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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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Wipplinger M, Mink S, Bublitz M, Gassner C. Regulation of the Lewis Blood Group Antigen Expression: A Literature Review Supplemented with Computational Analysis. Transfus Med Hemother 2024; 51:225-236. [PMID: 39135855 PMCID: PMC11318966 DOI: 10.1159/000538863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 08/15/2024] Open
Abstract
Background The Lewis (Le) blood group system, unlike most other blood groups, is not defined by antigens produced internally to the erythrocytes and their precursors but rather by glycan antigens adsorbed on to the erythrocyte membrane from the plasma. These oligosaccharides are synthesized by the two fucosyltransferases FUT2 and FUT3 mainly in epithelial cells of the digestive tract and transferred to the plasma. At their place of synthesis, some Lewis blood group carbohydrate antigen variants also seem to be involved in various gastrointestinal malignancies. However, relatively little is known about the transcriptional regulation of FUT2 and FUT3. Summary To address this question, we screened existing literature and additionally used in silico prediction tools to identify novel candidate regulators for FUT2 and FUT3 and combine these findings with already known data on their regulation. With this approach, we were able to describe a variety of transcription factors, RNA binding proteins and microRNAs, which increase FUT2 and FUT3 transcription and translation upon interaction. Key Messages Understanding the regulation of FUT2 and FUT3 is crucial to fully understand the blood group system Lewis (ISBT 007 LE) phenotypes, to shed light on the role of the different Lewis antigens in various pathologies, and to identify potential new diagnostic targets for these diseases.
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Affiliation(s)
- Martin Wipplinger
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Sylvia Mink
- Central Medical Laboratories, Feldkirch, Austria
- Medical-Scientific Faculty, Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Maike Bublitz
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Christoph Gassner
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
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Rapado-González Ó, Costa-Fraga N, Bao-Caamano A, López-Cedrún JL, Álvarez-Rodríguez R, Crujeiras AB, Muinelo-Romay L, López-López R, Díaz-Lagares Á, Suárez-Cunqueiro MM. Genome-wide DNA methylation profiling in tongue squamous cell carcinoma. Oral Dis 2024; 30:259-271. [PMID: 36398465 DOI: 10.1111/odi.14444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/14/2022] [Accepted: 11/05/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To provide a comprehensive characterization of DNA methylome of oral tongue squamous cell carcinoma (OTSCC) and identify novel tumor-specific DNA methylation markers for early detection using saliva. MATERIAL AND METHODS Genome-wide DNA methylation analysis including six OTSCC matched adjacent non-tumoral tissue and saliva was performed using Infinium MethylationEPIC array. Differentially methylated levels of selected genes in our OTSCC cohort were further validated using OTSCC methylation data from The Cancer Genome Atlas database (TCGA). The methylation levels of a set of tumor-specific hypermethylated genes associated with a downregulated expression were evaluated in saliva. Receiver operating characteristic (ROC) curves were performed to assess the diagnostic value of DNA methylation markers. RESULTS A total of 25,890 CpGs (20,505 hypomethylated and 5385 hypermethylated) were differentially methylated (DMCpGs) between OTSCC and adjacent non-tumoral tissue. Hypermethylation of 11 tumor-specific genes was validated in OTSCC TCGA cohort. Of these 11 genes, A2BP1, ANK1, ALDH1A2, GFRA1, TTYH1, and PDE4B were also hypermethylated in saliva. These six salivary methylated genes showed high diagnostic accuracy (≥0.800) for discriminating patients from controls. CONCLUSIONS This is the first largest genome-wide DNA methylation study on OTSCC that identifies a group of novel tumor-specific DNA methylation markers with diagnostic potential in saliva.
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Affiliation(s)
- Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Nicolás Costa-Fraga
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS, SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS, SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - José Luis López-Cedrún
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña (CHUAC, SERGAS), A Coruña, Spain
| | - Roberto Álvarez-Rodríguez
- Department of Pathology, Complexo Hospitalario Universitario de A Coruña (CHUAC, SERGAS), A Coruña, Spain
| | - Ana Belén Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS, SERGAS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Laura Muinelo-Romay
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rafael López-López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), Santiago de Compostela, Spain
| | - Ángel Díaz-Lagares
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS, SERGAS), Santiago de Compostela, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), Santiago de Compostela, Spain
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Sorroche BP, Miranda KC, Beltrami CM, Arantes LMRB, Kowalski LP, Marchi FA, Rogatto SR, Almeida JD. HOXA1 3'UTR Methylation Is a Potential Prognostic Biomarker in Oral Squamous cell Carcinoma. Cancers (Basel) 2024; 16:874. [PMID: 38473236 DOI: 10.3390/cancers16050874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND HOXA1 is a prognostic marker and a potential predictive biomarker for radioresistance in head and neck tumors. Its overexpression has been associated with promoter methylation and a worse prognosis in oral squamous cell carcinoma (OSCC) patients. However, opposite outcomes are also described. The effect of the methylation of this gene on different gene regions, other than the promoter, remains uncertain. We investigated the methylation profile at different genomic regions of HOXA1 in OSCC and correlated differentially methylated CpG sites with clinicopathological data. METHODS The HOXA1 DNA methylation status was evaluated by analyzing data from The Cancer Genome Atlas and three Gene Expression Omnibus datasets. Significant differentially methylated CpG sites were considered with a |∆β| ≥ 0.10 and a Bonferroni-corrected p-value < 0.01. Differentially methylated CpGs were validated by pyrosequencing using two independent cohorts of 15 and 47 OSCC patients, respectively. RESULTS Compared to normal tissues, we found significantly higher DNA methylation levels in the 3'UTR region of HOXA1 in OSCC. Higher methylation levels in tumor samples were positively correlated with smoking habits and patients' overall survival. CONCLUSIONS Our findings suggest that HOXA1 gene body methylation is a promising prognostic biomarker for OSCC with potential clinical applications in patient monitoring.
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Affiliation(s)
- Bruna Pereira Sorroche
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil
| | - Keila Cristina Miranda
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos 12224-300, Brazil
| | | | | | - Luiz Paulo Kowalski
- Head and Neck Surgery and Otorhinolaryngology Department, AC Camargo Cancer Center, Latin American Cooperative Oncology Group, São Paulo 01509-010, Brazil
- Head and Neck Surgery Department and LIM 28, University of São Paulo Medical School, São Paulo 01246-903, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo 01246-000, Brazil
- Clinical Hospital of the University of Sao Paulo Medical School (HCFMUSP), São Paulo 05403-010, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos 12224-300, Brazil
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5
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Rasouli M, Safari F, Sobhani N, Alavi M, Roudi R. Regulation of Cellular-Signaling Pathways by Mammalian Proteins Containing Bacterial EPIYA or EPIYA-Like Motifs Predicted to be Phosphorylated. DNA Cell Biol 2024; 43:74-84. [PMID: 38153368 DOI: 10.1089/dna.2023.0350] [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] [Indexed: 12/29/2023] Open
Abstract
The effector proteins of several pathogenic bacteria contain the Glu-Pro-Ile-Tyr-Ala (EPIYA) motif or other similar motifs. The EPIYA motif is delivered into the host cells by type III and IV secretion systems, through which its tyrosine residue undergoes phosphorylation by host kinases. These motifs atypically interact with a wide range of Src homology 2 (SH2) domain-containing mammalian proteins through tyrosine phosphorylation, which leads to the perturbation of multiple signaling cascades, the spread of infection, and improved bacterial colonization. Interestingly, it has been reported that EPIYA (or EPIYA-like) motifs exist in mammalian proteomes and regulate mammalian cellular-signaling pathways, leading to homeostasis and disease pathophysiology. It is possible that pathogenic bacteria have exploited EPIYA (or EPIYA-like) motifs from mammalian proteins and that the mammalian EPIYA (or EPIYA-like) motifs have evolved to have highly specific interactions with SH2 domain-containing proteins. In this review, we focus on the regulation of mammalian cellular-signaling pathways by mammalian proteins containing these motifs.
