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Shen-Gunther J, Easley A. HPV, HBV, and HIV-1 Viral Integration Site Mapping: A Streamlined Workflow from NGS to Genomic Insights of Carcinogenesis. Viruses 2024; 16:975. [PMID: 38932267 PMCID: PMC11209625 DOI: 10.3390/v16060975] [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: 05/27/2024] [Revised: 06/14/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Viral integration within the host genome plays a pivotal role in carcinogenesis. Various disruptive mechanisms are involved, leading to genomic instability, mutations, and DNA damage. With next-generation sequencing (NGS), we can now precisely identify viral and host genomic breakpoints and chimeric sequences, which are useful for integration site analysis. In this study, we evaluated a commercial hybrid capture NGS panel specifically designed for detecting three key viruses: HPV, HBV, and HIV-1. We also tested workflows for Viral Hybrid Capture (VHC) and Viral Integration Site (VIS) analysis, leveraging customized viral databases in CLC Microbial Genomics. By analyzing sequenced data from virally infected cancer cell lines (including SiHa, HeLa, CaSki, C-33A, DoTc2, 2A3, SCC154 for HPV; 3B2, SNU-182 for HBV; and ACH-2 for HIV-1), we precisely pinpointed viral integration sites. The workflow also highlighted disrupted and neighboring human genes that may play a crucial role in tumor development. Our results included informative virus-host read mappings, genomic breakpoints, and integration circular plots. These visual representations enhance our understanding of the integration process. In conclusion, our seamless end-to-end workflow bridges the gap in understanding viral contributions to cancer development, paving the way for improved diagnostics and treatment strategies.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA
| | - Acarizia Easley
- Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA;
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2
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Singh AK, Walavalkar K, Tavernari D, Ciriello G, Notani D, Sabarinathan R. Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers. Mol Oncol 2024; 18:1189-1208. [PMID: 38013620 PMCID: PMC11076994 DOI: 10.1002/1878-0261.13559] [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: 10/10/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023] Open
Abstract
Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated HPV DNA on host chromatin structure and gene regulation remains less understood. We investigated genome-wide patterns of HPV integrations and associated host gene expression changes in the context of host chromatin states and topologically associating domains (TADs). HPV integrations were significantly enriched in active chromatin regions and depleted in inactive ones. Interestingly, regardless of chromatin state, genomic regions flanking HPV integrations showed transcriptional upregulation. Nevertheless, upregulation (both local and long-range) was mostly confined to TADs with integration, but not affecting adjacent TADs. Few TADs showed recurrent integrations associated with overexpression of oncogenes within them (e.g. MYC, PVT1, TP63 and ERBB2) regardless of proximity. Hi-C and 4C-seq analyses in cervical cancer cell line (HeLa) demonstrated chromatin looping interactions between integrated HPV and MYC/PVT1 regions (~ 500 kb apart), leading to allele-specific overexpression. Based on these, we propose HPV integrations can trigger multimodal oncogenic activation to promote cancer progression.
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Affiliation(s)
- Anurag Kumar Singh
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Kaivalya Walavalkar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Daniele Tavernari
- Department of Computational BiologyUniversity of Lausanne (UNIL)Switzerland
- Swiss Cancer Center LemanLausanneSwitzerland
- Swiss Institute for Experimental Cancer Research (ISREC), EPFLLausanneSwitzerland
| | - Giovanni Ciriello
- Department of Computational BiologyUniversity of Lausanne (UNIL)Switzerland
- Swiss Cancer Center LemanLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Dimple Notani
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
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Kim KD, Lieberman PM. Viral remodeling of the 4D nucleome. Exp Mol Med 2024; 56:799-808. [PMID: 38658699 PMCID: PMC11058267 DOI: 10.1038/s12276-024-01207-0] [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: 11/17/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 04/26/2024] Open
Abstract
The dynamic spatial organization of genomes across time, referred to as the four-dimensional nucleome (4DN), is a key component of gene regulation and biological fate. Viral infections can lead to a reconfiguration of viral and host genomes, impacting gene expression, replication, latency, and oncogenic transformation. This review provides a summary of recent research employing three-dimensional genomic methods such as Hi-C, 4C, ChIA-PET, and HiChIP in virology. We review how viruses induce changes in gene loop formation between regulatory elements, modify chromatin accessibility, and trigger shifts between A and B compartments in the host genome. We highlight the central role of cellular chromatin organizing factors, such as CTCF and cohesin, that reshape the 3D structure of both viral and cellular genomes. We consider how viral episomes, viral proteins, and viral integration sites can alter the host epigenome and how host cell type and conditions determine viral epigenomes. This review consolidates current knowledge of the diverse host-viral interactions that impact the 4DN.
