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Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India: Identification of Epigenetically Altered Gene Expression Reveals Potential Biomarkers.
Marthong, Lastborn; Ghosh, Sahana; Palodhi, Arindam; Imran, Mohamed; Shunyu, Neizekhotuo Brian; Maitra, Arindam; Ghosh, Srimoyee.
Afiliación
  • Marthong L; Department of Zoology, North Eastern Hill University (NEHU), Shillong, India.
  • Ghosh S; National Institute of Biomedical Genomics (NIBMG), Kalyani, India.
  • Palodhi A; National Institute of Biomedical Genomics (NIBMG), Kalyani, India.
  • Imran M; National Institute of Biomedical Genomics (NIBMG), Kalyani, India.
  • Shunyu NB; Department of Otorhinolaryngology (ENT), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Shillong, India.
  • Maitra A; National Institute of Biomedical Genomics (NIBMG), Kalyani, India.
  • Ghosh S; Department of Zoology, North Eastern Hill University (NEHU), Shillong, India.
Front Genet ; 11: 986, 2020.
Article en En | MEDLINE | ID: mdl-33133131
Oropharyngeal cancer is a subtype of head and neck squamous cell carcinoma that is associated with unique risk exposures like consumption of smokeless tobacco and areca nut and is highly prevalent in the northeastern region of India, especially Meghalaya. However, the underlying epigenetic and transcriptomic changes in this cancer type is yet to be delineated. We have undertaken a study on genome wide somatic alterations in the DNA methylation and transcriptome in oropharyngeal cancer patients from this region using genome wide techniques in paired tumors and adjacent normal tissues. By using integrative approaches, we have identified 194 epigenetically silenced and 241 epigenetically overexpressed genes in the tumor tissue of these patients. Pathways that are significantly enriched by these genes include the pathways of immune systems, such as the interleukin signaling pathways and Toll-like receptor signaling pathway. Also, osteoclast differentiation pathway was found to be epigenetically upregulated. The pathways enriched by the epigenetically downregulated genes were found to be predominantly those involved in xenobiotic metabolism and keratinization. Two major transcription factors - SPI1 and RUNX1 were identified as epigenetically dysregulated, which further modulates 129 downstream genes. Comparison of our observations with the head and neck cancer data from TCGA revealed distinct DNA methylation and gene expression landscapes which might be specific for oropharyngeal cancer. HPV DNA sequences were not detected in any of the tumor samples in RNA-Seq data. The results obtained in this study might provide improved understanding of the disease.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Tipo de estudio: Diagnostic_studies / Prognostic_studies Idioma: En Revista: Front Genet Año: 2020 Tipo del documento: Article País de afiliación: India Pais de publicación: Suiza
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Tipo de estudio: Diagnostic_studies / Prognostic_studies Idioma: En Revista: Front Genet Año: 2020 Tipo del documento: Article País de afiliación: India Pais de publicación: Suiza