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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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2
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Reda O, Monde K, Sugata K, Rahman A, Sakhor W, Rajib SA, Sithi SN, Tan BJY, Niimura K, Motozono C, Maeda K, Ono M, Takeuchi H, Satou Y. HIV-Tocky system to visualize proviral expression dynamics. Commun Biol 2024; 7:344. [PMID: 38509308 PMCID: PMC10954732 DOI: 10.1038/s42003-024-06025-8] [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: 09/05/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
Determinants of HIV-1 latency establishment are yet to be elucidated. HIV reservoir comprises a rare fraction of infected cells that can survive host and virus-mediated killing. In vitro reporter models so far offered a feasible means to inspect this population, but with limited capabilities to dissect provirus silencing dynamics. Here, we describe a new HIV reporter model, HIV-Timer of cell kinetics and activity (HIV-Tocky) with dual fluorescence spontaneous shifting to reveal provirus silencing and reactivation dynamics. This unique feature allows, for the first time, identifying two latent populations: a directly latent, and a recently silenced subset, with the latter having integration features suggestive of stable latency. Our proposed model can help address the heterogeneous nature of HIV reservoirs and offers new possibilities for evaluating eradication strategies.
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Affiliation(s)
- Omnia Reda
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Microbiology Department, High Institute of Public Health, Alexandria University, Alexandria, Egypt
| | - Kazuaki Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenji Sugata
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Akhinur Rahman
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Wajihah Sakhor
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Samiul Alam Rajib
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Sharmin Nahar Sithi
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Benjy Jek Yang Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Koki Niimura
- School of Medicine, Kumamoto University, Kumamoto, Japan
| | - Chihiro Motozono
- Division of Infection and Immunology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kenji Maeda
- Division of Antiviral Therapy, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Masahiro Ono
- Department of Life Sciences, Imperial College London, London, UK
| | - Hiroaki Takeuchi
- Department of High-risk Infectious Disease Control, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
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Taga K, Takeuchi H. Novel role of host protein SLC25A42 in the HIV-1 reactivation of latent HIV-1 provirus. Microbiol Immunol 2024; 68:90-99. [PMID: 38244193 DOI: 10.1111/1348-0421.13114] [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: 11/15/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/22/2024]
Abstract
Despite the effectiveness of combination antiretroviral therapy, human immunodeficiency virus (HIV) infection remains incurable. To seek new strategies to overcome HIV type 1 (HIV-1) latency, one of the major barriers to HIV elimination, it is crucial to better understand how this state is maintained. Here, by means of an RNA interference screen employing an HIV-1 latency model using monocytic cell lines, we identified solute carrier family 25 member 42 (SLC25A42) as a potential host factor not previously known to affect HIV-1 latency. SLC25A42 knockdown resulted in increased HIV-1 expression, whereas forced expression of exogenous SLC25A42 suppressed it in SLC25A42-depleted cells. SLC25A42 depletion increased HIV-1 proviral transcriptional elongation but did not cause HIV-1 activation in an HIV-1 Tat-depleted latency model. This suggests that the role of SLC25A42 in HIV-1 transcription depends on HIV-1 Tat. Chromatin immunoprecipitation-qPCR analysis further revealed that SLC25A42 accumulated on or near the HIV-1 5' long terminal repeat promoter region of the HIV-1 provirus, suggesting a possible role in regulating HIV-1 Tat near this promoter region. These results indicate that SLC25A42 plays a novel role in HIV-1 latency maintenance in monocytic HIV-1 reservoirs.
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Affiliation(s)
- Kei Taga
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroaki Takeuchi
- Department of High-risk Infectious Disease Control, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- TMDU Center for Infectious Disease Education and Analysis (TCIDEA), Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Konno Y, Uriu K, Chikata T, Takada T, Kurita JI, Ueda MT, Islam S, Yang Tan BJ, Ito J, Aso H, Kumata R, Williamson C, Iwami S, Takiguchi M, Nishimura Y, Morita E, Satou Y, Nakagawa S, Koyanagi Y, Sato K. Two-step evolution of HIV-1 budding system leading to pandemic in the human population. Cell Rep 2024; 43:113697. [PMID: 38294901 DOI: 10.1016/j.celrep.2024.113697] [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: 07/04/2023] [Revised: 11/19/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
The pandemic HIV-1, HIV-1 group M, emerged from a single spillover event of its ancestral lentivirus from a chimpanzee. During human-to-human spread worldwide, HIV-1 diversified into multiple subtypes. Here, our interdisciplinary investigation mainly sheds light on the evolutionary scenario of the viral budding system of HIV-1 subtype C (HIV-1C), a most successfully spread subtype. Of the two amino acid motifs for HIV-1 budding, the P(T/S)AP and YPxL motifs, HIV-1C loses the YPxL motif. Our data imply that HIV-1C might lose this motif to evade immune pressure. Additionally, the P(T/S)AP motif is duplicated dependently of the level of HIV-1 spread in the human population, and >20% of HIV-1C harbored the duplicated P(T/S)AP motif. We further show that the duplication of the P(T/S)AP motif is caused by the expansion of the CTG triplet repeat. Altogether, our results suggest that HIV-1 has experienced a two-step evolution of the viral budding process during human-to-human spread worldwide.
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Affiliation(s)
- Yoriyuki Konno
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Takayuki Chikata
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Toru Takada
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Saiful Islam
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Benjy Jek Yang Tan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Hirofumi Aso
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Ryuichi Kumata
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan; MIRAI, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Yorifumi Satou
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan; CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan.
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Matsuda K, Tan BJY, Rajib SA, Tsuchiya K, Satou Y, Maeda K. Assessing the effects of antiretroviral therapy-latency-reversing agent combination therapy on eradicating replication-competent HIV provirus in a Jurkat cell culture model. STAR Protoc 2023; 4:102547. [PMID: 37751354 PMCID: PMC10520926 DOI: 10.1016/j.xpro.2023.102547] [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: 04/20/2023] [Revised: 06/26/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023] Open
Abstract
Eradication of HIV-1 latently infected cells is an important issue in HIV treatment. However, there are limited models available to assess therapeutic efficacy in vitro. Here, we present a protocol for establishing a variety of HIV-infected Jurkat cells, including productive and latent status, evaluating the efficacy of antiviral agents, followed by PCR/sequencing-based detection of replication competent HIV provirus. This protocol is useful for optimization of treatment of HIV-1 and provides insights into the mechanisms of clonal selection of heterogeneous HIV-1-infected cells. For complete details on the use and execution of this protocol, please refer to Matsuda et al. (2021).1.