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Affiliation(s)
- Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea.
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Wang Z, Liu C, Liu W, Lv X, Hu T, Yang F, Yang W, He L, Huang X. Long-read sequencing reveals the structural complexity of genomic integration of HPV DNA in cervical cancer cell lines. BMC Genomics 2024; 25:198. [PMID: 38378450 PMCID: PMC10877919 DOI: 10.1186/s12864-024-10101-y] [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: 06/16/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Cervical cancer (CC) causes more than 311,000 deaths annually worldwide. The integration of human papillomavirus (HPV) is a crucial genetic event that contributes to cervical carcinogenesis. Despite HPV DNA integration is known to disrupt the genomic architecture of both the host and viral genomes in CC, the complexity of this process remains largely unexplored. RESULTS In this study, we conducted whole-genome sequencing (WGS) at 55-65X coverage utilizing the PacBio long-read sequencing platform in SiHa and HeLa cells, followed by comprehensive analyses of the sequence data to elucidate the complexity of HPV integration. Firstly, our results demonstrated that PacBio long-read sequencing effectively identifies HPV integration breakpoints with comparable accuracy to targeted-capture Next-generation sequencing (NGS) methods. Secondly, we constructed detailed models of complex integrated genome structures that included both the HPV genome and nearby regions of the human genome by utilizing PacBio long-read WGS. Thirdly, our sequencing results revealed the occurrence of a wide variety of genome-wide structural variations (SVs) in SiHa and HeLa cells. Additionally, our analysis further revealed a potential correlation between changes in gene expression levels and SVs on chromosome 13 in the genome of SiHa cells. CONCLUSIONS Using PacBio long-read sequencing, we have successfully constructed complex models illustrating HPV integrated genome structures in SiHa and HeLa cells. This accomplishment serves as a compelling demonstration of the valuable capabilities of long-read sequencing in detecting and characterizing HPV genomic integration structures within human cells. Furthermore, these findings offer critical insights into the complex process of HPV16 and HPV18 integration and their potential contribution to the development of cervical cancer.
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Affiliation(s)
- Zhijie Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Chen Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Wanxin Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xinyi Lv
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Ting Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Fan Yang
- Wuhan Kandwise Biotechnology, Inc. Wuhan, Hubei, China
| | - Wenhui Yang
- Wuhan Kandwise Biotechnology, Inc. Wuhan, Hubei, China
| | - Liang He
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Xiaoyuan Huang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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Zhao J, Zheng W, Wang L, Jiang H, Wang X, Hou J, Xu A, Cong J. Human papillomavirus (HPV) integration signature in cervical lesions: identification of MACROD2 gene as HPV hot spot integration site. Arch Gynecol Obstet 2023; 307:1115-1123. [PMID: 36008642 DOI: 10.1007/s00404-022-06748-1] [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: 06/24/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND High-risk HPV is clearly associated with cervical cancer. Integration of HPV DNA into the host genome is considered a key event in driving cervical carcinogenesis. However, the mechanism on how HR-HPV integration influences the host genome structure has remained enigmatic. METHODS In our study, 25 DNA samples including 11 from fresh-frozen cervical carcinomas and 14 from fresh-frozen high-grade squamous intraepithelial lesion (HSILs) were detected using the method of HPV capture combined with next generation sequencing. RESULTS We calculated the frequency in each viral gene or region and found that breakpoints were prone to occur in L1 and L2 instead of E2 in the cervical cancer (P = 0.0004 and P = 5.15 × 10-40) and HSIL group (P = 2.1 × 10-32 and P = 7.06 × 10-13). The results revealed that HPV16 showed a strong tendency toward intronic region (P = 5.02 × 10-64) but a subtle tendency toward intergenic region (P = 0.04). The most frequent integration site was in the MACROD2 gene (introns 2, 4, 5, 6, 8 and 9), which in MACROD2 functional domain. CONCLUSION Our results revealed that MACROD2 is HPV hot spot integration site in cervical lesions, and its deficiency alter DNA repair and sensitivity to DNA damage thought impaired PARP1 activity resulting in chromosome instability.
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Affiliation(s)
- Junwei Zhao
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Wei Zheng
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Liqian Wang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Haiyang Jiang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Xiuli Wang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Jianqing Hou
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Anli Xu
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China.
| | - Jianglin Cong
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China.
