Multi-omics analyses of MEN1 missense mutations identify disruption of menin-MLL and menin-JunD interactions as critical requirements for molecular pathogenicity

Loss of function mutations of the multiple endocrine neoplasia type 1 (MEN1) gene are causal to the MEN1 syndrome and also commonly found in sporadic pancreatic neuroendocrine tumors and other types of cancer. The MEN1 gene product, menin, is involved in transcriptional regulation, most prominently as an integral component of MLL1 and MLL2 containing COMPASS-like histone methyltransferase complexes. In a mutually exclusive fashion, menin interacts with the transcription factor JunD. Whereas loss of menin function is known to result in endocrine tumorigenesis, the exact pathogenic mechanism remains poorly understood. After in silico screening of 253 disease-related MEN1 missense mutations, we selected a series of mutant forms of menin that were predicted to be stable and to affect menin-MLL1 and/or menin-JunD interactions. By studying this set of mutations using affinity-purification of protein complexes combined with mass spectrometry in HeLa cells, we aimed to identify critical requirements for pathogenic loss of menin function. While disruption of menin-MLL1/2 complex interaction was observed as a result of most MEN1 mutations, complete loss of the menin-JunD interaction was observed infrequently. We identified three MEN1 gene missense mutations: R52G, E255K and E359K that are characterized by predominant MLL1/2-menin interaction loss. This observation was supported by pronounced loss of binding of the R52G, E255K and E359K mutant proteins at menin sites co-occupied by JunD using genome-wide analyses. These findings support the importance of the menin-MLL1/2 interaction in MEN1 gene-associated tumor development.