Department of Pediatric Surgery, The Six Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China.
Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China.
PeerJ. 2024 Oct 30;12:e18376. doi: 10.7717/peerj.18376. eCollection 2024.
Hirschsprung's disease (HSCR) is a congenital disorder characterized by aganglionosis in the intermuscular and submucosal nerve plexuses of the gut, leading to impaired gastrointestinal function. Although the precise cause and pathophysiology of HSCR remain elusive, increasing evidence points to a significant role of autophagy in its development, warranting further investigation into its underlying mechanisms.
This study utilized publicly available microarray expression profiling datasets, GSE96854 and GSE98502, from the Gene Expression Omnibus (GEO). The R software (version 4.2.0) was employed to identify autophagy-related genes potentially showing differential expression in HSCR. Subsequent analyses included correlation analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analysis using the STRING database (version 11.0) and Cytoscape software (version 3.8.2). Ultimately, HSCR samples were used to verify the mRNA levels of important genes by quantitative real-time polymerase chain reaction (qRT-PCR) in a laboratory setting.
We have discovered 20 genes that are involved in autophagy and show variable expression. Among these genes, 15 are up-regulated and five are down-regulated. The enrichment analysis using the GO and KEGG pathways revealed a notable enrichment in pathways related to the control of autophagy. Nine hub genes were found the investigation of the PPI network constructed from STRING database and module analysis using Cytoscape. Moreover, the concordance between SIRT1 expression in the HSCR model and the bioinformatics analysis of mRNA chip findings was validated using qRT-PCR.
Utilizing bioinformatics analysis, we identified 20 potential genes associated with Hirschsprung's disease that play a role in autophagy. Notably, the upregulation of SIRT1 may profoundly influence the progression of HSCR by regulating autophagy-related pathways, offering a novel perspective on the disease's pathogenesis.
先天性巨结肠（HSCR）是一种以肠壁内、黏膜下肌间神经丛的神经节缺失为特征的先天性疾病，导致胃肠道功能受损。尽管 HSCR 的确切病因和病理生理学仍不清楚，但越来越多的证据表明自噬在其发生发展中起着重要作用，值得进一步研究其潜在机制。
本研究利用基因表达综合数据库（GEO）中公开的微阵列表达谱数据集 GSE96854 和 GSE98502。使用 R 软件（版本 4.2.0）鉴定可能在 HSCR 中表现出差异表达的自噬相关基因。随后的分析包括相关性分析、基因本体论（GO）和京都基因与基因组百科全书（KEGG）通路富集分析，以及使用 STRING 数据库（版本 11.0）和 Cytoscape 软件（版本 3.8.2）进行的蛋白质-蛋白质相互作用（PPI）网络分析。最终，在实验室环境中，通过定量实时聚合酶链反应（qRT-PCR）验证了重要基因在 HSCR 样本中的 mRNA 水平。
我们发现了 20 个参与自噬且表达可变的基因。其中 15 个基因上调，5 个基因下调。GO 和 KEGG 通路的富集分析显示，与自噬控制相关的途径显著富集。通过 STRING 数据库构建的 PPI 网络和 Cytoscape 中的模块分析发现了 9 个枢纽基因。此外，通过 qRT-PCR 验证了 SIRT1 在 HSCR 模型中的表达与 mRNA 芯片生物信息学分析结果的一致性。
利用生物信息学分析，我们鉴定了 20 个与先天性巨结肠相关的潜在基因，这些基因在自噬中发挥作用。值得注意的是，SIRT1 的上调可能通过调节自噬相关途径对 HSCR 的进展产生深远影响，为该疾病的发病机制提供了新的视角。
