RNA sequencing reveals widespread transcriptome changes in a renal carcinoma cell line

Oncotarget
Agata Lichawska-CieslarJolanta Jura

Abstract

We used RNA sequencing (RNA-Seq) technology to investigate changes in the transcriptome profile in the Caki-1 clear cell renal cell carcinoma (ccRCC) cells, which overexpress monocyte chemoattractant protein-induced protein 1 (MCPIP1). RNA-Seq data showed changes in 11.6% and 41.8% of the global transcriptome of Caki-1 cells overexpressing wild-type MCPIP1 or its D141N mutant, respectively. Gene ontology and KEGG pathway functional analyses showed that these transcripts encoded proteins involved in cell cycle progression, protein folding in the endoplasmic reticulum, hypoxia response and cell signalling. We identified 219 downregulated transcripts in MCPIP1-expressing cells that were either unchanged or upregulated in D141N-expressing cells. We validated downregulation of 15 transcripts belonging to different functional pathways by qRT-PCR. The growth and viability of MCPIP1-expressing cells was reduced because of elevated p21Cip1levels. MCPIP1-expressing cells also showed reduced levels of DDB1 transcript that encodes component of the E3 ubiquitin ligase that degrades p21Cip1. These results demonstrate that MCPIP1 influences the growth and viability of ccRCC cells by increasing or decreasing the transcript levels for proteins ...Continue Reading

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Citations

Dec 13, 2018·Journal of Crohn's & Colitis·Jerzy OstrowskiMichal Mikula
Apr 17, 2019·RNA·Mateusz WawroAneta Kasza
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Datasets Mentioned

BETA
PRJEB20908

Methods Mentioned

BETA
RNA-Seq
PCR
protein folding
nucleotide exchange
Assay
electrophoresis
chips

Software Mentioned

DESeq2
PURO
htseq
R
clusterProfiler
Torrent Suite
BioConductor package
GraphPad Prism
Pathview
GOplot R - package

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