Transcriptional and Functional Analyses of Intramuscular, Subcutaneous, and Visceral Adipose Tissue in Finished Beef Cattle

Abstract Intramuscular adipose tissue (IMAT; marbling) deposition is a highly desired trait in beef cattle. Unlike excessive subcutaneous (SCAT) and visceral (VIAT) adipose tissue, which have relatively low value, increased marbling is associated with meat sensory traits and is a primary factor influencing beef quality grading in the U.S. However, this trait is difficult to achieve. Our objective was to assess depot-specific characteristics and gene profile of IMAT, SCAT, and VIAT in beef cattle. IMAT and SCAT samples from the longissimus muscle (9-11th ribs), and VIAT from the greater omentum were collected from four beef animals at harvest. Adipose tissue (AT) samples were flash frozen in liquid nitrogen, followed by RNA extraction (Trizol reagent) and RNA sequencing analysis on an Illumina Novaseq 6000 platform to generate 150 bp paired-end reads. DESeq2 R package was used for differential gene expression analysis (DEG) and DEG (P ≤ 0.05, log2FC ≥ 1) were evaluated for KEGG enrichment pathways. Remainder tissue samples were assessed for viscoelasticity (rheometer), collagen fibrillogenesis (kinetics), and adipocyte size (K2 Cellometer). Transcriptome analysis revealed over 4,000 DEG between IMAT and SCAT, over 3,000 DEG between VIAT and IMAT, and 1,018 DEG between VIAT and SCAT, thus indicating substantial transcriptional diversity among AT depots (Figure 1). Top upregulated genes in SCAT vs. IMAT were associated with increased lipid accumulation and regulation such as LIPE, LEP, ADIPOQ, PPARG, and extracellular matrix (ECM) remodeling, including collagens, MMP14, and TIMP4. Accordingly, enrichment analysis revealed an activation of PPARG signaling pathways and fatty acid metabolism in SCAT vs. IMAT, which are key for lipogenesis and adipogenesis (Figure 2). IMAT showed activation of pathways for thermogenesis and oxidative phosphorylation compared with both SCAT and VIAT, indicating that IMAT utilization may be more directed towards muscle function and development (Figure 2 and 3). Top VIAT DEG were primarily associated with immune cell adhesion, and immune response (CDHR1, TENM2, and TNFRSF9), suggesting a pro-inflammatory profile of visceral adiposity. Notably, enrichment analysis showed an activation of the immune function in VIAT compared with IMAT and SCAT (Figures 3 and 4). In agreement with transcriptome analysis, adipocyte size was increased in SCAT vs. IMAT and VIAT, implying higher lipid accumulation (Figure 5). SCAT was also stiffer and had increased collagen fibrillogenesis compared with IMAT, suggesting a key role for ECM in mechanisms of AT adipogenesis and lipogenesis (Figure 5). In summary, these results indicate that AT anatomical location impacts AT transcriptome, which may translate into functional differences in adipogenesis and ECM remodeling. Understanding transcriptional and functional differences among IMAT, SCAT and VIAT can help on the identification of target genes to modulate AT deposition in distinct areas of the body, therefore, improving quality of beef carcasses and industry profitability.