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Sastre-Garau X, Estrada-Virrueta L, Radvanyi F. HPV DNA Integration at Actionable Cancer-Related Genes Loci in HPV-Associated Carcinomas. Cancers (Basel) 2024; 16:1584. [PMID: 38672666 PMCID: PMC11048798 DOI: 10.3390/cancers16081584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
In HPV-associated carcinomas, some examples of cancer-related genes altered by viral insertion and corresponding to potential therapeutic targets have been described, but no quantitative assessment of these events, including poorly recurrent targets, has been reported to date. To document these occurrences, we built and analyzed a database comprised of 1455 cases, including HPV genotypes and tumor localizations. Host DNA sequences targeted by viral integration were classified as "non-recurrent" (one single reported case; 838 loci), "weakly recurrent" (two reported cases; 82 loci), and highly recurrent (≥3 cases; 43 loci). Whereas the overall rate of cancer-related target genes was 3.3% in the Gencode database, this rate increased to 6.5% in "non-recurrent", 11.4% in "weakly recurrent", and 40.1% in "highly recurrent" genes targeted by integration (p = 4.9 × 10-4). This rate was also significantly higher in tumors associated with high-risk HPV16/18/45 than other genotypes. Among the genes targeted by HPV insertion, 30.2% corresponded to direct or indirect druggable targets, a rate rising to 50% in "highly recurrent" targets. Using data from the literature and the DepMap 23Q4 release database, we found that genes targeted by viral insertion could be new candidates potentially involved in HPV-associated oncogenesis. A more systematic characterization of HPV/host fusion DNA sequences in HPV-associated cancers should provide a better knowledge of HPV-driven carcinogenesis and favor the development of personalize patient treatments.
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Affiliation(s)
- Xavier Sastre-Garau
- Department of Pathology, Centre Hospitalier Intercommunal de Créteil, 40, Avenue de Verdun, 94010 Créteil, France
| | - Lilia Estrada-Virrueta
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
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2
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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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Guo C, Qu X, Tang X, Song Y, Wang J, Hua K, Qiu J. Spatiotemporally deciphering the mysterious mechanism of persistent HPV-induced malignant transition and immune remodelling from HPV-infected normal cervix, precancer to cervical cancer: Integrating single-cell RNA-sequencing and spatial transcriptome. Clin Transl Med 2023; 13:e1219. [PMID: 36967539 PMCID: PMC10040725 DOI: 10.1002/ctm2.1219] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND The mechanism underlying cervical carcinogenesis that is mediated by persistent human papillomavirus (HPV) infection remains elusive. AIMS Here, for the first time, we deciphered both the temporal transition and spatial distribution of cellular subsets during disease progression from normal cervix tissues to precursor lesions to cervical cancer. MATERIALS & METHODS We generated scRNA-seq profiles and spatial transcriptomics data from nine patient samples, including two HPV-negative normal, two HPV-positive normal, two HPV-positive HSIL and three HPV-positive cancer samples. RESULTS We not only identified three 'HPV-related epithelial clusters' that are unique to normal, high-grade squamous intraepithelial lesions (HSIL) and cervical cancer tissues but also discovered node genes that potentially regulate disease progression. Moreover, we observed the gradual transition of multiple immune cells that exhibited positive immune responses, followed by dysregulation and exhaustion, and ultimately established an immune-suppressive microenvironment during the malignant program. In addition, analysis of cellular interactions further verified that a 'homeostasis-balance-malignancy' change occurred within the cervical microenvironment during disease progression. DISCUSSION We for the first time presented a spatiotemporal atlas that systematically described the cellular heterogeneity and spatial map along the four developmental steps of HPV-related cervical oncogenesis, including normal, HPV-positive normal, HSIL and cancer. We identified three unique HPV-related clusters, discovered critical node genes that determined the cell fate and uncovered the immune remodeling during disease escalation. CONCLUSION Together, these findings provided novel possibilities for accurate diagnosis, precise treatment and prognosis evaluation of patients with precancer and cervical cancer.
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Affiliation(s)
- Chenyan Guo
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Xinyu Qu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Xiaoyan Tang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Yu Song
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Jue Wang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Keqin Hua
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Junjun Qiu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
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Ji F, Zhu X, Liao H, Ouyang L, Huang Y, Syeda MZ, Ying S. New Era of Mapping and Understanding Common Fragile Sites: An Updated Review on Origin of Chromosome Fragility. Front Genet 2022; 13:906957. [PMID: 35669181 PMCID: PMC9164283 DOI: 10.3389/fgene.2022.906957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic loci prone to forming gaps or breakages upon replication perturbation, which correlate well with chromosomal rearrangement and copy number variation. CFSs have been actively studied due to their important pathophysiological relevance in different diseases such as cancer and neurological disorders. The genetic locations and sequences of CFSs are crucial to understanding the origin of such unstable sites, which require reliable mapping and characterizing approaches. In this review, we will inspect the evolving techniques for CFSs mapping, especially genome-wide mapping and sequencing of CFSs based on current knowledge of CFSs. We will also revisit the well-established hypotheses on the origin of CFSs fragility, incorporating novel findings from the comprehensive analysis of finely mapped CFSs regarding their locations, sequences, and replication/transcription, etc. This review will present the most up-to-date picture of CFSs and, potentially, a new framework for future research of CFSs.
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Affiliation(s)
- Fang Ji
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinli Zhu
- Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Liao
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Liujian Ouyang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingfei Huang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Madiha Zahra Syeda
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Songmin Ying
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
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5
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Xu X, Han Z, Ruan Y, Liu M, Cao G, Li C, Li F. HPV16-LINC00393 Integration Alters Local 3D Genome Architecture in Cervical Cancer Cells. Front Cell Infect Microbiol 2021; 11:785169. [PMID: 34950609 PMCID: PMC8691139 DOI: 10.3389/fcimb.2021.785169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/04/2021] [Indexed: 11/30/2022] Open
Abstract
High-risk human papillomavirus (hrHPV) infection and integration were considered as essential onset factors for the development of cervical cancer. However, the mechanism on how hrHPV integration influences the host genome structure remains not fully understood. In this study, we performed in situ high-throughput chromosome conformation capture (Hi-C) sequencing, chromatin immunoprecipitation and sequencing (ChIP-seq), and RNA-sequencing (RNA-seq) in two cervical cells, 1) NHEK normal human epidermal keratinocyte; and 2) HPV16-integrated SiHa tumorigenic cervical cancer cells. Our results reveal that the HPV-LINC00393 integrated chromosome 13 exhibited significant genomic variation and differential gene expression, which was verified by calibrated CTCF and H3K27ac ChIP-Seq chromatin restructuring. Importantly, HPV16 integration led to differential responses in topologically associated domain (TAD) boundaries, with a decrease in the tumor suppressor KLF12 expression downstream of LINC00393. Overall, this study provides significant insight into the understanding of HPV16 integration induced 3D structural changes and their contributions on tumorigenesis, which supplements the theory basis for the cervical carcinogenic mechanism of HPV16 integration.
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Affiliation(s)
- Xinxin Xu
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhiqiang Han
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yetian Ruan
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Min Liu
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guangxu Cao
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chao Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fang Li
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
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6
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Human Papillomaviruses-Associated Cancers: An Update of Current Knowledge. Viruses 2021; 13:v13112234. [PMID: 34835040 PMCID: PMC8623401 DOI: 10.3390/v13112234] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022] Open
Abstract
Human papillomaviruses (HPVs), which are small, double-stranded, circular DNA viruses infecting human epithelial cells, are associated with various benign and malignant lesions of mucosa and skin. Intensive research on the oncogenic potential of HPVs started in the 1970s and spread across Europe, including Croatia, and worldwide. Nowadays, the causative role of a subset of oncogenic or high-risk (HR) HPV types, led by HPV-16 and HPV-18, of different anogenital and head and neck cancers is well accepted. Two major viral oncoproteins, E6 and E7, are directly involved in the development of HPV-related malignancies by targeting synergistically various cellular pathways involved in the regulation of cell cycle control, apoptosis, and cell polarity control networks as well as host immune response. This review is aimed at describing the key elements in HPV-related carcinogenesis and the advances in cancer prevention with reference to past and on-going research in Croatia.
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7
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Expression of Retroelements in Cervical Cancer and Their Interplay with HPV Infection and Host Gene Expression. Cancers (Basel) 2021; 13:cancers13143513. [PMID: 34298727 PMCID: PMC8306386 DOI: 10.3390/cancers13143513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022] Open
Abstract
Retroelements are expressed in diverse types of cancer and are related to tumorigenesis and to cancer progression. We characterized the expression of retroelements in cervical cancer and explored their interplay with HPV infection and their association with expression of neighboring genes. Forty biopsies of invasive cervical carcinoma (squamous cell carcinomas and adenocarcinomas) with genotyped HPV were selected and analyzed for human endogenous retrovirus (HERV) and long interspersed nuclear element 1 (L1) expression through RNA-seq data. We found 8060 retroelements expressed in the samples and a negative correlation of DNA methyltransferase 1 expression with the two most expressed L1 elements. A total of 103 retroelements were found differentially expressed between tumor histological types and between HPV types, including several HERV families (HERV-K, HERV-H, HERV-E, HERV-I and HERV-L). The comparison between HPV mono- and co-infections showed the highest proportion of differentially expressed L1 elements. The location of retroelements affected neighboring gene expression, such as shown for the interleukin-20 gene family. Three HERVs and seven L1 were located close to this gene family and two L1 showed a positive association with IL20RB expression. This study describes the expression of retroelements in cervical cancer and shows their association with HPV status and host gene expression.