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Affiliation(s)
- Kouki Matsuda
- Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima 890-8544, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo 162-8655, Japan; Japan Foundation for AIDS Prevention, Chiyoda-ku, Tokyo 101-0064, Japan.
| | - Benjy Jek Yang Tan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-8556, Japan
| | - Samiul Alam Rajib
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kiyoto Tsuchiya
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Yorifumi Satou
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-8556, Japan.
| | - Kenji Maeda
- Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima 890-8544, Japan.
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Clone Dynamics and Its Application for the Diagnosis of Enzootic Bovine Leukosis. J Virol 2023; 97:e0154222. [PMID: 36533951 PMCID: PMC9888225 DOI: 10.1128/jvi.01542-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bovine leukemia virus (BLV) infection results in polyclonal expansion of infected B lymphocytes, and ~5% of infected cattle develop enzootic bovine leukosis (EBL). Since BLV is a retrovirus, each individual clone can be identified by using viral integration sites. To investigate the distribution of tumor cells in EBL cattle, we performed viral integration site analysis by using a viral DNA capture-sequencing method. We found that the same tumor clones existed in peripheral blood, with a dominance similar to that in lymphoma tissue. Additionally, we observed that multiple tumor tissues from different sites harbored the identical clones, indicating that tumor cells can circulate and distribute systematically in EBL cattle. To investigate clonal expansion of BLV-infected cells during a long latent period, we collected peripheral blood samples from asymptomatic cattle every 2 years, among which several cattle developed EBL. We found that no detectable EBL clone existed before the diagnosis of EBL in some cases; in the other cases, clones that were later detected as malignant clones at the EBL stage were present several months or even years before the disease onset. To establish a feasible clonality-based method for the diagnosis of EBL, we simplified a quick and cost-effective method, namely, rapid amplification of integration sites for BLV infection (BLV-RAIS). We found that the clonality values (Cvs) were well correlated between the BLV-RAIS and viral DNA capture-sequencing methods. Furthermore, receiver operating characteristic (ROC) curve analysis identified an optimal Cv cutoff value of 0.4 for EBL diagnosis, with excellent diagnostic sensitivity (94%) and specificity (100%). These results indicated that the RAIS method efficiently and reliably detected expanded clones not only in lymphoma tissue but also in peripheral blood. Overall, our findings elucidated the clonal dynamics of BLV- infected cells during EBL development. In addition, Cvs of BLV-infected cells in blood can be used to establish a valid and noninvasive diagnostic test for potential EBL onset. IMPORTANCE Although BLV has been eradicated in some European countries, BLV is still endemic in other countries, including Japan and the United States. EBL causes huge economic damage to the cattle industry. However, there are no effective drugs or vaccines to control BLV infection and related diseases. The strategy of eradication of infected cattle is not practical due to the high endemicity of BLV. Furthermore, how BLV-infected B cell clones proliferate during oncogenesis and their distribution in EBL cattle have yet to be elucidated. Here, we provided evidence that tumor cells are circulating in the blood of diseased cattle. Thus, the Cv of virus-infected cells in blood is useful information for the evaluation of the disease status. The BLV-RAIS method provides quantitative and accurate clonality information and therefore is a promising method for the diagnosis of EBL.
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Kitamura H, Sukegawa S, Matsuda K, Tanimoto K, Kobayakawa T, Takahashi K, Tamamura H, Tsuchiya K, Gatanaga H, Maeda K, Takeuchi H. 4-phenylquinoline-8-amine induces HIV-1 reactivation and apoptosis in latently HIV-1 infected cells. Biochem Biophys Res Commun 2023; 641:139-147. [PMID: 36527748 DOI: 10.1016/j.bbrc.2022.12.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Combinational antiretroviral therapy (cART) dramatically suppresses the viral load to undetectable levels in human immunodeficiency virus (HIV)-infected patients. However, HIV-1 reservoirs in CD4+T cells and myeloid cells, which can evade cART and host antiviral immune systems, are still significant obstacles to HIV-1 eradication. The "Shock and Kill" approach using latently-reversing agents (LRAs) is therefore currently developing strategies for effective HIV-1 reactivation from latency and inducing cell death. Here, we performed small-molecular chemical library screening with monocytic HIV-1 latently-infected model cells, THP-1 Nluc #225, and identified 4-phenylquinoline-8-amine (PQA) as a novel LRA candidate. PQA induced efficient HIV-1 reactivation in combination with PKC agonists including Prostratin and showed a similar tendency for HIV-1 activation in primary HIV-1 reservoirs. Furthermore, PQA induced killing of HIV-1 latently-infected cells. RNA-sequencing analysis revealed PQA had different functional mechanisms from PKC agonists, and oxidative stress-inducible genes including DDIT3 or CTSD were only involved in PQA-mediated cell death. In summary, PQA is a potential LRA lead compound that exerts novel functions related to HIV-1 activation and apoptosis-mediated cell death to eliminate HIV-1 reservoirs.
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Affiliation(s)
- Haruki Kitamura
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Sukegawa
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan; Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kouki Matsuda
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan; Japan Foundation for AIDS Prevention, Tokyo, Japan
| | - Kousuke Tanimoto
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuho Takahashi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kiyoto Tsuchiya
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kenji Maeda
- Division of Antiviral Therapy, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan.
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan; Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan.