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Affiliation(s)
- Mohammad Rasouli
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Fatemeh Safari
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Navid Sobhani
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mana Alavi
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Raheleh Roudi
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology, Stanford University, Stanford, California, USA
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Sapkota D, Wang D, Schreurs O, Vallenari EM, Pandey Dhakal S, Küntziger T, Toközlü BS, Utheim TP, Chaudhry FA. Investigation of Roles of SLC38A1 in Proliferation and Differentiation of Mouse Tongue Epithelium and Expression in Human Oral Tongue Squamous Cell Carcinoma. Cancers (Basel) 2024; 16:405. [PMID: 38254895 PMCID: PMC10814082 DOI: 10.3390/cancers16020405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The aerobic glycolytic pathway, boosting lactate formation, and glutamine addiction are two hallmarks of cancer pathophysiology. Consistent with this, several cell membrane glutamine transporters, belonging to different solute carrier (SLC) families, have been shown to be upregulated in a cell-specific manner to furnish the cells with glutamine and glutamine-derived metabolic intermediates. Among them, the system A transporter Slc38a1 has a higher affinity for glutamine compared to other SLC transporters, and it undergoes highly multifaceted regulation at gene and protein levels. The current study aimed to investigate the functional role of Slc38a1 in the proliferation and maturation of the mouse tongue epithelium. Secondly, we aimed to examine the expression of SLC38A1 and its regulation in human tongue oral squamous cell carcinoma (OTSCC). Employing Slc38a1 wild-type and knockout mice, we showed that Slc38a1 was not directly linked to the regulation of the proliferation and differentiation of the mouse tongue epithelium. External transcriptomic datasets and Western blot analyses showed upregulation of SLC38A1 mRNA/protein in human OTSCC and oral cancer cell lines as compared to the corresponding controls. Further, an investigation of external datasets indicated that mechanisms other than the amplification of the SLC38A1 chromosomal locus or hypomethylation of the SLC38A1 promoter region might be important for the upregulation of SLC38A1 in OTSCC.
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Affiliation(s)
- Dipak Sapkota
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Daxin Wang
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway
| | - Olaf Schreurs
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Evan M. Vallenari
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Sushma Pandey Dhakal
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Thomas Küntziger
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Burcu Sengüven Toközlü
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
- Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara 06510, Turkey
| | - Tor Paaske Utheim
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0372 Oslo, Norway
| | - Farrukh Abbas Chaudhry
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway
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Xu Z, Chen X, Song X, Kong X, Chen J, Song Y, Xue M, Qiu L, Geng M, Xue C, Zhang W, Zhang R. ATHENA: an independently validated autophagy-related epigenetic prognostic prediction model of head and neck squamous cell carcinoma. Clin Epigenetics 2023; 15:97. [PMID: 37296474 PMCID: PMC10257287 DOI: 10.1186/s13148-023-01501-0] [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: 11/16/2022] [Accepted: 05/09/2023] [Indexed: 06/12/2023] Open
Abstract
The majority of these existing prognostic models of head and neck squamous cell carcinoma (HNSCC) have unsatisfactory prediction accuracy since they solely utilize demographic and clinical information. Leveraged by autophagy-related epigenetic biomarkers, we aim to develop a better prognostic prediction model of HNSCC incorporating CpG probes with either main effects or gene-gene interactions. Based on DNA methylation data from three independent cohorts, we applied a 3-D analysis strategy to develop An independently validated auTophagy-related epigenetic prognostic prediction model of HEad and Neck squamous cell carcinomA (ATHENA). Compared to prediction models with only demographic and clinical information, ATHENA has substantially improved discriminative ability, prediction accuracy and more clinical net benefits, and shows robustness in different subpopulations, as well as external populations. Besides, epigenetic score of ATHENA is significantly associated with tumor immune microenvironment, tumor-infiltrating immune cell abundances, immune checkpoints, somatic mutation and immunity-related drugs. Taken together these results, ATHENA has the demonstrated feasibility and utility of predicting HNSCC survival ( http://bigdata.njmu.edu.cn/ATHENA/ ).
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Affiliation(s)
- Ziang Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, China
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinlei Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, China
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaomeng Song
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, China
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinxin Kong
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, SPH Building Room 406, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, China
| | - Jiajin Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, SPH Building Room 406, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, China
| | - Yunjie Song
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, SPH Building Room 406, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, China
| | - Maojie Xue
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, SPH Building Room 406, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, China
| | - Lin Qiu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, China
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mingzhu Geng
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, China
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changyue Xue
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, China.
- Department of Implant Dentistry, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Wei Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, China.
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, SPH Building Room 406, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, China.
- China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China.
- Changzhou Medical Center, Nanjing Medical University, Changzhou, 213164, Jiangsu, China.
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8
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Vatsa PP, Jindal Y, Bhadwalkar J, Chamoli A, Upadhyay V, Mandoli A. Role of epigenetics in OSCC: an understanding above genetics. Med Oncol 2023; 40:122. [PMID: 36941511 DOI: 10.1007/s12032-023-01992-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023]
Abstract
Oral cavity cancer is categorized under head and neck cancer that frequently develops from squamous cells hence also known as oral squamous cell carcinoma (OSCC). Although molecular markers for oral cavity cancer are already known, epigenetic signatures for the same haven't been explored much. Epigenetic and genetic alterations were initially thought to be discrete mechanisms driving the tumour but the whole exome sequencing of various cancers has revealed the interdependency of epigenetics and genetic alterations. The reversible nature of these epigenetic changes makes them an alluring target for cancer therapeutics. The primary epigenetic alterations in cancer include DNA methylation and histone modifications. These alterations are useful for patient early detection and prognostication. This review summarizes the epigenetic perspective to understand the etiology, epigenetic biomarkers, and epi-drugs for better predictive diagnosis and treatment of OSCC.
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Affiliation(s)
- Priyanka P Vatsa
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Yogita Jindal
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Janhavi Bhadwalkar
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Ambika Chamoli
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Vinal Upadhyay
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Amit Mandoli
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India.
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9
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Chen L, Liu H, Li Y, Lin X, Xia S, Wanggou S, Li X. Functional characterization of TSPAN7 as a novel indicator for immunotherapy in glioma. Front Immunol 2023; 14:1105489. [PMID: 36845098 PMCID: PMC9947846 DOI: 10.3389/fimmu.2023.1105489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Glioma is the most common primary malignant tumor of the central nervous system in clinical practice. Most adult diffuse gliomas have poor efficacy after standard treatment, especially glioblastoma. With the in-depth understanding of brain immune microenvironment, immunotherapy as a new treatment has attracted much attention. In this study, through analyzing a large number of glioma cohorts, we reported that TSPAN7, a member of the tetraspanin family, decreased in high-grade gliomas and low expression was associated with poor prognosis in glioma patients. Meanwhile, the expression pattern of TSPAN7 was verified in glioma clinical samples and glioma cell lines by qPCR, Western Blotting and immunofluorescence. In addition, functional enrichment analysis showed that cell proliferation, EMT, angiogenesis, DNA repair and MAPK signaling pathways were activated in the TSPAN7 lower expression subgroup. Lentiviral plasmids were used to overexpress TSPAN7 in U87 and LN229 glioma cell lines to explore the anti-tumor role of TSPAN7 in glioma. Moreover, by analyzing the relationship between TSPAN7 expression and immune cell infiltration in multiple datasets, we found that TSPAN7 was significantly negatively correlated with the immune infiltration of tumor-related macrophages, especially M2-type macrophages. Further analysis of immune checkpoints showed that, the expression level of TSPAN7 was negatively correlated with the expression of PD-1, PD-L1 and CTLA-4. Using an independent anti-PD-1 immunotherapy cohorts of GBM, we demonstrated that TSPAN7 expression may had a synergistic effect with PD-L1 on the response to immunotherapy. Based on the above findings, we speculate that TSPAN7 can serve as a biomarker for prognosis and a potential immunotherapy target in glioma patients.
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Affiliation(s)
- Long Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongwei Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanwen Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Xuelei Lin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shunjin Xia
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
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10
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DNA Methylation as a Diagnostic, Prognostic, and Predictive Biomarker in Head and Neck Cancer. Int J Mol Sci 2023; 24:ijms24032996. [PMID: 36769317 PMCID: PMC9917637 DOI: 10.3390/ijms24032996] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a term collectively used to describe all cancers that develop in the oral and nasal cavities, the paranasal sinuses, the salivary glands, the pharynx, and the larynx. The majority (75%) of all newly diagnosed cases are observed in patients with locally advanced and aggressive disease, associated with significant relapse rates (30%) and poor prognostic outcomes, despite advances in multimodal treatment. Consequently, there is an unmet need for the identification and application of tools that would enable diagnosis at the earliest possible stage, accurately predict prognostic outcomes, contribute to the timely detection of relapses, and aid in the decision for therapy selection. Recent evidence suggests that DNA methylation can alter the expression of genes in a way that it favors tumorigenesis and tumor progression in HNSCC, and therefore represents a potential source for biomarker identification. This study summarizes the current knowledge on how abnormally methylated DNA profiles in HNSCC patients may contribute to the pathogenesis of HNSCC and designate the methylation patterns that have the potential to constitute clinically valuable biomarkers for achieving significant advances in the management of the disease and for improving survival outcomes in these patients.