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Abstract
Common fragile sites (CFSs) are large chromosomal regions that exhibit breakage on metaphase chromosomes upon replication stress. They become preferentially unstable at the early stage of cancer development and are hotspots for chromosomal rearrangements in cancers. Increasing evidence has highlighted the complexity underlying the instability of CFSs, and a combination of multiple mechanisms is believed to cause CFS fragility. We will review recent advancements in our understanding of the molecular mechanisms underlying the maintenance of CFS stability and the relevance of CFSs to cancer-associated genome instability. We will emphasize the contribution of the structure-prone AT-rich sequences to CFS instability, which is in line with the recent genome-wide study showing that structure-forming repeat sequences are principal sites of replication stress.
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Affiliation(s)
- Shibo Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, San Diego, CA 92037 USA
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, San Diego, CA 92037 USA
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9
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Jia XY, Xue YR, Zhang CX, Luo Q, Wu Y. Highly sensitive detection of the human papillomavirus E6 protein by DNA-protected silver nanoclusters and the intrinsic mechanism. NEW J CHEM 2019. [DOI: 10.1039/c9nj03241j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present study not only supplies a good approach for the early diagnosis of HPV-related cancer but also enriches the biological application of AgNCs–dsDNA.
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Affiliation(s)
- Xiang-Yu Jia
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130012
- China
| | - Ya-Rong Xue
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130012
- China
| | - Chun-Xia Zhang
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130012
- China
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130012
- China
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130012
- China
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10
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Irony-Tur Sinai M, Kerem B. Genomic instability in fragile sites-still adding the pieces. Genes Chromosomes Cancer 2018; 58:295-304. [PMID: 30525255 DOI: 10.1002/gcc.22715] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/19/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic regions in normal chromosomes that exhibit genomic instability under DNA replication stress. As replication stress is an early feature of cancer development, CFSs are involved in the signature of genomic instability found in malignant tumors. The landscape of CFSs is tissue-specific and differs under different replication stress inducers. Nevertheless, the features underlying CFS sensitivity to replication stress are shared. Here, we review the events generating replication stress and discuss the unique characteristics of CFS regions and the cellular responses aimed to stabilizing these regions.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
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Wang H, Li S, Zhang H, Wang Y, Hao S, Wu X. BLM prevents instability of structure-forming DNA sequences at common fragile sites. PLoS Genet 2018; 14:e1007816. [PMID: 30496191 PMCID: PMC6289451 DOI: 10.1371/journal.pgen.1007816] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/11/2018] [Accepted: 11/07/2018] [Indexed: 01/04/2023] Open
Abstract
Genome instability often arises at common fragile sites (CFSs) leading to cancer-associated chromosomal rearrangements. However, the underlying mechanisms of how CFS protection is achieved is not well understood. We demonstrate that BLM plays an important role in the maintenance of genome stability of structure-forming AT-rich sequences derived from CFSs (CFS-AT). BLM deficiency leads to increased DSB formation and hyper mitotic recombination at CFS-AT and induces instability of the plasmids containing CFS-AT. We further showed that BLM is required for suppression of CFS breakage upon oncogene expression. Both helicase activity and ATR-mediated phosphorylation of BLM are important for preventing genetic instability at CFS-AT sequences. Furthermore, the role of BLM in protecting CFS-AT is not epistatic to that of FANCM, a translocase that is involved in preserving CFS stability. Loss of BLM helicase activity leads to drastic decrease of cell viability in FANCM deficient cells. We propose that BLM and FANCM utilize different mechanisms to remove DNA secondary structures forming at CFS-AT on replication forks, thereby preventing DSB formation and maintaining CFS stability. Common fragile sites (CFSs) are large chromosomal regions which are more prone to breakage than other places in the genome. They are a part of normal chromosome structure and are present in all human beings, but are also hotspots for chromosomal rearrangement during oncogenesis. Understanding how CFSs are protected to prevent genome instability is thus extremely important for revealing the mechanism underlying cancer development. We found that Bloom syndrome protein BLM is involved in resolving DNA secondary structures that arise at AT-rich sequences in CFSs, suggesting a critical function of BLM in protecting CFSs. We also found that this BLM function is distinct from the role of Fanconi anemia protein FANCM in protecting CFSs, and loss of both BLM and FANCM activities leads to cell death. These studies reveal important mechanisms of the maintenance of CFS stability in mammalian cells.
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Affiliation(s)
- Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Shibo Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Huimin Zhang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ya Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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Hu Z, Ma D. The precision prevention and therapy of HPV-related cervical cancer: new concepts and clinical implications. Cancer Med 2018; 7:5217-5236. [PMID: 30589505 PMCID: PMC6198240 DOI: 10.1002/cam4.1501] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/14/2018] [Accepted: 03/21/2018] [Indexed: 12/14/2022] Open
Abstract
Cervical cancer is the third most common cancer in women worldwide, with concepts and knowledge about its prevention and treatment evolving rapidly. Human papillomavirus (HPV) has been identified as a major factor that leads to cervical cancer, although HPV infection alone cannot cause the disease. In fact, HPV-driven cancer is a small probability event because most infections are transient and could be cleared spontaneously by host immune system. With persistent HPV infection, decades are required for progression to cervical cancer. Therefore, this long time window provides golden opportunity for clinical intervention, and the fundament here is to elucidate the carcinogenic pattern and applicable targets during HPV-host interaction. In this review, we discuss the key factors that contribute to the persistence of HPV and cervical carcinogenesis, emerging new concepts and technologies for cancer interventions, and more urgently, how these concepts and technologies might lead to clinical precision medicine which could provide prediction, prevention, and early treatment for patients.
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Affiliation(s)
- Zheng Hu
- Department of Gynecological oncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd RoadYuexiu, GuangzhouGuangdongChina
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan, Hubei430030China
| | - Ding Ma
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan, Hubei430030China
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Jeannot E, Harlé A, Holmes A, Sastre-Garau X. Nuclear factor I X is a recurrent target for HPV16 insertions in anal carcinomas. Genes Chromosomes Cancer 2018; 57:638-644. [PMID: 30264502 DOI: 10.1002/gcc.22675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 12/25/2022] Open
Abstract
Anal carcinomas (AC) are associated with human papillomavirus (HPV) DNA sequences, but little is known about the physical state of the viral genome in carcinoma cells. To define the integration status and gene(s) targeted by viral insertions in AC, tumor DNAs extracted from 35 tumor specimen samples in patients with HPV16-associated invasive carcinoma were analyzed using the detection of integrated papillomavirus sequences-PCR approach. The genomic status at integration sites was assessed using comparative genomic hybridization-array assay and gene expression using reverse transcription quantitative PCR (RT-qPCR). HPV16 DNA was found integrated in 25/35 (71%) cases and the integration locus could be determined at the molecular level in 19 cases (29 total integration loci). HPV DNA was inserted on different chromosomes, but 5 cases harbored viral sequences at 19p13.2, within the nuclear factor I X (NFIX) locus. Viral DNA mapped between the most distal and the two proximal alternatively expressed exons of this gene in three cases (CA21, CA04, and CA35) and upstream of this gene (663 kb and 2.3 Mb) in the others. CGH arrays showed genomic gains/amplifications at the NFIX region, associated with HPV within the gene and RT-qPCR, revealed NFIX mRNA overexpression. Other genes targeted by integration were IL20RB, RPS6KA2, MSRA1, PIP5K1B, SLX4IP, CECR1, BCAR3, ATF6, CSNK1G1, APBA2, AGK, ILF3, PVT1, TRMT1, RAD51B, FASN, CCDC57, DSG3, and ZNF563. We identified recurrent targeting of NFIX by HPV16 insertion in anal carcinomas, supporting a role for this gene in oncogenesis, as reported for non-HPV tumors.
