1
|
Jansz N, Faulkner GJ. Viral genome sequencing methods: benefits and pitfalls of current approaches. Biochem Soc Trans 2024; 52:1431-1447. [PMID: 38747720 DOI: 10.1042/bst20231322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/27/2024]
Abstract
Whole genome sequencing of viruses provides high-resolution molecular insights, enhancing our understanding of viral genome function and phylogeny. Beyond fundamental research, viral sequencing is increasingly vital for pathogen surveillance, epidemiology, and clinical applications. As sequencing methods rapidly evolve, the diversity of viral genomics applications and catalogued genomes continues to expand. Advances in long-read, single molecule, real-time sequencing methodologies present opportunities to sequence contiguous, haplotype resolved viral genomes in a range of research and applied settings. Here we present an overview of nucleic acid sequencing methods and their applications in studying viral genomes. We emphasise the advantages of different viral sequencing approaches, with a particular focus on the benefits of third-generation sequencing technologies in elucidating viral evolution, transmission networks, and pathogenesis.
Collapse
Affiliation(s)
- Natasha Jansz
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
2
|
Catalán-Castorena O, Garibay-Cerdenares OL, Illades-Aguiar B, Castillo-Sánchez R, Zubillaga-Guerrero MI, Leyva-Vazquez MA, Encarnacion-Guevara S, Flores-Alfaro E, Ramirez-Ruano M, del Carmen Alarcón-Romero L. Bioinformatics Analysis of Human Papillomavirus 16 Integration in Cervical Cancer: Changes in MAGI-1 Expression in Premalignant Lesions and Invasive Carcinoma. Cancers (Basel) 2024; 16:2225. [PMID: 38927930 PMCID: PMC11202195 DOI: 10.3390/cancers16122225] [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: 03/28/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
HPV 16 integration is crucial for the onset and progression of premalignant lesions to invasive squamous cell carcinoma (ISCC) because it promotes the amplification of proto-oncogenes and the silencing of tumor suppressor genes; some of these are proteins with PDZ domains involved in homeostasis and cell polarity. Through a bioinformatics approach based on interaction networks, a group of proteins associated with HPV 16 infection, PDZ domains, and direct physical interaction with E6 and related to different hallmarks of cancer were identified. MAGI-1 was selected to evaluate the expression profile and subcellular localization changes in premalignant lesions and ISCC with HPV 16 in an integrated state in cervical cytology; the profile expression of MAGI-1 diminished according to lesion grade. Surprisingly, in cell lines CaSki and SiHa, the protein localization was cytoplasmic and nuclear. In contrast, in histological samples, a change in subcellular localization from the cytoplasm in low-grade squamous intraepithelial lesions (LSIL) to the nucleus in the high-grade squamous intraepithelial lesion (HSIL) was observed; in in situ carcinomas and ISCC, MAGI-1 expression was absent. In conclusion, MAGI-1 expression could be a potential biomarker for distinguishing those cells with normal morphology but with HPV 16 integrated from those showing morphology-related uterine cervical lesions associated with tumor progression.
Collapse
Affiliation(s)
- Oscar Catalán-Castorena
- Cytopathology and Histochemistry Research Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (O.C.-C.); (M.I.Z.-G.)
| | - Olga Lilia Garibay-Cerdenares
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (B.I.-A.); (M.A.L.-V.)
- CONAHCyT-Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico
| | - Berenice Illades-Aguiar
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (B.I.-A.); (M.A.L.-V.)
| | - Rocio Castillo-Sánchez
- Cell Biology Department, CINVESTAV-IPN Research Institute, Ciudad de México 07360, Mexico;
| | - Ma. Isabel Zubillaga-Guerrero
- Cytopathology and Histochemistry Research Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (O.C.-C.); (M.I.Z.-G.)
| | - Marco Antonio Leyva-Vazquez
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (B.I.-A.); (M.A.L.-V.)
| | - Sergio Encarnacion-Guevara
- Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca 62210, Morelos, Mexico;
| | - Eugenia Flores-Alfaro
- Clinical and Molecular Epidemiology Research Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico;
| | - Mónica Ramirez-Ruano
- Functional Genomics and Proteomics Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico;
| | - Luz del Carmen Alarcón-Romero
- Cytopathology and Histochemistry Research Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (O.C.-C.); (M.I.Z.-G.)
| |
Collapse
|
3
|
Zhao Q, Yang S, Hao S, Chen Z, Tang L, Wu Z, Wu J, Xu M, Ma Z, Zhou L, Xu J, Qin Q. Identification of transcriptionally-active human papillomavirus integrants through nanopore sequencing reveals viable targets for gene therapy against cervical cancer. J Med Virol 2024; 96:e29769. [PMID: 38932482 DOI: 10.1002/jmv.29769] [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: 04/09/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Integration of the human papillomavirus (HPV) genome into the cellular genome is a key event that leads to constitutive expression of viral oncoprotein E6/E7 and drives the progression of cervical cancer. However, HPV integration patterns differ on a case-by-case basis among related malignancies. Next-generation sequencing technologies still face challenges for interrogating HPV integration sites. In this study, utilizing Nanopore long-read sequencing, we identified 452 and 108 potential integration sites from the cervical cancer cell lines (CaSki and HeLa) and five tissue samples, respectively. Based on long Nanopore chimeric reads, we were able to analyze the methylation status of the HPV long control region (LCR), which controls oncogene E6/E7 expression, and to identify transcriptionally-active integrants among the numerous integrants. As a proof of concept, we identified an active HPV integrant in between RUNX2 and CLIC5 on chromosome 6 in the CaSki cell line, which was supported by ATAC-seq, H3K27Ac ChIP-seq, and RNA-seq analysis. Knockout of the active HPV integrant, by the CRISPR/Cas9 system, dramatically crippled cell proliferation and induced cell senescence. In conclusion, identifying transcriptionally-active HPV integrants with Nanopore sequencing can provide viable targets for gene therapy against HPV-associated cancers.
