Identifying Key Genes and Functionally Enriched Pathways of Diverse Adipose Tissue Types in Cattle

Abstract

Background: Fat is a tissue that not just stores energy and plays a protective role; it is also a vital endocrine organ that generates and integrates signals to influence metabolism. Meanwhile, the excessive accumulation of lipids in adipose tissue can lead to metabolic disturbance and diseases. To date, the complicated molecular mechanisms of bovine adipose tissue are still unknown. This study aimed to identify key genes and functionally enriched pathways in various adipose tissue types.Results: The RNAseq data of 264 samples were downloaded from Gene Expression Omnibus (GEO) and analyzed by weighted gene co-expression network analysis (WGCNA). We identified 19 modules that significantly associated with at least one adipose tissue type. The brown module from GSE39618 was most closely associated with intramuscular fat tissue, which contained 550 genes. These genes were significantly enriched in pathways that related to inflammation and disease, such as TNF signaling pathway, IL-17 signaling pathway, and NF-kappa B signaling pathway. The pink module (GSE39618) that contained 58 genes was most closely associated with omental fat tissue. The turquoise (GSE39618), blue (GSE116775), and yellow (GSE65125) module were most closely associated with subcutaneous fat tissue. Genes in these modules were significantly enriched in pathways related to fat metabolism, such as the PPAR signaling pathway, fatty acid metabolism and PI3K-Akt signaling pathway. At last, key genes for intramuscular fat (PTGS2 and IL6), omental fat (ARHGEF5 and WT1), and subcutaneous fat (KIT, QR6Q1, PKD2L1, etc.) were obtained and verified. In addition, it was found that IL10 and VCAM1 might be potential genes to distinguish adipose and muscle.Conclusion: The study applied WGCNA to generate a landscape of adipose tissue and provide a basis for identifying potential pathways and hub genes of different adipose tissue types.

Weighted Gene Co-expression Network Analysis Revealed That CircMARK3 Is a Potential CircRNA Affects Fat Deposition in Buffalo

“…Among these, circRNA 21:6969877|69753491 has been shown to be involved in lipid metabolism in a previous study, therefore it likely affects fat deposition. Gene significance (GS>0.8) ( 37 , 38 ) and module membership (MM>0.8) ( 37 – 39 ) values showed a high correlation between circRNA 21:6969877|69753491 and two traits (month and weight) of buffalo Figure 1F .…”

Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18

“…In this study, we found a strong positive correlation ( r > 0.9, p < 3.40 × 10 −14 ) between ARID4A and genes such as AHI1 , AKAP9 , ANKRD12 , CCDC18 , ENSSSCG00000037142 , IFT74 , KIAA2026 , NEXN , PPIG , ROCK1 , SMC4 , TWISTNB , BAZ1A , EIF5B , NSRP1 , and BBX . Among these genes, AHI1 , AKAP9 , ANKRD12 , CCDC18 , IFT74 , NEXN , etc., have been shown to play an important role in adipose deposition or obesity [ 48 , 49 , 50 , 51 , 52 , 53 ]. Moreover, AHI1 , AKAP9 , ANKRD12 , CCDC18 , IFT74 , KIAA2026 , NEXN , PPIG , ROCK1 , SMC4 , TWISTNB , EIF5B , and NSRP1 were also identified as potentially related to adipose deposition in this study.…”

“…Among them, ANKRD12 , ARID4A , IFT74 , KIAA2026 , and ROCK1 are located in multiple fat-related QTLs, and ANKRD12 , CCDC18 , NEXN , PPIG , and ROCK1 , are present in the intramuscular fat content QTL. Reports have already shown that ANKRD12, NEXN, IFT74, and ROCK1 play an important role in adipose deposition or obesity [ 50 , 52 , 53 , 56 ]. While CCDC18 is a new marker gene for fatty liver in chicken [ 51 ], its role in fat deposition has been rarely reported.…”

Identification of key genes in bovine muscle development by co-expression analysis

“…The gene co-expression network was constructed by using WGCNA software package in R ( Pan et al, 2022 ). First, a similarity matrix was constructed by calculating Pearson correlation coefficients.…”