Advances in pediatric non-alcoholic fatty liver disease: From genetics to lipidomics

Table 1 Main genes and changes in methylation found in human epigenomics studies in non-alcoholic fatty liver disease

Gene	Changes	Methods	Ref.
FGFR2	Hypomethylation	Bisulfite pyrosequencing and liver biopsy	Zhang et al[112]
MAT1A	Hypomethylation	Bisulfite pyrosequencing and liver biopsy	Zhang et al[112]
CASP1	Hypomethylation	Bisulfite pyrosequencing and liver biopsy	Zhang et al[108]
MTND6	Hypomethylation	Methylation-specific PCR and liver biopsy	Pirola et al[109]
PARVB	Hypomethylation	Targeted-bisulfite sequencing and liver biopsy	Kitamoto et al[111]
PNPLA3	Hypomethylation	Targeted-bisulfite sequencing and liver biopsy	Kitamoto et al[111]
PPARα	Hypomethylation	Bisulfite pyrosequencing and liver biopsy	Zeybel et al[112]
TGFβ1	Hypomethylation	Bisulfite pyrosequencing and liver biopsy	Zeybel et al[112]
Collagen 1A1	Hypomethylation	Bisulfite pyrosequencing and liver biopsy	Zeybel et al[112]
PDGFα	Hypomethylation	Bisulfite pyrosequencing and liver biopsy	Zeybel et al[112]
PPARGC1A	Hypomethylation	Methylation-specific PCR and liver biopsy	Sookoian et al[113]
cg08309687 (LINC00649)	Hypomethylation	Illumina BeadChip for array analyses	Ma et al[114]
NPC1L1	Methylation	Illumina human methylation 450 Beadchip and liver biopsy	Mwinyi et al[116]
STARD	Methylation	Illumina human methylation 450 Beadchip and liver biopsy	Mwinyi et al[116]
GRHL	Methylation	Illumina human methylation 450 Beadchip and liver biopsy	Mwinyi et al[116]

PCR: Polymerase chain reaction.

Table 2 Main findings of human transcriptomics studies and microRNAs in non-alcoholic fatty liver disease

Ref.	Study design	Population (n)	Main findings
Yamada et al[118]	Cross-sectional study	403 male subjects (median age 68.2 ± 10.3 yr); 48 NAFLD subjects (median age 66.2 ± 9.1 yr); 221 female patients (median age 65.5 ± 9.6 yr); 44 women with NAFLD (median age 65.0 ± 8.93 yr). Hepatic steatosis was assessed by ultrasound	Increased serum levels of miR-21, miR-34a, miR-122, and miR-451 were found in NAFLD patients
Cheung et al[119]	Cross-sectional study	50 patients with NASH (median age 52.5 yr) and 25 normal controls (median age 40.3 yr). NAFLD was suspected if abnormal liver enzymes or radiological evidence of a fatty liver and negative study for other common causes of liver disease and absence of clinically significant alcohol consumption	miR-34a and miR-146b were overexpressed in the liver of NASH patients, while miR-122 was underexpressed; miR-451 was not significantly different among the two groups
Pirola et al[120]	Case-control study	48 control patients (median age 47.8 ± 6.81 yr); 16 patients with simple steatosis (median age 51.5 ± 6.81 yr); 16 patients with NASH (median age 49.1 ± 8.6 yr). NAFLD was proven by biopsy	Increased levels of miR-122, miR-19a, miR-192, miR-19b, miR-125b, and miR-375 in serum either in SS or NASH patients were found. Reduced miR-122 levels in the liver of NASH patients were detected
Prats-Puig et al[122]	Cross-sectional study	10 lean children (median age 9.9 ± 1 yr), 5 obese children (median age 8.8 ± 1.8 yr)	Increased miR-486-5p, miR-486-3p, miR-142-3p, miR-130b, miR-423-5p, miR-532-5p, miR140-5p, miR-16-1, miR-222, miR-363, and miR-122; decreased miR-221, miR-28–3p, miR-125b, and miR-328 in obese children
Can et al[123]	Case-control study	86 non obese children (median age 14.44 ± 1.62 yr); 45 obese children (median age 14.71 ± 1.76 yr)	Reduced miR-335, miR-143, miR-758 and increased miR-27, miR-378, and miR-370 in the serum of obese children were detected
Cui et al[124]	Cross-sectional study	535 obese patients (median age 61.0 ± 10.4 yr); 106 OW patients (median age 59.6 ± 11.0 yr); 101 patients with T2D (median age 57.5 ± 12.2 yr); 82 with NGT (median age 49.3 ± 7.73 yr); 146 normal controls (median age 60.4 ± 11.1 yr)	miR-486, miR-146b and miR-15b were increased in the serum of obese children and T2D patients
Iacomino et al[125]	Cross-sectional study	189 children (median age 12.0 ± 1.6 yr) and 94 OW/Ob children (median age 12.3 ± 1.8 yr)	Increased miR-551a and miR-501-5p and reduced miR-10b-5p, miR-191-3p, miR-215-5p, and miR-874-3p levels in the serum of OW/Ob children were found

NASH: Non-alcoholic steatohepatitis; miR: MicroRNA; NAFLD: Non-alcoholic fatty liver disease; SS: Simple steatosis; T2D: Type 2 diabetes; NGT: Normal glucose tolerance controls; OW/Ob: overweight/obese.

Table 3 Main results of human proteomics studies in non-alcoholic fatty liver disease

Ref.	Study design	Population (n)	Main findings
Cusi et al[129]	Case-control study	300 subjects with NAFLD (median age 52 ± 1 yr) and 124 without NAFLD (median age 51 ± 1 yr). NAFLD was proven by MRS, biopsy, or US	Increased plasma CK-18 in steatosis, inflammation, and fibrosis
Sookoian et al[130]	Cross- sectional study	101 subjects with simple steatosis (median age 52.3 yr) and 60 NASH patients (median age 54.6 yr). NAFLD was proven by biopsy	sICAM-1 is able to differentiate between patients with simple steatosis and NASH
Rodriguez-Suarez et al[131]	Cross- sectional study	18 controls, 6 obese patients with NAFLD, 6 obese patients with early stage of NASH. Liver disease diagnosis was by biopsy	CPS1 could stratify different phenotypes associated with liver disease severity
Małecki et al[134]	Cross- sectional study	30 children (mean age 10.62 yr), 16 children with NAFLD (mean age 11.06 yr). NAFLD was proven by US	Afamin, retinol-binding protein-4, complement components, and hemopexin were upregulated; serum protease inhibitors, clusterin, immunoglobulin chains, vitamin D binding protein were down-regulated
Bălănescu et al[135]	Cross- sectional study	68 overweight and obese children (mean age 10 yr) and 10 healthy controls. NAFLD was proven by US or elevated alanine transaminase levels	HSP-90 isoforms could be used as NAFLD biomarkers in obese and overweight patients

NASH: Non-alcoholic steatohepatitis; miR: MicroRNA; NAFLD: Non-alcoholic fatty liver disease; MRS: Magnetic resonance spectroscopy; US: Ultrasound; CK-18: Cytokeratin-18; sICAM-1: Soluble intercellular adhesion molecule-1; CPS1: Carbamoyl-phosphate synthase 1; HSP-90: Heat shock protein-90.