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Affiliation(s)
- Emmanuelle Jeannot
- Department of Theranostic and Diagnostic Medicine, Institut Curie, PSL Research University, Paris, Saint-Cloud, France
| | - Alexandre Harlé
- Université de Lorraine, Nancy, France.,CNRS UMR 7039 CRAN, Vandoeuvre-Lès-Nancy, France.,Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre-Lès-Nancy, France
| | - Allyson Holmes
- Centre National de la Recherche Scientifique UMR3244, Sorbonne Universités, Institut Curie, PSL Research University, Paris, France
| | - Xavier Sastre-Garau
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre-Lès-Nancy, France
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14
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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15
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Bhowmick R, Hickson ID. The "enemies within": regions of the genome that are inherently difficult to replicate. F1000Res 2017; 6:666. [PMID: 28620461 PMCID: PMC5461909 DOI: 10.12688/f1000research.11024.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/11/2017] [Indexed: 12/23/2022] Open
Abstract
An unusual feature of many eukaryotic genomes is the presence of regions that appear intrinsically difficult to copy during the process of DNA replication. Curiously, the location of these difficult-to-replicate regions is often conserved between species, implying a valuable role in some aspect of genome organization or maintenance. The most prominent class of these regions in mammalian cells is defined as chromosome fragile sites, which acquired their name because of a propensity to form visible gaps/breaks on otherwise-condensed chromosomes in mitosis. This fragility is particularly apparent following perturbation of DNA replication-a phenomenon often referred to as "replication stress". Here, we review recent data on the molecular basis for chromosome fragility and the role of fragile sites in the etiology of cancer. In particular, we highlight how studies on fragile sites have provided unexpected insights into how the DNA repair machinery assists in the completion of DNA replication.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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16
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Walline HM, Goudsmit CM, McHugh JB, Tang AL, Owen JH, Teh BT, McKean E, Glover TW, Graham MP, Prince ME, Chepeha DB, Chinn SB, Ferris RL, Gollin SM, Hoffmann TK, Bier H, Brakenhoff R, Bradford CR, Carey TE. Integration of high-risk human papillomavirus into cellular cancer-related genes in head and neck cancer cell lines. Head Neck 2017; 39:840-852. [PMID: 28236344 DOI: 10.1002/hed.24729] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 11/16/2016] [Accepted: 12/29/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Human papillomavirus (HPV)-positive oropharyngeal cancer is generally associated with excellent response to therapy, but some HPV-positive tumors progress despite aggressive therapy. The purpose of this study was to evaluate viral oncogene expression and viral integration sites in HPV16- and HPV18-positive squamous cell carcinoma lines. METHODS E6/E7 alternate transcripts were assessed by reverse transcriptase-polymerase chain reaction (RT-PCR). Detection of integrated papillomavirus sequences (DIPS-PCR) and sequencing identified viral insertion sites and affected host genes. Cellular gene expression was assessed across viral integration sites. RESULTS All HPV-positive cell lines expressed alternate HPVE6/E7 splicing indicative of active viral oncogenesis. HPV integration occurred within cancer-related genes TP63, DCC, JAK1, TERT, ATR, ETV6, PGR, PTPRN2, and TMEM237 in 8 head and neck squamous cell carcinoma (HNSCC) lines but UM-SCC-105 and UM-GCC-1 had only intergenic integration. CONCLUSION HPV integration into cancer-related genes occurred in 7 of 9 HPV-positive cell lines and of these 6 were from tumors that progressed. HPV integration into cancer-related genes may be a secondary carcinogenic driver in HPV-driven tumors. © 2017 Wiley Periodicals, Inc. Head Neck 39: 840-852, 2017.
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Affiliation(s)
- Heather M Walline
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, Michigan.,Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Christine M Goudsmit
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Jonathan B McHugh
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Alice L Tang
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan.,Department of Otolaryngology, University of Cincinnati, Cincinnati, Ohio
| | - John H Owen
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Bin T Teh
- National Cancer Centre - Cancer Science Institute of Singapore, Duke-NUS Graduate Medical School, Singapore
| | - Erin McKean
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Thomas W Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Martin P Graham
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Mark E Prince
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Douglas B Chepeha
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Steven B Chinn
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Robert L Ferris
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Susanne M Gollin
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Thomas K Hoffmann
- Department of Otolaryngology, Heinrich Heine University, Dusseldorf, Germany.,Department of Otolaryngology, University of Ulm, Ulm, Germany
| | - Henning Bier
- Department of Otolaryngology, Heinrich Heine University, Dusseldorf, Germany.,Department of Otolaryngology, Technical University Medical Center, Munich, Germany
| | - Ruud Brakenhoff
- Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands
| | - Carol R Bradford
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Thomas E Carey
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
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17
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Abstract
Persistent infection with high-risk human papillomavirus (HPV) genotypes is the leading cause of cervical cancer development. To this end several studies have focused on designing molecular assays for HPV genotyping, which are considered as the gold standard for the early diagnosis of HPV infection. Moreover, the tendency of HPV DNA to be integrated into the host chromosome is a determining event for cervical oncogenesis. Thus, the establishment of molecular techniques was promoted in order to investigate the physical status of the HPV DNA and the locus of viral insertion into the host chromosome. The molecular approaches that have been developed recently facilitate the collection of a wide spectrum of valuable information specific to each individual patient and therefore can significantly contribute to the establishment of a personalised prognosis, diagnosis and treatment of HPV-positive patients. The present review focuses on state of the art molecular assays for HPV detection and genotyping for intra-lesion analyses, it examines molecular approaches for the determination of HPV-DNA physical status and it discusses the criteria for selecting the most appropriate regions of viral DNA to be incorporated in HPV genotyping and in the determination of HPV-DNA physical status.
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18
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Michmerhuizen NL, Birkeland AC, Bradford CR, Brenner JC. Genetic determinants in head and neck squamous cell carcinoma and their influence on global personalized medicine. Genes Cancer 2016; 7:182-200. [PMID: 27551333 PMCID: PMC4979591 DOI: 10.18632/genesandcancer.110] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
While sequencing studies have provided an improved understanding of the genetic landscape of head and neck squamous cell carcinomas (HNSCC), there remains a significant lack of genetic data derived from non-Caucasian cohorts. Additionally, there is wide variation in HNSCC incidence and mortality worldwide both between and within various geographic regions. These epidemiologic differences are in part accounted for by varying exposure to environmental risk factors such as tobacco, alcohol, high risk human papilloma viruses and betel quid. However, inherent genetic factors may also play an important role in this variability. As limited sequencing data is available for many populations, the involvement of unique genetic factors in HNSCC pathogenesis from epidemiologically diverse groups is unknown. Here, we review current knowledge about the epidemiologic, environmental, and genetic variation in HNSCC cohorts globally and discuss future studies necessary to further our understanding of these differences. Long-term, a more complete understanding of the genetic drivers found in diverse HNSCC cohorts may help the development of personalized medicine protocols for patients with rare or complex genetic events.
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Affiliation(s)
- Nicole L Michmerhuizen
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andrew C Birkeland
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Carol R Bradford
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - J Chad Brenner
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
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19
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Bodelon C, Untereiner ME, Machiela MJ, Vinokurova S, Wentzensen N. Genomic characterization of viral integration sites in HPV-related cancers. Int J Cancer 2016; 139:2001-11. [PMID: 27343048 DOI: 10.1002/ijc.30243] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/20/2016] [Accepted: 06/09/2016] [Indexed: 01/14/2023]
Abstract
Persistent infection with carcinogenic human papillomaviruses (HPV) causes the majority of anogenital cancers and a subset of head and neck cancers. The HPV genome is frequently found integrated into the host genome of invasive cancers. The mechanisms of how it may promote disease progression are not well understood. Thoroughly characterizing integration events can provide insights into HPV carcinogenesis. Individual studies have reported limited number of integration sites in cell lines and human samples. We performed a systematic review of published integration sites in HPV-related cancers and conducted a pooled analysis to formally test for integration hotspots and genomic features enriched in integration events using data from the Encyclopedia of DNA Elements (ENCODE). Over 1,500 integration sites were reported in the literature, of which 90.8% (N = 1,407) were in human tissues. We found 10 cytobands enriched for integration events, three previously reported ones (3q28, 8q24.21 and 13q22.1) and seven additional ones (2q22.3, 3p14.2, 8q24.22, 14q24.1, 17p11.1, 17q23.1 and 17q23.2). Cervical infections with HPV18 were more likely to have breakpoints in 8q24.21 (p = 7.68 × 10(-4) ) than those with HPV16. Overall, integration sites were more likely to be in gene regions than expected by chance (p = 6.93 × 10(-9) ). They were also significantly closer to CpG regions, fragile sites, transcriptionally active regions and enhancers. Few integration events occurred within 50 Kb of known cervical cancer driver genes. This suggests that HPV integrates in accessible regions of the genome, preferentially genes and enhancers, which may affect the expression of target genes.
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Affiliation(s)
- Clara Bodelon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Michael E Untereiner
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Svetlana Vinokurova
- Laboratory of Molecular Biology of Viruses, NN Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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20
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Integration of HIV in the Human Genome: Which Sites Are Preferential? A Genetic and Statistical Assessment. Int J Genomics 2016; 2016:2168590. [PMID: 27294106 PMCID: PMC4880676 DOI: 10.1155/2016/2168590] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/24/2016] [Indexed: 12/17/2022] Open
Abstract
Chromosomal fragile sites (FSs) are loci where gaps and breaks may occur and are preferential integration targets for some viruses, for example, Hepatitis B, Epstein-Barr virus, HPV16, HPV18, and MLV vectors. However, the integration of the human immunodeficiency virus (HIV) in Giemsa bands and in FSs is not yet completely clear. This study aimed to assess the integration preferences of HIV in FSs and in Giemsa bands using an in silico study. HIV integration positions from Jurkat cells were used and two nonparametric tests were applied to compare HIV integration in dark versus light bands and in FS versus non-FS (NFSs). The results show that light bands are preferential targets for integration of HIV-1 in Jurkat cells and also that it integrates with equal intensity in FSs and in NFSs. The data indicates that HIV displays different preferences for FSs compared to other viruses. The aim was to develop and apply an approach to predict the conditions and constraints of HIV insertion in the human genome which seems to adequately complement empirical data.
