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 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.
Highlights
Clear cell renal cell carcinoma is the most frequent kidney cancer, which is highly vascularized and characterized by malignant renal epithelial cells with clear cytoplasm
These results demonstrate that monocyte chemoattractant protein-induced protein 1 (MCPIP1) influences the growth and viability of clear cell renal cell carcinoma (ccRCC) cells by increasing or decreasing the transcript levels for proteins involved in cell cycle progression, protein folding, hypoxia response, and cell signaling
HIF-2α is negatively regulated during hypoxia by Monocyte Chemoattractant Protein-induced protein 1 (MCPIP1) in the ccRCC cell line, Caki-1 [4]
Summary
Clear cell renal cell carcinoma (ccRCC) is the most frequent kidney cancer, which is highly vascularized and characterized by malignant renal epithelial cells with clear cytoplasm. Deletion of the short arm of chromosome 3 that includes the von Hippel Lindau tumor suppressor (VHL) gene correlates with increased expression and activity of HIF-1α and HIF-2α in 90% of the ccRCC patient samples [1] This is because the VHL protein is part of an active E3 ubiquitin ligase complex that targets HIF-1α for ubiquitin-mediated degradation [2]. HIF-2α is negatively regulated during hypoxia by Monocyte Chemoattractant Protein-induced protein 1 (MCPIP1) in the ccRCC cell line, Caki-1 [4]. MCPIP1 inhibits growth of ccRCC and neuroblastoma cell lines [4, 12] by enhancing the decay of anti-apoptotic gene transcripts, including Bcl2L1, Bcl2A1, RelB, Birc, and Bcl3 [13] and negatively regulating the rate of metabolism and angiogenesis [4]. In this study, we investigated the role of MCPIP1 in global transcriptional regulation by performing RNA-Seq analysis of Caki cells that overexpress wild type or RNase-deficient MCPIP1 proteins
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