Identification of potential obese-specific biomarkers and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy.
Yongli YangXiaoyi WangMingli LiShuyan WangHuiyu WangQiang ChenShaoxiong LuPublished in: PeerJ (2024)
Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in the pig industry but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. The present study aims to identify obese-specific biomarkers and key pathways correlated with ASFD in pigs. The ASF-related mRNA expression dataset GSE136754 was retrieved from the Gene Expression Omnibus (GEO) database and systematically analyzed using a comprehensive bioinformatics method. A total of 565 differentially expressed genes (DEGs) were identified between three obese and three lean pigs, and these DEGs were mainly involved in the p53 signaling pathway, MAPK signaling pathway and fatty acid metabolism. A protein-protein interaction (PPI) network, consisting of 540 nodes and 1,065 edges, was constructed, and the top ten genes with the highest degree scores- ABL1 , HDAC1 , CDC42 , HDAC2 , MRPS5 , MRPS10 , MDM2 , JUP , RPL7L1 and UQCRFS1 -were identified as hub genes in the whole PPI network. Especially HDAC1 , MDM2 , MRPS10 and RPL7L1 were identified as potential robust obese-specific biomarkers due to their significant differences in single gene expression levels and high ROC area; this was further verified by quantitative real-time PCR (qRT-PCR) on abdominal subcutaneous fat samples from obese-type (Saba) and lean-type (Large White) pigs. Additionally, a mRNA-miRNA-lncRNA ceRNA network consisting of four potential biomarkers, 15 miRNAs and 51 lncRNAs was established, and two targeted lncRNAs with more connections, XIST and NEAT1 , were identified as potentially important regulatory factors. The findings of this study may provide novel insights into the molecular mechanism involved in ASFD.
Keyphrases
- adipose tissue
- human health
- gene expression
- bioinformatics analysis
- signaling pathway
- protein protein
- weight loss
- metabolic syndrome
- fatty acid
- risk assessment
- type diabetes
- obese patients
- real time pcr
- genome wide identification
- genome wide
- dna methylation
- pi k akt
- network analysis
- small molecule
- epithelial mesenchymal transition
- genome wide analysis
- bariatric surgery
- climate change
- histone deacetylase
- cancer therapy
- tyrosine kinase
- mass spectrometry
- early stage
- bone mineral density
- drug delivery
- cell cycle
- drug induced