Integrated gene expression analysis identifies shared inflammatory and metabolic pathways in polycystic ovarian syndrome, rheumatoid arthritis, and osteoarthritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41613858", "kind": "science-record", "revision": 4, "content_hash": "sha256:2e9c5b8c38551749ff4955837fd71a95362dda3f4a38ea79084ecec240515e8f", "created_at": "2026-11-01T20:31:43Z", "updated_at": "2026-11-01T22:57:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated gene expression analysis identifies shared inflammatory and metabolic pathways in polycystic ovarian syndrome, rheumatoid arthritis, and osteoarthritis.", "doi": "10.5114/bta/214378", "pmid": "41613858", "authors": ["Sri Chandana Mavulati", "Sujatha Dodoala"], "journal": "Biotechnologia", "year": 2025, "abstract": "Background: Polycystic ovary syndrome (PCOS) affects millions of women worldwide and is primarily known for its reproductive and hormonal symptoms. However, growing evidence suggests a strong link between PCOS and inflammation. Rheumatoid arthritis (RA) and osteoarthritis (OA) similarly involve systemic inflammation and immune dysregulation. Despite their distinct clinical manifestations, these disorders may share overlapping biological pathways. This study aimed to identify shared transcriptomic signatures between PCOS and autoimmune joint diseases such as RA and OA.\nMaterials and methods: RNA sequencing datasets were downloaded from the publicly available Gene Expression Omnibus (GEO) database. After processing and quality filtering, a total of 73 samples from the GSE277906 and GSE89408 datasets were selected. DEG analysis was conducted using the DE-Seq2 package in RStudio by adjusting for a significant p-value < 0.1 and |log2 fold change| > 0.5. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine functional enrichment of genes and common pathways associated with the diseases.\nResults: A total of 10,492 and 9,892 DEGs were identified in PCOS vs. RA and PCOS vs. OA, respectively. Key genes dysregulated among the diseases included TOMM34, DHCR24, CMAS, RBP1, and HSD3B2, and the enrichment analysis revealed overlapping pathways involving immune regulation, mitochondrial dysfunction, oxidative stress, and proteasome activity. Notably, 201 GO pathways were shared by PCOS and OA, 123 by RA and OA, and 267 by PCOS and RA. All three conditions shared a set of 57 GO pathways, including mitophagy and ER stress.\nConclusion: The identified common pathways signify the overlap between PCOS, RA, and OA. These findings support the hypothesis of systemic immunometabolic involvement in PCOS.", "claims": [{"id": "claim-method", "statement": "The analysis included normalization through estimation of size factors, dispersion estimation, fitting of the negative binomial generalized linear model, and application of the Wald test for final hypothesis testing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41613858", "locator": "sections[4] \"Identification of common genes of PCOS and arthritis\" paragraph 2", "quote": "The analysis included normalization through estimation of size factors, dispersion estimation, fitting of the negative binomial generalized linear model, and application of the Wald test for final hypothesis testing."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE277906 comprises mRNA-sequencing (RNA-seq) expression data of cumulus cells from 22 PCOS and 17 healthy control samples (Chen et al. 2024).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41613858", "locator": "sections[3] \"Data collection and processing\" paragraph 2", "quote": "GSE277906 comprises mRNA-sequencing (RNA-seq) expression data of cumulus cells from 22 PCOS and 17 healthy control samples (Chen et al. 2024)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 10,492 DEGs in PCOS vs. RA and 9,892 DEGs in PCOS vs. OA.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41613858", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 10,492 and 9,892 DEGs were identified in PCOS vs. RA and PCOS vs. OA, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 10,492 DEGs in PCOS vs. RA and 9,892 DEGs in PCOS vs. OA.", "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:41613858"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE277906"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE277906"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41613858", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.5114/bta/214378", "sha256": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:41613858", "data:geo:GSE277906"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE277906"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:11:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 9091, "completion_tokens": 1532, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:41613858", "type": "paper", "label": "pmid:41613858"}, {"id": "source:pmid:41613858", "type": "manuscript", "label": "PMID 41613858 full text"}, {"id": "data:geo:GSE277906", "type": "dataset", "label": "GEO GSE277906"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41613858", "type": "paper", "label": "pmid:41613858"}, {"id": "source:pmid:41613858", "type": "manuscript", "label": "PMID 41613858 full text"}, {"id": "data:geo:GSE277906", "type": "dataset", "label": "GEO GSE277906"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41613858", "type": "extraction", "used": ["source:pmid:41613858"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE277906", "type": "accession_resolution", "used": ["data:geo:GSE277906"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41613858", "parent_hash": "sha256:fca8e6719ea727a1f99eb47a469e3233a3078f347b3eb7e857a864a30211e8c4", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE277906 licence not read", "asset:data:geo:GSE277906 not downloaded", "asset:data:geo:GSE89408 licence not read", "asset:data:geo:GSE89408 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["es such as RA and OA. 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