incremental cost-effectiveness ratio (ICER) was calculated and presented for the year 2023. Additionally, a series of sensitivity analyses were performed to assess the robustness of the results. Results: Pharmacist intervention resulted in higher quality-adjusted life years (4.05 vs. 2.93) and likewise higher annual intervention costs than usual care (1979 USD vs. 429 USD) (532,894 PKR vs. 115,518 PKR). This yielded the ICER of 1383 USD/quality-adjusted life years (QALY) (372,406 PKR/QALY), which is well below the willingness-to-pay threshold of 1658 USD (446,456 PKR/QALY) recommended by the World Health Organization Choosing Interventions that are Cost-Effective. Probabilistic sensitivity analysis reported that more than 68% of iterations were below the lower limit of threshold. Sensitivity analysis reported intervention cost is the most important parameter influencing the ICER the most. Conclusion: The study suggests that involving pharmacists in HIV care could be a cost-effective approach. These findings could help shape healthcare policies and plans, possibly making pharmacist interventions a regular part of care for people with HIV in Pakistan.
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Affiliation(s)
- Ali Ahmed
- Monash University Health Economics Group (MUHEG), School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Road, Melbourne, VIC 3004, Australia
- School of Pharmacy, Monash University, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad 44000, Pakistan
| | - Juman Abdulelah Dujaili
- School of Pharmacy, Monash University, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
- Swansea University Medical School, Singleton Campus, Swansea University, Wales SA1 8EN, UK
| | - Lay Hong Chuah
- School of Pharmacy, Monash University, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | - Furqan Khurshid Hashmi
- Punjab University College of Pharmacy, University of Punjab, Allama Iqbal Campus, Lahore 54000, Pakistan
| | - Long Khanh Dao Le
- Monash University Health Economics Group (MUHEG), School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Road, Melbourne, VIC 3004, Australia
| | - Zeenat Fatima Chatha
- Department of Community Medicine and Global Health, University of Oslo, 0318 Oslo, Norway
| | - Saval Khanal
- Health Economics Consulting, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Ahmed Awaisu
- Department of Clinical Pharmacy & Practice, College of Pharmacy, QU Health, Qatar University, Doha 2713, Qatar
| | - Nathorn Chaiyakunapruk
- College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
- IDEAS Center, Veterans Affairs Salt Lake City Healthcare System, Salt Lake City, UT 84108, USA
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10
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Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping. Nat Commun 2023; 14:5156. [PMID: 37620325 PMCID: PMC10449902 DOI: 10.1038/s41467-023-40724-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Host-pathogen interactions are pivotal in regulating establishment, progression, and outcome of an infection. While affinity-purification mass spectrometry has become instrumental in characterizing such interactions, it suffers from limitations in scalability and biological authenticity. Here we present the use of co-fractionation mass spectrometry for high throughput analysis of host-pathogen interactions from native viral infections of two jumbophages (ϕKZ and ϕPA3) in Pseudomonas aeruginosa. This approach enabled the detection of > 6000 unique host-pathogen interactions for each phage, encompassing > 50% of their respective proteomes. This deep coverage provided evidence for interactions between KZ-like phage proteins and the host ribosome, and revealed protein complexes for previously undescribed phage ORFs, including a ϕPA3 complex showing strong structural and sequence similarity to ϕKZ non-virion RNA polymerase. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction ( https://phagemap.ucsf.edu/ ). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of host-pathogen interactomes and protein complex dynamics upon infection.
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Affiliation(s)
- Andrea Fossati
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Deepto Mozumdar
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Claire Kokontis
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Melissa Mèndez-Moran
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Eliza Nieweglowska
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Adrian Pelin
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Yuping Li
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Baron Guo
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - David A Agard
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Joseph Bondy-Denomy
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA.
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA.
