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Das S, Karuri S, Chakraborty J, Basu B, Chandra A, Aravindan S, Chakraborty A, Paul D, Ray JG, Lechner M, Beck S, Teschendorff EA, Chatterjee R. Universal penalized regression (Elastic-net) model with differentially methylated promoters for oral cancer prediction. Eur J Med Res 2024; 29:458. [PMID: 39261895 PMCID: PMC11389552 DOI: 10.1186/s40001-024-02047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 09/01/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND DNA methylation showed notable potential to act as a diagnostic marker in many cancers. Many studies proposed DNA methylation biomarker in OSCC detection, while most of these studies are limited to specific cohorts or geographical location. However, the generalizability of DNA methylation as a diagnostic marker in oral cancer across different geographical locations is yet to be investigated. METHODS We used genome-wide methylation data from 384 oral cavity cancer and normal tissues from TCGA HNSCC and eastern India. The common differentially methylated CpGs in these two cohorts were used to develop an Elastic-net model that can be used for the diagnosis of OSCC. The model was validated using 812 HNSCC and normal samples from different anatomical sites of oral cavity from seven countries. Droplet Digital PCR of methyl-sensitive restriction enzyme digested DNA (ddMSRE) was used for quantification of methylation and validation of the model with 22 OSCC and 22 contralateral normal samples. Additionally, pyrosequencing was used to validate the model using 46 OSCC and 25 adjacent normal and 21 contralateral normal tissue samples. RESULTS With ddMSRE, our model showed 91% sensitivity, 100% specificity, and 95% accuracy in classifying OSCC from the contralateral normal tissues. Validation of the model with pyrosequencing also showed 96% sensitivity, 91% specificity, and 93% accuracy for classifying the OSCC from contralateral normal samples, while in case of adjacent normal samples we found similar sensitivity but with 20% specificity, suggesting the presence of early disease methylation signature at the adjacent normal samples. Methylation array data of HNSCC and normal tissues from different geographical locations and different anatomical sites showed comparable sensitivity, specificity, and accuracy in detecting oral cavity cancer with across. Similar results were also observed for different stages of oral cavity cancer. CONCLUSIONS Our model identified crucial genomic regions affected by DNA methylation in OSCC and showed similar accuracy in detecting oral cancer across different geographical locations. The high specificity of this model in classifying contralateral normal samples from the oral cancer compared to the adjacent normal samples suggested applicability of the model in early detection.
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Affiliation(s)
- Shantanab Das
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700 108, India
| | - Saikat Karuri
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700 108, India
| | - Joyeeta Chakraborty
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700 108, India
| | - Baidehi Basu
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700 108, India
| | - Aditi Chandra
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700 108, India
- Univeristy of Pennsylvania, Philadelphia, 19104, USA
| | - S Aravindan
- Department of Oral Pathology, Dr. R. Ahmed Dental College & Hospital, Kolkata, India
| | | | - Debashis Paul
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700 108, India
- Department of Statistics, U C Davis, 4222 Mathematical Sciences Building, Davis, CA, 95616, USA
| | - Jay Gopal Ray
- Department of Oral Pathology, Dr. R. Ahmed Dental College & Hospital, Kolkata, India
| | - Matt Lechner
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Stephan Beck
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - E Andrew Teschendorff
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700 108, India.
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Huang G, Zhan X, Shen L, Lou L, Dai Y, Jiang A, Gao Y, Wang Y, Xie X, Zhang J. APOBEC family reshapes the immune microenvironment and therapy sensitivity in clear cell renal cell carcinoma. Clin Exp Med 2024; 24:212. [PMID: 39249558 PMCID: PMC11383847 DOI: 10.1007/s10238-024-01465-2] [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: 07/01/2024] [Accepted: 08/11/2024] [Indexed: 09/10/2024]
Abstract
Emerging evidence suggests that the APOBEC family is implicated in multiple cancers and might be utilized as a new target for cancer detection and treatment. However, the dysregulation and clinical implication of the APOBEC family in clear cell renal cell cancer (ccRCC) remain elusive. TCGA multiomics data facilitated a comprehensive exploration of the APOBEC family across cancers, including ccRCC. Remodeling analysis classified ccRCC patients into two distinct subgroups: APOBEC family pattern cancer subtype 1 (APCS1) and subtype 2 (APCS2). The study investigated differences in clinical parameters, tumor immune microenvironment, therapeutic responsiveness, and genomic mutation landscapes between these subtypes. An APOBEC family-related risk model was developed and validated for predicting ccRCC patient prognosis, demonstrating good sensitivity and specificity. Finally, the overview of APOBEC3B function was investigated in multiple cancers and verified in clinical samples. APCS1 and APCS2 demonstrated considerably distinct clinical features and biological processes in ccRCC. APCS1, an aggressive subtype, has advanced clinical stage and a poor prognosis. APCS1 exhibited an oncogenic and metabolically active phenotype. APCS1 also exhibited a greater tumor mutation load and immunocompromised condition, resulting in immunological dysfunction and immune checkpoint treatment resistance. The genomic copy number variation of APCS1, including arm gain and loss, was much more than that of APCS2, which may help explain the tired immune system. Furthermore, the two subtypes have distinct drug sensitivity patterns in clinical specimens and matching cell lines. Finally, we developed a predictive risk model based on subtype biomarkers that performed well for ccRCC patients and validated the clinical impact of APOBEC3B. Aberrant APOBEC family expression patterns might modify the tumor immune microenvironment by increasing the genome mutation frequency, thus inducing an immune-exhausted phenotype. APOBEC family-based molecular subtypes could strengthen the understanding of ccRCC characterization and guide clinical treatment. Targeting APOBEC3B may be regarded as a new therapeutic target for ccRCC.
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Affiliation(s)
- Guiying Huang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Clinical Laboratory, Lishui Central Hospital, Lishui, Zhejiang, China
| | - Xianlin Zhan
- Department of Clinical Laboratory, PLA Navy Medical Center, Shanghai, China
| | - Lihong Shen
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Luping Lou
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yuehong Dai
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Aiming Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yuzhen Gao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yanzhong Wang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xinyou Xie
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China.
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China.
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Liu H, Yue W, Shao S, Sun J, Yang Y, Dai X. Global analysis of DNA methylation changes during experimented lingual carcinogenesis. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2024; 42:319-328. [PMID: 39049651 PMCID: PMC11190864 DOI: 10.7518/hxkq.2024.2023416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/05/2024] [Indexed: 07/27/2024]
Abstract
OBJECTIVES This study aims to assess the role of DNA methylation changes in tongue cancer through a comprehensive analysis of global DNA methylation alterations during experimental lingual carcinogenesis. METHODS C57BL/6J mice were subjected to 16-week oral administration of 4-nitroquinoline-1-oxide (4NQO, 50 mg/L). Lingual mucosa samples, being representative of normal tissue (week 0) and early (week 12) and advanced (week 28) tumorigenesis, were harvested for microarray and methylated DNA immunoprecipitation sequencing (MeDIP-Seq). The mRNA and promoter methylation of transforming growth factor-beta-signaling protein 1 (SMAD1) were evaluated with real-time quantitative reverse transcription polymerase chain reaction and Massarray in human lingual mucosa and tongue cancer cell lines. RESULTS The cytosine guanine island (CGI) methylation level observed at 28 weeks surpassed that of both 12 weeks and 0 weeks. The promoter methylation level at 12 weeks exceeded that at 0 weeks. Notably, 208 differentially expressed genes were negatively correlated to differential methylation in promoters among 0, 12, and 28 weeks. The mRNA of SMAD1 was upregulated, concurrent with a decrease in promoter methylation levels in cell lines compared to normal mucosa. CONCLUSIONS DNA methylation changed during lingual carcinogenesis. Overexpression of SMAD1 was correlated to promoter hypomethylation in tongue cancer cell lines.
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Affiliation(s)
- Hua Liu
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China
| | - Wanyuan Yue
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China
| | - Shuai Shao
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China
| | - Jiaping Sun
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China
| | - Ying Yang
- Dept. of Pathology, First Affiliated Hospital of Kunming Medical University, Kunming 650031, China
| | - Xiaoming Dai
- Maxillofacial Service of Department of Plastic Surgery, First Affiliated Hospital of Kunming Medical University, Kunming 650031, China
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Lim I, Tan J, Alam A, Idrees M, Brenan PA, Coletta RD, Kujan O. Epigenetics in the diagnosis and prognosis of head and neck cancer: A systematic review. J Oral Pathol Med 2024; 53:90-106. [PMID: 38316046 DOI: 10.1111/jop.13513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/01/2024] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Aberrant epigenetic modifications significantly develop and progress human malignancies including head and neck squamous cell carcinoma (HNSCC). Taking into account issues of late diagnosis and poor prognosis associated with HNSCC, this systematic review is designed to provide an up-to-date insight of epigenetic changes in the management of HNSCC. METHODS All studies that assessed the diagnostic and prognostic utilities of epigenetic changes (DNA methylation and histone modifications) among patients diagnosed with HNSCC or oral potentially malignant disorders (OPMDs) were considered for inclusion till June 2023. Pre-defined Medical Subject Headings terms were used to search Web of Science, Pubmed, Scopus and Embase Ovid databases. RESULTS Twenty-five studies were deemed eligible for inclusion with a total number of 3790 samples (2123 HNSCCs, 334 OPMDs and 1333 as controls). DNA methylation was investigated in 18 studies while the role of histone modifications was assessed in seven studies. The most investigated biomarkers among the studies were H3, DAPK and TIMP3. The diagnostic accuracy of the epigenetic biomarkers in detecting HNSCC was assessed in eight studies where the following biomarkers showed the highest area under the curve values: TIPM3, DCC, DAPK, SEPT9, SHOX9, HOXA9 and TRH. None of the studies assessed the predictability of the epigenetic biomarkers in HNSCC and OPMDs. CONCLUSION Although initial promising results were seen using the epigenetic biomarkers in the early detection of HNSCC, the limited number of patients and the absence of well-designed longitudinal studies limit the clinical applicability of the outcomes.
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Affiliation(s)
- Isaac Lim
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Jade Tan
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Anneka Alam
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Majdy Idrees
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Peter A Brenan
- Department of Oral and Maxillofacial Surgery, Queen Alexandra Hospital, Portsmouth, UK
| | - Ricardo Della Coletta
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Omar Kujan
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
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Inchanalkar M, Srivatsa S, Ambatipudi S, Bhosale PG, Patil A, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers. Clin Epigenetics 2023; 15:93. [PMID: 37245006 DOI: 10.1186/s13148-023-01510-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/21/2023] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Gingivobuccal complex oral squamous cell carcinoma (GBC-OSCC) is an aggressive malignancy with high mortality often preceded by premalignant lesions, including leukoplakia. Previous studies have reported genomic drivers in OSCC, but much remains to be elucidated about DNA methylation patterns across different stages of oral carcinogenesis. RESULTS There is a serious lack of biomarkers and clinical application of biomarkers for early detection and prognosis of gingivobuccal complex cancers. Hence, in search of novel biomarkers, we measured genome-wide DNA methylation in 22 normal oral tissues, 22 leukoplakia, and 74 GBC-OSCC tissue samples. Both leukoplakia and GBC-OSCC had distinct methylation profiles as compared to normal oral tissue samples. Aberrant DNA methylation increases during the different stages of oral carcinogenesis, from premalignant lesions to carcinoma. We identified 846 and 5111 differentially methylated promoters in leukoplakia and GBC-OSCC, respectively, with a sizable fraction shared between the two sets. Further, we identified potential biomarkers from integrative analysis in gingivobuccal complex cancers and validated them in an independent cohort. Integration of genome, epigenome, and transcriptome data revealed candidate genes with gene expression synergistically regulated by copy number and DNA methylation changes. Regularised Cox regression identified 32 genes associated with patient survival. In an independent set of samples, we validated eight genes (FAT1, GLDC, HOXB13, CST7, CYB5A, MLLT11, GHR, LY75) from the integrative analysis and 30 genes from previously published reports. Bisulfite pyrosequencing validated GLDC (P = 0.036), HOXB13 (P < 0.0001) promoter hypermethylation, and FAT1 (P < 0.0001) hypomethylation in GBC-OSCC compared to normal controls. CONCLUSIONS Our findings identified methylation signatures associated with leukoplakia and gingivobuccal complex cancers. The integrative analysis in GBC-OSCC identified putative biomarkers that enhance existing knowledge of oral carcinogenesis and may potentially help in risk stratification and prognosis of GBC-OSCC.
