BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells

The CCCTC-binding factor (CTCF), which anchors DNA loops that organize the genome into structural domains, has a central role in gene control by facilitating or constraining interactions between genes and their regulatory elements 1 , 2 . In cancer cells, the disruption of CTCF binding at specific loci by somatic mutation 3 , 4 or DNA hypermethylation 5 results in the loss of loop anchors and consequent activation of oncogenes. By contrast, the germ-cell-specific paralogue of CTCF , BORIS (brother of the regulator of imprinted sites, also known as CTCFL ) 6 , is overexpressed in several cancers 7 – 9 , but its contributions to the malignant phenotype remain unclear. Here we show that aberrant upregulation of BORIS promotes chromatin interactions in ALK -mutated, MYCN -amplified neuroblastoma 10 cells that develop resistance to ALK inhibition. These cells are reprogrammed to a distinct phenotypic state during the acquisition of resistance, a process defined by the initial loss of MYCN expression followed by subsequent overexpression of BORIS and a concomitant switch in cellular dependence from MYCN to BORIS. The resultant BORIS-regulated alterations in chromatin looping lead to the formation of super-enhancers that drive the ectopic expression of a subset of proneural transcription factors that ultimately define the resistance phenotype. These results identify a previously unrecognized role of BORIS—to promote regulatory chromatin interactions that support specific cancer phenotypes.