Genomic translocations, super-enhancer hijacking and oncogene activiation : from mechanism to therapy

Abstract

Epigenomic profiling has revealed exceptionally large cis-regulatory elements genome-wide, broad H3K4me3 domains (H3K4me3-BDs), that extend from gene promoters, and clusters of enhancers called super-enhancers (SEs). The high transcriptional activity of both is associated with cell-type specific regulation and control of tumour suppressor genes in healthy cells. In some cancers, protooncogenes hijack SEs, leading to dysregulation of transcription and the appearance of H3K4me3-BDs across the genic sequence. SEs of the immunoglobulin heavy chain locus (IGH) are frequently translocated with over 25 proto-oncogenes, a mechanism of SE hijacking, which challenges gene-centric treatment options. We propose that treating multiple translocations of this kind will be possible via directed targeting of the common denominator, the SEs. However, questions remain unanswered, such as how similar their genomic environment is, whether active SEs maintain H3K4me3-BDs, whether targeting SEs is a viable option, and where are the regions to target within these large elements. To address some of these questions, I investigated the location of H3K4me3-BDs and SEs within the human Blymphoblastoid cell line, GM12878, and in mouse embryonic stem cells. I show that they often co-localised within insulated topologically associating domains in both species. Using feature association of genome-wide profiles of histone modifications and chromatin proteins, I developed a method to characterise the poorly understood overlapping SEs and H3K4me3-BDs, SE-BD-hybrids. I also identified several candidates for the identification of the ‘Achilles heel’ of hybrid genes. I targeted two epigenetic modifiers, KMT2D and p300 in addition to developing an IGH SE translocation cell line model expressing a dCas9-KRAB repressor complex. I show that repressing the IGH Eµ SE leads to a marginal effect on proto-oncogene expression. Overall, my work will aid the future of SE targeting by developing novel experimental models, uncovering viable methods, and which proteins to target.