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Affiliation(s)
- Mayuri Inchanalkar
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Sumana Srivatsa
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Srikant Ambatipudi
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
| | - Priyanka G Bhosale
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Centre for Gene Therapy and Regenerative Medicine, Guy's Hospital, King's College London, Tower Wing, London, UK
| | - Asawari Patil
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, and National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Manoj B Mahimkar
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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Zhang Z, Zhang Y, Hu X, Chen Y, Zhuang L, Zhang S. ZNF677 inhibits oral squamous cell carcinoma growth and tumor stemness by regulating FOXO3a. Hum Cell 2023:10.1007/s13577-023-00910-w. [PMID: 37129799 DOI: 10.1007/s13577-023-00910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/23/2023] [Indexed: 05/03/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is a common cancer with an increasing incidence worldwide. Zinc-finger proteins 677 (ZNF677) is involved in the progression and methylation of various cancers, but its role and mechanism in OSCC remain indeterminate. The expression of ZNF677 was analyzed by online database and immunohistochemistry, while the methylation level of ZNF677 was determined by the methylation-specific PCR. The role and mechanism of ZNF677 in the tumor cell growth, migration, invasion and stemness were addressed by cell counting kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU) incorporation, Transwell, wound-healing, sphere‑formation, and western blot assays. In addition, its function was also investigated in a xenografted mice model. The results showed that ZNF677 was lowly expressed in OSCC with a hypermethylation level, which predicted poor overall survival in patients with HNSC. Upregulation of ZNF677 reduced the cell viability, Edu positive cells, numbers of invasion cells, the migration ability, numbers of spheres formation and the expression of proliferation, migration and stemness related proteins in CAL-27 and SCC25 cells. Mechanically, the relative levels of p-AKT/AKT were decreased and the levels of p-FOXO3a/FOXO3a were increased in both cells overexpressed with ZNF677, which were reversed by the SC79 treatment. Moreover, interference of FOXO3a recovered the suppressive effects of ZNF677 overexpression on cell proliferation, migration, invasion and stemness of OSCC cells. Furthermore, overexpression of ZNF677 reduced the tumor volume and weight, and the relative protein level of p-AKT/AKT with an increased level of p-FOXO3a/FOXO3a, and improved pathological symptoms in vivo. Collectively, ZNF677 suppressed OSCC cells growth, migration, invasion and stemness through inhibiting AKT/FOXO3a pathway.
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Affiliation(s)
- Zebiao Zhang
- Department of Stomatology, Quanzhou First Hospital Affiliated to Fujian Medical University, No. 250, East Street, Quanzhou, 362000, Fujian, China
| | - Ying Zhang
- Department of Stomatology, Quanzhou First Hospital Affiliated to Fujian Medical University, No. 250, East Street, Quanzhou, 362000, Fujian, China.
| | - Xiaoyan Hu
- Department of Prosthodontics, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, 350000, Fujian, China
| | - Yanru Chen
- Department of Stomatology, Quanzhou First Hospital Affiliated to Fujian Medical University, No. 250, East Street, Quanzhou, 362000, Fujian, China
| | - Liangliang Zhuang
- Department of Stomatology, Quanzhou First Hospital Affiliated to Fujian Medical University, No. 250, East Street, Quanzhou, 362000, Fujian, China
| | - Shuqin Zhang
- Department of Stomatology, Jinjiang Stomatological Hospital, Quanzhou, 362200, Fujian, China
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Abstract
Head and neck cancers are a heterogeneous group of highly aggressive tumors and collectively represent the sixth most common cancer worldwide. Most head and neck cancers are squamous cell carcinomas (HNSCCs). Current multimodal treatment concepts combine surgery, chemotherapy, irradiation, immunotherapy, and targeted therapeutics. Recent scientific advancements have enabled a more precise molecular characterization of HNSCC and revealed novel therapeutic targets and prognostic/predictive biomarkers. Notably, HNSCC is characterized by complex relations between stromal, epithelial, and immune cells within the tumor microenvironment (TME). The TME consists of different subsets of immune cells that infiltrate the tumors and interact with the tumor cells or with each other. Understanding multiple pivotal factors in HNSCC tumorigenesis and tumor progression may help define novel targets and develop more effective therapies for patients. This review provides a comprehensive overview of the latest advances in the molecular biology of HNSCC and their effects on clinical oncology; it is meant for a broad readership in the head and neck cancers field.
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Affiliation(s)
- Subramanya Pandruvada
- Department of Oral Health Sciences, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, United States.
| | - Remi Kessler
- Department of Oral Health Sciences, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Ann Thai
- Department of Oral Health Sciences, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, United States
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Huang K, Han L, Xu H, Xu R, Guo H, Wang H, Xu Z. The prognostic role and metabolic function of GGPS1 in oral squamous cell carcinoma. Front Mol Biosci 2023; 10:1109403. [PMID: 37033446 PMCID: PMC10081451 DOI: 10.3389/fmolb.2023.1109403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Background: GGPS1(geranylgeranyl diphosphate synthase 1) is a member of the prenyltransferase family. Abnormal expression of GGPS1 can disrupt the balance between protein farnesylation and geranylgeranylation, thereby affecting a variety of cellular physiologic and pathological processes. However, it is still unknown how this gene could contribute to the prognosis of oral squamous cell carcinoma (OSCC). This study aimed to explore the prognostic role of GGPS1 in OSCC and its relationship with clinical features. Methods: The RNA-seq data and clinical data were obtained from TCGA. The survival analyses, Cox regression analyses, ROC curves, nomograms, calibration curves, and gene function enrichments were established by R software. Results: The results showed that the high expression of GGPS1 in OSCC is related to poor prognosis. At the same time, multivariate Cox regression analyses showed that GGPS1 could be an independent prognostic biomarker, and its gene expression level is closely related to the histological stage of cancer. GGPS1 may promote tumorigenesis because of its metabolic function. Conclusion: This study came to a conclusion that GGPS1, whose high expression has a significantly unfavorable meaning toward the prognosis of OSCC, can act as a novel independent biomarker for OSCC.
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Affiliation(s)
- Ke Huang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Liang Han
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Huimei Xu
- Lanzhou University Second Hospital, Lanzhou University, Lanzhou, Gansu, China
| | - Ruiming Xu
- The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hao Guo
- School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Huihui Wang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Huihui Wang, ; Zhaoqing Xu,
| | - Zhaoqing Xu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- *Correspondence: Huihui Wang, ; Zhaoqing Xu,
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Epigenetics and Gut Microbiota Crosstalk: A potential Factor in Pathogenesis of Cardiovascular Disorders. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120798. [PMID: 36551003 PMCID: PMC9774431 DOI: 10.3390/bioengineering9120798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Cardiovascular diseases (CVD) are the leading cause of mortality, morbidity, and "sudden death" globally. Environmental and lifestyle factors play important roles in CVD susceptibility, but the link between environmental factors and genetics is not fully established. Epigenetic influence during CVDs is becoming more evident as its direct involvement has been reported. The discovery of epigenetic mechanisms, such as DNA methylation and histone modification, suggested that external factors could alter gene expression to modulate human health. These external factors also influence our gut microbiota (GM), which participates in multiple metabolic processes in our body. Evidence suggests a high association of GM with CVDs. Although the exact mechanism remains unclear, the influence of GM over the epigenetic mechanisms could be one potential pathway in CVD etiology. Both epigenetics and GM are dynamic processes and vary with age and environment. Changes in the composition of GM have been found to underlie the pathogenesis of metabolic diseases via modulating epigenetic changes in the form of DNA methylation, histone modifications, and regulation of non-coding RNAs. Several metabolites produced by the GM, including short-chain fatty acids, folates, biotin, and trimethylamine-N-oxide, have the potential to regulate epigenetics, apart from playing a vital role in normal physiological processes. The role of GM and epigenetics in CVDs are promising areas of research, and important insights in the field of early diagnosis and therapeutic approaches might appear soon.
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Luo Z, Zhang Y, Sun Y. A Penalization Method for Estimating Heterogeneous Covariate Effects in Cancer Genomic Data. Genes (Basel) 2022; 13:genes13040702. [PMID: 35456506 PMCID: PMC9025588 DOI: 10.3390/genes13040702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 11/16/2022] Open
Abstract
In high-throughput profiling studies, extensive efforts have been devoted to searching for the biomarkers associated with the development and progression of complex diseases. The heterogeneity of covariate effects associated with the outcomes across subjects has been noted in the literature. In this paper, we consider a scenario where the effects of covariates change smoothly across subjects, which are ordered by a known auxiliary variable. To this end, we develop a penalization-based approach, which applies a penalization technique to simultaneously select important covariates and estimate their unique effects on the outcome variables of each subject. We demonstrate that, under the appropriate conditions, our method shows selection and estimation consistency. Additional simulations demonstrate its superiority compared to several competing methods. Furthermore, applying the proposed approach to two The Cancer Genome Atlas datasets leads to better prediction performance and higher selection stability.
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Affiliation(s)
- Ziye Luo
- School of Statistics, Renmin University of China, No. 59 Zhongguancun Street, Beijing 100872, China; (Z.L.); (Y.Z.)
| | - Yuzhao Zhang
- School of Statistics, Renmin University of China, No. 59 Zhongguancun Street, Beijing 100872, China; (Z.L.); (Y.Z.)
| | - Yifan Sun
- Center for Applied Statistics, School of Statistics, Renmin University of China, No. 59 Zhongguancun Street, Beijing 100872, China
- Correspondence:
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11
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Abstract
Purpose of Review This study assesses the current state of knowledge of head and neck squamous cell carcinomas (HNSCC), which are malignancies arising from the orifices and adjacent mucosae of the aerodigestive tracts. These contiguous anatomical areas are unique in that 2 important human oncoviruses, Epstein-Barr virus (EBV) and human papillomavirus (HPV), are causally associated with nasopharyngeal and oropharyngeal cancers, respectively. Mortality rates have remained high over the last 4 decades, and insufficient attention paid to the unique viral and clinical oncology of the different subgroups of HNSCC. Recent Findings We have compared and contrasted the 2 double-stranded DNA viruses and the relevant molecular oncogenesis of their respective cancers against other head and neck cancers. Tobacco and alcohol ingestion are also reviewed, as regard the genetic progression/mutation accumulation model of carcinogenesis. The importance of stringent stratification when searching for cancer mutations and biomarkers is discussed. Evidence is presented for a dysplastic/pre-invasive cancerous phase for HPV+ oropharyngeal cancers, and analogous with other HPV+ cancers. This raises the possibility of strategies for cancer screening as early diagnosis will undoubtedly save lives. Summary Staging and prognostication have changed to take into account the distinct biological and prognostic pathways for viral+ and viral− cancers. Diagnosis of pre-cancers and early stage cancers will reduce mortality rates. Multi-modal treatment options for HNSCC are reviewed, especially recent developments with immunotherapies and precision medicine strategies. Knowledge integration of the viral and molecular oncogenic pathways with sound planning, hypothesis generation, and clinical trials will continue to provide therapeutic options in the future.
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On the Cutting Edge of Oral Cancer Prevention: Finding Risk-Predictive Markers in Precancerous Lesions by Longitudinal Studies. Cells 2022; 11:cells11061033. [PMID: 35326482 PMCID: PMC8947091 DOI: 10.3390/cells11061033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 02/06/2023] Open
Abstract
Early identification and management of precancerous lesions at high risk of developing cancers is the most effective and economical way to reduce the incidence, mortality, and morbidity of cancers as well as minimizing treatment-related complications, including pain, impaired functions, and disfiguration. Reliable cancer-risk-predictive markers play an important role in enabling evidence-based decision making as well as providing mechanistic insight into the malignant conversion of precancerous lesions. The focus of this article is to review updates on markers that may predict the risk of oral premalignant lesions (OPLs) in developing into oral squamous cell carcinomas (OSCCs), which can logically be discovered only by prospective or retrospective longitudinal studies that analyze pre-progression OPL samples with long-term follow-up outcomes. These risk-predictive markers are different from those that prognosticate the survival outcome of cancers after they have been diagnosed and treated, or those that differentiate between different lesion types and stages. Up-to-date knowledge on cancer-risk-predictive markers discovered by longitudinally followed studies will be reviewed. The goal of this endeavor is to use this information as a starting point to address some key challenges limiting our progress in this area in the hope of achieving effective translation of research discoveries into new clinical interventions.