Collapse
Affiliation(s)
- Qianqian Zhao
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, China
| | - Shuaibing Yang
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Shijia Hao
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Zejia Chen
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Lihua Tang
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Zhaoting Wu
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jiaxin Wu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Mingqian Xu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Zebiao Ma
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Li Zhou
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jianzhen Xu
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, China
| | - Qingsong Qin
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
- International Science and Technology Collaboration Center for Emerging Infectious Diseases, Shantou University Medical College, Shantou, China
| |
Collapse
|
4
|
Satapathy P, Khatib MN, Gaidhane S, Zahiruddin QS, Serhan HA, Sharma RK, Sharma D, Arora M, Rustagi S, Na A, Alsayyah A, Al-Hajeili M, Al-Subaie MF, Alfaresi M, Alissa M, Rabaan AA. Prevalence of human papillomavirus in head and neck cancer patients in India: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:516. [PMID: 38783184 PMCID: PMC11112865 DOI: 10.1186/s12879-024-09357-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Human papillomavirus (HPV) is increasingly recognized as a significant risk factor in the development of head and neck cancers (HNCs), with varying prevalence and impact. This study aims to systematically review and analyze the prevalence of HPV in HNCs in India, providing insights into regional variations. METHODS A comprehensive literature search was carried out using PubMed, Embase, and Web of Science up to November 10, 2023. Inclusion criteria focused on original research reporting HPV-positive cases among HNC patients in India. We used Nested-Knowledge software, for screening, and data extraction. The modified Newcastle-Ottawa Scale was used for quality assessment of included studies. We pooled the prevalence of HPV among HNC patients and performed a random-effects model meta-analysis using R software (version 4.3). RESULTS The search yielded 33 studies, encompassing 4654 HNC patients. The pooled prevalence of HPV infection was found to be 33% (95% CI: 25.8-42.6), with notable heterogeneity (I² = 95%). Analysis of subgroups according to geographical location indicated varying prevalence rates. Specifically, the prevalence was 47% (95% CI: 32.2-62.4) in the eastern regions and 19.8% (95% CI: 10.8-33.4) in the western regions. No evidence of publication bias was detected. CONCLUSION The observed considerable regional disparities on the prevalence of HPV in HNC patients in India emphasizes the need for integrated HPV vaccination and screening programs in public health strategies. The findings underline the necessity for further research to explore regional variations and treatment responses in HPV-associated HNCs, considering the impact of factors such as tobacco use and the potential benefits of HPV vaccination.
Collapse
Affiliation(s)
- Prakasini Satapathy
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospital, Saveetha University, Chennai, India.
- Medical Laboratories Techniques Department, AL-Mustaqbal University, Hillah, Babil, 51001, Iraq.
| | - Mahalaqua Nazli Khatib
- Division of Evidence Synthesis, Global Consortium of Public Health and Research, Datta Meghe Institute of Higher Education, Wardha, India
| | - Shilpa Gaidhane
- One Health Centre (COHERD), Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education, Wardha, India
| | - Quazi Syed Zahiruddin
- Global South Asia Infant Feeding Research Network (SAIFRN), Division of Evidence Synthesis, Global Consortium of Public Health and Research, Datta Meghe Institute of Higher Education, Wardha, India
| | - Hashem Abu Serhan
- Department of Ophthalmology, Hamad Medical Corporation, Doha, Qatar.
| | - Rakesh Kumar Sharma
- Graphic Era (Deemed to be University), Clement Town, Dehradun, India
- Graphic Era Hill University, Clement Town, Dehradun, India
| | - Divya Sharma
- Centre of Research Impact and Outcome, Chitkara University, Rajpura, 140417, Punjab, India
| | - Mithhil Arora
- Chitkara Centre for Research and Development, Chitkara University, Himachal Pradesh, 174103, India
| | - Sarvesh Rustagi
- School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - AlKaabi Na
- College of Medicine and Health Science, Khalifa University, 127788, Abu Dhabi, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), 51900, Abu Dhabi, United Arab Emirates
| | - Ahmed Alsayyah
- Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Marwan Al-Hajeili
- Department of Medicine, College of Medicine, King Abdulaziz University, 23624, Jeddah, Saudi Arabia
| | - Maha F Al-Subaie
- Research Center, Dr. Sulaiman Alhabib Medical Group, 13328, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia
| | - Mubarak Alfaresi
- Department of Microbiology, National Reference laboratory, Cleveland clinic Abu Dhabi, 92323, Abu Dhabi, United Arab Emirates
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, 505055, Dubai, United Arab Emirates
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | - Ali A Rabaan
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, 22610, Haripur, Pakistan
| |
Collapse
|
5
|
Yu L, Majerciak V, Lobanov A, Mirza S, Band V, Liu H, Cam M, Hughes SH, Lowy DR, Zheng ZM. HPV oncogenes expressed from only one of multiple integrated HPV DNA copies drive clonal cell expansion in cervical cancer. mBio 2024; 15:e0072924. [PMID: 38624210 PMCID: PMC11077993 DOI: 10.1128/mbio.00729-24] [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: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
The integration of HPV DNA into human chromosomes plays a pivotal role in the onset of papillomavirus-related cancers. HPV DNA integration often occurs by linearizing the viral DNA in the E1/E2 region, resulting in the loss of a critical viral early polyadenylation signal (PAS), which is essential for the polyadenylation of the E6E7 bicistronic transcripts and for the expression of the viral E6 and E7 oncogenes. Here, we provide compelling evidence that, despite the presence of numerous integrated viral DNA copies, virus-host fusion transcripts originate from only a single integrated HPV DNA in HPV16 and HPV18 cervical cancers and cervical cancer-derived cell lines. The host genomic elements neighboring the integrated HPV DNA are critical for the efficient expression of the viral oncogenes that leads to clonal cell expansion. The fusion RNAs that are produced use a host RNA polyadenylation signal downstream of the integration site, and almost all involve splicing to host sequences. In cell culture, siRNAs specifically targeting the host portion of the virus-host fusion transcripts effectively silenced viral E6 and E7 expression. This, in turn, inhibited cell growth and promoted cell senescence in HPV16+ CaSki and HPV18+ HeLa cells. Showing that HPV E6 and E7 expression from a single integration site is instrumental in clonal cell expansion sheds new light on the mechanisms of HPV-induced carcinogenesis and could be used for the development of precision medicine tailored to combat HPV-related malignancies. IMPORTANCE Persistent oncogenic HPV infections lead to viral DNA integration into the human genome and the development of cervical, anogenital, and oropharyngeal cancers. The expression of the viral E6 and E7 oncogenes plays a key role in cell transformation and tumorigenesis. However, how E6 and E7 could be expressed from the integrated viral DNA which often lacks a viral polyadenylation signal in the cancer cells remains unknown. By analyzing the integrated HPV DNA sites and expressed HPV RNAs in cervical cancer tissues and cell lines, we show that HPV oncogenes are expressed from only one of multiple chromosomal HPV DNA integrated copies. A host polyadenylation signal downstream of the integrated viral DNA is used for polyadenylation and stabilization of the virus-host chimeric RNAs, making the oncogenic transcripts targetable by siRNAs. This observation provides further understanding of the tumorigenic mechanism of HPV integration and suggests possible therapeutic strategies for the development of precision medicine for HPV cancers.
Collapse
Affiliation(s)
- Lulu Yu
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR), National Cancer Institute, Bethesda, Maryland, USA
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Haibin Liu
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR), National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Douglas R. Lowy
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| |
Collapse
|
6
|
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.
