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Mallick S, Choi Y, Taylor AM, Cosper PF. Human Papillomavirus-Induced Chromosomal Instability and Aneuploidy in Squamous Cell Cancers. Viruses 2024; 16:501. [PMID: 38675844 PMCID: PMC11053578 DOI: 10.3390/v16040501] [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: 02/04/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Chromosomal instability (CIN) and aneuploidy are hallmarks of cancer. CIN is defined as a continuous rate of chromosome missegregation events over the course of multiple cell divisions. CIN causes aneuploidy, a state of abnormal chromosome content differing from a multiple of the haploid. Human papillomavirus (HPV) is a well-known cause of squamous cancers of the oropharynx, cervix, and anus. The HPV E6 and E7 oncogenes have well-known roles in carcinogenesis, but additional genomic events, such as CIN and aneuploidy, are often required for tumor formation. HPV+ squamous cancers have an increased frequency of specific types of CIN, including polar chromosomes. CIN leads to chromosome gains and losses (aneuploidies) specific to HPV+ cancers, which are distinct from HPV- cancers. HPV-specific CIN and aneuploidy may have implications for prognosis and therapeutic response and may provide insight into novel therapeutic vulnerabilities. Here, we review HPV-specific types of CIN and patterns of aneuploidy in squamous cancers, as well as how this impacts patient prognosis and treatment.
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Affiliation(s)
- Samyukta Mallick
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032, USA
| | - Yeseo Choi
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Cancer Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Alison M. Taylor
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Pippa F. Cosper
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI 53705, USA
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Mima M, Okabe A, Hoshii T, Nakagawa T, Kurokawa T, Kondo S, Mizokami H, Fukuyo M, Fujiki R, Rahmutulla B, Yoshizaki T, Hanazawa T, Misawa K, Kaneda A. Tumorigenic activation around HPV integrated sites in head and neck squamous cell carcinoma. Int J Cancer 2023; 152:1847-1862. [PMID: 36650703 DOI: 10.1002/ijc.34439] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/18/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023]
Abstract
Human papillomavirus (HPV) is causally involved in the development of head and neck squamous cell carcinoma (HNSCC). The integration of HPV drives tumorigenesis through expression of oncogenic viral genes as well as genomic alterations in surrounding regions. To elucidate involvement of epigenetic dysregulation in tumorigenesis, we here performed integrated analyses of the epigenome, transcriptome and interactome using ChIP-seq, RNA-seq and Hi-C and 4C-seq for HPV(+) HNSCCs. We analyzed clinical HNSCC using The Cancer Genome Atlas data and found that genes neighboring HPV integration sites were significantly upregulated and were correlated with oncogenic phenotypes in HPV(+) HNSCCs. While we found four HPV integration sites in HPV(+) HNSCC cell line UPCI-SCC-090 through target enrichment sequencing, 4C-seq revealed 0.5 to 40 Mb of HPV-interacting regions (HPVIRs) where host genomic regions interacted with integrated HPV genomes. While 9% of the HPVIRs were amplified and activated epigenetically forming super-enhancers, the remaining non-amplified regions were found to show a significant increase in H3K27ac levels and an upregulation of genes associated with GO terms, for example, Signaling by WNT and Cell Cycle. Among those genes, ITPR3 was significantly upregulated, involving UPCI-SCC-090-specific super-enhancer formation around the ITPR3 promoter and in the 80-kb-downstream region. The knockdown of ITPR3 by siRNA or CRISPR deletions of the distant enhancer region led to a significant suppression of cell proliferation. The epigenetic activation of HPVIRs was also confirmed in other cell lines, UM-SCC-47 and UM-SCC-104. These data indicate that epigenetic activation in HPVIRs contributes, at least partially, to genesis of HPV(+) HNSCC.
