Failure to repair damaged NAD(P)H blocks de novo serine synthesis in human cells#

Authors#

Adhish Walvekar, Marc Omer Warmoes, Dean Cheung, Tim Sikora, Gemma Gomez Giro, Sebastian Perrone, Lisa Dengler, Francois Unger, Bruno Filipe Rodrigues Dos Santos, Floriane Gavotto, Xiangyi Dong, Julia Becker-Kettern, Yong-Jun Kwon, Christian Jäger, Jens Christian Schwamborn, Nicole J Van Bergen, John Christodoulou, Carole Linster

Abstract#

Metabolism is error prone. The central metabolic cofactors NADH and NADPH for instance can undergo enzymatically catalyzed or spontaneous hydration, converting them into redox-inactive products designated NADHX and NADPHX. The metabolite repair enzymes NAXD and NAXE convert these damaged compounds back to the functional NAD(P)H cofactors. Pathogenic loss-of-function variants in NAXE and NAXD lead to development of the neurometabolic disorders named as progressive, early-onset encephalopathy with brain edema and/or leukoencephalopathy (PEBEL1 and PEBEL2, respectively). To gain insights into the molecular disease mechanisms, we investigated the metabolic impact of NAXD deficiency in human cell models. HAP1 NAXD knockout (NAXDko) cells showed growth impairment specifically in a basal medium containing galactose instead of glucose. Surprisingly, the galactose-grown NAXDko cells displayed only subtle signs of mitochondrial impairment, whereas metabolomic analyses revealed a strong inhibition of the cytosolic, de novo serine synthesis pathway in those cells as well as in NAXD patient-derived fibroblasts. We identified inhibition of 3-phosphoglycerate dehydrogenase as the root cause for this metabolic perturbation. The NAD precursor nicotinamide riboside (NR) and inosine exerted beneficial effects on HAP1 cell viability under galactose stress, with more pronounced effects in NAXDko cells. Metabolomic profiling in supplemented cells indicated that NR and inosine act via different mechanisms that at least partially involve the serine synthesis pathway. Taken together, our study identified a metabolic vulnerability in NAXD deficient cells that can be targeted by small molecules such as NR or inosine, opening perspectives in the search for mechanism-based therapeutic interventions in PEBEL disorders.