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RNA-seq of coding RNA from MCF7 breast cancer cells and samples derived from normal breast tissues

ABSTRACT: To improve our understanding of the effect of differential methylation on gene expression between normal and tumor breast cells, we carried out RNA sequencing evaluate mRNA expression changes in normal breast tissue and MCF7 breast cancer cell line. We identified 6632 protein-coding genes to be significantly differentially expressed (FDR threshold of 0.05) in the MCF7 cells. IPA Bio-Function enrichment analysis showed the 'cell death and survival' and 'cellular growth and proliferation' are the top 2 terms associated with differentially expressed genes. Cancer versus normal analysis of The Cancer Genome Atlas (TCGA) Breast data revealed genes that were differentially up and down-regulated in MCF7 are mostly respectively over- and under-expressed in clinical specimens.

ORGANISM(S): Homo sapiens

SUBMITTER: Lin IH

PROVIDER: S-ECPF-MTAB-1961 | biostudies-other | 2015

REPOSITORIES: biostudies-other

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Project description:Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the protein-coding genes for CALD1, FTX, and HNRNPH1. In conclusion, a number of differentially expressed lncRNAs have been identified with relation to cancer-related protein-coding genes.

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RNA-seq of coding RNA from MCF7 breast cancer cells and samples derived from normal breast tissues

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