Thermogenic Gene Expression in Human Neck Adipose Tissue in Relation to Circulating and Local Thyroid Hormone Levels

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This repository includes supplemental data from our study "Thermogenic gene expression in human neck adipose tissue in relation to circulating and local thyroid hormone levels".

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We collected cervical adipose tissue from 16 patients undergoing thyroid surgery between 11/2020 and 10/2022. Deep neck and subcutaneous (SC) adipose tissue were collected from 15 patients, while only SC adipose tissue was collected from one. Neck adipose tissue samples were frozen at –80°C for targeted LC-MS/MS analysis of tissue thyroid hormones (T3, T4) and bulk RNA-sequencing to assess gene expression. Correlations between thyroid hormone levels and gene expression were analyzed. Liquid Chromatography/Mass Spectrometry (LC-MS/MS) Adipose tissue T3 and T4 levels were quantified using an AB/SCIEX 6500 QTRAP system with internal and external standards. Missing values were imputed using the lowest detectable concentration per hormone. Bulk RNA-Sequencing RNA integrity was checked before processing with rRNA depletion and library preparation. Samples underwent paired-end sequencing (2x150 PE) using an Illumina platform. Data were processed using kallisto for transcript quantification, tximport for gene counts, and Limma for statistical modeling. Data Processing & Statistical Analysis RNA-seq data were filtered for expression levels, normalized using TMM, and transformed via Voom. Linear modeling assessed associations between gene expression and thyroid hormone levels, adjusting for clinical covariates. Differential gene expression between deep and SC adipose tissue was analyzed using DESeq2, with significant genes defined by absolute log2 fold change >1 and adjusted p-value ≤0.05. Gene set enrichment analysis (GSEA) identified pathways with FDR <0.05. Code is available at https://github.com/camara-h/Salej_2025.

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