转录组分析揭示牙周炎和甲状腺功能减退症之间的遗传相互作用。
Transcriptomic Analysis Reveals Genetic Cross-Talk between Periodontitis and Hypothyroidism.
机构信息
Department of Stomatology, Changzhi Medical College, Changzhi, 046000 Shanxi Province, China.
Department of Stomatology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, 046000 Shanxi Province, China.
出版信息
Dis Markers. 2022 Apr 11;2022:5736394. doi: 10.1155/2022/5736394. eCollection 2022.
BACKGROUND
Aim of this bioinformatics study based on transcriptomic analysis was to reveal the cross-talk between periodontitis (PD) and hypothyroidism (HT).
METHODS
The gene expression datasets GSE18152 and GSE176153 of HT and GSE10334, GSE16134, and GSE173078 of PD were downloaded through the Gene Expression Omnibus (GEO) database. Differential Expression Genes (DEG) between cases and controls in each microarray were assessed by using the "limma" (linear models for microarray data) R package (|log2 fold change (FC)| >0 and -value <0.05). To analyze the cross-talk effect between HT and PD, the intersection of DEG of HT and PD was selected. To investigate the biological function of cross-talk genes, the gene ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied. Protein-Protein Interaction (PPI) network was constructed using Cytoscape software. Top 10 cross-talk genes were screened, and the expression values of these 10 genes were extracted. ROC analysis was performed by using the pROC package and GGplot2 package of R language to predict the classification accuracy.
RESULTS
The overlapping DEG between HT and PD were 107 cross-talk genes. The results revealed that developmental process (-value =1.06E-21) was the most significantly enriched biological process, followed by cell differentiation (-value =8.49E-18) and immune system process (-value =6.78E-11). KEGG analysis showed that Complement and coagulation cascades (-value =2.29E-05), Hematopoietic cell lineage (-value =2.66E-05), Phospholipase D signaling pathway (-value =0.034367878) and Chemokine signaling pathway (-value =0.04946333) were significantly enriched. The top 10 genes with most connections were LCE1B, LCE2B, LCE2A, LCE2C, LCE1C, LCE1F, ITGAM, C1QB, TREM2, and CD19. The AUC values of the two datasets of HT were both greater than 65% (GSE18152 = 81.42%, GSE176153 = 68.75%). AUC values of three datasets of PD were all greater than 60% (GSE10334 = 69.23%, GSE16134 = 73.72%, GSE173078 = 81.6%).
CONCLUSIONS
A genetic cross-talk between HT and PD was detected, whereby LCE family genes appeared to play the most important role.
背景
本基于转录组分析的生物信息学研究旨在揭示牙周炎（PD）和甲状腺功能减退症（HT）之间的相互作用。
方法
通过基因表达综合数据库（GEO）下载 HT 的基因表达数据集 GSE18152 和 GSE176153，以及 PD 的 GSE10334、GSE16134 和 GSE173078。使用“limma”（微阵列数据的线性模型）R 包评估每个微阵列中病例与对照之间的差异表达基因（DEG）（|log2 倍变化（FC）|>0 和 -值 <0.05）。为了分析 HT 和 PD 之间的相互作用效应，选择 HT 和 PD 的 DEG 的交集。为了研究相互作用基因的生物学功能，应用基因本体（GO）功能富集分析和京都基因与基因组百科全书（KEGG）途径分析。使用 Cytoscape 软件构建蛋白质-蛋白质相互作用（PPI）网络。筛选前 10 个相互作用基因，并提取这些 10 个基因的表达值。通过 R 语言的 pROC 包和 GGplot2 包进行 ROC 分析，以预测分类准确性。
结果
HT 和 PD 之间重叠的 DEG 为 107 个相互作用基因。结果表明，发育过程（-值=1.06E-21）是最显著富集的生物学过程，其次是细胞分化（-值=8.49E-18）和免疫系统过程（-值=6.78E-11）。KEGG 分析显示，补体和凝血级联（-值=2.29E-05）、造血细胞谱系（-值=2.66E-05）、磷脂酶 D 信号通路（-值=0.034367878）和趋化因子信号通路（-值=0.04946333）明显富集。连接最多的前 10 个基因是 LCE1B、LCE2B、LCE2A、LCE2C、LCE1C、LCE1F、ITGAM、C1QB、TREM2 和 CD19。HT 的两个数据集的 AUC 值均大于 65%（GSE18152=81.42%，GSE176153=68.75%）。PD 的三个数据集的 AUC 值均大于 60%（GSE10334=69.23%，GSE16134=73.72%，GSE173078=81.6%）。
结论
检测到 HT 和 PD 之间存在遗传相互作用，其中 LCE 家族基因似乎起着最重要的作用。
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