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Barbosa S, Laureano NK, Hadiwikarta WW, Visioli F, Bonrouhi M, Pajdzik K, Conde-Lopez C, Herold-Mende C, Eidt G, Langie R, Lamers ML, Stögbauer F, Hess J, Kurth I, Jou A. The Role of SOX2 and SOX9 in Radioresistance and Tumor Recurrence. Cancers (Basel) 2024; 16:439. [PMID: 38275880 PMCID: PMC10814462 DOI: 10.3390/cancers16020439] [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: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) exhibits considerable variability in patient outcome. It has been reported that SOX2 plays a role in proliferation, tumor growth, drug resistance, and metastasis in a variety of cancer types. Additionally, SOX9 has been implicated in immune tolerance and treatment failures. SOX2 and SOX9 induce treatment failure by a molecular mechanism that has not yet been elucidated. This study explores the inverse association of SOX2/SOX9 and their distinct expression in tumors, influencing the tumor microenvironment and radiotherapy responses. Through public RNA sequencing data, human biopsy samples, and knockdown cellular models, we explored the effects of inverted SOX2 and SOX9 expression. We found that patients expressing SOX2LowSOX9High showed decreased survival compared to SOX2HighSOX9Low. A survival analysis of patients stratified by radiotherapy and human papillomavirus brings additional clinical relevance. We identified a gene set signature comprising newly discovered candidate genes resulting from inverted SOX2/SOX9 expression. Moreover, the TGF-β pathway emerges as a significant predicted contributor to the overexpression of these candidate genes. In vitro findings reveal that silencing SOX2 enhances tumor radioresistance, while SOX9 silencing enhances radiosensitivity. These discoveries lay the groundwork for further studies on the therapeutic potential of transcription factors in optimizing HNSCC treatment.
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Affiliation(s)
- Silvia Barbosa
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Department of Morphological Sciences, Institute of Basic Health Science, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, RS, Brazil
| | - Natalia Koerich Laureano
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Department of Oral Pathology, Faculty of Dental Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 90035-004, RS, Brazil
| | - Wahyu Wijaya Hadiwikarta
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, 69120 Heidelberg, Germany
| | - Fernanda Visioli
- Department of Oral Pathology, Faculty of Dental Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 90035-004, RS, Brazil
| | - Mahnaz Bonrouhi
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kinga Pajdzik
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Cristina Conde-Lopez
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christel Herold-Mende
- Department of Neurosurgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Gustavo Eidt
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Renan Langie
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Oral Pathology, Faculty of Dental Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 90035-004, RS, Brazil
| | - Marcelo Lazzaron Lamers
- Department of Morphological Sciences, Institute of Basic Health Science, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, RS, Brazil
| | - Fabian Stögbauer
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Germany and Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Institute of Pathology, School of Medicine, Technical University of Munich (TUM), 80337 Munich, Germany
| | - Jochen Hess
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Ina Kurth
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), 69120 Heidelberg, Germany
| | - Adriana Jou
- Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Dentistry, Institute of Toxicology and Pharmacology, Pontifícial Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, RS, Brazil
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2
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Qualliotine JR, Nakagawa T, Rosenthal SB, Sadat S, Ballesteros-Merino C, Xu G, Mark A, Nasamran A, Gutkind JS, Fisch KM, Guo T, Fox BA, Khan Z, Molinolo AA, Califano JA. A Network Landscape of HPVOPC Reveals Methylation Alterations as Significant Drivers of Gene Expression via an Immune-Mediated GPCR Signal. Cancers (Basel) 2023; 15:4379. [PMID: 37686653 PMCID: PMC10486378 DOI: 10.3390/cancers15174379] [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: 07/15/2023] [Revised: 08/17/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
HPV-associated oropharynx carcinoma (HPVOPC) tumors have a relatively low mutational burden. Elucidating the relative contributions of other tumor alterations, such as DNA methylation alterations, alternative splicing events (ASE), and copy number variation (CNV), could provide a deeper understanding of carcinogenesis drivers in this disease. We applied network propagation analysis to multiple classes of tumor alterations in a discovery cohort of 46 primary HPVOPC tumors and 25 cancer-unaffected controls and validated our findings with TCGA data. We identified significant overlap between differential gene expression networks and all alteration classes, and this association was highest for methylation and lowest for CNV. Significant overlap was seen for gene clusters of G protein-coupled receptor (GPCR) pathways. HPV16-human protein interaction analysis identified an enriched cluster defined by an immune-mediated GPCR signal, including CXCR3 cytokines CXCL9, CXCL10, and CXCL11. CXCR3 was found to be expressed in primary HPVOPC, and scRNA-seq analysis demonstrated CXCR3 ligands to be highly expressed in M2 macrophages. In vivo models demonstrated decreased tumor growth with antagonism of the CXCR3 receptor in immunodeficient but not immunocompetent mice, suggesting that the CXCR3 axis can drive tumor proliferation in an autocrine fashion, but the effect is tempered by an intact immune system. In conclusion, methylation, ASE, and SNV alterations are highly associated with network gene expression changes in HPVOPC, suggesting that ASE and methylation alterations have an important role in driving the oncogenic phenotype. Network analysis identifies GPCR networks, specifically the CXCR3 chemokine axis, as modulators of tumor-immune interactions that may have proliferative effects on primary tumors as well as a role for immunosurveillance; however, CXCR3 inhibition should be used with caution, as these agents may both inhibit and stimulate tumor growth considering the competing effects of this cytokine axis. Further investigation is needed to explore opportunities for targeted therapy in this setting.
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Affiliation(s)
- Jesse R. Qualliotine
- Department of Otolaryngology—Head and Neck Surgery, University of California San Diego, La Jolla, CA 92093, USA
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Takuya Nakagawa
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba 263-8522, Japan
| | - Sara Brin Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sayed Sadat
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Guorong Xu
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam Mark
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Art Nasamran
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - J. Silvio Gutkind
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Theresa Guo
- Department of Otolaryngology—Head and Neck Surgery, University of California San Diego, La Jolla, CA 92093, USA
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernard A. Fox
- Earle A. Chiles Research Institute, Providence Cancer Center, Portland, OR 97213, USA
| | - Zubair Khan
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alfredo A. Molinolo
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Joseph A. Califano
- Department of Otolaryngology—Head and Neck Surgery, University of California San Diego, La Jolla, CA 92093, USA
- Gleiberman Head and Neck Cancer Center, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
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3
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DSouza G, Tewari SR, Troy T, Waterboer T, Struijk L, Castillo R, Wright H, Shen M, Miles B, Johansson M, Robbins HA, Fakhry C. Prevalence of oral and blood oncogenic human papillomavirus biomarkers among an enriched screening population: Baseline results of the MOUTH study. Cancer 2023; 129:2373-2384. [PMID: 37032449 PMCID: PMC10330354 DOI: 10.1002/cncr.34783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 04/11/2023]
Abstract
BACKGROUND Human papillomavirus (HPV)-related oropharyngeal cancer screening is being explored in research studies, but strategies to identify an appropriate population are not established. The authors evaluated whether a screening population could be enriched for participants with oncogenic HPV biomarkers using risk factors for oral HPV. METHODS Participants were enrolled at Johns Hopkins Hospitals and Mount Sinai Icahn School of Medicine. Eligible participants were either men aged 30 years or older who had two or more lifetime oral sex partners and a personal history of anogenital dysplasia/cancer or partners of patients who had HPV-related cancer. Oral rinse and serum samples were tested for oncogenic HPV DNA, RNA, and E6 or E7 antibodies, respectively. Participants with any biomarker were considered at-risk. RESULTS Of 1108 individuals, 7.3% had any oncogenic oral HPV DNA, and 22.9% had serum antibodies for oncogenic HPV E6 or E7. Seventeen participants (1.5%) had both oral and blood biomarkers. HPV type 16 (HPV16) biomarkers were rarer, detected in 3.7% of participants, including 20 with oral HPV16 DNA and 22 with HPV16 E6 serum antibodies (n = 1 had both). In adjusted analysis, living with HIV (adjusted odds ratio, 2.65; 95% CI, 1.60-4.40) and older age (66-86 vs. 24-45 years; adjusted odds ratio, 1.70; 95% CI, 1.07-2.70) were significant predictors of being at risk. Compared with the general population, the prevalence of oral HPV16 (1.8% vs. 0.9%), any oncogenic oral HPV DNA (7.3% vs. 3.5%), and HPV16 E6 antibodies (2.2% vs. 0.3%) was significantly elevated. CONCLUSIONS Enrichment by the eligibility criteria successfully identified a population with higher biomarker prevalence, including HPV16 biomarkers, that may be considered for screening trials. Most in this group are still expected to have a low risk of oropharyngeal cancer.
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Affiliation(s)
- Gypsyamber DSouza
- Departments of Epidemiology & Otolaryngology-Head and Neck Surgery, Johns Hopkins, Baltimore, Maryland
| | - Sakshi R Tewari
- Departments of Epidemiology & Otolaryngology-Head and Neck Surgery, Johns Hopkins, Baltimore, Maryland
| | - Tanya Troy
- Departments of Epidemiology & Otolaryngology-Head and Neck Surgery, Johns Hopkins, Baltimore, Maryland
| | - Tim Waterboer
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Linda Struijk
- Viroclinics-DDL Diagnostic Laboratory, Rijswijk, Netherlands
| | - Rachel Castillo
- Departments of Epidemiology & Otolaryngology-Head and Neck Surgery, Johns Hopkins, Baltimore, Maryland
| | - Hannah Wright
- Departments of Epidemiology & Otolaryngology-Head and Neck Surgery, Johns Hopkins, Baltimore, Maryland
| | - Michael Shen
- Departments of Epidemiology & Otolaryngology-Head and Neck Surgery, Johns Hopkins, Baltimore, Maryland
| | - Brett Miles
- Department of Otolaryngology-Head and Neck Surgery, Northwell Health, New York, NY
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Hilary A Robbins
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Carole Fakhry
- Departments of Epidemiology & Otolaryngology-Head and Neck Surgery, Johns Hopkins, Baltimore, Maryland
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4
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Brown G. Deregulation of All- Trans Retinoic Acid Signaling and Development in Cancer. Int J Mol Sci 2023; 24:12089. [PMID: 37569466 PMCID: PMC10419198 DOI: 10.3390/ijms241512089] [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: 07/05/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Cancer stem cells are the root cause of cancer, which, in essence, is a developmental disorder. All-trans retinoic acid (ATRA) signaling via ligand-activation of the retinoic acid receptors (RARs) plays a crucial role in tissue patterning and development during mammalian embryogenesis. In adults, active RARγ maintains the pool of hematopoietic stem cells, whereas active RARα drives myeloid cell differentiation. Various findings have revealed that ATRA signaling is deregulated in many cancers. The enzymes for ATRA synthesis are downregulated in colorectal, gastric, lung, and oropharyngeal cancers. ATRA levels within breast, ovarian, pancreatic, prostate, and renal cancer cells were lower than within their normal counterpart cells. The importance is that 0.24 nM ATRA activates RARγ (for stem cell stemness), whereas 100 times more is required to activate RARα (for differentiation). Moreover, RARγ is an oncogene regarding overexpression within colorectal, cholangiocarcinoma, hepatocellular, ovarian, pancreatic, and renal cancer cells. The microRNA (miR) 30a-5p downregulates expression of RARγ, and miR-30a/miR-30a-5p is a tumor suppressor for breast, colorectal, gastric, hepatocellular, lung, oropharyngeal, ovarian, pancreatic, prostate, and renal cancer. These complementary findings support the view that perturbations to ATRA signaling play a role in driving the abnormal behavior of cancer stem cells. Targeting ATRA synthesis and RARγ has provided promising approaches to eliminating cancer stem cells because such agents have been shown to drive cell death.
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Affiliation(s)
- Geoffrey Brown
- School of Biomedical Sciences, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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5
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MacLennan SA, Marra MA. Oncogenic Viruses and the Epigenome: How Viruses Hijack Epigenetic Mechanisms to Drive Cancer. Int J Mol Sci 2023; 24:ijms24119543. [PMID: 37298494 DOI: 10.3390/ijms24119543] [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: 05/04/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Globally, viral infections substantially contribute to cancer development. Oncogenic viruses are taxonomically heterogeneous and drive cancers using diverse strategies, including epigenomic dysregulation. Here, we discuss how oncogenic viruses disrupt epigenetic homeostasis to drive cancer and focus on how virally mediated dysregulation of host and viral epigenomes impacts the hallmarks of cancer. To illustrate the relationship between epigenetics and viral life cycles, we describe how epigenetic changes facilitate the human papillomavirus (HPV) life cycle and how changes to this process can spur malignancy. We also highlight the clinical impact of virally mediated epigenetic changes on cancer diagnosis, prognosis, and treatment.