Collapse
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.)
| |
Collapse
|
7
|
Shi R, Chang L, Shi L, Zhang Z, Zhang L, Li X. Development and validation of a prognostic model for cervical cancer by combination of machine learning and high-throughput sequencing. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2024; 50:108241. [PMID: 38452717 DOI: 10.1016/j.ejso.2024.108241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/02/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Cervical cancer holds the highest morbidity and mortality rates among female reproductive tract tumors. However, the curative outcomes for patients with persistent, recurrent, or metastatic cervical cancer remain unsatisfactory. There is a lack of comprehensive prognostic indicators for cervical cancer. This study aims to develop a model that evaluates the prognosis of cervical cancer in combination of high-throughput sequencing and various machine learning algorithms. METHODS In this study, we combined two single-cell RNA sequencing (scRNA-seq) projects and TCGA data for cervical cancer to obtain shared differentially expressed genes (DEGs). A LASSO regression and several learners were applied for signature feature selection. Six machine learning algorithms including Linear Discriminant Analysis, Naive Bayes, K Nearest Neighbors, Decision Tree, Random Forest, and eXtreme Gradient Boosting were utilized to construct a prognostic model for cervical cancer. External validation was conducted using the CGCI-HTMCP-CC dataset, and the accuracy of the model was assessed through ROC curve analysis. RESULTS The results demonstrated the successful construction of a prognostic model based on DEGs from bulk- and scRNA-seq data. Ten genes CXCL8, DLC1, GRN, MPLKIP, PRDX1, RUNX1, SNX3, TFRC, UBE2V2, and UQCRC1 were screened by feature selection and applied for model construction. Random Forest exhibited the best performance in predicting the risk of cervical cancer. Patients in the high-risk group presented worse overall survival compared to those in the low-risk group. CONCLUSION Conclusively, our model based on DEGs from bulk-seq and scRNA-seq data effectively evaluates the prognosis of cervical cancer and provides valuable insights for comprehensive clinical management.
Collapse
Affiliation(s)
- Rui Shi
- Department of Obstetrics and Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Linlin Chang
- Department of Obstetrics and Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Liya Shi
- Department of Reproductive Medicine Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Zhouxiang Zhang
- Department of Obstetrics and Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Limin Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China; Department of Obstetrics and Gynecology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
| | - Xiaona Li
- Department of Obstetrics and Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| |
Collapse
|
8
|
Vallejo-Ruiz V, Gutiérrez-Xicotencatl L, Medina-Contreras O, Lizano M. Molecular aspects of cervical cancer: a pathogenesis update. Front Oncol 2024; 14:1356581. [PMID: 38567159 PMCID: PMC10985348 DOI: 10.3389/fonc.2024.1356581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Cervical cancer (CC) is a significant health problem, especially in low-income countries. Functional studies on the human papillomavirus have generated essential advances in the knowledge of CC. However, many unanswered questions remain. This mini-review discusses the latest results on CC pathogenesis, HPV oncogenesis, and molecular changes identified through next-generation technologies. Interestingly, the percentage of samples with HPV genome integrations correlates with the degree of the cervical lesions, suggesting a role in the development of CC. Also, new functions have been described for the viral oncoproteins E5, E6, and E7, resulting in the acquisition and maintenance of cancer hallmarks, including proliferation, immune response evasion, apoptosis, and genomic instability. Remarkably, E5 oncoprotein affects signaling pathways involved in the expression of interferon-induced genes and EGFR-induced proliferation, while E6 and E7 oncoproteins regulate the DNA damage repair and cell cycle continuity pathways. Furthermore, next-generation technologies provide vast amounts of information, increasing our knowledge of changes in the genome, transcriptome, proteome, metabolome, and epigenome in CC. These studies have identified novel molecular traits associated with disease susceptibility, degree of progression, treatment response, and survival as potential biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Verónica Vallejo-Ruiz
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Lourdes Gutiérrez-Xicotencatl
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Oscar Medina-Contreras
- Epidemiology, Endocrinology & Nutrition Research Unit, Mexico Children’s Hospital, Mexico City, Mexico
| | - Marcela Lizano
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Mexico City, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
9
|
Li M, Wu S, Niu J, Luo H, Chen W, Cao L, Yan Y, Tu H, He Y. Identification of hepatitis B virus infection and integration and its oncogenic role in gastric cancer. Clin Transl Med 2024; 14:e1601. [PMID: 38451008 PMCID: PMC10918734 DOI: 10.1002/ctm2.1601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Affiliation(s)
- Mengge Li
- Department of Medical OncologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Shusheng Wu
- Department of Medical OncologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Jiayu Niu
- Department of Medical OncologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Huiqin Luo
- Department of Medical OncologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Wenju Chen
- Department of Medical OncologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Lulu Cao
- Department of Medical OncologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Ying Yan
- Department of Medical OncologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Hong Tu
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRenji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yifu He
- Department of Medical OncologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Nittala MR, Yang J, Velazquez AE, Salvemini JD, Vance GR, Grady CC, Hathaway B, Roux JA, Vijayakumar S. Precision Population Cancer Medicine in Cancer of the Uterine Cervix: A Potential Roadmap to Eradicate Cervical Cancer. Cureus 2024; 16:e53733. [PMID: 38455773 PMCID: PMC10919943 DOI: 10.7759/cureus.53733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2024] [Indexed: 03/09/2024] Open
Abstract
With the success of the Human Genome Project, the era of genomic medicine (GM) was born. Later on, as GM made progress, there was a feeling of exhilaration that GM could help resolve many disease processes. It also led to the conviction that personalized medicine was possible, and a relatively synonymous word, precision medicine (PM), was coined. However, the influence of environmental factors and social determinants of diseases was only partially given their due importance in the definition of PM, although more recently, this has been recognized. With the rapid advances in GM, big data, data mining, wearable devices for health monitoring, telemedicine, etc., PM can be more easily extended to population-level health care in disease management, prevention, early screening, and so on.and the term precision population medicine (PPM) more aptly describes it. PPM's potential in cancer care was posited earlier,and the current authors planned a series of cancer disease-specific follow-up articles. These papers are mainly aimed at helping emerging students in health sciences (medicine, pharmacy, nursing, dentistry, public health, population health), healthcare management (health-focused business administration, nonprofit administration, public institutional administration, etc.), and policy-making (e.g., political science), although not exclusively. This first disease-specific report focuses on the cancer of the uterine cervix (CC). It describes how recent breakthroughs can be leveraged as force multipliers to improve outcomes in CC - by improving early detection, better screening for CC, potential GM-based interventions during the stage of persistent Human papillomavirus (HPV) infection and treatment interventions - especially among the disadvantaged and resource-scarce populations. This work is a tiny step in our attempts to improve outcomes in CC and ultimately eradicate CC from the face of the earth.