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Ferraguti G, Terracina S, Petrella C, Greco A, Minni A, Lucarelli M, Agostinelli E, Ralli M, de Vincentiis M, Raponi G, Polimeni A, Ceccanti M, Caronti B, Di Certo MG, Barbato C, Mattia A, Tarani L, Fiore M. Alcohol and Head and Neck Cancer: Updates on the Role of Oxidative Stress, Genetic, Epigenetics, Oral Microbiota, Antioxidants, and Alkylating Agents. Antioxidants (Basel) 2022; 11:145. [PMID: 35052649 PMCID: PMC8773066 DOI: 10.3390/antiox11010145] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/27/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
Head and neck cancer (HNC) concerns more than 890,000 patients worldwide annually and is associated with the advanced stage at presentation and heavy outcomes. Alcohol drinking, together with tobacco smoking, and human papillomavirus infection are the main recognized risk factors. The tumorigenesis of HNC represents an intricate sequential process that implicates a gradual acquisition of genetic and epigenetics alterations targeting crucial pathways regulating cell growth, motility, and stromal interactions. Tumor microenvironment and growth factors also play a major role in HNC. Alcohol toxicity is caused both directly by ethanol and indirectly by its metabolic products, with the involvement of the oral microbiota and oxidative stress; alcohol might enhance the exposure of epithelial cells to carcinogens, causing epigenetic modifications, DNA damage, and inaccurate DNA repair with the formation of DNA adducts. Long-term markers of alcohol consumption, especially those detected in the hair, may provide crucial information on the real alcohol drinking of HNC patients. Strategies for prevention could include food supplements as polyphenols, and alkylating drugs as therapy that play a key role in HNC management. Indeed, polyphenols throughout their antioxidant and anti-inflammatory actions may counteract or limit the toxic effect of alcohol whereas alkylating agents inhibiting cancer cells' growth could reduce the carcinogenic damage induced by alcohol. Despite the established association between alcohol and HNC, a concerning pattern of alcohol consumption in survivors of HNC has been shown. It is of primary importance to increase the awareness of cancer risks associated with alcohol consumption, both in oncologic patients and the general population, to provide advice for reducing HNC prevalence and complications.
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Affiliation(s)
- Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (S.T.); (M.L.)
| | - Sergio Terracina
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (S.T.); (M.L.)
| | - Carla Petrella
- Institute of Biochemistry and Cell Biology, IBBC—CNR, 000185 Rome, Italy; (C.P.); (M.G.D.C.); (C.B.)
| | - Antonio Greco
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy; (A.G.); (A.M.); (E.A.); (M.R.); (M.d.V.)
| | - Antonio Minni
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy; (A.G.); (A.M.); (E.A.); (M.R.); (M.d.V.)
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (S.T.); (M.L.)
| | - Enzo Agostinelli
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy; (A.G.); (A.M.); (E.A.); (M.R.); (M.d.V.)
| | - Massimo Ralli
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy; (A.G.); (A.M.); (E.A.); (M.R.); (M.d.V.)
| | - Marco de Vincentiis
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy; (A.G.); (A.M.); (E.A.); (M.R.); (M.d.V.)
| | - Giammarco Raponi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy;
| | - Antonella Polimeni
- Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Mauro Ceccanti
- SITAC, Società Italiana per il Trattamento dell’Alcolismo, 00184 Rome, Italy;
- SIFASD, Società Italiana Sindrome Feto-Alcolica, 00184 Rome, Italy
| | - Brunella Caronti
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Maria Grazia Di Certo
- Institute of Biochemistry and Cell Biology, IBBC—CNR, 000185 Rome, Italy; (C.P.); (M.G.D.C.); (C.B.)
| | - Christian Barbato
- Institute of Biochemistry and Cell Biology, IBBC—CNR, 000185 Rome, Italy; (C.P.); (M.G.D.C.); (C.B.)
| | - Alessandro Mattia
- Ministero dell’Interno, Dipartimento della Pubblica Sicurezza, Direzione Centrale di Sanità, Centro di Ricerche e Laboratorio di Tossicologia Forense, 00185 Rome, Italy;
| | - Luigi Tarani
- Department of Pediatrics, Sapienza University Hospital of Rome, 00185 Rome, Italy;
| | - Marco Fiore
- Institute of Biochemistry and Cell Biology, IBBC—CNR, 000185 Rome, Italy; (C.P.); (M.G.D.C.); (C.B.)
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14
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Zhang Z, Zhu R, Sun W, Wang J, Liu J. Analysis of Methylation-driven Genes in Pancreatic Ductal Adenocarcinoma for Predicting Prognosis. J Cancer 2021; 12:6507-6518. [PMID: 34659542 PMCID: PMC8489123 DOI: 10.7150/jca.53208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose: Considerable variations in methylation profile have been found in various cancers to modulate tumorigenesis and affect prognosis. To provide a theoretical basis for early detection, prognosis evaluation and targeted treatment for patients with pancreatic ductal adenocarcinoma: PDAC, this study identified methylation-driven genes in PDAC and explored their prognostic performance. Methods: The methylation, expression and clinical data of PDAC patients were extracted from TCGA database. Based on the β-mixture model of the MethylMix R package, the differential methylation status and connection between methylation and expression degree were examined to screen out methylation-driven genes in PDAC. COX analyses and lasso regressions were applied to construct a linear risk model based on methylation-driven genes. Univariate and multivariate analyses were performed to ensure the risk model was an independent prognostic factor. Joint survival analyses of methylation and gene expression were conducted to explore the prognostic value of component genes. The methylation sites in the key genes were also investigated. Results: A total of 118 methylation-driven genes in PDAC were identified, and two genes (FOXI2, MYEOV) constituted the risk model whose AUC was 0.722 at one year of overall survival rate, displaying a better performance on survival prediction than other clinical features. Further survival analyses demonstrated that the expression of MYEOV and combined methylation and expression levels of the genes MYEOV and FOXI2 can be potential biomarkers for survival prediction and targets of drug manipulation of PDAC patients. Close relationships were discovered between two sites in MYEOV and one site in FOXI2 and the prognosis of PDAC patients. Conclusion: Concentrating on DNA methylation, our study identified potential biomarkers and developed a reliable short-term predictive model for prognosis of PDAC patients.
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Affiliation(s)
- Zihan Zhang
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Rui Zhu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wentian Sun
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jun Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jin Liu
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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15
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Hoes L, Dok R, Verstrepen KJ, Nuyts S. Ethanol-Induced Cell Damage Can Result in the Development of Oral Tumors. Cancers (Basel) 2021; 13:cancers13153846. [PMID: 34359747 PMCID: PMC8345464 DOI: 10.3390/cancers13153846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Alcohol consumption is linked to 26.4% of all lip and oral cavity cancer cases worldwide. Despite this clear causal relationship, the exact molecular mechanisms by which ethanol damages cells are still under investigation. It is well-established that the metabolism of ethanol plays an important role. Ethanol metabolism yields reactive metabolites that can directly damage the DNA. If the damage is repaired incorrectly, mutations can be fixed in the DNA sequence. Whenever mutations affect key regulatory genes, for instance cell cycle regulating genes, uncontrolled cell growth can be the consequence. Recently, global patterns of mutations have been identified. These so-called mutational signatures represent a fingerprint of the different mutational processes over time. Interestingly, there were ethanol-related signatures discovered that did not associate with ethanol metabolism. This finding highlights there might be other molecular effects of ethanol that are yet to be discovered. Abstract Alcohol consumption is an underestimated risk factor for the development of precancerous lesions in the oral cavity. Although alcohol is a well-accepted recreational drug, 26.4% of all lip and oral cavity cancers worldwide are related to heavy drinking. Molecular mechanisms underlying this carcinogenic effect of ethanol are still under investigation. An important damaging effect comes from the first metabolite of ethanol, being acetaldehyde. Concentrations of acetaldehyde detected in the oral cavity are relatively high due to the metabolization of ethanol by oral microbes. Acetaldehyde can directly damage the DNA by the formation of mutagenic DNA adducts and interstrand crosslinks. Additionally, ethanol is known to affect epigenetic methylation and acetylation patterns, which are important regulators of gene expression. Ethanol-induced hypomethylation can activate the expression of oncogenes which subsequently can result in malignant transformation. The recent identification of ethanol-related mutational signatures emphasizes the role of acetaldehyde in alcohol-associated carcinogenesis. However, not all signatures associated with alcohol intake also relate to acetaldehyde. This finding highlights that there might be other effects of ethanol yet to be discovered.
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Affiliation(s)
- Lore Hoes
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium; (L.H.); (K.J.V.)
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium;
| | - Rüveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium;
| | - Kevin J. Verstrepen
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium; (L.H.); (K.J.V.)
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium;
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospital Leuven, 3000 Leuven, Belgium
- Correspondence: ; Tel.: +32-1634-7600; Fax: +32-1634-7623
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Bruixola G, Remacha E, Jiménez-Pastor A, Dualde D, Viala A, Montón JV, Ibarrola-Villava M, Alberich-Bayarri Á, Cervantes A. Radiomics and radiogenomics in head and neck squamous cell carcinoma: Potential contribution to patient management and challenges. Cancer Treat Rev 2021; 99:102263. [PMID: 34343892 DOI: 10.1016/j.ctrv.2021.102263] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/06/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022]
Abstract
The application of imaging biomarkers in oncology is still in its infancy, but with the expansion of radiomics and radiogenomics a revolution is expected in this field. This may be of special interest in head and neck cancer, since it can promote precision medicine and personalization of treatment by overcoming several intrinsic obstacles in this pathology. Our goal is to provide the medical oncologist with the basis to approach these disciplines and appreciate their main uses in clinical research and clinical practice in the medium term. Aligned with this objective we analyzed the most relevant studies in the field, also highlighting novel opportunities and current challenges.
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Affiliation(s)
- Gema Bruixola
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - Elena Remacha
- Quantitative Imaging Biomarkers in Medicine (QUIBIM SL), Valencia, Spain
| | - Ana Jiménez-Pastor
- Quantitative Imaging Biomarkers in Medicine (QUIBIM SL), Valencia, Spain
| | - Delfina Dualde
- Department of Radiology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - Alba Viala
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - Jose Vicente Montón
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain
| | - Maider Ibarrola-Villava
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
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Flausino CS, Daniel FI, Modolo F. DNA methylation in oral squamous cell carcinoma: from its role in carcinogenesis to potential inhibitor drugs. Crit Rev Oncol Hematol 2021; 164:103399. [PMID: 34147646 DOI: 10.1016/j.critrevonc.2021.103399] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is one of epigenetic changes most frequently studied nowadays, together with its relationship with oral carcinogenesis. A group of enzymes is responsible for methylation process, known as DNA methyltransferases (DNMT). Although essential during embryogenesis, DNA methylation pattern alterations, including global hypomethylation or gene promoter hypermethylation, can be respectively associated with chromosomal instability and tumor suppressor gene silencing. Higher expression of DNA methyltransferases is a common finding in oral cancer and may contribute to inactivation of important tumor suppressor genes, influencing development, progression, metastasis, and prognosis of the tumor. To control these alterations, inhibitor drugs have been developed as a way to regulate DNMT overexpression, and they are intended to be associated with ongoing chemo- and radiotherapy in oral cancer treatments. In this article, we aimed to highlight the current knowledge about DNA methylation in oral cancer, including main hyper/hypomethylated genes, DNMT expression and its inhibitor treatments.
