Nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease in children and adolescents, increasing the risk of its progression toward nonalcoholic steatohepatitis (NASH), cirrhosis, and cancer. There is an urgent need for noninvasive early diagnostic and prognostic tools such as epigenetic marks (epimarks), which would replace liver biopsy in the future. We used plasma samples from 67 children with biopsy-proven NAFLD, and as controls we used samples from 20 children negative for steatosis by ultrasound. All patients were genotyped for patatin-like phospholipase domain containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), membrane bound O-acyltransferase domain containing 7 (MBOAT7), and klotho-β (KLB) gene variants, and data on anthropometric and biochemical parameters were collected. Furthermore, plasma cell-free DNA (cfDNA) methylation was quantified using a commercially available kit, and ImageStream(X) was used for the detection of free circulating histone complexes and variants. We found a significant enrichment of the levels of histone macroH2A1.2 in the plasma of children with NAFLD compared to controls, and a strong correlation between cfDNA methylation levels and NASH. Receiver operating characteristic curve analysis demonstrated that combination of cfDNA methylation, PNPLA3 rs738409 variant, coupled with either high-density lipoprotein cholesterol or alanine aminotransferase levels can strongly predict the progression of pediatric NAFLD to NASH with area under the curve >0.87. Conclusion: Our pilot study combined epimarks and genetic and metabolic markers for a robust risk assessment of NAFLD development and progression in children, offering a promising noninvasive tool for the consistent diagnosis and prognosis of pediatric NAFLD. Further studies are necessary to identify their pathogenic origin and function.

Department of Adaptive Biotechnologies Global Change Research Institute CAS Brno Czech Republic

Department of Internal Diseases 1 Medical University of Varna Varna Bulgaria

Department of Life Health and Environmental Sciences MESVA School of Emergency and Urgency Medicine University of L'Aquila L'Aquila Italy

Department of Translational Stem Cell Biology Research Institute of the Medical University of Varna Varna Bulgaria

Hepatology Gastroenterology and Nutrition Unit Bambino Gesù Children's Hospital IRCCS Rome Italy

International Clinical Research Center St Anne's University Hospital Brno Czech Republic

Laboratory of Bioinformatics Fondazione IRCCS Casa Sollievo della Sofferenza San Giovanni Rotondo Italy

Liverpool Center for Cardiovascular Science Liverpool Johns Moore University Liverpool UK

Unit of Molecular Genetics of Complex Phenotypes Bambino Gesù Children's Hospital IRCCS Rome Italy

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