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11
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Antra, Parashar P, Hungyo H, Jain A, Ahmad S, Tandon V. Unraveling molecular mechanisms of Head and neck cancer. Crit Rev Oncol Hematol 2022; 178:103778. [PMID: 35932993 DOI: 10.1016/j.critrevonc.2022.103778] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/02/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Malignancies that develop from mucosal epithelium of the upper aerodigestive tract are known as head and neck squamous cell carcinomas (HNSCC). Heterogeneity, late stage diagnosis and high recurrence rate are big hurdles in head and neck treatment regimen. Presently, the biomarkers available for diagnosis and prognosis of HNSCC are based on smoking as the major risk habit. This review shed light on the differential environment of HNSCC in smokeless tobacco consuming Indian patients. Frequent mutation in genes involved in DNA repair pathway (p53), cell proliferation (PIK3CA, HRAS) and cell death (CASP8, FADD) are common in western population. On the contrary, the genes involved in metastasis (MMPs, YAP1), lymphocyte proliferation (TNFRSF4, CD80), cell-cell adhesion (DCC, EDNRB), miRNA processing (DROSHA) and inflammatory responses (TLR9, IL-9) are mutated in Indian HNSCC patients. Gene ontology enrichment analysis highlighted that responses to chemical stimulus, immune pathways and stress pathways are highly enriched in Indian patients.
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Affiliation(s)
- Antra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Palak Parashar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Hungharla Hungyo
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067.
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12
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Ma B, Chai B, Dong H, Qi J, Wang P, Xiong T, Gong Y, Li D, Liu S, Song F. Diagnostic classification of cancers using DNA methylation of paracancerous tissues. Sci Rep 2022; 12:10646. [PMID: 35739223 PMCID: PMC9226137 DOI: 10.1038/s41598-022-14786-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The potential role of DNA methylation from paracancerous tissues in cancer diagnosis has not been explored until now. In this study, we built classification models using well-known machine learning models based on DNA methylation profiles of paracancerous tissues. We evaluated our methods on nine cancer datasets collected from The Cancer Genome Atlas (TCGA) and utilized fivefold cross-validation to assess the performance of models. Additionally, we performed gene ontology (GO) enrichment analysis on the basis of the significant CpG sites selected by feature importance scores of XGBoost model, aiming to identify biological pathways involved in cancer progression. We also exploited the XGBoost algorithm to classify cancer types using DNA methylation profiles of paracancerous tissues in external validation datasets. Comparative experiments suggested that XGBoost achieved better predictive performance than the other four machine learning methods in predicting cancer stage. GO enrichment analysis revealed key pathways involved, highlighting the importance of paracancerous tissues in cancer progression. Furthermore, XGBoost model can accurately classify nine different cancers from TCGA, and the feature sets selected by XGBoost can also effectively predict seven cancer types on independent GEO datasets. This study provided new insights into cancer diagnosis from an epigenetic perspective and may facilitate the development of personalized diagnosis and treatment strategies.
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Affiliation(s)
- Baoshan Ma
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China.
| | - Bingjie Chai
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Heng Dong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Jishuang Qi
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Pengcheng Wang
- Department of Mechanical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Tong Xiong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Yi Gong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Di Li
- Department of Neuro Intervention, Dalian Medical University Affiliated Dalian Municipal Central Hospital, Dalian, 116033, China
| | - Shuxin Liu
- Department of Nephrology, Dalian Medical University Affiliated Dalian Municipal Central Hospital, Dalian, 116033, China.
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
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13
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Cao Y, Ye D, Shen Z, Li Z, Li Q, Rong H. The Expression Profile, Clinical Application and Potential Tumor Suppressing Mechanism of hsa_circ_0001675 in Head and Neck Carcinoma. Front Oncol 2022; 12:769666. [PMID: 35600372 PMCID: PMC9121769 DOI: 10.3389/fonc.2022.769666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose This study sought to identify circular RNAs (circRNA) that participate in the regulation of head and neck cancer (HNC), analyze their clinical application, and predict their molecular mechanism during HNC. Materials and Methods High-throughput sequencing was used to analyze circRNA expression in 18 matched HNC and adjacent normal tissues. Target circRNAs with significantly differential expression were obtained. In 103 HNC and adjacent normal tissues, real-time fluorescent quantitative PCR (qRT-PCR) was used to verify the differential expression of target circRNAs. This data was combined with clinicopathological information to analyze the diagnostic value of target circRNA. Bioinformatics was used to find target circRNAs that acted as competitive endogenous RNA (ceRNA) and construct a circRNA-miRNA-mRNA regulatory network. mRNA expression was verified by immunohistochemistry (IHC). Results A total of 714 differentially expressed circRNAs were detected in HNC, and the low expression of hsa_circ_0001675 was particularly significant (fold change [FC] = -4.85, P = 6.305E-05). hsa_circ_0001675 had significantly lower expression in HNC than in normal tissue (P < 0.01). Low hsa_circ_0001675 expression was positively associated with tumor invasion and clinical staging (P < 0.05), and its area under the ROC curve (AUC) was 0.7776. Low hsa_circ_0001675 expression also correlated with the overall survival (OS) rate and the progression-free survival (PFS) rate of HNC patients (P < 0.001). Bioinformatics was used to construct a ceRNA network of hsa_circ_0001675 with six differentially expressed miRNAs (hsa-miR-330-5p, hsa-miR-498, hsa-miR-532-3p, hsa-miR-577, hsa-miR-1248, and hsa-miR-1305) and 411 differentially expressed mRNAs and found that the neuroactive ligand-receptor interaction, and the cAMP and calcium signaling pathways were particularly enriched. Further bioinformatics and IHC analysis showed that miR577/TESC is the likely downstream signaling pathway for hsa_circ_0001675. Conclusion This study showed that hsa_circ_0001675 is downregulated in HNC and could be an effective biomarker for HNC diagnosis. In addition, hsa_circ_0001675 may have a potential ceRNA mechanism and suppress HNC disease progression through the hsa_circ_0001675-miRNA-mRNA axis.
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Affiliation(s)
- Yujie Cao
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital , Ningbo, China
- Medical School of Ningbo University, Ningbo, China
| | - Dong Ye
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital , Ningbo, China
| | - Zhisen Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital , Ningbo, China
- *Correspondence: Zhisen Shen, ; Zan Li,
| | - Zan Li
- The Affiliated Cancer Hospital of Xiangya School of Medical, Central South University, Changsha, China
- *Correspondence: Zhisen Shen, ; Zan Li,
| | - Qun Li
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital , Ningbo, China
| | - Hao Rong
- Medical School of Ningbo University, Ningbo, China
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14
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Yang F, Shi J, Zhang L, Wang H, Li Y. Role of fibulin-1 gene promoter methylation in the carcinogenesis and development of tongue squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2022; 133:432-440. [PMID: 35153187 DOI: 10.1016/j.oooo.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/26/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Recently, fibulin-1 (FBLN1) has been shown to be downregulated in various cancers via promoter hypermethylation. Our study aimed to determine the expression and methylation status of FBLN1 in tongue squamous cell carcinoma (TSCC) tissues and cells. METHODS Methylation-specific polymerase chain reaction was implemented to detect the methylation status of the FBLN1 gene in TSCC tissues and Western blot analysis was used to detect the expression of FBLN1 protein. The human TSCC cell lines CAL27 and SCC9 were cultured in vitro and treated with 5-aza-deoxycytidine (5-Aza-dC). CCK-8, colony formation, and Transwell assays were performed to test TSCC cell proliferation, migration, and invasion following 5-Aza-dC treatment or overexpression of FBLN1, which was further verified in in vivo experiments. RESULTS FBLN1 was hypermethylated and the protein expression was reduced in TSCC tissues. After human TSCC cell lines (CAL27 and SCC9) were treated with 5-Aza-dC or overexpressed FBLN1, FBLN1 expression was upregulated and the TSCC cell proliferation, migration, and invasion abilities were suppressed. In vivo experiments further showed that demethylation or overexpression of FBLN1 slowed tumor growth in nude mice. CONCLUSION This study demonstrated that 5-Aza-dC treatment or overexpression of FBLN1 inhibited the growth of human TSCC.