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Visualization of clonal expansion after massive depletion of cells carrying the bovine leukemia virus (BLV) integration sites during the course of disease progression in a BLV naturally-infected cow: a case report. Retrovirology 2022; 19:24. [PMID: 36329491 PMCID: PMC9635170 DOI: 10.1186/s12977-022-00609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022] Open
Abstract
Bovine leukemia virus (BLV) infects cattle, integrates into host DNA as a provirus, and induces malignant B-cell lymphoma. Previous studies have addressed the impact of proviral integration of BLV on BLV-induced leukemogenesis. However, no studies have monitored sequential changes in integration sites in which naturally infected BLV individuals progress from the premalignant stage to the terminal disease. Here, we collected blood samples from a single, naturally infected Holstein cow at three disease progression stages (Stage I: polyclonal stage, Stage II: polyclonal toward oligoclonal stage, Stage III: oligoclonal stage) and successfully visualized the kinetics of clonal expansion of cells carrying BLV integration sites using our BLV proviral DNA-capture sequencing method. Although 24 integration sites were detected in Stages I and II, 92% of these sites experienced massive depletion in Stage III. Of these sites, 46%, 37%, and 17% were located within introns of Refseq genes, intergenic regions, and repetitive sequences, respectively. At Stage III cattle with lymphoma, only two integration sites were generated de novo in the intergenic region of Chr1, and the intron of the CHEK2 gene on Chr17 was significantly increased. Our results are the first to demonstrate clonal expansion after the massive depletion of cells carrying BLV integration sites in a naturally infected cow.
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Khanal S, Cao D, Zhang J, Zhang Y, Schank M, Dang X, Nguyen LNT, Wu XY, Jiang Y, Ning S, Zhao J, Wang L, Gazzar ME, Moorman JP, Yao ZQ. Synthetic gRNA/Cas9 Ribonucleoprotein Inhibits HIV Reactivation and Replication. Viruses 2022; 14:1902. [PMID: 36146709 PMCID: PMC9500661 DOI: 10.3390/v14091902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
The current antiretroviral therapy (ART) for human immunodeficiency virus (HIV) can halt viral replication but cannot eradicate HIV infection because proviral DNA integrated into the host genome remains genetically silent in reservoir cells and is replication-competent upon interruption or cessation of ART. CRISPR/Cas9-based technology is widely used to edit target genes via mutagenesis (i.e., nucleotide insertion/deletion and/or substitution) and thus can inactivate integrated proviral DNA. However, CRISPR/Cas9 delivery systems often require viral vectors, which pose safety concerns for therapeutic applications in humans. In this study, we used synthetic guide RNA (gRNA)/Cas9-ribonucleoprotein (RNP) as a non-viral formulation to develop a novel HIV gene therapy. We designed a series of gRNAs targeting different HIV genes crucial for HIV replication and tested their antiviral efficacy and cellular cytotoxicity in lymphoid and monocytic latent HIV cell lines. Compared with the scramble gRNA control, HIV-gRNA/Cas9 RNP-treated cells exhibited efficient viral suppression with no apparent cytotoxicity, as evidenced by the significant inhibition of latent HIV DNA reactivation and RNA replication. Moreover, HIV-gRNA/Cas9 RNP inhibited p24 antigen expression, suppressed infectious viral particle production, and generated specific DNA cleavages in the targeted HIV genes that are confirmed by DNA sequencing. Because of its rapid DNA cleavage, low off-target effects, low risk of insertional mutagenesis, easy production, and readiness for use in clinical application, this study provides a proof-of-concept that synthetic gRNA/Cas9 RNP drugs can be utilized as a novel therapeutic approach for HIV eradication.
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Affiliation(s)
- Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Yi Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Xiao Y. Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Yong Jiang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jonathan P. Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
| | - Zhi Q. Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
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10
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Munyuza C, Ji H, Lee ER. Probe Capture Enrichment Methods for HIV and HCV Genome Sequencing and Drug Resistance Genotyping. Pathogens 2022; 11:pathogens11060693. [PMID: 35745547 PMCID: PMC9228464 DOI: 10.3390/pathogens11060693] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 01/01/2023] Open
Abstract
Human immunodeficiency virus (HIV) infections remain a significant public health concern worldwide. Over the years, sophisticated sequencing technologies such as next-generation sequencing (NGS) have emerged and been utilized to monitor the spread of HIV drug resistance (HIVDR), identify HIV drug resistance mutations, and characterize transmission dynamics. Similar applications also apply to the Hepatitis C virus (HCV), another bloodborne viral pathogen with significant intra-host genetic diversity. Several advantages to using NGS over conventional Sanger sequencing include increased data throughput, scalability, cost-effectiveness when batched sample testing is performed, and sensitivity for quantitative detection of minority resistant variants. However, NGS alone may fail to detect genomes from pathogens present in low copy numbers. As with all sequencing platforms, the primary determinant in achieving quality sequencing data is the quality and quantity of the initial template input. Samples containing degraded RNA/DNA and/or low copy number have been a consistent sequencing challenge. To overcome this limitation probe capture enrichment is a method that has recently been employed to target, enrich, and sequence the genome of a pathogen present in low copies, and for compromised specimens that contain poor quality nucleic acids. It involves the hybridization of sequence-specific DNA or RNA probes to a target sequence, which is followed by an enrichment step via PCR to increase the number of copies of the targeted sequences after which the samples are subjected to NGS procedures. This method has been performed on pathogens such as bacteria, fungus, and viruses and allows for the sequencing of complete genomes, with high coverage. Post NGS, data analysis can be performed through various bioinformatics pipelines which can provide information on genetic diversity, genotype, virulence, and drug resistance. This article reviews how probe capture enrichment helps to increase the likelihood of sequencing HIV and HCV samples that contain low viral loads and/or are compromised.
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Affiliation(s)
- Chantal Munyuza
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (C.M.); (H.J.)
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (C.M.); (H.J.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (C.M.); (H.J.)
- Correspondence: ; Tel.: +1-204-789-6512
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11
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Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AA, Mahmoud M, Paulin LF, Raza MS, Pfeifer SP, Agustinho DP, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LC, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DM, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRR, Kubica J, Lakra P, Lattimer D, Liew CS, Lo BW, Lo C, Lötter A, Majidian S, Mendem SK, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon CL, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, Busby B. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res 2022; 11:530. [PMID: 36262335 PMCID: PMC9557141 DOI: 10.12688/f1000research.110194.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 01/25/2023] Open
Abstract
In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.