Collapse
Affiliation(s)
- Mary R Nittala
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | - Johnny Yang
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | | | - John D Salvemini
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | - Gregory R Vance
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | - Camille C Grady
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | - Bradley Hathaway
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | - Jeffrey A Roux
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | | |
Collapse
|
12
|
Trammel J, Amusan O, Hultgren A, Raikhy G, Bodily JM. Epidermal growth factor receptor-dependent stimulation of differentiation by human papillomavirus type 16 E5. Virology 2024; 590:109952. [PMID: 38103269 PMCID: PMC10842332 DOI: 10.1016/j.virol.2023.109952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/19/2023]
Abstract
Human papillomaviruses (HPVs) infect keratinocytes of stratified squamous epithelia, and persistent infection with high-risk HPV types, such as HPV16, may lead to the development of malignancies. HPV evades host immunity in part by linking its gene expression to the host differentiation program, and therefore relies on differentiation to complete its life cycle. Based on previous reports indicating that the HPV16 protein E5 is important in the late stages of the differentiation-dependent life cycle, we found that organotypic cultures harboring HPV16 genomes lacking E5 showed reduced markers of terminal differentiation compared to wild type HPV16-containing cultures. We found that epidermal growth factor receptor (EGFR) levels and activation were increased in an E5-depdendent manner in these tissues, and that EGFR promoted terminal differentiation and expression of the HPV16 L1 gene. These findings suggest a function for E5 in preserving the ability of HPV16 containing keratinocytes to differentiate, thus facilitating the production of new virus progeny.
Collapse
Affiliation(s)
- Jessica Trammel
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA, 71103, USA
| | - Oluwamuyiwa Amusan
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA, 71103, USA
| | - Allison Hultgren
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA, 71103, USA; School of Medicine, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA, 71103, USA
| | - Gaurav Raikhy
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA, 71103, USA
| | - Jason M Bodily
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA, 71103, USA.
| |
Collapse
|
13
|
Xu S, Shi C, Zhou R, Han Y, Li N, Qu C, Xia R, Zhang C, Hu Y, Tian Z, Liu S, Wang L, Li J, Zhang Z. Mapping the landscape of HPV integration and characterising virus and host genome interactions in HPV-positive oropharyngeal squamous cell carcinoma. Clin Transl Med 2024; 14:e1556. [PMID: 38279874 PMCID: PMC10819103 DOI: 10.1002/ctm2.1556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Human papillomavirus (HPV) integration into the host genome is an important factor in HPV(+)OPSCC carcinogenesis, in conjunction with HPV oncoproteins E6/E7. However, a well-studied investigation about virus-host interaction still needs to be completed. Our objective is to characterise HPV integration to investigate potential mechanisms of tumourigenesis independent of E6/E7 oncoproteins. MATERIALS AND METHODS High-throughput viral integration detection was performed on 109 HPV(+)OPSCC tumours with relevant clinicopathological information. Of these tumours, 38 tumours underwent targeted gene sequencing, 29 underwent whole exome sequencing and 26 underwent RNA sequencing. RESULTS HPV integration was detected in 94% of tumours (with a mean integration count of 337). Tumours occurring at the tonsil/oropharyngeal wall that exhibit higher PD-L1 expression demonstrated increased integration sites (p = .024). HPV exhibited a propensity for integration at genomic sites located within specific fragile sites (FRA19A) or genes associated with functional roles such as cell proliferation and differentiation (PTEN, AR), immune evasion (CD274) and glycoprotein biosynthesis process (FUT8). The viral oncogenes E2, E4, E6 and E7 tended to remain intact. HPV fragments displayed enrichment within host copy number variation (CNV) regions. However, insertions into genes related to altered homologous recombination repair were infrequent. Genes with integration had distinct expression levels. Fifty-nine genes whose expression level was affected by viral integration were identified, for example, EPHB1, which was reported to be involved in cellular protein metabolic process. CONCLUSIONS HPV can promote oncogenesis through recurrent integration into functional host genome regions, leading to subsequent genomic aberrations and gene expression disruption. This study characterises viral integrations and virus-host interactions, enhancing our understanding of HPV-related carcinogenesis mechanisms.
Collapse
Affiliation(s)
- Shengming Xu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Chaoji Shi
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Rong Zhou
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Yong Han
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - NianNian Li
- Department of BioinfomaticsSequantaShanghaiChina
| | - Chuxiang Qu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Ronghui Xia
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Chunye Zhang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Yuhua Hu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhen Tian
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Shuli Liu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Lizhen Wang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Jiang Li
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhiyuan Zhang
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| |
Collapse
|
14
|
Ye R, Wang A, Bu B, Luo P, Deng W, Zhang X, Yin S. Viral oncogenes, viruses, and cancer: a third-generation sequencing perspective on viral integration into the human genome. Front Oncol 2023; 13:1333812. [PMID: 38188304 PMCID: PMC10768168 DOI: 10.3389/fonc.2023.1333812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
The link between viruses and cancer has intrigued scientists for decades. Certain viruses have been shown to be vital in the development of various cancers by integrating viral DNA into the host genome and activating viral oncogenes. These viruses include the Human Papillomavirus (HPV), Hepatitis B and C Viruses (HBV and HCV), Epstein-Barr Virus (EBV), and Human T-Cell Leukemia Virus (HTLV-1), which are all linked to the development of a myriad of human cancers. Third-generation sequencing technologies have revolutionized our ability to study viral integration events at unprecedented resolution in recent years. They offer long sequencing capabilities along with the ability to map viral integration sites, assess host gene expression, and track clonal evolution in cancer cells. Recently, researchers have been exploring the application of Oxford Nanopore Technologies (ONT) nanopore sequencing and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) sequencing in cancer research. As viral integration is crucial to the development of cancer via viruses, third-generation sequencing would provide a novel approach to studying the relationship interlinking viral oncogenes, viruses, and cancer. This review article explores the molecular mechanisms underlying viral oncogenesis, the role of viruses in cancer development, and the impact of third-generation sequencing on our understanding of viral integration into the human genome.
