IDENTIFICATION OF CANCER- AND METASTASIS-RELATED EPIGENETIC DYNAMICS USING PATIENT-DERIVED ORGANOIDS

Tumor initiation and progression imply radical changes of cell identity that can’t be entirely explained by specific genetic mutations. This suggests that cells might be epigenetically reprogrammed to undergo those phenotypic alterations. Regarding this, enhancers are crucial since their activation is tightly cell-type-specific. Accordingly, we have recently identified a group of enhancers selectively activated in colorectal cancer (CRC) patient-derived organoids (PDOs) with respect to the normal counterpart that are also conserved among different CRC subtypes, suggesting the presence of shared epigenetic mechanisms that are activated despite heterogeneous mutational landscapes. Aiming at investigating the role of epigenetic reprogramming in the context of the poorly understood process of metastasization, we generated PDOs from different types of metastases and characterized their histone mark profiling through chromatin immunoprecipitation followed by sequencing (ChIP-seq). In order to provide a global genome-wide annotation of chromatin regions, we evaluated the combinatorial distribution of five histone marks (H3K27ac, H3K4me1, H3K4me3, H3K36me3 and H3K27me3) through ChromHMM, modelling chromatin into 12 biologically distinct states. We then focused on active enhancers to perform a differential analysis between primary and metastatic CRC PDOs. Next, we annotated the enhancers gained in metastasis to their target genes and performed pathway analysis and motif binding analysis. Interestingly, pathways relative to tissue development and intermediate filaments organization were enriched. As trans modulators of these enhancers, we identified transcription factors belonging to the Wnt/β-catenin pathway and AP-1 complex. We also observed epigenomic and transcriptomic inter-metastases heterogeneity, that seemed to be mirrored by the different invasive capability of organoids in an in vitro 3D assay. In parallel, in order to perform a more accurate annotation of enhancers to their target genes and to address the formation of hubs of interacting enhancers, we performed enhancer capture-HiC on CRC PDOs. As proof of concept, we identified a group of highly interconnected enhancers that established hubs of interactions with other enhancers and concomitantly regulated the expression of cancer-relevant genes. Promoter capture-HiC has also been performed to provide future insights into the global 3D chromatin organization in cancer and metastasis.