Context: Skeletal muscle is an important target tissue for thyroid hormone (TH). It is currently unknown which genes are regulated by physiological TH levels.

Objective: We examined the effects of L-thyroxine on human skeletal muscle transcriptome.

Design: Microarray analysis of transcript levels was performed using skeletal muscle biopsies from patients under euthyroid and hypothyroid conditions.

Setting: University hospital laboratory.

Patients: We studied skeletal muscle obtained from 10 thyroidectomized patients with differentiated thyroid carcinoma on and after 4 weeks off L-thyroxine replacement.

Mean outcome measures: Gene expression changes were measured using microarrays. Results were analyzed using dedicated statistical methods.

Results: We detected 607 differentially expressed genes on L-thyroxine treatment, of which 60% were positively and 40% negatively regulated. Representative genes were validated by qPCR. Genes involved in energy and fuel metabolism were overrepresented among the upregulated genes, of which a large number were newly associated with thyroid state. L-thyroxine therapy induced a large downregulation of the primary transcripts of the non-coding microRNA pair miR-206/miR-133b.

Conclusion: We demonstrated that physiological levels of TH regulate a myriad of genes in human skeletal muscle. The identification of novel putatively TH-responsive genes may provide the molecular basis of clinical effects in subjects with different TH status. The observation that TH regulates microRNAs reveals a new layer of complexity by which TH influences cellular processes.