Collapse
Affiliation(s)
- Ruichen Ye
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
- Einstein Pathology Single-cell & Bioinformatics Laboratory, Bronx, NY, United States
- Stony Brook University, Stony Brook, NY, United States
| | - Angelina Wang
- Tufts Friedman School of Nutrition, Boston, MA, United States
| | - Brady Bu
- Horace Mann School, Bronx, NY, United States
| | - Pengxiang Luo
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjun Deng
- Clinical Proteomics Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Xinyi Zhang
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shanye Yin
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
- Einstein Pathology Single-cell & Bioinformatics Laboratory, Bronx, NY, United States
| |
Collapse
|
15
|
Cui X, Li Y, Zhang C, Qi Y, Sun Y, Li W. Multiple HPV integration mode in the cell lines based on long-reads sequencing. Front Microbiol 2023; 14:1294146. [PMID: 38169727 PMCID: PMC10758443 DOI: 10.3389/fmicb.2023.1294146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Background The integration of human papillomavirus (HPV) is closely related to the occurrence of cervical cancer. However, little is known about the complete state of HPV integration into the host genome. Methods In this study, three HPV-positive cell lines, HeLa, SiHa, and CaSki, were subjected to NANOPORE long-read sequencing to detect HPV integration. Analysis of viral integration patterns using independently developed software (HPV-TSD) yielded multiple complete integration patterns for the three HPV cell lines. Results We found distinct differences between the integration patterns of HPV18 and HPV16. Furthermore, the integration characteristics of the viruses were significantly different, even though they all belonged to HPV16 integration. The HPV integration in the CaSki cells was relatively complex. The HPV18 integration status in HeLa cells was the dominant, whereas the percentage of integrated HPV 16 in SiHa and CaSki cells was significantly lower. In addition, the virus sequences in the HeLa cells were incomplete and existed in an integrated state. We also identified a large number of tandem repeats in HPV16 and HPV18 integration. Our study not only clarified the feasibility of high-throughput long-read sequencing in the study of HPV integration, but also explored a variety of HPV integration models, and confirmed that viral integration is an important form of HPV in cell lines. Conclusion Elucidating HPV integration patterns will provide critical guidance for developing a detection algorithm for HPV integration, as well as the application of virus integration in clinical practice and drug research and development.
Collapse
Affiliation(s)
- Xiaofang Cui
- Jining Medical University, Jining, Shandong, China
- Department of Bioinformatics, School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | | | - Chuanpeng Zhang
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Yanwei Qi
- School of Control and Computer Engineering, North China Electric Power University, Beijing, China
| | | | - Weiyang Li
- Jining Medical University, Jining, Shandong, China
- Department of Bioinformatics, School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| |
Collapse
|
16
|
Li X, Wei X, Liu X, Wang N, Xu F, Liu X, Li Y, Zhou Y, Tang H, Bian M, Hou Y, Zhang L, Wang W, Liu Q. The analysis of HPV integration sites based on nanopore sequencing and the profiling changes along the course of photodynamic therapy. BMC Cancer 2023; 23:1052. [PMID: 37914994 PMCID: PMC10621124 DOI: 10.1186/s12885-023-11538-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
OBJECTIVE To detect the HPV genotype and integration sites in patients with high-risk HPV infection at different stages of photodynamic therapy using nanopore technology and to evaluate the treatment effect. METHODS Four patients with HPV infection were selected and subjected to photodynamic therapy, and cervical exfoliated cell was sampled at before treatment, after three courses of treatment and six courses of treatment, their viral abundance and insertion sites were analyzed by nanopore technology, and pathological examinations were performed before and after treatment. In this study, we developed a novel assay that combined viral sequence enrichment and Nanopore sequencing for identification of HPV genotype and integration sites at once. The assay has obvious advantages over qPCR or NGS-based methods, as it has better sensitivity after viral sequences enrichment and can generate long-reads (kb to Mb) for better detection rate of structure variations, moreover, fast turn-around time for real-time viral sequencing and analysis. RESULTS The pathological grade was reduced in all four patients after photodynamic therapy. Virus has been cleared in two cases after treatment, the virus amount reduced after treatment but not completely cleared in one case, and two type viruses were cleared and one type virus persisted after treatment in the last patient with multiple infection. Viral abundance and the number of integration sites were positively correlated. Gene enrichment analysis showed complete viral clearance in 1 patient and 3 patients required follow-up. CONCLUSION Nanopore sequencing can effectively monitor the abundance of HPV viruses and integration sites to show the presence status of viruses, and combined with the results of gene enrichment analysis, the treatment effect can be dynamically assessed.
Collapse
Affiliation(s)
- Xiulan Li
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xiaoke Wei
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China
| | - Xin Liu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Nan Wang
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Fuqiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xingyu Liu
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China
| | - Yanmei Li
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Yuxiang Zhou
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Huadong Tang
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Meina Bian
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Ying Hou
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Lili Zhang
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China.
| | - Weiwei Wang
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China.
| | - Qing Liu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
| |
Collapse
|
17
|
Gauthier MA, Kadam A, Leveque G, Golabi N, Zeitouni A, Richardson K, Mascarella M, Sadeghi N, Loganathan SK. Long-read sequencing of oropharyngeal squamous cell carcinoma tumors reveal diverse patterns of high-risk Human Papillomavirus integration. Front Oncol 2023; 13:1264646. [PMID: 37916168 PMCID: PMC10616875 DOI: 10.3389/fonc.2023.1264646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction In North America and in most European countries, Human Papillomavirus (HPV) is responsible for over 70% of oropharyngeal squamous cell carcinomas. The burden of OPSCC, in high-income countries, has been steadily increasing over the past 20 years. As a result, in the USA and in the UK, the burden of HPV-related oropharyngeal squamous cell carcinoma in men has now surpassed that of cervical cancer in women. However, the oncogenic impact of high-risk HPV integration in oropharyngeal squamous cell carcinomas hasn't been extensively studied. The present study aimed to explore the patterns of HPV integration in oropharyngeal squamous cell carcinomas and to assess the feasibility and reliability of long-read sequencing technology in detecting viral integration events in oropharyngeal head and neck cancers. Methods A cohort of eight HPV-positive OPSCC pre-treatment patient tumors (four males and four females), were selected. All patients received a p16INK4A positive OPSCC diagnosis and were treated at the McGill University Health Centre, a quaternary center in Montreal. A minimum of 20mg of tumor tissue was used for DNA extraction. Extracted DNA was subjected to Nanopore long-read sequencing to detect and analyze for the presence of high-risk HPV sequences. PCR and Sanger sequencing experiments were performed to confirm Nanopore long-read sequencing readings. Results Nanopore long-read sequencing showed that seven out of eight patient samples displayed either integrated or episomal high-risk HPV sequences. Out of these seven samples, four displayed verifiable integration events upon bioinformatic analysis. Integration confirmation experiments were designed for all four samples using PCR-based methods. Sanger sequencing was also performed. Four distinct HPV integration patterns were identified: concatemer chromosomal integration in a single chromosome, bi-chromosomal concatemer integration, single chromosome complete integration and bi-chromosomal complete integration. HPV concatemer integration also proved more common than full HPV integration events. Conclusion and relevance Long-read sequencing technologies can be effectively used to assess HPV integration patterns in OPSCC tumors. Clinically, more research should be conducted on the prognostication value of high-risk HPV integration in OPSCC tumors using long-read sequencing technology.
