Research Article: Abnormal expression of mRNA, microRNA alteration and aberrant DNA methylation patterns in rectal adenocarcinoma

Date Published: March 28, 2017

Publisher: Public Library of Science

Author(s): Yang Hua, Xiukun Ma, Xianglong Liu, Xiangfei Yuan, Hai Qin, Xipeng Zhang, Javier S Castresana.

http://doi.org/10.1371/journal.pone.0174461

Abstract

Rectal adenocarcinoma (READ) is a malignancy cancer with the high morbidity and motility worldwide. Our study aimed to explore the potential pathogenesis of READ through integrated analysis of gene expression profiling and DNA methylation data.

The miRNA, mRNA expression profiling and corresponding DNA methylation data were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed mRNAs/ miRNAs/methylated regions (DEmRNA/DEmiRNAs) were identified in READ. The negatively correlation of DEmiRNA-DEmRNAs and DNA methylation-DEmRNAs were obtained. DEmRNAs expression was validated through quantitative real-time polymerase chain reaction (qRT-PCR) and microarray expression profiling analyses.

1192 dysregulated DEmRNAs, 27 dysregulated DEmiRNAs and 6403 aberrant methylation CpG sites were screened in READ compared to normal controls. 1987 negative interaction pairs among 27 DEmiRNAs and 668 DEmRNAs were predicted. 446 genes with aberrant methylation were annotated. Eventually, 50 DEmRNAs (39 down- and 11 up-regulated DEmRNAs) with hypermethylation, synchronously negatively targeted by DEmiRNAs, were identified through the correlation analysis among 446 genes with aberrant methylation and 668 DEmRNAs. 50 DEmRNAs were significantly enriched in cAMP signaling pathway, circadian entrainment and glutamatergic synapse. The validation results of expression levels of DEmRNAs through qRT-PCR and microarray analyses were compatible with our study.

7 genes of SORCS1, PDZRN4, LONRF2, CNGA3, HAND2, RSPO2 and GNAO1 with hypermethylation and negatively regulation by DEmiRNAs might contribute to the tumorigenesis of READ. Our work might provide valuable foundation for the READ in mechanism elucidation, early diagnosis and therapeutic target identification.

Partial Text

Colorectal cancer (CRC) is a leading cause of cancers with high morbidity and mortality. CRC is the third leading cause of cancer both in male and female and worldwide number of death in 2012 is more than 690,000 [1]. Australia/New Zealand, Europe and Northern America possess the highest incident rates, Africa and Northern America possess the low incidence rates of CRC [1, 2].

In our study, DEmiRNAs, DEmRNAs and differentially methylated genes were identified in READ compared with normal control tissues based on the TCGA database. DEmiRNA-DEmRNA regulatory network was constructed and DEmRNAs associated with differentially methylated genes were recognized. qRT-PCR was applied to verify the dysregulated genes through bioinformatics analysis. 9 candidate genes were randomly selected for qRT-PCR examination, ATP2B4, NR3C1, ROR1 and PPKCB were down-regulated in READ, TCF7, SLC6A6, PDPN, WNT2 and ONECUT2 were up-regulated in READ compared to paired adjacent non-tumor tissues, which were accordance with our analyses. In order to further validate the expression levels of DEmRNAs in READ, microarray expression profiling with larger sample size of READ and matched mucosa tissues generated from GEO database were applied for validation. The expression status of 33 representative DEmRNAs in READ tissues based on microarray analyses were completely compatible with our bioinformatics analyses based on TCGA datasets. Both of qRT-PCR validation and microarray analyses indicated our bioinformatics analyses based on TCGA datasets was acceptable.

 

Source:

http://doi.org/10.1371/journal.pone.0174461

 

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