We have identified the genomic sequences and the locations bound by the mutated transcription factor STAT6 in several cHL cell lines, and several gene networks specifically altered by mutants STAT6. Interestingly, we have uncovered that STAT6 mutants binds and deregulates several important genes known to be involved in cHL pathogenesis. For example they upregulate the expression of genes for some chemokines and receptors involved in pro-survival signals, and some proteins with immuno-suppressive functions, while they downregulate some tumor suppressors known to be involved in haematological malignencies. We have found that the binding of STAT6 mutants drives local epigenetic chromatin changes, and activates genomic regions that are normally less accessible for transcription, which in turn results in deregulation of some relevant genes for cHL. We have also identified some newly formed long-range chromatin interactions in proximity of STAT6 mutants binding, confirming that the mutants are able to bind different regions not bound by the STAT6 wild type protein, which directly drive chromatin rearrangements that impact gene transcription of the nearby genes, including some known to be important for cHL cells survival.
Moreover, we have mapped the regions outside the genes (non-coding genome) which have regulatory function in gene transcription (promoters, enhancers, superenhancers) in 10 cHL cell lines, and evaluated their activation state. This allowed us to build a cathalog of important functional non-coding regions that could be interested by mutations affecting their function, and so that could have important role in the pathogenesis. We are now selecting mutations found in these regulatory non-coding regions of samples from cHL patients that we have sequenced, to identify some recurrent ones to investigate.
