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Liu L, Xie Y, Yang H, Lin A, Dong M, Wang H, Zhang C, Liu Z, Cheng Q, Zhang J, Yuan S, Luo P. HPVTIMER: A shiny web application for tumor immune estimation in human papillomavirus-associated cancers. IMETA 2023; 2:e130. [PMID: 38867938 PMCID: PMC10989930 DOI: 10.1002/imt2.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 06/14/2024]
Abstract
The tumor immune microenvironment (TIME) is closely associated with tumor formation, particularly linked to the human papillomavirus (HPV), and regulates tumor initiation, proliferation, infiltration, and metastasis. With the rise of immunotherapy, an increasing amount of sample data used for TIME exploration is available in databases. However, no currently available web tool enables a comprehensive exploration of the TIME of HPV-associated cancers by leveraging these data. We have developed a web tool called HPV-associated Tumor Immune MicroEnvironment ExploreR (HPVTIMER), which provides a comprehensive analysis platform that integrates over 10,000 genes and 2290 tumor samples from 65 transcriptome data sets across 8 cancer types sourced from the Gene Expression Omnibus (GEO) database. The tool features four built-in analysis modules, namely, the differential expression analysis module, correlation analysis module, immune infiltration analysis module, and pathway analysis module. These modules enable users to perform systematic and vertical analyses. We used several analytical modules in HPVTIMER to briefly explore the role of CDKN2A in head and neck squamous cell carcinomas. We expect that HPVTIMER will help users explore the immune microenvironment of HPV-associated cancers and uncover potential immune regulatory mechanisms and immunotherapeutic targets. HPVTIMER is available at http://www.hpvtimer.com/.
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Affiliation(s)
- Liying Liu
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yanan Xie
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
- The Second Clinical Medicine SchoolSouthern Medical UniversityGuangzhouGuangdongChina
| | - Hong Yang
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Anqi Lin
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Minjun Dong
- Department of Surgical OncologySir Run Run Shaw Hospital Affiliated to Zhejiang University, School of MedicineHang ZhouChina
| | - Haitao Wang
- Thoracic Surgery BranchCenter for Cancer Research, National Institutes of HealthBethesdaMarylandUSA
| | - Cangang Zhang
- Department of Pathogenic Microbiology and ImmunologyXi'an Jiaotong UniversityXi'anShaanxiChina
| | - Zaoqu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Quan Cheng
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityHunanChina
| | - Jian Zhang
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Shuofeng Yuan
- Department of Infectious Disease and MicrobiologyThe University of Hong Kong‐Shenzhen HospitalShenzhenChina
- State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologySchool of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Peng Luo
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
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2
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Abstract
In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.
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Affiliation(s)
- Tharcísio Soares de Amorim
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Daniel Longhi Fernandes Pedro
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil.
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3
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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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Zhang Q, Li X, Su X, Zhang H, Wang H, Yin S, Pei X, Yang A, Zuo Z. HNCDB: An Integrated Gene and Drug Database for Head and Neck Cancer. Front Oncol 2019; 9:371. [PMID: 31139565 PMCID: PMC6527845 DOI: 10.3389/fonc.2019.00371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Head and neck cancer (HNC) is the sixth most common cancer worldwide. Over the last decade, an enormous amount of well-annotated gene and drug data has accumulated for HNC. However, a comprehensive repository is not yet available. Here, we constructed the Head and Neck Cancer Database (HNCDB: http://hncdb.cancerbio.info) using text mining followed by manual curation of the literature to collect reliable information on the HNC-related genes and drugs. The high-throughput gene expression data for HNC were also integrated into HNCDB. HNCDB includes the following three separate but closely related components: “HNC GENE,” “Connectivity Map,” and “ANALYSIS.” The “HNC GENE” component contains comprehensive information for the 1,173 HNC-related genes manually curated from 2,564 publications. The “Connectivity Map” includes information on the potential connections between the 176 drugs manually curated from 2,032 publications and the 1,173 HNC-related genes. The “ANALYSIS” component allows users to conduct correlation, differential expression, and survival analyses in the 2,403 samples from 78 HNC gene expression datasets. Taken together, we believe that HNCDB will be of significant benefit for the HNC community and promote further advances for precision medicine research on HNC.
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Affiliation(s)
- Qingbin Zhang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xingyang Li
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuan Su
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongwan Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hanbing Wang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Sanjun Yin
- Department of Cancer Biology, Health Time Gene Institute, Shenzhen, China
| | - Xiaoqing Pei
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ankui Yang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
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Abstract
One of the most important resources for researchers of noncoding RNAs is the information available in public databases spread over the internet. However, the effective exploration of this data can represent a daunting task, given the large amount of databases available and the variety of stored data. This chapter describes a classification of databases based on information source, type of RNA, source organisms, data formats, and the mechanisms for information retrieval, detailing the relevance of each of these classifications and its usability by researchers. This classification is used to update a 2012 review, indexing now more than 229 public databases. This review will include an assessment of the new trends for ncRNA research based on the information that is being offered by the databases. Additionally, we will expand the previous analysis focusing on the usability and application of these databases in pathogen and disease research. Finally, this chapter will analyze how currently available database schemas can help the development of new and improved web resources.
