Project description:Transcriptional lineage factors are a prominent class of essential genes in cancer, but the mechanisms that maintain lineage fidelity in advanced cancer clones, and whether lineage factor pathways could be broadly exploited for cancer therapy remain poorly understood. Here, we have used clear cell renal cell carcinoma (ccRCC) as a model to characterise the mechanisms that underlie lineage factor dependence in cancer. Through CRISPR/Cas9 loss-of-function screening and functional validation we find that loss of SMARCB1, a member of the SWI/SNF chromatin remodelling complex, can confer an advantage to ccRCC cells upon inhibition of the essential renal lineage factor PAX8. PAX8 inhibition resistant cells formed tumours with a dramatically altered histology showing neuroendocrine differentiation. Based on ATAC-seq and RNA-seq analysis, SMARCB1 inactivation leads to large-scale loss of kidney-specific epigenetic programmes, acquisition of a cellular state resembling that of rhabdoid tumours, and eventual activation of proliferative pathways. We show that these pathways are supported by the adoption of new transcriptional dependencies on IRF2, BHLHE40, and ZNFX1, factors that represent rare essential genes across different lineage-specific and oncogenic pathways, a principle validated in a large-scale CRISPR/Cas9 screening data set comprising hundreds of cancer cell lines. Thus, lineage factor requirements in cancer can switch upon challenge. The rules governing such lineage switching should be considered when designing novel lineage factor-targeted cancer therapies.
Project description:Transcriptional lineage factors are a prominent class of essential genes in cancer, but the mechanisms that maintain lineage fidelity in advanced cancer clones, and whether lineage factor pathways could be broadly exploited for cancer therapy remain poorly understood. Here, we have used clear cell renal cell carcinoma (ccRCC) as a model to characterise the mechanisms that underlie lineage factor dependence in cancer. Through CRISPR/Cas9 loss-of-function screening and functional validation we find that loss of SMARCB1, a member of the SWI/SNF chromatin remodelling complex, can confer an advantage to ccRCC cells upon inhibition of the essential renal lineage factor PAX8. PAX8 inhibition resistant cells formed tumours with a dramatically altered histology showing neuroendocrine differentiation. Based on ATAC-seq and RNA-seq analysis, SMARCB1 inactivation leads to large-scale loss of kidney-specific epigenetic programmes, acquisition of a cellular state resembling that of rhabdoid tumours, and eventual activation of proliferative pathways. We show that these pathways are supported by the adoption of new transcriptional dependencies on IRF2, BHLHE40, and ZNFX1, factors that represent rare essential genes across different lineage-specific and oncogenic pathways, a principle validated in a large-scale CRISPR/Cas9 screening data set comprising hundreds of cancer cell lines. Thus, lineage factor requirements in cancer can switch upon challenge. The rules governing such lineage switching should be considered when designing novel lineage factor-targeted cancer therapies.
Project description:Lineage switching can induce therapy resistance in cancer. Yet, how lineage fidelity is maintained and how it can be lost remain poorly understood. Here, we have used CRISPR-Cas9-based genetic screening to demonstrate that loss of SMARCB1, a member of the SWI/SNF chromatin remodeling complex, can confer an advantage to clear cell renal cell carcinoma (ccRCC) cells upon inhibition of the renal lineage factor PAX8. Lineage factor inhibition-resistant ccRCC cells formed tumors with morphological features, but not molecular markers, of neuroendocrine differentiation. SMARCB1 inactivation led to large-scale loss of kidney-specific epigenetic programs and restoration of proliferative capacity through the adoption of new dependencies on factors that represent rare essential genes across different cancers. We further developed an analytical approach to systematically characterize lineage fidelity using large-scale CRISPR-Cas9 data. An understanding of the rules that govern lineage switching could aid the development of more durable lineage factor-targeted and other cancer therapies.
