Characterizing the transcriptional and chromatin landscapes of cancer metastasis

Abstract

Cancer cells must overcome numerous challenges in order to establish distant metastatic lesions. Thus, distinct molecular programs are required to provide cancer cells with the ability to adapt and develop overt metastases. Previous work has pointed toward epigenetic adaptations, as opposed to additional genetic mutations, in driving metastatic outgrowth. To better understand large-scale transcriptional and chromatin landscape changes in metastasis, we performed unbiased RNA-seq and ATAC-seq on matched primary and metastatic tumors from an established PDAC mouse model. This model uniquely develops rapid metastatic lesions, unlikely to carry de novo mutations, in both the liver and lung. RNA-sequencing analysis identified significantly differentially expressed gene signatures, including a common pro-metastatic gene signature regardless of metastatic site. Parallel ATAC-seq analysis revealed differential chromatin accessibility, the majority of which occurred outside of promoter regions. We used combined RNA-seq and ATAC-seq analysis to define specific gene sets based on differential gene expression and chromatin accessibility, and we revealed a subset of genes that are combinatorially regulated by both poised and newly opened genomic elements. Using transcription factor motif analysis, we identified top shared and lung-specific transcription factors of interest, which included the AP-1 and CNC families. Lastly, the additional analysis of a breast cancer (BC) mouse model revealed that both PDAC and BC lung mets show an enrichment for ETS family transcription factor motifs, highlighting potentially shared regulatory programs that could be driven by their shared metastatic niche. Finally, in addition to investigating the large-scale regulation of metastasis, we followed up on one driver of PDAC liver metastasis, DPYS. DPYS (dihydropyrimidinase) is the second enzyme involved in pyrimidine breakdown, and RNA-seq analysis of both bulk tissue and sorted tumor cells showed significant upregulation of DPYS expression in PDAC liver metastases. Through shRNA knockdown and rescue overexpression, we show that DPYS is important for PDAC liver metastasis formation both in vitro and in vivo. Additionally, we propose a unique mechanism where the synthesis of methylmalonic acid mediates the effect of pyrimidine catabolism on EMT maintenance in established liver metastases.