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Pradhan S, Das S, Singh AK, Das C, Basu A, Majumder PP, Biswas NK. dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6287646. [PMID: 34048545 PMCID: PMC8163239 DOI: 10.1093/database/baab034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 11/18/2022]
Abstract
Oral cancer is highly prevalent in India and is the most frequent cancer type among Indian males. It is also very common in southeast Asia. India has participated in the International Cancer Genome Consortium (ICGC) and some national initiatives to generate large-scale genomic data on oral cancer patients and analyze to identify associations and systematically catalog the associated variants. We have now created an open, web-accessible database of these variants found significantly associated with Indian oral cancer patients, with a user-friendly interface to enable easy mining. We have value added to this database by including relevant data collated from various sources on other global populations, thereby providing opportunities of comparative geographical and/or ethnic analyses. Currently, no other database of similar nature is available on oral cancer. We have developed Database of GENomic Variants of Oral Cancer, a browsable online database framework for storage, retrieval and analysis of large-scale data on genomic variants and make it freely accessible to the scientific community. Presently, the web-accessible database allows potential users to mine data on ∼24 million clinically relevant somatic and germline variants derived from exomes (n = 100) and whole genomes (n = 5) of Indian oral cancer patients; all generated by us. Variant data from The Cancer Genome Atlas and data manually curated from peer-reviewed publications were also incorporated into the database for comparative analyses. It allows users to query the database by a single gene, multiple genes, multiple variant sites, genomic region, patient ID and pathway identities. Database URL: http://research.nibmg.ac.in/dbcares/dbgenvoc/
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Affiliation(s)
- Sanchari Pradhan
- Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Subrata Das
- Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Animesh K Singh
- Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Chitrarpita Das
- Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Analabha Basu
- Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Partha P Majumder
- Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India.,Human Genetics Unit, Indian Statistical Institute, Kolkata, West Bengal 700108, India
| | - Nidhan K Biswas
- Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
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Zhuang Z, Huang J, Wang W, Wang C, Yu P, Hu J, Liu H, Yin H, Hou J, Liu X. Down-Regulation of Long Non-Coding RNA TINCR Induces Cell Dedifferentiation and Predicts Progression in Oral Squamous Cell Carcinoma. Front Oncol 2021; 10:624752. [PMID: 33732637 PMCID: PMC7959775 DOI: 10.3389/fonc.2020.624752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/30/2020] [Indexed: 01/22/2023] Open
Abstract
Objectives Recently long non-coding RNAs (lncRNAs) have emerged as novel gene regulators involved in tumorigenic processes, including oral squamous cell carcinoma (OSCC). Here, we identified a differentiation-related lncRNA, terminal differentiation-induced non-coding RNA (TINCR). However, its biological function and clinicopathological significance in OSCC still remain unclear. Methods The lncRNA expression profiles in OSCC tissues and paired adjacent non-tumor tissues (NATs) from 10 patients were detected by lncRNA microarrays. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) enrichment were performed to identify the most significant module and module functional annotation, respectively. Potential differentiation-related lncRNAs were screened by differential expression analysis. TINCR was further confirmed in OSCC cell lines and tissues of another patient cohort by using qRT-PCR. The correlation between the TINCR expression level and clinicopathological characteristics was analyzed. The effects of TINCR on cell differentiation, migration and invasion were assessed by knockdown or knock-in in vitro and in vivo. Results WGCNA and GO enrichment analysis showed that one co-expression network was significantly enriched for epithelial cell differentiation, among which, TINCR was significantly downregulated. qRT-PCR analyses validated down-regulation of TINCR in tumor tissues compared with paired NATs, and its expression was closely correlated with pathological differentiation and lymph node metastasis in patients with OSCC. Patients with lower TINCR expression levels had worse survival. Cell function experiments showed that TINCR played a crucial role in epithelial differentiation. Both TINCR and epithelial differentiation-associated genes, including IVL and KRT4, were significantly upregulated during OSCC cell calcium-induced differentiation but were reduced when cell dedifferentiation occurred in tumor spheres. Overexpression of TINCR dramatically suppressed cell dedifferentiation, migration and invasion in vitro, while knockdown of TINCR had the opposite effects. Upregulation of TINCR significantly elevated the expression of terminal differentiation genes and repressed tumor growth in vivo. Moreover, TINCR significantly suppressed the activation of JAK2/STAT3 signaling in OSCC cells. Conclusion Our study suggests that TINCR functions as a tumor suppressor by inducing cell differentiation through modulating JAK2/STAT3 signaling in OSCC. TINCR may serve as a prognostic biomarker and therapeutic target for OSCC.