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21
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Sarni D, Kerem B. The complex nature of fragile site plasticity and its importance in cancer. Curr Opin Cell Biol 2016; 40:131-136. [PMID: 27062332 DOI: 10.1016/j.ceb.2016.03.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/21/2016] [Accepted: 03/28/2016] [Indexed: 01/12/2023]
Abstract
Common fragile sites (CFSs) are chromosomal regions characterized as hotspots for breakage and chromosomal rearrangements following DNA replication stress. They are preferentially unstable in pre-cancerous lesions and during cancer development. Recently CFSs were found to be tissue- and even oncogene-induced specific, thus indicating an unforeseen complexity. Here we review recent developments in CFS research that shed new light on the molecular basis of their instability and their importance in cancer development.
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Affiliation(s)
- Dan Sarni
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem 91904, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem 91904, Israel.
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22
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Possible contributing role of Epstein-Barr virus (EBV) as a cofactor in human papillomavirus (HPV)-associated cervical carcinogenesis. J Clin Virol 2015; 73:70-76. [PMID: 26551071 DOI: 10.1016/j.jcv.2015.10.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Persistent infection with EBV has been linked to the development of malignancies including HPV-associated cervical carcinoma. However, the role of EBV in HPV-associated cervical cancer is still poorly understood. OBJECTIVE To determine the possible contributing role of EBV in HPV-associated cervical carcinogenesis according to HPV genotypes, HPV genome status and EBV localization. STUDY DESIGN Cervical tissues, including 82 with no squamous intraepithelial lesions (noSILs), 85 low-grade SILs (LSILs), 85 high grade SILs (HSILs) and 40 squamous cell carcinoma samples (SCC) were investigated using PCR and dot blot hybridization for EBV detection and PCR and reverse line blot hybridization for HPV genotyping. The amplification of papillomavirus oncogene transcripts assay and in situ hybridization were used to determine HPV physical status and EBV EBER localization, respectively. RESULTS EBV was detected increasingly from noSIL (13.4%), LSIL (29.4%) to HSIL (49.4%) samples. The prevalence of HPV-EBV co-infection was significantly higher in any grade of lesion than in noSIL samples (p<0.05) including noSIL (1.2%; 95% confidence intervals [CI]=0.0-3.6%, relative risk [RR]=1), LSIL (18.8%, 95% CI=10.5-27.1%, RR=15.4), HSIL (41.2%, 95% CI=30.7-51.6%, RR=33.8) and SCC (30.0%, 95% CI=15.8-44.2%, RR=24.6). Interestingly, HPV-EBV co-infection was more common in cases with episomal forms of high-risk (HR) HPV whereas HPV alone was more common in cases with integrated HR-HPV. In addition, EBER staining demonstrated that EBV was mainly present in infiltrating lymphocytes. CONCLUSION Infiltrating EBV-infected lymphocytes may play a role in cancer progression of cervical lesion containing episomal HR-HPV.
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23
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Han L, Maimaitiming T, Husaiyin S, Wang L, Wusainahong K, Ma C, Niyazi M. Comparative study of HPV16 integration in cervical lesions between ethnicities with high and low rates of infection with high-risk HPV and the correlation between integration rate and cervical neoplasia. Exp Ther Med 2015; 10:2169-2174. [PMID: 26668611 DOI: 10.3892/etm.2015.2740] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 08/10/2015] [Indexed: 12/19/2022] Open
Abstract
The etiology of a high incidence of cervical cancer in populations with a low human papillomavirus (HPV) infection rate is unclear. The current study aimed to investigate the role of HPV16 DNA integration in cervical lesions in women of Han and Uygur ethnicity and to explore the association between viral integration and a high cervical cancer morbidity with a low HPV infection rate. DNA was extracted from the biopsy specimens of cervical lesions of 379 patients of Uygur ethnicity and 464 patients of Han ethnicity, and multiple quantitative polymerase chain reaction (qPCR) assays were performed to determine the copy numbers of the HPV16 E2 and E6 genes. The copy number of the HPV16 DNA was evaluated according to the E2/E6 ratio. Among these cases, 122 Uygur and 121 Han specimens were found to be HPV16 positive. In the two populations, the percentage of cases with HPV16 integration (the sum of integrated-type infection only or a mixture of free-and integrated-type infection) increased with the grade of the cervical lesions (P<0.001). Within groups with the same cervical lesion grade, no significant differences in HPV16 integration were found between women of Uygur and Han ethnicity (rank sum test, P>0.05). No significant differences in the distribution of the HPV16 integration rate according to lesion grade were found in either population (P>0.05). When the two subpopulations were considered as one sample population, the integration rate significantly increased with lesion grade (P=0.02). These results indicate that the integration rate of HPV16 E2 may serve as a molecular biological marker for the development of cervical lesions.
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Affiliation(s)
- Lili Han
- Postgraduate College of Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China ; Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830054, P.R. China
| | - Tuerxunayi Maimaitiming
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830054, P.R. China
| | - Sulaiya Husaiyin
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830054, P.R. China
| | - Lin Wang
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830054, P.R. China
| | - Kunduozi Wusainahong
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830054, P.R. China
| | - Chunhua Ma
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830054, P.R. China
| | - Mayinuer Niyazi
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830054, P.R. China
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24
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Scheel A, Lin GC, McHugh JB, Komarck CM, Walline HM, Prince ME, Zacharek MA, Carey TE. Human papillomavirus infection and biomarkers in sinonasal inverted papillomas: clinical significance and molecular mechanisms. Int Forum Allergy Rhinol 2015; 5:701-7. [PMID: 26077310 PMCID: PMC4526407 DOI: 10.1002/alr.21524] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/09/2015] [Accepted: 02/19/2015] [Indexed: 12/27/2022]
Abstract
BACKGROUND The role of human papillomavirus (HPV) in sinonasal inverted papillomas (IPs) is controversial. Determining the prevalence of HPV infection and its impact on the molecular biology of these tumors is critical to characterizing its role in the pathogenesis of IPs. METHODS A total of 112 paraffin-embedded IPs from 90 patients were studied. A tissue microarray was constructed and stained for p16, p53, epidermal growth factor receptor (EGFR), and cyclin D1. HPV presence and types were determined using PGMY 09/11 primers and integration using HPV 11 detection of integrated papillomavirus sequences by ligation-mediated polymerase chain reaction (DIPS-PCR). RESULTS HPV was detected in 11 of 90 (12%) patients. HPV 11 was found in 9 samples. HPV 6 and HPV 27 were found in 1 sample each. EGFR staining proportion was higher in HPV-positive IPs vs HPV-negative specimens (56.2% vs 23.6%; p = 0.009). Differences in p16, p53, and cyclin D1 staining were not significant. HPV-positive lesions tend to progress to malignancy (p = 0.064). Three samples were analyzed for integration. Viral integration was found in both malignant tumors but not in the precursor IP. CONCLUSION Degradation of p53 and p16/cyclin D1 dysregulation are not important mechanisms in low-risk HPV-related IP. The low prevalence of HPV in this series indicates it is not a main etiological factor for IPs; however, when present, low-risk HPV may contribute to the biology of IPs through an increase of EGFR expression and a predisposition for malignant progression by integration into the cellular genome.
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Affiliation(s)
- Adam Scheel
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Giant C. Lin
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Jonathan B. McHugh
- Department of Pathology, University of Michigan Health Systems, Ann Arbor, MI
| | - Christine M. Komarck
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Heather M. Walline
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Mark E. Prince
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Mark A. Zacharek
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Thomas E. Carey
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
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25
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HPVbase--a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Sci Rep 2015. [PMID: 26205472 PMCID: PMC4513345 DOI: 10.1038/srep12522] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human papillomaviruses (HPVs) are extremely associated with different carcinomas. Despite consequential accomplishments, there is still need to establish more promising biomarkers to discriminate cancerous progressions. Therefore, we have developed HPVbase (http://crdd.osdd.net/servers/hpvbase/), a comprehensive resource for three major efficacious cancer biomarkers i.e. integration and breakpoint events, HPVs methylation patterns and HPV mediated aberrant expression of distinct host microRNAs (miRNAs). It includes clinically important 1257 integrants and integration sites from different HPV types i.e. 16, 18, 31, 33 and 45 associated with distinct histological conditions. An inclusive HPV integrant and breakpoints browser was designed to provide easy browsing and straightforward analysis. Our study also provides 719 major quantitative HPV DNA methylation observations distributed in 5 distinct HPV genotypes from higher to lower in numbers namely HPV 16 (495), HPV 18 (113), HPV45 (66), HPV 31 (34) and HPV 33 (11). Additionally, we have curated and compiled clinically significant aberrant expression profile of 341 miRNAs including their target genes in distinct carcinomas, which can be utilized for miRNA therapeutics. A user-friendly web interface has been developed for easy data retrieval and analysis. We foresee that HPVbase an integrated and multi-comparative platform would facilitate reliable cancer diagnostics and prognosis.