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Affiliation(s)
- Fang Yang
- Department of Oncology, Daqing Oilfield General Hospital, Daqing, China
| | - Jing Shi
- Department of Stomatology, Daqing Oilfield General Hospital, Daqing, China
| | - Liangyu Zhang
- Department of Oncology, Daqing Oilfield General Hospital, Daqing, China.
| | - Hongyan Wang
- Department of Stomatology, Daqing Oilfield General Hospital, Daqing, China
| | - Yang Li
- Department of Stomatology, Daqing Oilfield General Hospital, Daqing, China
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15
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Yu Y, Tang H, Franceschi D, Mujagond P, Acharya A, Deng Y, Lethaus B, Savkovic V, Zimmerer R, Ziebolz D, Li S, Schmalz G. Immune Checkpoint Gene Expression Profiling Identifies Programmed Cell Death Ligand-1 Centered Immunologic Subtypes of Oral and Squamous Cell Carcinoma With Favorable Survival. Front Med (Lausanne) 2022; 8:759605. [PMID: 35127742 PMCID: PMC8810827 DOI: 10.3389/fmed.2021.759605] [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: 08/16/2021] [Accepted: 12/20/2021] [Indexed: 12/23/2022] Open
Abstract
Objective This study aimed to identify the programmed death ligand-1 (PDL1, also termed as CD274) and its positively correlated immune checkpoint genes (ICGs) and to determine the immune subtypes of CD274-centered ICG combinations in oral and squamous cell carcinoma (OSCC). Materials and Methods Firstly, the 95 ICGs obtained via literature reviews were identified in the Cancer Genome Atlas (TCGA) database in relation to OSCC, and such 88 ICG expression profiles were extracted. ICGs positively correlated with CD274 were utilized for subsequent analysis. The relationship between ICGs positively correlated with CD274 and immunotherapy biomarkers (tumor mutation burden (TMB), and adaptive immune resistance pathway genes) was investigated, and the relationships of these genes with OSCC clinical features were explored. The prognostic values of CD274 and its positively correlated ICGs and also their associated gene pairs were revealed using the survival analysis. Results Eight ICGs, including CTLA4, ICOS, TNFRSF4, CD27, B- and T-lymphocyte attenuator (BTLA), ADORA2A, CD40LG, and CD28, were found to be positively correlated with CD274. Among the eight ICGs, seven ICGs (CTLA4, ICOS, TNFRSF4, CD27, BTLA, CD40LG, and CD28) were significantly negatively correlated with TMB. The majority of the adaptive immune resistance pathway genes were positively correlated with ICGs positively correlated with CD274. The survival analysis utilizing the TCGA-OSCC data showed that, although CD274 was not significantly associated with overall survival (OS), the majority of ICGs positively correlated with CD274 (BTLA, CD27, CTLA4, CD40LG, CD28, ICOS, and TNFRSF4) were significantly correlated with OS, whereby their low-expression predicted a favorable prognosis. The survival analysis based on the gene pair subtypes showed that the combination subtypes of CD274_low/BTLA_low, CD274_low/CD27_low, CD274_low/CTLA4_low, CD8A_high/BTLA_low, CD8A_high/CD27_low, and CD8A_high/CTLA4_low predicted favorable OS. Conclusion The results in this study provide a theoretical basis for prognostic immune subtyping of OSCC and highlight the importance of developing future immunotherapeutic strategies for treating oral cancer.
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Affiliation(s)
- Yang Yu
- Department of Stomatology, Qunli Branch, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Yang Yu
| | - Huiwen Tang
- Department of Stomatology, Qunli Branch, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Debora Franceschi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Prabhakar Mujagond
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, India
| | - Aneesha Acharya
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pune, India
| | - Yupei Deng
- Laboratory of Molecular Cell Biology, China Tibetology Research Center, Beijing Tibetan Hospital, Beijing, China
| | - Bernd Lethaus
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Vuk Savkovic
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Rüdiger Zimmerer
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Dirk Ziebolz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Simin Li
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
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16
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Li S, Mai Z, Gu W, Ogbuehi AC, Acharya A, Pelekos G, Ning W, Liu X, Deng Y, Li H, Lethaus B, Savkovic V, Zimmerer R, Ziebolz D, Schmalz G, Wang H, Xiao H, Zhao J. Molecular Subtypes of Oral Squamous Cell Carcinoma Based on Immunosuppression Genes Using a Deep Learning Approach. Front Cell Dev Biol 2021; 9:687245. [PMID: 34422810 PMCID: PMC8375681 DOI: 10.3389/fcell.2021.687245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/04/2021] [Indexed: 12/21/2022] Open
Abstract
Background: The mechanisms through which immunosuppressed patients bear increased risk and worse survival in oral squamous cell carcinoma (OSCC) are unclear. Here, we used deep learning to investigate the genetic mechanisms underlying immunosuppression in the survival of OSCC patients, especially from the aspect of various survival-related subtypes. Materials and methods: OSCC samples data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and OSCC-related genetic datasets with survival data in the National Center for Biotechnology Information (NCBI). Immunosuppression genes (ISGs) were obtained from the HisgAtlas and DisGeNET databases. Survival analyses were performed to identify the ISGs with significant prognostic values in OSCC. A deep learning (DL)-based model was established for robustly differentiating the survival subpopulations of OSCC samples. In order to understand the characteristics of the different survival-risk subtypes of OSCC samples, differential expression analysis and functional enrichment analysis were performed. Results: A total of 317 OSCC samples were divided into one inferring cohort (TCGA) and four confirmation cohorts (ICGC set, GSE41613, GSE42743, and GSE75538). Eleven ISGs (i.e., BGLAP, CALCA, CTLA4, CXCL8, FGFR3, HPRT1, IL22, ORMDL3, TLR3, SPHK1, and INHBB) showed prognostic value in OSCC. The DL-based model provided two optimal subgroups of TCGA-OSCC samples with significant differences (p = 4.91E-22) and good model fitness [concordance index (C-index) = 0.77]. The DL model was validated by using four external confirmation cohorts: ICGC cohort (n = 40, C-index = 0.39), GSE41613 dataset (n = 97, C-index = 0.86), GSE42743 dataset (n = 71, C-index = 0.87), and GSE75538 dataset (n = 14, C-index = 0.48). Importantly, subtype Sub1 demonstrated a lower probability of survival and thus a more aggressive nature compared with subtype Sub2. ISGs in subtype Sub1 were enriched in the tumor-infiltrating immune cells-related pathways and cancer progression-related pathways, while those in subtype Sub2 were enriched in the metabolism-related pathways. Conclusion: The two survival subtypes of OSCC identified by deep learning can benefit clinical practitioners to divide immunocompromised patients with oral cancer into two subpopulations and give them target drugs and thus might be helpful for improving the survival of these patients and providing novel therapeutic strategies in the precision medicine area.
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Affiliation(s)
- Simin Li
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhaoyi Mai
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Wenli Gu
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | | | - Aneesha Acharya
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pune, India
| | - George Pelekos
- Faculty of Dentistry, University of Hong Kong, Hong Kong, China
| | - Wanchen Ning
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Xiangqiong Liu
- Laboratory of Molecular Cell Biology, Beijing Tibetan Hospital, China Tibetology Research Center, Beijing, China
| | - Yupei Deng
- Laboratory of Molecular Cell Biology, Beijing Tibetan Hospital, China Tibetology Research Center, Beijing, China
| | - Hanluo Li
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Bernd Lethaus
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Vuk Savkovic
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Rüdiger Zimmerer
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Dirk Ziebolz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Hao Wang
- Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Hui Xiao
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Jianjiang Zhao
- Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, China
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17
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Cui SH, Hu XD, Yan Y. Wnt/β-catenin signaling pathway participates in the effect of miR-626 on oral squamous cell carcinoma by targeting RASSF4. J Oral Pathol Med 2021; 50:1005-1017. [PMID: 34121238 DOI: 10.1111/jop.13216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND The role of miR-626 in oral squamous cell carcinoma (OSCC) was investigated by targeting RASSF4. METHODS The miR-626 and RASSF4 expression was detected in normal oral mucosa or OSCC tissues and OSCC or normal cells. The methylation status of RASSF4 was analyzed using methylation-specific polymerase chain reaction (PCR). The cytoplasmic/nuclear ratios (C/N ratios) targeted by miR-626 were examined using microarray, followed by a dual-luciferase reporter assay. The subcellular localization of RASSF4 and miR-626 in OSCC cells was determined using RNA fluorescence in situ hybridization (FISH) and immunocytochemistry (ICC), respectively. Ca9-22 and HSC2 cells were divided into mock, inhibitor NC, miR-626 inhibitor, scramble, RASSF4 and miR-626 mimic + RASSF4 groups, and then CCK-8, Annexin V-FITC/PI, wound healing, Transwell, qRT-PCR and western blotting assays were performed. RESULTS OSCC tissues and cells had increased miR-626 expression and decreased RASSF4 expression. Patients with RASSF4 methylation had lower RASSF4 expression than those without methylation. In addition, a negative correlation between miR-626 and RASSF4 was found in OSCC tissues, both of which were correlated with the pathological grade, pathological stage, lymph node metastasis and patient prognosis. MiR-626 targeted RASSF4 in OSCC cells. Overexpressed RASSF4 inhibited the proliferation, invasion, migration and epithelial-mesenchymal transition (EMT) of OSCC cells, promoted cell apoptosis, and blocked the Wnt/β-Catenin pathway, which was reversed by miR-626 overexpression. CONCLUSIONS Inhibiting miR-626 can regulate the biological characteristics of OSCC cells, including proliferation, invasion, migration, EMT and apoptosis, by targeting RASSF4, which may be related to the Wnt/β-Catenin pathway.
