Integrated transcriptomic and proteomic analysis of gene expression changes in brown adipose tissue during cold acclimatization in rats

Objective This study aims to conduct a combined analysis of differentially expressed genes in the transcriptome and proteome of brown adipose tissue in cold-tolerant rats, exploring potential biomarkers and therapeutic targets for cold acclimatization. Methods Male SD rats underwent intermittent cold exposure. Blood and brown/white adipose tissue samples were collected after 21 days. Differentially expressed genes and proteins in brown adipose tissue were identified through high-throughput mRNA transcriptome sequencing and tandem mass tag (TMT) mass spectrometry analysis, combined with detection of glucometabolic markers in blood samples. Results Transcriptome analysis identified 2031 differentially expressed genes, comprising 344 upregulated and 1687 downregulated genes. Proteomic mass spectrometry analysis identified 376 differentially expressed proteins, comprising 217 upregulated and 159 downregulated proteins. Integrated analysis revealed 13 synergistically upregulated genes and 11 synergistically downregulated genes. GO and KEGG enrichment analyses indicated that upregulated genes predominantly clustered in fatty acid metabolism processes and PPAR signaling pathways, while downregulated genes were enriched in adipocyte lipolysis regulation pathways. Protein–protein interaction (PPI) network analysis indicated that Lpl, Plin1, Ckb, Fabp3, and Ldha may play pivotal roles in brown adipose tissue metabolism. Conclusion This study reveals expression alterations in multiple genes within brown adipose tissue during rat cold adaptation, suggesting these genes may collectively regulate cold adaptation responses in physiological processes involving fat metabolism, conversion, and energy balance.