ATAC-seq deconvolution with CiberATAC identifies a prognostic regulon of HMG20B in metastatic colorectal adenocarcinoma

We used a sequential metastasis model of colorectal cancer cell lines and tumours to understand epigenomic regulators of metastasis. We performed scRNA-seq, scATAC-seq, and bulk ATAC-seq on these samples and discovered the deregulation of HMG20B and its regulon. Overall design: We used colorectal cancer SW480 and LS174T cell lines. We injected the cell lines to NOD/SCID Gamma male mice. We re-injected the xenografted tumours to new mice to obtain sequential lineages of colorectal cancer liver metastasis. Therefore all samples have a parental, LvM1, and LvM2 forms. We performed scRNA-seq on the pool of parental and LvM lineages from each sample (total of 2 samples, each containing parental and LvM lineages within the library). We performed scATAC-seq on SW480 parental and LvM2 as different libraries. We also performed bulk ATAC-seq for parental, LvM1, and LvM2 samples of SW480 as well as LS174T.