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Affiliation(s)
- Signe A MacLennan
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
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6
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Goričan L, Büdefeld T, Čelešnik H, Švagan M, Lanišnik B, Potočnik U. Gene Expression Profiles of Methyltransferases and Demethylases Associated with Metastasis, Tumor Invasion, CpG73 Methylation, and HPV Status in Head and Neck Squamous Cell Carcinoma. Curr Issues Mol Biol 2023; 45:4632-4646. [PMID: 37367043 DOI: 10.3390/cimb45060294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/12/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Epigenetic studies on the role of DNA-modifying enzymes in HNSCC tumorigenesis have focused on a single enzyme or a group of enzymes. To acquire a more comprehensive insight into the expression profile of methyltransferases and demethylases, in the present study, we examined the mRNA expression of the DNA methyltransferases DNMT1, DNMT3A, and DNMT3B, the DNA demethylases TET1, TET2, TET3, and TDG, and the RNA methyltransferase TRDMT1 by RT-qPCR in paired tumor-normal tissue samples from HNSCC patients. We characterized their expression patterns in relation to regional lymph node metastasis, invasion, HPV16 infection, and CpG73 methylation. Here, we show that tumors with regional lymph node metastases (pN+) exhibited decreased expression of DNMT1, 3A and 3B, and TET1 and 3 compared to non-metastatic tumors (pN0), suggesting that metastasis requires a distinct expression profile of DNA methyltransferases/demethylases in solid tumors. Furthermore, we identified the effect of perivascular invasion and HPV16 on DNMT3B expression in HNSCC. Finally, the expression of TET2 and TDG was inversely correlated with the hypermethylation of CpG73, which has previously been associated with poorer survival in HNSCC. Our study further confirms the importance of DNA methyltransferases and demethylases as potential prognostic biomarkers as well as molecular therapeutic targets for HNSCC.
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Affiliation(s)
- Larisa Goričan
- Centre for Human Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Tomaž Büdefeld
- Centre for Human Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Helena Čelešnik
- Centre for Human Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, 2000 Maribor, Slovenia
| | - Matija Švagan
- Department of Otorhinolaryngology, Cervical and Maxillofacial Surgery, University Medical Centre Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia
| | - Boštjan Lanišnik
- Department of Otorhinolaryngology, Cervical and Maxillofacial Surgery, University Medical Centre Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia
| | - Uroš Potočnik
- Centre for Human Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, 2000 Maribor, Slovenia
- Department for Science and Research, University Medical Centre Maribor, 2000 Maribor, Slovenia
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7
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Kumari S, Mishra S, Anand N, Hadi R, Rastogi M, Husain N. Circulating free DNA integrity index and promoter methylation of tumor suppressor gene P16, DAPK and RASSF1A as a biomarker for oropharyngeal squamous cell carcinoma. Pathol Res Pract 2023; 246:154489. [PMID: 37150134 DOI: 10.1016/j.prp.2023.154489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
Circulating free DNA (cfDNA) is in use for the non-invasive diagnosis of tumors. Methylation of tumor suppressor genes (TSGs) is an early event in carcinogenesis and may serve as tumor biomarker. We have investigated cfDNA integrity and methylation of tumor suppressor genes P16, DAPK and RASSF1A in serum cfDNA of oropharyngeal squamous cell carcinoma (OPSCC) comparing paired serum and tumor tissue samples to evaluate their diagnostic use. Prospective case-control study, paired serum and tissue samples from 56 OPSCC, and 15 normal controls (NC). Sybr green Quantitate real time PCR was used for cfDNA quantification through amplification ALU 115 and 247 fragments. Promoter methylation of was analyzed in paired samples using methylation specific PCR. There was significantly high cfDNA integrity in OPSCC compared to normal control (p = < 0.0001). The cfDNA integrity values were significantly higher and associated with nodal status (p = 0.016). The AUC for cfDNA integrity was 0.967. The P16, DAPK and RASSF1 promoters were significantly hypermethylated in serum of OPSCC compared to NC with high concordance in tissue (up to 96.55 %). The gene promoter methylation of P16 was associated with smoking (p = 0.030), RASSF1A with stage (p = 0.011). The combination of ALU115 with cfDNA integrity and combination of gene methylation increases diagnostic sensitivity. In followup samples the cfDNA change was not different. Liquid biopsy approach including cfDNA integrity, methylation profiling in cfDNA, in combination or separately can assist in the diagnosis of OPSCC along with radio diagnostic scan. Serum changes represent changes in tissue with very high concordance.
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Affiliation(s)
- Swati Kumari
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Sridhar Mishra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Nidhi Anand
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Rahat Hadi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Madhup Rastogi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India.
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8
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Barnekow E, Hasslow J, Liu W, Bryant P, Thutkawkorapin J, Wendt C, Czene K, Hall P, Margolin S, Lindblom A. A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31. Int J Mol Sci 2023; 24:ijms24054468. [PMID: 36901898 PMCID: PMC10003706 DOI: 10.3390/ijms24054468] [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: 12/13/2022] [Revised: 02/01/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Most breast cancer heritability is unexplained. We hypothesized that analysis of unrelated familial cases in a GWAS context could enable the identification of novel susceptibility loci. In order to examine the association of a haplotype with breast cancer risk, we performed a genome-wide haplotype association study using a sliding window analysis of window sizes 1-25 SNPs in 650 familial invasive breast cancer cases and 5021 controls. We identified five novel risk loci on 9p24.3 (OR 3.4; p 4.9 × 10-11), 11q22.3 (OR 2.4; p 5.2 × 10-9), 15q11.2 (OR 3.6; p 2.3 × 10-8), 16q24.1 (OR 3; p 3 × 10-8) and Xq21.31 (OR 3.3; p 1.7 × 10-8) and confirmed three well-known loci on 10q25.13, 11q13.3, and 16q12.1. In total, 1593 significant risk haplotypes and 39 risk SNPs were distributed on the eight loci. In comparison with unselected breast cancer cases from a previous study, the OR was increased in the familial analysis in all eight loci. Analyzing familial cancer cases and controls enabled the identification of novel breast cancer susceptibility loci.
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Affiliation(s)
- Elin Barnekow
- Department of Clinical Science and Education, Karolinska Institutet, 11883 Stockholm, Sweden
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden
- Correspondence: (E.B.); (A.L.)
| | - Johan Hasslow
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden
| | - Wen Liu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
- Department of Neuroscience, Uppsala University, 75237 Uppsala, Sweden
| | - Patrick Bryant
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, 17165 Stockholm, Sweden
- Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Jessada Thutkawkorapin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Camilla Wendt
- Department of Clinical Science and Education, Karolinska Institutet, 11883 Stockholm, Sweden
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Per Hall
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Sara Margolin
- Department of Clinical Science and Education, Karolinska Institutet, 11883 Stockholm, Sweden
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
- Correspondence: (E.B.); (A.L.)
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9
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Ling Y, Li J, Zhou L. Smoking-related epigenetic modifications are associated with the prognosis and chemotherapeutics of patients with bladder cancer. Int J Immunopathol Pharmacol 2023; 37:3946320231166774. [PMID: 37011378 PMCID: PMC10074629 DOI: 10.1177/03946320231166774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
OBJECTIVE Epidemiologic studies have linked smoking to various malignancies, including bladder cancer, but its underlying biological functions remain elusive. Currently, we aimed to identify the smoking-related epigenetic modifications and disclose their impacts on prognosis and therapies in bladder cancer. METHODS DNA methylation, transcriptome, and clinical profiles were acquired from The Cancer Genome Atlas (TCGA) using "TCGAbiolinks" Differential expression analyses were performed with "limma" and visualized by the "pheatmap" package. Smoking-related interactions were displayed using Cytoscape. Least absolute shrinkage and selection operator (LASSO) algorithm was for generation of a smoking-related prognostic model. Kaplan-Meier analysis with log-rank test was for survival analysis, followed by a prognostic nomogram. The Gene Set Enrichment Analysis (GSEA) was used for functional analysis. The "oncoPredict" package was applied for drug sensitivity analysis. RESULTS We recruited all types of bladder cancers and found that smoking was involved in poor prognosis, with the hazard ratio (HR) of 1.600 (95%CI: 1.028-2.491). A total of 1078 smoking-related DNA methylations (526 hypermethylation and 552 hypomethylation) were identified and 9 methylation-driven genes differentially expressed in bladder cancer. Also, 506lncRNAs (448 upregulated and 58 downregulated lncRNAs) and 102 miRNAs (74 upregulated and 28 downregulated miRNAs) were determined as smoking-related ncRNAs. We then calculated the smoking-related risk score and observed that cases of high risk were predicted with poor prognosis. We constructed a prognostic nomogram to predict the 1-, 3-, and 5-year overall survival rates. Several cancer-related pathways were enriched in the high-risk group, and patients with high-risk were more sensitive to Gemcitabine, Wnt-C59, JAK1_8709, KRAS (G12C) Inhibitor-12, and LY2109761. Whereas, those with low-risk were more sensitive to Cisplatin, AZ960, and Buparlisib. CONCLUSIONS Totally, we initially identified the smoking-related epigenetic modifications in bladder cancer and constructed a corresponding prognostic model, which was also linked to disparate sensitivities to chemotherapeutics. Our findings would provide novel insights into the carcinogenesis, prognosis, and therapies in bladder cancer.
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Affiliation(s)
- Ya Ling
- 74566The first Affiliated Hospital of Soochow University, Suzhou, China
| | - Jindong Li
- 372209Taizhou People's Hospital, Taizhou, China
| | - Lijuan Zhou
- 74566The first Affiliated Hospital of Soochow University, Suzhou, China
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10
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Diez-Fraile A, De Ceulaer J, Derpoorter C, Spaas C, De Backer T, Lamoral P, Abeloos J, Lammens T. Tracking the Molecular Fingerprint of Head and Neck Cancer for Recurrence Detection in Liquid Biopsies. Int J Mol Sci 2022; 23:ijms23052403. [PMID: 35269544 PMCID: PMC8910330 DOI: 10.3390/ijms23052403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 02/04/2023] Open
Abstract
The 5-year relative survival for patients with head and neck cancer, the seventh most common form of cancer worldwide, was reported as 67% in developed countries in the second decade of the new millennium. Although surgery, radiotherapy, chemotherapy, or combined treatment often elicits an initial satisfactory response, relapses are frequently observed within two years. Current surveillance methods, including clinical exams and imaging evaluations, have not unambiguously demonstrated a survival benefit, most probably due to a lack of sensitivity in detecting very early recurrence. Recently, liquid biopsy monitoring of the molecular fingerprint of head and neck squamous cell carcinoma has been proposed and investigated as a strategy for longitudinal patient care. These innovative methods offer rapid, safe, and highly informative genetic analysis that can identify small tumors not yet visible by advanced imaging techniques, thus potentially shortening the time to treatment and improving survival outcomes. In this review, we provide insights into the available evidence that the molecular tumor fingerprint can be used in the surveillance of head and neck squamous cell carcinoma. Challenges to overcome, prior to clinical implementation, are also discussed.
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Affiliation(s)
- Araceli Diez-Fraile
- Division of Oral and Maxillofacial Surgery, Department of Surgery, General Hospital Sint-Jan Brugge-Oostende A.V., 8000 Bruges, Belgium; (A.D.-F.); (J.D.C.); (C.S.); (T.D.B.); (P.L.); (J.A.)
| | - Joke De Ceulaer
- Division of Oral and Maxillofacial Surgery, Department of Surgery, General Hospital Sint-Jan Brugge-Oostende A.V., 8000 Bruges, Belgium; (A.D.-F.); (J.D.C.); (C.S.); (T.D.B.); (P.L.); (J.A.)
| | - Charlotte Derpoorter
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, 9000 Ghent, Belgium;
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (C.R.I.G.), 9000 Ghent, Belgium
| | - Christophe Spaas
- Division of Oral and Maxillofacial Surgery, Department of Surgery, General Hospital Sint-Jan Brugge-Oostende A.V., 8000 Bruges, Belgium; (A.D.-F.); (J.D.C.); (C.S.); (T.D.B.); (P.L.); (J.A.)
| | - Tom De Backer
- Division of Oral and Maxillofacial Surgery, Department of Surgery, General Hospital Sint-Jan Brugge-Oostende A.V., 8000 Bruges, Belgium; (A.D.-F.); (J.D.C.); (C.S.); (T.D.B.); (P.L.); (J.A.)
| | - Philippe Lamoral
- Division of Oral and Maxillofacial Surgery, Department of Surgery, General Hospital Sint-Jan Brugge-Oostende A.V., 8000 Bruges, Belgium; (A.D.-F.); (J.D.C.); (C.S.); (T.D.B.); (P.L.); (J.A.)
| | - Johan Abeloos
- Division of Oral and Maxillofacial Surgery, Department of Surgery, General Hospital Sint-Jan Brugge-Oostende A.V., 8000 Bruges, Belgium; (A.D.-F.); (J.D.C.); (C.S.); (T.D.B.); (P.L.); (J.A.)
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, 9000 Ghent, Belgium;
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (C.R.I.G.), 9000 Ghent, Belgium
- Correspondence: ; Tel.: +32-9-332-2480
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11
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Dong H, Shu X, Xu Q, Zhu C, Kaufmann AM, Zheng ZM, Albers AE, Qian X. Current Status of Human Papillomavirus-Related Head and Neck Cancer: From Viral Genome to Patient Care. Virol Sin 2021. [PMID: 34152564 DOI: 10.1007/s12250-021-00413-8/figures/2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Human papillomavirus (HPV) infection identified as a definitive human carcinogen is increasingly being recognized for its role in carcinogenesis of human cancers. Up to 38%-80% of head and neck squamous cell carcinoma (HNSCC) in oropharyngeal location (OPSCC) and nearly all cervical cancers contain the HPV genome which is implicated in causing cancer through its oncoproteins E6 and E7. Given by the biologically distinct HPV-related OPSCC and a more favorable prognosis compared to HPV-negative tumors, clinical trials on de-escalation treatment strategies for these patients have been studied. It is therefore raised the questions for the patient stratification if treatment de-escalation is feasible. Moreover, understanding the crosstalk of HPV-mediated malignancy and immunity with clinical insights from the proportional response rate to immune checkpoint blockade treatments in patients with HNSCC is of importance to substantially improve the treatment efficacy. This review discusses the biology of HPV-related HNSCC as well as successful clinically findings with promising candidates in the pipeline for future directions. With the advent of various sequencing technologies, further biomolecules associated with HPV-related HNSCC progression are currently being identified to be used as potential biomarkers or targets for clinical decisions throughout the continuum of cancer care.
