Computational analysis for identification of the extracellular matrix molecules involved in endometrial cancer progression

Vijesh Kumar Yadav, Tzong Yi Lee, Justin Bo Kai Hsu, Hsien Da Huang, Wei Chung Vivian Yang, Tzu Hao Chang

Research output: Contribution to journalArticlepeer-review

Abstract

Recurrence and poorly differentiated (grade 3 and above) and atypical cell type endometrial cancer (EC) have poor prognosis outcome. The mechanisms and characteristics of recurrence and distal metastasis of EC remain unclear. The extracellular matrix (ECM) of the reproductive tract in women undergoes extensive structural remodelling changes every month. Altered ECMs surrounding cells were believed to play crucial roles in a cancer progression. To decipher the associations between ECM and EC development, we generated a PAN-ECM Data list of 1516 genes including ECM molecules (ECMs), synthetic and degradation enzymes for ECMs, ECM receptors, and soluble molecules that regulate ECM and used RNA-Seq data from The Cancer Genome Atlas (TCGA) for the studies. The alterations of PAN-ECM genes by comparing the RNA-Seq expressions profiles of EC samples which have been grouped as tumorigenesis and metastasis group based on their pathological grading were identified. Differential analyses including functional enrichment, co-expression network, and molecular network analysis were carried out to identify the specific PAN-ECM genes that may involve in the progression of EC. Eight hundred and thirty-one and 241 PAN-ECM genes were significantly involved in tumorigenesis (p-value <1.571e-15) and metastasis (p-value <2.2e-16), respectively, whereas 140 genes were in the intersection of tumorigenesis and metastasis. Interestingly, 92 of the 140 intersecting PAN-ECM genes showed contrasting fold changes between the tumorigenesis and metastasis datasets. Enrichment analysis for the contrast PAN-ECM genes indicated pathways such as GP6 signaling, ILK signaling, and interleukin (IL)-8 signaling pathways were activated in metastasis but inhibited in tumorigenesis. The significantly activated ECM and ECM associated genes in GP6 signaling, ILK signaling, and interleukin (IL)-8 signaling pathways may play crucial roles in metastasis of EC. Our study provides a better understanding of the etiology and the progression of EC.

Original languageEnglish
Article numbere0231594
Pages (from-to)e0231594
JournalPLoS ONE
Volume15
Issue number4
DOIs
Publication statusPublished - Apr 1 2020

Keywords

  • Carcinogenesis/genetics
  • Computational Biology
  • Disease Progression
  • Endometrial Neoplasms/genetics
  • Endometrium/metabolism
  • Extracellular Matrix/genetics
  • Female
  • Gene Expression Regulation, Neoplastic/genetics
  • Humans
  • Neoplasm Metastasis
  • Neoplasm Proteins/genetics
  • RNA-Seq
  • Receptors, Cell Surface/genetics
  • Signal Transduction/genetics

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • General
  • Biochemistry, Genetics and Molecular Biology(all)

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