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Affiliation(s)
- Sheng-Hai Cui
- Department of Oral and Maxillofacial Surgery, Yantai Stomatological Hospital, Yantai, China
| | - Xiao-Di Hu
- Department of Stomatology, Yantaishan Hospital, Yantai, China
| | - Yan Yan
- Department of Stomatology, Yantaishan Hospital, Yantai, China
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18
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Saidak Z, Lailler C, Testelin S, Chauffert B, Clatot F, Galmiche A. Contribution of Genomics to the Surgical Management and Study of Oral Cancer. Ann Surg Oncol 2021; 28:5842-5854. [PMID: 33846893 PMCID: PMC8460589 DOI: 10.1245/s10434-021-09904-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/07/2021] [Indexed: 02/06/2023]
Abstract
Background Oral squamous cell carcinoma (OSCC) is the most frequent type of tumor arising from the oral cavity. Surgery is the cornerstone of the treatment of these cancers. Tumor biology has long been overlooked as an important contributor to the outcome of surgical procedures, but recent studies are challenging this concept. Molecular analyses of tumor DNA or RNA provide a rich source of information about the biology of OSCC. Methods We searched for relevant articles using PubMed. We examined in particular the prospect of applying molecular methods for minimally invasive exploration of OSCC biology. Results We examined five potential applications of genomics to the surgical management and study of OSCC: i) assessing oral potentially malignant lesions; ii) tumor staging prior to surgery; iii) predicting postoperative risk in locally advanced tumors; iv) measuring minimal residual disease and optimizing the longitudinal monitoring of OSCC; and v) predicting the efficacy of medical treatment. Conclusions Genomic information can be harnessed in order to identify new biomarkers that could improve the staging, choice of therapy and management of OSCC. The identification of new biomarkers is awaited for better personalization of the surgical treatment of OSCC.
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Affiliation(s)
- Zuzana Saidak
- UR7516 "CHIMERE, Université de Picardie Jules Verne", Amiens, France. .,Centre de Biologie Humaine, CHU Amiens, Amiens, France.
| | - Claire Lailler
- UR7516 "CHIMERE, Université de Picardie Jules Verne", Amiens, France.,Centre de Biologie Humaine, CHU Amiens, Amiens, France
| | - Sylvie Testelin
- UR7516 "CHIMERE, Université de Picardie Jules Verne", Amiens, France.,Department of Maxillofacial Surgery, CHU Amiens, Amiens, France
| | - Bruno Chauffert
- UR7516 "CHIMERE, Université de Picardie Jules Verne", Amiens, France.,Department of Oncology, CHU Amiens, Amiens, France
| | - Florian Clatot
- Centre Henri Becquerel, Rouen, France.,INSERM U1245/Team IRON, Rouen, France
| | - Antoine Galmiche
- UR7516 "CHIMERE, Université de Picardie Jules Verne", Amiens, France.,Centre de Biologie Humaine, CHU Amiens, Amiens, France
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19
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Yu X, Li S, Pang M, Du Y, Xu T, Bai T, Yang K, Hu J, Zhu S, Wang L, Liu X. TSPAN7 Exerts Anti-Tumor Effects in Bladder Cancer Through the PTEN/PI3K/AKT Pathway. Front Oncol 2021; 10:613869. [PMID: 33489923 PMCID: PMC7821430 DOI: 10.3389/fonc.2020.613869] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 11/27/2020] [Indexed: 01/21/2023] Open
Abstract
The tetraspanin protein superfamily participate in the dynamic regulation of cellular membrane compartments expressed in a variety of tumor types, which may alter the biological properties of cancer cells such as cell development, activation, growth and motility. The role of tetraspanin 7 (TSPAN7) has never been investigated in bladder cancer (BCa). In this study, we aimed to investigate the biological function of TSPAN7 and its therapeutic potential in human BCa. First, via reverse transcription and quantitative real-time PCR (qRT-PCR), we observed downregulation of TSPAN7 in BCa tissues samples and cell lines and found that this downregulation was associated with a relatively high tumor stage and tumor grade. Low expression of TSPAN7 was significantly correlated with a much poorer prognosis for BCa patients than was high expression. Immunohistochemistry (IHC) showed that low TSPAN7 expression was a high-risk predictor of BCa patient overall survival. Furthermore, the inhibitory effects of TSPAN7 on the proliferation and migration of BCa cell lines were detected by CCK-8, wound-healing, colony formation and transwell assays in vitro. Flow cytometry analysis revealed that TSPAN7 induced BCa cell lines apoptosis and cell cycle arrest. In vivo, tumor growth in nude mice bearing tumor xenografts could be obviously affected by overexpression of TSPAN7. Western blotting showed that overexpression of TSPAN7 activated Bax, cleaved caspase-3 and PTEN but inactivated Bcl-2, p-PI3K, and p-AKT to inhibit BCa cell growth via the PTEN/PI3K/AKT pathway. Taken together, our study will help identify a potential marker for BCa diagnosis and supply a target molecule for BCa treatment.
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Affiliation(s)
- Xi Yu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shenglan Li
- Department of Radiography, Renmin Hospital of Wuhan University, Wuhan, China
| | - Mingrui Pang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yang Du
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tao Xu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tao Bai
- Department of Urology, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Juncheng Hu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shaoming Zhu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lei Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
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20
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Patak J, Faraone SV, Zhang-James Y. Sodium hydrogen exchanger 9 NHE9 (SLC9A9) and its emerging roles in neuropsychiatric comorbidity. Am J Med Genet B Neuropsychiatr Genet 2020; 183:289-305. [PMID: 32400953 DOI: 10.1002/ajmg.b.32787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 12/09/2019] [Accepted: 02/22/2020] [Indexed: 12/16/2022]
Abstract
Variations in SLC9A9 gene expression and protein function are associated with multiple human diseases, which range from Attention-deficit/hyperactivity disorder (ADHD) to glioblastoma multiforme. In an effort to determine the full spectrum of human disease associations with SLC9A9, we performed a systematic review of the literature. We also review SLC9A9's biochemistry, protein structure, and function, as well as its interacting partners with the goal of identifying mechanisms of disease and druggable targets. We report gaps in the literature regarding the genes function along with consistent trends in disease associations that can be used to further research into treating the respective diseases. We report that SLC9A9 has strong associations with neuropsychiatric diseases and various cancers. Interestingly, we find strong overlap in SLC9A9 disease associations and propose a novel role for SLC9A9 in neuropsychiatric comorbidity. In conclusion, SLC9A9 is a multifunctional protein that, through both its endosome regulatory function and its protein-protein interaction network, has the ability to modulate signaling axes, such as the PI3K pathway, among others.