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Affiliation(s)
- Haoru Dong
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinhua Shu
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Qiang Xu
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Chen Zhu
- Department of Cancer Prevention, Cancer Hospital University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Andreas M Kaufmann
- Clinic for Gynecology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, 12203, Germany
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Andreas E Albers
- Department of Otolaryngology, Head and Neck Surgery, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, 13353, Germany
| | - Xu Qian
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
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12
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Head and Neck Cancers Are Not Alike When Tarred with the Same Brush: An Epigenetic Perspective from the Cancerization Field to Prognosis. Cancers (Basel) 2021; 13:cancers13225630. [PMID: 34830785 PMCID: PMC8616074 DOI: 10.3390/cancers13225630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Squamous cell carcinomas affect different head and neck subsites and, although these tumors arise from the same epithelial lining and share risk factors, they differ in terms of clinical behavior and molecular carcinogenesis mechanisms. Differences between HPV-negative and HPV-positive tumors are those most frequently explored, but further data suggest that the molecular heterogeneity observed among head and neck subsites may go beyond HPV infection. In this review, we explore how alterations of DNA methylation and microRNA expression contribute to head and neck squamous cell carcinoma (HNSCC) development and progression. The association of these epigenetic alterations with risk factor exposure, early carcinogenesis steps, transformation risk, and prognosis are described. Finally, we discuss the potential application of the use of epigenetic biomarkers in HNSCC. Abstract Head and neck squamous cell carcinomas (HNSCC) are among the ten most frequent types of cancer worldwide and, despite all efforts, are still diagnosed at late stages and show poor overall survival. Furthermore, HNSCC patients often experience relapses and the development of second primary tumors, as a consequence of the field cancerization process. Therefore, a better comprehension of the molecular mechanisms involved in HNSCC development and progression may enable diagnosis anticipation and provide valuable tools for prediction of prognosis and response to therapy. However, the different biological behavior of these tumors depending on the affected anatomical site and risk factor exposure, as well as the high genetic heterogeneity observed in HNSCC are major obstacles in this pursue. In this context, epigenetic alterations have been shown to be common in HNSCC, to discriminate the tumor anatomical subsites, to be responsive to risk factor exposure, and show promising results in biomarker development. Based on this, this review brings together the current knowledge on alterations of DNA methylation and microRNA expression in HNSCC natural history, focusing on how they contribute to each step of the process and on their applicability as biomarkers of exposure, HNSCC development, progression, and response to therapy.
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13
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Zhou R, Chen Z, Xiao ZR, Wang SL, Rong C. HPV-Related Promoter Methylation-Based Gene Signature Predicts Clinical Prognosis of Patients With Cervical Cancer. Front Oncol 2021; 11:753102. [PMID: 34745985 PMCID: PMC8566918 DOI: 10.3389/fonc.2021.753102] [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: 08/04/2021] [Accepted: 10/06/2021] [Indexed: 01/16/2023] Open
Abstract
Persistent high-risk HPV infection drives tumorigenesis in various human malignancies, including cervical, oropharyngeal, anal, and vulvar carcinomas. Although HPV-related tumors arise in several different sites, they share many common genetic and epigenetic events. Complex and heterogeneous genomic aberrations and mutations induced by high-risk HPV contribute to the initiation and progression of cervical cancer (CC). However, the associations between high-risk HPV infection and DNA methylation have not been clearly investigated. In the present study, HPV-related gene promoter methylation signature was comprehensively analyzed using multiple interactive platforms. CC patients were successfully classified into high-risk and low-risk groups with significant differences in clinical outcomes based on the HPV-related gene promoter methylation signature. Moreover, the protein levels of ALDH1A2 and clinical prognostic value were confirmed in the CC patients cohort. In summary, our study provides compelling evidence that HPV-related gene promoter methylation signature serves as a strong prognostic signature for CC patients. Clinical investigations in large CC patient cohorts are greatly needed to pave the way to implement epigenetic biomarkers into better clinical management.
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Affiliation(s)
- Ran Zhou
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhuo Chen
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zuo-Run Xiao
- Department of Pathology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | - Shou-Li Wang
- Department of Pathology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | - Chao Rong
- Department of Pathology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
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14
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Ma W, Cao Q, She W. Identification and clinical validation of gene signatures with grade and survival in head and neck carcinomas. Braz J Med Biol Res 2021; 54:e11069. [PMID: 34550272 PMCID: PMC8457684 DOI: 10.1590/1414-431x2020e11069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/15/2021] [Indexed: 11/22/2022] Open
Abstract
This study aimed to explore gene expression profiles that drive malignancy from low- to high-grade head and neck carcinomas (HNC), as well as to analyze their correlations with survival. Gene expressions and clinical data of HNC were downloaded from the Gene Expression Omnibus (GEO) repository. The significantly differential genes (SDGs) between low- and high-grade HNC were screened. Cox regressions were performed to identify prognostic SDGs of progression-free survival (PFS) and disease-specific survival (DSS). The genes were experimentally validated by RT-PCR in clinical tissue specimens. Thirty-five SDGs were identified in 47 low-grade and 30 high-grade HNC samples. Cox regression analyses showed that CXCL14, SLC44A1, and UBD were significantly associated with DSS, and PPP2R2C and SLC44A1 were associated with PFS. Patients were grouped into high-risk or low-risk groups for prognosis based on gene signatures. High-risk patients had significantly shorter DSS and PFS than low-risk patients (P=0.033 and P=0.010, respectively). Multivariate Cox regression showed HPV (P=0.033), lymph node status (P=0.032), and residual status (P<0.044) were independent risk factors for PFS. ROC curves showed the risk score had better efficacy to predict survival both for DSS and PFS (AUC=0.858 and AUC=0.901, respectively). The results showed CXCL14 and SLC44A1 were significantly overexpressed in the low-grade HNC tissues and the UBD were overexpressed in the high-grade HNC tissues. Our results suggested that SDGs had different expression profiles between the low-grade and high-grade HNC, and these genes may serve as prognostic biomarkers to predict survival.
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Affiliation(s)
- Wei Ma
- Department of Otolaryngology - Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Otolaryngology - Head and Neck Surgery, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qing Cao
- Department of Otolaryngology - Head and Neck Surgery, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Wandong She
- Department of Otolaryngology - Head and Neck Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
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15
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Camuzi D, Buexm LA, Lourenço SDQC, Esposti DD, Cuenin C, Lopes MDSA, Manara F, Talukdar FR, Herceg Z, Ribeiro Pinto LF, Soares-Lima SC. HPV Infection Leaves a DNA Methylation Signature in Oropharyngeal Cancer Affecting Both Coding Genes and Transposable Elements. Cancers (Basel) 2021; 13:3621. [PMID: 34298834 PMCID: PMC8306428 DOI: 10.3390/cancers13143621] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/04/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022] Open
Abstract
HPV oncoproteins can modulate DNMT1 expression and activity, and previous studies have reported both gene-specific and global DNA methylation alterations according to HPV status in head and neck cancer. However, validation of these findings and a more detailed analysis of the transposable elements (TEs) are still missing. Here we performed pyrosequencing to evaluate a 5-CpG methylation signature and Line1 methylation in an oropharyngeal squamous cell carcinoma (OPSCC) cohort. We further evaluated the methylation levels of the TEs, their correlation with gene expression and their impact on overall survival (OS) using the TCGA cohort. In our dataset, the 5-CpG signature distinguished HPV-positive and HPV-negative OPSCC with 66.67% sensitivity and 84.33% specificity. Line1 methylation levels were higher in HPV-positive cases. In the TCGA cohort, Line1, Alu and long terminal repeats (LTRs) showed hypermethylation in a frequency of 60.5%, 58.9% and 92.3%, respectively. ZNF541 and CCNL1 higher expression was observed in HPV-positive OPSCC, correlated with lower methylation levels of promoter-associated Alu and LTR, respectively, and independently associated with better OS. Based on our findings, we may conclude that a 5-CpG methylation signature can discriminate OPSCC according to HPV status with high accuracy and TEs are differentially methylated and may regulate gene expression in HPV-positive OPSCC.
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Affiliation(s)
- Diego Camuzi
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro CEP 20231-050, Brazil; (D.C.); (L.A.B.); (M.d.S.A.L.); (L.F.R.P.)
| | - Luisa Aguirre Buexm
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro CEP 20231-050, Brazil; (D.C.); (L.A.B.); (M.d.S.A.L.); (L.F.R.P.)
| | - Simone de Queiroz Chaves Lourenço
- Department of Pathology, Dental School, Fluminense Federal University, Rua Mario Santos Braga, 30, Centro, Niterói CEP 24040-110, Brazil;
| | - Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (D.D.E.); (C.C.); (F.M.); (F.R.T.); (Z.H.)
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (D.D.E.); (C.C.); (F.M.); (F.R.T.); (Z.H.)
| | - Monique de Souza Almeida Lopes
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro CEP 20231-050, Brazil; (D.C.); (L.A.B.); (M.d.S.A.L.); (L.F.R.P.)
| | - Francesca Manara
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (D.D.E.); (C.C.); (F.M.); (F.R.T.); (Z.H.)
| | - Fazlur Rahman Talukdar
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (D.D.E.); (C.C.); (F.M.); (F.R.T.); (Z.H.)
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (D.D.E.); (C.C.); (F.M.); (F.R.T.); (Z.H.)
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro CEP 20231-050, Brazil; (D.C.); (L.A.B.); (M.d.S.A.L.); (L.F.R.P.)
| | - Sheila Coelho Soares-Lima
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro CEP 20231-050, Brazil; (D.C.); (L.A.B.); (M.d.S.A.L.); (L.F.R.P.)
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16
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Dong H, Shu X, Xu Q, Zhu C, Kaufmann AM, Zheng ZM, Albers AE, Qian X. Current Status of Human Papillomavirus-Related Head and Neck Cancer: From Viral Genome to Patient Care. Virol Sin 2021; 36:1284-1302. [PMID: 34152564 PMCID: PMC8692589 DOI: 10.1007/s12250-021-00413-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022] Open
Abstract
Human papillomavirus (HPV) infection identified as a definitive human carcinogen is increasingly being recognized for its role in carcinogenesis of human cancers. Up to 38%–80% of head and neck squamous cell carcinoma (HNSCC) in oropharyngeal location (OPSCC) and nearly all cervical cancers contain the HPV genome which is implicated in causing cancer through its oncoproteins E6 and E7. Given by the biologically distinct HPV-related OPSCC and a more favorable prognosis compared to HPV-negative tumors, clinical trials on de-escalation treatment strategies for these patients have been studied. It is therefore raised the questions for the patient stratification if treatment de-escalation is feasible. Moreover, understanding the crosstalk of HPV-mediated malignancy and immunity with clinical insights from the proportional response rate to immune checkpoint blockade treatments in patients with HNSCC is of importance to substantially improve the treatment efficacy. This review discusses the biology of HPV-related HNSCC as well as successful clinically findings with promising candidates in the pipeline for future directions. With the advent of various sequencing technologies, further biomolecules associated with HPV-related HNSCC progression are currently being identified to be used as potential biomarkers or targets for clinical decisions throughout the continuum of cancer care.
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Affiliation(s)
- Haoru Dong
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinhua Shu
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Qiang Xu
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Chen Zhu
- Department of Cancer Prevention, Cancer Hospital University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Andreas M Kaufmann
- Clinic for Gynecology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, 12203, Germany
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Andreas E Albers
- Department of Otolaryngology, Head and Neck Surgery, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, 13353, Germany
| | - Xu Qian
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
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17
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Nakagawa T, Kurokawa T, Mima M, Imamoto S, Mizokami H, Kondo S, Okamoto Y, Misawa K, Hanazawa T, Kaneda A. DNA Methylation and HPV-Associated Head and Neck Cancer. Microorganisms 2021; 9:microorganisms9040801. [PMID: 33920277 PMCID: PMC8069883 DOI: 10.3390/microorganisms9040801] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC), especially oropharyngeal squamous cell carcinoma (OPSCC), has recently been found to be significantly associated with human papillomavirus (HPV) infection. The incidence of OPSCC has been increasing and surpassed the number of cervical cancer cases in the United States. Although HPV-associated OPSCC has a relatively better prognosis than HPV-negative cancer, approximately 20% of HPV-associated HNSCC patients show a poor prognosis or therapeutic response, and the molecular mechanism behind this outcome in the intermediate-risk group is yet to be elucidated. These biological differences between HPV-associated HNSCC and HPV-negative HNSCC are partly explained by the differences in mutation patterns. However, recent reports have revealed that epigenetic dysregulation, such as dysregulated DNA methylation, is a strikingly common pathological feature of human malignancy. Notably, viral infections can induce aberrant DNA methylation, leading to carcinogenesis, and HPV-associated HNSCC cases tend to harbor a higher amount of aberrantly methylated DNA than HPV-negative HNSCC cases. Furthermore, recent comprehensive genome-wide DNA-methylation analyses with large cohorts have revealed that a sub-group of HPV-associated HNSCC correlates with increased DNA methylation. Accordingly, in this review, we provide an overview of the relationship between DNA methylation and HPV-associated HNSCC.