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Affiliation(s)
- Kimberly Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
| | | | - Guangyi Chen
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany,Center for Bioinformatics, Saarland University, Saarbrücken, Germany,
| | - David Molik
- Tropical Crop and Commodity Protection Research Unit, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Daniela C. Soto
- Biochemistry & Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, Davis, CA, 95616, USA
| | - Fawaz Dabbaghie
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany,Institute for Medical Biometry and Bioinformatics, University hospital Düsseldorf, Düsseldorf, Germany
| | - Ahmad Al Khleifat
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Muhammad Sohail Raza
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Susanne P. Pfeifer
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Daniel Paiva Agustinho
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Elbay Aliyev
- Research Department, Sidra Medicine, Doha, Qatar
| | - Pavel Avdeyev
- Computational Biology Institute, The George Washington University, Washington, DC, 20052, USA
| | - Enrico R. Barrozo
- Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Li Chuin Chong
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, Turkey
| | - Deepak Choubey
- Department of Technology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium,Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Alejandro R. Gener
- Association of Public Health Labs, Centers for Disease Control and Prevention, Downey, CA, USA
| | - Timothy Hefferon
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Morgan Henke
- Department Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wolfram Höps
- EMBL Heidelberg, Genome Biology Unit, Heidelberg, Germany
| | | | - Michael D. Jochum
- Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Jose
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India
| | - Rupesh K. Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | - Priya Lakra
- Department of Zoology, University of Delhi, Delhi, India
| | - Damaris Lattimer
- University of Applied Sciences Upper Austria - FH Hagenberg, Mühlkreis, Austria
| | - Chia-Sin Liew
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Bai-Wei Lo
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Chunhsuan Lo
- Human Genetics Laboratory, National Institute of Genetics, Japan, Mishima City, Japan
| | - Anneri Lötter
- Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Rajarshi Mondal
- Department of Biotechnology, The University of Burdwan, West Bengal, India
| | - Hiroko Ohmiya
- Genetic Reagent Development Unit, Medical & Biological Laboratories Co., Ltd., Tokoyo, Japan
| | - Nasrin Parvin
- Department of Biotechnology, The University of Burdwan, West Bengal, India
| | | | | | | | - Marie Saitou
- Center of Integrative Genetics (CIGENE),Faculty of Biosciences, Norwegian University of Life Sciences, As, Norway
| | - Aditi Sammi
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Philippe Sanio
- University of Applied Sciences Upper Austria - FH Hagenberg, Hagenberg im Mühlkreis, Austria
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Najeeb Syed
- Research Department, Sidra Medicine, Doha, Qatar
| | - Todd Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Tiancheng Xu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Jianzhi Yang
- Department of Quantitative and Computational Biology,, University of Southern California, Los Angeles, CA, USA
| | - Shangzhe Zhang
- School of Biology, University of St Andrews, St Andrews, UK
| | - Weiyu Zhou
- Department of Statistical Science, George Mason University, Fairfax, Virginia, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
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12
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Comprehensive Comparison of Novel Bovine Leukemia Virus (BLV) Integration Sites between B-Cell Lymphoma Lines BLSC-KU1 and BLSC-KU17 Using the Viral DNA Capture High-Throughput Sequencing Method. Viruses 2022; 14:v14050995. [PMID: 35632737 PMCID: PMC9143949 DOI: 10.3390/v14050995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Bovine leukemia virus (BLV) infects cattle and integrates into host DNA, causing enzootic bovine leukosis (EBL), an aggressive B-cell lymphoma. Here, we developed a novel proviral DNA-capture sequencing (proviral DNA-capture-seq) method investigating BLV proviral integration in two B-cell lymphoma lines, BLSC-KU1 and BLSC-KU17, derived from BLV-infected cattle with EBL. We designed BLV-specific biotinylated probes to capture the provirus genome and enrich libraries for next-generation sequencing. Validation showed high specificity and efficient enrichment of target sequence reads as well as identification of three BLV proviral integration sites on BLV persistently infected FLK-BLV cells as a positive control. We successfully detected a single BLV proviral integration site on chromosome 19 of BLSC-KU1 and chromosome 9 of BLSC-KU17, which were confirmed by standard PCR and Sanger sequencing. Further, a defective provirus in BLSC-KU1 and complete BLV proviral sequence in BLSC-KU17 were confirmed using long PCR and sequencing. This is the first study to provide comprehensive information on BLV proviral structure and viral integration in BLSC-KU1 and BLSC-KU17. Moreover, the proposed method can facilitate understanding of the detailed mechanisms underlying BLV-induced leukemogenesis and may be used as an innovative tool to screen BLV-infected cattle at risk at an earlier stage than those that have already developed lymphoma.
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13
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Gulati GK, Panpradist N, Stewart SWA, Beck IA, Boyce C, Oreskovic AK, García-Morales C, Avila-Ríos S, Han PD, Reyes-Terán G, Starita LM, Frenkel LM, Lutz BR, Lai JJ. Simultaneous monitoring of HIV viral load and screening of SARS-CoV-2 employing a low-cost RT-qPCR test workflow. Analyst 2022; 147:3315-3327. [PMID: 35762367 PMCID: PMC10143869 DOI: 10.1039/d2an00405d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This new workflow enables co-extraction of HIV and SARS-CoV2 RNAs from clinical pooled plasma/nasal secretion samples that allows sensitive detection of SARS-CoV-2 and HIV infections in the patients-living with HIV.
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Affiliation(s)
- Gaurav K. Gulati
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, USA
| | - Samuel W. A. Stewart
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ceejay Boyce
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Santiago Avila-Ríos
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Peter D. Han
- Department of Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gustavo Reyes-Terán
- Coordination of the Mexican National Institutes of Health and High Specialty Hospitals, Mexico City, Mexico
| | - Lea M. Starita
- Department of Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Departments of Medicine, Pediatrics, Laboratory Medicine and Pathology, Global Health and Medicine, University of Washington, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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14
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Rodari A, Poli G, Van Lint C. Jurkat-Derived (J-Lat, J1.1, and Jurkat E4) and CEM-Derived T Cell Lines (8E5 and ACH-2) as Models of Reversible Proviral Latency. Methods Mol Biol 2022; 2407:3-15. [PMID: 34985653 DOI: 10.1007/978-1-0716-1871-4_1] [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] [Indexed: 06/14/2023]
Abstract
The introduction of combination antiretroviral therapy (cART) has switched HIV-1 infection from a lethal disease to a chronic one. Indeed, cART is a lifelong treatment since its interruption is always followed by a rapid rebound of viremia from both cellular and anatomical viral reservoirs where the integrated HIV-1 provirus remains transcriptionally silent or maintains low-levels of viral replication, thereby preventing HIV-1 eradication. As therapeutic approach, the "shock and kill" strategy has emerged with the main objective to reactivate HIV-1 transcription from latency by using latency reversing agents (LRAs) prior to kill the reactivated infected cells by improving host immune responses. In this context, the development of tools such as HIV-1 latently infected cell lines have drastically increased our knowledge about HIV-1 latency and how to counteract this highly heterogeneous phenomenon. In this chapter, we will describe several chronically HIV-1 infected T-lymphocytic cell lines as useful surrogate models to study reversible HIV-1 proviral latency in CD4+ T cells in vitro before approaching more complex and expensive models.
