RNA sequencing reveals widespread transcriptome changes in a renal carcinoma cell line
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Agata Lichawska-Cieslar1, Roza Pietrzycka1, Janusz Ligeza1, Maria Kulecka2, Agnieszka Paziewska2, Agata Kalita1, Dobrochna D. Dolicka1, Mateusz Wilamowski1, Katarzyna Miekus1, Jerzy Ostrowski2,3, Michal Mikula3 and Jolanta Jura1
1Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
2Departments of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
3Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
Jolanta Jura, email: email@example.com
Michal Mikula, email: firstname.lastname@example.org
Keywords: MCPIP1; clear cell renal cell carcinoma; transcriptome profile; Regnase-1
Received: May 24, 2017 Accepted: December 30, 2017 Published: January 16, 2018
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 p21Cip1 levels. 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 involved in cell cycle progression, protein folding, hypoxia response, and cell signaling.
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