Background: Crohn's disease (CD) is a chronic idiopathic inflammatory bowel disease affecting the entire gastrointestinal tract from the mouth to the anus. These patients often experience a period of symptomatic relapse and remission. A 20–30% symptomatic recurrence rate is reported in the first year after surgery, with a 10% increase each subsequent year. Thus, surgery is done only to relieve symptoms and not for the complete cure of the disease. The determinants and the genetic factors of this disease recurrence are also not well-defined. Therefore, enhanced diagnostic efficiency and prognostic outcome are critical for confronting CD recurrence. Methods: We analysed ileal mucosa samples collected from neo-terminal ileum six months after surgery (M6=121 samples) from Crohn's disease dataset (GSE186582). The primary aim of this study is to identify the potential genes and critical pathways in post-operative recurrence of Crohn’s disease. We combined the differential gene expression analysis with Recursive feature elimination (RFE), a machine learning approach to get five critical genes for the postoperative recurrence of Crohn's disease. The features (genes) selected by different methods were validated using five binary classifiers for recurrence and remission samples: Logistic Regression (LR), Decision tree classifier (DT), Support Vector Machine (SVM), Random Forest classifier (RF), and K-nearest neighbor (KNN) with 10-fold cross-validation. We also performed weighted gene co-expression network analysis (WGCNA) to select specific modules and feature genes associated with Crohn's disease postoperative recurrence, smoking, and biological sex. Combined with other biological interpretations, including Gene Ontology (GO) analysis, pathway enrichment, and protein-protein interaction (PPI) network analysis, our current study sheds light on the indepth research of CD diagnosis and prognosis in postoperative recurrence. Results: PLOD2, ZNF165, BOK, CX3CR1, and ARMCX4, are the important genes identified from the machine learning approach. These genes are reported to be involved in the viral protein interaction with cytokine and cytokine receptors, lysine degradation, and apoptosis. They are also linked with various cellular and molecular functions such as Peptidyl-lysine hydroxylation, Central nervous system maturation, G protein-coupled chemoattractant receptor activity, BCL-2 homology (BH) domain binding, Gliogenesis and negative regulation of mitochondrial depolarization. WGCNA identified a gene co-expression module that was primarily involved in mitochondrial translational elongation, mitochondrial translational termination, mitochondrial translation, mitochondrial respiratory chain complex, mRNA splicing via spliceosome pathways, etc.; Both the analysis result emphasizes that the mitochondrial depolarization pathway is linked with CD recurrence leading to oxidative stress in promoting inflammation in CD patients. Conclusion: These key genes serve as the novel diagnostic biomarker for the postoperative recurrence of Crohn’s disease. Thus, among other treatment options present until now, these biomarkers would provide success in both diagnosis and prognosis, aiming for a long-lasting remission to prevent further complications in CD.

中文翻译：

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通过机器学习和WGCNA网络分析识别克罗恩病术后复发的潜在基因和关键通路

背景：克罗恩病（CD）是一种慢性特发性炎症性肠病，影响从口腔到肛门的整个胃肠道。这些患者经常经历一段症状复发和缓解期。据报道，术后第一年症状复发率为 20-30%，随后每年增加 10%。因此，手术只是为了缓解症状，而不是为了彻底治愈疾病。这种疾病复发的决定因素和遗传因素也尚未明确。因此，提高诊断效率和预后结果对于对抗 CD 复发至关重要。方法：我们分析了克罗恩病数据集 (GSE186582) 术后六个月从新末端回肠收集的回肠粘膜样本（M6 = 121 个样本）。本研究的主要目的是确定克罗恩病术后复发的潜在基因和关键途径。我们将差异基因表达分析与递归特征消除（RFE）（一种机器学习方法）相结合，以获得克罗恩病术后复发的五个关键基因。使用五个二元分类器对复发和缓解样本验证不同方法选择的特征（基因）：逻辑回归（LR）、决策树分类器（DT）、支持向量机（SVM）、随机森林分类器（RF）和K -具有10倍交叉验证的最近邻（KNN）。我们还进行了加权基因共表达网络分析（WGCNA），以选择与克罗恩病术后复发、吸烟和生物性别相关的特定模块和特征基因。结合其他生物学解释，包括基因本体（GO）分析、通路富集和蛋白质-蛋白质相互作用（PPI）网络分析，我们当前的研究为CD术后复发诊断和预后的深入研究提供了线索。结果：PLOD2、ZNF165、BOK、CX3CR1 和 ARMCX4 是通过机器学习方法鉴定的重要基因。据报道，这些基因参与病毒蛋白与细胞因子和细胞因子受体的相互作用、赖氨酸降解和细胞凋亡。它们还与各种细胞和分子功能相关，例如肽基赖氨酸羟基化、中枢神经系统成熟、G 蛋白偶联趋化剂受体活性、BCL-2 同源 (BH) 结构域结合、胶质细胞生成和线粒体去极化的负调节。WGCNA鉴定出一个基因共表达模块，主要参与线粒体翻译延伸、线粒体翻译终止、线粒体翻译、线粒体呼吸链复合体、通过剪接体途径的mRNA剪接等；这两项分析结果都强调线粒体去极化途径与 CD 复发有关，导致氧化应激促进 CD 患者炎症。结论：这些关键基因可作为克罗恩病术后复发的新型诊断生物标志物。因此，在迄今为止存在的其他治疗选择中，这些生物标志物将在诊断和预后方面提供成功，旨在实现持久缓解以预防 CD 的进一步并发症。