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核心技术专利:CN118964589B侵权必究
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综合生物信息学结合机器学习分析银屑病和宫颈鳞状细胞癌中的共享生物标志物和通路。

Integrated bioinformatics combined with machine learning to analyze shared biomarkers and pathways in psoriasis and cervical squamous cell carcinoma.

机构信息

Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.

Department of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, China.

出版信息

Front Immunol. 2024 May 28;15:1351908. doi: 10.3389/fimmu.2024.1351908. eCollection 2024.


DOI:10.3389/fimmu.2024.1351908
PMID:38863714
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11165063/
Abstract

BACKGROUND: Psoriasis extends beyond its dermatological inflammatory manifestations, encompassing systemic inflammation. Existing studies have indicated a potential risk of cervical cancer among patients with psoriasis, suggesting a potential mechanism of co-morbidity. This study aims to explore the key genes, pathways, and immune cells that may link psoriasis and cervical squamous cell carcinoma (CESC). METHODS: The cervical squamous cell carcinoma dataset (GSE63514) was downloaded from the Gene Expression Omnibus (GEO). Two psoriasis-related datasets (GSE13355 and GSE14905) were merged into one comprehensive dataset after removing batch effects. Differentially expressed genes were identified using Limma and co-expression network analysis (WGCNA), and machine learning random forest algorithm (RF) was used to screen the hub genes. We analyzed relevant gene enrichment pathways using GO and KEGG, and immune cell infiltration in psoriasis and CESC samples using CIBERSORT. The miRNA-mRNA and TFs-mRNA regulatory networks were then constructed using Cytoscape, and the biomarkers for psoriasis and CESC were determined. Potential drug targets were obtained from the cMAP database, and biomarker expression levels in hela and psoriatic cell models were quantified by RT-qPCR. RESULTS: In this study, we identified 27 key genes associated with psoriasis and cervical squamous cell carcinoma. NCAPH, UHRF1, CDCA2, CENPN and MELK were identified as hub genes using the Random Forest machine learning algorithm. Chromosome mitotic region segregation, nucleotide binding and DNA methylation are the major enrichment pathways for common DEGs in the mitotic cell cycle. Then we analyzed immune cell infiltration in psoriasis and cervical squamous cell carcinoma samples using CIBERSORT. Meanwhile, we used the cMAP database to identify ten small molecule compounds that interact with the central gene as drug candidates for treatment. By analyzing miRNA-mRNA and TFs-mRNA regulatory networks, we identified three miRNAs and nine transcription factors closely associated with five key genes and validated their expression in external validation datasets and clinical samples. Finally, we examined the diagnostic effects with ROC curves, and performed experimental validation in hela and psoriatic cell models. CONCLUSIONS: We identified five biomarkers, , and , which may play important roles in the common pathogenesis of psoriasis and cervical squamous cell carcinoma, furthermore predict potential therapeutic agents. These findings open up new perspectives for the diagnosis and treatment of psoriasis and squamous cell carcinoma of the cervix.

摘要

背景:银屑病不仅表现为皮肤炎症,还伴有系统性炎症。现有的研究表明,银屑病患者患宫颈癌的风险可能增加,这表明两者之间可能存在共同的发病机制。本研究旨在探讨可能将银屑病与宫颈鳞状细胞癌(CESC)联系起来的关键基因、途径和免疫细胞。

方法:从基因表达综合数据库(GEO)中下载宫颈鳞状细胞癌数据集(GSE63514)。合并两个银屑病相关数据集(GSE13355 和 GSE14905),去除批次效应后得到一个综合数据集。使用 Limma 和共表达网络分析(WGCNA)鉴定差异表达基因,使用随机森林算法(RF)筛选关键基因。使用 GO 和 KEGG 分析相关基因富集途径,使用 CIBERSORT 分析银屑病和 CESC 样本中的免疫细胞浸润。使用 Cytoscape 构建 miRNA-mRNA 和 TFs-mRNA 调控网络,并确定银屑病和 CESC 的生物标志物。从 cMAP 数据库中获得潜在的药物靶点,并通过 RT-qPCR 定量测定 hela 和银屑病细胞模型中生物标志物的表达水平。

结果:本研究共鉴定出 27 个与银屑病和宫颈鳞状细胞癌相关的关键基因。使用随机森林机器学习算法鉴定出 NCAPH、UHRF1、CDCA2、CENPN 和 MELK 为关键基因。在有丝分裂细胞周期中,共同差异表达基因的主要富集途径是染色体有丝分裂区分离、核苷酸结合和 DNA 甲基化。然后我们使用 CIBERSORT 分析了银屑病和宫颈鳞状细胞癌样本中的免疫细胞浸润。同时,我们使用 cMAP 数据库识别出与中央基因相互作用的十个小分子化合物作为治疗候选药物。通过分析 miRNA-mRNA 和 TFs-mRNA 调控网络,我们鉴定出三个与五个关键基因密切相关的 miRNA 和九个转录因子,并在外部验证数据集和临床样本中验证了它们的表达。最后,我们使用 ROC 曲线进行了诊断效果评估,并在 hela 和银屑病细胞模型中进行了实验验证。

结论:我们鉴定出五个生物标志物、、、和,它们可能在银屑病和宫颈鳞状细胞癌的共同发病机制中发挥重要作用,进一步预测了潜在的治疗药物。这些发现为银屑病和宫颈鳞状细胞癌的诊断和治疗开辟了新的视角。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/dcf5a9542879/fimmu-15-1351908-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/ede47df567c1/fimmu-15-1351908-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/80e33d6636b9/fimmu-15-1351908-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/617b511b2bf3/fimmu-15-1351908-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/7e1ae9273c47/fimmu-15-1351908-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/9b43ad1d138c/fimmu-15-1351908-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/dca2d5ca76c8/fimmu-15-1351908-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/d4e0346be0e5/fimmu-15-1351908-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/a53b37893538/fimmu-15-1351908-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/dcf5a9542879/fimmu-15-1351908-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/ede47df567c1/fimmu-15-1351908-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/80e33d6636b9/fimmu-15-1351908-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/617b511b2bf3/fimmu-15-1351908-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/7e1ae9273c47/fimmu-15-1351908-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/9b43ad1d138c/fimmu-15-1351908-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/dca2d5ca76c8/fimmu-15-1351908-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/d4e0346be0e5/fimmu-15-1351908-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/a53b37893538/fimmu-15-1351908-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/788b/11165063/dcf5a9542879/fimmu-15-1351908-g009.jpg

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引用本文的文献

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Discov Oncol. 2025-8-27

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Exploring immune-inflammation markers in psoriasis prediction using advanced machine learning algorithms.

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[3]
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[6]
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Inflammation. 2025-3-3

[7]
Pan-cancer analysis and single-cell analysis identifies the CENPN as a biomarker for survival prognosis and immunotherapy.

Discov Oncol. 2025-1-17

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