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Affiliation(s)
- Takuya Nakagawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (T.N.); (T.K.); (S.I.); (Y.O.)
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (M.M.); (H.M.); (S.K.)
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92037, USA
| | - Tomoya Kurokawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (T.N.); (T.K.); (S.I.); (Y.O.)
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (M.M.); (H.M.); (S.K.)
- Clinical Research Center, Chiba University Hospital, Chiba 260-8677, Japan
| | - Masato Mima
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (M.M.); (H.M.); (S.K.)
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Hamamatsu University, Hamamatsu 431-3192, Japan;
| | - Sakiko Imamoto
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (T.N.); (T.K.); (S.I.); (Y.O.)
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (M.M.); (H.M.); (S.K.)
| | - Harue Mizokami
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (M.M.); (H.M.); (S.K.)
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan
| | - Satoru Kondo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (M.M.); (H.M.); (S.K.)
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan
| | - Yoshitaka Okamoto
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (T.N.); (T.K.); (S.I.); (Y.O.)
- Chiba Rosai Hospital, Ichihara 290-0003, Japan
| | - Kiyoshi Misawa
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Hamamatsu University, Hamamatsu 431-3192, Japan;
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (T.N.); (T.K.); (S.I.); (Y.O.)
- Correspondence: (T.H.); (A.K.); Tel./Fax: +81-43-226-2039
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (M.M.); (H.M.); (S.K.)
- Correspondence: (T.H.); (A.K.); Tel./Fax: +81-43-226-2039
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18
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Uysal D, Kowalewski KF, Kriegmair MC, Wirtz R, Popovic ZV, Erben P. A comprehensive molecular characterization of the 8q22.2 region reveals the prognostic relevance of OSR2 mRNA in muscle invasive bladder cancer. PLoS One 2021; 16:e0248342. [PMID: 33711044 PMCID: PMC7954304 DOI: 10.1371/journal.pone.0248342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/25/2021] [Indexed: 12/27/2022] Open
Abstract
Technological advances in molecular profiling have enabled the comprehensive identification of common regions of gene amplification on chromosomes (amplicons) in muscle invasive bladder cancer (MIBC). One such region is 8q22.2, which is largely unexplored in MIBC and could harbor genes with potential for outcome prediction or targeted therapy. To investigate the prognostic role of 8q22.2 and to compare different amplicon definitions, an in-silico analysis of 357 patients from The Cancer Genome Atlas, who underwent radical cystectomy for MIBC, was performed. Amplicons were generated using the GISTIC2.0 algorithm for copy number alterations (DNA_Amplicon) and z-score normalization for mRNA gene overexpression (RNA_Amplicon). Kaplan-Meier survival analysis, univariable, and multivariable Cox proportional hazard ratios were used to relate amplicons, genes, and clinical parameters to overall (OS) and disease-free survival (DFS). Analyses of the biological functions of 8q22.2 genes and genomic events in MIBC were performed to identify potential targets. Genes with prognostic significance from the in silico analysis were validated using RT-qPCR of MIBC tumor samples (n = 46). High 8q22.2 mRNA expression (RNA-AMP) was associated with lymph node metastases. Furthermore, 8q22.2 DNA and RNA amplified patients were more likely to show a luminal subtype (DNA_Amplicon_core: p = 0.029; RNA_Amplicon_core: p = 0.01). Overexpression of the 8q22.2 gene OSR2 predicted shortened DFS in univariable (HR [CI] 1.97 [1.2; 3.22]; p = 0.01) and multivariable in silico analysis (HR [CI] 1.91 [1.15; 3.16]; p = 0.01) and decreased OS (HR [CI] 6.25 [1.37; 28.38]; p = 0.0177) in RT-qPCR data analysis. Alterations in different levels of the 8q22.2 region are associated with manifestation of different clinical characteristics in MIBC. An in-depth comprehensive molecular characterization of genomic regions involved in cancer should include multiple genetic levels, such as DNA copy number alterations and mRNA gene expression, and could lead to a better molecular understanding. In this study, OSR2 is identified as a potential biomarker for survival prognosis.
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Affiliation(s)
- Daniel Uysal
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Karl-Friedrich Kowalewski
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | | | - Ralph Wirtz
- STRATIFYER Molecular Pathology GmbH, Köln, Germany
| | - Zoran V. Popovic
- Institute of Pathology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Philipp Erben
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- * E-mail:
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19
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[Tumor biology of oropharyngeal carcinoma]. HNO 2020; 69:249-255. [PMID: 33215226 DOI: 10.1007/s00106-020-00964-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Etiologically, oropharyngeal squamous cell carcinoma (OPSCC) can be divided into OPSCC caused by noxious agents and human papillomavirus (HPV)-driven carcinoma. These types differ with regard to clinical features and prognosis-differences which are rooted in the underlying molecular biology of the tumor. OBJECTIVE The aim of this work is to provide an overview of the molecular biological characteristics of the genetics, epigenetics, and immunology of OPSCC. MATERIALS AND METHODS A literature review was performed on a selection of genetic, epigenetic, and immunological factors characterizing OPSCC. RESULTS The understanding of genetic aberrations and their consequences for cancerogenesis and tumor biology is increasing. Epigenetic phenomena are complementing functional relationships. However, epigenetic mechanisms of gene regulation are complex and much research is still required in this field. Immunological aspects of cancer molecular biology have moved into the focus in light of recent advances in the field of immunotherapy. CONCLUSION The tumor biology of OPSCC is primarily defined by its HPV status. Additionally, HPV-independent genetic, epigenetic, and immunological signatures are being defined. From these advances, rationales for new treatment concepts may evolve.
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20
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Cobzeanu BM, Cobzeanu MD, Moscalu M, Palade OD, Rădulescu L, Negru D, Moisii LG, Cobzeanu LM, Ungureanu LB, Vonica P, Matei DV, Rusu DC, Volovaț C, Costan VV. Predictive Value of HPV, p53, and p16 in the Post-Treatment Evolution of Malignant Tumors of the Oropharynx and Retromolar Trigone-Oropharynx Junction. ACTA ACUST UNITED AC 2020; 56:medicina56100542. [PMID: 33076537 PMCID: PMC7602815 DOI: 10.3390/medicina56100542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022]
Abstract
Background and objectives: Knowledge of the interactions and influences of infectious, genetic, and environmental factors on the evolution and treatment response of malignant tumors is essential for improving the management of the disease and increasing patient survival. The objective of this study was to establish the contribution of human papillomavirus (HPV), as well as p53 and p16 tumor markers, alongside associated factors (smoking and alcohol consumption), in the progression of malignancies located in the oropharynx and at the retromolar trigone–oropharyngeal junction. Materials and Methods: We performed a prospective study including 50 patients with malignant tumors of the oropharynx and retromolar trigone–oropharyngeal junction. In all patients, the presence and type of HPV were determined, as well as the status of the tumor markers p53 and p16. The associated risk factors, biopsy results, treatment method, and post-treatment evolution were all documented. Statistical analyses were performed to evaluate the correlations between the determining factors and their influence on the post-treatment evolution. An overall increased survival rate was found in HPV(+) patients. Results: Our study outlined the prevalence of different high-risk subtypes of HPV from the ones presented by other studies, suggesting a possible geographic variation. Correlations between the p53 and p16 statuses and patient survival could be established. The association of smoking and alcohol consumption strongly correlated with an unfavorable evolution. Conclusions: Awareness of the differences in the post-treatment evolution of the patients in relation to the presence of the factors determined in our study could change the future management of such cases for ensuring improved treatment outcomes.
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21
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Liu X, Liu P, Chernock RD, Kuhs KA, Lewis JS, Luo J, Gay HA, Thorstad WL, Wang X. A prognostic gene expression signature for oropharyngeal squamous cell carcinoma. EBioMedicine 2020; 61:102805. [PMID: 33038770 PMCID: PMC7648117 DOI: 10.1016/j.ebiom.2020.102805] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Robust prognostic stratification of patients with oropharyngeal squamous cell carcinoma (OPSCC) is important for developing individualized treatment plans. This study was conducted to develop and validate a clinically feasible prognostic classifier based on transcriptome-wide gene expression profiles. METHODS Tumor tissues were collected from 208 OPSCC patients treated at Washington University in St. Louis and 130 OPSCC patients treated at Vanderbilt University, used for model training and validation, respectively. OPSCC patients (n = 70) from the TCGA cohort were also included for independent validation. Based on RNA-seq profiling data, Cox proportional hazards regression analysis was performed to identify genes associated with disease outcomes. Then, Lasso-penalized multivariate survival models were constructed to identify biomarker genes for developing a prognostic gene signature. FINDINGS A 60-gene signature was identified by RNA-seq profiling analysis. Computed risk score of the gene signature was significantly predictive of 5-year overall survival of the training cohort (Hazard ratio (HR) 28·32, P = 4·3E-41). Subgroup analysis stratified by HPV status revealed that the signature was prognostic in HPV-positive OPSCC patients (HR 30·55, P = 7·0E-37) and was independent of clinical features. Importantly, the gene signature was validated in two independent patient cohorts, including the TCGA cohort (HR 3·94, P = 0·0018) and the Vanderbilt cohort (HR 8·50, P = 5·7E-09) for overall survival. INTERPRETATION The prognostic gene signature is a robust tool for risk stratification of OPSCC patients. The signature remains prognostic among HPV-positive OPSCC patients. FUNDING National Institutes of Health.
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Affiliation(s)
- Xinyi Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ping Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca D. Chernock
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Krystle A.Lang Kuhs
- Department of Otolaryngology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James S. Lewis
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jingqin Luo
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Hiram A. Gay
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Wade L. Thorstad
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.
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22
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Plath M, Gass J, Hlevnjak M, Li Q, Feng B, Hostench XP, Bieg M, Schroeder L, Holzinger D, Zapatka M, Freier K, Weichert W, Hess J, Zaoui K. Unraveling most abundant mutational signatures in head and neck cancer. Int J Cancer 2020; 148:115-127. [PMID: 32930393 DOI: 10.1002/ijc.33297] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022]
Abstract
Genomic alterations are a driving force in the multistep process of head and neck cancer (HNC) and result from the interaction of exogenous environmental exposures and endogenous cellular processes. Each of these processes leaves a characteristic pattern of mutations on the tumor genome providing the unique opportunity to decipher specific signatures of mutational processes operative during HNC pathogenesis and to address their prognostic value. Computational analysis of whole exome sequencing data of the HIPO-HNC (Heidelberg Center for Personalized Oncology-head and neck cancer) (n = 83) and TCGA-HNSC (The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma) (n = 506) cohorts revealed five common mutational signatures (Catalogue of Somatic Mutations in Cancer [COSMIC] Signatures 1, 2, 3, 13 and 16) and demonstrated their significant association with etiological risk factors (tobacco, alcohol and HPV16). Unsupervised hierarchical clustering identified four clusters (A, B, C1 and C2) of which Subcluster C2 was enriched for cases with a higher frequency of signature 16 mutations. Tumors of Subcluster C2 had significantly lower p16INK4A expression accompanied by homozygous CDKN2A deletion in almost one half of cases. Survival analysis revealed an unfavorable prognosis for patients with tumors characterized by a higher mutation burden attributed to signature 16 as well as cases in Subcluster C2. Finally, a LASSO-Cox regression model was applied to prioritize clinically relevant signatures and to establish a prognostic risk score for head and neck squamous cell carcinoma patients. In conclusion, our study provides a proof of concept that computational analysis of somatic mutational signatures is not only a powerful tool to decipher environmental and intrinsic processes in the pathogenesis of HNC, but could also pave the way to establish reliable prognostic patterns.
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Affiliation(s)
- Michaela Plath
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Johanna Gass
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Mario Hlevnjak
- Division Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Qiaoli Li
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Bohai Feng
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Xavier Pastor Hostench
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology, DKFZ-HIPO, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology, DKFZ-HIPO, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lea Schroeder
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dana Holzinger
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Zapatka
- Division Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kolja Freier
- Department of Oral and Cranio-Maxillofacial Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Jochen Hess
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karim Zaoui
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
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23
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Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffmann TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA. Analysis, identification and visualization of subgroups in genomics. Brief Bioinform 2020; 22:5909009. [PMID: 32954413 PMCID: PMC8138884 DOI: 10.1093/bib/bbaa217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact hans.kestler@uni-ulm.de, phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502
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Affiliation(s)
| | | | | | | | | | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Donna S Neuberg
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Verena Gaidzik
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Medical Center, Germany
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24
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Negroni C, Hilton DA, Ercolano E, Adams CL, Kurian KM, Baiz D, Hanemann CO. GATA-4, a potential novel therapeutic target for high-grade meningioma, regulates miR-497, a potential novel circulating biomarker for high-grade meningioma. EBioMedicine 2020; 59:102941. [PMID: 32810829 PMCID: PMC7452696 DOI: 10.1016/j.ebiom.2020.102941] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/06/2020] [Accepted: 07/22/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Meningiomas are the most common primary intracranial tumours. They are classified as grade I, II, and III based on their histopathological features. While most meningiomas can be managed by surgery alone, adjuvant treatment may be required in case of recurrent, or high-grade tumours. To date, chemotherapy has proven ineffective in meningioma patients, reinforcing the need for novel therapeutic targets and molecular biomarkers. METHODS Using meningioma tissues and in vitro models, we investigated microRNA levels in meningioma samples of different grades, as well as their regulation. Based on this, we also investigated candidate miRNAs expression in serum, and their potential as biomarkers. FINDINGS We found that miR-497~195 cluster expression in meningioma decreases with increasing malignancy grade, and that Cyclin D1 overexpression correlated with downregulation of the miR-497~195 cluster. GATA binding protein 4, a transcription factor upregulated in malignant meningioma, caused increased cell viability by controlling the expression of the miR-497~195 cluster, resulting in increased Cyclin D1 expression. Accordingly, GATA-4 inhibition via the small-molecule inhibitor NSC140905 restored miR-497~195 cluster expression, resulting in decreased viability, and Cyclin D1 downregulation. Analysis of the miR-497~195 cluster expression in serum exosomes derived from high-grade meningioma patients, revealed lower levels of miR-497 compared to those of benign origin. INTERPRETATION Our data suggest that GATA-4 could be a novel potential therapeutic target, and miR-497 could serve as a potential non-invasive biomarker for high-grade meningioma.