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Affiliation(s)
- Jameson Patak
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York, USA.,College of Medicine, MD Program, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Stephen V Faraone
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York, USA.,Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Yanli Zhang-James
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
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21
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Das D, Ghosh S, Maitra A, Biswas NK, Panda CK, Roy B, Sarin R, Majumder PP. Epigenomic dysregulation-mediated alterations of key biological pathways and tumor immune evasion are hallmarks of gingivo-buccal oral cancer. Clin Epigenetics 2019; 11:178. [PMID: 31796082 PMCID: PMC6889354 DOI: 10.1186/s13148-019-0782-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/17/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Gingivo-buccal oral squamous cell carcinoma (OSCC-GB) is the most common cancer among men in India and is associated with high mortality. Although OSCC-GB is known to be quite different from tongue cancer in its genomic presentation and its clinical behavior, it is treated identically as tongue cancer. Predictive markers of prognosis and therapy that are specific to OSCC-GB are, therefore, required. Although genomic drivers of OSCC-GB have been identified by whole exome and whole genome sequencing, no epigenome-wide study has been conducted in OSCC-GB; our study has filled this gap, and has discovered and validated epigenomic hallmarks of gingivobuccal oral cancer. METHODS We have carried out integrative analysis of epigenomic (n = 87) and transcriptomic (n = 72) profiles of paired tumor-normal tissues collected from OSCC-GB patients from India. Genome-wide DNA methylation assays and RNA-sequencing were performed on high-throughput platforms (Illumina) using a half-sample of randomly selected patients to discover significantly differentially methylated probes (DMPs), which were validated on the remaining half-sample of patients. RESULTS About 200 genes showed significant inverse correlation between promoter methylation and expression, of which the most significant genes included genes that act as transcription factors and genes associated with other cancer types. Novel findings of this study include identification of (a) potential immunosuppressive effect in OSCC-GB due to significant promoter hypomethylation driven upregulation of CD274 and CD80, (b) significant dysregulation by epigenetic modification of DNMT3B (upregulation) and TET1 (downregulation); and (c) known drugs that can reverse the direction of dysregulation of gene expression caused by promoter methylation. CONCLUSIONS In OSCC-GB patients, there are significant alterations in expression of key genes that (a) regulate normal cell division by maintenance of balanced DNA methylation and transcription process, (b) maintain normal physiological signaling (PPAR, B cell receptor) and metabolism (arachidonic acid) pathways, and (c) provide immune protection against antigens, including tumor cells. These findings indicate novel therapeutic targets, including immunotherapeutic, for treatment of OSCC-GB.
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Affiliation(s)
- Debodipta Das
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | | | - Bidyut Roy
- Indian Statistical Institute, Kolkata, India
| | - Rajiv Sarin
- Advanced Centre for Treatment Research and Education in Cancer, Mumbai, India
| | - Partha P Majumder
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India. .,Indian Statistical Institute, Kolkata, India.
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22
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Zhou Y, Zheng S, Luo Q, Huang X, Zhou Y, Li Z. Hypermethylation of DcR1, DcR2, DR4, DR5 gene promoters and clinical significance in tongue carcinoma. Am J Otolaryngol 2019; 40:102258. [PMID: 31399243 DOI: 10.1016/j.amjoto.2019.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 06/10/2019] [Accepted: 07/01/2019] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Tongue squamous cell carcinoma (TSCC) is one of the most common malignancies in the oral cavity, and its incidence and mortality have been constantly increasing these years. A large number of tumor suppressor genes are involved in the development of the TSCC and it has been reported that the aberrant hypermethylation of tumor suppressor genes may play a key role in the process of the TSCC. In this study, we sought to analyze the association of methylation of DcR1, DcR2, DR4 and DR5 gene promoters and clinical significance in the TSCC to evaluate association between methylation of DcR1, DcR2, DR4 and DR5 gene and Clinical Significance in tongue squamous cell carcinoma. METHODS Methylation-specific PCR(MSP) was used to analyze the methylation of the promoters of TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) receptors in 45 TSCC cases. Real-Time PCR was used to detect the expression of the DcR1, DcR2, DR4 and DR5 gene. RESULTS All the four genes (DcR1, DcR2, DR4 and DR5) showed different methylation of promoters in TSCC, while methylation of these promoters in paired adjacent normal tissues were almost undetectable. Patients with high methylation index were diagnosed at younger age when compared with the ones with low methylation index. DcR1 and DR4 hypermethylation was correlated significantly with patients' TNM stage. CONCLUSIONS Methylation of DcR1, DcR2,DR4 and DR5 promoters are found in TSCC and may associate with its occurrence and development. Taking the reversibility of methylation into account,methylation is a potential targeted therapy of TSCC.
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23
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Zhong P, Liu L, Shen A, Chen Z, Hu X, Cai Y, Lin J, Wang B, Li J, Chen Y, Peng J. Five extracellular matrix-associated genes upregulated in oral tongue squamous cell carcinoma: An integrated bioinformatics analysis. Oncol Lett 2019; 18:5959-5967. [PMID: 31788070 PMCID: PMC6865669 DOI: 10.3892/ol.2019.10982] [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: 11/03/2018] [Accepted: 07/26/2019] [Indexed: 12/16/2022] Open
Abstract
Despite advancements in treatment regimens, the mortality rate of patients with oral tongue squamous cell carcinoma (OTSCC) is high. In addition, the signaling pathways and oncoproteins involved in OTSCC progression remain largely unknown. Therefore, the aim of the present study was to identify specific prognostic marker for patients at a high risk of developing OTSCC. The present study used four original microarray datasets to identify the key candidate genes involved in OTSCC pathogenesis. Expression profiles of 93 OTSCC tissues and 76 normal tissues from GSE9844, GSE13601, GSE31056 and GSE75538 datasets were investigated. Differentially expressed genes (DEGs) were determined, and gene ontology enrichment and gene interactions were analyzed. The four GSE datasets reported five upregulated and six downregulated DEGs. Five upregulated genes (matrix metalloproteinase 1, 3, 10 and 12 and laminin subunit gamma 2) were localized in the extracellular region of cells and were associated with extracellular matrix disassembly. Furthermore, analysis for The Cancer Genome Atlas database revealed that the aforementioned five upregulated genes were also highly expressed in OTSCC and head and neck squamous cell carcinoma tissues. These results demonstrated that the five upregulated genes may be considered as potential prognostic biomarkers of OTSCC and may serve at understanding OTSCC progression. Upregulated DEGs may therefore represent valuable therapeutic targets to prevent or control OTSCC pathogenesis.
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Affiliation(s)
- Pingping Zhong
- Department of Orthodontics, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, P.R. China.,Key Laboratory of Stomatology, Fujian Province University, Fuzhou, Fujian 350002, P.R. China.,Fujian Biological Materials Engineering and Technology Center of Stomatology, Fuzhou, Fujian 350002, P.R. China.,Institute of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, P.R. China
| | - Liya Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Aling Shen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Zhongxin Chen
- West China School of Stomatology Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaoyan Hu
- Key Laboratory of Stomatology, Fujian Province University, Fuzhou, Fujian 350002, P.R. China.,Fujian Biological Materials Engineering and Technology Center of Stomatology, Fuzhou, Fujian 350002, P.R. China.,Institute of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, P.R. China
| | - Yichao Cai
- Key Laboratory of Stomatology, Fujian Province University, Fuzhou, Fujian 350002, P.R. China.,Fujian Biological Materials Engineering and Technology Center of Stomatology, Fuzhou, Fujian 350002, P.R. China.,Institute of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, P.R. China
| | - Jie Lin
- Key Laboratory of Stomatology, Fujian Province University, Fuzhou, Fujian 350002, P.R. China.,Fujian Biological Materials Engineering and Technology Center of Stomatology, Fuzhou, Fujian 350002, P.R. China.,Institute of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, P.R. China
| | - Bangyan Wang
- Key Laboratory of Stomatology, Fujian Province University, Fuzhou, Fujian 350002, P.R. China.,Fujian Biological Materials Engineering and Technology Center of Stomatology, Fuzhou, Fujian 350002, P.R. China.,Institute of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, P.R. China
| | - Jiesen Li
- Key Laboratory of Stomatology, Fujian Province University, Fuzhou, Fujian 350002, P.R. China.,Fujian Biological Materials Engineering and Technology Center of Stomatology, Fuzhou, Fujian 350002, P.R. China.,Institute of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, P.R. China
| | - Youqin Chen
- Department of Pediatrics, Case Western Reserve University School of Medicine, Rainbow Babies and Children's Hospital, Cleveland, OH 44106, USA
| | - Jun Peng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
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24
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Ma J, Li R, Wang J. Characterization of a prognostic four‑gene methylation signature associated with radiotherapy for head and neck squamous cell carcinoma. Mol Med Rep 2019; 20:622-632. [PMID: 31180552 PMCID: PMC6579992 DOI: 10.3892/mmr.2019.10294] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 03/15/2019] [Indexed: 12/29/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) remains one of the most common malignancies associated with poor prognosis. DNA methylation has emerged as an important mechanism underlying the radio-resistance of tumors. Prognostic biomarkers based on radiotherapy-related aberrant DNA methylation are limited. Methylation profiles of 388 patients with HNSCC were acquired from The Cancer Genome Atlas (TCGA) portal. Genes with differentially methylated CpG sites (DMGs) were screened between patients with a favorable and poor prognosis with or without radiotherapy. A weight gene co-methylation network was constructed using a Weighted Gene Co-expression Network Analysis (WGCNA) package. A lasso Cox-PH model was used to identify the optimal panel of genes with the ability to predict survival in these patients. Prognostic performance of the multi-gene methylation signature was assessed in a training set and confirmed in a validation set. A total of 976 DMGs were observed between favorable and poor prognostic samples. Four DMG-enriched co-methylation modules were identified. A four-gene methylation signature was determined by the lasso Cox-PH model that consisted of ZNF10, TMPRSS12, ERGIC2, and RNF215. The risk score based on the four-gene signature was able to divide the training or validation set into two risk groups with significantly different overall survival. Thus, the present study revealed a radiotherapy-related four-gene methylation signature to predict survival outcomes of patients with HNSCC, providing candidate therapeutic targets for novel therapy against HNSCC. However, substantial validation experiments are required.
