基于 miRNA 和 mRNA 表达谱的生物信息学分析揭示骨关节炎中的关键 miRNA 和基因
Bioinformatics analysis of miRNA and mRNA expression profiles to reveal the key miRNAs and genes in osteoarthritis.
机构信息
Department of Orthopaedic Surgery, Shanghai Fifth People's Hospital Affiliated to Fudan University, No. 128 Ruili Road, Minhang District, Shanghai, 200240, China.
出版信息
J Orthop Surg Res. 2021 Jan 19;16(1):63. doi: 10.1186/s13018-021-02201-2.
BACKGROUND
Osteoarthritis (OA) is a chronic degenerative joint disease and the most frequent type of arthritis. This study aimed to identify the key miRNAs and genes associated with OA progression.
METHODS
The GSE105027 (microRNA [miRNA/miR] expression profile; 12 OA samples and 12 normal samples) and GSE48556 (messenger RNA [mRNA] expression profile; 106 OA samples and 33 normal samples) datasets were selected from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and miRNAs (DEMs) were analyzed using the limma and ROCR packages in R, respectively. The target genes that negatively correlated with the DEMs were predicted, followed by functional enrichment analysis and construction of the miRNA-gene and miRNA-transcription factor (TF)-gene regulatory networks. Additionally, key miRNAs and genes were screened, and their expression levels were verified by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR).
RESULTS
A total of 1696 DEGs (739 upregulated and 957 downregulated) and 108 DEMs (56 upregulated and 52 downregulated) were identified in the OA samples. Furthermore, 56 target genes that negatively correlated with the DEMs were predicted and found to be enriched in three functional terms (e.g., positive regulation of intracellular protein transport) and three pathways (e.g., human cytomegalovirus infection). In addition, three key miRNAs (miR-98-5p, miR-7-5p, and miR-182-5p) and six key genes (murine double minute 2, MDM2; glycogen synthase kinase 3-beta, GSK3B; transmembrane P24-trafficking protein 10, TMED10; DDB1 and CUL4-associated factor 12, DCAF12; caspase 3, CASP3; and ring finger protein 44, RNF44) were screened, among which the miR-7-5p → TMED10/DCAF12, miR-98-5p → CASP3/RNF44, and miR-182-5p → GSK3B pairs were observed in the regulatory network. Moreover, the expression levels of TMED10, miR-7-5p, CASP3, miR-98-5p, GSK3B, and miR-182-5p showed a negative correlation with qRT-PCR verification.
CONCLUSION
MiR-98-5p, miR-7-5p, miR-182-5p, MDM2, GSK3B, TMED10, DCAF12, CASP3, and RNF44 may play critical roles in OA progression.
背景
骨关节炎（OA）是一种慢性退行性关节疾病，也是最常见的关节炎类型。本研究旨在确定与 OA 进展相关的关键 miRNA 和基因。
方法
从基因表达综合数据库中选择 GSE105027（miRNA [miRNA/miR] 表达谱；12 个 OA 样本和 12 个正常样本）和 GSE48556（信使 RNA [mRNA] 表达谱；106 个 OA 样本和 33 个正常样本）数据集。使用 R 中的 limma 和 ROCR 包分别分析差异表达基因（DEGs）和 miRNA（DEMs）。预测与 DEMs 呈负相关的靶基因，然后进行功能富集分析，并构建 miRNA-基因和 miRNA-转录因子（TF）-基因调控网络。此外，筛选关键 miRNA 和基因，并通过实时定量逆转录聚合酶链反应（qRT-PCR）验证其表达水平。
结果
在 OA 样本中鉴定出 1696 个 DEGs（739 个上调和 957 个下调）和 108 个 DEMs（56 个上调和 52 个下调）。此外，预测并发现 56 个与 DEMs 呈负相关的靶基因富集在三个功能术语（例如，细胞内蛋白质运输的正调节）和三个途径（例如，人类巨细胞病毒感染）中。此外，筛选出三个关键 miRNA（miR-98-5p、miR-7-5p 和 miR-182-5p）和六个关键基因（鼠双微体 2，MDM2；糖原合酶激酶 3-β，GSK3B；跨膜 P24 转运蛋白 10，TMED10；DDB1 和 CUL4 相关因子 12，DCAF12；半胱天冬酶 3，CASP3；和环指蛋白 44，RNF44），其中观察到 miR-7-5p→TMED10/DCAF12、miR-98-5p→CASP3/RNF44 和 miR-182-5p→GSK3B 三个调控网络。此外，TMED10、miR-7-5p、CASP3、miR-98-5p、GSK3B 和 miR-182-5p 的表达水平与 qRT-PCR 验证呈负相关。
结论
miR-98-5p、miR-7-5p、miR-182-5p、MDM2、GSK3B、TMED10、DCAF12、CASP3 和 RNF44 可能在 OA 进展中起关键作用。
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