Integrative Network Analysis Revealed Genetic Impact of Pyruvate Kinase L/R on Hepatocyte Proliferation and Graft Survival after Liver Transplantation

Figure 2

Comprehensive analysis on targeted metabolomic results in cells with PKLR variations. (a) PCA revealed clear separation in targeted metabolomic data from hepatocytes with overexpressed PKLR (OV), dots in green [2] represented the samples with overexpressed PKLR, and dots in blue [1] represented the corresponded NC samples. (b) Validation of OPLS-DA model by class permutation analysis for (a). (c) PCA revealed clear separation in targeted metabolomic data from hepatocytes with downregulated PKLR (SI), dots in green [2] represented the samples with downregulated PKLR, and dots in blue [1] represented the corresponded NC samples. (d) Validation of OPLS-DA model by class permutation analysis for (c). (e) Heatmap for comparison between samples from OV group and corresponded NC in all enrolled metabolites. (f) Heatmap for comparison between samples from SI group and corresponded NC in all enrolled metabolites. (g) Heatmap for comparison between samples from OV and SI groups in all enrolled metabolites. (h) Correlations on log-transformed FCs of each metabolite from OV and SI groups. (i) Overlapped positive metabolites compared in (f)/(g)/(h). (j) Correlation heatmap for all enrolled metabolites from targeted metabolomics; the table is color coded by correlation according to the color legend; legend on intensity and direction of correlations is indicated on the right side of the heatmap. (k) Correlation heatmap for positive metabolites from targeted metabolomics that are associated with PKLR variations; the table is color coded by correlation according to the color legend; legend on intensity and direction of correlations is indicated on the right side of the heatmap. (l) Details on variations of positive metabolites in different comparisons categorized by PKLR expression (OV vs. NC/SI vs. NC/OV vs. SI); # represented insignificant FC in comparison. (m) Rank of pathways based on positive metabolites from targeted metabolomics by enrichment ratios. (n) Pathway analysis based on positive metabolites from targeted metabolomics that are associated with PKLR expression. (o) Details of pathway on TCA cycle and positive metabolites that are associated with PKLR expression. (p) Details of pathway on pyruvate metabolism and positive metabolites that are associated with PKLR expression. (q) Venn plot for those overlapped across the positive metabolites from pathways A (TCA cycle), B (pyruvate metabolism), and C (glycolysis). (r) PEP-to-pyruvate ratio presented in different comparisons (OV vs. NC/SI vs. NC). (s) ATP-to-ADP ratio presented in different comparisons (OV vs. NC/SI vs. NC). (t) NADPH-to-NADP+ ratio presented in different comparisons (OV vs. NC/SI vs. NC). Abbreviations: FC: fold change; NC: negative control; OV: overexpression; PCA: principal component analysis; PEP: phosphoenolpyruvate; SI: silence; TCA: tricarboxylic acid cycle.

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