Differences in gene expression in CRPC cell line C4-2 before and after Cyclin-Dependent Kinase 12 (CDK12) knockdown using CRISPR-Cas9

CDK12 is a transcription-related CDK that is commonly mutated in different types of cancers. In prostate cancer, defective CDK12 has been identified as a new subtype with a worse prognosis and widespread drug resistance. CRPC is a malignant stage of recurrent prostate cancer following treatment, with a higher frequency of CDK12 mutations compared to early-stage prostate cancer. To investigate the impact of CDK12 defects on the overall gene expression in CRPC cells, we used CRISPR-Cas9 technology to generate CDK12 knockout and control C4-2 cell lines, followed by high-throughput transcriptome sequencing (RNA-seq). Our results demonstrate that CDK12 defects affect the expression of numerous genes in CRPC cells, providing insights into the regulatory role of CDK12 in prostate cancer development. Overall design: To investigate the effects of CDK12 deficiency on CRPC cells. We constructed CDK12 knockout and control cell lines using CRISPR-Cas9 technology. Next, we extracted total RNA from the cells and performed high-throughput transcriptome sequencing. We then performed gene expression profiling analysis using data obtained from RNA-seq and comparative gene expression profiling analysis of RNA-seg data for C4-2 VEC cell and its KO derivatives (VEC, CDK12KO)—three replicates per sample.