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Affiliation(s)
- Jiabao Ma
- Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
| | - Rui Li
- Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
| | - Jie Wang
- Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
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25
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Palve V, Bagwan J, Krishnan NM, Pareek M, Chandola U, Suresh A, Siddappa G, James BL, Kekatpure V, Kuriakose MA, Panda B. Detection of High-Risk Human Papillomavirus in Oral Cavity Squamous Cell Carcinoma Using Multiple Analytes and Their Role in Patient Survival. J Glob Oncol 2019; 4:1-33. [PMID: 30398949 PMCID: PMC7010445 DOI: 10.1200/jgo.18.00058] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Accurate detection of human papillomavirus (HPV) in oral cavity squamous cell carcinoma (OSCC) is essential to understanding the role of HPV in disease prognosis and management of patients. We used different analytes and methods to understand the true prevalence of HPV in a cohort of patients with OSCC with different molecular backgrounds, and we correlated HPV data with patient survival. METHODS We integrated data from multiple analytes (HPV DNA, HPV RNA, and p16), assays (immunohistochemistry, polymerase chain reaction [PCR], quantitative PCR [qPCR], and digital PCR), and molecular changes (somatic mutations and DNA methylation) from 153 patients with OSCC to correlate p16 expression, HPV DNA, and HPV RNA with HPV incidence and patient survival. RESULTS High prevalence (33% to 58%) of HPV16/18 DNA did not correlate with the presence of transcriptionally active viral genomes (15%) in tumors. Eighteen percent of the tumors were p16 positive and only 6% were both HPV DNA and HPV RNA positive. Most tumors with relatively high copy number HPV DNA and/or HPV RNA, but not with HPV DNA alone (irrespective of copy number), were wild-type for TP53 and CASP8 genes. In our study, p16 protein, HPV DNA, and HPV RNA, either alone or in combination, did not correlate with patient survival. Nine HPV-associated genes stratified the virus-positive from the virus-negative tumor group with high confidence ( P < .008) when HPV DNA copy number and/or HPV RNA were considered to define HPV positivity, and not HPV DNA alone, irrespective of copy number ( P < .2). CONCLUSION In OSCC, the presence of both HPV RNA and p16 is rare. HPV DNA alone is not an accurate measure of HPV positivity and therefore may not be informative. HPV DNA, HPV RNA, and p16 do not correlate with patients' outcome.
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Affiliation(s)
- Vinayak Palve
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Jamir Bagwan
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Neeraja M Krishnan
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Manisha Pareek
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Udita Chandola
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Amritha Suresh
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Gangotri Siddappa
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Bonney L James
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Vikram Kekatpure
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Moni Abraham Kuriakose
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Binay Panda
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
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Krishnan NM, I M, Hariharan J, Panda B. CAFE MOCHA: An Integrated Platform for Discovering Clinically Relevant Molecular Changes in Cancer-An Example of Distant Metastasis- and Recurrence-Linked Classifiers in Head and Neck Squamous Cell Carcinoma. JCO Clin Cancer Inform 2019; 2:1-11. [PMID: 30652568 DOI: 10.1200/cci.17.00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE With large amounts of multidimensional molecular data on cancers generated and deposited into public repositories such as The Cancer Genome Atlas and International Cancer Genome Consortium, a cancer type agnostic and integrative platform will help to identify signatures with clinical relevance. We devised such a platform and showcase it by identifying a molecular signature for patients with metastatic and recurrent (MR) head and neck squamous cell carcinoma (HNSCC). METHODS We devised a statistical framework accompanied by a graphical user interface-driven application, Clinical Association of Functionally Established MOlecular CHAnges ( CAFE MOCHA; https://github.com/binaypanda/CAFEMOCHA), to discover molecular signatures linked to a specific clinical attribute in a cancer type. The platform integrates mutations and indels, gene expression, DNA methylation, and copy number variations to discover a classifier first and then to predict an incoming tumor for the same by pulling defined class variables into a single framework that incorporates a coordinate geometry-based algorithm called complete specificity margin-based clustering, which ensures maximum specificity. CAFE MOCHA classifies an incoming tumor sample using either its matched normal or a built-in database of normal tissues. The application is packed and deployed using the install4j multiplatform installer. We tested CAFE MOCHA in HNSCC tumors (n = 513) followed by validation in tumors from an independent cohort (n = 18) for discovering a signature linked to distant MR. RESULTS CAFE MOCHA identified an integrated signature, MR44, associated with distant MR HNSCC, with 80% sensitivity and 100% specificity in the discovery stage and 100% sensitivity and 100% specificity in the validation stage. CONCLUSION CAFE MOCHA is a cancer type and clinical attribute agnostic statistical framework to discover integrated molecular signatures.
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Affiliation(s)
- Neeraja M Krishnan
- All authors: Ganit Labs; and Binay Panda, Strand Life Sciences, Bangalore, Karnataka, India
| | - Mohanraj I
- All authors: Ganit Labs; and Binay Panda, Strand Life Sciences, Bangalore, Karnataka, India
| | - Janani Hariharan
- All authors: Ganit Labs; and Binay Panda, Strand Life Sciences, Bangalore, Karnataka, India
| | - Binay Panda
- All authors: Ganit Labs; and Binay Panda, Strand Life Sciences, Bangalore, Karnataka, India
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Chen Y, Hei N, Zhao J, Peng S, Yang K, Chen H, Cui Z, Jin L, Sun R, Guo J. A two‐CpG‐based prognostic signature for oral squamous cell carcinoma overall survival. J Cell Biochem 2018; 120:9082-9090. [PMID: 30548666 DOI: 10.1002/jcb.28182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Yanping Chen
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - Naiheng Hei
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - Jianguang Zhao
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - Shixiong Peng
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - Kaicheng Yang
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - He Chen
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - Zifeng Cui
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - Linyu Jin
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - Ran Sun
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
| | - Jingxin Guo
- Oral and Maxillofacial Surgery The Fourth Hospital of Hebei Medical University Shijiazhuang People's Republic of China
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Palve V, Pareek M, Krishnan NM, Siddappa G, Suresh A, Kuriakose MA, Panda B. A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma. PeerJ 2018; 6:e5207. [PMID: 30128175 PMCID: PMC6097490 DOI: 10.7717/peerj.5207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/20/2018] [Indexed: 12/25/2022] Open
Abstract
Selection of the right reference gene(s) is crucial in the analysis and interpretation of gene expression data. The aim of the present study was to discover and validate a minimal set of internal control genes in head and neck tumor studies. We analyzed data from multiple sources (in house whole-genome gene expression microarrays, previously published quantitative real-time PCR (qPCR) data and RNA-seq data from TCGA) to come up with a list of 18 genes (discovery set) that had the lowest variance, a high level of expression across tumors, and their matched normal samples. The genes in the discovery set were ranked using four different algorithms (BestKeeper, geNorm, NormFinder, and comparative delta Ct) and a web-based comparative tool, RefFinder, for their stability and variance in expression across tissues. Finally, we validated their expression using qPCR in an additional set of tumor:matched normal samples that resulted in five genes (RPL30, RPL27, PSMC5, MTCH1, and OAZ1), out of which RPL30 and RPL27 were most stable and were abundantly expressed across the tissues. Our data suggest that RPL30 or RPL27 in combination with either PSMC5 or MTCH1 or OAZ1 can be used as a minimal set of control genes in head and neck tumor gene expression studies.
