Fig. 4: lincNMR depletion downregulates key dNTP metabolism enzymes.

a Triple-label SILAC-MS: scatter plot showing normalized M/L ratios representing deregulated proteins 48 h after lincNMR knockdown in replicates 1 and 2 with 10 nM siPOOLs in HLE cells (M/L = si-lincNMR-A/si-Neg Ctrl). b Triple-label SILAC-MS: scatter plot showing normalized H/L ratios representing deregulated proteins 48 h after lincNMR knockdown in replicates 1 and 2 with 10 nM siPOOLs in HLE cells (H/L = si-lincNMR-B/si-Neg Ctrl). c Western blot validation of SILAC-MS data depicting downregulation of RRM2, TK1, and TYMS proteins in HLE cells 72 h after lincNMR knockdown with 10 nM siPOOLs (n = 3). Vinculin was used as a loading control. d Quantitative comparison of SILAC-MS (i) and western blot (ii) results confirming consistent downregulation of RRM2, TK1 and TYMS (n = 3). log2 fold change was calculated and normalized to negative control siPOOL. e YBX1 silencing inhibits the expression of RRM2, TK1, and TYMS at 72 h post transfection with 10 nM siPOOL in HLE cells documented by western blotting (n = 3). GAPDH was used as a loading control. f Quantification of western blot from (e): protein fold change was calculated by normalizing the RRM2, TK1, and TYMS signal to loading control GAPDH and to negative control siPOOL (n = 3). a, b Data represent log2 fold change normalized to negative control siPOOL from two independent replicates. Highlighted proteins represent key deregulated players in purine and pyrimidine metabolism according to KEGG pathway annotations. Color key: red = upregulated proteins; blue = downregulated proteins. d, f Data represent mean, and error bars represent SEM. Significance was calculated by unpaired, two-tailed t test with *P < 0.05; **P < 0.01; ***P < 0.001.