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Affiliation(s)
- Anthony Rodari
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Guido Poli
- Viral Pathogenesis Group, San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium.
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15
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New Approaches to Multi-Parametric HIV-1 Genetics Using Multiple Displacement Amplification: Determining the What, How, and Where of the HIV-1 Reservoir. Viruses 2021; 13:v13122475. [PMID: 34960744 PMCID: PMC8709494 DOI: 10.3390/v13122475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022] Open
Abstract
Development of potential HIV-1 curative interventions requires accurate characterization of the proviral reservoir, defined as host-integrated viral DNA genomes that drive rebound of viremia upon halting ART (antiretroviral therapy). Evaluation of such interventions necessitates methods capable of pinpointing the rare, genetically intact, replication-competent proviruses within a background of defective proviruses. This evaluation can be achieved by identifying the distinct integration sites of intact proviruses within host genomes and monitoring the dynamics of these proviruses and host cell lineages over longitudinal sampling. Until recently, molecular genetic approaches at the single proviral level have been generally limited to one of a few metrics, such as proviral genome sequence/intactness, host-proviral integration site, or replication competency. New approaches, taking advantage of MDA (multiple displacement amplification) for WGA (whole genome amplification), have enabled multiparametric proviral characterization at the single-genome level, including proviral genome sequence, host-proviral integration site, and phenotypic characterization of the host cell lineage, such as CD4 memory subset and antigen specificity. In this review, we will examine the workflow of MDA-augmented molecular genetic approaches to study the HIV-1 reservoir, highlighting technical advantages and flexibility. We focus on a collection of recent studies in which investigators have used these approaches to comprehensively characterize intact and defective proviruses from donors on ART, investigate mechanisms of elite control, and define cell lineage identity and antigen specificity of infected CD4+ T cell clones. The highlighted studies exemplify how these approaches and their future iterations will be key in defining the targets and evaluating the impacts of HIV curative interventions.
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16
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Emerging Single-cell Approaches to Understand HIV in the Central Nervous System. Curr HIV/AIDS Rep 2021; 19:113-120. [PMID: 34822063 PMCID: PMC8613726 DOI: 10.1007/s11904-021-00586-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 11/23/2022]
Abstract
Purpose of Review This review highlights emerging single-cell sequencing methods relevant to translational studies of HIV in the central nervous system (CNS), summarizes limited single-cell studies of HIV in the CNS, and discusses opportunities for future HIV translational CNS studies. Recent Findings Innovative methods utilizing single-cell technologies have advanced the study of genomes, proteomes, transcriptomes, and epigenomes at an enhanced resolution and depth. Single-cell analyses of central nervous system tissue, including autopsy brain and CSF cells, may shed light on CNS perturbations in people living with HIV. New strategies can distinguish distinct molecular identifies of rare infected cells at single-cell level, suggesting an opportunity to uncloak the molecular identity of hidden HIV in the CNS reservoir. Summary Adoption of multimodal “omics” analyses to translational HIV studies and tissue compartments beyond blood will be critical to advancing our understanding of viral establishment, persistence, and eradication.
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17
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Gulati GK, Panpradist N, Stewart SWA, Beck IA, Boyce C, Oreskovic AK, García-Morales C, Avila-Ríos S, Han PD, Reyes-Terán G, Starita LM, Frenkel LM, Lutz BR, Lai JJ. Inexpensive workflow for simultaneous monitoring of HIV viral load and detection of SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.18.21256786. [PMID: 34462759 PMCID: PMC8404901 DOI: 10.1101/2021.08.18.21256786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
BACKGROUND COVID-19 pandemic interrupted routine care for individuals living with HIV, putting them at risk of becoming virologically unsuppressed and ill. Often they are at high risk for exposure to SARS-CoV-2 infection and severe disease once infected. For this population, it is urgent to closely monitor HIV plasma viral load ( VL ) and screen for SARS-COV-2 infection. METHOD We have developed a non-proprietary method to isolate RNA from plasma, nasal secretions ( NS ), or both. HIV, SARS-CoV-2, and human RP targets in extracted RNA are then RT-qPCR to estimate the VL and classify HIV/SARS-CoV-2 status ( i . e ., HIV as VL failure or suppressed; SARS-CoV-2 as positive, presumptive positive, negative, or indeterminate). We evaluated this workflow on 133 clinical specimens: 40 plasma specimens (30 HIV-seropositive), 67 NS specimens (31 SARS-CoV-2-positive), and 26 pooled plasma/NS specimens (26 HIV-positive with 10 SARS-CoV-2-positive), and compared the results obtained using the in-house extraction to those using a commercial extraction kit. RESULTS In-house extraction had a detection limit of 200-copies/mL for HIV and 100-copies/mL for SARS-CoV-2. In-house and commercial methods yielded positively correlated HIV VL (R 2 : 0.98 for contrived samples; 0.81 for seropositive plasma). SARS-CoV-2 detection had 100% concordant classifications in contrived samples, and in clinical NS extracted by in-house method, excluding indeterminate results, was 95% concordant (25 positives, 6 presumptive positives, and 31 negatives) to those using the commercial method. Analysis of pooled plasma/NS showed R 2 of 0.91 (contrived samples) and 0.71 (clinical specimens) for HIV VL correlations obtained by both extraction methods, while SARS-CoV-2 detection showed 100% concordance in contrived and clinical specimens. INTERPRETATION Our low-cost workflow for molecular testing of HIV and SARS-CoV-2 could serve as an alternative to current standard assays for laboratories in low-resource settings.
