Screening of Potential Key Genes Related to Tubal Factor Infertility Based on Competitive Endogenous RNA Network

Genetic insights into Staphylococcus aureus resistance: exploring AMR genes and molecular interactions

Antimicrobial resistance (AMR) among microorganisms remains a significant global concern in this century, posing an ongoing challenge for humanity. To solve this issue effectively, it is crucial to understand the genes responsible for AMR and how they create resistance. Staphylococcus aureus, which has AMR genes imparting resistance against numerous antibiotics, was the main subject of our investigation. We conducted a phylogenetic investigation to explore the evolutionary history of the gene network comprising rpl, rpoC, parE, and gyrB, providing insights into their genetic relationships and evolutionary connections. A gene interaction network with 46 functional partners was built and examined from the STRING Database and Cytoscape to increase our understanding. According to Cluego's enrichment analysis, 20 genes are significantly involved in biological processes, as are 14 genes in cellular components and 16 genes in molecular functions. RpoB, RpoC, FusA, RplI, and RpsL had the most interactions by Cytohubba when the degree and closeness of the network were studied, according to the gene interaction network analysis. Understanding the molecular basis of AMR requires analysis of the enriched pathways and Gene Ontologies (GO). The proposed study may also help researchers find new ways to battle the multidrug resistance of Staphylococcus aureus.

miR-424-5p combined with miR-17-5p has high diagnostic efficacy for endometriosis

PURPOSE

Endometriosis (EMT) is a chronic benign disease with high prevalence. This study investigated the diagnostic value of serum miR-17-5p, miR-424-5p, and their combined expressions for EMT.

METHODS

Total 80 EMT patients of reproductive age who underwent laparoscopy or laparotomy and were confirmed by pathological examination were included as the study subjects, and another 80 healthy women of reproductive age receiving gynecological examination and ultrasonography with no pelvic abnormalities were selected as the control group. The whole blood samples of enrolled subjects were collected and clinical characteristics were recorded. The miR-17-5p, miR-424-5p, VEGFA, IL-4, and IL-6 levels in the serum were measured. ROC curve was used to evaluate the diagnostic efficacy of miR-17-5p and miR-424-5p expressions for EMT. Pearson correlation was performed to analyze the correlation of miR-17-5p and miR-424-5p with clinical indexes in EMT patients.

RESULTS

miR-17-5p and miR-424-5p were downregulated in EMT patients. For diagnosing EMT, the AUC of miR-17-5p was 0.865 and cutoff value was 0.890 (91.3% sensitivity and 85% specificity), the AUC of miR-424-5p was 0.737, and cutoff value was 0.915 (98.8% sensitivity and 61.2% specificity), and the AUC of miR-424-5p combined with miR-17-5p was 0.938 and cutoff value was 2.205 (93.8% sensitivity and 88.7% specificity), with the diagnostic efficacy higher than miR-424-5p or miR-17-5p alone. miR-17-5p and miR-424-5p expressions were negatively correlated with dysmenorrhea, infertility, pelvic pain, and rASRM stage, but not with age, BMI, menstrual disorder, and nulliparity. VEGFA, IL-4, IL-6, and CA-125 were increased in EMT patients and were inversely associated with miR-17-5p and miR-424-5p.

CONCLUSION

miR-424-5p combined with miR-17-5p has high diagnostic efficacy for EMT.

Construction of ceRNA network and key gene screening in cervical squamous intraepithelial lesions

BACKGROUND

This study aimed to construct an endogenous competition network for cervical squamous intraepithelial lesions using differential gene screening.

METHODS

GSE149763 was used to screen differentially expressed long non-coding RNAs (lncRNAs) and mRNAs to predict correlated microRNAs (miRNAs). The correlated miRNAs and GSE105409 were used to screen differentially expressed miRNAs for differential co-expression analysis, and the co-expressed differentially expressed miRNAs were used to predict correlated mRNAs. Differentially expressed mRNAs, miRNAs, and lncRNAs were visualized, and differential gene screening, enrichment, and pathway analysis were performed.

RESULTS

The ceRNA network of cervical squamous intraepithelial was successfully established and a potential differentially expressed network was identified. The key genes were VEGFA and FOS, and the key pathway was the MAPK signaling pathway.

