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基于网络的综合多组学表达数据分析在先天性巨结肠病中的生物信息学预测。

Bioinformatics Prediction for Network-Based Integrative Multi-Omics Expression Data Analysis in Hirschsprung Disease.

机构信息

Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain.

Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain.

出版信息

Biomolecules. 2024 Jan 30;14(2):164. doi: 10.3390/biom14020164.

DOI:10.3390/biom14020164
PMID:38397401
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10886964/
Abstract

Hirschsprung's disease (HSCR) is a rare developmental disorder in which enteric ganglia are missing along a portion of the intestine. HSCR has a complex inheritance, with as the major disease-causing gene. However, the pathogenesis of HSCR is still not completely understood. Therefore, we applied a computational approach based on multi-omics network characterization and clustering analysis for HSCR-related gene/miRNA identification and biomarker discovery. Protein-protein interaction (PPI) and miRNA-target interaction (MTI) networks were analyzed by DPClusO and BiClusO, respectively, and finally, the biomarker potential of miRNAs was computationally screened by miRNA-BD. In this study, a total of 55 significant gene-disease modules were identified, allowing us to propose 178 new HSCR candidate genes and two biological pathways. Moreover, we identified 12 key miRNAs with biomarker potential among 137 predicted HSCR-associated miRNAs. Functional analysis of new candidates showed that enrichment terms related to gene ontology (GO) and pathways were associated with HSCR. In conclusion, this approach has allowed us to decipher new clues of the etiopathogenesis of HSCR, although molecular experiments are further needed for clinical validations.

摘要

先天性巨结肠症（HSCR）是一种罕见的发育障碍，其沿部分肠段缺失肠神经节。HSCR 具有复杂的遗传特征， 是主要的致病基因。然而，HSCR 的发病机制仍不完全清楚。因此，我们应用了一种基于多组学网络特征描述和聚类分析的计算方法，用于识别与 HSCR 相关的基因/miRNA 并发现生物标志物。通过 DPClusO 和 BiClusO 分别分析蛋白质-蛋白质相互作用（PPI）和 miRNA 靶标相互作用（MTI）网络，最后通过 miRNA-BD 计算筛选 miRNA 的生物标志物潜力。在这项研究中，共鉴定出 55 个显著的基因疾病模块，使我们能够提出 178 个新的 HSCR 候选基因和两个生物学途径。此外，我们在 137 个预测的 HSCR 相关 miRNA 中确定了 12 个具有生物标志物潜力的关键 miRNA。对新候选基因的功能分析表明，与基因本体论（GO）和途径相关的富集术语与 HSCR 相关。总之，尽管还需要进行分子实验来进行临床验证，但这种方法使我们能够破解 HSCR 发病机制的新线索。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/788a550864ba/biomolecules-14-00164-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/33750137fda4/biomolecules-14-00164-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/b105e0b4c340/biomolecules-14-00164-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/ee727a1c4cdc/biomolecules-14-00164-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/fd66018f49f9/biomolecules-14-00164-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/4dea993a40b3/biomolecules-14-00164-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/788a550864ba/biomolecules-14-00164-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/33750137fda4/biomolecules-14-00164-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/b105e0b4c340/biomolecules-14-00164-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/ee727a1c4cdc/biomolecules-14-00164-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/fd66018f49f9/biomolecules-14-00164-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/4dea993a40b3/biomolecules-14-00164-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3f5/10886964/788a550864ba/biomolecules-14-00164-g006.jpg

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Up-Regulation of microRNA-424 Causes an Imbalance in AKT Phosphorylation and Impairs Enteric Neural Crest Cell Migration in Hirschsprung Disease.微小 RNA-424 的上调导致 AKT 磷酸化失衡，损害先天性巨结肠症中的肠神经嵴细胞迁移。
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UniProt Tools: BLAST, Align, Peptide Search, and ID Mapping.UniProt 工具：BLAST、Align、肽搜索和 ID 映射。
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