Endocrine Abstracts

Thyroid hormones play a key role in cellular growth, development, and metabolism, and are known regulators of gene expression through genomic and non-genomic processes including DNA methylation. Using eight cohorts from the ThyroidOmics-Consortium and a standardized meta-analysis quality control pipeline, we conducted an epigenome-wide association study between blood-based leucocyte DNA methylation sites and thyroid hormones (TSH, free T3 and free T4) in up to 7,073 participants of European and African ancestry. Significant associations were replicated in independent samples. The validated findings were correlated with gene expression levels and genetic variants. Causal influence of thyroid hormones on the DNA methylation levels was assessed by Mendelian randomization. Epigenome-wide significant associations (P-value < 1.1E-7) of 3 CpGs for free T4, 5 for free T3, and 2 for TSH were discovered and replicated (combined P-values = 1.5E-9 to 4.3E-28). The associations included CpG-sites annotated to KLF9 (cg00049440) and DOT1L (cg04173586) that overlap with all three traits with consistent effect directions. Associations were also found for CpG-sites in FKBP5 for free T4, and at CSNK1D/lINCO1970 and LRRC8D for free T3. Differences in circulating TSH levels have a causal effect on DNA methylation of KLF9. DNA methylation of cg00049440 in KLF9 was inversely correlated with KLF9 gene expression in blood. The CpG-site at CSNK1D/lINC01970 overlapped with THRA binding peaks in liver cells. The total additive heritability of the methylation levels of the six significant CpG-sites is between 25% and 57%. Significant methylation QTLs were identified for CpG-sites at KLF9, FKBP5, LRRC8D and CSNK1D/lINC01970. We report novel associations between TSH, thyroid hormones and blood-based DNA methylation. This study advances our understanding of thyroid hormone action and serves as a proof-of-concept that similar integrations of EWAS and other omics techniques can provide a valuable tool for unravelling thyroid hormone signaling next to classical in-vitro and animal studies.