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11
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Borrmann H, Ulkar G, Kliszczak AE, Ismed D, Schilling M, Magri A, Harris JM, Balfe P, Vasudevan S, Borrow P, Zhuang X, McKeating JA. Molecular components of the circadian clock regulate HIV-1 replication. iScience 2023; 26:107007. [PMID: 37534138 PMCID: PMC10391662 DOI: 10.1016/j.isci.2023.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/24/2023] [Accepted: 05/26/2023] [Indexed: 08/04/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) causes major health burdens worldwide and still lacks curative therapies and vaccines. Circadian rhythms are endogenous daily oscillations that coordinate an organism's response to its environment and invading pathogens. Peripheral viral loads of HIV-1 infected patients show diurnal variation; however, the underlying mechanisms remain unknown. Here, we demonstrate a role for the cell-intrinsic clock to regulate rhythmic HIV-1 replication in circadian-synchronized systems. Silencing the circadian activator Bmal1 abolishes this phenotype, and we observe BMAL1 binding to the HIV-1 promoter. Importantly, we show differential binding of the nuclear receptors REV-ERB and ROR to the HIV-long terminal repeat at different circadian times, demonstrating a dynamic interplay in time-of-day regulation of HIV-1 transcription. Bioinformatic analysis shows circadian regulation of host factors that control HIV-1 replication, providing an additional mechanism for rhythmic viral replication. This study increases our understanding of the circadian regulation of HIV-1, which can ultimately inform new therapies.
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Affiliation(s)
- Helene Borrmann
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Görkem Ulkar
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Anna E. Kliszczak
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dini Ismed
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mirjam Schilling
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Andrea Magri
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - James M. Harris
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Peter Balfe
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Jane A. McKeating
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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12
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. Cell Rep 2023; 42:112556. [PMID: 37227817 PMCID: PMC10592456 DOI: 10.1016/j.celrep.2023.112556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4+ T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4+ T cells by performing CRISPR-knockout screens with a custom library that specifically targets ISGs expressed in CD4+ T cells. Our investigation identifies previously undescribed HIV-restricting ISGs (HM13, IGFBP2, LAP3) and finds that two factors characterized in other HIV infection models (IFI16 and UBE2L6) mediate IFN restriction in T cells. Inactivation of these five ISGs in combination further diminishes IFN's protective effect against diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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13
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Imamichi T, Chen Q, Sowrirajan B, Yang J, Laverdure S, Mele AR, Watkins C, Adelsberger JW, Higgins J, Sui H. Interleukin-27-induced HIV-resistant dendritic cells suppress reveres transcription following virus entry in an SPTBN1, Autophagy, and YB-1 independent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544550. [PMID: 37546823 PMCID: PMC10402176 DOI: 10.1101/2023.06.12.544550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Interleukin (IL)-27, a member of the IL-12 family of cytokines, induces human immunodeficiency virus (HIV)-resistant monocyte-derived macrophages and T cells. This resistance is mediated via the downregulation of spectrin beta, non-erythrocytic 1 (SPTBN1), induction of autophagy, or suppression of the acetylation of Y-box binding protein-1 (YB-1); however, the role of IL-27 administration during the induction of immature monocyte-derived dendritic cells (iDC) is poorly investigated. In the current study, we investigated the function of IL-27-induced iDC (27DC) on HIV infection. 27DC inhibited HIV infection by 95 ± 3 % without significant changes in the expression of CD4, CCR5, and SPTBN1 expression, autophagy induction and acetylation of YB-1 compared to iDC. An HIV proviral DNA copy number assay displayed that 27DC suppressed reverse transcriptase (RT) reaction without influencing the virus entry. A DNA microarray analysis was performed to identify the differentially expressed genes between 27DC and iDC. Compared to iDC, 51 genes were differentially expressed in 27DC, with more than 3-fold changes in four independent donors. Cross-reference analysis with the reported 2,214 HIV regulatory host genes identified nine genes as potential interests: Ankyrin repeat domain 22, Guanylate binding protein (GBP)-1, -2, -4, -5, Stabilin 1, Serpin family G member 1 (SERPING1), Interferon alpha inducible protein 6, and Interferon-induced protein with tetratricopeptide repeats 3. A knock-down study using si-RNA failed to determine a key factor associated with the anti-HIV activity due to the induction of robust amounts of off-target effects. Overexpression of each protein in cells had no impact on HIV infection. Thus, we could not define the mechanism of the anti-HIV effect in 27DC. However, our findings indicated that IL-27 differentiates monocytes into HIV-resistant DC, and the inhibitory mechanism differs from IL-27-induced HIV-resistant macrophages and T cells.
