title: Transcriptional coexpression network reveals the involvement of varying stem cell features with different dysregulations in different gastric cancer subtypes.
abstract: Despite the advancements in the cancer therapeutics, gastric cancer ranks as the second most common cancers with high global mortality rate. Integrative functional genomic investigation is a powerful approach to understand the major dysregulations and to identify the potential targets toward the development of targeted therapeutics for various cancers. Intestinal and diffuse type gastric tumors remain the major subtypes and the molecular determinants and drivers of these distinct subtypes remain unidentified. In this investigation, by exploring the network of gene coexpression association in gastric tumors, mRNA expressions of 20,318 genes across 200 gastric tumors were categorized into 21 modules. The genes and the hub genes of the modules show gastric cancer subtype specific expression. The expression patterns of the modules were correlated with intestinal and diffuse subtypes as well as with the differentiation status of gastric tumors. Among these, G1 module has been identified as a major driving force of diffuse type gastric tumors with the features of (i) enriched mesenchymal, mesenchymal stem cell like, and mesenchymal derived multiple lineages, (ii) elevated OCT1 mediated transcription, (iii) involvement of Notch activation, and (iv) reduced polycomb mediated epigenetic repression. G13 module has been identified as key factor in intestinal type gastric tumors and found to have the characteristic features of (i) involvement of embryonic stem cell like properties, (ii) Wnt, MYC and E2F mediated transcription programs, and (iii) involvement of polycomb mediated repression. Thus the differential transcription programs, differential epigenetic regulation and varying stem cell features involved in two major subtypes of gastric cancer were delineated by exploring the gene coexpression network. The identified subtype specific dysregulations could be optimally employed in developing subtype specific therapeutic targeting strategies for gastric cancer.
authors.affiliation: Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India.
authors.forename: Kalaivani
authors.initials: K
authors.lastname: Kalamohan
authors.affiliation: Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India.
authors.forename: Jayaprakash
authors.initials: J
authors.lastname: Periasamy
authors.affiliation: Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India.
authors.forename: Divya
authors.initials: D
authors.lastname: Bhaskar Rao
authors.affiliation: Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India.
authors.forename: Georgina D
authors.initials: GD
authors.lastname: Barnabas
authors.affiliation: Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India.
authors.forename: Srigayatri
authors.initials: S
authors.lastname: Ponnaiyan
authors.affiliation: Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, India. Electronic address: kumar@oncocellomics.org.
authors.forename: Kumaresan
authors.initials: K
authors.lastname: Ganesan
mesh_terms: D002454:Cell Differentiation; D045744:Cell Line, Tumor; D044127:Epigenesis, Genetic; D005753:Gastric Mucosa / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D014411:Neoplastic Stem Cells / Q000166:cytology / Q000378:metabolism / Q000473:pathology*; D013270:Stomach / Q000473:pathology*; D013274:Stomach Neoplasms / Q000235:genetics* / Q000473:pathology
keywords: Diffuse subtype; Embryonic stem cells; Gastric cancer; Intestinal subtype; Mesenchymal stem cell differentiation; Mesenchymal stem cells; Notch signaling; Polycomb repression