Screening for rare variants in the PNPLA3 gene in obese liver biopsy patients

NAFLD: genetics and its clinical implications

Worldwide non-alcoholic fatty liver disease (NAFLD) is recognized as the most common type of liver disease and its burden increasing at an alarming rate. NAFLD entails steatosis, fibrosis, cirrhosis, and, finally, hepatocellular carcinoma (HCC). The substantial inter-patient variation during disease progression is the hallmark of individuals with NAFLD. The variability of NAFLD development and related complications among individuals is determined by genetic and environmental factors. Genome-wide association studies (GWAS) have discovered reproducible and robust associations between gene variants such as PNPLA3, TM6SF2, HSD17B13, MBOAT7, GCKR and NAFLD. Evidences have provided the new insights into the NAFLD biology and underlined potential pharmaceutical targets. Ideally, the candidate genes associated with the hereditability of NAFLD are mainly involved in assembly of lipid droplets, lipid remodeling, lipoprotein packing and secretion, redox status mitochondria, and de novo lipogenesis. In recent years, the ability to translate genetics into a clinical context has emerged substantially by combining genetic variants primarily associated with NAFLD into polygenic risk scores (PRS). These score in combination with metabolic factors could be utilized to identify the severe liver diseases in patients with the gene regulatory networks (GRNs). Hereby, we even have highlighted the current understanding related to the schedule therapeutic approach of an individual based on microbial colonization and dysbiosis reversal as a therapy for NAFLD. The premise of this review is to concentrate on the potential of genetic factors and their translation into the design of novel therapeutics, as well as their implications for future research into personalized medications using microbiota.

Association between the CYBA and NOX4 genes of NADPH oxidase and its relationship with metabolic syndrome in non-alcoholic fatty liver disease in Brazilian population

BACKGROUND

Oxidative stress has been implicated in the progression of severe forms of non-alcoholic fatty liver disease (NAFLD). NADPH oxidase produces reactive oxygen species. In the present study, we investigated for the first time two single nucleotide polymorphisms (SNPs) in the regulatory region of genes encoding NADPH oxidase 4 (NOX4) and p22phox (CYBA) in NAFLD.

METHODS

A total of 207 biopsy-proven NAFLD patients [simple steatosis (n = 27); nonalcoholic steatohepatitis (NASH) (n = 180)] were evaluated. Genomic DNA was extracted from peripheral blood cells, and polymorphisms in CYBA (unregistered) and NOX4 (rs3017887) were determined by direct sequencing of PCR.

RESULTS

Associations of CYBA-675 T/A with high-density lipoprotein (HDL) (TT vs TA vs AA; P < 0.01) and triglycerides (TGL) (TT vs XA; P < 0.01) were observed only in NASH patients. For polymorphisms in the NOX4 gene, NOX4 (rs3017887) CA + AA genotypes was significant associated with alanine aminotransferase (ALT) (CA + AA vs CC; P = 0.02). However, there was no association of SNPs in the CYBA and NOX4 genes encoding the NADPH oxidase system proteins and the presence of NASH. Regarding the clinical results, it was observed that the most advanced degrees of fibrosis occurred in patients diagnosed with type 2 diabetes mellitus (66.9% vs 37.5%, P < 0.01) and those who were more obese (32.2 vs 29.0 kg/m², P < 0.01). In addition, serum glucose and insulin levels increased significantly in the presence of NASH.

CONCLUSIONS

There were associations between the presence of the allele A in the NOX4 SNP and a higher concentration of ALT in the NAFLD population; between the presence of the AA genotype in the polymorphism of the CYBA-675 T/A CYBA gene and a higher level of TGL and lower HDL in NASH patients. The presence of metabolic syndrome was associated with advanced degrees of fibrosis in NAFLD patients.

Identification of deleterious rare variants in MTTP, PNPLA3, and TM6SF2 in Japanese males and association studies with NAFLD

Background

Non-alcoholic fatty liver disease (NAFLD) is a disorder characterized by excessive fat deposits in hepatocytes without excessive alcohol intake. NAFLD is influenced by genetic factors, and the heritability has been estimated at 0.35 to 0.6 by twin studies. We explored rare variants in known NAFLD-associated genes to investigate whether these rare variants are involved in the susceptibility to NAFLD.

Methods

The target genes for re-sequencing were PNPLA3, TM6SF2, and MTTP. All exons of these three genes were amplified from a discovery panel of 950 Japanese males, and the identified rare variants were further tested for genetic association in 3014 individuals from the Japanese general population and for in vitro functional evaluation.

Results

Target re-sequencing analysis using next-generation sequencing identified 29 rare variants in 65 Japanese males (6.84%), 12 of which were newly identified base substitutions. A splicing mutation in TM6SF2 that resulted in deletion of 31 amino acids was identified in an NAFLD case. Among eight genotyped rare single-nucleotide polymorphisms (SNPs; minor allele frequency < 0.02), rs143392071 (Tyr220Cys, PNPLA3) significantly increased (odds ratio = 3.52, P = 0.008) and rs756998920 (Val42Ile, MTTP) significantly decreased (odds ratio = 0.03, P = 0.019) the NAFLD risk. Functional assays showed that these two SNPs disrupted protein functions and supported the genetic association.

Conclusion

Collectively, 1.79% of individuals in our studied population were estimated carriers of rare variants that are potentially associated with NAFLD.

Electronic supplementary material

The online version of this article (10.1186/s12944-017-0570-y) contains supplementary material, which is available to authorized users.