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Affiliation(s)
- Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Qian Chen
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Bharatwaj Sowrirajan
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Jun Yang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Sylvain Laverdure
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Anthony R. Mele
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Catherine Watkins
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Joseph W. Adelsberger
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Jeanette Higgins
- AIDS monitoring Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Hongyan Sui
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
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14
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Zhou L, Yao S. Recent advances in therapeutic CRISPR-Cas9 genome editing: mechanisms and applications. MOLECULAR BIOMEDICINE 2023; 4:10. [PMID: 37027099 PMCID: PMC10080534 DOI: 10.1186/s43556-023-00115-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/04/2023] [Indexed: 04/08/2023] Open
Abstract
Recently, clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 derived editing tools had significantly improved our ability to make desired changes in the genome. Wild-type Cas9 protein recognizes the target genomic loci and induced local double strand breaks (DSBs) in the guidance of small RNA molecule. In mammalian cells, the DSBs are mainly repaired by endogenous non-homologous end joining (NHEJ) pathway, which is error prone and results in the formation of indels. The indels can be harnessed to interrupt gene coding sequences or regulation elements. The DSBs can also be fixed by homology directed repair (HDR) pathway to introduce desired changes, such as base substitution and fragment insertion, when proper donor templates are provided, albeit in a less efficient manner. Besides making DSBs, Cas9 protein can be mutated to serve as a DNA binding platform to recruit functional modulators to the target loci, performing local transcriptional regulation, epigenetic remolding, base editing or prime editing. These Cas9 derived editing tools, especially base editors and prime editors, can introduce precise changes into the target loci at a single-base resolution and in an efficient and irreversible manner. Such features make these editing tools very promising for therapeutic applications. This review focuses on the evolution and mechanisms of CRISPR-Cas9 derived editing tools and their applications in the field of gene therapy.
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Affiliation(s)
- Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
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15
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Boehm D, Lam V, Schnolzer M, Ott M. The lysine methyltransferase SMYD5 amplifies HIV-1 transcription and is post-transcriptionally upregulated by Tat and USP11. Cell Rep 2023; 42:112234. [PMID: 36897778 PMCID: PMC10124996 DOI: 10.1016/j.celrep.2023.112234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/22/2022] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
A successful HIV-1 cure strategy may require enhancing HIV-1 latency to silence HIV-1 transcription. Modulators of gene expression show promise as latency-promoting agents in vitro and in vivo. Here, we identify Su(var)3-9, enhancer-of-zeste, and trithorax (SET) and myeloid, Nervy, and DEAF-1 (MYND) domain-containing protein 5 (SMYD5) as a host factor required for HIV-1 transcription. SMYD5 is expressed in CD4+ T cells and activates the HIV-1 promoter with or without the viral Tat protein, while knockdown of SMYD5 decreases HIV-1 transcription in cell lines and primary T cells. SMYD5 associates in vivo with the HIV-1 promoter and binds the HIV trans-activation response (TAR) element RNA and Tat. Tat is methylated by SMYD5 in vitro, and in cells expressing Tat, SMYD5 protein levels are increased. The latter requires expression of the Tat cofactor and ubiquitin-specific peptidase 11 (USP11). We propose that SMYD5 is a host activator of HIV-1 transcription stabilized by Tat and USP11 and, together with USP11, a possible target for latency-promoting therapy.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Victor Lam
- Tetrad Graduate Program, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martina Schnolzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Melanie Ott
- Gladstone Institute of Virology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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16
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Stankey CT, Lee JC. Translating non-coding genetic associations into a better understanding of immune-mediated disease. Dis Model Mech 2023; 16:297044. [PMID: 36897113 PMCID: PMC10040244 DOI: 10.1242/dmm.049790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Genome-wide association studies have identified hundreds of genetic loci that are associated with immune-mediated diseases. Most disease-associated variants are non-coding, and a large proportion of these variants lie within enhancers. As a result, there is a pressing need to understand how common genetic variation might affect enhancer function and thereby contribute to immune-mediated (and other) diseases. In this Review, we first describe statistical and experimental methods to identify causal genetic variants that modulate gene expression, including statistical fine-mapping and massively parallel reporter assays. We then discuss approaches to characterise the mechanisms by which these variants modulate immune function, such as clustered regularly interspaced short palindromic repeats (CRISPR)-based screens. We highlight examples of studies that, by elucidating the effects of disease variants within enhancers, have provided important insights into immune function and uncovered key pathways of disease.