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Affiliation(s)
- Zehang Zhuang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jing Huang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Weiwang Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.,Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Cheng Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Pei Yu
- Department of Prothodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Jing Hu
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Haichao Liu
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Hanqi Yin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,South China Institute of Biomedine, Guangzhou, China
| | - Jinsong Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xiqiang Liu
- Department of Oral and Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, China
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Taunk K, Kalita B, Kale V, Chanukuppa V, Naiya T, Zingde SM, Rapole S. The development and clinical applications of proteomics: an Indian perspective. Expert Rev Proteomics 2020; 17:433-451. [PMID: 32576061 DOI: 10.1080/14789450.2020.1787157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic. AREAS COVERED This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed. EXPERT OPINION The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.
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Affiliation(s)
- Khushman Taunk
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Bhargab Kalita
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | - Vaikhari Kale
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | | | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Surekha M Zingde
- CH3-53, Kendriya Vihar, Sector 11, Kharghar , Navi Mumbai, Maharashtra, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
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The significance of gene mutations across eight major cancer types. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:88-99. [PMID: 31416581 DOI: 10.1016/j.mrrev.2019.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 04/11/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022]
Abstract
Mutations occur spontaneously, which can be induced by either chemicals (e.g. benzene) or biological factors (e.g. virus). Not all mutations cause noticeable changes in cellular functions. However, mutation in key cellular genes leads to developmental disorders. It is one of the main ways in which proto-oncogenes can be changed into their oncogenic state. The progressive accumulation of multiple mutations throughout life leads to cancer. In the past few decades, extensive research on cancer biology has discovered many genes and pathways having role in cancer development. In this review, we tried to summarize the current knowledge of mutational effect on different cancer types and its consequences in brief for future reference and guidance of researchers in cancer biology.
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Sarode GS, Sarode SC, Maniyar N, Anand R, Patil S. Oral cancer databases: A comprehensive review. J Oral Pathol Med 2017; 47:547-556. [PMID: 29193424 DOI: 10.1111/jop.12667] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2017] [Indexed: 01/14/2023]
Abstract
Cancer database is a systematic collection and analysis of information on various human cancers at genomic and molecular level that can be utilized to understand various steps in carcinogenesis and for therapeutic advancement in cancer field. Oral cancer is one of the leading causes of morbidity and mortality all over the world. The current research efforts in this field are aimed at cancer etiology and therapy. Advanced genomic technologies including microarrays, proteomics, transcrpitomics, and gene sequencing development have culminated in generation of extensive data and subjection of several genes and microRNAs that are distinctively expressed and this information is stored in the form of various databases. Extensive data from various resources have brought the need for collaboration and data sharing to make effective use of this new knowledge. The current review provides comprehensive information of various publicly accessible databases that contain information pertinent to oral squamous cell carcinoma (OSCC) and databases designed exclusively for OSCC. The databases discussed in this paper are Protein-Coding Gene Databases and microRNA Databases. This paper also describes gene overlap in various databases, which will help researchers to reduce redundancy and focus on only those genes, which are common to more than one databases. We hope such introduction will promote awareness and facilitate the usage of these resources in the cancer research community, and researchers can explore the molecular mechanisms involved in the development of cancer, which can help in subsequent crafting of therapeutic strategies.