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26
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Milutin Gašperov N, Sabol I, Planinić P, Grubišić G, Fistonić I, Ćorušić A, Grce M. Methylated Host Cell Gene Promoters and Human Papillomavirus Type 16 and 18 Predicting Cervical Lesions and Cancer. PLoS One 2015; 10:e0129452. [PMID: 26057381 PMCID: PMC4461273 DOI: 10.1371/journal.pone.0129452] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 05/08/2015] [Indexed: 12/18/2022] Open
Abstract
Change in the host and/or human papillomavirus (HPV) DNA methylation profile is probably one of the main factors responsible for the malignant progression of cervical lesions to cancer. To investigate those changes we studied 173 cervical samples with different grades of cervical lesion, from normal to cervical cancer. The methylation status of nine cellular gene promoters, CCNA1, CDH1, C13ORF18, DAPK1, HIC1, RARβ2, hTERT1, hTERT2 and TWIST1, was investigated by Methylation Specific Polymerase Chain Reaction (MSP). The methylation of HPV18 L1-gene was also investigated by MSP, while the methylated cytosines within four regions, L1, 5’LCR, enhancer, and promoter of the HPV16 genome covering 19 CpG sites were evaluated by bisulfite sequencing. Statistically significant methylation biomarkers distinguishing between cervical precursor lesions from normal cervix were primarily C13ORF18 and secondly CCNA1, and those distinguishing cervical cancer from normal or cervical precursor lesions were CCNA1, C13ORF18, hTERT1, hTERT2 and TWIST1. In addition, the methylation analysis of individual CpG sites of the HPV16 genome in different sample groups, notably the 7455 and 7694 sites, proved to be more important than the overall methylation frequency. The majority of HPV18 positive samples contained both methylated and unmethylated L1 gene, and samples with L1-gene methylated forms alone had better prognosis when correlated with the host cell gene promoters’ methylation profiles. In conclusion, both cellular and viral methylation biomarkers should be used for monitoring cervical lesion progression to prevent invasive cervical cancer.
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Affiliation(s)
| | - Ivan Sabol
- Rudjer Boskovic Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Pavao Planinić
- Department of Gynecologic Oncology, Clinic for Gynecology and Obstetrics, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Goran Grubišić
- Obstetrics and Gynaecology Clinic, Clinical Hospital “Sestre milosrdnice,” Zagreb, Croatia
| | | | - Ante Ćorušić
- Department of Gynecologic Oncology, Clinic for Gynecology and Obstetrics, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Magdalena Grce
- Rudjer Boskovic Institute, Division of Molecular Medicine, Zagreb, Croatia
- * E-mail:
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Chandrani P, Kulkarni V, Iyer P, Upadhyay P, Chaubal R, Das P, Mulherkar R, Singh R, Dutt A. NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome. Br J Cancer 2015; 112:1958-65. [PMID: 25973533 PMCID: PMC4580395 DOI: 10.1038/bjc.2015.121] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 03/03/2015] [Accepted: 03/07/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool 'HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets. METHODS We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a 'quick mode' to identify presence of HPV types and an 'integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html. RESULTS On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene E7, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71. CONCLUSIONS HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.
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Affiliation(s)
- P Chandrani
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - V Kulkarni
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - P Iyer
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - P Upadhyay
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - R Chaubal
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - P Das
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - R Mulherkar
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - R Singh
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - A Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
- E-mail:
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Cho NH. Human papillomavirus: wearisome or awesome issue? J Gynecol Oncol 2015; 25:265-6. [PMID: 25310030 PMCID: PMC4195292 DOI: 10.3802/jgo.2014.25.4.265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Nam Hoon Cho
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea.
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Tsakogiannis D, Gortsilas P, Kyriakopoulou Z, Ruether IGA, Dimitriou TG, Orfanoudakis G, Markoulatos P. Sites of disruption within E1 and E2 genes of HPV16 and association with cervical dysplasia. J Med Virol 2015; 87:1973-80. [PMID: 25959607 DOI: 10.1002/jmv.24256] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 04/28/2015] [Indexed: 12/25/2022]
Abstract
Integration of HPV16 DNA into the host chromosome usually disrupts the E1 and/or E2 genes. The present study investigated the disruption of E1, E2 genes in a total of eighty four HPV16-positive precancerous and cervical cancer specimens derived from Greek women (seventeen paraffin-embedded cervical biopsies and sixty seven Thin Prep samples). Complete E2 and E1 genes were amplified using three and nine overlapping primer sets respectively, in order to define the sites of disruption. Extensive mapping analysis revealed that disruption/deletion events within E2 gene occurred in high grade and cervical cancer samples (x(2) test, P < 0.01), while no evidence of E2 gene disruption was documented among low grade cervical intraepithelial neoplasias. In addition, disruptions within the E1 gene occur both in high and low grade cervical intraepithelial neoplasia. This leads to the assumption that in low grade cervical intraepithelial neoplasias only E1 gene disruption was involved (Fisher's exact test, P < 0.05), while in high grade malignancies and cervical cancer cases deletions in both E1 and E2 genes occurred. Furthermore, the most prevalent site of disruption of E1 gene was located between nucleotides 1059 and 1323, while the most prevalent deleted region of the E2 gene was located between nucleotides 3172 and 3649 (E2 hinge region). Therefore, it is proposed that each population has its own profile of frequencies and sites of disruptions and extensive mapping analysis of E1 and E2 genes is mandatory in order to determine suitable markers for HPV16 DNA integration analysis in distinct populations.
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Affiliation(s)
- D Tsakogiannis
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - P Gortsilas
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Z Kyriakopoulou
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - I G A Ruether
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - T G Dimitriou
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - G Orfanoudakis
- University of Strasbourg, Ecole Superieure de Biotechnologie de Strasbourg, CNRS FRE 3211-Oncoprotein Group, Illkirch, France
| | - P Markoulatos
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
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30
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Thys RG, Lehman CE, Pierce LCT, Wang YH. DNA secondary structure at chromosomal fragile sites in human disease. Curr Genomics 2015; 16:60-70. [PMID: 25937814 PMCID: PMC4412965 DOI: 10.2174/1389202916666150114223205] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 11/22/2022] Open
Abstract
DNA has the ability to form a variety of secondary structures that can interfere with normal cellular processes, and many of these structures have been associated with neurological diseases and cancer. Secondary structure-forming sequences are often found at chromosomal fragile sites, which are hotspots for sister chromatid exchange, chromosomal translocations, and deletions. Structures formed at fragile sites can lead to instability by disrupting normal cellular processes such as DNA replication and transcription. The instability caused by disruption of replication and transcription can lead to DNA breakage, resulting in gene rearrangements and deletions that cause disease. In this review, we discuss the role of DNA secondary structure at fragile sites in human disease.
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Affiliation(s)
- Ryan G Thys
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Christine E Lehman
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | | | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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31
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Guo Y, Hu J, Zhu L, Sun J, Xie L, Kong F, Han L, Li F. Physical Status and Variant Analysis of Human Papillomavirus 16 in Women from Shanghai. Gynecol Obstet Invest 2015; 81:61-70. [DOI: 10.1159/000381775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/18/2015] [Indexed: 11/19/2022]
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32
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Gao G, Smith DI. Very large common fragile site genes and their potential role in cancer development. Cell Mol Life Sci 2014; 71:4601-15. [PMID: 25300511 PMCID: PMC11113612 DOI: 10.1007/s00018-014-1753-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
Abstract
Common fragile sites (CFSs) are large chromosomal regions that are hot-spots for alterations especially within cancer cells. The three most frequently expressed CFS regions (FRA3B, FRA16D and FRA6E) contain genes that span extremely large genomic regions (FHIT, WWOX and PARK2, respectively), and these genes were found to function as important tumor suppressors. Many other CFS regions contain extremely large genes that are also targets of alterations in multiple cancers, but none have yet been demonstrated to function as tumor suppressors. The loss of expression of just FHIT or WWOX has been found to be associated with a worse overall clinical outcome. Studies in different cancers have revealed that some cancers have decreased expression of multiple large CFS genes. This loss of expression could have a profound phenotypic effect on these cells. In this review, we will summarize the known large common fragile site genes and discuss their potential relationship to cancer development.
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Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - David I. Smith
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
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Tsakogiannis D, Kyriakopoulou Z, Ruether IGA, Amoutzias GD, Dimitriou TG, Diamantidou V, Kotsovassilis C, Markoulatos P. Determination of human papillomavirus 16 physical status through E1/E6 and E2/E6 ratio analysis. J Med Microbiol 2014; 63:1716-1723. [DOI: 10.1099/jmm.0.076810-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Human papillomavirus (HPV) 16 genome integration into the host chromosome is a crucial event during the life cycle of the virus and a major step towards carcinogenesis. The integration of HPV16 DNA promotes a constitutive high expression level of E6 and E7 oncoproteins, resulting in the extensive proliferation of the infected epithelial cells. In the present report the physical status of the HPV16 genome was studied, through determination of E1/E6 and E2/E6 DNA copy number ratios in 61 cervical samples of low- and high-grade malignancy and 8 cervical cancer samples, all of them associated with HPV16 infection. The selection of E1, E2 and E6 amplification target regions was performed according to the most prevalent deleted/disrupted sites of E1 and E2 genes. For this target selection we also considered the most conserved regions of E1, E2 and E6 genes among the same HPV16 isolates that were recently reported by our group. The analysis of HPV16 DNA form revealed a significant association among the mixed DNA forms in low-grade and high-grade malignancies, (χ2, P<0.01). The comparative analysis of E1/E6 and E2/E6 in the same cervical samples provides an accurate picture of HPV16 DNA form and may reveal whether different HPV16 DNA integrants coexist in the same cervical sample or not. This study proposes that E1/E6 and E2/E6 ratios determine with accuracy the HPV16 DNA integration pattern and may predict multiple integration events in the examined sample, thus providing significant information about the progression of cervical dysplasia.