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Affiliation(s)
- Christina T Stankey
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - James C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Institute of Liver and Digestive Health, Royal Free Hospital, University College London, London NW3 2PF, UK
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17
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Duran-Castells C, Llano A, Kawana-Tachikawa A, Prats A, Martinez-Zalacain I, Kobayashi-Ishihara M, Oriol-Tordera B, Peña R, Gálvez C, Silva-Arrieta S, Clotet B, Riveira-Muñoz E, Ballana E, Prado JG, Martinez-Picado J, Sanchez J, Mothe B, Hartigan-O'Connor D, Wyss-Coray T, Meyerhans A, Gisslén M, Price RW, Soriano-Mas C, Muñoz-Moreno JA, Brander C, Ruiz-Riol M. Sirtuin-2, NAD-Dependent Deacetylase, Is a New Potential Therapeutic Target for HIV-1 Infection and HIV-Related Neurological Dysfunction. J Virol 2023; 97:e0165522. [PMID: 36719240 PMCID: PMC9972991 DOI: 10.1128/jvi.01655-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/20/2022] [Indexed: 02/01/2023] Open
Abstract
The implementation and access to combined antiretroviral treatment (cART) have dramatically improved the quality of life of people living with HIV (PLWH). However, some comorbidities, such as neurological disorders associated with HIV infection still represent a serious clinical challenge. Soluble factors in plasma that are associated with control of HIV replication and neurological dysfunction could serve as early biomarkers and as new therapeutic targets for this comorbidity. We used a customized antibody array for determination of blood plasma factors in 40 untreated PLWH with different levels of viremia and found sirtuin-2 (SIRT2), an NAD-dependent deacetylase, to be strongly associated with elevated viral loads and HIV provirus levels, as well as with markers of neurological damage (a-synuclein [SNCA], brain-derived neurotrophic factor [BDNF], microtubule-associated protein tau [MAPT], and neurofilament light protein [NFL]). Also, longitudinal analysis in HIV-infected individuals with immediate (n = 9) or delayed initiation (n = 10) of cART revealed that after 1 year on cART, SIRT2 plasma levels differed between both groups and correlated inversely with brain orbitofrontal cortex involution. Furthermore, targeting SIRT2 with specific small-molecule inhibitors in in vitro systems using J-LAT A2 and primary glial cells led to diminished HIV replication and virus reactivation from latency. Our data thus identify SIRT2 as a novel biomarker of uncontrolled HIV infection, with potential impact on neurological dysfunction and offers a new therapeutic target for HIV treatment and cure. IMPORTANCE Neurocognitive disorders are frequently reported in people living with HIV (PLWH) even with the introduction of combined antiretroviral treatment (cART). To identify biomarkers and potential therapeutic tools to target HIV infection in peripheral blood and in the central nervous system (CNS), plasma proteomics were applied in untreated chronic HIV-infected individuals with different levels of virus control. High plasma levels of sirtuin-2 (SIRT2), an NAD+ deacetylase, were detected in uncontrolled HIV infection and were strongly associated with plasma viral load and proviral levels. In parallel, SIRT2 levels in the peripheral blood and CNS were associated with markers of neurological damage and brain involution and were more pronounced in individuals who initiated cART later in infection. In vitro infection experiments using specific SIRT2 inhibitors suggest that specific targeting of SIRT2 could offer new therapeutic treatment options for HIV infections and their associated neurological dysfunction.