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Affiliation(s)
| | - Filipe Ivan Daniel
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil.
| | - Filipe Modolo
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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18
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Bhat GR, Hyole RG, Li J. Head and neck cancer: Current challenges and future perspectives. Adv Cancer Res 2021; 152:67-102. [PMID: 34353444 DOI: 10.1016/bs.acr.2021.05.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Head and neck cancers are a heterogeneous, aggressive and genetically complex collection of malignancies of the oral cavity, nasopharynx, oropharynx, hypopharynx, larynx, paranasal sinuses and salivary glands, which are difficult to treat. About 90% of all head and neck cancers are squamous cell carcinomas (HNSCC). Larynx and Oral cavity carcinomas are generally related with tobacco consumption, alcohol abuse (or both), but pharynx carcinomas are generally associated with infection of human papillomavirus (HPV), especially HPV-16 subtype. Thus, usually HNSCC can be separated into HPV-negative and HPV-positive categories. Despite substantial efforts invested into therapeutic development of HNSCC, the 5-year survival rate of patients with HNSCC still remains dismal. The primary reason being late diagnosis, recurrent metastasis, relapse and resistance to therapies. Currently surgery and radiotherapy represent the baseline treatment options for most initial stage HNSCC patients, but these treatments are associated with significant morbidity and poor prognosis. Moreover, the issue of resistance to both radiotherapy/chemotherapy and recurrent relapse are common in HNSCC. Elucidation of the genetic landscape, tumor microenvironment and aberrant signaling pathways have generated new insights into the molecular pathogenesis of this disease. Thus, the scientific research has therefore been focused on the understanding of HNSCC biology and immunobiology to identification of predictive/prognostic biomarkers, which will be key to develop more effective targeted therapies with less toxicity and high specificity.
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Affiliation(s)
- Gh Rasool Bhat
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Rosalie G Hyole
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Jiong Li
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States; Department of Oral and Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, VA, United States; Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, United States.
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Identification of Prognostic Risk Model Based on DNA Methylation-Driven Genes in Esophageal Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6628391. [PMID: 34222478 PMCID: PMC8213479 DOI: 10.1155/2021/6628391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/15/2021] [Accepted: 05/08/2021] [Indexed: 01/10/2023]
Abstract
Background DNA methylation is an important part of epigenetic modification, and its abnormality is closely related to esophageal adenocarcinoma (EAC). This study was aimed at using bioinformatics analysis to identify methylation-driven genes (MDGs) in EAC patients and establish a risk model as a biological indicator of EAC prognosis. Method Downloaded EAC DNA methylation, transcriptome, and related clinical data from TCGA database. MethylMix was used to identify MDGs. R package clusterProfiler and the ConsensusPathDB online database were used to analyze the rich functions and pathways of these MDGs. The prognostic risk model was established by univariate Cox regression, Lasso regression, and multivariate Cox regression analysis. Finally each MDG in the model were carried out through the survival R package. Results A total of 273 MDGs were identified, which were enriched in transcriptional regulation and embryonic organ morphogenesis. Cox regression analysis established a risk model consisting of GPBAR1, OLFM4, FOXI2, and CASP10. In addition, further survival analysis revealed that OLFM4 and its two related sites were significantly related to the EAC patients' survival. Conclusion In summary, this study used bioinformatics methods to identify EAC MDGs and established a reliable risk prognosis model. It provided potential biomarkers for the early treatment and prognosis evaluation of EAC.
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Novel prognostic prediction model constructed through machine learning on the basis of methylation-driven genes in kidney renal clear cell carcinoma. Biosci Rep 2021; 40:225719. [PMID: 32633782 PMCID: PMC7374278 DOI: 10.1042/bsr20201604] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is a common tumor with poor prognosis and is closely related to many aberrant gene expressions. DNA methylation is an important epigenetic modification mechanism and a novel research target. Thus, exploring the relationship between methylation-driven genes and KIRC prognosis is important. The methylation profile, methylation-driven genes, and methylation characteristics in KIRC was revealed through the integration of KIRC methylation, RNA-seq, and clinical information data from The Cancer Genome Atlas. The Lasso regression was used to establish a prognosis model on the basis of methylation-driven genes. Then, a trans-omics prognostic nomogram was constructed and evaluated by combining clinical information and methylated prognosis model. A total of 242 methylation-driven genes were identified. The Gene Ontology terms of these methylation-driven genes mainly clustered in the activation, adhesion, and proliferation of immune cells. The methylation prognosis prediction model that was established using the Lasso regression included four genes in the methylation data, namely, FOXI2, USP44, EVI2A, and TRIP13. The areas under the receiver operating characteristic curve of 1-, 3-, and 5-year survival rates were 0.810, 0.824, and 0.799, respectively, in the training group and 0.794, 0.752, and 0.731, respectively, in the testing group. An easy trans-omics nomogram was successfully established. The C-indices of the nomogram in the training and the testing groups were 0.8015 and 0.8389, respectively. The present study revealed the overall perspective of methylation-driven genes in KIRC and can help in the evaluation of the prognosis of KIRC patients and provide new clues for further study.
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21
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Chen L, Wang D. Identification of potential CpG sites for oral squamous cell carcinoma diagnosis via integrated analysis of DNA methylation and gene expression. World J Surg Oncol 2021; 19:16. [PMID: 33468155 PMCID: PMC7816501 DOI: 10.1186/s12957-021-02129-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) accounts for more than 90% of the oral carcinomas and has a high fatality rate. This study aimed to identify potentially diagnostic biomarkers of OSCC through integrated analysis of DNA methylation and gene expression profiles. METHODS The DNA methylation profiles of OSCC patients from The Cancer Genome Atlas (TCGA) were analyzed to screen patients with CpG island methylator phenotype (CIMP) and investigate the relationship between CIMP and survival probability of OSCC patients. Differential methylation and expression analyses of the paired OSCC tumor and paracancerous samples from TCGA were performed. Logistic regression model was established, and the accuracy of this diagnostic model for OSCC was evaluated in validation sets from Gene Expression Omnibus (GEO). RESULTS OSCC patients with CIMP had lower survival probability than those without CIMP. The cg02860732 and cg04342955 were determined as candidate diagnostic methylation sites for OSCC. Logistic regression model was established based on cg02860732 and cg04342955 showed relatively high diagnostic accuracy in OSCC. CONCLUSIONS A diagnostic model for OSCC was identified based on the methylation sites cg02860732 and cg04342955, which might be favorable for the diagnosis of OSCC.
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Affiliation(s)
- Le Chen
- Department of Stomatology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road Intersection, Hexi District, Tianjin, 300211, China
| | - Dong Wang
- Department of Stomatology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road Intersection, Hexi District, Tianjin, 300211, China.
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22
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Monteiro L, Mello FW, Warnakulasuriya S. Tissue biomarkers for predicting the risk of oral cancer in patients diagnosed with oral leukoplakia: A systematic review. Oral Dis 2020; 27:1977-1992. [PMID: 33290585 DOI: 10.1111/odi.13747] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/15/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES We performed a systematic review to evaluate the published biomarkers related to oral leukoplakia (OL), aiming to identify the biomarkers that indicate any future risk of cancer in patients with oral leukoplakia. METHODS A search strategy was developed for three main electronic databases: PubMed, Cochrane Library, and EBSCO, and also for Google Scholar, until February 28, 2020. The study selection was performed in a two-phase process aiming at studies assessing tissue biomarkers for "malignant transformation of OL." Risk of bias analysis of included studies was performed using the Quality in Prognosis Studies Tool. RESULTS From 3,130 articles initially identified by searching databases, a total of 46 studies were included in this systematic review, with a combined sample of 3,783 patients, of whom 1,047 presented with malignant transformation of a previously diagnosed OL as reported by the authors. The cancer incidence in the whole group was 27.6% (range: 5.4% to 54.1%). The studies were derived from different geographic areas, including Asia (n = 21), Europe (n = 15), North America (n = 9), and Oceania (n = 1). There were 49 different molecular biomarkers evaluated in the 46 included studies: p53 and podoplanin proteins were the most frequently reported, followed by abnormalities at particular chromosomal loci (e.g., LOH). Risk of bias analysis revealed concerns associated with "measurement of prognostic factor," "study confounding" and "statistical analysis and reporting." CONCLUSIONS Substantial heterogeneity and lack of standardized reporting of data among the studies were identified. The most promising biomarkers reported to have a significant association with the malignant transformation in OL included podoplanin and chromosomal loci abnormalities. A critical examination of the follow-up studies on OL published so far indicated that tissue biomarkers that could predict the risk of oral cancer in patients with OL are still in a discovery phase.
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Affiliation(s)
- Luis Monteiro
- Medicine and Oral Surgery Department, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS), IUCS - Instituto Universitário de Ciências da Saúde (CESPU), Gandra, Portugal
| | - Fernanda Weber Mello
- Postgraduate Program in Dentistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Saman Warnakulasuriya
- Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London and WHO Collaborating Centre for Oral Cancer, London, UK
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23
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Johnson DE, Burtness B, Leemans CR, Lui VWY, Bauman JE, Grandis JR. Head and neck squamous cell carcinoma. Nat Rev Dis Primers 2020; 6:92. [PMID: 33243986 PMCID: PMC7944998 DOI: 10.1038/s41572-020-00224-3] [Citation(s) in RCA: 1791] [Impact Index Per Article: 447.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Most head and neck cancers are derived from the mucosal epithelium in the oral cavity, pharynx and larynx and are known collectively as head and neck squamous cell carcinoma (HNSCC). Oral cavity and larynx cancers are generally associated with tobacco consumption, alcohol abuse or both, whereas pharynx cancers are increasingly attributed to infection with human papillomavirus (HPV), primarily HPV-16. Thus, HNSCC can be separated into HPV-negative and HPV-positive HNSCC. Despite evidence of histological progression from cellular atypia through various degrees of dysplasia, ultimately leading to invasive HNSCC, most patients are diagnosed with late-stage HNSCC without a clinically evident antecedent pre-malignant lesion. Traditional staging of HNSCC using the tumour-node-metastasis system has been supplemented by the 2017 AJCC/UICC staging system, which incorporates additional information relevant to HPV-positive disease. Treatment is generally multimodal, consisting of surgery followed by chemoradiotherapy (CRT) for oral cavity cancers and primary CRT for pharynx and larynx cancers. The EGFR monoclonal antibody cetuximab is generally used in combination with radiation in HPV-negative HNSCC where comorbidities prevent the use of cytotoxic chemotherapy. The FDA approved the immune checkpoint inhibitors pembrolizumab and nivolumab for treatment of recurrent or metastatic HNSCC and pembrolizumab as primary treatment for unresectable disease. Elucidation of the molecular genetic landscape of HNSCC over the past decade has revealed new opportunities for therapeutic intervention. Ongoing efforts aim to integrate our understanding of HNSCC biology and immunobiology to identify predictive biomarkers that will enable delivery of the most effective, least-toxic therapies.
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Affiliation(s)
- Daniel E. Johnson
- Department of Otolaryngology-Head and Neck Surgery, University of California at San Francisco, San Francisco, CA, USA
| | - Barbara Burtness
- Department of Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | - C. René Leemans
- Department of Otolaryngology-Head and Neck Surgery, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Vivian Wai Yan Lui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR
| | - Julie E. Bauman
- Department of Medicine-Hematology/Oncology, University of Arizona, Tucson, AZ, USA
| | - Jennifer R. Grandis
- Department of Otolaryngology-Head and Neck Surgery, University of California at San Francisco, San Francisco, CA, USA,
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24
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The 4-NQO mouse model: An update on a well-established in vivo model of oral carcinogenesis. Methods Cell Biol 2020; 163:197-229. [PMID: 33785166 DOI: 10.1016/bs.mcb.2020.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The early detection and management of oral premalignant lesions (OPMDs) improve their outcomes. Animal models that mimic histological and biological processes of human oral carcinogenesis may help to improve the identification of OPMD at-risk of progression into oral squamous cell carcinoma and to develop preventive strategies for the entire field of cancerization. No animal model is perfectly applicable for investigating human oral carcinogenesis. However, the 4-nitroquinoline 1-oxide (4-NQO) mouse model is well established and mimics several morphological, histological, genomic and molecular features of human oral carcinogenesis. Some of the reasons for the success of this model include its reproducible experimental conditions with limited variation, the possibility of realizing longitudinal studies with invasive intervention or gene manipulation, and sample availability for all stages of oral carcinogenesis, especially premalignant lesions. Moreover, the role of histological and molecular alterations in the field of cancerization (i.e., macroscopically healthy mucosa exposed to a carcinogen) during oral carcinogenesis can be easily explored using this model. In this review, we discuss the advantages and drawbacks of this model for studying human oral carcinogenesis. In summary, the 4-NQO-induced murine oral cancer model is relevant for investigating human oral carcinogenesis, including the immune microenvironment, and for evaluating therapeutic and chemoprevention agents.