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18
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Identification and characterization of Stathmin 1 as a host factor involved in HIV-1 latency. Biochem Biophys Res Commun 2021; 567:106-111. [PMID: 34146904 DOI: 10.1016/j.bbrc.2021.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/04/2021] [Indexed: 11/22/2022]
Abstract
Latency remains a barrier to achieving a sterilizing cure to HIV infection. It is thus important to find new host factor(s) to better understand maintenance of HIV latency and be exploited to develop new and more efficient latency reversing agents (LRAs). Here we employed RNA interference screening with a latently HIV-1-infected cell-line to identify Stathmin 1 (STMN1) as a host factor required for maintaining HIV-1 latency. Depletion of STMN1 significantly enhanced HIV-1 expression in a STMN1 depletion-dependent manner and forced expression of exogenous STMN1 suppressed it. We further showed that STMN1 depletion increases HIV-1 proviral transcriptional elongation. Moreover, chromatin immunoprecipitation (ChIP)-qPCR assays revealed STMN1 accumulation on/near the HIV-1 5' LTR region compared to other regions on the HIV-1 provirus, suggesting the possible contribution of STMN1 to HIV-1 transcription. These results suggest that STMN1 is required for the maintenance of HIV-1 latency and implicates STMN1 as a novel therapeutic target to eradicate HIV-1.
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19
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Abstract
![]()
Targeted
sequencing enables sensitive and cost-effective analysis
by focusing resources on molecules of interest. Existing methods,
however, are limited in enrichment power and target capture length.
Here, we present a novel method that uses compound nucleic acid cytometry
to achieve million-fold enrichments of molecules >10 kbp in length
using minimal prior target information. We demonstrate the approach
by sequencing HIV proviruses in infected individuals. Our method is
useful for rare target sequencing in research and clinical applications,
including for identifying cancer-associated mutations or sequencing
viruses infecting cells.
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Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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20
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Aso H, Nagaoka S, Kawakami E, Ito J, Islam S, Tan BJY, Nakaoka S, Ashizaki K, Shiroguchi K, Suzuki Y, Satou Y, Koyanagi Y, Sato K. Multiomics Investigation Revealing the Characteristics of HIV-1-Infected Cells In Vivo. Cell Rep 2021; 32:107887. [PMID: 32668246 DOI: 10.1016/j.celrep.2020.107887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
For eradication of HIV-1 infection, it is important to elucidate the detailed features and heterogeneity of HIV-1-infected cells in vivo. To reveal multiple characteristics of HIV-1-producing cells in vivo, we use a hematopoietic-stem-cell-transplanted humanized mouse model infected with GFP-encoding replication-competent HIV-1. We perform multiomics experiments using recently developed technology to identify the features of HIV-1-infected cells. Genome-wide HIV-1 integration-site analysis reveals that productive HIV-1 infection tends to occur in cells with viral integration into transcriptionally active genomic regions. Bulk transcriptome analysis reveals that a high level of viral mRNA is transcribed in HIV-1-infected cells. Moreover, single-cell transcriptome analysis shows the heterogeneity of HIV-1-infected cells, including CXCL13high cells and a subpopulation with low expression of interferon-stimulated genes, which can contribute to efficient viral spread in vivo. Our findings describe multiple characteristics of HIV-1-producing cells in vivo, which could provide clues for the development of an HIV-1 cure.
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Affiliation(s)
- Hirofumi Aso
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Shumpei Nagaoka
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Eiryo Kawakami
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan; Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba 2608670, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Saiful Islam
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Benjy Jek Yang Tan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Shinji Nakaoka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 0600810, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - Koichi Ashizaki
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan
| | - Katsuyuki Shiroguchi
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 5650874, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 2300045, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 2778561, Japan
| | - Yorifumi Satou
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan.
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21
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Artesi M, Hahaut V, Cole B, Lambrechts L, Ashrafi F, Marçais A, Hermine O, Griebel P, Arsic N, van der Meer F, Burny A, Bron D, Bianchi E, Delvenne P, Bours V, Charlier C, Georges M, Vandekerckhove L, Van den Broeke A, Durkin K. PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads. Genome Biol 2021; 22:97. [PMID: 33823910 PMCID: PMC8025556 DOI: 10.1186/s13059-021-02307-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/25/2021] [Indexed: 12/30/2022] Open
Abstract
The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
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Affiliation(s)
- Maria Artesi
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
- Laboratory of Human Genetics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
| | - Vincent Hahaut
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
| | - Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University, 9000 Ghent, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Fereshteh Ashrafi
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ambroise Marçais
- Service d’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Olivier Hermine
- Service d’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Philip Griebel
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, S7N 5E3 Canada
| | - Natasa Arsic
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, S7N 5E3 Canada
| | - Frank van der Meer
- Faculty of Veterinary Medicine: Ecosystem and Public Health, Calgary, AB Canada
| | - Arsène Burny
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
| | - Dominique Bron
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
| | - Elettra Bianchi
- Department of Pathology, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Department of Pathology, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Department of Human Genetics, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University, 9000 Ghent, Belgium
| | - Anne Van den Broeke
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
| | - Keith Durkin
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
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22
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A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP. Sci Rep 2021; 11:4521. [PMID: 33633166 PMCID: PMC7907107 DOI: 10.1038/s41598-021-83909-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/27/2021] [Indexed: 11/29/2022] Open
Abstract
Bovine leukemia virus (BLV) is an oncogenic retrovirus which induces malignant lymphoma termed enzootic bovine leukosis (EBL) after a long incubation period. Insertion sites of the BLV proviral genome as well as the associations between disease progression and polymorphisms of the virus and host genome are not fully understood. To characterize the biological coherence between virus and host, we developed a DNA-capture-seq approach, in which DNA probes were used to efficiently enrich target sequence reads from the next-generation sequencing (NGS) library. In addition, enriched reads can also be analyzed for detection of proviral integration sites and clonal expansion of infected cells since the reads include chimeric reads of the host and proviral genomes. To validate this DNA-capture-seq approach, a persistently BLV-infected fetal lamb kidney cell line (FLK-BLV), four EBL tumor samples and four non-EBL blood samples were analyzed to identify BLV integration sites. The results showed efficient enrichment of target sequence reads and oligoclonal integrations of the BLV proviral genome in the FLK-BLV cell line. Moreover, three out of four EBL tumor samples displayed multiple integration sites of the BLV proviral genome, while one sample displayed a single integration site. In this study, we found the evidence for the first time that the integrated provirus defective at the 5′ end was present in the persistent lymphocytosis cattle. The efficient and sensitive identification of BLV variability, integration sites and clonal expansion described in this study provide support for use of this innovative tool for understanding the detailed mechanisms of BLV infection during the course of disease progression.