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Affiliation(s)
- Clara Duran-Castells
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- Departament de Biologia, Cel·lular, Fisiologia i d'immunologia, Facultat de Medicina, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Anna Prats
- Fundació Lluita contra la Sida and Infectious Diseases Department, Hospital Germans Trias i Pujol, Badalona, Spain
| | | | - Mie Kobayashi-Ishihara
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Bruna Oriol-Tordera
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- Departament de Biologia, Cel·lular, Fisiologia i d'immunologia, Facultat de Medicina, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain
| | - Ruth Peña
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Cristina Gálvez
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Sandra Silva-Arrieta
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- Fundació Lluita contra la Sida and Infectious Diseases Department, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - Eva Riveira-Muñoz
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Esther Ballana
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Julia G Prado
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
- ICREA, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Sanchez
- Centro de Investigaciones Tecnologicas Biomedicas y Medioambientales, CITBM, Lima, Peru
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- Fundació Lluita contra la Sida and Infectious Diseases Department, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Dennis Hartigan-O'Connor
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Andreas Meyerhans
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Magnus Gisslén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden
| | - Richard W Price
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Carles Soriano-Mas
- Department of Psychiatry, Bellvitge Biomedical Research Institute-IDIBELL, Barcelona, Spain
- Department of Clinical Sciences, University of Barcelona, Barcelona, Spain
- Department of Psychobiology and Methodology in Health Sciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - José Antonio Muñoz-Moreno
- Fundació Lluita contra la Sida and Infectious Diseases Department, Hospital Germans Trias i Pujol, Badalona, Spain
- Faculty of Psychology and Education Sciences, Universitat Oberta de Catalunya (UOC), Barcelona, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
- ICREA, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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18
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A Virus-Packageable CRISPR System Identifies Host Dependency Factors Co-Opted by Multiple HIV-1 Strains. mBio 2023; 14:e0000923. [PMID: 36744886 PMCID: PMC9973025 DOI: 10.1128/mbio.00009-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
At each stage of the HIV life cycle, host cellular proteins are hijacked by the virus to establish and enhance infection. We adapted the virus packageable HIV-CRISPR screening technology at a genome-wide scale to comprehensively identify host factors that affect HIV replication in a human T cell line. Using a smaller, targeted HIV Dependency Factor (HIVDEP) sublibrary, we then performed screens across HIV strains representing different clades and with different biological properties to define which T cell host factors are important across multiple HIV strains. Nearly 90% of the genes selected across various host pathways validated in subsequent assays as bona fide host dependency factors, including numerous proteins not previously reported to play roles in HIV biology, such as UBE2M, MBNL1, FBXW7, PELP1, SLC39A7, and others. Our ranked list of screen hits across diverse HIV-1 strains form a resource of HIV dependency factors for future investigation of host proteins involved in HIV biology. IMPORTANCE With a small genome of ~9.2 kb that encodes 14 major proteins, HIV must hijack host cellular machinery to successfully establish infection. These host proteins necessary for HIV replication are called "dependency factors." Whole-genome, and then targeted screens were done to try to comprehensively identify all dependency factors acting throughout the HIV replication cycle. Many host processes were identified and validated as critical for HIV replication across multiple HIV strains.
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19
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Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523954. [PMID: 36711836 PMCID: PMC9882154 DOI: 10.1101/2023.01.13.523954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Host-pathogen interactions (HPIs) are pivotal in regulating establishment, progression, and outcome of an infection. Affinity-purification mass spectrometry has become instrumental for the characterization of HPIs, however the targeted nature of exogenously expressing individual viral proteins has limited its utility to the analysis of relatively small pathogens. Here we present the use of co-fractionation mass spectrometry (SEC-MS) for the high-throughput analysis of HPIs from native viral infections of two jumbophages ( ϕ KZ and ϕ PA3) in Pseudomonas aeruginosa . This enabled the detection > 6000 unique host-pathogen and > 200 pathogen-pathogen interactions for each phage, encompassing > 50% of the phage proteome. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. Prediction of novel ORFs revealed a ϕ PA3 complex showing strong structural and sequence similarity to ϕ KZ nvRNAp, suggesting ϕ PA3 also possesses two RNA polymerases acting at different stages of the infection cycle. We further expanded our understanding on the molecular organization of the virion packaged and injected proteome by identifying 23 novel virion components and 5 novel injected proteins, as well as providing the first evidence for interactions between KZ-like phage proteins and the host ribosome. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction ( https://phagemap.ucsf.edu/ ). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of hostpathogen interactomes and protein complex dynamics upon infection.
