Collateral lethality of NAD kinase in 1p36 deleted tumors drives vulnerability to NAD kinase 2 depletion

Abstract

The deletion of tumor suppressor genes often occurs in a tumor-specific manner and is accompanied by the unintended loss of adjacent genes. Nicotinamide adenine dinucleotide kinase (NADK), located at a tumor suppressive locus on chromosome 1p36, plays a pivotal role in the biosynthesis of NADP and NADPH and has a closely related paralog, NADK2, in human cells. Although synthetic lethality between NAD kinases was reported in yeast, the relationship between NADK and NADK2 in human cells remains unclear. Here, we investigated alterations of the NADK gene expression across various tumor types and assessed whether there is a synthetic lethal relationship between these NAD kinases in human cells. Analysis of The Cancer Genome Atlas dataset revealed NADK gene deletion in multiple tumor types. Depletion of both NADK and NADK2 using siRNA decreased cellular NADP(H) levels and inhibited cell proliferation, resulting in the induction of apoptosis. Notably, NADK2 knockdown alone markedly impaired cell proliferation and NADP(H) production in NADK homozygous-deleted tumor cells, and also reduced proliferation in NADK heterozygous-deleted tumor cells, whereas in NADK-intact tumor cells only de novo NADP synthesis, but not its intracellular levels or proliferation, was affected. These findings suggest that loss of the NADK gene in tumor cells confers vulnerability to NADK2 depletion.