Author information
1Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Private Bag 23, Hobart, TAS, 7000, Australia. phillip.melton@utas.edu.au.
2School of Global and Population Health, The University of Western Australia, Crawley, WA, Australia. phillip.melton@utas.edu.au.
3School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
4Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK.
5NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.
6MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK.
7Telethon Kids Institute, The University of Western Australia, Perth, Australia.
8School of Human Health and Development, Faculty of Medicine, University of Southampton, Southampton, UK.
9Medical School, The University of Western Australia, Perth, Australia.
10Department of Gastroenterology and Hepatology, Fiona Stanley and Fremantle Hospitals, Murdoch, WA, Australia.
11MCRI, Royal Children's Hospital, Flemington Road, Parkville, VIC, Australia.
12The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, Australia.
13School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
14University of Newcastle, Newcastle, NSW, Australia.
15Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Private Bag 23, Hobart, TAS, 7000, Australia.
16School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia.
Abstract
Background and aims: Epigenetic modifications are associated with hepatic fat accumulation and non-alcoholic fatty liver disease (NAFLD). However, few epigenetic modifications directly implicated in such processes have been identified during adolescence, a critical developmental window where physiological changes could influence future disease trajectory. To investigate the association between DNA methylation and NAFLD in adolescence, we undertook discovery and validation of novel methylation marks, alongside replication of previously reported marks.
Approach and results: We performed a DNA methylation epigenome-wide association study (EWAS) on DNA from whole blood from 707 Raine Study adolescents phenotyped for steatosis score and NAFLD by ultrasound at age 17. Next, we performed pyrosequencing validation of loci within the most 100 strongly associated differentially methylated CpG sites (dmCpGs) for which ≥ 2 probes per gene remained significant across four statistical models with a nominal p value < 0.007. EWAS identified dmCpGs related to three genes (ANK1, MIR10a, PTPRN2) that met our criteria for pyrosequencing. Of the dmCpGs and surrounding loci that were pyrosequenced (ANK1 n = 6, MIR10a n = 7, PTPRN2 n = 3), three dmCpGs in ANK1 and two in MIR10a were significantly associated with NAFLD in adolescence. After adjustment for waist circumference only dmCpGs in ANK1 remained significant. These ANK1 CpGs were also associated with γ-glutamyl transferase and alanine aminotransferase concentrations. Three of twenty-two differentially methylated dmCpGs previously associated with adult NAFLD were associated with NAFLD in adolescence (all adjusted p < 2.3 × 10-3).
Conclusions: We identified novel DNA methylation loci associated with NAFLD and serum liver biochemistry markers during adolescence, implicating putative dmCpG/gene regulatory pathways and providing insights for future mechanistic studies.