Transcriptome Comparison between Porcine Subcutaneous and Intramuscular Stromal Vascular Cells during Adipogenic Differentiation

Intramuscular fat (IMF) is an important trait influencing meat quality, and preadipocyte differentiation is a key factor affecting IMF deposition. Here we compared the transcriptome profiles of porcine intramuscular and subcutaneous preadipocytes during differentiation to gain insight into specific molecular and cellular events associated with intramuscular stromal vascular cell (MSVC) differentiation. RNA-Seq was used to screen for differentially expressed genes (DEGs) during the in vitro differentiation of MSVC and subcutaneous stromal vascular cell (ASVC) on days 0, 2 and 4. A total of 985 DEGs were identified during ASVC differentiation and 1469 DEGs during MSVC differentiation. Among these DEGs, 409 genes were specifically expressed during ASVC differentiation, 893 genes were specifically expressed during MSVC differentiation, and 576 DEGs were co-expressed during ASVC and MSVC differentiation. The expression profiles of DEGs during ASVC or MSVC differentiation were determined by cluster analysis based on Short Time-series Expression Miner (STEM). Four significant STEM profiles (profiles 1, 4, 5, and 14) were determined during ASVC differentiation, and four significant STEM profiles (profiles 1, 4, 11, and 14) were determined during MSVC differentiation. Gene ontology (GO) analysis indicated that DEGs related to adipocyte differentiation were identified to be significantly enriched in both adipose and muscle profile 14. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs in adipose profile 14 and muscle profiles 11 and 14 (STEM clustered them into one cluster) showed that the PPAR signaling pathway was significantly enriched in these profiles and four signaling pathways were specifically enriched in muscle profiles 11 and 14. Furthermore, analysis of transcription factor binding sites (TFBS) in the gene set revealed two over-represented transcription factors (NR3C4 and NR3C1), which were specifically significantly enriched in the promoter regions of genes within muscle gene expression profiles 11 and 14.

肌内脂肪（Intramuscular fat, IMF）是影响肉品质的重要性状，而前体脂肪细胞分化是调控肌内脂肪沉积的关键因素。本研究比较了猪肌内基质血管细胞（Intramuscular Stromal Vascular Cell, MSVC）与皮下基质血管细胞（Subcutaneous Stromal Vascular Cell, ASVC）在分化过程中的转录组谱，以解析与肌内基质血管细胞分化相关的特异性分子与细胞事件。研究采用RNA测序（RNA-Seq）筛选了MSVC与ASVC在体外分化第0、2、4天的差异表达基因（Differentially Expressed Genes, DEGs）。最终在ASVC分化过程中共鉴定到985个DEGs，MSVC分化过程中共鉴定到1469个DEGs。其中，409个基因仅在ASVC分化过程中特异性表达，893个基因仅在MSVC分化过程中特异性表达，另有576个DEGs在两类细胞分化过程中共同表达。基于短时间序列表达挖掘器（Short Time-series Expression Miner, STEM）的聚类分析，我们明确了ASVC或MSVC分化过程中DEGs的表达谱。ASVC分化过程中共得到4个显著富集的STEM聚类模块（模块1、4、5和14），MSVC分化过程中共得到4个显著富集的STEM聚类模块（模块1、4、11和14）。基因本体（Gene Ontology, GO）富集分析显示，与脂肪细胞分化相关的DEGs在脂肪相关模块14与肌肉相关模块14中均显著富集。此外，对脂肪模块14以及肌肉模块11和14（STEM将二者聚类为同一模块）内DEGs的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路富集分析表明，过氧化物酶体增殖物激活受体信号通路（PPAR signaling pathway）在上述模块中均显著富集，另有4条信号通路仅在肌肉模块11和14中特异性富集。进一步对该基因集开展转录因子结合位点（Transcription Factor Binding Sites, TFBS）分析，发现两个过度富集的转录因子NR3C4与NR3C1，它们在肌肉模块11和14内基因的启动子区域呈现特异性显著富集。