GSE130049
Transcriptome profiling of 786-O RCC cells transduced with control vector or PRDM16 lentivirus.
Recent large-scale data sets indicate the emerging importance of alterations of the epigenome in renal cell carcinoma (RCC).  Analysis of transcriptomic data of patient samples including normal kidney, primary tumor, and metastatic tumor deposits demonstrates epigenetic silencing of the gene encoding the transcription factor PR domain-containing 16 (PRDM16).  PRDM16 has a prominent role in adipocyte metabolism but is also highly expressed in the kidney.  The role of PRDM16 in renal cancer has not been investigated. RNAseq analysis reveals that PRDM16 imparts a predominantly repressive effect on the RCC transcriptome including suppression of SEMA5B (semaphorin 5B), a target gene of hypoxia inducible factor (HIF).  Collectively, our data uncover a novel epigenetic basis by which HIF target gene expression is amplified in kidney cancer.  Moreover, they demonstrate a new mechanism by which PRDM16 exerts its tumor suppressive effects. Overall design: Total RNA were isolated from 786-O RCC cells transduced with control vector or PRDM16 lentivirus. Two replicates were considered for both control and PRDM16 overexpressed cells. RNA-seq was performed to find out impact of PRDM16 overexpression on global transcriptome of RCC cells.