Collapse
Affiliation(s)
- Marc-Andre Gauthier
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Adway Kadam
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Gary Leveque
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Nahid Golabi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Anthony Zeitouni
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Keith Richardson
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Marco Mascarella
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Nader Sadeghi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Oncology, McGill University, Montreal, QC, Canada
| | - Sampath Kumar Loganathan
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Experimental Medicine, Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada
| |
Collapse
|
18
|
Li DY, Jiang YJ, Nie KH, Li J, Li YF, Huang CZ, Li CM. Rational design of genotyping nanodevice for HPV subtype distinction. Anal Chim Acta 2023; 1276:341651. [PMID: 37573127 DOI: 10.1016/j.aca.2023.341651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/14/2023]
Abstract
There are more than 200 subtypes of human papillomavirus (HPV), and high-risk HPVs are a leading cause of cervical cancer. Identifying the genotypes of HPV is significant for clinical diagnosis and cancer control. Herein, we used programmable and modified DNA as the backbone to construct fluorescent genotyping nanodevice for HPV subtype distinction. In our strategy, the dye-labeled single-stranded recognize-DNA (R-DNA) was hybridized with Black Hole Quencher (BHQ) labeled single-stranded link-DNA (L-DNA) to form three functionalized DNA (RL-DNA). Through the extension of polycytosine (poly-C) in L-DNA, three RL-DNAs can be more firmly adsorbed on graphene oxide to construct reliable genotyping nanodevice. The genotyping nanodevice had low background noise since the dual energy transfer, including Förster resonance energy transfer (FRET) from dye to BHQ and the resonance energy transfer (RET) from dye to graphene oxide. Meanwhile, the programmability of DNA allows the proposed strategy to simultaneously and selectively distinguish several HPV subtypes in solution using DNA labeled with different dyes. To demonstrate clinical potential, we show multiplexed assay of HPV subtypes in cervical scrapes, and it has been successfully applied in HPV-DNA analysis in cervical scrapes samples. The genotyping nanodevice could be developed for simultaneous and multiplex analysis of several oligonucleotides in a homogeneous solution by adjusting the recognition sequence, demonstrating its potential application in the rapid screening of multiple biomarkers.
Collapse
Affiliation(s)
- De Yu Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yong Jian Jiang
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Kun Han Nie
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Jing Li
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Yuan Fang Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Chun Mei Li
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| |
Collapse
|
19
|
Ye J, Zheng L, He Y, Qi X. Human papillomavirus associated cervical lesion: pathogenesis and therapeutic interventions. MedComm (Beijing) 2023; 4:e368. [PMID: 37719443 PMCID: PMC10501338 DOI: 10.1002/mco2.368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/19/2023] Open
Abstract
Human papillomavirus (HPV) is the most prevalent sexually transmitted virus globally. Persistent high-risk HPV infection can result in cervical precancerous lesions and cervical cancer, with 70% of cervical cancer cases associated with high-risk types HPV16 and 18. HPV infection imposes a significant financial and psychological burden. Therefore, studying methods to eradicate HPV infection and halt the progression of precancerous lesions remains crucial. This review comprehensively explores the mechanisms underlying HPV-related cervical lesions, including the viral life cycle, immune factors, epithelial cell malignant transformation, and host and environmental contributing factors. Additionally, we provide a comprehensive overview of treatment methods for HPV-related cervical precancerous lesions and cervical cancer. Our focus is on immunotherapy, encompassing HPV therapeutic vaccines, immune checkpoint inhibitors, and advanced adoptive T cell therapy. Furthermore, we summarize the commonly employed drugs and other nonsurgical treatments currently utilized in clinical practice for managing HPV infection and associated cervical lesions. Gene editing technology is currently undergoing clinical research and, although not yet employed officially in clinical treatment of cervical lesions, numerous preclinical studies have substantiated its efficacy. Therefore, it holds promise as a precise treatment strategy for HPV-related cervical lesions.
Collapse
Affiliation(s)
- Jiatian Ye
- Department of Gynecology and ObstetricsKey Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second Hospital, Sichuan UniversityChengduChina
| | - Lan Zheng
- Department of Pathology and Lab MedicineUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Yuedong He
- Department of Gynecology and ObstetricsKey Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second Hospital, Sichuan UniversityChengduChina
| | - Xiaorong Qi
- Department of Gynecology and ObstetricsKey Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second Hospital, Sichuan UniversityChengduChina
| |
Collapse
|
20
|
Li QS, Zheng PS. ESRRB Inhibits the TGFβ Signaling Pathway to Drive Cell Proliferation in Cervical Cancer. Cancer Res 2023; 83:3095-3114. [PMID: 37350664 PMCID: PMC10502452 DOI: 10.1158/0008-5472.can-23-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 06/24/2023]
Abstract
Estrogen-related receptor β (ESRRB) is a member of the orphan nuclear receptor family and mediates stem cell self-renewal and early embryonic development. Previous studies have also reported that ESRRB plays a role in the development and progression of breast cancer and prostate cancer. In this study, we observed that ESRRB was highly expressed in cervical cancer and was associated with disease progression. Knocking out ESRRB using CRISPR/Cas9 gene editing in cervical cancer cells induced cell-cycle arrest at the transition from the G0-G1 phase to the S phase, resulting in inhibition of cell proliferation in vitro and reduced tumor growth in vivo. Conversely, ectopic expression of ESRRB significantly promoted the proliferation of cervical cancer cells. ESRRB activated transcription of SMAD7, a TGFβ pathway inhibitor, which blocked phosphorylation and nuclear translocation of SMAD2/3 to the nucleus, thereby downregulating CDKN1A and upregulating CCNA2 and MYC. In turn, MYC transactivated ESRRB and upregulated SMAD7, thus forming a positive feedback loop with ESRRB. Together, these findings identify the tumor-promoting function of ESRRB in cervical cancer and reveal a mechanism by which ESRRB stimulates cell proliferation to promote cancer progression. SIGNIFICANCE The ESRRB/SMAD7/MYC-positive feedback loop inhibits TGFβ signaling to activate cell-cycle progression and promote proliferation in cervical cancer, thereby driving tumor growth.