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Affiliation(s)
- Caterina Negroni
- University of Plymouth, Faculty of Medicine and Dentistry, The Institute of Translational and Stratified Medicine, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK
| | - David A Hilton
- Cellular and Anatomical Pathology, University Hospitals Plymouth NHS Trust, Derriford Road, Plymouth PL6 8DH, UK
| | - Emanuela Ercolano
- University of Plymouth, Faculty of Medicine and Dentistry, The Institute of Translational and Stratified Medicine, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK
| | - Claire L Adams
- University of Plymouth, Faculty of Medicine and Dentistry, The Institute of Translational and Stratified Medicine, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK
| | - Kathreena M Kurian
- Institute of Clinical Neuroscience, University of Bristol and Southmead Hospital - North Bristol Trust, Bristol BS8 1QU, UK
| | - Daniele Baiz
- University of Plymouth, Faculty of Medicine and Dentistry, The Institute of Translational and Stratified Medicine, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK
| | - C Oliver Hanemann
- University of Plymouth, Faculty of Medicine and Dentistry, The Institute of Translational and Stratified Medicine, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK.
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25
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DNA Methylation Changes in Human Papillomavirus-Driven Head and Neck Cancers. Cells 2020; 9:cells9061359. [PMID: 32486347 PMCID: PMC7348958 DOI: 10.3390/cells9061359] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption of DNA methylation patterns is one of the hallmarks of cancer. Similar to other cancer types, human papillomavirus (HPV)-driven head and neck cancer (HNC) also reveals alterations in its methylation profile. The intrinsic ability of HPV oncoproteins E6 and E7 to interfere with DNA methyltransferase activity contributes to these methylation changes. There are many genes that have been reported to be differentially methylated in HPV-driven HNC. Some of these genes are involved in major cellular pathways, indicating that DNA methylation, at least in certain instances, may contribute to the development and progression of HPV-driven HNC. Furthermore, the HPV genome itself becomes a target of the cellular DNA methylation machinery. Some of these methylation changes appearing in the viral long control region (LCR) may contribute to uncontrolled oncoprotein expression, leading to carcinogenesis. Consistent with these observations, demethylation therapy appears to have significant effects on HPV-driven HNC. This review article comprehensively summarizes DNA methylation changes and their diagnostic and therapeutic indications in HPV-driven HNC.
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26
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[Organ preservation in advanced laryngeal/hypopharyngeal carcinoma: lessons from the DeLOS-II trial]. HNO 2020; 68:648-656. [PMID: 32468135 DOI: 10.1007/s00106-020-00890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Patients with locoregionally advanced laryngeal and hypopharyngeal squamous cell carcinomas (LHSCC) comprise two broad groups: those who are candidates for functional larynx preservation (LP) with avoidance of ablative surgery and those who are not. Currently, treatment depends on the patient's needs and wishes, the experience and recommendation of the surgeon, the philosophy of the institution, etc. The milestone VA trial established non-surgical LP in advanced LHSCC in the 1990s using induction chemotherapy (IC) with PF (cisplatin, P, plus 5‑fluorouracil, F) followed by irradiation (IC + RT) as an appropriate alternative treatment to total laryngectomy (TL). Even though the findings of the VA trial were verified by the EORTC 24891 trial, a debate persists regarding the best protocol for balancing survival and laryngectomy-free survival (LFS) with acceptable late toxicity and good functional outcome. In advanced LHSCC without surgical options for larynx preservation, only IC + RT or primary concurrent platin-based chemoradiotherapy (CRT) are accepted treatment options aiming to preserve a functional larynx. In the US, cisplatin-based CRT is exclusively recommended as the best curative protocol. With regards to long-term survival with functional organ preservation and persistently high failure rates, there is current discussion on the necessity of improving patient selection based on the current literature and the recently published data of the DeLOS-II trial.
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27
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Shiah SG, Hsiao JR, Chang HJ, Hsu YM, Wu GH, Peng HY, Chou ST, Kuo CC, Chang JY. MiR-30a and miR-379 modulate retinoic acid pathway by targeting DNA methyltransferase 3B in oral cancer. J Biomed Sci 2020; 27:46. [PMID: 32238162 PMCID: PMC7114797 DOI: 10.1186/s12929-020-00644-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/26/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Epigenetic silencing of retinoic acid (RA) signaling-related genes have been linked with the pathogenesis and clinical outcome in oral squamous cell carcinoma (OSCC) carcinogenesis. However, the precise mechanisms underlying the abnormal silencing of RA signaling-related genes in OSCC have not been well investigated. METHODS Using combined analysis of genome-wide gene expression and methylation profile from 40 matched normal-tumor pairs of OSCC specimens, we found a set of retinoid signaling related genes are frequently hypermethylated and downregulated in OSCC patient samples, including alcohol dehydrogenase, iron containing 1 (ADHFE1) and aldehyde dehydrogenase 1 family, member A2 (ALDH1A2), which are the important rate-limiting enzymes in synthesis of RA. The expression of ADHFE1 and ALDH1A2 in OSCC patients was determine by quantitative real-time PCR (qRT-PCR) and immunohistochemistry. The binding sites of miR-30a and miR-379 with DNA methyltransferase 3B (DNMT3B) were predicted using a series of bioinformatic tools, and validated using dual luciferase assay and Western blot analyses. The functions of miR-30a, miR-379, and DNMT3B were accessed by growth and colony formation analyses using gain- and loss-of-function approaches. Chromatin immunoprecipitation (ChIP) was performed to explore the molecular mechanisms by arecoline and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) treatment. RESULTS We demonstrated that deregulated miR-30a and miR-379 could represent a mechanism for the silencing of ADHFE1 and ALDH1A2 in OSCC through targeting DNMT3B. Ectopic expression of miR-30a and miR-379 could induce re-expression of methylation-silenced ADHFE1 and ALDH1A2, and lead to growth inhibition in oral cancer cells. Furthermore, the dysregulation of the miRNAs and DNMT-3B may result from exposure to tobacco smoking and betel quid chewing. CONCLUSIONS Our results demonstrate that tobacco smoking and betel quid chewing could repress miR-30a and miR-379, which upregulate the DNMT3B expression, in turn, lead to the hypermethylation of ADHFE1 and ALDH1A genes, consequently, promote the oncogenic activity. These findings highlight the potential use of retinoids in combination with epigenetic modifiers for the prevention or treatment of oral cancer.
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Affiliation(s)
- Shine-Gwo Shiah
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program in Environmental and Occupational Medicine|, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jenn-Ren Hsiao
- Department of Otolaryngology, Head and Neck Collaborative Oncology Group, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsiao-Ju Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Yuan-Ming Hsu
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Guan-Hsun Wu
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Hsuan-Yu Peng
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Sung-Tau Chou
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Jang-Yang Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan.
- Division of Hematology and Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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28
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Nakagawa T, Matsusaka K, Misawa K, Ota S, Fukuyo M, Rahmutulla B, Kunii N, Sakurai D, Hanazawa T, Matsubara H, Okamoto Y, Kaneda A. Stratification of HPV-associated and HPV-negative oropharyngeal squamous cell carcinomas based on DNA methylation epigenotypes. Int J Cancer 2020; 146:2460-2474. [PMID: 31997344 DOI: 10.1002/ijc.32890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/25/2019] [Accepted: 01/15/2020] [Indexed: 12/20/2022]
Abstract
While the incidence of oropharyngeal squamous cell carcinoma (OPSCC) has been increasing in these two decades, primarily due to human papillomavirus (HPV), stratification of OPSCC into molecular subgroups showing different clinicopathological features has not been fully investigated. We performed DNA methylome analysis using Infinium 450k for 170 OPSCC cases, including 89 cases in our cohort and 81 cases reported by The Cancer Genome Atlas, together with targeted exon sequencing analysis. We stratified OPSCC by hierarchical clustering analysis using methylome data. Methylation levels of classifier markers were validated quantitatively using pyrosequencing, and area under the curve (AUC) values of receiver operating characteristics (ROC) curves were calculated. OPSCC was stratified into four epigenotypes: HPV(+) high-methylation (OP1), HPV(+) intermediate-methylation (OP2), HPV(-) intermediate-methylation (OP3) and HPV(-) low-methylation (OP4). Ten methylation marker genes were generated: five to classify HPV(+) cases into OP1 and OP2, and five to classify HPV(-) cases into OP3 and OP4. AUC values of ROC curves were 0.969 and 0.952 for the two marker panels, respectively. While significantly higher TP53 mutation and CCND1 copy number gains were observed in HPV(-) than in HPV(+) groups (p < 0.01), no significant difference of genomic aberrations was observed between OP1 and OP2, or OP3 and OP4. The four epigenotypes showed significantly different prognosis (p = 0.0006), distinguishing the most favorable OPSCC subgroup (OP1) among generally favorable HPV(+) cases, and the most unfavorable OPSCC subgroup (OP3) among generally unfavorable HPV(-) cases. HPV(+) and HPV(-) OPSCC are further divided into distinct DNA methylation epigenotypes, showing significantly different prognosis.
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Affiliation(s)
- Takuya Nakagawa
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Chiba University, Chiba, Japan.,Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan.,Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoshi Ota
- Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Naoki Kunii
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Chiba University, Chiba, Japan
| | - Daiju Sakurai
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Chiba University, Chiba, Japan
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Chiba University, Chiba, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshitaka Okamoto
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
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Devaraja K, Aggarwal S, Verma SS, Gupta SC. Clinico-pathological peculiarities of human papilloma virus driven head and neck squamous cell carcinoma: A comprehensive update. Life Sci 2020; 245:117383. [PMID: 32007572 DOI: 10.1016/j.lfs.2020.117383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/17/2020] [Accepted: 01/28/2020] [Indexed: 01/11/2023]
Abstract
AIMS The current article provides a detailed account of the current understanding of molecular and clinico-pathological aspects of Human papilloma virus (HPV) driven head and neck squamous cell carcinoma (HNSCC). MATERIALS AND METHODS The literature review included most of the landmark trials and clinical studies related to the HPV driven HNSCC. KEY FINDINGS HPV positive HNSCC differ distinctly from HPV negative tobacco-related HNSCC, especially in oropharyngeal region. Therefore, the American joint committee on cancer`s latest manual for classification and staging of cancer suggests a separate staging system for HPV positive oropharyngeal cancers. Despite the younger patients being affected and the high propensity for cervical metastasis, the HPV positive oropharyngeal cancers respond much better to the treatment. The association with wild type TP53 and low EGFR expression confers the favorable prognosis in HPV driven HNSCC. Since the association is not universal, we suggest checking for p53 and EGFR expression status before considering de-intensification of therapy. In addition, the presence of matted lymph nodes and five or more nodes could mean relatively poorer prognosis, and are not suitable for de-intensification of therapy. The same is also true probably with higher T stage and co-existing tobacco use. The methods for the detection of p16, HPV DNA, HPV E6/E7 mRNA, anti-E6/E7 antibodies, in tissue, in serum and in saliva of patients, along with their clinical implications are also discussed. SIGNIFICANCE This article provides latest developments on the HPV driven HNSCC. 'Diagnosis of transcriptionally active HPV infection,' 'Modalities for surveillance,' 'Implication of de-escalation of therapy' are some of the critical issues that could serve the medical, the research as well as the patient communities.
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Affiliation(s)
- K Devaraja
- Department of Otorhinolaryngology and Head and Neck surgery, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India.
| | - Sadhna Aggarwal
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sumit Singh Verma
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, 221 005, India
| | - Subash Chandra Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, 221 005, India.
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30
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Sun X, Chen D, Jin Z, Chen T, Lin A, Jin H, Zhu Y, Lai M. Genome-wide methylation and expression profiling identify methylation-associated genes in colorectal cancer. Epigenomics 2019; 12:19-36. [PMID: 31833403 DOI: 10.2217/epi-2019-0133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: To identify methylation-associated genes in the carcinogenesis of colorectal cancer (CRC). Materials & methods: Genome-wide patterns of DNA methylation and gene expression in CRC tissues and adjacent normal tissues were determined and further validated in The Cancer Genome Atlas data and Chinese CRC patients, respectively. Gene overexpression and knockdown cells were constructed to investigate their biological roles in CRC. Results: After validations, hypermethylation of eight genes were found to be correlated with their reduced transcription, and hypomethyaltion of three genes were associated with their upregulation. CADM3, CNRIP1, GRHL2, GRIA4, GSTM2 and NRXN1 were associated with the overall survival of CRC patients. CNRIP1 and GSTM2 were mainly responsible for the proliferation in CRC cells. Conclusion: A total of 11 genes may be promising biomarkers for CRC.