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Affiliation(s)
- Vinayak Palve
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Manisha Pareek
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Neeraja M Krishnan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Gangotri Siddappa
- Head and Neck Oncology, Mazumdar Shaw Centre for Translational Research, Bangalore, India
| | - Amritha Suresh
- Head and Neck Oncology, Mazumdar Shaw Centre for Translational Research, Bangalore, India
| | - Moni A Kuriakose
- Head and Neck Oncology, Mazumdar Shaw Centre for Translational Research, Bangalore, India
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
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30
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Qiu Z, Sun W, Gao S, Zhou H, Tan W, Cao M, Huang W. A 16-gene signature predicting prognosis of patients with oral tongue squamous cell carcinoma. PeerJ 2017; 5:e4062. [PMID: 29158988 PMCID: PMC5695251 DOI: 10.7717/peerj.4062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/29/2017] [Indexed: 12/25/2022] Open
Abstract
Background Oral tongue squamous cell carcinoma (OTSCC) is the most common subtype of oral cancer. A predictive gene signature is necessary for prognosis of OTSCC. Methods Five microarray data sets of OTSCC from the Gene Expression Omnibus (GEO) and one data set from The Cancer Genome Atlas (TCGA) were obtained. Differentially expressed genes (DEGs) of GEO data sets were identified by integrated analysis. The DEGs associated with prognosis were screened in the TCGA data set by univariate survival analysis to obtain a gene signature. A risk score was calculated as the summation of weighted expression levels with coefficients by Cox analysis. The signature was used to distinguish carcinoma, estimated by receiver operator characteristic curves and the area under the curve (AUC). All were validated in the GEO and TCGA data sets. Results Integrated analysis of GEO data sets revealed 300 DEGs. A 16-gene signature and a risk score were developed after survival analysis. The risk score was effective to stratify patients into high-risk and low-risk groups in the TCGA data set (P < 0.001). The 16-gene signature was valid to distinguish the carcinoma from normal samples (AUC 0.872, P < 0.001). Discussion We identified a useful 16-gene signature for prognosis of OTSCC patients, which could be applied to clinical practice. Further studies were needed to prove the findings.
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Affiliation(s)
- Zeting Qiu
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China.,Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Wei Sun
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Shaowei Gao
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Huaqiang Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Wulin Tan
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Minghui Cao
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Wenqi Huang
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
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Sun W, Qiu Z, Huang W, Cao M. Gene expression profiles and protein‑protein interaction networks during tongue carcinogenesis in the tumor microenvironment. Mol Med Rep 2017; 17:165-171. [PMID: 29115421 PMCID: PMC5780107 DOI: 10.3892/mmr.2017.7843] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 07/07/2017] [Indexed: 12/02/2022] Open
Abstract
Oral tongue squamous cell carcinoma (OTSCC) has a high incidence and is associated with a high mortality rate. Studies regarding the potential molecular mechanism of OTSCC in the tumor microenvironment (TME) are required. The present study aimed to perform bioinformatic analysis to identify important nodes, clusters and functional pathways during tongue carcinogenesis in the TME. After downloading the gene expression data of GSE42780, differentially expressed genes (DEGs) among carcinoma, dysplastic and normal samples in epithelia and fibroblasts were identified using the affy and limma packages with R version 3.3. Subsequently, the Database for Annotation, Visualization and Integrated Discovery was employed to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Furthermore, a protein-protein interaction (PPI) network was constructed by using the Search Tool for the Retrieval of Interacting Genes/Proteins and analyzed by Cytoscape software. In total, 85 DEGs were identified for tongue epithelia and 46 DEGs were identified for fibroblasts. Neutrophil chemotaxis and inflammatory response from GO, and cytokine-cytokine receptor interaction from KEGG were enriched for epithelia and fibroblasts. The PPI network revealed that C-X-C motif chemokine ligand (Cxcl)1, Cxcl10, Cxcl13, Cxcl2 and pro-platelet basic protein were a key cluster for epithelia, and interleukin (Il)1β, Il1 receptor 2, Il1a and Il1 receptor antagonist were a key cluster for fibroblasts. Therefore, the results indicate that fibroblasts and cytokines associated with an inflammatory immune response contributed substantially to tongue carcinogenesis in the TME, which is useful for the development of OTSCC targeted therapy. However, further investigation is required to elucidate the molecular and cellular mechanisms underlying the inflammatory immune network in the TME.
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Affiliation(s)
- Wei Sun
- Department of Anesthesiology, Sun Yat‑sen Memorial Hospital, Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Zeting Qiu
- Department of Anesthesiology, Sun Yat‑sen Memorial Hospital, Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Wenqi Huang
- Department of Anesthesiology, Sun Yat‑sen Memorial Hospital, Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Minghui Cao
- Department of Anesthesiology, Sun Yat‑sen Memorial Hospital, Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
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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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Epigenetic Bases of Aberrant Glycosylation in Cancer. Int J Mol Sci 2017; 18:ijms18050998. [PMID: 28481247 PMCID: PMC5454911 DOI: 10.3390/ijms18050998] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 04/27/2017] [Accepted: 05/02/2017] [Indexed: 02/07/2023] Open
Abstract
In this review, the sugar portions of glycoproteins, glycolipids, and glycosaminoglycans constitute the glycome, and the genes involved in their biosynthesis, degradation, transport and recognition are referred to as “glycogenes“. The extreme complexity of the glycome requires the regulatory layer to be provided by the epigenetic mechanisms. Almost all types of cancers present glycosylation aberrations, giving rise to phenotypic changes and to the expression of tumor markers. In this review, we discuss how cancer-associated alterations of promoter methylation, histone methylation/acetylation, and miRNAs determine glycomic changes associated with the malignant phenotype. Usually, increased promoter methylation and miRNA expression induce glycogene silencing. However, treatment with demethylating agents sometimes results in silencing, rather than in a reactivation of glycogenes, suggesting the involvement of distant methylation-dependent regulatory elements. From a therapeutic perspective aimed at the normalization of the malignant glycome, it appears that miRNA targeting of cancer-deranged glycogenes can be a more specific and promising approach than the use of drugs, which broad target methylation/acetylation. A very specific type of glycosylation, the addition of GlcNAc to serine or threonine (O-GlcNAc), is not only regulated by epigenetic mechanisms, but is an epigenetic modifier of histones and transcription factors. Thus, glycosylation is both under the control of epigenetic mechanisms and is an integral part of the epigenetic code.
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Bhat S, Kabekkodu SP, Jayaprakash C, Radhakrishnan R, Ray S, Satyamoorthy K. Gene promoter-associated CpG island hypermethylation in squamous cell carcinoma of the tongue. Virchows Arch 2017; 470:445-454. [PMID: 28255813 DOI: 10.1007/s00428-017-2094-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/28/2016] [Accepted: 02/15/2017] [Indexed: 01/10/2023]
Abstract
The present study was undertaken to explore and validate novel hypermethylated DNA regions in squamous cell carcinoma of the tongue (SCCT). Genome-wide methylation changes were identified by differential methylation hybridization (DMH) microarray and validated by bisulfite genome sequencing (BGS). The results were compared against datasets from The Cancer Genome Atlas head and neck squamous cell carcinoma (TCGA-HNSCC), Gene Expression Omnibus (GSE26549), and ArrayExpress (E-MTAB-1328). DMH identified 116 hypomethylated and 241 hypermethylated regions. Of the latter, 24 were localized to promoter or 5'-UTR regions. By BGS, promoter sequences of DAPK1, LRPPRC, RAB6C, and ZNF471 were significantly hypermethylated in tumors when compared with matched normal tissues (P < 0.0001). A TCGA-HNSCC dataset (516 cases of cancer and 50 normal tissue samples) further confirmed hypermethylation of DAPK1, RAB6C, and ZNF471. Sensitivity and specificity of methylation markers for a diagnosis of cancer were in the range of 70-100% in our study and from TCGA-HNSCC datasets, with an area under curve (AUC) of 0.83 and above. Kaplan-Meier survival analysis of TCGA-HNSCC expression data revealed that patients with low expressions of DAPK1, RAB6C, and ZNF471 showed poorer survival than patients with high expression (P = 0.02). Human papillomavirus (HPV) was found in 55% of cases, HPV16 being the predominant genotype. DAPK1 immunohistochemical staining was lower in SCCT than in normal buccal epithelial cells. This is the first study to report hypermethylation of LRPPRC, RAB6C, and ZNF471 in SCCT and its diagnostic and prognostic potentials in a specific head and neck squamous cell carcinoma.
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Affiliation(s)
- Samatha Bhat
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Chinchu Jayaprakash
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal University, Manipal, 576104, India
| | - Satadru Ray
- Department of Surgical Oncology, Kasturba Medical College, Manipal University, Manipal, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India.
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