Collapse
Affiliation(s)
- Qin-Shu Li
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P.R. China
| | - Peng-Sheng Zheng
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P.R. China
- Section of Cancer Stem Cell Research, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of the People's Republic of China, Xi'an, Shaanxi, P.R. China
| |
Collapse
|
21
|
Mastrorosa FK, Miller DE, Eichler EE. Applications of long-read sequencing to Mendelian genetics. Genome Med 2023; 15:42. [PMID: 37316925 DOI: 10.1186/s13073-023-01194-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/18/2023] [Indexed: 06/16/2023] Open
Abstract
Advances in clinical genetic testing, including the introduction of exome sequencing, have uncovered the molecular etiology for many rare and previously unsolved genetic disorders, yet more than half of individuals with a suspected genetic disorder remain unsolved after complete clinical evaluation. A precise genetic diagnosis may guide clinical treatment plans, allow families to make informed care decisions, and permit individuals to participate in N-of-1 trials; thus, there is high interest in developing new tools and techniques to increase the solve rate. Long-read sequencing (LRS) is a promising technology for both increasing the solve rate and decreasing the amount of time required to make a precise genetic diagnosis. Here, we summarize current LRS technologies, give examples of how they have been used to evaluate complex genetic variation and identify missing variants, and discuss future clinical applications of LRS. As costs continue to decrease, LRS will find additional utility in the clinical space fundamentally changing how pathological variants are discovered and eventually acting as a single-data source that can be interrogated multiple times for clinical service.
Collapse
Affiliation(s)
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
22
|
Wu P, Ma D, Wu P. Oncogenic virus integration: Moving toward clinical applications. MED 2023; 4:347-352. [PMID: 37301195 DOI: 10.1016/j.medj.2023.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 06/12/2023]
Abstract
The majority of oncogenic viruses are capable of integrating into the host genome, posing significant challenges to clinical control. Recent conceptual and technological advances, however, offer promising clinical applications. Here, we summarize the advances in our understanding of oncogenic viral integration, their clinical relevance, and the future perspectives.
Collapse
Affiliation(s)
- Ping Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ding Ma
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Peng Wu
- Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| |
Collapse
|
23
|
Rossi NM, Dai J, Xie Y, Wangsa D, Heselmeyer-Haddad K, Lou H, Boland JF, Yeager M, Orozco R, Freites EA, Mirabello L, Gharzouzi E, Dean M. Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis. Cancer Res 2023; 83:1768-1781. [PMID: 36971511 PMCID: PMC10239328 DOI: 10.1158/0008-5472.can-22-3030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/18/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
SIGNIFICANCE Multimers of the HPV genome are generated in cervical tumors replicating as extrachromosomal episomes, which is associated with deletion and rearrangement of the HPV genome and provides a mechanism for oncogenesis without integration.
Collapse
Affiliation(s)
- Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jieqiong Dai
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Darawalee Wangsa
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerstin Heselmeyer-Haddad
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hong Lou
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph F. Boland
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Enrique Alvirez Freites
- Hospital Central Universitario “Dr. Antonio M Pineda,” Barquisimeto, Lara State, Venezuela, and Universidad Andino de Cusco, Cusco, Perú
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| |
Collapse
|
24
|
Evande R, Rana A, Biswas-Fiss EE, Biswas SB. Protein-DNA Interactions Regulate Human Papillomavirus DNA Replication, Transcription, and Oncogenesis. Int J Mol Sci 2023; 24:ijms24108493. [PMID: 37239839 DOI: 10.3390/ijms24108493] [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: 03/27/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Human papillomavirus (HPV) is a group of alpha papillomaviruses that cause various illnesses, including cancer. There are more than 160 types of HPV, with many being "high-risk" types that have been clinically linked to cervical and other types of cancer. "Low-risk" types of HPV cause less severe conditions, such as genital warts. Over the past few decades, numerous studies have shed light on how HPV induces carcinogenesis. The HPV genome is a circular double-stranded DNA molecule that is approximately 8 kilobases in size. Replication of this genome is strictly regulated and requires two virus-encoded proteins, E1 and E2. E1 is a DNA helicase that is necessary for replisome assembly and replication of the HPV genome. On the other hand, E2 is responsible for initiating DNA replication and regulating the transcription of HPV-encoded genes, most importantly the E6 and E7 oncogenes. This article explores the genetic characteristics of high-risk HPV types, the roles of HPV-encoded proteins in HPV DNA replication, the regulation of transcription of E6 and E7 oncogenes, and the development of oncogenesis.
Collapse
Affiliation(s)
- Roxanne Evande
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Anshul Rana
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Esther E Biswas-Fiss
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Subhasis B Biswas
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| |
Collapse
|
25
|
Chen D, Liang Y, Wang H, Wang H, Su F, Zhang P, Wang S, Liu W, Li Z. CRISPR-Cas-Driven Single Micromotor (Cas-DSM) Enables Direct Detection of Nucleic Acid Biomarkers at the Single-Molecule Level. Anal Chem 2023; 95:5729-5737. [PMID: 36944919 DOI: 10.1021/acs.analchem.2c05767] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The target-dependent endonuclease activity (also known as the trans-cleavage activity) of CRISPR-Cas systems has stimulated great interest in the development of nascent sensing strategies for nucleic acid diagnostics. Despite many attempts, the majority of the sensitive CRISPR-Cas diagnostics strategies mainly rely on nucleic acid preamplification, which generally needs complex probes/primers designs, multiple experimental steps, and a longer testing time, as well as introducing the risk of false-positive results. In this work, we propose the CRISPR-Cas-Driven Single Micromotor (Cas-DSM), which can directly detect the nucleic acid targets at a single-molecule level with high specificity. We have demonstrated that the Cas-DSM is a reliable and practical method for the quantitative detection of DNA/RNA in various complex clinical samples as well as in individual cells without any preamplification processes. Due to the excellent features of the CRISPR/Cas system, including constant temperature, simple design, high specificity, and flexible programmability, the Cas-DSM could serve as a simple and universal platform for nucleic acid detection. More importantly, this work will provide a breakthrough for the development of next-generation amplification-free CRISPR/Cas sensing toolboxes.
Collapse
Affiliation(s)
- Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yuanwen Liang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Pengbo Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Shuhui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Weiliang Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| |
Collapse
|
26
|
Nelson CW, Mirabello L. Human papillomavirus genomics: Understanding carcinogenicity. Tumour Virus Res 2023; 15:200258. [PMID: 36812987 PMCID: PMC10063409 DOI: 10.1016/j.tvr.2023.200258] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
Collapse
Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA; Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA.
