Integrative multi-omics analyses identify key genes and elucidate bidirectional regulatory mechanisms in thyroid dysfunction.

objectiveHyperthyroidism and hypothyroidism are globally prevalent endocrine disorders, with their pathogenesis involving multifactorial mechanisms including genetics, immunity, and metabolism. Although genome-wide association studies (GWAS) have identified risk genes such as PDE8B, critical gaps remain in the annotation of causal variants in non-coding regions, characterization of tissue-specific regulatory networks, and understanding of ethnic heterogeneity. This study aimed to systematically identify genes associated with hyperthyroidism and hypothyroidism and unravel their underlying molecular mechanisms through multi-omics integration.

methodsWe included data from the ThyroidOmics Consortium, comprising 1,840 hyperthyroidism cases (49,983 controls) and 3,340 hypothyroidism cases (49,983 controls). Core candidate genes were prioritized using a combination of SMR-HEIDI analysis, cross-tissue transcriptome-wide association study (TWAS), mBAT-combo rare variant analysis, and polygenic priority score (PoPS). GTEx colocalization (coloc) analysis was used to validate tissue-specific colocalization between these candidate genes and disease signals. Phenome-wide association study (PheWAS), KEGG pathway enrichment, and protein-protein interaction (PPI) network analyses were performed to explore gene functions, with potential targeted drugs predicted using the Drug Signatures Database (DSigDB).

resultsCross-validation by four methods identified FAM227B, PDE8B, and PDE10A as key genes for hyperthyroidism, and PDE8B as the critical gene for hypothyroidism. GTEx coloc analysis (with PP4 > 0.8 as the threshold) confirmed significant colocalization: FAM227B with hyperthyroidism signals in the adrenal gland, lung, and minor salivary gland; PDE8B with both hyperthyroidism and hypothyroidism signals in thyroid tissue; and PDE10A with hyperthyroidism signals in thyroid tissue. As a core member of the phosphodiesterase family, PDE8B exhibited bidirectional regulatory characteristics in thyroid hormone synthesis via the cAMP signaling pathway and nucleotide metabolism network: its inhibition promoted hormone synthesis in hypothyroidism, while its interaction with PDE10A suppressed overactive cAMP signaling in hyperthyroidism. PheWAS linked FAM227B to cardiovascular diseases and PDE10A to neurological pathways. KEGG enrichment analysis highlighted the "morphine addiction" pathway (p = 6.12 × 10 ⁻ ⁵), suggesting potential neuroendocrine crosstalk. Notably, potential drugs targeting FAM227B, PDE8B, and PDE10A were identified.

conclusionThrough multi-omics integration, this study identifies PDE8B as a central gene associated with thyroid dysfunction, characterized by tissue-specific colocalization, and elucidates its critical roles in signaling pathways, comorbidity associations, and drug targeting. These findings provide insights into the bidirectional regulatory mechanisms of hyperthyroidism and hypothyroidism and a theoretical basis for developing phosphodiesterase family-based precision therapies. It should be noted that all samples in this study are of European ancestry, and the generalizability of the results in other ethnic groups remains to be verified.