MAP3K14 (NIK) synonymous variants drive altered splicing to activate NF-κB in mature B-cell malignancies

Genetic alterations activating NF‑κB have been described in mature B‑cell malignancies. These alterations include loss of the negative regulator TRAF3, allowing NIK (NF‑κB-inducing kinase) to drive non-canonical NF‑κB (ncNF‑κB) signaling. In this study, we characterized two recurrent synonymous variants of MAP3K14, the gene encoding NIK, across mature B‑cell malignancies including chronic lymphocytic leukemia, lymphoplasmacytic lymphoma/Waldenström's macroglobulinemia, multiple myeloma and mantle cell lymphoma. These variants were shown to introduce splice donor sites that result in removal of the critical TRAF3 binding motif. Cell line models prime edited to contain the synonymous variants demonstrated NF‑κB activation and transcriptional reprogramming with enhanced cell proliferation and survival, as well as increased secretion of several cytokines/chemokines including IP10/CXCL10. We also characterized distinctive cell surface proteomic changes with NF‑κB activation, identifying candidate markers (e.g.,CD132/IL‑2Rγ) for assessing NF‑κB activation at a single cell level using flow cytometry. This study expands the spectrum of genetic lesions that result in activation of NF‑κB in mature B‑cell malignancies and highlights our incomplete understanding of NF‑κB drivers in mature B‑cell malignancies.