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Chalbatani GM, Dana H, Gharagozlo E, Mahmoodzad H, Zeinalinia E, Rezaeian O, Pilvar P, Ardaneh M, Meghdadi S, Memari F, Rad N. Microrna a New Gate in Cancer and Human Disease: A Review. ACTA ACUST UNITED AC 2017. [DOI: 10.3923/jbs.2017.247.254] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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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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Agarwal R, Kumar B, Jayadev M, Raghav D, Singh A. CoReCG: a comprehensive database of genes associated with colon-rectal cancer. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw059. [PMID: 27114494 PMCID: PMC4843536 DOI: 10.1093/database/baw059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 03/23/2016] [Indexed: 12/19/2022]
Abstract
Cancer of large intestine is commonly referred as colorectal cancer, which is also the third most frequently prevailing neoplasm across the globe. Though, much of work is being carried out to understand the mechanism of carcinogenesis and advancement of this disease but, fewer studies has been performed to collate the scattered information of alterations in tumorigenic cells like genes, mutations, expression changes, epigenetic alteration or post translation modification, genetic heterogeneity. Earlier findings were mostly focused on understanding etiology of colorectal carcinogenesis but less emphasis were given for the comprehensive review of the existing findings of individual studies which can provide better diagnostics based on the suggested markers in discrete studies. Colon Rectal Cancer Gene Database (CoReCG), contains 2056 colon-rectal cancer genes information involved in distinct colorectal cancer stages sourced from published literature with an effective knowledge based information retrieval system. Additionally, interactive web interface enriched with various browsing sections, augmented with advance search facility for querying the database is provided for user friendly browsing, online tools for sequence similarity searches and knowledge based schema ensures a researcher friendly information retrieval mechanism. Colorectal cancer gene database (CoReCG) is expected to be a single point source for identification of colorectal cancer-related genes, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. Database URL: lms.snu.edu.in/corecg
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Affiliation(s)
- Rahul Agarwal
- Department of Life Science, Shiv Nadar University, Greater Noida, India
| | - Binayak Kumar
- Department of Life Science, Shiv Nadar University, Greater Noida, India
| | - Msk Jayadev
- Department of Life Science, Shiv Nadar University, Greater Noida, India
| | - Dhwani Raghav
- Department of Health Research (Ministry of Health & Family Welfare), Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, Ansari Nagar, New Delhi, India
| | - Ashutosh Singh
- Department of Life Science, Shiv Nadar University, Greater Noida, India
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Mar-Aguilar F, Rodríguez-Padilla C, Reséndez-Pérez D. Web-based tools for microRNAs involved in human cancer. Oncol Lett 2016; 11:3563-3570. [PMID: 27284356 DOI: 10.3892/ol.2016.4446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/10/2016] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs/miRs) are a family of small, endogenous and evolutionarily-conserved non-coding RNAs that are involved in the regulation of several cellular and functional processes. miRNAs can act as oncogenes or tumor suppressors in all types of cancer, and could be used as prognostic and diagnostic biomarkers. Databases and computational algorithms are behind the majority of the research performed on miRNAs. These tools assemble and curate the relevant information on miRNAs and present it in a user-friendly manner. The current review presents 14 online databases that address every aspect of miRNA cancer research. Certain databases focus on miRNAs and a particular type of cancer, while others analyze the behavior of miRNAs in different malignancies at the same time. Additional databases allow researchers to search for mutations in miRNAs or their targets, and to review the naming history of a particular miRNA. All these databases are open-access, and are a valuable tool for those researchers working with these molecules, particularly those who lack access to an advanced computational infrastructure.
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Affiliation(s)
- Fermín Mar-Aguilar
- Departamento de Biología Celular y Genética, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León 66451, México
| | - Cristina Rodríguez-Padilla
- Departamento de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León 66451, México
| | - Diana Reséndez-Pérez
- Departamento de Biología Celular y Genética, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León 66451, México; Departamento de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León 66451, México
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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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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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Anomalous altered expressions of downstream gene-targets in TP53-miRNA pathways in head and neck cancer. Sci Rep 2014; 4:6280. [PMID: 25186767 PMCID: PMC5385823 DOI: 10.1038/srep06280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/11/2014] [Indexed: 01/21/2023] Open
Abstract
The prevalence of head and neck squamous cell carcinoma, HNSCC, continues to grow. Change in the expression of TP53 in HNSCC affects its downstream miRNAs and their gene targets, anomalously altering the expressions of the five genes, MEIS1, AGTR1, DTL, TYMS and BAK1. These expression alterations follow the repression of TP53 that upregulates miRNA-107, miRNA- 215, miRNA-34 b/c and miRNA-125b, but downregulates miRNA-155. The above five so far unreported genes are the targets of these miRNAs. Meta-analyses of microarray and RNA-Seq data followed by qRT-PCR validation unravel these new ones in HNSCC. The regulatory roles of TP53 on miRNA-155 and miRNA-125b differentiate the expressions of AGTR1 and BAK1in HNSCC vis-à-vis other carcinogenesis. Expression changes alter cell cycle regulation, angiogenic and blood cell formation, and apoptotic modes in affliction. Pathway analyses establish the resulting systems-level functional and mechanistic insights into the etiology of HNSCC.
