Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

BMC Genomics
Joshua D WelchJan F Prins

Abstract

Recent studies have shown that some pseudogenes are transcribed and contribute to cancer when dysregulated. In particular, pseudogene transcripts can function as competing endogenous RNAs (ceRNAs). The high similarity of gene and pseudogene nucleotide sequence has hindered experimental investigation of these mechanisms using RNA-seq. Furthermore, previous studies of pseudogenes in breast cancer have not integrated miRNA expression data in order to perform large-scale analysis of ceRNA potential. Thus, knowledge of both pseudogene ceRNA function and the role of pseudogene expression in cancer are restricted to isolated examples. To investigate whether transcribed pseudogenes play a pervasive regulatory role in cancer, we developed a novel bioinformatic method for measuring pseudogene transcription from RNA-seq data. We applied this method to 819 breast cancer samples from The Cancer Genome Atlas (TCGA) project. We then clustered the samples using pseudogene expression levels and integrated sample-paired pseudogene, gene and miRNA expression data with miRNA target prediction to determine whether more pseudogenes have ceRNA potential than expected by chance. Our analysis identifies with high confidence a set of 440 pseudogenes tha...Continue Reading

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Citations

Dec 15, 2015·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Xuefei ShiMing Sun
Sep 12, 2015·Journal of Medical Genetics·Xiaolong QiWang Ma
Apr 6, 2016·Cancer Letters·Mohammed L AbbaHeike Allgayer
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Aug 27, 2016·Journal of Cellular and Molecular Medicine·Yang AnShaoping Ji
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Jan 31, 2017·Molecular Therapy : the Journal of the American Society of Gene Therapy·Ming SunKai-Hua Lu
Aug 23, 2016·World Journal of Gastroenterology : WJG·Meng Zhang, Xiang Du
Dec 12, 2018·Journal of Cellular Physiology·Rasoul AbdollahzadehJavad Tavakkoly-Bazzaz
Jun 28, 2018·Breast Cancer Research and Treatment·Edna Ayerim Mandujano-TinocoVilma Maldonado
Apr 26, 2017·Pathology Oncology Research : POR·Yansong LiuLi Li
Nov 30, 2018·Biochemistry. Biokhimii︠a︡·T F Kovalenko, L I Patrushev
Oct 13, 2020·Cell Cycle·Marco De MartinoAlfredo Fusco

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

BLAST
GOrilla
SAM
Ensembl
GENCODE
psiDR
samr
GeneCards
Significance Analysis of Microarrays R package ( samr )
ENCODE

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