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25
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Ali A, Soares AB, Eymael D, Magalhaes M. Expression of invadopodia markers can identify oral lesions with a high risk of malignant transformation. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2020; 7:61-74. [PMID: 33001588 PMCID: PMC7737762 DOI: 10.1002/cjp2.182] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 01/31/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignant tumor of the oral cavity and is usually preceded by a range of premalignant tissue abnormalities termed oral potentially malignant disorders. Identifying malignant transformation is critical for early treatment and consequently improved survival and decreased morbidity. Invadopodia (INV) are specialized subcellular structures required for cancer cell invasion. We developed a new method to visualize INV in keratinocytes using fluorescent immunohistochemistry (FIHC) and semi‐automated images analysis. The presence of INV was used to determine the risk of malignant transformation. We analyzed 145 formalin‐fixed, paraffin‐embedded (FFPE) oral biopsy samples from 95 patients diagnosed as nondysplastic, dysplastic, and OSCC including 49 patients whose lesions transformed to OSCC (progressing) and 46 cases that did not transform to OSCC (control). All samples were stained for Cortactin, tyrosine kinase substrate with five SH3 domains (Tks5) and matrix metallopeptidase 14 (MMP14) using FIHC, imaged using confocal microscopy and analyzed using a multichannel colocalization analysis. The areas of colocalization were used to generate an INV score. Using the INV score, we were able to identify progressing lesions with a sensitivity of 75–100% and specificity of 72–76%. A positive INV score was associated with increased risk of progression to OSCC. Our results suggest that INV markers can be used in conjunction with the current diagnostic standard for early detection of OSCC.
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Affiliation(s)
- Aiman Ali
- Cancer Invasion and Metastasis Laboratory, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Andresa Borges Soares
- Cancer Invasion and Metastasis Laboratory, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.,Department of Oral Pathology, São Leopoldo Mandic Institute and Research Center, Campinas, Brazil
| | - Denise Eymael
- Cancer Invasion and Metastasis Laboratory, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Marco Magalhaes
- Cancer Invasion and Metastasis Laboratory, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.,Oral Pathology and Oral Medicine, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.,Dental and Maxillofacial Sciences Department, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
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26
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Increased expression of PD-1 and PD-L1 in oral lesions progressing to oral squamous cell carcinoma: a pilot study. Sci Rep 2020; 10:9705. [PMID: 32546692 PMCID: PMC7297711 DOI: 10.1038/s41598-020-66257-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
Oral cancer is a devastating disease and is commonly preceded by a range of oral premalignant disorders. We investigated the expression of PD-1 and PD-L1 in oral epithelial dysplasia (OED) that progressed to oral squamous cell carcinoma (OSCC) compared to non-progressing dysplasia. 49 oral biopsies were analyzed, including 19 progressing cases, 20 cases did not progress, and 10 OSCC. Samples were stained with monoclonal antibodies for PD-1 and PD-L1, followed by conventional peroxidase reaction immunohistochemistry (IHC) imaged under light microscopy or fluorescent immunohistochemistry (FIHC) imaged using a confocal microscope. Images were analyzed using a novel semi-automated analysis protocol. PD-1/PD-L1 expression was assessed at the epithelium/tumor cells (TC) and at inflammatory cells in lamina propria. Our results show a significant increase in PD-L1 expression in progressing compared to non-progressing dysplasia. Using FIHC, we showed increased PD-L1 expression, increased nuclear density in progressing dysplasia and a better interobserver agreement compared with IHC. We developed a new FIHC-based quantitative method to study PD-1/PD-L1 expression in FFPE samples and showed that PD-L1 is highly expressed in premalignant lesions progressing to cancer. Our results suggest that immunomodulation via PD-L1/PD-1 pathway occurs prior to malignant transformation.
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27
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Oral potentially malignant disorders: A scoping review of prognostic biomarkers. Crit Rev Oncol Hematol 2020; 153:102986. [PMID: 32682268 DOI: 10.1016/j.critrevonc.2020.102986] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 02/08/2023] Open
Abstract
This scoping review aimed to map evidence regarding biomarkers for malignant transformation of oral potentially malignant disorders (OPMD). Seventy-three longitudinal studies investigating prognostic biomarkers for OPMD malignant transformation were included, encompassing 5612 disorders and 108 biomarkers, of which 72 were investigated by immunohistochemistry. Most biomarkers were assessed in one or two studies, while five (p53, Ki-67, podoplanin, p16, and DNA ploidy) were analyzed in five or more studies. All studies investigating podoplanin (n = 8) reported a significant association between positive/high immunoexpression and malignant transformation. Similarly, all studies assessing DNA ploidy (n = 5) found that aneuploidy or gross genomic aberrations were significantly associated with malignant transformation. Included studies often presented mixed data from different OPMD subtypes, inadequate description of population characteristics, and lack of adjusted analysis for confounding factors. One hundred and eight biomarkers were identified and, from these, podoplanin immunoexpression and DNA ploidy were considered promising candidates for future long-term clinical research.
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28
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Dai Y, Lv Q, Qi T, Qu J, Ni H, Liao Y, Liu P, Qu Q. Identification of hub methylated-CpG sites and associated genes in oral squamous cell carcinoma. Cancer Med 2020; 9:3174-3187. [PMID: 32155325 PMCID: PMC7196066 DOI: 10.1002/cam4.2969] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/07/2020] [Accepted: 02/16/2020] [Indexed: 12/15/2022] Open
Abstract
To improve personalized diagnosis and prognosis for oral squamous cell carcinoma (OSCC) by identification of hub methylated‐CpG sites and associated genes, weighted gene comethylation network analysis (WGCNA) was performed to examine and identify hub modules and CpG sites correlated with OSCC. Here, WGCNA modeling yielded blue and brown comethylation modules that were significantly associated with OSCC status. Following screening of the differentially expressed genes (DEGs) from gene expression microarrays and differentially methylated‐CpG sites (DCGs), integrated multiomics analysis of the DEGs, DCGs, and hub CpG sites from the modules was performed to investigate their correlations. Expression levels of 16 CpG sites‐associated genes were negatively correlated with methylation patterns of promoter. Moreover, Kaplan‐Meier survival analysis of the hub CpG sites and associated genes was carried out using 2 public databases, MethSurv and GEPIA. Only 5 genes, ACTA1, ACTN2, OSR1, SYNGR1, and ZNF677, had significant overall survival using GEPIA. Hypermethylated‐CpG sites ACTN2‐cg21376883 and OSR1‐cg06509239 were found to be associated with poor survival by MethSurv. Methylation status of specific site and expression levels of associated genes were determined using clinical samples by quantitative methylation‐specific PCR and real‐time PCR. Pearson's correlation analysis showed that methylation levels of cg06509239 and cg18335068 were negatively related to OSR1 and ZNF677 expression levels, respectively. Our classification schema using multiomics analysis represents a screening framework for identification of hub CpG sites and associated genes.
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Affiliation(s)
- Yuxin Dai
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiaoli Lv
- Department of Science and Education, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Nanchang, Jiangxi, China
| | - Tingting Qi
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongli Ni
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yongkang Liao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Peng Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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29
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Diagnostic Adjuncts for Oral Cavity Squamous Cell Carcinoma and Oral Potentially Malignant Disorders. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-32316-5_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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30
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Li X, Wu N, Ji H, Huang Y, Hu H, Li J, Mi S, Duan S, Chen X. A male-specific association between AGTR1 hypermethylation and coronary heart disease. Bosn J Basic Med Sci 2020; 20:31-36. [PMID: 31538912 PMCID: PMC7029202 DOI: 10.17305/bjbms.2019.4321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/07/2019] [Indexed: 01/09/2023] Open
Abstract
The AGTR1 gene encodes angiotensin II receptor type 1, which is involved in cardiovascular diseases such as coronary heart disease (CHD). In the current study, we analyzed AGTR1 promoter methylation level in a Han Chinese population by SYBR green-based quantitative methylation-specific PCR (qMSP). We collected blood samples from 761 CHD patients and 398 non-CHD controls at the Ningbo First Hospital. A data mining analysis was also performed to explore the association between AGTR1 methylation and AGTR1 gene expression, using datasets from the cBioPortal for Cancer Genomics and the Gene Expression Omnibus (GEO) database. Our results showed a significantly higher percentage of methylated reference (PMR) of AGTR1 in male CHD patients compared with male non-CHD controls (median PMR: 2.12% vs. 0.59%, p = 0.037). The data mining analysis showed that AGTR1 expression was significantly increased in human hepatoma HepG2 cells treated with the demethylation agent 5-aza-2’-deoxycytidine (fold = 3.12, p = 0.009). Further data mining analysis using the cholangiocarcinoma (TCGA, PanCancer Atlas) data indicated an inverse association between AGTR1 methylation and AGTR1 expression (r = -0.595, p = 1.29E-04). Overall, our results suggest that AGTR1 methylation is involved in the regulation of AGTR1 gene expression and that AGTR1 hypermethylation is associated with CHD in males. These findings may provide new clues about the pathogenesis of CHD.
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Affiliation(s)
- Xiaojing Li
- Key Laboratory of Ningbo First Hospital and Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, China
| | - Nan Wu
- Key Laboratory of Ningbo First Hospital and Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, China
| | - Huihui Ji
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, China
| | - Yi Huang
- Key Laboratory of Ningbo First Hospital and Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, China
| | - Haochang Hu
- Key Laboratory of Ningbo First Hospital and Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, China
| | - Jiyi Li
- Key Laboratory of Ningbo First Hospital and Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, China
| | - Siyu Mi
- Key Laboratory of Ningbo First Hospital and Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, China.
| | - Xiaomin Chen
- Key Laboratory of Ningbo First Hospital and Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, China.
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31
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Villa A, Celentano A, Glurich I, Borgnakke WS, Jensen SB, Peterson DE, Delli K, Ojeda D, Vissink A, Farah CS. World Workshop on Oral Medicine VII: Prognostic biomarkers in oral leukoplakia: A systematic review of longitudinal studies. Oral Dis 2020; 25 Suppl 1:64-78. [PMID: 31140698 DOI: 10.1111/odi.13087] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/24/2019] [Accepted: 03/03/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To identify the prognostic biomarker candidates for stratification and long-term surveillance of oral leukoplakia progressing to cancer via a systematic literature review. MATERIALS AND METHODS Systematic searches with no date restrictions were conducted on March 29, 2018, targeting the databases PubMed (Ovid), EMBASE (Ovid), EBM (Ovid), and Web of Science (ISI). Bias was assessed using the Quality in Prognosis Studies tool. Biomarkers were stratified based on hallmarks of cancer. RESULTS Inclusion criteria were met by 25 of 3,415 studies. A range of biomarkers were evaluated experimentally for risk stratification, prognosis, and surveillance of oral leukoplakia in tissue, blood, and saliva. However, the studies were highly heterogeneous and require further validation. Biomarkers reported in these studies included inflammatory or oxidative markers, growth factors, ion channels, genetic and cellular regulatory factors, and epigenetic biomarkers. Studies tended to include small sample sizes, under-reported or variably reported histopathological data, did not address potential confounding, reported limited/variable follow-up data, or lacked a control group. Inclusion of subsets from chemoprevention trials may have introduced bias regarding reported malignant transformation rates and accuracy of prognostic biomarkers. CONCLUSIONS This review identified insufficient longitudinal evidence to support validated prognostic biomarkers for oral leukoplakia. Further studies are needed to identify molecular targets with the potential to mitigate risk of malignant transformation.