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Affiliation(s)
- Masato Mima
- Department of Otorhinolaryngology, Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuya Nakagawa
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoya Kurokawa
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoru Kondo
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Harue Mizokami
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ryoji Fujiki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomokazu Yoshizaki
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kiyoshi Misawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Single-Cell Transcriptome Analysis Reveals Different Immune Signatures in HPV- and HPV + Driven Human Head and Neck Squamous Cell Carcinoma. J Immunol Res 2022; 2022:2079389. [PMID: 36157879 PMCID: PMC9507777 DOI: 10.1155/2022/2079389] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is a significant health problem and related to poor long-term outcomes, indicating more research to be done to deeply understand the underlying pathways. Objective This current study aimed in the assessment of the viral- (especially human papilloma virus [HPV]) and carcinogen-driven head and neck squamous cell carcinoma (HNSCC) microenvironment based on single-cell sequencing analysis. Methods Data were downloaded from GEO database (GSE139324), including 131224 cells from 18 HP- HNSCC patients and 8 HPV+ HNSCC patients. Following data normalization, all highly variable genes in single cells were identified, and batch correction was applied. Differentially expressed genes were identified using Wilcoxon rank sum test. A gene enrichment analysis was performed in each cell cluster using KEGG analysis. Single-cell pseudotime trajectories were constructed with MONOCLE (version 2.6.4). Cell-cell interactions were analyzed with CellChat R package. Additionally, cell-cell communication patterns in key signal pathways were compared in different tissue groups. A hidden Markov model (HMM) was used to predict gene expression states (on or off) throughout pseudotime. Five-year overall survival outcomes were compared in both HPV+ and HPV- subsets. Results 20,978 high-quality individual cells passed quality control. RNA-seq data were used from 522 HNSCC primary tumor samples. 1,137 differentially expressed genes between HPV+ and HPV- HNSCC patients were investigated. 96 differentially expressed genes were associated with overall survival and highly enriched in B cell associated biological process. Cell composition differed between types of samples. MHC-I, MHC-II, and MIF signaling pathways were found to be most relevant. Within these pathways, some cells were either signal receiver or signal sender, depending on sample type, respectively. Six genes were obtained, AREG and TGFBI (upregulation), CD27, CXCR3, MS4A1, and CD19 (downregulation), whose expression and HPV types were highly associated with worse overall survival. AREG and TGFBI were pDC marker genes, CXCR3 and CD27 were significantly expressed in T cell-related cells, while MS4A1 and CD19 were mainly expressed in B naïve cells. Conclusions This study revealed dynamic changes in cell percentage and heterogeneity of cell subtypes of HNSCC. AREG, TGFBI, CD27, CXCR3, MS4A1, and CD19 were associated with worse overall survival in HPV-related HNSCC. Especially B-cell related pathways were revealed as particularly relevant in HPV-related HNSCC. These findings are a basis for the development of biomarkers and therapeutic targets in respective patients.
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LncRNA AWPPH as a prognostic predictor in human cancers in Chinese population: evidence from meta-analysis. Biosci Rep 2021; 41:228775. [PMID: 34042153 PMCID: PMC8188174 DOI: 10.1042/bsr20210012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/23/2022] Open
Abstract
Background: Long non-coding RNA associated with poor prognosis of hepatocellular carcinoma (AWPPH) is dysregulated in a variety of human cancers. However, the prognostic value of AWPPH in various cancers remains unclear. Methods: Comprehensive literature search was performed in PubMed, Web of Science, CNKI and Wangfang databases, and eligible studies were obtained according to the inclusion and exclusion criteria. The pooled hazard ratios (HRs) and odds ratios (ORs) were applied to assess the clinical value of AWPPH expression for overall survival (OS) and clinicopathological features. Results: A total of 19 articles including 1699 cancer patients were included in the study. The pooled results demonstrated that evaluated AWPPH expression was positively related to a poorer overall survival of patients with cancers (HR = 1.79, 95%CI: 1.44–2.14, P<0.001). Subgroup analysis revealed that tumor type and sample size affect the predictive value of AWPPH on OS, whereas cut-off value and HR estimation method have no impact on it. In addition, the pooled data also showed that AWPPH was positively linked to advanced TNM stage (OR = 2.50, 95%CI: 1.94–3.22, P<0.001), bigger tumor size (OR = 2.64, 95%CI: 1.47–4.73, P=0.001), macro-vascular invasion (OR = 2.08, 95%CI: 1.04–4.16, P=0.04) and lymph node metastasis (OR = 2.68, 95%CI: 1.82–3.96, P<0.001). Moreover, the results of the trim and fill analysis confirmed the reliability of our finding. Conclusions: Up-regulation of AWPPH was associated with advanced TNM stage, bigger tumor size, worse lymph node metastasis, macro-vascular invasion and shorter overall survival, suggesting that AWPPH may serve as a biomarker for prognosis and clinicopathological characteristics in human cancers among the Chinese population.