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Affiliation(s)
- Xiaohui Sun
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Diyu Chen
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, PR China
| | - Ziqi Jin
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Tianhui Chen
- Group of Molecular Epidemiology & Cancer Precision Prevention, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Aifen Lin
- Human Tissue Bank/Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, PR China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou 310020, PR China
| | - Yimin Zhu
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China.,Department of Respiratory Diseases, Sir Run Run Shaw Hospital Affiliated to School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310020, PR China
| | - Maode Lai
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PR China
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31
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Dietz A, Wiegand S, Kuhnt T, Wichmann G. Laryngeal Preservation Approaches: Considerations for New Selection Criteria Based on the DeLOS-II Trial. Front Oncol 2019; 9:625. [PMID: 31355142 PMCID: PMC6635549 DOI: 10.3389/fonc.2019.00625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/24/2019] [Indexed: 12/02/2022] Open
Abstract
In the locoregional advanced group of larynx and hypopharyngeal squamous cell carcinomas (LHSCC), there are two kinds of patients: those who are candidates for functional larynx organ preservation (LP) by avoiding ablative surgery and those who are not. Currently, the distinction between them is depending on the patient's needs and desires, the experience and recommendation of the surgeon, the philosophy of the institution and others. The milestone VA trial established non-surgical LP in advanced LHSCC utilizing induction-chemotherapy (IC) with PF (cisplatin, P plus 5-fluorouracil, F) followed by irradiation (IC+RT) as appropriate alternative treatment to total laryngectomy (TL) already in the 1990s. Even thou the VA trial's findings were verified by the EORTC 24891 trial we have an ongoing debate about the best protocol balancing survival and laryngectomy-free survival (LFS) with acceptable late toxicity and good functional outcome. In advanced LHSCC without surgical options preserving the larynx, only IC+RT and primary concurrent chemo-radiotherapy (CRT) are accepted treatment options aiming to preserve a functional larynx. In the US, cisplatin-based CRT is still recommended as best protocol to achieve cure of the disease and LP. But current views on long term survival with functional organ preservation and still high failure rates are addressing the need of better selection of patients which will be discussed as follows taking the current debate in literature and in particular the recently published data of the DeLOS-II trial in consideration.
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Affiliation(s)
- Andreas Dietz
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Susanne Wiegand
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Thomas Kuhnt
- Department of Radiation Oncology, University Hospital Leipzig, Leipzig, Germany
| | - Gunnar Wichmann
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany
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32
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Ma J, Li R, Wang J. Characterization of a prognostic four‑gene methylation signature associated with radiotherapy for head and neck squamous cell carcinoma. Mol Med Rep 2019; 20:622-632. [PMID: 31180552 PMCID: PMC6579992 DOI: 10.3892/mmr.2019.10294] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 03/15/2019] [Indexed: 12/29/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) remains one of the most common malignancies associated with poor prognosis. DNA methylation has emerged as an important mechanism underlying the radio-resistance of tumors. Prognostic biomarkers based on radiotherapy-related aberrant DNA methylation are limited. Methylation profiles of 388 patients with HNSCC were acquired from The Cancer Genome Atlas (TCGA) portal. Genes with differentially methylated CpG sites (DMGs) were screened between patients with a favorable and poor prognosis with or without radiotherapy. A weight gene co-methylation network was constructed using a Weighted Gene Co-expression Network Analysis (WGCNA) package. A lasso Cox-PH model was used to identify the optimal panel of genes with the ability to predict survival in these patients. Prognostic performance of the multi-gene methylation signature was assessed in a training set and confirmed in a validation set. A total of 976 DMGs were observed between favorable and poor prognostic samples. Four DMG-enriched co-methylation modules were identified. A four-gene methylation signature was determined by the lasso Cox-PH model that consisted of ZNF10, TMPRSS12, ERGIC2, and RNF215. The risk score based on the four-gene signature was able to divide the training or validation set into two risk groups with significantly different overall survival. Thus, the present study revealed a radiotherapy-related four-gene methylation signature to predict survival outcomes of patients with HNSCC, providing candidate therapeutic targets for novel therapy against HNSCC. However, substantial validation experiments are required.
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Affiliation(s)
- Jiabao Ma
- Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
| | - Rui Li
- Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
| | - Jie Wang
- Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
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33
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Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun 2019; 10:2188. [PMID: 31097695 PMCID: PMC6522544 DOI: 10.1038/s41467-019-09937-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 04/09/2019] [Indexed: 02/08/2023] Open
Abstract
Although promoter-associated CpG islands have been established as targets of DNA methylation changes in cancer, previous studies suggest that epigenetic dysregulation outside the promoter region may be more closely associated with transcriptional changes. Here we examine DNA methylation, chromatin marks, and transcriptional alterations to define the relationship between transcriptional modulation and spatial changes in chromatin structure. Using human papillomavirus-related oropharyngeal carcinoma as a model, we show aberrant enrichment of repressive H3K9me3 at the transcriptional start site (TSS) with methylation-associated, tumor-specific gene silencing. Further analysis identifies a hypermethylated subtype which shows a functional convergence on MYC targets and association with CREBBP/EP300 mutation. The tumor-specific shift to transcriptional repression associated with DNA methylation at TSSs was confirmed in multiple tumor types. Our data may show a common underlying epigenetic dysregulation in cancer associated with broad enrichment of repressive chromatin marks and aberrant DNA hypermethylation at TSSs in combination with MYC network activation. In tumours aberrant epigenetic modifications can alter the transcriptional state. Here, the authors identify a common tumour-specific shift to transcriptional repression associated with DNA methylation and chromatin dysregulation at the transcription start site.
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34
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Moinova HR, LaFramboise T, Lutterbaugh JD, Chandar AK, Dumot J, Faulx A, Brock W, De la Cruz Cabrera O, Guda K, Barnholtz-Sloan JS, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Thota PN, Willis JE, Chak A, Markowitz SD. Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett's esophagus. Sci Transl Med 2019; 10:10/424/eaao5848. [PMID: 29343623 DOI: 10.1126/scitranslmed.aao5848] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/08/2017] [Indexed: 12/17/2022]
Abstract
We report a biomarker-based non-endoscopic method for detecting Barrett's esophagus (BE) based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma. Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus. We tested CCNA1 DNA methylation as a BE biomarker in cytology brushings of the distal esophagus from 173 individuals with or without BE. CCNA1 DNA methylation demonstrated an area under the curve of 0.95 for discriminating BE-related metaplasia and neoplasia cases versus normal individuals, performing identically to methylation of VIM DNA, an established BE biomarker. When combined, the resulting two biomarker panel was 95% sensitive and 91% specific. These results were replicated in an independent validation cohort of 149 individuals who were assayed using the same cutoff values for test positivity established in the training population. To progress toward non-endoscopic esophageal screening, we engineered a well-tolerated, swallowable, encapsulated balloon device able to selectively sample the distal esophagus within 5 min. In balloon samples from 86 individuals, tests of CCNA1 plus VIM DNA methylation detected BE metaplasia with 90.3% sensitivity and 91.7% specificity. Combining the balloon sampling device with molecular assays of CCNA1 plus VIM DNA methylation enables an efficient, well-tolerated, sensitive, and specific method of screening at-risk populations for BE.
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Affiliation(s)
- Helen R Moinova
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Thomas LaFramboise
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - James D Lutterbaugh
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Apoorva Krishna Chandar
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - John Dumot
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Ashley Faulx
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Wendy Brock
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | | | - Kishore Guda
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Prasad G Iyer
- Barrett's Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcia I Canto
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Jean S Wang
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas J Shaheen
- Center for Esophageal Diseases and Swallowing, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Prashanti N Thota
- Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Joseph E Willis
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA. .,Department of Pathology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Amitabh Chak
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Sanford D Markowitz
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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35
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Weigel C, Chaisaingmongkol J, Assenov Y, Kuhmann C, Winkler V, Santi I, Bogatyrova O, Kaucher S, Bermejo JL, Leung SY, Chan TL, Lasitschka F, Bohrer MH, Marx A, Haußen RHV, Herold-Mende C, Dyckhoff G, Boukamp P, Delank KW, Hörmann K, Lippert BM, Baier G, Dietz A, Oakes CC, Plass C, Becher H, Schmezer P, Ramroth H, Popanda O. DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer. Clin Epigenetics 2019; 11:67. [PMID: 31053176 PMCID: PMC6499986 DOI: 10.1186/s13148-019-0666-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/15/2019] [Indexed: 12/23/2022] Open
Abstract
Background Genetic aberrations in DNA repair genes are linked to cancer, but less is reported about epigenetic regulation of DNA repair and functional consequences. We investigated the intragenic methylation loss at the three prime repair exonuclease 2 (TREX2) locus in laryngeal (n = 256) and colorectal cancer cases (n = 95) and in pan-cancer data from The Cancer Genome Atlas (TCGA). Results Significant methylation loss at an intragenic site of TREX2 was a frequent trait in both patient cohorts (p = 0.016 and < 0.001, respectively) and in 15 out of 22 TCGA studies. Methylation loss correlated with immunohistochemically staining for TREX2 (p < 0.0001) in laryngeal tumors and improved overall survival of laryngeal cancer patients (p = 0.045). Chromatin immunoprecipitation, demethylation experiments, and reporter gene assays revealed that the region of methylation loss can function as a CCAAT/enhancer binding protein alpha (CEBPA)-responsive enhancer element regulating TREX2 expression. Conclusions The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. Altered TREX2 protein levels in tumors may affect drug-induced DNA damage repair and provide new tailored therapies. Electronic supplementary material The online version of this article (10.1186/s13148-019-0666-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christoph Weigel
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Present Address: Division of Hematology Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Christine Kuhmann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Volker Winkler
- Institute of Public Health, University of Heidelberg, Heidelberg, Germany
| | - Irene Santi
- Institute of Public Health, University of Heidelberg, Heidelberg, Germany
| | - Olga Bogatyrova
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Simone Kaucher
- Institute of Public Health, University of Heidelberg, Heidelberg, Germany
| | - Justo L Bermejo
- Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Suet Y Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Tsun L Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China.,Department of Pathology, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong, China
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Alexander Marx
- Institute of Pathology, University Medical Centre Mannheim, Mannheim, Germany
| | | | - Christel Herold-Mende
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Heidelberg, Heidelberg, Germany.,Division of Neurosurgical Research, Neurosurgery, University of Heidelberg, Heidelberg, Germany
| | - Gerhard Dyckhoff
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Heidelberg, Heidelberg, Germany
| | - Petra Boukamp
- Division of Genetics of Skin Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute for Environmental Medicine, IUF, Düsseldorf, Germany
| | - Klaus W Delank
- Medical Hospital, Head and Neck Surgery, Ludwigshafen, Germany
| | - Karl Hörmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital of Mannheim, Mannheim, Germany
| | - Burkhard M Lippert
- Department of Otorhinolaryngology, Head and Neck Surgery, Heilbronn, Germany
| | - Gerald Baier
- Department of Otorhinolaryngology, Head and Neck Surgery, Academic Teaching Hospital, Darmstadt, Germany
| | - Andreas Dietz
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Leipzig, Leipzig, Germany
| | - Christopher C Oakes
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Present Address: Division of Hematology Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Heiko Becher
- Institute of Public Health, University of Heidelberg, Heidelberg, Germany.,Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Heribert Ramroth
- Institute of Public Health, University of Heidelberg, Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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36
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Liyanage C, Wathupola A, Muraleetharan S, Perera K, Punyadeera C, Udagama P. Promoter Hypermethylation of Tumor-Suppressor Genes p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 in Salivary DNA as a Quadruple Biomarker Panel for Early Detection of Oral and Oropharyngeal Cancers. Biomolecules 2019; 9:biom9040148. [PMID: 31013839 PMCID: PMC6523930 DOI: 10.3390/biom9040148] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 01/01/2023] Open
Abstract
Silencing of tumor-suppressor genes (TSGs) by DNA promoter hypermethylation is an early event in carcinogenesis; hence, TSGs may serve as early tumor biomarkers. We determined the promoter methylation levels of p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 TSGs in salivary DNA from oral cancer (OC) and oropharyngeal cancer (OPC) patients, using methylation-specific PCR coupled with densitometry analysis. We assessed the association between DNA methylation of individual TSGs with OC and OPC risk factors. The performance and the clinical validity of this quadruple-methylation marker panel were evaluated in discriminating OC and OPC patients from healthy controls using the CombiROC web tool. Our study reports that RASSF1A, TIMP3, and PCQAP/MED15 TSGs were significantly hypermethylated in OC and OPC cases compared to healthy controls. DNA methylation levels of TSGs were significantly augmented by smoking, alcohol use, and betel quid chewing, indicating the fact that frequent exposure to risk factors may drive oral and oropharyngeal carcinogenesis through TSG promoter hypermethylation. Also, this quadruple-methylation marker panel of p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 TSGs demonstrated excellent diagnostic accuracy in the early detection of OC at 91.7% sensitivity and 92.3% specificity and of OPC at 99.8% sensitivity and 92.1% specificity from healthy controls.
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Affiliation(s)
- Chamikara Liyanage
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Asanga Wathupola
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Sanjayan Muraleetharan
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Kanthi Perera
- National Cancer Institute of Sri Lanka, Maharagama, 10280, Sri Lanka.
