Fig. 1
From: Failure to repair damaged NAD(P)H blocks de novo serine synthesis in human cells

Metabolic profiling of a HAP1 cell model of NAXD deficiency in standard (Iscove’s modified Dulbecco’s medium, IMDM) medium. A Schematic presentation of the NAD(P)HX repair system. Hydration damage (enzymatic or nonenzymatic) of NAD(P)H generates S- or R-NAD(P)HX forms that can interconvert and further react to form cyclic forms designated collectively as cNAD(P)HX. The repair enzymes (NAXD and NAXE) are shown in blue. The NAXE epimerase accelerates interconversion between the S- and R-NAD(P)HX forms, whereas the NAXD dehydratase stereospecifically acts on S-NAD(P)HX in an ATP-dependent manner. B HAP1 NAXDko cells accumulate damaged forms of NADH. Control and NAXDko cells were grown in IMDM for 72 h or 96 h (Supplementary Fig. S1A), and NAD(H)(X) metabolites were measured by LC–MS. All values were normalized to an internal standard and cell counts from replicate plates, and are means ± SDs of three replicate wells. Statistical significance was calculated using an equal variance, unpaired Student’s t-test. **p < 0.01; ***p < 0.001; ns, not significant. C, D Metabolite extracts from HAP1 control and NAXDko cells grown for 72 h and 96 h in IMDM were analyzed using untargeted GC–MS (C) and LC–MS (D) methods (72 h data is shown here, whereas 96 h data is shown in Supplementary Fig. S1B, C). For both the GC–MS and LC–MS data, metabolites with significant changes between the control and NAXDko cells at both time points are presented. For the LC–MS data plotted in Fig.1D and Supplementary Fig. S1C, the presence of metabolites in significantly enriched metabolite sets was used as an additional selection filter. GC–MS data were first normalized using the internal standard [U-13C]-ribitol. LC–MS data were normalized using the summed MS1 intensities of all metabolites within each sample. For both GC–MS and LC–MS data, all values presented are relative to controls and are means ± SDs of six biological replicates. Pathway analysis for the differential metabolites detected by LC–MS is presented in Supplementary Fig. S2. The detailed list of metabolites is compiled in Additional file 1. NAXD, NAD(P)HX dehydratase; NAXE, NAD(P)HX epimerase; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; Acetyl-CoA, acetyl coenzyme A; ADP, adenosine diphosphate