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Affiliation(s)
- Alessandro Villa
- Division of Oral Medicine and Dentistry, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts
| | - Antonio Celentano
- Melbourne Dental School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid Glurich
- Center for Oral and Systemic Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | - Wenche S Borgnakke
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan
| | - Siri Beier Jensen
- Department of Dentistry and Oral Health, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Douglas E Peterson
- Oral Medicine Section, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, Connecticut
| | - Konstantina Delli
- Department of Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David Ojeda
- Department of Comprehensive Dentistry, School of Dentistry, UT Health San Antonio, San Antonio, Texas
| | - Arjan Vissink
- Department of Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Camile S Farah
- Australian Centre for Oral Oncology Research & Education, Perth, Westren Australia, Australia
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32
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Gaździcka J, Gołąbek K, Strzelczyk JK, Ostrowska Z. Epigenetic Modifications in Head and Neck Cancer. Biochem Genet 2019; 58:213-244. [PMID: 31712935 PMCID: PMC7113219 DOI: 10.1007/s10528-019-09941-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common human malignancy in the world, with high mortality and poor prognosis for patients. Among the risk factors are tobacco and alcohol intake, human papilloma virus, and also genetic and epigenetic modifications. Many studies show that epigenetic events play an important role in HNSCC development and progression, including DNA methylation, chromatin remodeling, histone posttranslational covalent modifications, and effects of non-coding RNA. Epigenetic modifications may influence silencing of tumor suppressor genes by promoter hypermethylation, regulate transcription by microRNAs and changes in chromatin structure, or induce genome instability through hypomethylation. Moreover, getting to better understand aberrant patterns of methylation may provide biomarkers for early detection and diagnosis, while knowledge about target genes of microRNAs may improve the therapy of HNSCC and extend overall survival. The aim of this review is to present recent studies which demonstrate the role of epigenetic regulation in the development of HNSCC.
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Affiliation(s)
- Jadwiga Gaździcka
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808, Zabrze, Katowice, Poland.
| | - Karolina Gołąbek
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808, Zabrze, Katowice, Poland
| | - Joanna Katarzyna Strzelczyk
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808, Zabrze, Katowice, Poland
| | - Zofia Ostrowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808, Zabrze, Katowice, Poland
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33
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Suzuki T, Yamazaki H, Honda K, Ryo E, Kaneko A, Ota Y, Mori T. Altered DNA methylation is associated with aberrant stemness gene expression in early‑stage HNSCC. Int J Oncol 2019; 55:915-924. [PMID: 31432153 DOI: 10.3892/ijo.2019.4857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/17/2019] [Indexed: 11/05/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is characterized by morphological and functional cellular heterogeneity, which are properties of progenitor cells, as opposed to cell alterations caused by accidental expression of stem cell‑related molecules. The expression levels of stemness molecules and their distribution in HNSCC are unclear. As regards sporadic cellular heterogeneity, methylation is an important factor for transcriptional regulation in tumors. Integrative screening analysis of mRNA expression and altered methylation status was performed with original microarrays in 12 tumor and non‑tumor pairs of oral squamous cell carcinoma (SCC) cases. From this data set, genes regulated via aberrant DNA methylation and classified proteins were validated by function clustering. Olfactomedin 4 (OLFM4), known as an intestinal stemness molecule and cell‑cell adhesion factor, was found to be highly expressed in tumors, with an mRNA expression ratio [tumor/normal (T/N)] of 40.7686 and low methylation (‑18.02%) in the promoter region. In addition, the OLFM4 expression levels increased following treatment with the demethylating agent 5‑azacytidine in two HNSCC cell lines. Furthermore, the expression levels of OLFM4 in 59 cases of early‑stage tongue SCC were analyzed using immunohistochemistry to examine protein expression corresponding to the histopathological definition of tumors and to evaluate prognosis. The aberrant stemness gene expression caused by altered DNA methylation appeared to regulate early‑stage HNSCC characteristics. The results of the present study indicated a correlation between OLFM4 expression and promoter methylation, and suggest that it plays an important role in tumor cell heterogeneity in HNSCC.
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Affiliation(s)
- Takatsugu Suzuki
- Department of Oral Surgery, Tokai University School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Hiroshi Yamazaki
- Department of Oral Surgery, Tokai University School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Kazufumi Honda
- Division of Biomarker for Cancer Early Detection, National Cancer Center Research Institute, Tokyo 104‑0045, Japan
| | - Eijitsu Ryo
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104‑0045, Japan
| | - Akihiro Kaneko
- Department of Oral Surgery, Tokai University School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Yoshihide Ota
- Department of Oral Surgery, Tokai University School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Taisuke Mori
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104‑0045, Japan
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Kim SY, Han YK, Song JM, Lee CH, Kang K, Yi JM, Park HR. Aberrantly hypermethylated tumor suppressor genes were identified in oral squamous cell carcinoma (OSCC). Clin Epigenetics 2019; 11:116. [PMID: 31405379 PMCID: PMC6689875 DOI: 10.1186/s13148-019-0715-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/22/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) is a genetic and epigenetic disease. There is growing evidence to suggest that environmental factors due to epigenetic changes can be involved in the OSCC pathogenesis. Although tumor suppressor genes (TSGs) are commonly inactivated by promoter hypermethylation in human cancers, the epigenetic changes and the mechanism of TSGs in human OSCC remain unclear. We therefore assessed the methylation status of the TSGs, which are associated with epigenetic silencing in human cancers, OSCC cell lines, primary tumors, and normal oral mucosa. RESULTS We used 14 TSGs that were originally identified in colon cancer to investigate the aberrant hypermethylation of these genes associated with transcriptional silencing in 10 OSCC cell lines. We found three TSGs, TFPI2, SOX17, and GATA4, that are robustly hypermethylated and are associated with transcriptional silencing in OSCC cell lines. The re-expression of the three genes was induced by 5-aza-2'-deoxycytidine (5-aza-dC) in cells in which these genes were not expressed or had a lack of expression. In 33 cases of primary OSCC tumors, promoter hypermethylation was detected for the TFPI2, SOX17, and GATA4 genes at (32/33) 97%, (22/33) 67%, and (11/33) 33%, respectively. Eleven normal oral mucosa samples showed no promoter hypermethylation for all three genes, which suggests that this promoter hypermethylation is cancer-specific. Bisulfite sequencing analysis confirmed the cancer-specific methylation of the TFPI2, SOX17, and GATA4 promoters in the OSCC cell lines and tumors but not in the normal oral mucosa samples. More importantly, the methylation status of TFPI2, GATA4, and SOX17 was significantly associated with OSCC patients' overall survival through TCGA DNA methylation database. CONCLUSIONS We identified that TFPI2, SOX17, and GATA4 are frequently hypermethylated in human OSCC cells in a cancer-specific manner and that the transcriptional expression of these genes is regulated by promoter hypermethylation in OSCC. Our results highlight the great potential used as a synergistic biomarker set to improve the prognosis and therapeutic treatment for patients with OSCC.
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Affiliation(s)
- Soo Yeon Kim
- Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan, 50612, Gyeongsangnam-do, Republic of Korea
| | - Yu Kyeong Han
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan, 47392, Republic of Korea
| | - Jae Min Song
- Department of Oral and Maxillofacial Surgery, Pusan National University, Yangsan, 50612, Gyeongsangnam-do, Republic of Korea.,Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan, 50612, Gyeongsangnam-do, Republic of Korea
| | - Chang Hun Lee
- Department of Pathology, School of Medicine, Pusan National University, Busan, 49241, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan, 47392, Republic of Korea.
| | - Hae Ryoun Park
- Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan, 50612, Gyeongsangnam-do, Republic of Korea. .,Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan, 50612, Gyeongsangnam-do, Republic of Korea.
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Tang D, Lin T, Wang Y, Cao H. High expression of proenkephalin is associated with favorable outcomes in patients with gastrointestinal stromal tumors. Cancer Manag Res 2019; 11:6681-6690. [PMID: 31410059 PMCID: PMC6643514 DOI: 10.2147/cmar.s202044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/11/2019] [Indexed: 01/01/2023] Open
Abstract
Purpose The aim of this study was to elucidate the prognostic value of proenkephalin (PENK) in gastrointestinal stromal tumors (GISTs). Patients and methods We collected data on 268 eligible postoperative patients diagnosed with GIST between January 1, 2002, and December 31, 2011. PENK expression was detected in GIST tissues classified using the United States National Institutes of Health (NIH) risk classification system. The associations between high PENK expression and the clinicopathological characteristics were assessed. Overall survival (OS) and recurrence-free survival (RFS) were estimated by Kaplan–Meier analysis, and the log-rank test was used to compare the differences between groups. Univariate and multivariate Cox regression analyses were conducted to assess the prognostic value of PENK in GIST patients. Results High PENK expression was more common in the low- and intermediate-risk GIST groups compared with the high-risk group (P<0.05). Additionally, PENK expression was associated with tumor size, mitosis count per 50 high-power fields, and tumor rupture (P<0.05). Kaplan–Meier analysis revealed that high PENK expression was associated with superior OS and RFS, while low PENK expression was associated with worse OS and RFS. Furthermore, PENK was shown to be an independent predictor of OS and RFS in the overall population (for OS, hazard ratio [HR], 1.596, 95% confidence interval [CI], 1.006–2.914, P<0.001; for RFS, HR, 1.910, 95% CI, 0.977–3.089, P<0.001). Conclusion PENK expression in GIST is closely associated with NIH risk grade and prognosis, indicating that PENK may act as a tumor suppressor and may serve as a new biomarker for predicting prognosis in postoperative GIST patients.
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Affiliation(s)
- Defeng Tang
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China.,Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, People's Republic of China
| | - Tianlong Lin
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Yangyang Wang
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Hui Cao
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
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Calabrese F, Lunardi F, Pezzuto F, Fortarezza F, Vuljan SE, Marquette C, Hofman P. Are There New Biomarkers in Tissue and Liquid Biopsies for the Early Detection of Non-Small Cell Lung Cancer? J Clin Med 2019; 8:jcm8030414. [PMID: 30917582 PMCID: PMC6463117 DOI: 10.3390/jcm8030414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/11/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is one of the most lethal malignancies worldwide, mainly due to its late diagnoses. The detection of molecular markers on samples provided from routine bronchoscopy including several liquid-based cytology tests (e.g., bronchoaspirate, bronchoalveolar lavage) and/or on easily obtained specimens such as sputum could represent a new approach to improve the sensitivity in lung cancer diagnoses. Recently growing interest has been reported for "noninvasive" liquid biopsy as a valuable source for molecular profiling. Unfortunately, a biomarker and/or composition of biomarkers capable of detecting early-stage lung cancer has yet to be discovered even if in the last few years there has been, through the use of revolutionary new technologies, an explosion of lung cancer biomarkers. Assay sensitivity and specificity need to be improved particularly when new approaches and/or tools are used. We have focused on the most important markers detected in tissue, and on several cytological specimens and liquid biopsies overall.
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Affiliation(s)
- Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Francesco Fortarezza
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Stefania Edith Vuljan
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Charles Marquette
- University Côte d'Azur, University Nice Hospital, FHU OncoAge, Department of Pneumology, Pasteur Hospital, 06001 Nice, France.
- University Côte d'Azur, CNRS, INSERM, IRCAN, Team 4, FHU OncoAge, 06001 Nice, France.
| | - Paul Hofman
- University Côte d'Azur, CNRS, INSERM, IRCAN, Team 4, FHU OncoAge, 06001 Nice, France.
- University Côte d'Azur, University Nice Hospital, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, 06001 Nice, France.
- University Côte d'Azur, Biobank (BB-0033-00025), FHU OncoAge, Pasteur Hospital, 06001 Nice, France.
