Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, which after breast, lung and, prostate cancers, is the fourth prevalent cancer in the United States. Long non-coding RNAs (lncRNAs) have an essential role in the pathogenesis of CRC. Therefore, bioinformatics studies on lncRNAs and their target genes have potential importance as novel biomarkers. In the current study, publicly available microarray gene expression data of colorectal cancer (GSE106582) was analyzed with the Limma, Geoquery, Biobase package. Afterward, identified differentially expressed lncRNAs and their target genes were inserted into Weighted correlation network analysis (WGCNA) to obtain modules and hub genes. A total of nine differentially expressed lncRNAs (LINC01018, ITCH-IT, ITPK1-AS1, FOXP1-IT1, FAM238B, PAXIP1-AS1, ATP2B1-AS1, MIR29B2CHG, and SNHG32) were identified using microarray data analysis. The WGCNA has identified several hub genes for black (LMOD3, CDKN2AIPNL, EXO5, ZNF69, BMS1P5, METTL21A, IL17RD, MIGA1, CEP19, FKBP14), blue (CLCA1, GUCA2A, UGT2B17, DSC2, CA1, AQP8, ITLN1, BEST4, KLF4, IQCF6) and turquoise (PAFAH1B1, LMNB1, CACYBP, GLO1, PUM3, POC1A, ASF1B, SDCCAG3, ASNS, PDCD2L) modules. The findings of the current study will help to improve our understanding of CRC. Moreover, the hub genes that we have identified could be considered as possible prognostic/diagnostic biomarkers. This study led to the determination of nine lncRNAs with no previous association with CRC development.
Highlights
Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, which after breast, lung and, prostate cancers, is the fourth prevalent cancer in the United States
Microarray gene expression data of colorectal cancer with the series number GSE106582 was obtained from the publicly available Gene Expression Omnibus (GEO) database to identify Long non-coding RNAs (lncRNAs) candidates .GSE106582 was provided by the University clinics Freiburg (Freiburg, Germany), and CRC patients were recruited at the University Hospital of Heidelberg
LncRNA expression data analysis of the GSE106582 dataset resulted in the identification of 32 differentially expressed lncRNAs (DELs) (Supplementary File 1), among which nine lncRNAs are detected as novel lncRNAs with no previous association with CRC development, including LINC01018, SNHG32, ITCH-IT1, ITPK1-AS1, FOXP1-IT1, FAM238B, PAXIP1DT, ATP2B1-AS1, and MIR29B2CHG (Table 1)
Summary
Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, which after breast, lung and, prostate cancers, is the fourth prevalent cancer in the United States. Publicly available microarray gene expression data of colorectal cancer (GSE106582) was analyzed with the Limma, Geoquery, Biobase package. LncRNAs were recently identified as regulatory molecules with a length of more than 200 nucleotides They bear some resemblances with mRNAs, including a cap at the 5′ end, having more than one exon, being transcribed by RNA polymerase II (RNA pol II), and being located in the cytoplasm or the nucleus. Forrest et al identified more than 200 differentially expressed lncRNAs by analyzing RNA sequencing data from The Cancer Genome Atlas (TCGA) dataset. They concluded these lncRNAs regulate cell cycle genes and increase resistance to apoptosis[14]. In addition to CRC cells, lncRNAs with altered expression level has been reported in peripheral blood components such as serum or p lasma[16]
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