The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer

Large-scale human genetic data(1-3) have shown that cancer mutations display strong tissue-selectivity, but how this selectivity arises remains unclear. Here, using experimental models, functional genomics and analyses of patient samples, we demonstrate that the lineage transcription factor paired box 8 (PAX8) is required for oncogenic signalling by two common genetic alterations that cause clear cell renal cell carcinoma (ccRCC) in humans: the germline variant rs7948643 at 11q13.3 and somatic inactivation of the von Hippel-Lindau tumour suppressor (VHL)(4-6). VHL loss, which is observed in about 90% of ccRCCs, can lead to hypoxia-inducible factor 2 alpha (HIF2A) stabilization(6,7). We show that HIF2A is preferentially recruited to PAX8-bound transcriptional enhancers, including a pro-tumorigenic cyclin D1 (CCND1) enhancer that is controlled by PAX8 and HIF2A. The ccRCC-protective allele Cat rs7948643 inhibits PAX8 binding at this enhancer and downstream activation of CCND1 expression. Co-option of a PAX8-dependent physiological programme that supports the proliferation of normal renal epithelial cells is also required for MYC expression from the ccRCC metastasis-associated amplicons at 8q21.3-q24.3 (ref. (8)). These results demonstrate that transcriptional lineage factors are essential for oncogenic signalling and that they mediate tissue-specific cancer risk associated with somatic and inherited genetic variants.Peer reviewe

Ageing and regeneration-associated transcriptional state transitions and tumour-stroma interaction in early renal carcinogenesis

Kidney cancer is the 14th most common cancers in the world, among which clear cell renal cell carcinoma (ccRCC) is the most common subtype. VHL inactivation is the most common mutation seen in ccRCC with more than 90% of tumours had clonal disruption of the VHL pathway. Although it is the initial oncogenic insult in ccRCC, it takes decades after VHL inactivation for ccRCC to develop. To investigate the molecular mechanisms of ccRCC development, a mouse model with inducible inactivation of Vhl and Pbrm1 genes in kidney epithelial cells was used. single cell RNA sequencing (scRNA-seq) was performed to track the phenotypic evolution of Vhl / Pbrm1 null cells towards early carcinomas. The first transition was seen 10 months after Vhl / Pbrm1 inactivation with upregulation of stress- related transcription factors (TFs) including Fos, Junb, Egr1 and Atf3. Interestingly, these 4 TFs showed upregulation in normal proximal tubule (PT) cells as mice get older. The second wave showed upregulation of Sox4 and Sox9, which are involved in kidney epithelial cell regeneration. Single cell ATAC sequencing (scATAC-seq) experiment confirmed the functional importance of these TFs in early ccRCC cells. Although the expression of these TFs in normal kidney epithelial cells decrease after some time, they continued to be expressed at high level in ccRCC. Therefore, it seems that the initiation of ccRCC could be induced by unresolved response to the cell injury and tissue repair.Rosetrees Trust MRC Cancer Uni

The SWI/SNF complex member SMARCB1 supports lineage fidelity in kidney cancer

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.Peer reviewe

The SWI/SNF complex member SMARCB1 supports lineage fidelity in kidney cancer.

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