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Rozek LS, Virani S, Bellile EL, Taylor JMG, Sartor MA, Zarins KR, Virani A, Cote C, Worden FP, Mark MEP, McLean SA, Duffy SA, Yoo GH, Saba NF, Shin DM, Kucuk O, Wolf GT. Soy Isoflavone Supplementation Increases Long Interspersed Nucleotide Element-1 (LINE-1) Methylation in Head and Neck Squamous Cell Carcinoma. Nutr Cancer 2019; 71:772-780. [PMID: 30862188 PMCID: PMC6513708 DOI: 10.1080/01635581.2019.1577981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/13/2018] [Accepted: 12/26/2018] [Indexed: 12/20/2022]
Abstract
AIM Soy isoflavones have been suggested as epigenetic modulating agents with effects that could be important in carcinogenesis. Hypomethylation of LINE-1 has been associated with head and neck squamous cell carcinoma (HNSCC) development from oral premalignant lesions and with poor prognosis. To determine if neoadjuvant soy isoflavone supplementation could modulate LINE-1 methylation in HNSCC, we undertook a clinical trial. METHODS Thirty-nine patients received 2-3 weeks of soy isoflavone supplements (300 mg/day) orally prior to surgery. Methylation of LINE-1, and 6 other genes was measured by pyrosequencing in biopsy, resection, and whole blood (WB) specimens. Changes in methylation were tested using paired t tests and ANOVA. Median follow up was 45 months. RESULTS LINE-1 methylation increased significantly after soy isoflavone (P < 0.005). Amount of change correlated positively with days of isoflavone taken (P = 0.04). Similar changes were not seen in corresponding WB samples. No significant changes in tumor or blood methylation levels were seen in the other candidate genes. CONCLUSION This is the first demonstration of in vivo increases in tissue-specific global methylation associated with soy isoflavone intake in patients with HNSCC. Prior associations of LINE-1 hypomethylation with genetic instability, carcinogenesis, and prognosis suggest that soy isoflavones maybe potential chemopreventive agents in HNSCC.
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Affiliation(s)
- Laura S Rozek
- a University of Michigan , Ann Arbor , Michigan, USA
| | - Shama Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - A Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | - C Cote
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - George H Yoo
- c Karmanos Cancer Institute , Wayne State University , Detroit , Michigan 48201, USA
| | - Nabil F Saba
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Dong M Shin
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Omer Kucuk
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
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Chaudhary M, Chaudhary S. Functional relevance of promoter CpG island of human Angiotensin II type 1 receptor (AT1R) gene. Mol Cell Biochem 2019; 457:31-40. [PMID: 30790131 DOI: 10.1007/s11010-019-03509-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/14/2019] [Indexed: 12/20/2022]
Abstract
Angiotensin II type 1 receptor can activate number of signalling pathways upon stimulation and consequently its involvement in cancer progression have also been revealed. But which epigenetic mechanisms are involved in its regulation, need to be further explored. In-silico analysis revealed a promoter CpG island (CGI) which was cloned and assayed for functional activity using reporter gene system. The effect of methylation on this CGI was analysed through varying degree of methyltransferase treatment of cloned fragment. Results thus obtained were validated by direct sequencing. To further establish the status of this effect, in-vivo analysis was done through screening of methylation pattern in the targeted region among hypertensives (HTN) and normotensives (NTN) using PCR-Bisulphite sequencing. Additionally, clinical details of all participants, biochemical parameters and lifestyle related information was also collected and statistically evaluated. Reporter gene assay assigned functional activity to the cloned promoter CpG island. Increased dose and durations of methyltransferase treatment decreased the expression of reporter gene indicating the role of promoter DNA methylation. Among all the human samples screened, only one of the HTN individual was found to have single hemi-methylated CpG site at a position which happens to be a part of Sp1 transcription factor binding site. To conclude, CpG island in the promoter region of AT1R (CpG.P.AT1R) gets regulated through epigenetic mechanism of DNA methylation.
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Affiliation(s)
- Mayank Chaudhary
- Department cum National Centre for Human Genome Studies and Research (NCHGSR), Panjab University, Chandigarh, 160 014, India
| | - Shashi Chaudhary
- Department cum National Centre for Human Genome Studies and Research (NCHGSR), Panjab University, Chandigarh, 160 014, India.
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Bhatia S, Sharma J, Bukkapatnam S, Oweida A, Lennon S, Phan A, Milner D, Uyanga N, Jimeno A, Raben D, Somerset H, Heasley L, Karam SD. Inhibition of EphB4-Ephrin-B2 Signaling Enhances Response to Cetuximab-Radiation Therapy in Head and Neck Cancers. Clin Cancer Res 2018; 24:4539-4550. [PMID: 29848571 DOI: 10.1158/1078-0432.ccr-18-0327] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/23/2018] [Accepted: 05/25/2018] [Indexed: 01/30/2023]
Abstract
Purpose: The clinical success of targeted therapies such as cetuximab and radiotherapy (RT) is hampered by the low response rates and development of therapeutic resistance. In the current study, we investigated the involvement of EphB4-ephrin-B2 protumorigenic signaling in mediating resistance to EGFR inhibition and RT in head and neck cancers.Experimental Design: We used patient-derived xenograft (PDX) models of head and neck squamous cell carcinoma (HNSCC) and HNSCC cell lines to test our hypothesis. Tumor tissues were subjected to PhosphoRTK array, and Western blotting to detect changes in EphB4-ephrin-B2 targets. mRNA sequencing and microarray data analysis were performed on PDX tumors and HNSCC cell lines, respectively, to determine differences in gene expression of molecules involved in tumor cell growth, proliferation, and survival pathways. Effects on cell growth were determined by MTT assay on HNSCC cells downregulated for EphB4/ephrin-B2 expression, with and without EGFR inhibitor and radiation.Results: Our data from locally advanced HNSCC patients treated with standard-of-care definitive chemo-RT show elevated EphB4 and ephrin-B2 levels after failure of treatment. We observed significant response toward cetuximab and RT following EphB4-ephrin-B2 inhibition, resulting in improved survival in tumor-bearing mice. Tumor growth inhibition was accompanied by a decrease in the levels of proliferation and prosurvival molecules and increased apoptosis.Conclusions: Our findings underscore the importance of adopting rational drug combinations to enhance therapeutic effect. Our study documenting enhanced response of HNSCC to cetuximab-RT with EphB4-ephrin-B2 blockade has the potential to translate into the clinic to benefit this patient population. Clin Cancer Res; 24(18); 4539-50. ©2018 AACR.
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Affiliation(s)
- Shilpa Bhatia
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Jaspreet Sharma
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Sanjana Bukkapatnam
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Ayman Oweida
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Shelby Lennon
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Andy Phan
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Dallin Milner
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Nomin Uyanga
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Antonio Jimeno
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - David Raben
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Hilary Somerset
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Lynn Heasley
- Department of Craniofacial Biology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Sana D Karam
- Department of Radiation Oncology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado.
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Jelinek J, Madzo J. DREAM: A Simple Method for DNA Methylation Profiling by High-throughput Sequencing. Methods Mol Biol 2018; 1465:111-27. [PMID: 27581143 DOI: 10.1007/978-1-4939-4011-0_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The digital restriction enzyme analysis of methylation (DREAM) is a simple method for DNA methylation analysis at tens of thousands of CpG sites across the genome. The method creates specific signatures at unmethylated and methylated CpG sites by sequential digests of genomic DNA with restriction endonucleases SmaI and XmaI, respectively. Both enzymes have the same CCCGGG recognition site; however, they differ in their sensitivity to CpG methylation and their cutting pattern. SmaI cuts only unmethylated sites leaving blunt 5'-GGG ends. XmaI cuts remaining methylated CC(me)CGG sites leaving 5'-CCGGG ends. Restriction fragments with distinct signatures at their ends are ligated to Illumina sequencing adaptors with sample-specific barcodes. High-throughput sequencing of pooled libraries follows. Sequencing reads are mapped to the restriction sites in the reference genome, and signatures corresponding to methylation status of individual DNA molecules are resolved. Methylation levels at target CpG sites are calculated as the proportion of sequencing reads with the methylated signature to the total number of reads mapping to the particular restriction site. Aligning the reads to the reference genome of any species is straightforward, since the method does not rely on bisulfite conversion of DNA. Sequencing of 25 million reads per human DNA library yields over 50,000 unique CpG sites with high coverage enabling accurate determination of DNA methylation levels. DREAM has a background less than 1 % making it suitable for accurate detection of low methylation levels. In summary, the method is simple, robust, highly reproducible, and cost-effective.
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Affiliation(s)
- Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 North Broad Street, Rm 339 F, PAHB, Philadelphia, PA, 19140, USA.
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
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Sun YW, Chen KM, Imamura Kawasawa Y, Salzberg AC, Cooper TK, Caruso C, Aliaga C, Zhu J, Gowda K, Amin S, El-Bayoumy K. Hypomethylated Fgf3 is a potential biomarker for early detection of oral cancer in mice treated with the tobacco carcinogen dibenzo[def,p]chrysene. PLoS One 2017; 12:e0186873. [PMID: 29073177 PMCID: PMC5658092 DOI: 10.1371/journal.pone.0186873] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/09/2017] [Indexed: 12/26/2022] Open
Abstract
Genetic and epigenetic alterations observed at end stage OSCC formation could be considered as a consequence of cancer development and thus changes in normal or premalignant tissues which had been exposed to oral carcinogens such as Dibenzo[def,p]chrysene (DBP) may better serve as predictive biomarkers of disease development. Many types of DNA damage can induce epigenetic changes which can occur early and in the absence of evident morphological abnormalities. Therefore we used ERRBS to generate genome-scale, single-base resolution DNA methylomes from histologically normal oral tissues of mice treated with DBP under experimental conditions known to induce maximum DNA damage which is essential for the development of OSCC induced by DBP in mice. After genome-wide correction, 30 and 48 differentially methylated sites (DMS) were identified between vehicle control and DBP treated mice using 25% and 10% differences in methylation, respectively. RT-PCR was further performed to examine the expressions of nine selected genes. Among them, Fgf3, a gene frequently amplified in head and neck cancer, showed most prominent and significant gene expression change (2.4× increases), despite the hypomethylation of Fgf3 was identified at >10kb upstream of transcription start site. No difference was observed in protein expression between normal oral tissues treated with DBP or vehicle as examined by immunohistochemistry. Collectively, our results indicate that Fgf3 hypomethylation and gene overexpression, but not protein expression, occurred in the early stage of oral carcinogenesis induced by DBP. Thus, Fgf3 hypomethylation may serve as a potential biomarker for early detection of OSCC.
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Affiliation(s)
- Yuan-Wan Sun
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Kun-Ming Chen
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Yuka Imamura Kawasawa
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Anna C. Salzberg
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Timothy K. Cooper
- Department of Comparative Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Carla Caruso
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Cesar Aliaga
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Junjia Zhu
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Krishne Gowda
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Shantu Amin
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Karam El-Bayoumy
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States of America
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AGTR1 promoter hypermethylation in lung squamous cell carcinoma but not in lung adenocarcinoma. Oncol Lett 2017; 14:4989-4994. [PMID: 29085512 DOI: 10.3892/ol.2017.6824] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 08/03/2017] [Indexed: 12/23/2022] Open
Abstract
Aberrant DNA methylation is associated with non-small cell lung cancer (NSCLC), suggesting that gene promoter methylation may be a potential biomarker for the detection or risk prediction of NSCLC. The present study aimed to evaluate the potential usage of angiotensin II receptor type 1 (AGTR1) methylation in two major pathologic subtypes: Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Quantitative methylation-specific polymerase chain reaction was used to investigate the effect of AGTR1 promoter methylation in the tumor and the paired adjacent non-tumor tissue samples from 42 patients with LUSC, and 69 with LUAD. The percentage of methylated reference was calculated and presented as the median (interquartile range 25th-75th percentile). The results of the current study revealed that there was significantly increased AGTR1 promoter methylation in the tumor tissues compared with the paired adjacent non-tumor tissue [97.4 (57.22-130.5) vs. 85 (48.25-123); P=0.024]. Furthermore, higher AGTR1 promoter methylation was observed in patients with LUSC compared with LUAD (odds ratio=2.483; 95% confidence interval=1.125-5.480; P=0.023). Significant differences were identified in AGTR1 methylation between non-tumor and the tumor tissues in LUSC [113.5 (68.33-148.73) vs. 93.04 (45.94-140); P=0.008]. In addition, the Cancer Genome Atlas data of 378 patients with LUSC and 477 with LUAD revealed an inverse correlation between gene expression and the methylation status of AGTR1 promoter.. These data suggest that AGTR1 hypermethylation is a promising biomarker to assist in LUSC detection and diagnosis.
