Bi-allelic Mutations in NADSYN1 Cause Multiple Organ Defects and Expand the Genotypic Spectrum of Congenital NAD Deficiency Disorders

Abstract

Birth defects occur in up to 3% of all live births and are the leading cause of infant death. Here we present five individuals from four unrelated families, individuals who share similar phenotypes with disease-causal bi-allelic variants in NADSYN1, encoding NAD synthetase 1, the final enzyme of the nicotinamide adenine dinucleotide (NAD) de novo synthesis pathway. Defects range from the isolated absence of both kidneys to multiple malformations of the vertebrae, heart, limbs, and kidney, and no affected individual survived for more than three months postnatally. NAD is an essential coenzyme for numerous cellular processes. Bi-allelic loss-of-function mutations in genes required for the de novo synthesis of NAD were previously identified in individuals with multiple congenital abnormalities affecting the heart, kidney, vertebrae, and limbs. Functional assessments of NADSYN1 missense variants, through a combination of yeast complementation and enzymatic assays, show impaired enzymatic activity and severely reduced NAD levels. Thus, NADSYN1 represents an additional gene required for NAD synthesis during embryogenesis, and NADSYN1 has bi-allelic missense variants that cause NAD deficiency-dependent malformations. Our findings expand the genotypic spectrum of congenital NAD deficiency disorders and further implicate mutation of additional genes involved in de novo NAD synthesis as potential causes of complex birth defects.

New cases that expand the genotypic and phenotypic spectrum of Congenital NAD Deficiency Disorder

“…pDONR201 HAAO was generated as described (Szot et al, 2020). Variants c.128G>A p.(Arg43Lys), c.141C>A p.(His47Gln), c.43del p.(Arg15Glyfs*99), c.301G>T p.(Gly101Trp), and c.323G>A p.(Arg108Gln) were introduced into pDONR201 HAAO cDNA by site‐directed mutagenesis with primers listed in Table .…”

“…Congenital NAD Deficiency Disorder is characterized by birth defects in humans most commonly involving the heart, kidney, vertebrae, and limbs, and stemming from an insufficient synthesis of NAD de novo during embryogenesis. To date, causes are limited to biallelic loss‐of‐function (LOF) variants in HAAO or KYNU (Shi et al, 2017), and LOF or reduced function variants in NADSYN1 (Szot et al, 2020). All three genes encode nonredundant enzymes of the de novo NAD biosynthesis pathway whose inactivation manifests downstream NAD deficiency in affected individuals.…”

“…All three genes encode nonredundant enzymes of the de novo NAD biosynthesis pathway whose inactivation manifests downstream NAD deficiency in affected individuals. Although there is significant phenotypic variability, individuals with biallelic NADSYN1 variants predicting LOF exhibit the most severe defects incompatible with life (Szot et al, 2020), likely owing to an inability to synthesize NAD from nicotinic acid via the Preiss‐Handler pathway, unlike those with HAAO or KYNU variants. In contrast, some patients with biallelic HAAO or KYNU LOF variants are surviving (Shi et al, 2017).…”

Targeting energy pathways in kidney disease: the roles of sirtuins, AMPK, and PGC1α

“…It is interesting that the de novo NAD þ biosynthetic pathway only accounts for roughly 10% of total NAD þ production, 130 yet in AKI, that pathway is specifically downregulated to a degree that becomes clinically relevant. Likewise, mutations in this otherwise minor pathway have been linked to renal developmental anomalies, [131][132][133] while mutations in nicotinamide mononucleotide adenylyltransferase 1 of the salvage pathway are not associated with renal anomalies despite that pathway's more significant contribution to NAD þ stores and other clinical findings in those patients consistent with NAD þ coactivator-1a (PGC1a) regulation of nicotinamide adenine dinucleotide (NAD) biosynthesis. NAD þ is metabolized through 3 pathways.…”

Dietary modification, penetrance, and the origins of congenital malformation

“…Cuny et al (2) start with the observation they made a few years ago (13) that multiple cases of a syndrome characterized by a combination of vertebral, cardiac, renal, and limb defects (VCRL1 and VCRL2), now also known as congenital nicotinamide adenine dinucleotide (NAD) deficiency disorder (OMIM 617660 and 617661), can be attributed to biallelic loss of function of the genes HAAO and KYNU, which encode essential enzymes involved in the kynurenine pathway of NAD synthesis. More recently, NADSYN1 has been added to the list (14). They reasoned that if low levels of fetal NAD are responsible, then dietary restriction of the NAD precursors tryptophan and vitamin B3 ought also to promote these birth defects.…”