Identification of molecular characteristics induced by radiotherapy in rectal cancer based on microarray data

Abstract

Abstract. The present study aimed to reveal the molecular characteristics induced by radiotherapy in rectal cancer at the transcriptome level. Microarray data (ID, GSE26027) downloaded from the Gene Expression Omnibus database were re-analyzed to identify differentially expressed genes (DEGs) between rectal cancer tissues during and prior to radiotherapy. The DEGs were then inputted into the database for annotation, visualization and integrated discovery, an online tool to perform enrichment analyses, and into the search tool for the retrieval of interacting genes/proteins database to identify protein-protein interactions (PPIs). Subsequently, a PPI network was constructed, which was screened for densely connected modules. Furthermore, protein domain enrichment analysis was performed. In total, 690 DEGs, including 179 upregulated and 511 downregulated DEGs, were found in rectal cancer tissues during and prior to radiotherapy. The upregulated DEGs were significantly enriched in 'positive regulation of transport' and 'regulation of cardiac muscle contraction', while the downregulated DEGs were most markedly enriched in 'cell migration', 'cell-cell signaling', 'extracellular matrix organization' and 'blood vessel development', including prostaglandin-endoperoxide synthase 2, transforming growth factor β-induced, 68 kDa endothelin receptor type A, brain-derived neurotrophic factor, TIMP metallopeptidase inhibitor 1, and serpin family E member 1, which were the top 6 hub nodes in the PPI network. Furthermore, 2 protein domains were significantly enriched by PPI modules, including: The collagen triple helix repeat (CTHR) family members collagen type (COL) 5A2, COL9A3, COL6A3, COL21A1, COL5A3, COL11A1, COL7A1 and CTHR-containing-1; and the olfactory receptor family (OR) members OR7E24, OR7A17, OR6A2, OR1F1, OR10H3 and OR7A10. A total of 7 upregulated DEGs were characterized as tumor suppressor genes, and 8 downregulated DEGs were characterized as oncogenes. The biological processes or protein domains enriched by upregulated or downregulated DEGs may improve the understanding of molecular characteristics in response to radiotherapy.

Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of esophageal squamous cell carcinoma

“…In addition, in X-linked adrenoleukodystrophy patients, the combination of methylation levels of SPG20 , UNC45A , and COL9A3 and also the expression levels of ID4 and MYRF would be a good marker for distinguishing the discriminating childhood from adult inflammatory phenotypes [ 24 ]. As for tumor-related research, COL9A3 was identified as tumor suppressor gene in rectal cancer [ 25 ], and it was also significantly associated with the prognosis of triple-negative breast cancer as an independent prognostic signature [ 26 ]. Seldom research about the relationship between COL9A3 and ESCC was taken by now.…”

Bioinformatic analysis identifying Endoplasmic Reticulum Stress-Related genes as a new diagnostic and prognostic indicator in clear cell Renal Cell Carcinoma

“…COL5A3 is a member of the collagen triple helical repeat family and plays a role in cell proliferation, differentiation, apoptosis, migration and carcinogenesis(18). It has been shown to play a key role in breast cancer brain metastases and radiosensitivity in rectal cancer (19,20). Manoj Amrutkar et al found that COL5A3 promotes chemoresistance of pancreatic cancer cells to gemcitabine (21).…”

Profiles of Immune Cell Infiltration and Immune-Related Genes in the Tumor Microenvironment of Esophageal Squamous Cell Carcinoma

“…In addition, in X-linked adrenoleukodystrophy patients, the combination of methylation levels of SPG20, UNC45A, and COL9A3 and also the expression levels of ID4 and MYRF would be a good marker for distinguishing the discriminating childhood from adult in ammatory phenotypes [24]. As for tumor-related research, COL9A3 was identi ed as tumor suppressor gene in rectal cancer [25], and it was also signi cantly associated with the prognosis of triple-negative breast cancer as an independent prognostic signature [26]. Seldom research about the relationship between COL9A3 and ESCC was taken by now.…”