Construction of miRNA-mRNA network for the identification of key biological markers and their associated pathways in IgA nephropathy by employing the integrated bioinformatics analysis

Abstract

Background: About half-century ago, Immunoglobulin A nephropathy (IgAN) was discovered as a complicated disease with frequent clinical symptoms. Until now, exact mechanism underlying the pathogenesis of IgAN is poorly known. Therefore, current study was aimed to understand the molecular mechanism of IgAN by identifying the key miRNAs and their targeted hub genes. The key miRNAs might contribute to the diagnosis and therapy of IgAN, and could turn out to be a new star in the field of IgAN.

Methods: The microarray datasets were downloaded from Gene Expresssion Omnibus (GEO) database and analyzed using R package (LIMMA) in order to obtain differential expressed genes (DEGs). Then, the hub genes were identified using cytoHubba plugin of cytoscpae tool and other bioinformatics approaches including protein-protein interaction (PPI) network analysis, module analysis, and miRNA-hub gene network construction was also performed.

Results: A total of 348 DEGs were identified, of which 107 were upregulated genes and 241 were downregulated genes. Subsequently, the 12 overlapped genes were predicted from cytoHubba, and considered as hub genes. Moreover, a network among miRNA-hub genes was created to explore the correlation between the hub genes and their targeted miRNAs. Network construction ultimately lead to the identification of nine gene named FN1, EGR1, FOS, JUN, SERPINE1, MMP2, ATF3, MYC, and IL1B and one novel key miRNA namely, has-miR-144-3p as biomarker for diagnosis and therapy of IgAN.

Conclusion: This study updates the information and yield a new perspective in context of understanding the pathogenesis and development of IgAN. In future, key miRNAs might be capable of improving the personalized detection and therapies for IgAN. In vivo and in vitro investigation of miRNAs and pathway interaction is essential to delineate the specific roles of the novel miRNAs, which may help to further reveal the mechanisms underlying IgAN.

Keywords: BP, Cellular components; Bioinformatics analysis; CC, Molecular function; DAVID, Gene Expression Omnibus; ENCORI, Molecular Complex Detection; GEO, MicroRNA; GO, Database for annotation visualizationand integrated discovery; Gene expression profiling; Hub genes; Hub genes-miRNA network; IgAN, Differential Expressed Genes; Immunoglobulin A nephropathy; KEGG, Gene Ontology; MCODE, Search Tool for the Retrieval of Interacting Genes/Proteins; MF, Kyoto Encyclopedia of Genes and Genomes; PPI, Immunoglobulin A nephropathy; Protein-protein interaction; STRING, Biological process; miRNA, Protein-Protein Interaction.

Fig. 1

Graphical synopsis of representing the overall strategy used in the prediction key miRNAs as potential biomarker.

Fig. 2

Representation of differential expressed genes in form of Volcano plot with red dots showing upregulated genes while blue dots showing downregulated genes. Black dots represent non-significant genes.

Fig. 3

Representation of GO enrichment and KEGG pathway analysis. (a) Gene ontology in terms of Biological processes (b) Gene ontology in terms of Cellular Components (c) Gene ontology in terms of Molecular function (d) KEGG pathway analysis.

Fig. 4

3 modules were selected having cutoff criteria node >5 and the score is ≥5. (a) First module constructed from MCDOE comprised of 11 genes. (b) Pathways associated with first module (c) Second module constructed from MCDOE comprised of 7 genes. (d) Pathways associated with the second modules. (e) Third module constructed from MCDOE comprised of 20 genes. (f) Pathways associated with the third modules.

Fig. 5

(a) Common differential expressed genes identified between 4 methods cytohubba (b) Construction of PPI network of 12 hub genes.

Fig. 6

Construction of network among miRNA-hub genes from cytoscape. Yellow circles in network represent the hub genes while the blue circle in network represent miRNA followed by arrows which shows the interaction among miRNA and hub genes.