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Affiliation(s)
- Dimitris Tsakogiannis
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Zaharoula Kyriakopoulou
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Irina Georgia Anna Ruether
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Grigoris D. Amoutzias
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Tilemachos G. Dimitriou
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Valentina Diamantidou
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | | | - Panayotis Markoulatos
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
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Ozeri-Galai E, Tur-Sinai M, Bester AC, Kerem B. Interplay between genetic and epigenetic factors governs common fragile site instability in cancer. Cell Mol Life Sci 2014; 71:4495-506. [PMID: 25297918 PMCID: PMC11113459 DOI: 10.1007/s00018-014-1719-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 11/28/2022]
Abstract
Common fragile sites (CFSs) are regions within the normal chromosomal structure that were characterized as hotspots for genomic instability in cancer almost 30 years ago. In recent years, many efforts have been made to understand the basis of CFS fragility and their involvement in the genomic signature of instability found in malignant tumors. CFSs are among the first regions to undergo genomic instability during cancer development because of their intrinsic sensitivity to replication stress conditions, which result from oncogene expression. The preferred sensitivity of CFSs to replication stress stems from various mechanisms including: replication fork arrest at AT-rich repeats, origin paucity along large genomic regions, failure in activation of dormant origins, late replication timing, collision between replication and transcription along large genes, all leading to incomplete replication of the CFS region and resulting in chromosomal instability. Here we review shared and unique characteristics of CFSs, their underlying causes and implications, particularly for the development of cancer.
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Affiliation(s)
- Efrat Ozeri-Galai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Michal Tur-Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Assaf C. Bester
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
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35
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Aromseree S, Chaiwongkot A, Ekalaksananan T, Kongyingyoes B, Patarapadungkit N, Pientong C. The three most common human papillomavirus oncogenic types and their integration state in Thai women with cervical precancerous lesions and carcinomas. J Med Virol 2014; 86:1911-9. [DOI: 10.1002/jmv.24034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Sirinart Aromseree
- Department of Microbiology; Faculty of Medicine; Khon Kaen University; Khon Kaen Thailand
| | - Arkom Chaiwongkot
- Department of Microbiology; Faculty of Medicine; Khon Kaen University; Khon Kaen Thailand
| | - Tipaya Ekalaksananan
- Department of Microbiology; Faculty of Medicine; Khon Kaen University; Khon Kaen Thailand
| | - Bunkerd Kongyingyoes
- Department of Pharmacology; Faculty of Medicine; Khon Kaen University; Khon Kaen Thailand
| | | | - Chamsai Pientong
- Department of Microbiology; Faculty of Medicine; Khon Kaen University; Khon Kaen Thailand
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36
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Raybould R, Fiander A, Wilkinson GWG, Hibbitts S. HPV integration detection in CaSki and SiHa using detection of integrated papillomavirus sequences and restriction-site PCR. J Virol Methods 2014; 206:51-4. [PMID: 24880069 DOI: 10.1016/j.jviromet.2014.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 05/17/2014] [Accepted: 05/20/2014] [Indexed: 01/10/2023]
Abstract
Human Papillomavirus (HPV) infection is the primary cause of cervical neoplasia. HPV DNA is integrated into the human genome in the majority of cervical cancers. The nature of integration may differ with integration incorporating a single copy of HPV or occurring in concatenated form. Our understanding of HPV tumorigenesis is largely based on studies using characterised cell lines with defined integration sites; these cell lines provide an invaluable standard for validation of diagnostic assays. Cell lines also further understanding of integration mechanisms in clinical samples. The objective of this study was to explore integration assays and to investigate integration events in cell lines where HPV is integrated in concatenated form. Restriction site PCR and detection of integrated papillomavirus sequences were performed on DNA from SiHa and CaSki. A novel integration site on Xq27.3 and HPV genome rearrangements were detected in CaSki DNA. However, where integration was previously detected by FISH in CaSki, and reported to be integrated in concatenated form, integration was not detected by DIPS or RS-PCR. The data presented illustrate that HPV copy number can hinder integration detection; this needs consideration when interpreting results from tests applied to clinical samples.
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Affiliation(s)
- Rachel Raybould
- Institute of Cancer Research and Genetics, Section of Obstetrics and Gynecology, Main Building, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom.
| | - Alison Fiander
- Institute of Cancer Research and Genetics, Section of Obstetrics and Gynecology, Main Building, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Gavin W G Wilkinson
- Institute of Infection and Immunity, Section of Medical Microbiology, Tenovus Building, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Sam Hibbitts
- Institute of Cancer Research and Genetics, Section of Obstetrics and Gynecology, Main Building, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
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HPV-16 E2 physical status and molecular evolution in vivo in cervical carcinomas. Int J Biol Markers 2014; 29:e78-85. [PMID: 24170557 DOI: 10.5301/jbm.5000051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2013] [Indexed: 11/20/2022]
Abstract
A key event in the development of cervical carcinoma is the deregulated expression of high-risk human papillomavirus (HR-HPV) oncogenes, most commonly due to HPV integration into host DNA. Here we explored whether HPV-16 E2 gene integrity is a biomarker of progressive disease with oncogenes expression. HPV-16 genome disruption was assessed by amplification of the entire E2 gene, while mRNA expression patterns of the E1, E2, E6, and E7 genes were evaluated by reverse transcription PCR (RT-PCR). As expected, E2 disruption was significantly higher among patients with cervical cancers than subjects with benign lesions (p=0.02). The status of the E2 gene correlated with tumorogenesis, and seemed also to correlate with the stage of the carcinomas, since integrated HPV-16 DNA was frequently detected in patients with advanced cancer stages (75% of stage III vs 60% stages I and II). In bivariate analysis, the lesions’ grade was most significantly associated with HPV-16 DNA disruption (p<0.05). In cervical carcinoma the deletion pattern involved more frequently the E2 gene rather than the E1 gene (62.5% vs 45.8%). The prevalence of the E6/E7 HPV-16 transcripts in cervical carcinoma specimens and in benign cervical lesions were detected with frequencies of, respectively, 91.6% and 45.4%. The mRNA levels of the HPV-16 E6/E7 genes were expressed at approximately the same levels in each physical state. We consistently observed that E6/E7 were absent or weakly detectable in the presence of E2. However, in the absence of E2 the levels of E6/E7 markedly increased (p<0.05). This study underscores the significance of investigating alternative mechanisms of E2 expression and oncogenes E6/E7 transcripts in vivo as biomarkers for disease severity in cervical carcinomas.
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Detection of the human papillomavirus 58 physical state using the amplification of papillomavirus oncogene transcripts assay. J Virol Methods 2013; 189:290-8. [PMID: 23466631 DOI: 10.1016/j.jviromet.2013.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 02/17/2013] [Accepted: 02/21/2013] [Indexed: 01/20/2023]
Abstract
HPV 58 is detected commonly in cervical cancer in East Asian countries. To evaluate the HPV 58 physical state, the amplification of papillomavirus oncogene transcripts (APOT) and hybridisation assays were established. Episome- and integrate-derived transcripts were confirmed by direct sequencing. Twenty-nine HPV 58 positive samples from various cervical lesions were used. The results showed that the episome-derived transcripts were recognised as two major specific amplified products (1040 and 714 bp). Two splice donor sites were mapped to the 5' splice site of the E1 gene on SD898 and SD899 and spliced to the 3' acceptor site of the E4 gene on SA3353, SA3356 and SA3365. The episome-derived transcripts were found 100% in normal cervical epithelia and low-grade lesions (9/9 cases) while the integrate-derived transcripts were detected in 13.3% of high-grade lesions (2/15 cases) and in 20% of carcinomas (1/5 cases). HPV 58 integration sites were found on chromosomes 4q21, 12q24 and 18q12. Using the established APOT assay, the results revealed not only novel information on the HPV 58 transcription patterns of episomal transcripts, but also integration site. The APOT assay is a reliable and useful tool for the detection of the HPV 58 physical state and its oncogene expression.
