Integrated Bioinformatics and Experimental Analysis Revealed Crosstalk Between IL-6, Autophagy, Ubiquitination, and Key miRNAs in Female Infertility: Insights from Ovarian Endometriosis and Polycystic Ovary Syndrome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41227338", "kind": "science-record", "revision": 2, "content_hash": "sha256:8f5b67fb30425ee21308d2d82d395d86ef8bb9d77fc98aff8d6bcd2d26287892", "created_at": "2026-11-01T20:31:15Z", "updated_at": "2026-11-01T21:36:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics and Experimental Analysis Revealed Crosstalk Between IL-6, Autophagy, Ubiquitination, and Key miRNAs in Female Infertility: Insights from Ovarian Endometriosis and Polycystic Ovary Syndrome.", "doi": "10.3390/cells14211693", "pmid": "41227338", "authors": ["Saber Nahdi", "Maria Arafah", "Abdel Halim Harrath"], "journal": "Cells", "year": 2025, "abstract": "Female infertility, affecting millions worldwide, involves complex molecular mechanisms such as chronic inflammation, impaired cellular death, and protein regulation. This study explores how the cytokine IL-6, the autophagy marker LC3, ubiquitination process, and three miRNAs, miR-146a-5p, miR-9-5p, and miR-9-3p, contribute to the control of ovarian function and female infertility. Two expression profile datasets (GSE199225 and GSE146856) were screened and downloaded from GEO. DEGs were screened using the GEO2R and ggVennDiagram tools. The three miRNAs were retrieved from datasets using the multiMiR tool, and IL6-targeted genes were retrieved from MSigDB. IL6 and miRNA interaction networks were constructed. Further, the cross-correlation of LC3 and ubiquitination with the DEGs associated miRNAs was demonstrated. Meanwhile, GO/KEGG pathway enrichment analyses and molecular network interaction analysis were performed. Lastly, immunohistochemistry and quantitative PCR (qPCR) were used to confirm the expression of IL6, LC3, and miRNA in ovarian endometrial tissues compared to control tissues. The results showed that IL-6 drives inflammation in conditions of PCOS and ovarian endometriosis, which then disrupts ovulation and embryo implantation. miR-146a-5p reduced inflammation by targeting the gene TRAF6, while miR-9-5p regulated protein degradation via SQSTM1. In agreement with the bioinformatic approach, experimental analysis revealed reduced IL6 protein expression in ovarian endometriosis tissues while the mRNA IL6 level was increased, suggesting the presence of post-transcriptional regulatory mechanisms that act to limit excessive inflammation, probably through miRNAs. Indeed, the levels of miR-146a-5, which plays a role in immune modulation and inflammatory signaling, were significantly upregulated. Interestingly, an alteration in autophagic markers revealed by elevated LC3 was also observed. Aligned with these experimental data, bioinformatic analysis showed that autophagy genes LC3 and ATG5 and ubiquitination processes were tightly linked to ovarian health, with disruptions accelerating follicle loss and oxidative damage. In conclusion, the results showed that IL-6, miRNAs, and autophagy processes work together to control inflammation and cellular repair in ovarian disorders. This study opens new avenues for targeted treatments to improve fertility outcomes by connecting molecular networks to clinical insights.", "claims": [{"id": "claim-method", "statement": "Raw expression data and metadata were extracted by using GEO2R [29,30]. Normalization and log2 conversion were carried out for each dataset to filter out the DEGs, which are displayed as volcano plots. The filtering conditions were as follows: |log2-fold change| ≥ 1 and adjusted p-value (adj. P) < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41227338", "locator": "sections[4] \"2.2. Analysis of Microarray Datasets\" paragraph 2", "quote": "Raw expression data and metadata were extracted by using GEO2R [29,30]. Normalization and log2 conversion were carried out for each dataset to filter out the DEGs, which are displayed as volcano plots. The filtering conditions were as follows: |log2-fold change| ≥ 1 and adjusted p-value (adj. 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P) < 0.05) after the deletion of duplicated genes, including 1148 upregulated and 1164 downregulated expression 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:41227338"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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Lastly, immunohistochemistry and quantitative PCR (qPCR) were used to con", "metriosis. Protein expression analysis using immunohistochemistry (IHC) revealed a paradoxical downregulation", "ression analysis using immunohistochemistry (IHC) revealed a paradoxical downregulation of IL", "restingly, protein expression analysis using IHC consistently showed a notable increase in LC"], "order_basis": "paper_text_order:1110", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [", immunohistochemistry and quantitative PCR (qPCR) were used to confirm the expression of IL6,", "crease in IL-6 mRNA revealed by quantitative real-time PCR (qRT-PCR) analysis was observed (Figure 14H)"], "order_basis": "paper_text_order:1153", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["according to the Human collection Biocarta, Apoptosis, and IL6 pathway gene sets category [25]. mi", "P7 were tied to hypoxia and ovarian follicle apoptosis. The MSigDB pathway analysis confirmed IL6 a"], "order_basis": "paper_text_order:4517", "id": "assay:3"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["is illustrated in Figure 1. 2.2. Analysis of Microarray Datasets Based on PCOS’s role in female infe"], "order_basis": "paper_text_order:5166", "id": "assay:4"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["pathway enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}