Non-genetic Alterations in Colorectal Cancer Liver Metastasis and Patient-derived Models

Abstract

Colorectal cancer (CRC) is the third most diagnosed type of cancer, and the 5-year survival rate drops significantly once the patient develops liver metastases. Notably, over the past decade, multiple patient-derived models of cancer (PDMC) have been developed and are widely accepted as preclinical models. Current chemotherapy does not distinguish the primary and metastatic loci, and there lack a direct comparison between different PDMC (e.g., patient-derived organoids (PDO), patient-derived xenografts (PDX) and PDO-derived xenografts (PDOX)) and the patient tumor (PT). Therefore, understanding the differences between the cells from metastasized CRC and the primary site, as well as the differences between the PDMC and the original patient specimen is of critical importance.In CRC, many conventional studies have focused on associating genetic mutations with clinical phenotypes. However, non-genetic alterations including changes in chromatin accessibility, transcriptome and histone modification markers provide an alternative and even faster way for the tumor cells to adapt to their microenvironment. In this dissertation, we first focused on how the liver microenvironment can affect the epigenetic transformations of the metastasized CRC. Using high-throughput sequencing such as ATAC-seq, RNA-seq and Mint-ChIP, we identified an HGF-PU.1-DPP4 epigenetic reprogramming axis that facilitates the metastatic tumor cells to adapt to the liver microenvironment. The results were validated by extensive numbers of patient samples and the precision epigenetic modification tools CRISPR/dCas9KRAB/HDAC. We identified several FDA approved drugs including Sitagliptin and Norleual, which can be repurposed to treat CRC liver metastases. Furthermore, using the similar set of tools, we revealed that each PDMC undergo distinctive epigenetic reprogramming following two modeling axes. The first axis delineates PDX and PDO from patient, while the second axis distinguishes PDX and PDO. We further identified that the transcription factors KLF14 and EGR2 are collectively more active in the PDOX than in PDO. Moreover, we demonstrated that the varied expression level of their common downstream targets EPHA4 led to distinct drug responses in PDO to 147 FDA approved compounds. We concluded that there are differences in growth and drug sensitivity between PDOX and PDO, which should be taken into consideration when using PDMC to predict clinical outcomes.