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Li H, Yang Y, Zhang R, Cai Y, Yang X, Wang Z, Li Y, Cheng X, Ye X, Xiang Y, Zhu B. Preferential sites for the integration and disruption of human papillomavirus 16 in cervical lesions. J Clin Virol 2013; 56:342-7. [PMID: 23290390 DOI: 10.1016/j.jcv.2012.12.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/03/2012] [Accepted: 12/10/2012] [Indexed: 11/16/2022]
Abstract
BACKGROUND Persistent infection with high-risk human papillomavirus (HPV) is necessary to cause cervical cancer, and integrating viral DNA into the host genome may contribute to the process of carcinogenesis. The underlying mechanisms are still unclear. OBJECTIVE In this study, we aimed to investigate the distribution of HPV 16 integration in the host genome and disrupted sites in the viral genome. STUDY DESIGN The physical status of HPV 16 genomes in 46 cervical precancerous and cancerous lesions was determined via ligation-mediated chain reaction (DIPS) using 15 previously published primer sets and 12 newly designed primer sets. RESULTS A total of 60 viral-cellular junctions were identified in 31 of 46 specimens, and over 80% of the integration sites in the human genome were located in regions of repetitive elements. The proportion of LSIL-, HSIL-, and SCC-containing integration sites near cancer-relevant genes was 10%, 18.8%, and 33.3%, respectively. The frequency of viral gene disruption was significantly higher (P < 0.05) in the L2 gene than in other regions of the viral genome. CONCLUSION There are sites of preferential HPV 16 integration. The integration sites tend to be located in repetitive regions of the host genome, and some sites are found near cancer-relevant genes. In addition, the HPV 16 genome is more likely to be disrupted in the L2 gene locus.
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Affiliation(s)
- Hui Li
- Microbial Genome Research Center, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Hernandez JM, Siegel EM, Riggs B, Eschrich S, Elahi A, Qu X, Ajidahun A, Berglund A, Coppola D, Grady WM, Giuliano AR, Shibata D. DNA methylation profiling across the spectrum of HPV-associated anal squamous neoplasia. PLoS One 2012; 7:e50533. [PMID: 23226306 PMCID: PMC3511539 DOI: 10.1371/journal.pone.0050533] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 09/27/2012] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Changes in host tumor genome DNA methylation patterns are among the molecular alterations associated with HPV-related carcinogenesis. However, there is little known about the epigenetic changes associated specifically with the development of anal squamous cell cancer (SCC). We sought to characterize broad methylation profiles across the spectrum of anal squamous neoplasia. METHODOLOGY/PRINCIPAL FINDINGS Twenty-nine formalin-fixed paraffin embedded samples from 24 patients were evaluated and included adjacent histologically normal anal mucosa (NM; n = 3), SCC-in situ (SCC-IS; n = 11) and invasive SCC (n = 15). Thirteen women and 11 men with a median age of 44 years (range 26-81) were included in the study. Using the SFP(10) LiPA HPV-typing system, HPV was detected in at least one tissue from all patients with 93% (27/29) being positive for high-risk HPV types and 14 (93%) of 15 invasive SCC tissues testing positive for HPV 16. Bisulfite-modified DNA was interrogated for methylation at 1,505 CpG loci representing 807 genes using the Illumina GoldenGate Methylation Array. When comparing the progression from normal anal mucosa and SCC-IS to invasive SCC, 22 CpG loci representing 20 genes demonstrated significant differential methylation (p<0.01). The majority of differentially methylated gene targets occurred at or close to specific chromosomal locations such as previously described HPV methylation "hotspots" and viral integration sites. CONCLUSIONS We have identified a panel of differentially methlylated CpG loci across the spectrum of HPV-associated squamous neoplasia of the anus. To our knowledge, this is the first reported application of large-scale high throughput methylation analysis for the study of anal neoplasia. Our findings support further investigations into the role of host-genome methylation in HPV-associated anal carcinogenesis with implications towards enhanced diagnosis and screening strategies.
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Affiliation(s)
- Jonathan M. Hernandez
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Erin M. Siegel
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Bridget Riggs
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Steven Eschrich
- Department of Biomedical Informatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Abul Elahi
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Xiaotao Qu
- Department of Biomedical Informatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Abidemi Ajidahun
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Anders Berglund
- Department of Biomedical Informatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Domenico Coppola
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - William M. Grady
- Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Anna R. Giuliano
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - David Shibata
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
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Abreu ALP, Souza RP, Gimenes F, Consolaro MEL. A review of methods for detect human Papillomavirus infection. Virol J 2012; 9:262. [PMID: 23131123 PMCID: PMC3507852 DOI: 10.1186/1743-422x-9-262] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 11/02/2012] [Indexed: 02/07/2023] Open
Abstract
Human Papillomavirus (HPV) is the most common sexually transmitted virus. Worldwide, the most common high-risk (HR)-HPV are -16/18, and approximately 70% of cervical cancers (CC) are due to infection by these genotypes. Persistent infection by HR-HPV is a necessary but not sufficient cause of this cancer, which develops over a long period through precursor lesions, which can be detected by cytological screening. Although this screening has decreased the incidence of CC, HPV-related cervical disease, including premalignant and malignant lesions, continues to be a major burden on health-care systems. Although not completely elucidated, the HPV-driven molecular mechanisms underlying the development of cervical lesions have provided a number of potential biomarkers for both diagnostic and prognostic use in the clinical management of women with HPV-related cervical disease, and these biomarkers can also be used to increase the positive predictive value of current screening methods. In addition, they can provide insights into the biology of HPV-induced cancer and thus lead to the development of nonsurgical therapies. Considering the importance of detecting HPV and related biomarkers, a variety of methods are being developed for these purposes. This review summarizes current knowledge of detection methods for HPV, and related biomarkers that can be used to discriminate lesions with a high risk of progression to CC.
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Affiliation(s)
- André L P Abreu
- Division of Clinical Cytology, Department of Clinical Analysis and Biomedicine, State University of Maringá, Av, Colombo 5790, 87020-900, Paraná, Brazil
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42
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Sabol I, Matovina M, Si-Mohamed A, Grce M. Characterization and whole genome analysis of human papillomavirus type 16 e1-1374^63nt variants. PLoS One 2012; 7:e41045. [PMID: 22911739 PMCID: PMC3404080 DOI: 10.1371/journal.pone.0041045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 06/20/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The variation of the most common Human papillomavirus (HPV) type found in cervical cancer, the HPV16, has been extensively investigated in almost all viral genes. The E1 gene variation, however, has been rarely studied. The main objective of the present investigation was to analyze the variability of the E6 and E1 genes, focusing on the recently identified E1-1374^63nt variant. METHODOLOGY/PRINCIPAL FINDINGS Variation within the E6 of 786 HPV16 positive cervical samples was analyzed using high-resolution melting, while the E1-1374^63nt duplication was assayed by PCR. Both techniques were supplemented with sequencing. The E1-1374^63nt duplication was linked with the E-G350 and the E-C109/G350 variants. In comparison to the referent HPV16, the E1-1374^63nt E-G350 variant was significantly associated with lower grade cervical lesions (p = 0.029), while the E1-1374^63nt E-C109/G350 variant was equally distributed between high and low grade lesions. The E1-1374^63nt variants were phylogenetically closest to E-G350 variant lineage (A2 sub-lineage based on full genome classification). The major differences between E1-1374^63nt variants were within the LCR and the E6 region. On the other hand, changes within the E1 region were the major differences from the A2 sub-lineage, which has been historically but inconclusively associated with high grade cervical disease. Thus, the shared variations cannot explain the particular association of the E1-1374^63nt variant with lower grade cervical lesions. CONCLUSIONS/SIGNIFICANCE The E1 region has been thus far considered to be well conserved among all HPVs and therefore uninteresting for variability studies. However, this study shows that the variations within the E1 region could possibly affect cervical disease, since the E1-1374^63nt E-G350 variant is significantly associated with lower grade cervical lesions, in comparison to the A1 and A2 sub-lineage variants. Furthermore, it appears that the silent variation 109T>C of the E-C109/G350 variant might have a significant role in the viral life cycle and warrants further study.
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Affiliation(s)
- Ivan Sabol
- Division of Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Mihaela Matovina
- Department of Microbiology and Parasitology, School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ali Si-Mohamed
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Magdalena Grce
- Division of Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia
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43
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Das P, Thomas A, Mahantshetty U, Shrivastava SK, Deodhar K, Mulherkar R. HPV genotyping and site of viral integration in cervical cancers in Indian women. PLoS One 2012; 7:e41012. [PMID: 22815898 PMCID: PMC3397968 DOI: 10.1371/journal.pone.0041012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 06/15/2012] [Indexed: 12/03/2022] Open
Abstract
Persistent HPV infection plays a major role in cervical cancer. This study was undertaken to identify HPV types in a cohort of Indian women with locally advanced cervical cancer as well as to determine the physical state and/or site of viral integration in the host genome. Pretreatment biopsies (n = 270) from patients were screened for HPV infection by a high throughput HPV genotyping assay based on luminex xMAP technology as well as MY09/11 PCR and SPF1/2 PCR. Overall HPV positivity was observed to be 95%, with HPV16 being most common (63%) followed by infection with HPV18. Integration status of the virus was identified using Amplification of Papillomavirus Oncogene Transcripts (APOT) assay in a subset of samples positive for HPV16 and/or HPV18 (n = 86) and with an adequate follow-up. The data was correlated with clinical outcome of the patients. Integration of the viral genome was observed in 79% of the cases and a preference for integration into the chromosomal loci 1p, 3q, 6q, 11q, 13q and 20q was seen. Clinical data revealed that the physical state of the virus (integrated or episomal) could be an important prognostic marker for cervical cancer.