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23
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Increased Proviral DNA in Circulating Cells Correlates with Plasma Viral Rebound in Simian Immunodeficiency Virus-Infected Rhesus Macaques after Antiretroviral Therapy Interruption. J Virol 2021; 95:JVI.02064-20. [PMID: 33408173 PMCID: PMC8094949 DOI: 10.1128/jvi.02064-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/18/2020] [Indexed: 12/30/2022] Open
Abstract
Viral reservoirs are involved in persistent HIV infection, and a small number of mosaic latent cellular reservoirs promote viral rebound upon analytical treatment interruption, which is the major obstacle to a cure. However, early indicators that can predict resurgence of viremia after treatment interruption may aid treatment decisions in people living with HIV. The human immunodeficiency virus (HIV) reservoir is responsible for persistent viral infection, and a small number of mosaic latent cellular reservoirs promote viral rebound upon antiretroviral therapy interruption, which is the major obstacle to a cure. However, markers that determine effective therapy and viral rebound posttreatment interruption remain unclear. In this study, we comprehensively and longitudinally tracked dynamic decay of cell-associated viral RNA/DNA in systemic and lymphoid tissues in simian immunodeficiency virus (SIV)-infected rhesus macaques on prolonged combined antiretroviral therapy (cART) and evaluated predictors of viral rebound after treatment cessation. The results showed that suppressive ART substantially reduced plasma SIV RNA, cell-associated unspliced, and multiply spliced SIV RNA to undetectable levels, yet viral DNA remained detectable in systemic tissues and lymphoid compartments throughout cART. Intriguingly, a rapid increase of integrated proviral DNA in peripheral mononuclear cells was detected once treatment was withdrawn, accompanied by the emergence of detectable plasma viral load. Notably, the increase of peripheral proviral DNA after treatment interruption correlated with the emergence and degree of viral rebound. These findings suggest that measuring total viral DNA in SIV infection may be a relatively simple surrogate marker of reservoir size and may predict viral rebound after treatment interruption and inform treatment strategies. IMPORTANCE Viral reservoirs are involved in persistent HIV infection, and a small number of mosaic latent cellular reservoirs promote viral rebound upon analytical treatment interruption, which is the major obstacle to a cure. However, early indicators that can predict resurgence of viremia after treatment interruption may aid treatment decisions in people living with HIV. Utilizing the rhesus macaque model, we demonstrated that increased proviral DNA in peripheral cells after treatment interruption, rather than levels of proviral DNA, was a useful marker to predict the emergence and degree of viral rebound after treatment interruption, providing a rapid approach for monitoring HIV rebound and informing decisions.
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24
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van Haasteren J, Munis AM, Gill DR, Hyde SC. Genome-wide integration site detection using Cas9 enriched amplification-free long-range sequencing. Nucleic Acids Res 2021; 49:e16. [PMID: 33290561 PMCID: PMC7897500 DOI: 10.1093/nar/gkaa1152] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/13/2020] [Accepted: 11/10/2020] [Indexed: 12/31/2022] Open
Abstract
The gene and cell therapy fields are advancing rapidly, with a potential to treat and cure a wide range of diseases, and lentivirus-based gene transfer agents are the vector of choice for many investigators. Early cases of insertional mutagenesis caused by gammaretroviral vectors highlighted that integration site (IS) analysis was a major safety and quality control checkpoint for lentiviral applications. The methods established to detect lentiviral integrations using next-generation sequencing (NGS) are limited by short read length, inadvertent PCR bias, low yield, or lengthy protocols. Here, we describe a new method to sequence IS using Amplification-free Integration Site sequencing (AFIS-Seq). AFIS-Seq is based on amplification-free, Cas9-mediated enrichment of high-molecular-weight chromosomal DNA suitable for long-range Nanopore MinION sequencing. This accessible and low-cost approach generates long reads enabling IS mapping with high certainty within a single day. We demonstrate proof-of-concept by mapping IS of lentiviral vectors in a variety of cell models and report up to 1600-fold enrichment of the signal. This method can be further extended to sequencing of Cas9-mediated integration of genes and to in vivo analysis of IS. AFIS-Seq uses long-read sequencing to facilitate safety evaluation of preclinical lentiviral vector gene therapies by providing IS analysis with improved confidence.
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Affiliation(s)
- Joost van Haasteren
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Altar M Munis
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Deborah R Gill
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen C Hyde
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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25
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Rosewick N, Hahaut V, Durkin K, Artesi M, Karpe S, Wayet J, Griebel P, Arsic N, Marçais A, Hermine O, Burny A, Georges M, Van den Broeke A. An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites. Front Microbiol 2020; 11:587306. [PMID: 33193242 PMCID: PMC7606357 DOI: 10.3389/fmicb.2020.587306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
The combined application of linear amplification-mediated PCR (LAM-PCR) protocols with next-generation sequencing (NGS) has had a large impact on our understanding of retroviral pathogenesis. Previously, considerable effort has been expended to optimize NGS methods to explore the genome-wide distribution of proviral integration sites and the clonal architecture of clinically important retroviruses like human T-cell leukemia virus type-1 (HTLV-1). Once sequencing data are generated, the application of rigorous bioinformatics analysis is central to the biological interpretation of the data. To better exploit the potential information available through these methods, we developed an optimized bioinformatics pipeline to analyze NGS clonality datasets. We found that short-read aligners, specifically designed to manage NGS datasets, provide increased speed, significantly reducing processing time and decreasing the computational burden. This is achieved while also accounting for sequencing base quality. We demonstrate the utility of an additional trimming step in the workflow, which adjusts for the number of reads supporting each insertion site. In addition, we developed a recall procedure to reduce bias associated with proviral integration within low complexity regions of the genome, providing a more accurate estimation of clone abundance. Finally, we recommend the application of a “clean-and-recover” step to clonality datasets generated from large cohorts and longitudinal studies. In summary, we report an optimized bioinformatics workflow for NGS clonality analysis and describe a new set of steps to guide the computational process. We demonstrate that the application of this protocol to the analysis of HTLV-1 and bovine leukemia virus (BLV) clonality datasets improves the quality of data processing and provides a more accurate definition of the clonal landscape in infected individuals. The optimized workflow and analysis recommendations can be implemented in the majority of bioinformatics pipelines developed to analyze LAM-PCR-based NGS clonality datasets.