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Affiliation(s)
- Gargi S Sarode
- Department of Oral Pathology and Microbiology, Dr. D. Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Sachin C Sarode
- Department of Oral Pathology and Microbiology, Dr. D. Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Nikunj Maniyar
- Department of Oral Pathology and Microbiology, Dr. D. Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Rahul Anand
- Department of Oral Pathology and Microbiology, Dr. D. Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Shankargouda Patil
- Division of Oral Pathology, Department of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia
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Mukherjee S, Bandyopadhyay A. Proteomics in India: the clinical aspect. Clin Proteomics 2016; 13:21. [PMID: 27822170 PMCID: PMC5097398 DOI: 10.1186/s12014-016-9122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 08/12/2016] [Indexed: 02/07/2023] Open
Abstract
Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human cancers and hematological disorders. Recently, some seminal works on clinical proteomics have been reported from several laboratories across India. This review aims to shed light on the increasing use of proteomics in India in a variety of biological conditions. It also highlights that India has the expertise and infrastructure needed for pursuing proteomics research in the country and to participate in global initiatives. Research in clinical proteomics is gradually picking up pace in India and its future seems very bright.
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Affiliation(s)
- Somaditya Mukherjee
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
| | - Arun Bandyopadhyay
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
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Christopher AF, Gupta M, Bansal P. Micronome revealed miR-19a/b as key regulator of SOCS3 during cancer related inflammation of oral squamous cell carcinoma. Gene 2016; 594:30-40. [PMID: 27581787 DOI: 10.1016/j.gene.2016.08.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/20/2016] [Accepted: 08/26/2016] [Indexed: 12/21/2022]
Abstract
Although significant advances have been established in molecular biology of Oral squamous cell carcinoma (OSCC), innovative strategies are still required to further understand detailed molecular mechanisms. Using bioinformatic approach, we aim to explore the potential miRNA-mRNA pairs in cancer related inflammatory response and investigate their potential roles as signature miRNA and proteins in the signaling pathway. Firstly, the differentially expressed genes of OSCC were selected which then underwent gene ontology to identify genes engaged in inflammatory response and its regulation. Validated miRNAs were retrieved and miRNAs with complete complementarily with their targets were visualized for miRNA-mRNA regulatory network. Protein-protein interactions of inflammatory and its regulatory genes were analyzed for interacting genes involved in signaling pathway. Eight universal miRNAs were obtained for inflammation and its regulation. miRNA-19a/b showed significant influence in controlling inflammatory response in OSCC. Therefore, micronome on deregulated genes in inflammation identifies miRNA-mRNA pairs which have high potential to be targeted for diagnostic and treatment applications in OSCC.
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Affiliation(s)
- Ajay Francis Christopher
- Division of Clinical Research, University Centre of Excellence in Research, Baba Farid University of Health Science, Faridkot 151203, Punjab, India
| | - Mridula Gupta
- Division of Clinical Research, University Centre of Excellence in Research, Baba Farid University of Health Science, Faridkot 151203, Punjab, India
| | - Parveen Bansal
- Division of Clinical Research, University Centre of Excellence in Research, Baba Farid University of Health Science, Faridkot 151203, Punjab, India.
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Bhartiya D, Kumar A, Singh H, Sharma A, Kaushik A, Kumari S, Mehrotra R. OrCanome: a Comprehensive Resource for Oral Cancer. Asian Pac J Cancer Prev 2016; 17:1333-6. [DOI: 10.7314/apjcp.2016.17.3.1333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Henrique T, José Freitas da Silveira N, Henrique Cunha Volpato A, Mioto MM, Carolina Buzzo Stefanini A, Bachir Fares A, Gustavo da Silva Castro Andrade J, Masson C, Verónica Mendoza López R, Daumas Nunes F, Paulo Kowalski L, Severino P, Tajara EH. HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw026. [PMID: 27013077 PMCID: PMC4806539 DOI: 10.1093/database/baw026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/19/2016] [Indexed: 12/19/2022]
Abstract
The total amount of scientific literature has grown rapidly in recent years. Specifically, there are several million citations in the field of cancer. This makes it difficult, if not impossible, to manually retrieve relevant information on the mechanisms that govern tumor behavior or the neoplastic process. Furthermore, cancer is a complex disease or, more accurately, a set of diseases. The heterogeneity that permeates many tumors is particularly evident in head and neck (HN) cancer, one of the most common types of cancer worldwide. In this study, we present HNdb, a free database that aims to provide a unified and comprehensive resource of information on genes and proteins involved in HN squamous cell carcinoma, covering data on genomics, transcriptomics, proteomics, literature citations and also cross-references of external databases. Different literature searches of MEDLINE abstracts were performed using specific Medical Subject Headings (MeSH terms) for oral, oropharyngeal, hypopharyngeal and laryngeal squamous cell carcinomas. A curated gene-to-publication assignment yielded a total of 1370 genes related to HN cancer. The diversity of results allowed identifying novel and mostly unexplored gene associations, revealing,for example, that processes linked to response to steroid hormone stimulus are significantly enriched in genes related to HN carcinomas. Thus, our database expands the possibilities for gene networks investigation, providing potential hypothesis to be tested. Database URL:http://www.gencapo.famerp.br/hndb.
