Comprehensive bioinformatics analysis of vitiligo melanocytes based on high-throughput sequencing

Yihuan PU; Yangmei CHEN; Xuenuo CHEN; Lingzhao ZHANG; Jiayi CHEN; Tianwen GAO; Jin CHEN

doi:10.16016/j.1000-5404.202101238

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Comprehensive bioinformatics analysis of vitiligo melanocytes based on high-throughput sequencing

Basic Medicine | 更新时间：2026-01-09

- Comprehensive bioinformatics analysis of vitiligo melanocytes based on high-throughput sequencing
- Journal of Third Military Medical University Vol. 43, Issue 16, Pages: 1566-1574(2021)
- 作者机构：
  
  1.400016 重庆，重庆医科大学附属第一医院: 皮肤科
  2.400016 重庆，重庆医科大学附属第一医院: 消化内科
  3.710032 西安，空军军医大学西京医院皮肤科
- 作者简介：
- 基金信息：
  
  the General Program of National Natural Science Foundation of China(81773307);the General Project of Frontier and Application Basic Research Plan of Chongqing Science and Technology Commission(cstc2018jcyjAX0195)
- DOI：10.16016/j.1000-5404.202101238
  CLC： R318.04;R394.3;R758.41
- Received：27 January 2021，
  
  Revised：2021-04-27，
  
  Published：30 August 2021
- 稿件说明：
移动端阅览
Yihuan PU, Yangmei CHEN, Xuenuo CHEN, et al. Comprehensive bioinformatics analysis of vitiligo melanocytes based on high-throughput sequencing[J]. Journal of Third Military Medical University, 2021, 43(16): 1566-1574.
DOI：

Yihuan PU, Yangmei CHEN, Xuenuo CHEN, et al. Comprehensive bioinformatics analysis of vitiligo melanocytes based on high-throughput sequencing[J]. Journal of Third Military Medical University, 2021, 43(16): 1566-1574. DOI： 10.16016/j.1000-5404.202101238.

摘要

目的

筛选人类白癜风黑素细胞中差异表达的编码和非编码RNAs，分析它们之间相互作用并对鉴定出的重要RNAs进行表达量验证，以探讨其在白癜风发病过程中可能扮演的角色。

方法

对人类白癜风黑素细胞株和正常黑素细胞株进行高通量测序，用R软件进行差异表达(differentially expressed

DE)分析，利用互作基因的检索工具STRING构建蛋白相互作用网络(protein-protein interaction

PPI)，用生物信息学算法miRanda鉴定miRNA-mRNA和miRNA-lncRNA的相互作用环。并用Cytoscape软件构建CeRNA网络，运用DAVID数据库对筛选获得的DE mRNAs进行功能富集和通路分析，最后对鉴定的关键RNAs进行RT-qPCR验证。

结果

差异表达分析共筛选出5 958个DE mRNAs，1650个DE LncRNAs和450个DE miRNAs。PPI网络中top10枢纽基因(JUN，HIST2H3PS2，SOX2，EGR1，MMP9，NGF，BMP2，HSPA5，EDN1，SERPINE1)显示与白癜风发病密切相关。本研究还挖掘了与top20枢纽基因有相互作用的LncRNAs，通过取它们的交集鉴定出7个关键LncRNAs，其中分子功能和信号通路富集最丰富的3个LncRNAs(ENST0000623111、NONHSAT245258.1和NONHSAT 189782.1)被分别构建了竞争性内源性RNA(CeRNA)子网络，CeRNA子网络中预测的hsa-miR-92b-5p在白癜风黑素细胞中的表达有显著差异。另外，RT-qPCR结果与我们分析结果基本一致。

结论

本研究经过层层鉴定及筛选出的枢纽基因以及关键的ncRNAs可能在白癜风发病中发挥重要作用，这些发现可能为白癜风的研究提供了新的见解和策略。

Abstract

Objective

To screen the differentially expressed (DE) coding and non-coding RNAs in human vitiligo melanocytes and analyze their interactions and verify the expression of the identified key RNAs in order to explore their possible role in the pathogenesis of vitiligo.

Methods

High throughput sequencing was performed on human vitiligo melanocyte lines and normal human melanocyte lines. DE analysis was performed by R software. Protein-protein interaction (PPI) network was constructed by using the search tool STRING. The interaction loop of miRNA-mRNA and miRNA-lncRNA was identified by bioinformatics algorithm miRanda. The competitive endogenous RNA (CeRNA) network was constructed by Cytoscape software

and the functional enrichment and pathway analysis of DE mRNAs were performed by David database. Finally

the identified key RNAs were verified by Q-PCR.

Results

A total of 5 958 DE mRNAs

1 650 DE lncRNAs and 450 DE miRNAs were screened out by DE analysis. The top10 hub genes (JUN

HIST2H3PS2

SOX2

EGR1

MMP9

NGF

BMP2

HSPA5

EDN1 and SERPINE1) in the PPI network are indicated closely related to the pathogenesis of vitiligo. Furthermore

7 key lncRNAs that interact with top 20 hub genes are found. Among them

3 lncRNAs (ENST0000623111

NONHSAT245258.1 and NONHSAT189782.1) with the most abundant molecular functions and signaling pathways were constructed into CeRNA subnetwork

and the expression of hsa-miR-92b-5p predicted in the CeRNA sub-network is significantly different in vitiligo melanocytes. In addition

the results of Q-PCR were basically consistent with our analysis.

Conclusion

The identified hub genes and non-coding RNAs in our study may play important roles in the pathogenesis of vitiligo. Our findings provide novel insights and strategies for researches on vitiligo.

关键词

Keywords

references

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