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20
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527545. [PMID: 36798236 PMCID: PMC9934674 DOI: 10.1101/2023.02.07.527545] [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: 02/10/2023]
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4 + T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4 + T cells. We performed CRISPR-knockout screens using a custom library that specifically targets ISGs expressed in CD4 + T cells and validated top hits. Our investigation identified new HIV-restricting ISGs (HM13, IGFBP2, LAP3) and found that two previously studied factors (IFI16, UBE2L6) are IFN effectors in T cells. Inactivation of these five ISGs in combination further diminished IFN’s protective effect against six diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L. Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA, 98109, USA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Present address: Tr1X Inc, La Jolla, CA, 92037, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
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21
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Ghanam RH, Eastep GN, Saad JS. Structural Insights into the Mechanism of HIV-1 Tat Secretion from the Plasma Membrane. J Mol Biol 2023; 435:167880. [PMID: 36370804 PMCID: PMC9822876 DOI: 10.1016/j.jmb.2022.167880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) trans-activator of transcription (Tat) is a small, intrinsically disordered basic protein that plays diverse roles in the HIV-1 replication cycle, including promotion of efficient viral RNA transcription. Tat is released by infected cells and subsequently absorbed by healthy cells, thereby contributing to HIV-1 pathogenesis including HIV-associated neurocognitive disorder. It has been shown that, in HIV-1-infected primary CD4 T-cells, Tat accumulates at the plasma membrane (PM) for secretion, a mechanism mediated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). However, the structural basis for Tat interaction with the PM and thereby secretion is lacking. Herein, we employed NMR and biophysical methods to characterize Tat86 (86 amino acids) interactions with PI(4,5)P2 and lipid nanodiscs (NDs). Our data revealed that Arg49, Lys50 and Lys51 (RKK motif) constitute the PI(4,5)P2 binding site, that Tat86 interaction with lipid NDs is dependent on PI(4,5)P2 and phosphatidylserine (PS), and that the arginine-rich motif (RRQRRR) preferentially interacts with PS. Furthermore, we show that Trp11, previously implicated in Tat secretion, penetrates deeply in the membrane; substitution of Trp11 severely reduced Tat86 interaction with membranes. Deletion of the entire highly basic region and Trp11 completely abolished Tat86 binding to lipid NDs. Our data support a mechanism by which HIV-1 Tat secretion from the PM is mediated by a tripartite signal consisting of binding of the RKK motif to PI(4,5)P2, arginine-rich motif to PS, and penetration of Trp11 in the membrane. Altogether, these findings provide new insights into the molecular requirements for Tat binding to membranes during secretion.
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Affiliation(s)
- Ruba H Ghanam
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Gunnar N Eastep
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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22
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Cisneros WJ, Cornish D, Hultquist JF. Application of CRISPR-Cas9 Gene Editing for HIV Host Factor Discovery and Validation. Pathogens 2022; 11:pathogens11080891. [PMID: 36015010 PMCID: PMC9415735 DOI: 10.3390/pathogens11080891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 12/04/2022] Open
Abstract
Human Immunodeficiency Virus (HIV) interacts with a wide array of host factors at each stage of its lifecycle to facilitate replication and circumvent the immune response. Identification and characterization of these host factors is critical for elucidating the mechanism of viral replication and for developing next-generation HIV-1 therapeutic and curative strategies. Recent advances in CRISPR-Cas9-based genome engineering approaches have provided researchers with an assortment of new, valuable tools for host factor discovery and interrogation. Genome-wide screening in a variety of in vitro cell models has helped define the critical host factors that play a role in various cellular and biological contexts. Targeted manipulation of specific host factors by CRISPR-Cas9-mediated gene knock-out, overexpression, and/or directed repair have furthermore allowed for target validation in primary cell models and mechanistic inquiry through hypothesis-based testing. In this review, we summarize several CRISPR-based screening strategies for the identification of HIV-1 host factors and highlight how CRISPR-Cas9 approaches have been used to elucidate the molecular mechanisms of viral replication and host response. Finally, we examine promising new technologies in the CRISPR field and how these may be applied to address critical questions in HIV-1 biology going forward.