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Buza T, Arick M, Wang H, Peterson DG. Computational prediction of disease microRNAs in domestic animals. BMC Res Notes 2014; 7:403. [PMID: 24970281 PMCID: PMC4091757 DOI: 10.1186/1756-0500-7-403] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 06/20/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The most important means of identifying diseases before symptoms appear is through the discovery of disease-associated biomarkers. Recently, microRNAs (miRNAs) have become highly useful biomarkers of infectious, genetic and metabolic diseases in human but they have not been well studied in domestic animals. It is probable that many of the animal homologs of human disease-associated miRNAs may be involved in domestic animal diseases. Here we describe a computational biology study in which human disease miRNAs were utilized to predict orthologous miRNAs in cow, chicken, pig, horse, and dog. RESULTS We identified 287 human disease-associated miRNAs which had at least one 100% identical animal homolog. The 287 miRNAs were associated with 359 human diseases referenced in 2,863 Pubmed articles. Multiple sequence analysis indicated that over 60% of known horse mature miRNAs found perfect matches in human disease-associated miRNAs, followed by dog (50%). As expected, chicken had the least number of perfect matches (5%). Phylogenetic analysis of miRNA precursors indicated that 85% of human disease pre-miRNAs were highly conserved in animals, showing less than 5% nucleotide substitution rates over evolutionary time. As an example we demonstrated conservation of human hsa-miR-143-3p which is associated with type 2 diabetes and targets AKT1 gene which is highly conserved in pig, horse and dog. Functional analysis of AKT1 gene using Gene Ontology (GO) showed that it is involved in glucose homeostasis, positive regulation of glucose import, positive regulation of glycogen biosynthetic process, glucose transport and response to food. CONCLUSIONS This data provides the animal and veterinary research community with a resource to assist in generating hypothesis-driven research for discovering animal disease-related miRNA from their datasets and expedite development of prophylactic and disease-treatment strategies and also influence research efforts to identify novel disease models in large animals. Integrated data is available for download at http://agbase.hpc.msstate.edu/cgi-bin/animal_mirna.cgi.
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Affiliation(s)
- Teresia Buza
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, P. O. Box 6100, Mississippi State 39762, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, P. O. Box 9627, Mississippi State 39762, USA
| | - Mark Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, P. O. Box 9627, Mississippi State 39762, USA
| | - Hui Wang
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, P. O. Box 9627, Mississippi State 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, P. O. Box 9627, Mississippi State 39762, USA
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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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16
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Dang J, Bian YQ, Sun JY, Chen F, Dong GY, Liu Q, Wang XW, Kjems J, Gao S, Wang QT. MicroRNA-137 promoter methylation in oral lichen planus and oral squamous cell carcinoma. J Oral Pathol Med 2012; 42:315-21. [PMID: 23121285 DOI: 10.1111/jop.12012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2012] [Indexed: 12/23/2022]
Abstract
Oral lichen planus (OLP) is a common oral mucosal disease, which is generally considered a potentially malignant lesion. To identify efficiently prognostic biomarker, we investigated the microRNA-137 (miR-137) promoter methylation in OLP and compared with the samples from healthy volunteers and patients with oral squamous cell carcinoma (OSCC). A total of 20 OLP and 12 patients with OSCC as well as 10 healthy subjects were subjected to miR-137 promoter methylation analysis using methylation-specific PCR (MSP). To address the malignancy prediction potential from miR-137 promoter methylation status, methylation of the p16 gene, a well-known tumor suppressor, was investigated in the same samples. The p16 methylation and miR-137 promoter methylation were found to be 25% and 35% in patients with OLP, 50% and 58.3% in patients with OSCC, and 0% and 0% in healthy subjects, respectively. The differences between miR-137 and p16 methylation levels were statistically significant between healthy controls and patients. Methylation levels of the two promoters were also influenced by age, gender, and lesion duration. Interestingly, aberrant promoter methylation of the p16 and miR-137 genes was only found in the epithelium but not in the connective tissue from patients with OLP. This raises the possibility to use miR-137 methylation as a biomarker for malignant prediction in patients with OLP.
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Affiliation(s)
- Jun Dang
- Department of Periodontics and Oral Medicine, School of Stomatology, Fourth Military Medical University, Xi'an 710032, China
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