Oral Presentation ESA-SRB-APEG-NZSE 2022

 Epigenome-wide association study of autoimmune thyroid disease highlights novel loci (#93)

Nicole Lafontaine 1 2 , Christopher Shore 3 , Purdey Campbell 1 , Benjamin H Mullin 1 4 , Suzanne J Brown 1 , Vijay Panicker 1 2 , Frank Dudbridge 5 , Thomas Brix 6 , Laszlo Hegedüs 6 , Scott G Wilson 1 4 , Jordana T Bell 3 , John P Walsh 1 2
  1. Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
  2. Medical School, University of Western Australia, Crawley, Western Australia, Australia
  3. Department of Twin Research & Genetic Epidemiology, King’s College London, London, UK
  4. School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia, Australia
  5. Department of Health Sciences, University of Leicester, Leicester, UK
  6. Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark

Autoimmune thyroid disease (AITD) demonstrates familial clustering, with both Graves’ disease (GD) and Hashimoto’s disease (HD) often present within the same family. The aetiology of AITD is incompletely understood, but genetic factors may account for up to 75% of phenotypic variance1 and epigenetics (including DNA methylation (DNAm)) probably contributes to the remaining variance. We aimed to perform an epigenome-wide association study (EWAS) comparing DNAm in GD versus HD, to identify differentially methylated positions (DMP) associated with AITD.

We measured whole blood DNAm using the Illumina EPIC array in 32 Australian participants with GD treated with antithyroid medications only, within 1.5 years from diagnosis and 30 with HD on levothyroxine replacement, within 8 years of diagnosis. We performed an EWAS, using linear models to test for associations between quantile normalised beta values of DNAm in GD and HD. Results were then replicated in 32 participants with GD and 32 HD from Denmark using the same methodology.

We identified epigenome-wide significant differences (p <9E-8) in 5 novel DMPs between GD and HD in the discovery study: cg00049440 in KLF9 was associated with reduced DNAm and cg06315208 in MDC1, cg03633435 near MTMR3/HORMAD2-AS1, cg27064684 near LINC01581 and cg13843840 in ZMIZ1 were associated with increased DNAm in GD compared with HD. In the replication study, data from all 5 DMPs provided additional evidence for the relevance for these CpGs and 2 DMPs were replicated (p <0.05).

Reduced DNAm in cg00049440 in KLF9 has been shown to be associated with free T3 by our group in a previous EWAS2. We provide further evidence of a close relationship between thyroid hormone and DNAm. These data highlight additional DMPs of potential clinical significance. Our other findings provide a basis for further larger well-designed EWAS of AITD and for functional studies to investigate the relationship between DNAm and AITD.

  1. Brix, T.H. and L. Hegedus, Twin studies as a model for exploring the aetiology of autoimmune thyroid disease. Clin Endocrinol (Oxf), 2012. 76(4): p. 457-64.
  2. Lafontaine, N., et al., Epigenome-Wide Association Study of Thyroid Function Traits Identifies Novel Associations of fT3 With KLF9 and DOT1L. The Journal of Clinical Endocrinology & Metabolism, 2021. 106(5): p. e2191-e2202.