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, 37 Kent Street, Woolloongabba, Brisbane, QLD 4102, Australia.
| | - Preethi Udagama
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
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Prakash R, Izraely S, Thareja NS, Lee RH, Rappaport M, Kawaguchi R, Sagi-Assif O, Ben-Menachem S, Meshel T, Machnicki M, Ohe S, Hoon DS, Coppola G, Witz IP, Carmichael ST. Regeneration Enhances Metastasis: A Novel Role for Neurovascular Signaling in Promoting Melanoma Brain Metastasis. Front Neurosci 2019; 13:297. [PMID: 31024232 PMCID: PMC6465799 DOI: 10.3389/fnins.2019.00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/15/2019] [Indexed: 12/12/2022] Open
Abstract
Neural repair after stroke involves initiation of a cellular proliferative program in the form of angiogenesis, neurogenesis, and molecular growth signals in the surrounding tissue elements. This cellular environment constitutes a niche in which regeneration of new blood vessels and new neurons leads to partial tissue repair after stroke. Cancer metastasis has similar proliferative cellular events in the brain and other organs. Do cancer and CNS tissue repair share similar cellular processes? In this study, we identify a novel role of the regenerative neurovascular niche induced by stroke in promoting brain melanoma metastasis through enhancing cellular interactions with surrounding niche components. Repair-mediated neurovascular signaling induces metastatic cells to express genes crucial to metastasis. Mimicking stroke-like conditions in vitro displays an enhancement of metastatic migration potential and allows for the determination of cell-specific signals produced by the regenerative neurovascular niche. Comparative analysis of both in vitro and in vivo expression profiles reveals a major contribution of endothelial cells in mediating melanoma metastasis. These results point to a previously undiscovered role of the regenerative neurovascular niche in shaping the tumor microenvironment and brain metastatic landscape.
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Affiliation(s)
- Roshini Prakash
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sivan Izraely
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nikita S Thareja
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Rex H Lee
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maya Rappaport
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Riki Kawaguchi
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, United States
| | - Orit Sagi-Assif
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shlomit Ben-Menachem
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tsipi Meshel
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Machnicki
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Shuichi Ohe
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, United States
| | - Dave S Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, United States
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, United States
| | - Isaac P Witz
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - S Thomas Carmichael
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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Huebbers CU, Verhees F, Poluschkin L, Olthof NC, Kolligs J, Siefer OG, Henfling M, Ramaekers FCS, Preuss SF, Beutner D, Seehawer J, Drebber U, Korkmaz Y, Lam WL, Vucic EA, Kremer B, Klussmann JP, Speel EJM. Upregulation of AKR1C1 and AKR1C3 expression in OPSCC with integrated HPV16 and HPV-negative tumors is an indicator of poor prognosis. Int J Cancer 2019; 144:2465-2477. [PMID: 30367463 DOI: 10.1002/ijc.31954] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 09/14/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022]
Abstract
Different studies have shown that HPV16-positive OPSCC can be subdivided based on integration status (integrated, episomal and mixed forms). Because we showed that integration neither affects the levels of viral genes, nor those of virally disrupted human genes, a genome-wide screen was performed to identify human genes which expression is influenced by viral integration and have clinical relevance. Thirty-three fresh-frozen HPV-16 positive OPSCC samples with known integration status were analyzed by mRNA expression profiling. Among the genes of interest, Aldo-keto-reductases 1C1 and 1C3 (AKR1C1, AKR1C3) were upregulated in tumors with viral integration. Additionally, 141 OPSCC, including 48 HPV-positive cases, were used to validate protein expression by immunohistochemistry. Results were correlated with clinical and histopathological data. Non-hierarchical clustering resulted in two main groups differing in mRNA expression patterns, which interestingly corresponded with viral integration status. In OPSCC with integrated viral DNA, often metabolic pathways were deregulated with frequent upregulation of AKR1C1 and AKR1C3 transcripts. Survival analysis of 141 additionally immunostained OPSCC showed unfavorable survival rates for tumors with upregulation of AKR1C1 or AKR1C3 (both p <0.0001), both in HPV-positive (p ≤0.001) and -negative (p ≤0.017) tumors. OPSCC with integrated HPV16 show upregulation of AKR1C1 and AKR1C3 expression, which strongly correlates with poor survival rates. Also in HPV-negative tumors, upregulation of these proteins correlates with unfavorable outcome. Deregulated AKR1C expression has also been observed in other tumors, making these genes promising candidates to indicate prognosis. In addition, the availability of inhibitors of these gene products may be utilized for drug treatment.
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Affiliation(s)
- Christian U Huebbers
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
| | - Femke Verhees
- Department of Otorhinolaryngology and Head and Neck Surgery, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Leonard Poluschkin
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
| | - Nadine C Olthof
- Department of Otorhinolaryngology and Head and Neck Surgery, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands.,Department of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Jutta Kolligs
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
| | - Oliver G Siefer
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
| | - Mieke Henfling
- Department of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Frans C S Ramaekers
- Department of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Simon F Preuss
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital of Cologne, Cologne, Germany
| | - Dirk Beutner
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Göttingen, Germany
| | - Julia Seehawer
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital of Cologne, Cologne, Germany
| | - Uta Drebber
- Institute for Pathology, University Hospital of Cologne, Cologne, Germany
| | - Yüksel Korkmaz
- Institute for Experimental Dental Research and Oral Musculoskeletal Biology, University Hospital of Cologne, Cologne, Germany.,Department I of Anatomy, University Hospital of Cologne, Cologne, Germany.,Center for Biochemistry, University Hospital of Cologne, Cologne, Germany
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Emily A Vucic
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Bernd Kremer
- Department of Otorhinolaryngology and Head and Neck Surgery, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Jens P Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital of Cologne, Cologne, Germany
| | - Ernst-Jan M Speel
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
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Ding W, Chen G, Shi T. Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis. Epigenetics 2019; 14:67-80. [PMID: 30696380 DOI: 10.1080/15592294.2019.1568178] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC > 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC > 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC > 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (p-value < 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.
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Affiliation(s)
- Wubin Ding
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China
| | - Geng Chen
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China
| | - Tieliu Shi
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China.,b National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy , Guangxi Medical University , Nanning , China
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40
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Kanazawa T, Misawa K, Shinmura K, Misawa Y, Kusaka G, Maruta M, Sasaki T, Watanabe Y, Carey TE. Promoter methylation of galanin receptors as epigenetic biomarkers for head and neck squamous cell carcinomas. Expert Rev Mol Diagn 2019; 19:137-148. [PMID: 30640567 DOI: 10.1080/14737159.2019.1567334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION While remarkable progress has been made in standard treatments for head and neck squamous cell carcinomas (HNSCCs), the long-term survival remains at an unsatisfactory 40-50%. To improve the survival rate, biomarkers for optimal treatment selection and prognostic prediction, as well as novel, low-toxicity treatment strategies, are required. Galanin receptor (GALR) 1 and GALR2 are well-studied tumor suppressors in HNSCCs. Compared with other clinicopathological factors, the epigenetic variants of GALRs have been found to be the most powerful markers to predict the prognosis of HNSCC patients. Areas covered: This review outlines the functions and signaling pathways of GALRs and explains the potential of GALR promoter methylation as a biomarker for HNSCC prognosis. We also summarize recent developments in promoter methylation studies in HNSCC and indicate future directions for GALR promoter methylation studies. Expert commentary: GALR studies have highlighted two major aspects with implications in HNSCC - that G-protein coupled receptors (GPCRs) act as tumor suppressor genes and that GALR promoter methylation is significantly related to the carcinogenesis of HNSCC. The findings of GALR studies can be applied to studies on other GPCRs and further in-depth DNA methylation studies. Deeper insights into GPCR epigenetics are expected to markedly improve HNSCC treatment.
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Affiliation(s)
- Takeharu Kanazawa
- a Department of Otolaryngology-Head and Neck Surgery , International University of Health and Welfare , Tokyo , Japan.,b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Kiyoshi Misawa
- c Department of Otolaryngology/Head and Neck Surgery , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Kazuya Shinmura
- d Department of Tumor Pathology , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Yuki Misawa
- c Department of Otolaryngology/Head and Neck Surgery , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Gen Kusaka
- e Department of Neurosurgery , Jichi Medical University Saitama Medical Center , Saitama , Saitama , Japan
| | - Mikiko Maruta
- b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Toru Sasaki
- b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Yusuke Watanabe
- a Department of Otolaryngology-Head and Neck Surgery , International University of Health and Welfare , Tokyo , Japan
| | - Thomas E Carey
- f Laboratory of Head and Neck Center Biology, Department of Otolaryngology, Head and Neck Surgery , The University of Michigan , Ann Arbor , MI , USA
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Abstract
Since their discovery as the etiologic agents of cervical cancer in the mid-1970s, human papillomaviruses (HPVs) have been linked with a growing number of epithelial-derived tumors, including head and neck squamous cell carcinomas. HPV demonstrates a particular predilection for causing tumors of the oropharynx, with the majority of cases involving infection with high-oncogenic risk HPV-16. People living with HIV are at increased risk of infection with HPV- and HPV-related oral complications even with adequate control of their HIV infection with antiretroviral therapy. In this chapter, we discuss the molecular mechanisms that underlie HPV-mediated oncogenesis in the oropharynx. We also describe the progress that has been made in understanding the epidemiology of oral HPV infection and the determinants of oral HPV-related pathology. Finally, we examine what can be done to treat and prevent oral HPV infection, benign lesions, and cancer, particularly in the context of the HIV-positive patient.
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Horn D, Gross M, Dyckhoff G, Fuchs J, Grabe N, Weichert W, Herpel E, Herold‐Mende C, Lichter P, Hoffmann J, Hess J, Freier K. Cortactin expression: Association with disease progression and survival in oral squamous cell carcinoma. Head Neck 2018; 40:2685-2694. [DOI: 10.1002/hed.25515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/21/2018] [Accepted: 10/06/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Dominik Horn
- Department of Oral and Cranio‐Maxillofacial SurgeryUniversity Hospital Heidelberg Heidelberg Germany
| | - Madeleine Gross
- Department of Oral and Cranio‐Maxillofacial SurgeryUniversity Hospital Heidelberg Heidelberg Germany
- Division of Molecular GeneticsGerman Cancer Research Center (DKFZ) Heidelberg Germany
| | - Gerhard Dyckhoff
- Department of Otorhinolaryngology, Head and Neck SurgeryUniversity Hospital Heidelberg Heidelberg Germany
- Molecular Cell Biology Group, Department of Otorhinolaryngology, Head and Neck SurgeryUniversity Hospital Heidelberg Heidelberg Germany
| | - Jennifer Fuchs
- Department of Oral and Cranio‐Maxillofacial SurgeryUniversity Hospital Heidelberg Heidelberg Germany
| | - Niels Grabe
- Hamamatsu Tissue Imaging and Analysis Center (TIGA)BIOQUANT, University of Heidelberg Heidelberg Germany
| | - Wilko Weichert
- Institute of PathologyUniversity Hospital Heidelberg Heidelberg Germany
| | - Esther Herpel
- Institute of PathologyUniversity Hospital Heidelberg Heidelberg Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg Germany
| | - Christel Herold‐Mende
- Molecular Cell Biology Group, Department of Otorhinolaryngology, Head and Neck SurgeryUniversity Hospital Heidelberg Heidelberg Germany
| | - Peter Lichter
- Division of Molecular GeneticsGerman Cancer Research Center (DKFZ) Heidelberg Germany
| | - Jürgen Hoffmann
- Department of Oral and Cranio‐Maxillofacial SurgeryUniversity Hospital Heidelberg Heidelberg Germany
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck SurgeryUniversity Hospital Heidelberg Heidelberg Germany
- Research Group Molecular Mechanisms of Head and Neck TumorsGerman Cancer Research Center (DKFZ) Heidelberg Germany
| | - Kolja Freier
- Department of Oral and Cranio‐Maxillofacial SurgeryUniversity Hospital Heidelberg Heidelberg Germany
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43
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Abstract
Rising incidence rates in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) and a significantly improved prognosis have brought this entity into scientific focus. At this year's American Society of Clinical Oncology (ASCO) Annual Meeting, 291 studies with the keyword "HPV" were presented, the majority of which were in head and neck cancer. Due to high rates of late toxicities after conventional therapy, de-intensified treatment concepts are being increasingly discussed, although data from prospective phase III studies were not presented. Retrospective data on the latest TNM staging (downstaging in many HPV-associated patients) and other risk stratification systems were presented. HPV diagnostics based solely on p16 immunohistochemistry were discussed. Many groups presented work on the HPV association and its prognostic relevance not only in oropharyngeal carcinoma, but also in oral cavity, hypopharyngeal, and locally advanced laryngeal squamous cell carcinoma. New prognostic biomarkers such as methylation signatures appear to be promising. New data suggest equal survival rates in HPV-associated stage I OPSCC treated with surgery alone in comparison to patients who received adjuvant therapy after surgery. A possible negative effect on overall survival in stage III HPV-associated OPSCC with a cisplatin dose ≤200 mg/m2 was discussed. Results of de-escalation studies are urgently awaited, in order to be able to treat HPV-associated OPSCC patients as precisely and as specifically as possible and ensure long-term quality of life.