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Shen S, Wang G, Shi Q, Zhang R, Zhao Y, Wei Y, Chen F, Christiani DC. Seven-CpG-based prognostic signature coupled with gene expression predicts survival of oral squamous cell carcinoma. Clin Epigenetics 2017; 9:88. [PMID: 28852427 PMCID: PMC5571486 DOI: 10.1186/s13148-017-0392-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/16/2017] [Indexed: 12/18/2022] Open
Abstract
Background DNA methylation has started a recent revolution in genomics biology by identifying key biomarkers for multiple cancers, including oral squamous cell carcinoma (OSCC), the most common head and neck squamous cell carcinoma. Methods A multi-stage screening strategy was used to identify DNA-methylation-based signatures for OSCC prognosis. We used The Cancer Genome Atlas (TCGA) data as training set which were validated in two independent datasets from Gene Expression Omnibus (GEO). The correlation between DNA methylation and corresponding gene expression and the prognostic value of the gene expression were explored as well. Results The seven DNA methylation CpG sites were identified which were significantly associated with OSCC overall survival. Prognostic signature, a weighted linear combination of the seven CpG sites, successfully distinguished the overall survival of OSCC patients and had a moderate predictive ability for survival [training set: hazard ratio (HR) = 3.23, P = 5.52 × 10−10, area under the curve (AUC) = 0.76; validation set 1: HR = 2.79, P = 0.010, AUC = 0.67; validation set 2: HR = 3.69, P = 0.011, AUC = 0.66]. Stratification analysis by human papillomavirus status, clinical stage, age, gender, smoking status, and grade retained statistical significance. Expression of genes corresponding to candidate CpG sites (AJAP1, SHANK2, FOXA2, MT1A, ZNF570, HOXC4, and HOXB4) was also significantly associated with patient’s survival. Signature integrating of DNA methylation, gene expression, and clinical information showed a superior ability for prognostic prediction (AUC = 0.78). Conclusion Prognostic signature integrated of DNA methylation, gene expression, and clinical information provides a better prognostic prediction value for OSCC patients than that with clinical information only. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0392-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sipeng Shen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Health, Harvard School of Public Health, Boston, MA USA
| | - Guanrong Wang
- National Health and Family Planning Commission Contraceptives Adverse Reaction Surveillance Center, Jiangsu Institute of Planned Parenthood Research, Nanjing, China
| | - Qianwen Shi
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruyang Zhang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Yang Zhao
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Yongyue Wei
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China.,Ministry of Education Key Laboratory for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,101 Longmian Avenue, Nanjing, Jiangsu 211136 China
| | - David C Christiani
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Health, Harvard School of Public Health, Boston, MA USA
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Wang J, Li W, Zhao Y, Kang D, Fu W, Zheng X, Pang X, Du G. Members of FOX family could be drug targets of cancers. Pharmacol Ther 2017; 181:183-196. [PMID: 28830838 DOI: 10.1016/j.pharmthera.2017.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FOX families play important roles in biological processes, including metabolism, development, differentiation, proliferation, apoptosis, migration, invasion and longevity. Here we are focusing on roles of FOX members in cancers, FOX members and drug resistance, FOX members and stem cells. Finally, FOX members as drug targets of cancer treatment were discussed. Future perspectives of FOXC1 research were described in the end.
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Affiliation(s)
- Jinhua Wang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Wan Li
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Ying Zhao
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - De Kang
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Weiqi Fu
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Xiangjin Zheng
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Xiaocong Pang
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China
| | - Guanhua Du
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China; Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, 100050 Beijing, China.
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Morandi L, Gissi D, Tarsitano A, Asioli S, Gabusi A, Marchetti C, Montebugnoli L, Foschini MP. CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel. Clin Epigenetics 2017; 9:85. [PMID: 28814981 PMCID: PMC5558660 DOI: 10.1186/s13148-017-0386-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/07/2017] [Indexed: 02/08/2023] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is usually diagnosed at an advanced stage and is commonly preceded by oral premalignant lesions. The mortality rates have remained unchanged (50% within 5 years after diagnosis), and it is related to tobacco smoking and alcohol intake. Novel molecular markers for early diagnosis are urgently needed. The purpose of this study was to evaluate the diagnostic value of methylation level in a set of 18 genes by bisulfite next-generation sequencing. Methods With minimally invasive oral brushing, 28 consecutive OSCC, one squamous cell carcinoma with sarcomatoid features, six high-grade squamous intraepithelial lesions (HGSIL), 30 normal contralateral mucosa from the same patients, and 65 healthy donors were evaluated for DNA methylation analyzing 18 target genes by quantitative bisulfite next-generation sequencing. We further evaluated an independent cohort (validation dataset) made of 20 normal donors, one oral fibroma, 14 oral lichen planus (OLP), three proliferative verrucous leukoplakia (PVL), and two OSCC. Results Comparing OSCC with normal healthy donors and contralateral mucosa in 355 CpGs, we identified the following epigenetically altered genes: ZAP70, ITGA4, KIF1A, PARP15, EPHX3, NTM, LRRTM1, FLI1, MIR193, LINC00599, PAX1, and MIR137HG showing hypermethylation and MIR296, TERT, and GP1BB showing hypomethylation. The behavior of ZAP70, GP1BB, H19, EPHX3, and MIR193 fluctuated among different interrogated CpGs. The gap between normal and OSCC samples remained mostly the same (Kruskal-Wallis P values < 0.05), but the absolute values changed conspicuously. ROC curve analysis identified the most informative CpGs, and we correctly stratified OSCC and HGSIL from normal donors using a multiclass linear discriminant analysis in a 13-gene panel (AUC 0.981). Only the OSCC with sarcomatoid features was negative. Three contralateral mucosa were positive, a sign of a possible field cancerization. Among imprinted genes, only MIR296 showed loss of imprinting. DNMT1, TERC, and H19 together with the global methylation of long interspersed element 1 were unchanged. In the validation dataset, values over the threshold were detected in 2/2 OSCC, in 3/3 PVL, and in 2/14 OLP. Conclusions Our data highlight the importance of CpG location and correct estimation of DNA methylation level for highly accurate early diagnosis of OSCC. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0386-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luca Morandi
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
| | - Davide Gissi
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Achille Tarsitano
- Unit of Maxillofacial Surgery, S. Orsola Hospital Bologna, Bologna, Italy
| | - Sofia Asioli
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
| | - Andrea Gabusi
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Claudio Marchetti
- Unit of Maxillofacial Surgery, S. Orsola Hospital Bologna, Bologna, Italy
| | - Lucio Montebugnoli
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Maria Pia Foschini
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
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The promising impact of molecular profiling on treatment strategies in oral cancers. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2017; 118:242-247. [PMID: 28576460 DOI: 10.1016/j.jormas.2017.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 12/19/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is a major cause of cancer-associated morbidity and mortality. Although OSCC may develop from easily accessible oral preneoplastic lesions (OPLs), no intervention has been reported so far that reduces the rate of malignant transformation. A comprehensive molecular characterization of oral carcinogenesis may help refining treatment strategies both in patients with OPLs and OSCC. Herein, we review main molecular alterations occurring at different steps during oral carcinogenesis and show how molecularly-based medicine and surgery may impact the outcome of OSCC in the future.
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Kumar A, Sarode SC, Sarode GS, Majumdar B, Patil S, Sharma NK. Beyond gene dictation in oral squamous cell carcinoma progression and its therapeutic implications. TRANSLATIONAL RESEARCH IN ORAL ONCOLOGY 2017. [DOI: 10.1177/2057178x17701463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ajay Kumar
- Cancer and Translational Research Lab, Dr D.Y. Patil Biotechnology and Bioinformatics Institute, Dr D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Sachin C Sarode
- Department of Oral Pathology, Dr D.Y. Patil Dental College and Research, Pimpri, Pune, Maharashtra, India
| | - Gargi S Sarode
- Department of Oral Pathology, Dr D.Y. Patil Dental College and Research, Pimpri, Pune, Maharashtra, India
| | - Barnali Majumdar
- Department of Oral Pathology and Microbiology, Bhojia Dental College and Hospital, Baddi, Himachal Pradesh, India
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr D.Y. Patil Biotechnology and Bioinformatics Institute, Dr D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
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Chatterjee A, Rodger EJ, Stockwell PA, Le Mée G, Morison IM. Generating Multiple Base-Resolution DNA Methylomes Using Reduced Representation Bisulfite Sequencing. Methods Mol Biol 2017; 1537:279-298. [PMID: 27924600 DOI: 10.1007/978-1-4939-6685-1_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Reduced representation bisulfite sequencing (RRBS) is an effective technique for profiling genome-wide DNA methylation patterns in eukaryotes. RRBS couples size selection, bisulfite conversion, and second-generation sequencing to enrich for CpG-dense regions of the genome. The progressive improvement of second-generation sequencing technologies and reduction in cost provided an opportunity to examine the DNA methylation patterns of multiple genomes. Here, we describe a protocol for sequencing multiple RRBS libraries in a single sequencing reaction to generate base-resolution methylomes. Furthermore, we provide a brief guideline for base-calling and data analysis of multiplexed RRBS libraries. These strategies will be useful to perform large-scale, genome-wide DNA methylation analysis.
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Affiliation(s)
- Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.
- Gravida: National Centre for Growth and Development, University of Auckland, 85 Park Road, Grafton, Auckland, New Zealand.
| | - Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Peter A Stockwell
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Gwenn Le Mée
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Ian M Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.
- Gravida: National Centre for Growth and Development, University of Auckland, 85 Park Road, Grafton, Auckland, New Zealand.
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Schulz CA, Christensson A, Ericson U, Almgren P, Hindy G, Nilsson PM, Struck J, Bergmann A, Melander O, Orho-Melander M. High Level of Fasting Plasma Proenkephalin-A Predicts Deterioration of Kidney Function and Incidence of CKD. J Am Soc Nephrol 2016; 28:291-303. [PMID: 27401687 DOI: 10.1681/asn.2015101177] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/20/2016] [Indexed: 11/03/2022] Open
Abstract
High levels of proenkephalin-A (pro-ENK) have been associated with decreased eGFR in an acute setting. Here, we examined whether pro-ENK levels predict CKD and decline of renal function in a prospective cohort of 2568 participants without CKD (eGFR>60 ml/min per 1.73 m2) at baseline. During a mean follow-up of 16.6 years, 31.7% of participants developed CKD. Participants with baseline pro-ENK levels in the highest tertile had significantly greater yearly mean decline of eGFR (Ptrend<0.001) and rise of cystatin C (Ptrend=0.01) and creatinine (Ptrend<0.001) levels. Furthermore, compared with participants in the lowest tertile, participants in the highest tertile of baseline pro-ENK concentration had increased CKD incidence (odds ratio, 1.51; 95% confidence interval, 1.18 to 1.94) when adjusted for multiple factors. Adding pro-ENK to a model of conventional risk factors in net reclassification improvement analysis resulted in reclassification of 14.14% of participants. Genome-wide association analysis in 4150 participants of the same cohort revealed the strongest association of pro-ENK levels with rs1012178 near the PENK gene, where the minor T-allele associated with a 0.057 pmol/L higher pro-ENK level per allele (P=4.67x10-21). Furthermore, the T-allele associated with a 19% increased risk of CKD per allele (P=0.03) and a significant decrease in the instrumental variable estimator for eGFR (P<0.01) in a Mendelian randomization analysis. In conclusion, circulating plasma pro-ENK level predicts incident CKD and may aid in identifying subjects in need of primary preventive regimens. Additionally, the Mendelian randomization analysis suggests a causal relationship between pro-ENK level and deterioration of kidney function over time.
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Affiliation(s)
- Christina-Alexandra Schulz
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | - Anders Christensson
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | - Ulrika Ericson
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | - Peter Almgren
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | - George Hindy
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | - Peter M Nilsson
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | | | - Andreas Bergmann
- Sphingotec GmbH, Hennigsdorf, Germany; and.,Waltraut Bergmann Foundation, Hohen Neuendorf, Germany
| | - Olle Melander
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | - Marju Orho-Melander
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden;
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