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Affiliation(s)
- Poulami Das
- Mulherkar Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Asha Thomas
- Mulherkar Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Umesh Mahantshetty
- Department of Radiation Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Shyam K. Shrivastava
- Department of Radiation Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Kedar Deodhar
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Rita Mulherkar
- Mulherkar Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
- * E-mail:
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44
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Schmitz M, Driesch C, Jansen L, Runnebaum IB, Dürst M. Non-random integration of the HPV genome in cervical cancer. PLoS One 2012; 7:e39632. [PMID: 22761851 PMCID: PMC3384597 DOI: 10.1371/journal.pone.0039632] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 05/24/2012] [Indexed: 12/19/2022] Open
Abstract
HPV DNA integration into the host genome is a characteristic but not an exclusive step during cervical carcinogenesis. It is still a matter of debate whether viral integration contributes to the transformation process beyond ensuring the constitutive expression of the viral oncogenes. There is mounting evidence for a non-random distribution of integration loci and the direct involvement of cellular cancer-related genes. In this study we addressed this topic by extending the existing data set by an additional 47 HPV16 and HPV18 positive cervical carcinoma. We provide supportive evidence for previously defined integration hotspots and have revealed another cluster of integration sites within the cytogenetic band 3q28. Moreover, in the vicinity of these hotspots numerous microRNAs (miRNAs) are located and may be influenced by the integrated HPV DNA. By compiling our data and published reports 9 genes could be identified which were affected by HPV integration at least twice in independent tumors. In some tumors the viral-cellular fusion transcripts were even identical with respect to the viral donor and cellular acceptor sites used. However, the exact integration sites are likely to differ since none of the integration sites analysed thus far have shown more than a few nucleotides of homology between viral and host sequences. Therefore, DNA recombination involving large stretches of homology at the integration site can be ruled out. It is however intriguing that by sequence alignment several regions of the HPV16 genome were found to have highly homologous stretches of up to 50 nucleotides to the aforementioned genes and the integration hotspots. One common region of homologies with cellular sequences is between the viral gene E5 and L2 (nucleotides positions 4100 to 4240). We speculate that this and other regions of homology are involved in the integration process. Our observations suggest that targeted disruption, possibly also of critical cellular genes, by HPV integration remains an issue to be fully resolved.
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Affiliation(s)
- Martina Schmitz
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
| | - Corina Driesch
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
| | - Lars Jansen
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
| | - Ingo B. Runnebaum
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
| | - Matthias Dürst
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Jena, Jena, Germany
- * E-mail:
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45
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Leonard SM, Wei W, Collins SI, Pereira M, Diyaf A, Constandinou-Williams C, Young LS, Roberts S, Woodman CB. Oncogenic human papillomavirus imposes an instructive pattern of DNA methylation changes which parallel the natural history of cervical HPV infection in young women. Carcinogenesis 2012; 33:1286-93. [DOI: 10.1093/carcin/bgs157] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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46
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Ozeri-Galai E, Bester AC, Kerem B. The complex basis underlying common fragile site instability in cancer. Trends Genet 2012; 28:295-302. [PMID: 22465609 DOI: 10.1016/j.tig.2012.02.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
Abstract
Common fragile sites (CFSs) were characterized almost 30 years ago as sites undergoing genomic instability in cancer. Recently, in vitro studies have found that oncogene-induced replication stress leads to CFS instability. In vivo, CFSs were found to be preferentially unstable during early stages of cancer development and to leave a unique signature of instability. It is now increasingly clear that, along the spectrum of replication features characterizing CFSs, failure of origin activation is a common feature. This and other features of CFSs, together with the replication stress characterizing early stages of cancer development, lead to incomplete replication that results in genomic instability preferentially at CFSs. Here, we review the shared and unique characteristics of CFSs, their underlying causes and their implications, particularly with respect to the development of cancer.
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Affiliation(s)
- Efrat Ozeri-Galai
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University, Jerusalem 91904, Israel
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47
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Annunziata C, Buonaguro L, Buonaguro FM, Tornesello ML. Characterization of the human papillomavirus (HPV) integration sites into genital cancers. Pathol Oncol Res 2012; 18:803-8. [PMID: 22451136 DOI: 10.1007/s12253-012-9507-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 02/16/2012] [Indexed: 12/24/2022]
Abstract
Oncogenic HPVs have been found frequently integrated into human genome of invasive cancers and chromosomal localization has been extensively investigated in cervical carcinoma. Few studies have analyzed the HPV integration loci in other genital cancers. We have characterized the integration sites of HPV16 in invasive penile carcinoma by means of Alu-HPV-based PCR. Nucleotide sequence analysis of viral-human DNA junctions showed that HPV integration occurred in one case within the chromosome 8q21.3 region, in which the FAM92A1 gene is mapped, and in the second case inside the chromosome 16p13.3, within the intronic region of TRAP1 gene. These results confirm previous observations, summarized in a systematic review of the literature, on the HPV integration events in gene loci relevant to cancer pathogenesis.
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Affiliation(s)
- Clorinda Annunziata
- Molecular Biology and Viral Oncology and AIDS Reference Centre, National Cancer Institute Fondazione Pascale, Cappella Cangiani, 80131, Naples, Italy
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48
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Schmitz M, Driesch C, Beer-Grondke K, Jansen L, Runnebaum IB, Dürst M. Loss of gene function as a consequence of human papillomavirus DNA integration. Int J Cancer 2012; 131:E593-602. [PMID: 22262398 DOI: 10.1002/ijc.27433] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Accepted: 12/23/2011] [Indexed: 11/10/2022]
Abstract
Integration of the human papillomavirus (HPV) genome into the host chromatin is a characteristic step in cervical carcinogenesis. Integration ensures constitutive expression of the viral oncogenes E6 and E7 which drive carcinogenesis. However, integration has also an impact on host DNA. There is increasing evidence that integration not only occurs in fragile sites and translocation breakpoints but also in transcriptionally active regions. Indeed, a substantial number of integration sites actually disrupt host genes and may thereby affect gene expression. No doubt, even subtle changes in gene expression may influence the cell phenotype but small fold changes are difficult to quantify reliably in biopsy material. We have, therefore, addressed the question whether a complete loss of gene function that is insertional mutagenesis in combination with deletion or epigenetic modification of the second allele is also a phenomenon pertinent to cervical cancer. Out of the ten preselected squamous cell carcinomas analyzed, all viral integration sites were located within the intron sequences of known genes, giving rise to viral-cellular fusion transcripts of sense orientation. Moreover, for two tumors, we provide evidence for complete functional loss of the gene affected by HPV integration. Of particular note is that one of the genes involved is the recently described novel tumor suppressor gene castor zinc finger 1. Although our study provides no functional proof that any of the genes affected by HPV integration are causally involved in the transformation process, an exhaustive systematic look at the role of insertional mutagenesis in cervical cancer appears to be warranted.
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Affiliation(s)
- Martina Schmitz
- Klinik für Geburtshilfe und Frauenheilkunde, Universitätsklinikum Jena, Jena, Germany
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49
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Sequence variation analysis of the E2 gene of human papilloma virus type 16 in cervical lesions from women in Greece. Arch Virol 2012; 157:825-32. [DOI: 10.1007/s00705-012-1236-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 12/15/2011] [Indexed: 10/14/2022]
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50
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Li K, Jin X, Fang Y, Wang C, Gong M, Chen P, Liu J, Deng D, Ai J. Correlation between physical status of human papilloma virus and cervical carcinogenesis. ACTA ACUST UNITED AC 2012; 32:97-102. [PMID: 22282253 DOI: 10.1007/s11596-012-0017-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Indexed: 11/29/2022]
Abstract
The prevalence of human papilloma virus (HPV)-16 in patients with cervical cancer, the physical status of HPV-16 in patients with cervical lesions, and the role of HPV-16 integration in cervical carcinogenesis were investigated. HPV genotyping was performed by using PCR approach with the primer GP5+/GP6+ and type-specific primer on biopsy specimens taken operatively from 198 women. Multiple PCR was done to detect physical status of HPV-16 in a series of cervical liquid-based cytology samples and biopsy specimens obtained from different cervical lesions with HPV-16 infection, including 112 specimens with cervical cancer, 151 specimens with CIN I, 246 specimens with CIN and 120 specimens with CINIII. The results showed that there were 112 cervical cancer samples (56.57% of total cervical cancer patients) with HPV-16 infection. The frequency of HPV-16 pure integration was 65.18% (73/112), 56.57% (47/120), 23.58% (58/246) and 7.95% (12/151) in cervical cancer, CINIII, CINII and CINI patients respectively. In situ hybridization was performed on some paraffin-embedded sections of CINII, CINIII and cervical cancer to verify the physical status of HPV-16 infection. Significant difference was observed between cervical cancer and CIN I, CINII, CINIII in the frequency of HPV-16 integration (P<0.01). It is suggested that HPV-16 is the most prevalent type and is associated with cervical cancer. In the case of HPV-16 infection there are close associations between the severity of cervical lesions and the frequency of HPV-16 integration. The application of testing HPV genotyping and physical status based on detection of HC-II HPV DNA would be in favor of predicting the prognosis of cervical precancerosis and enhancing the screening accuracy of cervical cancer.
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Affiliation(s)
- Kezhen Li
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xin Jin
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yong Fang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Changyu Wang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Mei Gong
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Pingbo Chen
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jia Liu
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dongrui Deng
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jihui Ai
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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