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de Carvalho AC, Melendez ME, da Silva Sabato C, Palmero EI, Arantes LMRB, Neto CS, Carvalho AL. Clinical and Molecular Characterization of Surgically Treated Oropharynx Squamous Cell Carcinoma Samples. Pathol Oncol Res 2018; 25:1047-1058. [PMID: 30099696 DOI: 10.1007/s12253-018-0462-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
Abstract
A better understanding of the clinical and molecular features of oropharyngeal squamous cell carcinomas (OPSCC) may help in the development of strategies for a better patient management, improving survival rates. This retrospective study conducted a clinical and molecular characterization of surgically treated OPSCC samples. Paraffin-embedded samples from a series of cases were screened for high-risk (HR) human papillomavirus (HPV) infection, methylation of a 5-gene panel, p53 expression, and TP53 mutation. The study was conducted at Barretos Cancer Hospital. Twenty-five surgically treated OPSCC with available tissue were included in the study. Samples were classified according to HPV status and molecular features and some of these characteristics were associated to clinical data. Twenty percent of the cases were HR-HPV positive and 62.5% presented TP53 mutations. DAPK hypermethylation was associated with HPV status (p = 0.023), while methylated CCNA1 was inversely related to TP53 mutations in primary tumors (p = 0.042) and associated with a better disease-free survival (22.3% vs. 100.0%; p = 0.028) and overall survival (8.0% vs. 100.0%; p = 0.012). The results show differences regarding molecular and clinical characteristics in the oropharynx cases identified that should be validated in more cases to confirm whether these differences are able to classify patients according to outcome and help in a more thorough patient management.
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Affiliation(s)
- Ana Carolina de Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil.
| | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil
| | | | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil
- Center of Molecular Diagnosis, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil
| | | | - Cristovam Scapulatempo Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil
- Department of Pathology, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil
- Department of Head and Neck Surgery, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil
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Perez-Campos Mayoral E, Mayoral-Andrade G, Pérez-Campos Mayoral L, Canseco SP, Cruz RM, Hernández-Huerta MT, Rodriguez AM, Cabrera-Fuentes HA, Pérez-Campos E. Diagnosis of Transient/Latent HPV Infections - A Point of View! Arch Med Res 2018. [DOI: 10.1016/j.arcmed.2018.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Li K, Zeng L, Wei H, Hu J, Jiao L, Zhang J, Xiong Y. Identification of gene-specific DNA methylation signature for Colorectal Cancer. Cancer Genet 2018; 228-229:5-11. [PMID: 30553473 DOI: 10.1016/j.cancergen.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/22/2018] [Accepted: 05/08/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND Colorectal Cancer (CC), a common disease causing approximately million deaths annually, has been the third most frequent type of malignancy. We aimed to identify gene-specific DNA methylation signature to function as prognostic and predictive markers for CC patient survival. METHODS Expression profiles of gene-specific DNA methylation and the corresponding clinical information of 201 CC patients were downloaded from The Cancer Genome Atlas (TCGA) dataset and differentially expressed gene-specific DNA methylation was identified after tumor subtype classification. A risk score model was further built by analyzing the expression data of these gene-specific DNA methylations from the training dataset of CC patients. RESULTS Totally, 214 gene-specific DNA methylations were found to be expressed significantly between different subtypes of CC, including 150 up-regulated and 64 down-regulated ones. Up-regulated gene-specific DNA methylation accounted for 70.1% and the down-regulated gene-specific DNA methylation accounted for 29.9%. Hereinto, six gene-specific DNA methylations were obtained, including methy_vimentin and methy_ TFPI2, which were found significantly correlated with overall survival status of patients with CC. CONCLUSIONS With the six gene-specific DNA methylation signatures, patients in the training set were divided into low-risk and high- risk groups. What's more, gene-specific DNA methylation target genes were highly associated with protein phosphorylation, which indicated that further research on phosphorylation of target gene-coding protein might provide new sight on the treatment of CC.
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Affiliation(s)
- Kaixue Li
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Li Zeng
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Hong Wei
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Jingjing Hu
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Lu Jiao
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Juan Zhang
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Ying Xiong
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.
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47
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Wichmann G, Lehmann C, Herchenhahn C, Kolb M, Hofer M, Wiegand S, Dietz A. Development of a Human Leukocyte Antigen Score to Predict Progression-Free Survival in Head and Neck Squamous Cell Carcinoma Patients. Front Oncol 2018; 8:168. [PMID: 29868484 PMCID: PMC5966661 DOI: 10.3389/fonc.2018.00168] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/01/2018] [Indexed: 01/09/2023] Open
Abstract
Background In personalized medicine and treatment stratification of head and neck squamous cell carcinoma (HNSCC), the heterogeneous genetic background of patients is not considered. Human leukocyte antigen (HLA) alleles and HLA haplotypes (HLA traits) are linked to development of HNSCC and affect progression-free survival (PFS) of HNSCC patients but most head and neck oncologists are not familiar with HLA typing. Hence, we developed an HLA-score abstracting from complexity of HLA-typing results to facilitate potential use of HLA-associated hazard ratios (HR) for prognostic stratification. Methods The HR for PFS of 8 HLA traits shown to be independent predictors (Pi) of PFS in a test cohort (TC) of 90 HNSCC patients were used to build the HLA-score based on the natural logarithm (ln) of the Pi-associated HR. Crude ln-transformed HR of the eight Pi, alleles B*13 (2), B*35 (1), B*51 (2), DQB1*06 (1), homozygous Cw (1), homozygous DRB4 (2), and haplotypes A*01/B*08 (−6) and B*08/C*07 (4), were summed up to yield the individual patient’s HLA-score. Receiver operating characteristic (ROC) and Kaplan–Meier curves were used to proof the suitability of the HLA-score as prognostic marker for PFS. An independent validation cohort (iVC) of 32 patients treated in the larynx-organ preservation trial DeLOS-II was utilized for validation. Results The individual HLA-scores (range −2 to 6) in TC classified HNSCC patients regarding PFS. ROC analysis (area under the curve = 0.750, 95% CI 0.665–0.836; P = 0.0000034) demonstrated an optimum cutoff for the HLA-score at 0.5 (97.9% sensitivity, 34.7% specificity), and 70/90 patients in TC with HLA-score > 0 had significant reduced PFS (P = 0.001). Applying the same classifier (HLA-score > 0) confirmed these findings in the iVC revealing reduced PFS of 25/32 patients (P = 0.040). Conclusion HLA traits constitute critical Pi. Considering the HLA-score may potentially facilitate the use of genetic information from HLA typing for prognostic stratification, e.g., within clinical trials.
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Affiliation(s)
- Gunnar Wichmann
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany.,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Claudia Lehmann
- Institute for Transfusion Medicine, University Hospital Leipzig, Leipzig, Germany
| | - Cindy Herchenhahn
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany.,Clinic for Anesthesiology and Intensive Care, University Hospital Leipzig, Leipzig, Germany
| | - Marlen Kolb
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Mathias Hofer
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Susanne Wiegand
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Andreas Dietz
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Hospital Leipzig, Leipzig, Germany.,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
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48
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Ma X, Sheng S, Wu J, Jiang Y, Gao X, Cen X, Wu J, Wang S, Tang Y, Tang Y, Liang X. LncRNAs as an intermediate in HPV16 promoting myeloid-derived suppressor cell recruitment of head and neck squamous cell carcinoma. Oncotarget 2018; 8:42061-42075. [PMID: 28159935 PMCID: PMC5522049 DOI: 10.18632/oncotarget.14939] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/27/2016] [Indexed: 02/05/2023] Open
Abstract
The emerging evidence showed that long noncoding RNAs (lncRNAs) are involved in cell growth and apoptosis as well as cancer progression and metastasis of malignant tumor, however, limited data are available on the role of lncRNAs in human papillomavirus (HPV)-associated Head and neck squamous cell carcinomas (HNSCC). Here, we demonstrated that 23.98% of 196 HNSCC cases in Southwest China could be classified as HPV16 infection. The number of MDSCs in HPV-positive HNSCC was significantly higher than normal control, indicating that HPV infection may promote MDSCs aggregation. Then, we applied an array-based approach to monitor the lncRNA expression between HPV-positive HNSCC, HPV-negative HNSCC and normal oral mucous, and obtained 132 different lncRNAs in different HPV infected states of HNSCC. HOTAIR, PROM1, CCAT1, and MUC19 mRNA levels, determined by qRT-PCR were inversely correlated with MDSCs collection of HPV-associated HNSCC in 2 independent patient cohorts. The results may provide a rationale for the further evaluation of lncRNAs as a molecular target to elucidate the molecular mechanism of HPV promoting MDSCs collection of HNSCC.
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Affiliation(s)
- Xiangrui Ma
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Binzhou Medical College, Binzhou, Shandong 256600, China
| | - Surui Sheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China
| | - Jingbiao Wu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China
| | - Yaping Jiang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China.,Department of Implant, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Xiaolei Gao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China
| | - Xiao Cen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China
| | - Jiashun Wu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China
| | - Shasha Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China
| | - Yajie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Yaling Tang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China.,Department of Oral Pathology, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China
| | - Xinhua Liang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China.,Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology (Sichuan University), Chengdu, Sichuan 610041, China
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49
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Wittekindt C, Wagner S, Sharma SJ, Würdemann N, Knuth J, Reder H, Klußmann JP. [HPV - A different view on Head and Neck Cancer]. Laryngorhinootologie 2018; 97:S48-S113. [PMID: 29905354 PMCID: PMC6540966 DOI: 10.1055/s-0043-121596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Head and neck cancer is the sixth most common cancer with over 500000 annually reported incident cases worldwide. Besides major risk factors tobacco and alcohol, oropharyngeal squamous cell carcinomas (OSCC) show increased association with human papillomavirus (HPV). HPV-associated and HPV-negative OSCC are 2 different entities regarding biological characteristics, therapeutic response, and patient prognosis. In HPV OSCC, viral oncoprotein activity, as well as genetic (mutations and chromosomal aberrations) and epigenetic alterations plays a key role during carcinogenesis. Based on improved treatment response, the introduction of therapy de-intensification and targeted therapy is discussed for patients with HPV OSCC. A promising targeted therapy concept is immunotherapy. The use of checkpoint inhibitors (e.g. anti-PD1) is currently investigated. By means of liquid biopsies, biomarkers such as viral DNA or tumor mutations in the will soon be available for disease monitoring, as well as detection of treatment failure. By now, primary prophylaxis of HPV OSCC can be achieved by vaccination of girls and boys.
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Affiliation(s)
- Claus Wittekindt
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Steffen Wagner
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Shachi Jenny Sharma
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Nora Würdemann
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Jennifer Knuth
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Henrike Reder
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Jens Peter Klußmann
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
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50
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Boda D, Docea AO, Calina D, Ilie MA, Caruntu C, Zurac S, Neagu M, Constantin C, Branisteanu DE, Voiculescu V, Mamoulakis C, Tzanakakis G, Spandidos DA, Drakoulis N, Tsatsakis AM. Human papilloma virus: Apprehending the link with carcinogenesis and unveiling new research avenues (Review). Int J Oncol 2018; 52:637-655. [PMID: 29393378 PMCID: PMC5807043 DOI: 10.3892/ijo.2018.4256] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/28/2017] [Indexed: 12/17/2022] Open
Abstract
Human papilloma viruses (HPV) are a small group of non‑enveloped viruses belonging to the Papillomaviridae family with strong similarities to polyoma viruses. The viral particles consist of a genome in the form of a circular double‑stranded DNA, encompassing eight open reading frames, as well as a non‑enveloped icosahedral capsid. HPV infection is considered the most common sexually transmitted disease in both sexes and is strongly implicated in the pathogenesis of different types of cancer. 'High‑risk' mucosal HPV types, predominantly types 16, 18, 31, 33 and 35, are associated with most cervical, penile, vulvar, vaginal, anal, oropharyngeal cancers and pre‑cancers. Screening for HPV is necessary for the prognosis and for determining treatment strategies for cancer. Novel HPV markers, including proteomic and genomic markers, as well as anti‑papillomavirus vaccines are currently available. The aim of this comprehensive review was to thoroughly present the updated information on virus development, cancer occurrence, treatment and prevention strategies, in an attempt to shed further light into the field, including novel research avenues.
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Affiliation(s)
- Daniel Boda
- Dermatology Research Laboratory, ‘Carol Davila’ University of Medicine and Pharmacy, 030167 Bucharest
- Department of Dermatology, ‘Prof. N. Paulescu’ National Institute of Diabetes, Nutrition and Metabolic Diseases, 011233 Bucharest
| | | | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova
| | - Mihaela Adriana Ilie
- Dermatology Research Laboratory, ‘Carol Davila’ University of Medicine and Pharmacy, 030167 Bucharest
- Department of Biochemistry
| | - Constantin Caruntu
- Dermatology Research Laboratory, ‘Carol Davila’ University of Medicine and Pharmacy, 030167 Bucharest
- Department of Dermatology, ‘Prof. N. Paulescu’ National Institute of Diabetes, Nutrition and Metabolic Diseases, 011233 Bucharest
- Department of Physiology
| | - Sabina Zurac
- Department of Pathology, ‘Carol Davila’ University of Medicine and Pharmacy, 030167 Bucharest
- Colentina University Hospital, Sector 2 19-21, Bucharest
| | - Monica Neagu
- ‘Victor Babes’ National Institute of Pathology, 050096 Bucharest
| | | | | | - Vlad Voiculescu
- Department of Dermatology and Allergology, Elias Emergency University Hospital, 011461 Bucharest, Romania
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete Medical School
| | | | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Crete
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens
| | - Aristides M. Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Crete, Greece
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