CONCLUSIONS

The differential expression and potential effects of the lncRNA BACH1-IT1/miR-140-5p/VEGFA axis, key genes, VEGFA and FOS, and MAPK signaling in CIN were clarified, and the occurrence and potential effects of CIN were further clarified. The underlying molecular mechanism provides a certain degree of reference for subsequent treatments and experimental research.

Construction of a ceRNA network in polycystic ovary syndrome (PCOS) driven by exosomal lncRNA

Polycystic ovary syndrome (PCOS), a common and frustrating syndrome in women of reproductive age, is characterized by symptoms including hyperandrogenemia, ovulation dysfunction, and polycystic ovaries. The role of competitive endogenous RNA (ceRNA) networks is receiving increasing attention and has been reported in multiple complicated diseases, such as various carcinomas, endometriosis, and tubal factor infertility. However, the association of ceRNA networks with the pathogenesis of PCOS remains unclear. This study aimed to construct a ceRNA network orchestrated by exosomal lnRNA and circRNA in PCOS. We screened RNA data of 34 samples from the Gene Expression Omnibus (GEO) database for differentially expressed lncRNAs (DELs), miRNAs (DEMs), mRNAs (DEGs), and circRNA associated with the progression of PCOS (PCOS, n = 17 vs. normal, n = 17). A protein-protein interaction (PPI) network, gene set enrichment analysis (GSEA), and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted. Importantly, the function of the ceRNA network was explored using GO and KEGG enrichment analyses. We identified 46 DELs (25 upregulated and 21 downregulated), 31 DEMs (20 upregulated and 11 downregulated), 165 DEGs (52 upregulated and 113 downregulated), and 1 differentially expressed circRNA. The PPI network had 79 nodes and 112 edges. The GSEA results showed that these genes were mainly related to oxidative phosphorylation; TNF signaling pathways; and valine, leucine, and isoleucine degradation. GO and KEGG analyses revealed that the DEGs were significantly enriched in lipid metabolism, peroxisome proliferator-activated receptor (PPAR) signaling pathways, and fatty acid metabolism. Additionally, we constructed a novel PCOS-associated lncRNA-miRNA-mRNA ceRNA triple network and a circRNA-related network. Thereafter, we described the potential roles played by follicular fluid exosomes in PCOS. Our present study describes the molecular pathogenesis of PCOS in human ovarian granulosa cells at the post-transcriptional level, which provides new insights for the clinical diagnosis and treatment of PCOS and further scientific research.

Candidate genes for infertility: an in-silico study based on cytogenetic analysis

Background

The cause of infertility remains unclear in a significant proportion of reproductive-age couples who fail to conceive naturally. Chromosomal aberrations have been identified as one of the main genetic causes of male and female infertility. Structural chromosomal aberrations may disrupt the functioning of various genes, some of which may be important for fertility. The present study aims to identify candidate genes and putative functional interaction networks involved in male and female infertility using cytogenetic data from cultured peripheral blood lymphocytes of infertile patients.

Methods

Karyotypic analyses was done in 201 infertile patients (100 males and 101 females) and 201 age and gender matched healthy controls (100 males and 101 females) after 72 h peripheral lymphocyte culturing and GTG banding, followed by bioinformatic analysis using Cytoscape v3.8.2 and Metascape.

Results

Several chromosomal regions with a significantly higher frequency of structural aberrations were identified in the infertile males (5q2, 10q2, and 17q2) and females (6q2, 16q2, and Xq2). Segregation of the patients based on type of infertility (primary v/s secondary infertility) led to the identification of chromosomal regions with a significantly higher frequency of structural aberrations exclusively within the infertile males (5q2, 17q2) and females (16q2) with primary infertility. Cytoscape identified two networks specific to these regions: a male specific network with 99 genes and a female specific network with 109 genes. The top enriched GO terms within the male and female infertility networks were “skeletal system morphogenesis” and “mRNA transport” respectively. PSME3, PSMD3, and CDC27 were the top 3 hub genes identified within the male infertility network. Similarly, UPF3B, IRF8, and PSMB1 were the top 3 hub genes identified with the female infertility network. Among the hub genes identified in the male- and female-specific networks, PSMB1, PSMD3, and PSME3 are functional components of the proteasome complex. These hub genes have a limited number of reports related to their respective roles in maintenance of fertility in mice model and humans and require validation in further studies.

Conclusion

The candidate genes predicted in the present study can serve as targets for future research on infertility.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01320-x.