成纤维细胞增殖通路相关9个基因可以预测糖尿病足的发生

Nine genes related to fibroblast proliferation pathway can predict occurrence of diabetic foot

目的基于血浆游离DNA(cfDNA)探究成纤维细胞增殖通路相关的5-羟甲基胞嘧啶修饰基因对糖尿病足(Diabetic foot ulcer,DFU)和糖尿病(Diabetic mellitus,DM)患者的区分。方法收集2021年1-12月就诊于北京大学第三附属医院确诊为DFU患者血浆6例和DM患者血浆14例,提取cfDNA,使用5hmC-Seal技术建立文库后,依托Illumina高通量测序平台进行测序,筛选差异羟甲基化修饰基因(DhMGs)。采用GSVA富集分析方法对DhMGs富集分析,使用STRING数据库和Cytoscape3.9.0对GSVA富集中|log_(2)FoldChange|变化最大的成纤维细胞增殖通路中的18个DhMGs进行分析,使用STRING数据库和Cytoscape3.9.0得到9个关键枢纽基因(Hub基因),最后使用Hub基因通过岭回归建模区分DFU组和DM组,并使用RNA-seq数据验证。结果分析得出DFU组与DM组DhMGs共有5748个,通过GSVA富集中|log_(2)FoldChange|变化最大的成纤维细胞增殖通路中的18个DhMGs进行分析,使用STRING数据库和Cytoscape3.9.0得到9个Hub基因,使用岭回归建模得到AUC为1.000,使用RNA-seq数据对9个基因建模的AUC为0.962。结论本研究基于5hmC-Seal技术探究DFU和DM患者血浆cfDNA中5hmC变化,在5hmC的水平发现成纤维细胞增殖通路的重要性,通路中的9个基因能够预测糖尿病足患者。

Objective The differentiation of 5-hydroxymethylcytosine-modified genes related to fibroblast proliferation pathway in patients with Diabetic Foot Ulcer(DFU)and Diabetic Mellitus(DM)were explored based on plasma cell-free DNA(cfDNA).Methods The plasma of 6 patients with DFU and 14 patients with DM who were admitted to the hospital from January to December 2021 were collected,to screen for differentially hydroxymethylated modified genes(DhMGs).The GSVA enrichment analysis method was used to analyze the enrichment of DhMGs,and STRING database and Cytoscape3.9.0 were used to analyze 18 DhMGs in|log_(2)FoldChange|most changed fibroblast proliferation pathway in the GSVA enrichment,which were obtained to use STRING database and Cytoscape3.9.09 key hub genes(Hub genes),and finally the Hub genes were used to distinguish DFU group and DM group by glm-net modeling and validated with using RNA-seq data.ResultsThe analysis showed that there were a total of 5748DhMGs inDFU group and DM group.The 18 DhMGs in|log_(2)FoldChange|fibroblast proliferation pathway with thegreatest change in GSVA enrichment were analyzed,and 9 Hub genes were obtained to use STRING database andCytoscape3.9.0.Glmnetmodeling yielded anAUCof 1.000 and anAUCof 0.962 for 9 genes modeled with usingRNA-seq data.ConclusionBased on 5hmC-Seal technology,this study explored the changes of 5hmC in plasmacfDNA of DFU and DM patients,and it found the importance of fibroblast proliferation pathway at the level of 5hmC.Nine genes in pathway could predict diabetic foot in patients.