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Homo sapiens

ABSTRACT: PRPF6 regulated alternative splicing in colon cancer cell lines

OTHER RELATED OMICS DATASETS IN: EGAC00001000055EGAS00001000761EGAD00001000817

PROVIDER: PRJNA244759 | ENA |

REPOSITORIES: ENA

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PRPF6 regulated alternative splicing in colon cancer cell lines

Project description:PRPF6, an RNA binding component of the pre-mRNA spliceosome, is an essential driver of oncogenesis in colon cancer. PRPF6 is both amplified and overexpressed in colon cancer and cells with high PRPF6 levels are sensitive to its loss. Here we investigate alternative splicing changes in colon cancer cell lines following PRPF6 silencing by three different siRNA sequences. Two colon cancer cell lines (SW620 and KM-12), silencing of PRPF6 and control, 3 biological replicate samples for each group.

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RNAseq data to study PRPF6 regulated splice forms in colon cancer cell lines

Project description:Description Alternative splicing plays critical roles in differentiation, development, and cancer. Using an integrated genomic approach, we have identified PRPF6, an RNA binding component of the pre-mRNA spliceosome, as an essential driver of oncogenesis in colon cancer. Importantly, PRPF6 is both amplified and overexpressed in colon cancer, and only colon cancer cells with high PRPF6 levels are sensitive to its loss. Our data clearly point to an important role for PRPF6 in colon cancer growth and suggest that a better understanding of its role in alternative splicing in colon cancer is warranted. To determine the specific alternative splice forms that PRPF6 regulates in colon cancer, we conducted the following experiment: Using two colon cancer cell lines (KM-12 and SW620) that have high PRPF6 levels, we inhibited PRPF6 expression using 2 independent siRNAs. We also tested the effect of U2 snRNP inhibition using both a siRNA targeting SF3B1 as well as spliceostatin A (a small molecule inhibitor of SF3B1). We then conducted RNA-seq to determine the gene expression and exonic changes that occur relative to either the non-targeting control siRNA (for siSF3B1 and siPRPF6) or the vehicle control (for spliceostatin A).

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