Identification of potential biomarkers and pathways for asthenozoospermia by bioinformatics analysis and experiments.

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Despite previous bioinformatics analysis identifying potential key lncRNAs, miRNAs, hub genes, and pathways associated with asthenospermia, there is still a need to explore additional molecular mechanisms and potential biomarkers for this condition.\nMethods: We integrated data from Gene Expression Omnibus (GEO) (GSE22331, GSE34514, and GSE160749) and performed bioinformatics analysis to identify differentially expressed genes (DEGs) between normozoospermia and asthenozoospermia. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to gain insights into biological processes and signaling pathways. Weighted Gene Co-expression Network Analysis (WGCNA) identified gene modules associated with asthenozoospermia. Expression levels of key genes were assessed using datasets and experimental data. Gene Set Enrichment Analysis (GSEA) and correlation analysis identified pathways associated with the hub gene and explore the relationship between the ZNF764 and COQ9 and mitochondrial autophagy-related genes. Competitive endogenous RNA (ceRNA) networks were constructed, and in vitro experiments using exosome samples were conducted to validate this finding.\nResults: COQ9 was identified as a marker gene in asthenozoospermia, involved in autophagy, ATP-dependent chromatin remodeling, endocytosis, and cell cycle, etc. The ceRNA regulatory network (LINC00893/miR-125a-5p/COQ9) was constructed, and PCR demonstrated that LINC00893 and COQ9 were downregulated in asthenozoospermia, while miR-125a-5p and m6A methylation level of LINC00893 were upregulated in asthenozoospermia compared to normozoospermic individuals.\nConclusion: The ceRNA regulatory network (LINC00893/miR-125a-5p/COQ9) likely plays a crucial role in the mechanism of asthenozoospermia. However, further functional experiments are needed to fully understand its significance.", "claims": [{"id": "claim-method", "statement": "DEGs were identified using the “limma” packages of the R language, with a significance threshold of p-value < 0.05 and |log2FC| > 0.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38863929", "locator": "sections[4] \"Identification of key DEGs\" paragraph 2", "quote": "DEGs were identified using the “limma” packages of the R language, with a significance threshold of p-value < 0.05 and |log2FC| > 0.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38863929", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 2,070 DEGs were identified between asthenozoospermic and normozoospermic groups, including 159 upregulated genes and 1,911 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38863929", "locator": "sections[15] \"Identification of key DEGs\" paragraph 2", "quote": "Normalization and integration of the mRNA expression datasets GSE22331, GSE34514, and GSE160749 resulted in a total of 17,415 genes."}, {"asset": "source:pmid:38863929", "locator": "sections[15] \"Identification of key DEGs\" paragraph 2", "quote": "A total of 2,070 DEGs were identified between asthenozoospermic and normozoospermic groups, including 159 upregulated genes and 1,911 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 2,070 DEGs were identified between asthenozoospermic and normozoospermic groups, including 159 upregulated genes and 1,911 downregulated genes.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38863929"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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