Jiayi Yao:
Investigation of acid adaptation in the tumor microenvironment at gene, promoter and enhancer levels

Date: 30-04-2023    Supervisor: Albin Sandelin

Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy. Recent studies have revealed that the tumor microenvironment (TME) plays a critical role in its progression. Meanwhile, acidosis often occurs in TME as a consequence of elevated metabolic activities and poor perfusion. While low pH has been generally reported to drive aggressive traits in cancer cells, its impacts need to be better understood in the context of other components. To this end, we aim to investigate the role of acidic TME in PDAC progression on the transcriptional level. In particular, we adapted cancer models with different genotypes and growth conditions to low extracellular pH and employed high-throughput sequencing methods to profile gene, promoter, and enhancer expression.

We first established the generality of acid-induced transcriptional change across various cancer types. Gene expression changes shared in three acid-adapted human cancer cell lines were found to be correlated to tumor-specific tissue expression profiles and overall patient survival. (Paper I) We then studied the impact of acid adaption and its interplay with p53 mutation using mouse organoids. By analyzing RNA-seq data from samples collected at various pH levels, we observed upregulation in drug resistance pathways in low pH and the subsequent restoration to normal pH. This occurred only in wild-type p53 organoids, suggesting a genotype-specific pattern. Furthermore, we identified two potential regulators driven by acidic pH in Gemcitabine and Erlotinib resistance. (Paper II)

In addition, we investigated another component of TME, the extracellular matrix (ECM). We utilized CAGE sequencing to study promoter and enhancer usage in acid-adapted Panc02 cells, cultured in spheroids or in matrigel ECM. Strikingly, the two growth conditions resulted in highly diverging expression changes of both elements and transcriptional factor binding motif enrichment patterns, suggesting that acid response is dependent on cell media. (Paper III)