cMYC protein interactions and chromatin association in NUT carcinoma

Abstract The oncogene c MYC (HGNC:7553) is a critical genomic target of the BRD4-NUT (B4N) protein that defines many of the NUTM1-rearrangement cancer subtypes in NUT carcinoma (NC). Previously, we reported that B4N interacts with the EP300 lysine acetyltransferase (KAT3B) and creates hyperacetylated “megadomains” that activate downstream genes such as cMYC . Here we ask how misregulated cMYC in turn interacts with protein partners and target genes in patient-derived NC797 cells, and whether these interactions change in response to B4N inactivation. We used CRISPR-Cas9 mediated knock-in of a BioTAP affinity tag to analyze cMYC protein expressed from its normal chromosomal context. This allowed us to implement a crosslinking purification method termed BioTAP-XL to preserve cMYC integrity and chromatin association for genomic and mass spectrometry-based proteomic analyses. We found that in the NC797 cell line, cMYC interacts primarily with the NuA4 KAT5 lysine acetyltransferase complex, with interactions that are maintained despite a decrease in cMYC levels after JQ1 treatment. We propose that a cascade of aberrant acetyltransferase activities in NC797 cells, first via EP300 recruitment by B4N to mis-regulate cMYC , and then by KAT5 interaction with the resulting overexpressed cMYC protein, drive NC cell proliferation and blockade to differentiation. Graphical Abstract Simple Summary A longstanding goal in biology is to understand how protein interactions influence and reflect cellular disease states. MYC is a critical regulator of cellular proliferation that is mis-regulated in many cancers, including those with NUTM1-rearrangements featured in this issue. NUT carcinoma cells are dependent on MYC expression, which blocks differentiation. Using a crosslinking approach to identify MYC protein interactions in a NUTM1-rearranged patient cell line, we found that MYC interacts primarily with subunits of the NuA4 lysine acetyltransferase (KAT5), one of two KAT complexes previously discovered as MYC interactors in non-NUTM1 cell lines.