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Affiliation(s)
- Nicolas Rosewick
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Vincent Hahaut
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Keith Durkin
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Maria Artesi
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Snehal Karpe
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Jérôme Wayet
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Philip Griebel
- VIDO-Intervac, University of Saskatchewan, Saskatoon, SK, Canada
| | - Natasa Arsic
- VIDO-Intervac, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ambroise Marçais
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, Paris, France
| | - Olivier Hermine
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, Paris, France.,Institut Imagine, INSERM U1163, CNRS ERL8654, Paris, France
| | - Arsène Burny
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Anne Van den Broeke
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
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26
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Modern diagnostic technologies for HIV. Lancet HIV 2020; 7:e574-e581. [PMID: 32763220 DOI: 10.1016/s2352-3018(20)30190-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
Novel diagnostic technologies, including nanotechnology, microfluidics, -omics science, next-generation sequencing, genomics big data, and machine learning, could contribute to meeting the UNAIDS 95-95-95 targets to end the HIV epidemic by 2030. Novel technologies include multiplexed technologies (including biomarker-based point-of-care tests and molecular platform technologies), biomarker-based combination antibody and antigen technologies, dried-blood-spot testing, and self-testing. Although biomarker-based rapid tests, in particular antibody-based tests, have dominated HIV diagnostics since the development of the first HIV test in the mid-1980s, targets such as nucleic acids and genes are now used in nanomedicine, biosensors, microfluidics, and -omics to enable early diagnosis of HIV. These novel technologies show promise as they are associated with ease of use, high diagnostic accuracy, rapid detection, and the ability to detect HIV-specific markers. Additional clinical and implementation research is needed to generate evidence for use of novel technologies and a public health approach will be required to address clinical and operational challenges to optimise their global deployment.
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27
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Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda. Viruses 2020; 12:v12030331. [PMID: 32197553 PMCID: PMC7150763 DOI: 10.3390/v12030331] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Across sub-Saharan Africa, key populations with elevated HIV-1 incidence and/or prevalence have been identified, but their contribution to disease spread remains unclear. We performed viral deep-sequence phylogenetic analyses to quantify transmission dynamics between the general population (GP), fisherfolk communities (FF), and women at high risk of infection and their clients (WHR) in central and southwestern Uganda. Between August 2014 and August 2017, 6185 HIV-1 positive individuals were enrolled in 3 GP and 10 FF communities, 3 WHR enrollment sites. A total of 2531 antiretroviral therapy (ART) naïve participants with plasma viral load >1000 copies/mL were deep-sequenced. One hundred and twenty-three transmission networks were reconstructed, including 105 phylogenetically highly supported source–recipient pairs. Only one pair involved a WHR and male participant, suggesting that improved population sampling is needed to assess empirically the role of WHR to the transmission dynamics. More transmissions were observed from the GP communities to FF communities than vice versa, with an estimated flow ratio of 1.56 (95% CrI 0.68–3.72), indicating that fishing communities on Lake Victoria are not a net source of transmission flow to neighboring communities further inland. Men contributed disproportionally to HIV-1 transmission flow regardless of age, suggesting that prevention efforts need to better aid men to engage with and stay in care.
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28
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Miyazato P, Matsuo M, Tan BJY, Tokunaga M, Katsuya H, Islam S, Ito J, Murakawa Y, Satou Y. HTLV-1 contains a high CG dinucleotide content and is susceptible to the host antiviral protein ZAP. Retrovirology 2019; 16:38. [PMID: 31842935 PMCID: PMC6915898 DOI: 10.1186/s12977-019-0500-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
Background Human T cell leukaemia virus type 1 (HTLV-1) is a retrovirus associated with human diseases such as adult T-cell leukaemia/lymphoma and HTLV-1 associated myelopathy/tropical spastic paraparesis. In contrast to another human retrovirus, human immunodeficiency virus type 1 (HIV-1), HTLV-1 persists in the host not via vigorous virus production but mainly via proliferation and/or long-term survival in the form of silent proviruses in infected host cells. As a result, HTLV-1-infected cells rarely produce virus particles in vivo even without anti-retroviral treatment. That should be an advantage for the virus to escape from the host immune surveillance by minimizing the expression of viral antigens in host cells. However, why HIV-1 and HTLV-1 behave so differently during natural infection is not fully understood. Results We performed cap analysis of gene expression (CAGE) using total RNAs and nascent, chromatin-associated, RNAs in the nucleus and found that HTLV-1 RNAs were processed post-transcriptionally in infected cells. RNA processing was evident for the sense viral transcripts but not the anti-sense ones. We also found a higher proportion of CG di-nucleotides in proviral sequences of HTLV-1-infected cells, when compared to the HIV-1 genomic sequence. It has been reported recently that CG dinucleotide content of viral sequence is associated with susceptibility to the antiviral ZC3HAV1 (ZAP), suggesting the involvement of this protein in the regulation of HTLV-1 transcripts. To analyse the effect of ZAP on HTLV-1 transcripts, we over-expressed it in HTLV-1-infected cells. We found there was a dose-dependent reduction in virus production with ZAP expression. We further knocked down endogenous ZAP with two independent targeting siRNAs and observed a significant increase in virus production in the culture supernatant. Other delta-type retroviruses such as simian T-cell leukaemia virus and bovine leukaemia virus, also contain high CG-dinucleotide contents in their viral genomes, suggesting that ZAP-mediated suppression of viral transcripts might be a common feature of delta-type retroviruses, which cause minimal viremia in their natural hosts. Conclusions The post-transcriptional regulatory mechanism involving ZAP might allow HTLV-1 to maintain a delicate balance required for prolonged survival in infected individuals.
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Affiliation(s)
- Paola Miyazato
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Misaki Matsuo
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Benjy J Y Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Michiyo Tokunaga
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Hiroo Katsuya
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Saiful Islam
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan. .,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.
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