Pan-cancer 3D genomic analysis revealed extremely long Polycomb loops as the biomarker for sensitivity to Polycomb inhibition

Polycomb targeted loci form long-range chromatin interactions independent of CTCF-cohesion and are demarcated by low DNA methylation. Polycomb targets form extremely long-range loops (long Polycomb loops) that can span up to 60 Mb. These loops predominantly occur in cells of self-renewal status, such as human hematopoietic stem cells (HSC) and mouse embryonic stem cells (ESC). But it was rarely studied in any cancers, in which extensive epigenetic alterations of DNA hypermethylation and loss of Polycomb binding occurs at Polycomb target loci.To identify long Polycomb loops in cancer, we initiated a pan-cancer survey of long Polycomb loops in a collection of 247 tumor samples (33 acute myeloid leukemias, 29 Breast cancer samples, 63 pediatric brain tumors, 70 prostate cancers, and 42 colon cancers). We found most cancers, displayed reduced levels of long Polycomb interactions in comparison with the normal HSC. Solid tumors including all prostate cancers and colon cancers, lack detectable level long Polycomb loops. Additionally, the long Polycomb loop signals are the weakest in cancer cell lines. Pediatric brain tumors and certain AMLs however displayed high long Polycomb loops similar or even stronger than HSC. In pediatric brain tumors, we found the over 20% ependymoma PFA subtypes ( in which EZHIP over expression drives Polycomb protein segregation at the canonical Polycomb target loci) notably displayed strong long Polycomb loop interactions with low differentiation. AML displayed more diverse levels of long Polycomb loop interactions. Most AMLs lost both long Polycomb loops with Polycomb binding loss at the loop anchors. Whereas 10% of AMLs retain long Polycomb loops as strong as in HSCs. These AMLs recurrently carry mutations in CEBPA and STAG2 , which are not associated with the Polycomb complex or DNA methylation machinery. Further, while the normal HSC and developing brains contain strong long Polycomb loop, such signal is undetectable in normal colon, suggesting the strong long Polycomb loop is inherited from the tissue of origin. The deletion or inhibition of Polycomb repressive complex (PRC) 1/2 have been shown to eradicate the long Polycomb loops. We found that long Polycomb loop strong AML is sensitive to PRC2 key enzyme EZH2 inhibition, which inhibits cell cycle and induces cell differentiation. Conversely, CRISPR DepMap PRC1 component dependency can be used to predict long Polycomb loop formation in cell lines, identifying cell lines with rare occurrence of long Polycomb loops. Our analysis suggests that the oncogenesis process antagonizes the long Polycomb loop maintenance in most cancers, yet certain cancers may still preserve strong long Polycomb loops from cell-of-origin. The maintenance of long Polycomb loops sensitizes cells to Polycomb inhibition, indicating that such loops could be an epigenomic biomarker for pharmacological or genetic Polycomb inhibition.