空间与加权基因共表达分析揭示跨种属的缺血性心力衰竭机制

Spatial and weighted gene co-expression analysis revealed the mechanism of cross-species ischemic heart failure

[目的]从空间与基因共表达网络的角度揭示跨种属的缺血性心力衰竭机制。[方法]从美国国立生物技术信息中心基因表达数据库(NCBI-GEO)中检索获得GSE210374和GSE57338高通量测序数据,利用R语言软件程序包分析筛选在心肌梗死大鼠不同心肌区域中差异表达基因(DEG)以及缺血性心力衰竭患者与健康对照者的心肌样本间的DEG,分析共同基因的分区域表达情况。利用加权基因共表达网络分析(WGCNA)筛选心肌梗死相关的基因并进行富集分析,构建蛋白质-蛋白质相互作用网络(PPI)筛选核心基因(HG)。[结果]在心肌梗死大鼠和正常对照组中共筛选出4835个差异基因,在缺血性心力衰竭患者和正常对照样本共筛选出51个差异基因,揭示心肌梗死后左心室心肌梗死区(I区)、边缘区(BZ区)及远端区(R区)的代表性基因集。空间表达分析发现两个种属样本:在每个心肌分区均有20个共表达基因,其中16个在3个分区均有表达,在I区、BZ区和R区特异表达的基因数分别为2、0和2个。富集分析显示:各分区的共表达基因功能各异,I、BZ区与胶原纤维组装、应激诱导的心肌细胞肥大、下调c-Jun氨基末端激酶(JNK信号)与细胞增殖等功能以及补体信号通路相关;而I、R区则富集于Wnt和胶原结合;作为非缺血的远端R区,共表达基因显著富集于细胞外基质的抗压性、细胞溶解以及抑制T细胞增殖等功能。此外值得注意的是:3个分区的共表达基因的产物大部分位于细胞外空间和细胞外基质当中,提示可能存在活化的细胞分泌与互作调控。进一步PPI分析提示无孢蛋白(ASPN)、骨诱导因子(OGN)和ⅩⅣ型胶原蛋白α链(COL14A1)基因可能是前述机制的核心基因。[结论]大鼠和人类缺血性心力衰竭的共性机制涉及补体与凝血级联信号、Wnt等多种信号通路;可能与细胞外基质、外泌体介导的细胞凋亡密切相关;ASPN、OGN和COL14A1可能是其中的核心基因。本工作有望为缺血性心力衰竭相关转化研究中的干预靶点与路径选择提供空间与通路参考。

Aim To reveal the mechanism of cross-species ischemic heart failure from the perspective of spatial and gene co-expression networks.Methods GSE210374 and GSE57338 high-throughput sequencing datas were retrieved from the national center for biotechnology information gene expression database(NCBI-GEO),and R language software packages was used to analyze and screen differentially expressed genes(DEG)in different myocardial regions of myocardial infarction rats,as well as DEG of myocardial samples from patients with ischemic heart failure and healthy controls,and the regional expression of common genes was analyzed.Weighted gene co-expression network analysis(WGCNA)was used to screen the genes related to myocardial infarction and to carry out enrichment analysis,protein-protein interaction network(PPI)was constructed to screen core genes(HG).Results A total of 4835 differentially expressed genes were screened out in myocardial infarction rats and normal controls,and 51 differentially expressed genes were screened out in ischemic heart failure patients and normal control samples,which revealed representative gene sets in the left ventricular myocardial infarction area(I area),border area(BZ area),and remote area(R area)after myocardial infarction.Spatial expression analysis revealed that there were 20 co-expressed genes in each myocardial region,16 of which were expressed in all three regions,the number of genes specifically expressed in I,BZ and R regions were 2,0 and 2,respectively.Enrichment analysis showed that the functions of co-expressed genes were different in different region.The I and BZ regions were related to collagen fiber assembly,stress-induced cardiomyocyte hypertrophy,down-regulation of c-Jun amino terminal kinase(JNK signal)and cell proliferation,and complement signaling pathways;The I and R regions were enriched in the binding of Wnt and collagen;As a non-ischemic distal R region,the co-expressed genes were significantly enriched in the extracellular matrix for functions such as compressive resistance,cytolysis and inhibition of T cell proliferation.Furthermore,it was worth noting that the products of co-expressed genes in the three regions were mostly located in the extracellular space and extracellular matrix,suggesting that there may be active cellular secretion and interaction regulation.Further PPI analysis suggested that asporin(ASPN),osteoglycin(OGN)and collagentypeⅩⅣalpha chain(COL14A1)gene might be the core genes of the mechanism mentioned above.Conclusions The common mechanism of ischemic heart failure in rats and human involves multiple signaling pathways such as complement and coagulation cascade signaling and Wnt;which may be closely related to cell apoptosis mediated by extracellular matrix and exosomes;ASPN,OGN,and COL14A1 may be the core genes.This work is expected to provide spatial and pathway reference for the selection of intervention targets and pathway in the transformation research related to ischemic heart failure.