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Affiliation(s)
- William J. Cisneros
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Daphne Cornish
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
- Correspondence:
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23
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Stam JC, de Maat S, de Jong D, Arens M, van Lint F, Gharu L, van Roosmalen MH, Roovers RC, Strokappe NM, Wagner R, Kliche A, de Haard HJ, van Bergen En Henegouwen PM, Nijhuis M, Verrips CT. Directing HIV-1 for degradation by non-target cells, using bi-specific single-chain llama antibodies. Sci Rep 2022; 12:13413. [PMID: 35927444 PMCID: PMC9352707 DOI: 10.1038/s41598-022-15993-y] [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: 02/03/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
While vaccination against HIV-1 has been so far unsuccessful, recently broadly neutralizing antibodies (bNAbs) against HIV-1 envelope glycoprotein were shown to induce long-term suppression in the absence of antiretroviral therapy in patients with antibody-sensitive viral reservoirs. The requirement of neutralizing antibodies indicates that the antibody mediated removal (clearance) of HIV-1 in itself is not efficient enough in these immune compromised patients. Here we present a novel, alternative approach that is independent of a functional immune system to clear HIV-1, by capturing the virus and redirecting it to non-target cells where it is internalized and degraded. We use bispecific antibodies with domains derived from small single chain Llama antibodies (VHHs). These bind with one domain to HIV-1 envelope proteins and with the other domain direct the virus to cells expressing epidermal growth factor receptor (EGFR), a receptor that is ubiquitously expressed in the body. We show that HIV envelope proteins, virus-like particles and HIV-1 viruses (representing HIV-1 subtypes A, B and C) are efficiently recruited to EGFR, internalized and degraded in the lysosomal pathway at low nM concentrations of bispecific VHHs. This directed degradation in non-target cells may provide a clearance platform for the removal of viruses and other unwanted agents from the circulation, including toxins, and may thus provide a novel method for curing.
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Affiliation(s)
- Jord C Stam
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.
| | - Steven de Maat
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Dorien de Jong
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mathia Arens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Fenna van Lint
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Lavina Gharu
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark H van Roosmalen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.,Intervet, Wim de Körverstraat 35, 5831 AN, Boxmeer, The Netherlands
| | - Rob C Roovers
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.,LAVA Therapeutics, Yalelaan 60, 3584CM, Utrecht, The Netherlands
| | - Nika M Strokappe
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Ralf Wagner
- Molecular Microbiology and Gene Therapy, Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Alexander Kliche
- Molecular Microbiology and Gene Therapy, Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Hans J de Haard
- Argenx, Industriepark Zwijnaarde 7, 9052, Zwijnaarde, Belgium
| | - Paul M van Bergen En Henegouwen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Monique Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C Theo Verrips
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.,QVQ Holding BV, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
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Closing the Door with CRISPR: Genome Editing of CCR5 and CXCR4 as a Potential Curative Solution for HIV. BIOTECH 2022; 11:biotech11030025. [PMID: 35892930 PMCID: PMC9326690 DOI: 10.3390/biotech11030025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection can be controlled by anti-retroviral therapy. Suppressing viral replication relies on life-long medication, but anti-retroviral therapy is not without risks to the patient. Therefore, it is important that permanent cures for HIV infection are developed. Three patients have been described to be completely cured from HIV infection in recent years. In all cases, patients received a hematopoietic stem cell (HSC) transplantation due to a hematological malignancy. The HSCs were sourced from autologous donors that expressed a homozygous mutation in the CCR5 gene. This mutation results in a non-functional receptor, and confers resistance to CCR5-tropic HIV strains that rely on CCR5 to enter host cells. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is one of the methods of choice for gene editing, and the CRISPR/Cas system has been employed to target loci of interest in the context of HIV. Here, the current literature regarding CRISPR-mediated genome editing to render cells resistant to HIV (re)-infection by knocking out the co-receptors CCR5 and CXCR4 is summarized, and an outlook is provided regarding future (research) directions.
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