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Affiliation(s)
- Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, SP, Brazil Av Brigadeiro Faria Lima n° 5416 Vila Sao Pedro 15090-000 - São José do Rio Preto, SP - Brazil
| | - Nelson José Freitas da Silveira
- Institute of Exact Science, Federal University of Alfenas, MG, Brazil, Rua Gabriel Monteiro da Silva, 700 Centro 37130-000 - Alfenas, MG - Brazil
| | - Arthur Henrique Cunha Volpato
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, SP, Brazil Av Brigadeiro Faria Lima n° 5416 Vila Sao Pedro 15090-000 - São José do Rio Preto, SP - Brazil
| | - Mayra Mataruco Mioto
- Department of Dermatological, Infectious, and Parasitic Diseases, School of Medicine of São José do Rio Preto, SP, Brazil Av Brigadeiro Faria Lima n° 5416 Vila Sao Pedro 15090-000 - São José do Rio Preto, SP - Brazil
| | - Ana Carolina Buzzo Stefanini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, SP, Brazil Av Brigadeiro Faria Lima n° 5416 Vila Sao Pedro 15090-000 - São José do Rio Preto, SP - Brazil Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil R. do Matão Butantã 05508-090 - São Paulo, SP, Brazil
| | - Adil Bachir Fares
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, SP, Brazil Av Brigadeiro Faria Lima n° 5416 Vila Sao Pedro 15090-000 - São José do Rio Preto, SP - Brazil
| | - João Gustavo da Silva Castro Andrade
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, SP, Brazil Av Brigadeiro Faria Lima n° 5416 Vila Sao Pedro 15090-000 - São José do Rio Preto, SP - Brazil
| | - Carolina Masson
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, SP, Brazil Av Brigadeiro Faria Lima n° 5416 Vila Sao Pedro 15090-000 - São José do Rio Preto, SP - Brazil
| | - Rossana Verónica Mendoza López
- State of São Paulo Cancer Institute - ICESP, SP, Brazil Av. Dr. Arnaldo, 251 Pacaembu 01246-000 - São Paulo, SP - Brazil
| | - Fabio Daumas Nunes
- Department of Stomatology School of Dentistry, University of São Paulo, SP, Brazil Avenida Professor Lineu Prestes, 2227 Butantã 05508-000 - São Paulo, SP - Brazil
| | - Luis Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, Cancer Hospital A.C. Camargo, SP, Brazil Rua Prof Antonio Prudente, 211 Liberdade 01509-010 - São Paulo, SP - Brazil and
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, SP, Brazil Av. Albert Einstein, 627 Morumbi 05652-000 - São Paulo, SP - Brazil
| | - Eloiza Helena Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, SP, Brazil Av Brigadeiro Faria Lima n° 5416 Vila Sao Pedro 15090-000 - São José do Rio Preto, SP - Brazil Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil R. do Matão Butantã 05508-090 - São Paulo, SP, Brazil
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Zingde SM. Has Proteomics come of age in India? J Proteomics 2015; 127:3-6. [PMID: 25748142 DOI: 10.1016/j.jprot.2015.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/25/2015] [Indexed: 12/24/2022]
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Comprehensive network analysis of genes expressed in human oropharyngeal cancer. Am J Otolaryngol 2015; 36:235-41. [PMID: 25484365 DOI: 10.1016/j.amjoto.2014.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/13/2014] [Indexed: 01/02/2023]
Abstract
PURPOSE Oropharyngeal cancer (OPC) is the eighth most common cancer worldwide, however the genes involved in the development of OPC have been reported few. We constructed a co-expression network to extend knowledge of the molecular biomarkers in OPC development. MATERIALS AND METHODS Microarray data of HPV-active, -inactive, -negative OPC and normal benign tissue (uvula, tonsil) (Series GSE55550) were retrieved from NCBI GEO DataSets. We performed co-expression analysis of OPC transcriptome data by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off using 13 guide genes. RESULTS The OPC subnetwork contained three clusters: cell cycle (62 node genes and 125 edge genes), immune system (44 node genes and 70 edge genes) and organ morphogenesis (128 node gene and 215 edge genes) process separately. CONCLUSION Our co-expression analysis includes separated transcriptomes of OPC, which is a useful resource for OPC researchers to elucidate important and complex biological events, to prevent and to predict cancer.
