Table 1.
The principal effects of siRNA-PNPLA3 silencing on the global metabolome of Huh-7 hepatoma cells
| Main Pathway | Subpathway | Metabolites | Fold Change | Nominal P Value | Empirical P Value (FDR) |
|---|---|---|---|---|---|
| Amino acid metabolism | Alanine and aspartate metabolism | Asparagine | 0.4 | 0.0008 | 0.01 |
| Alanine | 0.5 | 0.0001 | 0.02 | ||
| α-Amino Acids and Derivatives | γ-Glutamyl-glutamine | 0.4 | 0.0006 | 0.01 | |
| γ-Glutamyl-leucine | 0.6 | 0.004 | 0.03 | ||
| γ-Glutamyl-isoleucine | 0.6 | 0.02 | NS | ||
| γ-Glutamyl-threonine | 0.6 | 0.04 | NS | ||
| Putrescine | 0.5 | 0.04 | NS | ||
| 5-oxoproline | 0.7 | 0.04 | NS | ||
| Cysteine, methionine, SAM, taurine metabolism | Methionine | 0.5 | 0.007 | 0.04 | |
| Cysteine sulfinic acid | 2.5 | 0.007 | 0.04 | ||
| N-acetylmethionine | 0.6 | 0.009 | 0.04 | ||
| Serine | 0.7 | 0.05 | NS | ||
| Dipeptides | Glycyl-tryptophan | 0.1 | 0.0007 | 0.01 | |
| Glycyl-phenylalanine | 0.3 | 0.0007 | 0.01 | ||
| Alanyl-threonine | 0.3 | 0.002 | 0.02 | ||
| Glycyl-tyrosine | 0.3 | 0.003 | 0.03 | ||
| Aspartyl-phenylalanine | 0.5 | 0.005 | 0.03 | ||
| Glycyl-isoleucine | 0.3 | 0.007 | 0.04 | ||
| Glycyl-valine | 0.3 | 0.01 | 0.05 | ||
| Glycyl-leucine | 0.4 | 0.02 | NS | ||
| Alanyl-valine | 0.3 | 0.04 | NS | ||
| Glutamate metabolism | Glutamine | 0.3 | 0.00008 | 0.006 | |
| Glutamate | 0.5 | 0.0002 | 0.007 | ||
| N-acetylglutamate | 1.2 | 0.02 | NS | ||
| Histidine metabolism | Histidine | 0.5 | 0.0003 | 0.007 | |
| Lysine metabolism | Lysine | 0.4 | 0.002 | 0.02 | |
| 2-Aminoadipate | 2.0 | 0.002 | 0.02 | ||
| Other amino acids | Proline | 0.7 | 0.0004 | 0.008 | |
| Leucine | 0.5 | 0.003 | 0.03 | ||
| Isoleucine | 0.6 | 0.009 | 0.04 | ||
| Valine | 0.6 | 0.01 | 0.05 | ||
| Phenylalanine metabolism | Tyrosine | 0.6 | 0.005 | 0.03 | |
| Phenylalanine | 0.6 | 0.005 | 0.03 | ||
| Tryptophan metabolism | Kynurenine | 0.6 | 0.0009 | 0.01 | |
| Tryptophan | 0.5 | 0.004 | 0.03 | ||
| Urea cycle and Arginine metabolism | Arginine | 0.4 | 0.0004 | 0.007 | |
| Assymetricdimethylarginine (ADMA) | 0.6 | 0.03 | NS | ||
| Carbohydrate metabolism | Glycolysis, gluconeogenesis, pyruvate metabolism | Isobar: fructose 1,6-diphosphate, glucose 1,6-diphosphate | 0.4 | 0.005 | 0.03 |
| Sedoheptulose-7-phosphate | 1.8 | 0.007 | 0.04 | ||
| Lactate | 0.7 | 0.01 | 0.05 | ||
| Inositol metabolism | Myo-inositol | 2.1 | 0.003 | 0.02 | |
| Nucleotide, sugars, pentose metabolism | Hypoxanthine | 0.9 | 0.0001 | 0.007 | |
| Uridine | 0.6 | 0.0003 | 0.007 | ||
| Cytidine | 0.5 | 0.006 | 0.04 | ||
| Guanine | 0.6 | 0.02 | NS | ||
| Thymidine 5¢-monophosphate | 1.5 | 0.03 | NS | ||
| Ribose 5-phosphate | 0.5 | 0.03 | NS | ||
| Flavin adenine dinucleotide (FAD) | 1.2 | 0.05 | NS | ||
| Vitamins | Pantothenate | 0.8 | 0.006 | 0.04 | |
| Lipid metabolism | Bile acid metabolism | Taurolithocholate | 0.5 | 0.003 | 0.03 |
| Cholesterol | 0.7 | 0.006 | 0.03 | ||
| Choline metabolism | Choline | 0.7 | 0.002 | 0.02 | |
| Choline phosphate | 0.7 | 0.04 | NS | ||
| Free fatty acids | Margarate (17:0) | 0.8 | 0.00006 | 0.006 | |
| Stearate (18:0) | 0.8 | 0.0001 | 0.007 | ||
| Palmitate (16:0) | 0.8 | 0.0003 | 0.007 | ||
| Azelate (nonanedioate) | 0.6 | 0.0007 | 0.01 | ||
| Docosahexaenoate (DHA; 22:6n3) | 0.8 | 0.001 | 0.01 | ||
| Docosatrienoate (22:3n3) | 1.3 | 0.004 | 0.03 | ||
| Laurate (12:0) | 0.7 | 0.01 | 0.05 | ||
| Eicosapentaenoate (EPA; 20:5n3) | 0.8 | 0.01 | 0.05 | ||
| Glycerol derivatives | Glycerophosphorylcholine (GPC) | 0.5 | 0.006 | 0.03 | |
| Glycerol 3-phosphate (G3P) | 0.8 | 0.010 | 0.05 | ||
| Lysolipids | 1-Stearoyl-glycero-phosphoinositol | 0.6 | 0.00003 | 0.006 | |
| 1-Arachidonoyl-glycero-phosphoethanolamine | 2.3 | 0.0002 | 0.007 | ||
| 1-Oleoyl-glycero-phosphoinositol | 0.7 | 0.001 | 0.01 | ||
| 1-Palmitoyl-glycero-phosphoinositol | 0.6 | 0.003 | 0.03 | ||
| 2-Palmitoyl-glycero-phosphoethanolamine | 3.4 | 0.02 | NS | ||
| 2-Arachidonoyl-glycero-phosphoinositol | 2.0 | 0.02 | NS | ||
| 1-Arachidonoyl-glycero-phosphoinositol | 1.5 | 0.02 | NS | ||
| 2-Linoleoyl-glycero-phosphocholine | 4.2 | 0.03 | NS | ||
| 1-Linoleoyl-glycero-phosphocholine | 3.8 | 0.04 | NS | ||
| 2-Oleoyl-glycero-phosphoethanolamine | 1.6 | 0.04 | NS | ||
| Sphingolipids | Sphinganine | 3.0 | 0.02 | NS |
Using LC/MS and GC/MS analysis, 234 distinct metabolites in the sample matched a named structure in the metabolomic reference library but one was filtered out because of lack of informative variation. Fold change refers to the ratio of the metabolite level between siRNA against PNPLA3-treated cells vs. control cells. After log transformation of the variables with equal variances, unpaired 2-sample t-test was used for comparing silencing vs. control group (nominal P value); similar results were obtained by a nonparametric test. FDR, false discovery rate; NS, not significant; SAM, S-adenosyl-methionine.