Research Article

Hyperlipidemia May Synergize with Hypomethylation in Establishing Trained Immunity and Promoting Inflammation in NASH and NAFLD

Table 1

Ingenuity Pathway Analysis (IPA) for top 20 pathways of significantly modulated genes in each dataset of human NASH studies and mouse models of NAFLD. Leukocyte extravasation was shared by both human NASH studies and in the MCD+HFD mouse model; LXR/RXR activation was shared by HFCD model of NAFLD; and fatty acid β-oxidation was shared by the GNMT-KO and HFCD models of NAFLD. IL-8 signaling was shared by the second human NASH study and the MCD+HFD model. Fatty acid β-oxidation I and stearate biosynthesis I were shared by the first human NASH study and GNMT-KO and HFCD models. Nicotine degradation II was shared by the first human NASH study and the MAT1A-KO model.
(a)

HumanMouse
GEO IDGSE17470GSE63067GSE35961GSE63027GSE63027GSE53381
ComparisonNASH vs. healthyNASH vs. healthyMCD+HFDGNMT-KOMAT1A-KOHFCD

Pathways
 Serotonin degradation
 Ethanol degradation II
 Synaptic long-term depression
 Noradrenaline and adrenaline degradation
 Sperm motility
 Phospholipases
 LXR/RXR activation
 Fatty acid β-oxidation I
 Nicotine degradation II
 eNOS signaling
 Leukocyte extravasation signaling
 p70S6K signaling
 Retinol biosynthesis
 Stearate biosynthesis I (animals)
 Histamine degradation
 Aldosterone signaling in epithelial cells
 HIPPO signaling
 cAMP-mediated signaling
 Synaptic long-term potentiation
 Fcγ receptor-mediated phagocytosis in macrophages and monocytes
 IL-8 signaling
 Rac signaling
 NF-κB activation by viruses
 Salvage pathways of pyrimidine ribonucleotides
 Gαq signaling
 Pyridoxal 5-phosphate salvage pathway
 GP6 signaling pathway
 Colorectal cancer metastasis signaling
 ILK signaling
 Integrin signaling
 mTOR signaling
 Phospholipase C signaling
 Cardiac hypertrophy signaling (enhanced)
 ERK5 signaling
 Sphingosine-1-phosphate signaling
 Small cell lung cancer signaling
 Gα12/13 signaling
 Signaling by rho family GTPases
 Superpathway of cholesterol biosynthesis
 PPAR signaling
 Nicotine degradation III
 Melatonin degradation I
 Superpathway of melatonin degradation
 Xenobiotic metabolism CAR signaling pathway
 Xenobiotic metabolism PXR signaling pathway
 Cholesterol biosynthesis I
 Cholesterol biosynthesis II (via 24,25-dihydrolanosterol)
 Cholesterol biosynthesis III (via desmosterol)

(b)

HumanMouse
GEO IDGSE17470GSE63067GSE35961GSE63027GSE63027GSE53381
ComparisonNASH vs. healthyNASH vs. healthyMCD+HFD vs. NCDGNMT-KO vs. WTMAT1A-KO vs. WTHFCD vs. NCD

Pathways
 Superpathway of geranylgeranyl diphosphate biosynthesis I (via mevalonate)
 Estrogen biosynthesis
 Acetone degradation I (to methylglyoxal)
 Mevalonate pathway I
 Tryptophan degradation III (eukaryotic)
 Antioxidant action of vitamin C
 Oxidative phosphorylation
 Glutaryl-CoA degradation
 Valine degradation I
 Isoleucine degradation I
 RhoA signaling
 Mitotic roles of polo-like kinase
 Triacylglycerol biosynthesis
 TCA cycle II (eukaryotic)
 Role of CHK proteins in cell cycle checkpoint control
 Sumoylation pathway
 Apelin adipocyte signaling pathway
 Glutathione-mediated detoxification
 Tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate
 CMP-N-acetylneuraminate biosynthesis I (eukaryotes)
 EIF2 signaling
 tRNA charging
 Folate transformations I
 Endocannabinoid cancer inhibition pathway
 Pyrimidine ribonucleotide interconversion
 Pyrimidine ribonucleotide de novo biosynthesis
 NAD salvage pathway II
 PPARα/RXRα activation
 NRF2-mediated oxidative stress response
 Glutathione redox reactions I
 Pancreatic adenocarcinoma signaling
 Estrogen-mediated S-phase entry
 Type II diabetes mellitus signaling
 PCP pathway
 PDGF signaling
 NF-κB signaling
 Neuroinflammation signaling pathway
 Tec kinase signaling
 B cell receptor signaling
 Osteoarthritis pathway
 Th17 activation pathway
 Role of pattern recognition receptors in recognition of bacteria and viruses
 Apelin endothelial signaling pathway
 Cholecystokinin/gastrin-mediated signaling
 T cell exhaustion signaling pathway
 Endothelin-1 signaling
 B cell activating factor signaling
 RANK signaling in osteoclasts
 Toll-like receptor signaling
 Renin-angiotensin signaling