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Varesano S, Pulliero A, Martorana E, Pizzino G, Raciti G, Coco S, Vellone VG, Izzotti A. Screening of Precancerous Lesions in Women with Human Papillomavirus (HPV) Infection by Molecular Typing and MicroRNA Analysis. J Pers Med 2023; 13:jpm13030531. [PMID: 36983713 PMCID: PMC10058065 DOI: 10.3390/jpm13030531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Human papillomavirus (HPV) is causatively associated with cervical cancer, the fourth most common malignant disease of women worldwide: (1) The aim of the proposed study is to implement routine diagnostics of HPV precancerous cervical lesions by introducing new molecular diagnostic tools. (2) Methods: This is a retrospective cohort study with a total of twenty-two formalin-fixed paraffin-embedded (FFPE) cervical samples of various sample type (nine biopsy and thirteen conization) each patient had a previous abnormal results of pap test or HPV DNA test. Genotyping, viral load and co-infections were determined. For each patient, the individual expression of 2549 microRNAs were evaluated by microarray and qPCR. (3) Results: Our data demonstrates that the microRNAs were commonly expressed in tissues biopsies. miR 4485-5p, miR4485-3p and miR-4497 were highly down-regulated in tissue biopsies with HPV precancerous cervical lesions. (4) Conclusions: the introduction of a microRNA analysis panel can improve early diagnosis, understand the nature of the lesion and, consequently, improve the clinical management of patients with HPV precancerous cervical lesions.
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Affiliation(s)
| | - Alessandra Pulliero
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy
- Correspondence: ; Tel.: +39-0103538509
| | | | | | - Gabriele Raciti
- Istituto Oncologico del Mediterraneo, 95029 Viagrande, Italy
- Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina (ME), 98122 Messina, Italy
| | - Simona Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Valerio Gaetano Vellone
- Department of Integrated Surgical and Diagnostic Sciences (DISC), University of Genoa, 16132 Genoa, Italy
- Fetal and Perinatal Pathology Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, 16147 Genoa, Italy
| | - Alberto Izzotti
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Experimental Medicine, University of Genoa, 16132 Genoa, Italy
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Shao L, Shi R, Zhao Y, Liu H, Lu A, Ma J, Cai Y, Fuksenko T, Pelayo A, Shah NN, Kochenderfer JN, Norberg SM, Hinrichs C, Highfill SL, Somerville RP, Panch SR, Jin P, Stroncek DF. Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products. J Transl Med 2022; 20:514. [DOI: 10.1186/s12967-022-03729-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
Clinical CAR T-cell therapy using integrating vector systems represents a promising approach for the treatment of hematological malignancies. Lentiviral and γ-retroviral vectors are the most commonly used vectors in the manufacturing process. However, the integration pattern of these viral vectors and subsequent effect on CAR T-cell products is still unclear.
Methods
We used a modified viral integration sites analysis (VISA) pipeline to evaluate viral integration events around the whole genome in pre-infusion CAR T-cell products. We compared the differences of integration pattern between lentiviral and γ-retroviral products. We also explored whether the integration sites correlated with clinical outcomes.
Results
We found that γ-retroviral vectors were more likely to insert than lentiviral vectors into promoter, untranslated, and exon regions, while lentiviral vector integration sites were more likely to occur in intron and intergenic regions. Some integration events affected gene expression at the transcriptional and post-transcriptional level. Moreover, γ-retroviral vectors showed a stronger impact on the host transcriptome. Analysis of individuals with different clinical outcomes revealed genes with differential enrichment of integration events. These genes may affect biological functions by interrupting amino acid sequences and generating abnormal proteins, instead of by affecting mRNA expression. These results suggest that vector integration is associated with CAR T-cell efficacy and clinical responses.
Conclusion
We found differences in integration patterns, insertion hotspots and effects on gene expression vary between lentiviral and γ-retroviral vectors used in CAR T-cell products and established a foundation upon which we can conduct further analyses.
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Linden N, Jones RB. Potential multi-modal effects of provirus integration on HIV-1 persistence: lessons from other viruses. Trends Immunol 2022; 43:617-629. [PMID: 35817699 PMCID: PMC9429957 DOI: 10.1016/j.it.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
Despite antiretroviral therapy (ART), HIV-1 persists as proviruses integrated into the genomic DNA of CD4+ T cells. The mechanisms underlying the persistence and clonal expansion of these cells remain incompletely understood. Cases have been described in which proviral integration can alter host gene expression to drive cellular proliferation. Here, we review observations from other genome-integrating human viruses to propose additional putative modalities by which HIV-1 integration may alter cellular function to favor persistence, such as by altering susceptibility to cytotoxicity in virus-expressing cells. We propose that signals implicating such mechanisms may have been masked thus far by the preponderance of defective and/or nonreactivatable HIV-1 proviruses, but could be revealed by focusing on the integration sites of intact proviruses with expression potential.
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Affiliation(s)
- Noemi Linden
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA.
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