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Noel Z, Hoeller S, Bihl M, Muller L. TP53 and PTEN as driver mutations in Zenker's carcinoma-a clinical presentation. Clin Case Rep 2020; 8:2791-2797. [PMID: 33363824 PMCID: PMC7752333 DOI: 10.1002/ccr3.3169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
Zenker carcinoma is still being treated empirically because of the lack of evidence- based guidelines. We report for the first time about the genetic examination of this rare entity. The revealed mutations show genetic similarities with HPV(-)HNSCC which suggests that well-known therapeutic strategies may be applicable for this disease.
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Affiliation(s)
- Zsanett Noel
- Department of SurgeryUniversity Hospitals BaselBaselSwitzerland
| | - Sylvia Hoeller
- Department of PathologyUniversity Hospitals BaselBaselSwitzerland
| | - Michel Bihl
- Department of PathologyUniversity Hospitals BaselBaselSwitzerland
| | - Laurent Muller
- Department of Otorhinolaryngology and BiomedicineUniversity Hospitals BaselBaselSwitzerland
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Lerch S, Berthold S, Ziemann F, Dreffke K, Subtil FSB, Senger Y, Jensen A, Engenhart-Cabillic R, Dikomey E, Wittig A, Eberle F, Schötz U. HPV-positive HNSCC cell lines show strongly enhanced radiosensitivity after photon but not after carbon ion irradiation. Radiother Oncol 2020; 151:134-140. [PMID: 32717362 DOI: 10.1016/j.radonc.2020.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND PURPOSE HPV positive (pos.) HNSCC cells are significantly more radiosensitive to photon irradiation as compared to HPV negative (neg.) cells. Functionally, this is considered to result from a reduced DSB repair capacity. It was now tested, whether such a difference is also observed when using carbon ion (12C) irradiation. MATERIAL AND METHODS Five HPV pos. and five HPV neg. HNSCC cell lines were irradiated with photons or 12C-ions using 2D or 3D cell culture conditions. Clonogenic survival was determined by colony formation assay and DSB repair by immunofluorescence using co-staining of γH2AX and 53BP1 foci. RESULTS The pronounced difference in radiosensitivity known for these two entities when exposed to photons in 2D cell culture, was reduced when treated under 3D conditions. Irradiation with 12C-ions strongly enhanced cell killing, whereby increase was more pronounced for the HPV neg. when compared to the HPV pos. cell line (RBE = 2.81 vs. 2.14). As a consequence, after 12C-irradiation clonogenic survival was almost identical for the two entities as was demonstrated for all cell lines at a dose of 3 Gy. In line with this, the significant difference in DSB repair capacity between HPV pos. and neg. HNSCC cells, as seen after photon irradiation, was abrogated after 12C-irradiation. CONCLUSION While HPV pos. cells are significantly more radiosensitive to photons than HPV neg. cells, no significant difference was seen after 12C-irradiation. This needs to be considered when planning new clinical protocols for the treatment of HPV neg. and pos. tumors with 12C-ions.
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Affiliation(s)
- Stefan Lerch
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | - Sophie Berthold
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | - Frank Ziemann
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | - Kristin Dreffke
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | | | | | - Alexandra Jensen
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | | | - Ekkehard Dikomey
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany; Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Andrea Wittig
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany; Department of Radiotherapy and Radiation Oncology, University Hospital Jena, Friedrich-Schiller-University, Germany
| | - Fabian Eberle
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | - Ulrike Schötz
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany.
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