Combining Gene Variants to Improve Risk Prediction for Metabolic (Dysfunction)- Associated Fatty Liver Disease and Its Progression to Cirrhosis in Indian Individuals With Type 2 Diabetes

Type 2 diabetes and metabolic (dysfunction)-associated fatty liver disease (MAFLD) often exist together. The prevalence of MAFLD is about 15-30% in healthy people and around 60-70% in people with type 2 diabetes. Moreover, type 2 diabetes accelerates the progression of liver disease in MAFLD.

MAFLD is a spectrum of liver conditions, ranging from simple fatty liver (low risk for progression), progressing to steatohepatitis (MASH) with no or mild fibrosis, advanced liver fibrosis, cirrhosis, and hepatocellular carcinoma. Although diabetes is the strongest predictor of advanced fibrosis in MAFLD, however, only a small proportion of people with type 2 diabetes and MAFLD (about 5-7%) develop a clinically significant liver disease, but the burden of MAFLD is such that even a small proportion of patients developing cirrhosis will lead to a huge strain on the health care system in India. MAFLD is predicted to be the leading indication for liver transplantation in coming years. At present, MAFLD/MASH is the second most common indication for liver transplantation in the USA as well as in India.

The question is why around 5-7% patients amongst MAFLD population develop fibrosis and cirrhosis. A growing body of evidence suggest that the disease develops because of a complex process in which several factors, including genetic susceptibility and environmental insults, are involved. There are several gene variants that have been incriminated in the development and progression of MAFLD. The most common genes associated with MAFLD are PNPLA3, TM6SF2, GCKR, and MBOAT7. The loss-of-function gene variant HSD17B13 seems to protect from NAFLD. There are a few studies from India about the role of PNPLA3 and TM6SF2 in MAFLD. However, these studies used USG for the diagnosis of MAFLD, which does not provide any information regarding fibrosis of the liver. The data regarding other three genetic variants are scarce from Indian individuals.

1. PNPLA3 rs738409 C/G polymorphism: The nonsynonymous rs738409 C/G variant in PNPLA3 (patatin-like phospholipase domain containing 3), which encodes the amino acid substitution I148M, is regarded as the major genetic component of MAFLD and MASH. The risk effect of rs738409 on developing fatty liver in the context of MAFLD is the strongest ever reported for a common variant modifying the genetic susceptibility of MAFLD (5.3% of the total variance). The rs738409 is not only significantly associated with the accumulation of fat in the liver (the lipid fat content in carriers of the GG homozygous genotype is 73% higher compared with that measured in the carriers of the CC genotype) but also with the histological disease severity and progression of MAFLD (odds ratio-OR 1.88 per G allele; 95% confidence interval-CI 1.03-3.43; GG vs. CC homozygous carriers OR 3.488, 95% CI 1.859-6.545). PNPLA3 is a lipase involved in hepatocellular lipid remodelling and retinol metabolism.
2. TM6SF2: In 2014, two exome and genome wide association studies identified the rs58542926 C > T genetic variant of the transmembrane 6 superfamily member 2 gene (TM6SF2), which encodes the loss-of-function lysine (E) to glutamic acid (K) at position 167 substitution (E167K), as a determinant of hepatic fat content, serum aminotransferases, and lower serum lipoproteins. The same studies demonstrated that silencing of TM6SF2 reduces secretion of VLDL resulting in intrahepatic retention of triglycerides and steatosis in mice and in hepatocytes in vitro. TM6SF2 is involved in hepatic VLDL secretion.
3. GCKR: A variant in GCKR locus (glucokinase regulatory gene) has recently gained attention of researchers due to its biological plausibility in the disease pathogenesis. Specifically, the missense variant rs780094 was associated with a modest risk of having a fatty liver. Interestingly, GCKR mutations have been involved in the maturity-onset diabetes in young individuals, given that diabetes/glucose intolerance/insulin resistance is a well-known risk factor for MAFLD. No Indian data.
4. MBOAT7 rs641738 C/T polymorphism: The MBOAT7 polymorphism rs641738 was identified as a risk factor for MAFLD, especially in people of European decent. This association is mediated by lower hepatic protein expression of MBOAT7 resulting in changes in the hepatic phosphatidylinositol acyl-chain remodeling. The mechanism linking altered PI remodeling to MAFLD development and progression is not clear. The data form India is scarce.
5. HSD17B13 rs72613567:TA: A gene variant that describes a link between hepatic phospholipids and the risk of advanced MAFLD is the splicing variant rs72613567 (T > TA) with an adenine insertion in HSD17B13 that encodes for the hepatic lipid droplet protein hydroxysteroid 17-beta dehydrogenase 13. The HSD17B13 rs72613567 variant leads to the synthesis of a truncated loss-of-function enzyme that protects against advanced MAFLD, MASH and fibrosis. Surprisingly, the gene variant does not influence the development of steatosis, as several studies showed no difference in the degree of steatosis between rs72613567 carriers and noncarriers; however, it decreases the risk of chronic liver damage in MAFLD patients we aimed to assess the role of these five gene variants (PNPLA3, TM6SF2, GCKR, MBOAT7 and HSD17B13) in the development of steatosis and fibrosis (as assessed by transient elastography), and correlation of these gene variants with body composition (body fat percentage, lean mass and bone mineral content- as assessed by dual-energy X-ray absorptiometry), in Indian individuals with type 2 diabetes