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

// Agata Lichawska-Cieslar 1 , Roza Pietrzycka 1 , Janusz Ligeza 1 , Maria Kulecka 2 , Agnieszka Paziewska 2 , Agata Kalita 1 , Dobrochna D. Dolicka 1 , Mateusz Wilamowski 1 , Katarzyna Miekus 1 , Jerzy Ostrowski 2, 3 , Michal Mikula 3 and Jolanta Jura 1 1 Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland 2 Departments of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland 3 Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland Correspondence to: Jolanta Jura, email: jolanta.jura@uj.edu.pl Michal Mikula, email: mikula.michal@coi.pl Keywords: MCPIP1; clear cell renal cell carcinoma; transcriptome profile; Regnase-1 Received: May 24, 2017      Accepted: December 30, 2017      Published: January 16, 2018 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 p21 Cip1 levels. MCPIP1-expressing cells also showed reduced levels of DDB1 transcript that encodes component of the E3 ubiquitin ligase that degrades p21 Cip1 . 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.