Microarray and bioinformatic analysis reveal the parental genes of m6A modified circRNAs as novel prognostic signatures in colorectal cancer

Abstract

BackgroundAccumulating evidences have revealed that the abnormal N6-methyladenosine (m6A) modification is closely associated with the occurrence, development, progression and prognosis of cancer. It is noteworthy that m6A modification is widely existed in circRNAs and found its key biological functions in regulating circRNAs metabolism. However, the role of m6A modified circRNAs in colorectal cancer (CRC) remains unknown. To better understand the role of circRNAs in the pathogenesis of CRC, we focus on the relationship between m6A-modified circRNAs and their parental genes.MethodsArraystar m6A-circRNA epitranscriptomic microarray was used to identify differentially m6A modified circRNAs between CRC and the control group. In addition, TCGA-COAD and GSE106582 cohort were used to identify differentially expressed mRNAs. In this study, we screened the parental genes for which both circRNAs and mRNAs were down-regulated further to analyze, including gene expression, survival prognosis, enrichment analysis. Additionally, Western Blotting was used to further validate the role of the parental gene in CRC.ResultsWe found that 1405 significantly downregulated circRNAs in CRC by our microarray data. Moreover, we obtained 113 parental genes for which both circRNAs and mRNAs were down-regulated to analyze the relationship with the prognosis of CRC based on TCGA-COAD cohort. And we identified nine potential prognostic genes, including ABCD3, ABHD6, GAB1, MIER1, MYOCD, PDE8A, RPS6KA5, TPM1 and WDR78. And low expression of these genes was associated with poor survival prognosis of the patients with CRC. In addition, we found that TPM1 is downregulated in CRC by western blotting experiment. And the calcium-signaling pathway may involve the process of the CRC progression.ConclusionsWe identified nine potential prognostic genes, after analyzed the relationship between the parental genes of m6A modified circRNAs and the progression of CRC. Above all, our study further validated TPM1 can serve as a potentail signature for CRC patients.

Epithelial Gab1 calibrates RIPK3-dependent necroptosis to prevent intestinal inflammation

“…A previous study reported that Gab1 overexpression in DLD-1 colon carcinoma cells promoted tumor growth in a subcutaneous model ( 71 ), which is consistent with the in vitro findings from Bai et al ( 72 ). In contrast, Liang et al delineated the tumor-suppressing role for Gab1 in CRC ( 73 ). In our study, we generated mice with Gab1 -KO in normal intestinal epithelium, followed by AOM/DSS induction to mimic the progression of inflammation-associated carcinogenesis.…”

Analysis approaches for the identification and prediction of N 6 -methyladenosine sites

“…Meanwhile, computational methods are developed based on the MeRIP-seq data to map m 6 A modifications in circRNA [ 151 , 152 ]. In addition, due to its unique property of low total RNA input, m 6 A-circRNA epitranscriptomic microarray [ 153 , 154 ] is coming into vogue. However, microarray based on the hybridization of probes must have the sequence of the samples in advance.…”