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基于加权基因共表达网络分析的银屑病潜在关键分子和信号通路的鉴定

Identification of potential key molecules and signaling pathways for psoriasis based on weighted gene co-expression network analysis.

作者信息

Shu Xin, Chen Xiao-Xia, Kang Xin-Dan, Ran Min, Wang You-Lin, Zhao Zhen-Kai, Li Cheng-Xin

机构信息

Department of Dermatology, The Third Medical Center of Chinese PLA General Hospital, Beijing 100039, China.

Department of Radiology, The Third Medical Center of Chinese PLA General Hospital, Beijing 100039, China.

出版信息

World J Clin Cases. 2022 Jun 26;10(18):5965-5983. doi: 10.12998/wjcc.v10.i18.5965.

Abstract

BACKGROUND

Psoriasis is a chronic inflammatory skin disease, the pathogenesis of which is more complicated and often requires long-term treatment. In particular, moderate to severe psoriasis usually requires systemic treatment. Psoriasis is also associated with many diseases, such as cardiometabolic diseases, malignant tumors, infections, and mood disorders. Psoriasis can appear at any age, and lead to a substantial burden for individuals and society. At present, psoriasis is still a treatable, but incurable, disease. Previous studies have found that microRNAs (miRNAs) play an important regulatory role in the progression of various diseases. Currently, miRNAs studies in psoriasis and dermatology are relatively new. Therefore, the identification of key miRNAs in psoriasis is helpful to elucidate the molecular mechanism of psoriasis.

AIM

To identify key molecular markers and signaling pathways to provide potential basis for the treatment and management of psoriasis.

METHODS

The miRNA and mRNA data were obtained from the Gene Expression Omnibus database. Then, differentially expressed mRNAs (DEmRNAs) and differentially expressed miRNAs (DEmiRNAs) were screened out by limma R package. Subsequently, DEmRNAs were analyzed for Gene Ontology and Kyoto Encyclopedia of Genes and Genomics functional enrichment. The "WGCNA" R package was used to analyze the co-expression network of all miRNAs. In addition, we constructed miRNA-mRNA regulatory networks based on identified hub miRNAs. Finally, validation was performed. All experimental procedures were approved by the ethics committee of Chinese PLA General Hospital (S2021-012-01).

RESULTS

A total of 639 DEmRNAs and 84 DEmiRNAs were identified. DEmRNAs screening criteria were adjusted (adj. value < 0.01 and |logFoldChange| (|logFC|) > 1. DEmiRNAs screening criteria were adj. value < 0.01 and |logFC| > 1.5. KEGG functional analysis demonstrated that DEmRNAs were significantly enriched in immune-related biological functions, for example, toll-like receptor signaling pathway, cytokine-cytokine receptor interaction, and chemokine signaling pathway. In weighted gene co-expression network analysis, turquoise module was the hub module. Moreover, 10 hub miRNAs were identified. Among these 10 hub miRNAs, only 8 hub miRNAs predicted the corresponding target mRNAs. 97 negatively regulated miRNA-mRNA pairs were involved in the miRNA-mRNA regulatory network, for example, hsa-miR-21-5p-claudin 8 (CLDN8), hsa-miR-30a-3p-interleukin-1B (IL-1B), and hsa-miR-181a-5p/hsa-miR-30c-2-3p-C-X-C motif chemokine ligand 9 (CXCL9). Real-time polymerase chain reaction results showed that IL-1B and CXCL9 were up-regulated and CLDN8 was down-regulated in psoriasis with statistically significant differences.

CONCLUSION

The identification of potential key molecular markers and signaling pathways provides potential research directions for further understanding the molecular mechanisms of psoriasis. This may also provide new research ideas for the prevention and treatment of psoriasis in the future.

摘要

背景

银屑病是一种慢性炎症性皮肤病,其发病机制较为复杂,通常需要长期治疗。特别是中重度银屑病通常需要系统治疗。银屑病还与许多疾病相关,如心脏代谢疾病、恶性肿瘤、感染和情绪障碍。银屑病可在任何年龄出现,给个人和社会带来沉重负担。目前,银屑病仍是一种可治疗但无法治愈的疾病。先前的研究发现,微小RNA(miRNA)在各种疾病的进展中发挥着重要的调节作用。目前,miRNA在银屑病和皮肤病学中的研究相对较新。因此,鉴定银屑病中的关键miRNA有助于阐明银屑病的分子机制。

目的

鉴定关键分子标志物和信号通路,为银屑病的治疗和管理提供潜在依据。

方法

从基因表达综合数据库获取miRNA和mRNA数据。然后,使用limma R包筛选差异表达的mRNA(DEmRNA)和差异表达的miRNA(DEmiRNA)。随后,对DEmRNA进行基因本体论和京都基因与基因组百科全书功能富集分析。使用“WGCNA”R包分析所有miRNA的共表达网络。此外,我们基于鉴定出的枢纽miRNA构建了miRNA-mRNA调控网络。最后,进行验证。所有实验程序均获得中国人民解放军总医院伦理委员会批准(S2021-012-01)。

结果

共鉴定出639个DEmRNA和84个DEmiRNA。DEmRNA的筛选标准为调整后P值(adj.P值)<0.01且|log倍变化|(|logFC|)>1。DEmiRNA的筛选标准为adj.P值<0.01且|logFC|>1.5。KEGG功能分析表明,DEmRNA在免疫相关生物学功能中显著富集,例如Toll样受体信号通路、细胞因子-细胞因子受体相互作用和趋化因子信号通路。在加权基因共表达网络分析中,绿松石模块是枢纽模块。此外,鉴定出10个枢纽miRNA。在这10个枢纽miRNA中,只有8个枢纽miRNA预测了相应的靶mRNA。97个负调控的miRNA-mRNA对参与了miRNA-mRNA调控网络,例如hsa-miR-21-5p-闭合蛋白8(CLDN8)、hsa-miR-30a-3p-白细胞介素-1β(IL-1β)和hsa-miR-181a-5p/hsa-miR-30c-2-3p-C-X-C基序趋化因子配体9(CXCL9)。实时聚合酶链反应结果显示,银屑病中IL-1β和CXCL9上调,CLDN8下调,差异具有统计学意义。

结论

潜在关键分子标志物和信号通路的鉴定为进一步了解银屑病的分子机制提供了潜在的研究方向。这也可能为未来银屑病的预防和治疗提供新的研究思路。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf1d/9254198/e4a1cbc557e3/WJCC-10-5965-g001.jpg

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