Abstract

  Esophageal Cancer (EC) represents the third most common G.I malignancy and ranks among the ten most common cancers worldwide. The highest incidence of this cancer in India has been reported from Assam in the North-east region where it is the second leading cancer in men and third leading cancer in women.   A familial aggregation of  esophagial  cancer has been reported in Assam region of North East India along with high consumption of beetle quid, tobacco  and alcohal suggesting that environmental carcinogens in addition to geographic and genetic factors may play major etiological role. Integrated genomic approaches have been under taken to understand molecular carcinogenesis and to identify biomarker.

   Analysis of gene expression profile of tumour tissue from 16 non familial betel quid/tobacco chewing patients of esophageal cancer from Dr. B. Borooah cancer Hospital, Guwahati, Assam showed up regulation of MAPK pathway, G-protein coupled receptor family, ion transport activity, and serine or threonine kinase activity and down regulation of structural constituent of ribosome, endopeptidase inhibitor activity, structural constituent of cytoskeleton, antioxidant activity, acyl group transferase activity, eukaryotic translation elongation factor activit Gene expression profile of  patients having family history of esophageal cancer showed downregulation of genes involved in humoral immune response (PF4), extracellular matrix organization (COL4A4), metabolism of xenobiotics (EPHX1), TGF-ß signaling (SMAD1) and calcium signaling pathways (VDAC1) and up regulation of genes involved in regulation of actin cytoskeleton (WASL), neuroactive ligand receptor interaction (GRM3), Toll-like receptor (CD14), B-cell receptor (IFITM1) and insulin signaling pathways (FOXO1A). Study of high-resolution chromosomal instability profile showed amplifications on chromosomes arms 1p36.13, 1q21.1, 2p14, 3q28, 3q27, 3q26.1, 5p15.2, 5q11.2, 6p25.3, 7q11.21, 9q31.3, and17p13.1 and frequent deletions on chromosome arms 3p, 4p, 5q, 8p, 9p, 11q, 13q, 17p, and 18q. In this study we identified five genes COL11A1, FGF12, PAK1, DLC1 and NPHP4 by using different bioinformatics tools. In which gene enrichment analysis showed FGF12 was more suitable candidate marker for esophageal cancer among the all other cancer. On the basis of the insilico analysis, validations of candidate biomarker FGF12 gene by siRNA knockdown was done in  esophageal cancer cell lines KYSE410 followed by Proliferation assay, colony formation assay, and wound healing assay. 

Since DNA methylation, histone modification and miRNA-mediated epigenetic processes alter the gene expression, we investigated genome wide differential methylation profiling and differential expression profiling of chromatin modification enzymes in tumor and normal tissue collected ESCC patients. Genome wide differential methylation profiling of esophageal squamous cell carcinoma (ESCC) patients from Northeast India had been done along with integeration of data with gene expression data studied earlier. To prepare a network of genes displaying enriched pathways together with list of genes for each case i.e. hypermethylation with downregulation and hypomethylation with upregulation an Integrome analysis was also done. The study resulted in 23 Integrome network enriched genes having relevance to tumor progression as they are associated with the processes involved in metastasis like cell adhesion, integrin signaling, cytoskeleton organization and extracellular matrix organizations. To further scale down the most relevant genes to ESCC Methylation Efficiency Index (MEI) was calculated for all 23 genes found in Integrome analysis. Further higher expression of enzymes regulating methylation (DOT1L and PRMT1) and acetylation (KAT7, KAT8, KAT2A and KAT6A) of histone was found associated with ESCC risk. Tissue microarray done in independent cohort o