In-silico analysis and validation of differentially expressed imprinting gene, co-expression network of mRNAs-miRNAs-lncRNA, and finding the suitable drug in recurrent implantation failure of endometrial tissue
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1.
University of Tehran
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2.
Royan Institute
Description
The primers used for KBTBD3, DHCR7, PPP1R9A, RASGRF1, MARP2, NTM, NPAP1, and ADAM were created and are listed in Supplementary 1.
Supplementary 2 and Figure 2 illustrates changes in mRNA, miRNA, and lncRNA expression.
Notably, KBTBD3, PTPN14, and DHCR7 exhibited changes in the context of RSA (see Figure 3d and Supplementary 3 and Figure 2).
Furthermore, our analysis revealed that the up/down-regulated DEGs were enriched in four cellular compound terms. Specifically, the enriched cellular compound terms in RIF included PAR Polarity Complex, Neuron Projection, Nuclear Outer Membrane, GABA-ergic Synapse, Myofibril, and Synaptic Membrane (as depicted in Figure 5 and supplementary data 4).
The functional enrichment terms for upregulated DEGs in RSA were predominantly related to Oxidoreductase Activity, Adenyl Nucleotide Binding, NADP Binding, and Receptor Tyrosine Kinase Binding (as shown in Figure 5A). In terms of cellular compound terms, the enriched categories in RSA included Nuclear Outer Membrane, Organelle Outer Membrane, and Nuclear Membrane (as indicated in Figure 5B and supplementary data 5).
Within this section, after the identification of 7 genes (KBTBD3, PPP1R9A, PYY2, MEST, HOXA3, KCNQ1, and SOX8), we isolated and selected the most relevant lncRNAs, namely LINC01502, AC243960.3, SLC7A11-AS1, AC097375.4, and AC097375.4, which exhibited clearer associations compared to other lncRNAs (as depicted in Figure 7a). In addition, following the identification of 8 genes (NLRP2, PPP1R9A, TFPI2, PEG13, NNAT, KCNQ1, HTR2A, and ANO1), we isolated and selected the most relevant microRNAs, including hsa-miR-374c-5p, hsa-miR-455-5p, hsa-miR-9-5p, hsa-miR-4306, hsa-miR-4306, hsa-miR-142-3p, hsa-miR-142-3p, and hsa-miR-144-5p (as illustrated in Figure 7b and supplementary 6).
In supplemantry 7, domain and pocket of proteins are shown. We find and dock protein domains, Dbl homology (DH) domain in RASGRF, Ig-like domain in NMT and BTB domain in KBTBD3. For this study, 2400 drugs were selected from the DrugBank database for screening.
As in Supplementary 8, low or no toxicity was reported for many drugs such as Lidoflazine, Glimepiride, Eltrombopag, Cabozantinib, Drospirenone, Maraviroc, Cabozantinib, Glimepiride, Lidoflazine, Rimegepant, Tucatinib, Rupatadine and Delamanid using this web server.
We upload drugs (Lidoflazine, Glimepiride, Eltrombopag, Cabozantinib, Drospirenone, Maraviroc, Cabozantinib, Glimepiride, Lidoflazine, Rimegepant, Tucatinib, Rupatadine, and Delamanid) in SMPDB database. The analysis show that drug can prevent coagulation, induce Pro-inflammatory Cytokines, induce Cell Adhesion Molecules, induce Chemotactic Factors Mast Cells (Supplementary 9).
Abstract (English)
Introduction:
Recurrent implantation failure (RIF) and recurrent spontaneous abortion (RSA) represent intricate issues within the realm of assisted reproductive technology (ART), and their underlying causes are often linked to compromised endometrial receptivity. Nevertheless, the precise pathophysiological mechanisms responsible for RIF and RSA remain incompletely understood.
Material and Method:
Eight microarray datasets related to RIF and RSA were retrieved from the Gene Expression Omnibus (GEO) database and were subsequently integrated employing the "sva" package in the R programming environment. The analysis encompassed the identification of Differentially Expressed Genes (DEGs), Differentially Expressed miRNA, and Differentially Expressed long non-coding RNA (lncRNA) using the "limma" package. Subsequently, Gene Ontology (GO), KEGG analyses, and exploration of lncRNA-miRNA-mRNA interactions were conducted to unravel functional and pathway enrichment in the context of RIF and RSA specifically considering genes influenced by imprinting. To finalize the investigation, central genes, miRNA, and lncRNA with imprinting significance were pinpointed through the application of CytoHubba, an algorithmic tool for identifying hub genes and regulatory RNAs in biological networks. Therefore, the present research used computational methods to find the best DEG inhibitor(s) among FDA-approved drugs.
Results:
In the endometrial tissue of individuals suffering from RIF and RSA, a noteworthy differential expression was observed in 33 genes, 49 microRNAs, and 137 long non-coding RNAs (lncRNA) that are associated with imprinted gene regulation. Through a meticulous functional enrichment analysis, it became evident that the altered gene expression profile in these two patient groups primarily pertained to significant modifications in biological processes. Specifically, these changes were predominantly linked to the G-protein coupled receptor signaling pathway, the regulation of interleukin-1 beta production, and the binding of phosphatidylinositol bisphosphate within the endometrial tissue. Furthermore, a subset of key DEGs, including KBTBD3, PPP1R9A, PYY2, MEST, HOXA3, KCNQ1, and SOX8, were identified as central hub genes implicated in the pathogenesis of RIF, while KBTBD3, PTPN14, and DHCR7 were singled out as hub genes specifically associated with RSA. The drug complexes of Lidoflazine, Maraviroc, and Drospirenone are suitable drugs for DEGs.
Conclusion:
These networks offer novel perspectives into the underlying pathophysiology of RIF. The molecules LINC01502, AC243960.3, SLC7A11-AS1, hsa-miR-374c-5p, hsa-miR-455-5p, and hsa-miR-9-5p emerge as promising candidates for further investigation as potential biomarkers for RIF and we suggest some drug for RIF.
Files
Supplementary 9.pdf
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