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Randhawa V, Kumar Singh A, Acharya V. A systematic approach to prioritize drug targets using machine learning, a molecular descriptor-based classification model, and high-throughput screening of plant derived molecules: a case study in oral cancer. MOLECULAR BIOSYSTEMS 2015; 11:3362-77. [DOI: 10.1039/c5mb00468c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Network-based and cheminformatics approaches identify novel lead molecules forCXCR4, a key gene prioritized in oral cancer.
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Affiliation(s)
- Vinay Randhawa
- Functional Genomics and Complex Systems Laboratory
- Biotechnology Division
- CSIR-Institute of Himalayan Bioresource Technology
- Council of Scientific and Industrial Research
- Palampur
| | - Anil Kumar Singh
- Biotechnology Division
- CSIR-Institute of Himalayan Bioresource Technology
- Council of Scientific and Industrial Research
- Palampur
- India
| | - Vishal Acharya
- Functional Genomics and Complex Systems Laboratory
- Biotechnology Division
- CSIR-Institute of Himalayan Bioresource Technology
- Council of Scientific and Industrial Research
- Palampur
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14
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Significant patterns for oral cancer detection: association rule on clinical examination and history data. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s13721-014-0050-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Bragazzi NL, Pechkova E, Nicolini C. Proteomics and Proteogenomics Approaches for Oral Diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:125-62. [DOI: 10.1016/b978-0-12-800453-1.00004-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Abdelfadil E, Cheng YH, Bau DT, Ting WJ, Chen LM, Hsu HH, Lin YM, Chen RJ, Tsai FJ, Tsai CH, Huang CY. Thymoquinone induces apoptosis in oral cancer cells through p38β inhibition. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2013; 41:683-96. [PMID: 23711149 DOI: 10.1142/s0192415x1350047x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oral cancer is a common malignancy associated with high morbidity and mortality. While p38 MAPK is reported to be involved in different cellular activities such as proliferation and differentiation, reports rarely define the roles of the individual members of the p38 MAPK family in cancer. We used two unique cell lines developed by our lab representing chemically induced oral cancer cells (T28) and non-tumor cells (N28) obtained from tissues surrounding the induced cancer as a model to screen out whether p38 MAPK is involved in the malignant transformation processes. The results suggest an association between p38β not p38α and oral cancer development. Additionally, the anti-cancer activity of thymoquinone (TQ) was screened out and we found evidences suggesting that the anti-tumor activity of TQ may be attributed to the downregulation of p38β MAPK.
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Affiliation(s)
- Ehab Abdelfadil
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
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Mitra S, Das S, Das S, Ghosal S, Chakrabarti J. HNOCDB: A comprehensive database of genes and miRNAs relevant to head and neck and oral cancer. Oral Oncol 2012; 48:117-9. [DOI: 10.1016/j.oraloncology.2011.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/22/2011] [Accepted: 09/27/2011] [Indexed: 10/16/2022]
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