| |
Collapse
|
27
|
Leiendecker L, Neumann T, Jung PS, Cronin SM, Steinacker TL, Schleiffer A, Schutzbier M, Mechtler K, Kervarrec T, Laurent E, Bachiri K, Coyaud E, Murali R, Busam KJ, Itzinger-Monshi B, Kirnbauer R, Cerroni L, Calonje E, Rütten A, Stubenrauch F, Griewank KG, Wiesner T, Obenauf AC. Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers. Cancer Discov 2023; 13:70-84. [PMID: 36213965 PMCID: PMC9827110 DOI: 10.1158/2159-8290.cd-22-0489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/24/2022] [Accepted: 10/04/2022] [Indexed: 01/13/2023]
Abstract
The skin is exposed to viral pathogens, but whether they contribute to the oncogenesis of skin cancers has not been systematically explored. Here we investigated 19 skin tumor types by analyzing off-target reads from commonly available next-generation sequencing data for viral pathogens. We identified human papillomavirus 42 (HPV42) in 96% (n = 45/47) of digital papillary adenocarcinoma (DPA), an aggressive cancer occurring on the fingers and toes. We show that HPV42, so far considered a nononcogenic, "low-risk" HPV, recapitulates the molecular hallmarks of oncogenic, "high-risk" HPVs. Using machine learning, we find that HPV-driven transformation elicits a germ cell-like transcriptional program conserved throughout all HPV-driven cancers (DPA, cervical carcinoma, and head and neck cancer). We further show that this germ cell-like transcriptional program, even when reduced to the top two genes (CDKN2A and SYCP2), serves as a fingerprint of oncogenic HPVs with implications for early detection, diagnosis, and therapy of all HPV-driven cancers. SIGNIFICANCE We identify HPV42 as a uniform driver of DPA and add a new member to the short list of tumorigenic viruses in humans. We discover that all oncogenic HPVs evoke a germ cell-like transcriptional program with important implications for detecting, diagnosing, and treating all HPV-driven cancers. See related commentary by Starrett et al., p. 17. This article is highlighted in the In This Issue feature, p. 1.
Collapse
Affiliation(s)
- Lukas Leiendecker
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.,Quantro Therapeutics, Vienna, Austria
| | - Pauline S. Jung
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Shona M. Cronin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas L. Steinacker
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Michael Schutzbier
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Thibault Kervarrec
- Department of Pathology, University Hospital Center of Tours, University of Tours, Tours, France
| | - Estelle Laurent
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Kamel Bachiri
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Etienne Coyaud
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Rajmohan Murali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Klaus J. Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Reinhard Kirnbauer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Lorenzo Cerroni
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Eduardo Calonje
- Department of Dermatopathology, St John's Institute of Dermatology, St Thomas’ Hospital, London, United Kingdom
| | - Arno Rütten
- Dermatopathology Friedrichshafen, Friedrichshafen, Germany
| | - Frank Stubenrauch
- University Hospital Tuebingen, Institute for Medical Virology and Epidemiology of Viral Diseases, Tuebingen, Germany
| | - Klaus G. Griewank
- Department of Dermatology, University Hospital Essen, University of Duisburg, German Cancer Consortium (DKTK), Partner Site, Essen, Germany
| | - Thomas Wiesner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Department of Pathology, Medical University of Vienna, Vienna, Austria.,Corresponding Authors: Anna C. Obenauf, Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria. Phone: 0043-179-730; E-mail: ; and Thomas Wiesner, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria. Phone: 0043-1404-0077-100; E-mail:
| | - Anna C. Obenauf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Corresponding Authors: Anna C. Obenauf, Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria. Phone: 0043-179-730; E-mail: ; and Thomas Wiesner, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria. Phone: 0043-1404-0077-100; E-mail:
| |
Collapse
|
28
|
Friedman MJ, Lee H, Kwon YC, Oh S. Dynamics of Viral and Host 3D Genome Structure upon Infection. J Microbiol Biotechnol 2022; 32:1515-1526. [PMID: 36398441 PMCID: PMC9843816 DOI: 10.4014/jmb.2208.08020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022]
Abstract
Eukaryotic chromatin is highly organized in the 3D nuclear space and dynamically regulated in response to environmental stimuli. This genomic organization is arranged in a hierarchical fashion to support various cellular functions, including transcriptional regulation of gene expression. Like other host cellular mechanisms, viral pathogens utilize and modulate host chromatin architecture and its regulatory machinery to control features of their life cycle, such as lytic versus latent status. Combined with previous research focusing on individual loci, recent global genomic studies employing conformational assays coupled with high-throughput sequencing technology have informed models for host and, in some cases, viral 3D chromosomal structure re-organization during infection and the contribution of these alterations to virus-mediated diseases. Here, we review recent discoveries and progress in host and viral chromatin structural dynamics during infection, focusing on a subset of DNA (human herpesviruses and HPV) as well as RNA (HIV, influenza virus and SARS-CoV-2) viruses. An understanding of how host and viral genomic structure affect gene expression in both contexts and ultimately viral pathogenesis can facilitate the development of novel therapeutic strategies.
Collapse
Affiliation(s)
- Meyer J. Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Haram Lee
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
| | - Young-Chan Kwon
- Center for Convergent Research of Emerging Virus Infections, Korean Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Soohwan Oh
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
| |
Collapse
|
29
|
Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
Collapse
Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
| |
Collapse
|
30
|
Liu T, Chen M, Li X, Wang H. Predict the Progression of Cervical Intraepithelial Neoplasia by a Novel Marker Folate Combine with FRα, p16 and Ki-67. Int J Gen Med 2022; 15:6529-6538. [PMID: 35971526 PMCID: PMC9375578 DOI: 10.2147/ijgm.s362685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To study the expression of serum folate and red blood cell (RBC) folate, folate receptor α (FRα), p16INK4a (p16), and Ki-67 at different levels of cervical intraepithelial neoplasia (CIN) and then analyze their role in the progression of CIN and their value as an early warning indicator of CIN progression. Patients and methods We randomly collected the data of patients at the Department of Gynecology in Guangxi Medical University Affiliated Cancer Hospital from January 2016 to December 2018: Normal controls (149 cases), CIN1 (150 cases), CIN2 (100 cases), and CIN3 (101 cases). [Ethical approval by Ethics Committee of the Second Hospital of Shanxi Medical University. (2013) No. (001–1)]. The expression of serum folate and RBC folate was detected by the chemiluminescence method, while the expression of FRα, p16, and Ki-67 was detected by Streptavidin-Perosidase (SP) immunohistochemistry. Results There was no statistically significant difference in serum folate levels between different grades of CIN (P=0.784), but the RBC folate levels were statistically significant (P=0.015), and there was a negative correlation between RBC folate levels and CIN lesion grades (P<0.05). The FRα, p16, and Ki-67 levels in the CIN group were significantly different from those in the normal control group (P <0.01), and a positive correlation was found (P <0.01); FRα positivity (P=0.000), Ki-67 positivity (P=0.000), and low-level RBC folate (P=0.000) were independent risk factors for the progression of CIN; these indicators were combined to establish a random forest (RF) model in which the Ki-67+FRα model was used as the early warning model of CIN progression. Conclusion RBC folate, FRα, p16, and Ki-67 can be used as valuable clinical test indicators for predicting the progression of CIN; the combined detection model of Ki-67+FRα can be used as an early warning model for predicting the progression of CIN.
Collapse
Affiliation(s)
- Tingting Liu
- Department of Gynecology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Mengjie Chen
- Department of Gynecology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Xueqin Li
- Department of Gynecology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - He Wang
- Department of Gynecology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| |
Collapse
|