Screening and identification of potential hub genes and immune cell infiltration in the synovial tissue of rheumatoid arthritis by bioinformatic approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36699262", "kind": "science-record", "revision": 4, "content_hash": "sha256:3d5cbac4212f16056f398f68bf274af45b9edcb8ec2097b9f0c33bb015c07082", "created_at": "2026-11-01T19:01:15Z", "updated_at": "2026-11-01T22:51:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and identification of potential hub genes and immune cell infiltration in the synovial tissue of rheumatoid arthritis by bioinformatic approach.", "doi": "10.1016/j.heliyon.2023.e12799", "pmid": "36699262", "authors": ["Zhi-Wei Feng", "Yu-Chen Tang", "Xiao-Yun Sheng", "Sheng-Hong Wang", "Yao-Bin Wang", "Zhong-Cheng Liu", "Jin-Min Liu", "Bin Geng", "Ya-Yi Xia"], "journal": "Heliyon", "year": 2023, "abstract": "Background: Rheumatoid arthritis (RA) is an autoimmune disease that affects individuals of all ages. The basic pathological manifestations are synovial inflammation, pannus formation, and erosion of articular cartilage, bone destruction will eventually lead to joint deformities and loss of function. However, the specific molecular mechanisms of synovitis tissue in RA are still unclear. Therefore, this study aimed to screen and explore the potential hub genes and immune cell infiltration in RA.\nMethods: Three microarray datasets (GSE12021, GSE55457, and GSE55235), from the Gene Expression Omnibus (GEO) database, have been analyzed to explore the potential hub genes and immune cell infiltration in RA. First, the LIMMA package was used to screen the differentially expression genes (DEGs) after removing the batch effect. Then the clusterProfiler package was used to perform functional enrichment analyses. Second, through weighted coexpression network analysis (WGCNA), the key module was identified in the coexpression network of the gene set. Third, the protein-protein interaction (PPI) network was constructed through STRING website and the module analysis was performed using Cytoscape software. Fourth, the CIBERSORT and ssGSEA algorithm were used to analyze the immune status of RA and healthy synovial tissue, and the associations between immune cell infiltration and RA-related diagnostic biomarkers were evaluated. Fifth, we used the quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to validate the expression levels of the hub genes, and ROC curve analysis of hub genes for discriminating between RA and healthy tissue. Finally, the gene-drug interaction network was constructed using DrugCentral database, and identification of drug molecules based on hub genes using the Drug Signature Database (DSigDB) by Enrichr.\nResults: A total of 679 DEGs were identified, containing 270 downregulated genes and 409 upregulated genes. DEGs were primarily enriched in immune response and chemokine signaling pathways, according to functional enrichment analysis of DEGs. WGCNA explored the co-expression network of the gene set and identified key modules, the blue module was selected as the key module associated with RA. Seven hub genes are identified when PPI network and WGCNA core modules are intersected. Immune infiltration analysis using CIBERSORT and ssGSEA algorithms revealed that multiple types of immune infiltration were found to be upregulated in RA tissue compared to normal tissue. Furthermore, the levels of 7 hub genes were closely related to the relative proportions of multiple immune cells in RA. The results of the qRT-PCR demonstrated that the relative expression levels of 6 hub genes (CD27, LCK, CD2, GZMB, IL7R, and IL2RG) were up-regulated in RA synovial tissue, compared with normal tissue. Simultaneously, ROC curves indicated that the above 6 hub genes had strong biomarker potential for RA (AUC >0.8).\nConclusions: Through bioinformatics analysis and qRT-PCR experiment, our study ultimately discovered 6 hub genes (CD27, LCK, CD2, GZMB, IL7R, and IL2RG) that closely related to RA. These findings may provide valuable direction for future RA clinical diagnosis, treatment, and associated research.", "claims": [{"id": "claim-method", "statement": "Limma package [12] (version: 3.5) of R software (version: 4.1.2) was utilized to identify the DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36699262", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "Limma package [12] (version: 3.5) of R software (version: 4.1.2) was utilized to identify the DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and analyzed during the current study are available from NCBI GEO: GSE12021, GSE55235 and GSE55457. The following datasets from NCBI GEO were used in this work and were analyzed: GSE12021, GSE55235, and GSE55457. The Supplementary Files contain the code.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36699262", "locator": "sections[33] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and analyzed during the current study are available from NCBI GEO: GSE12021, GSE55235 and GSE55457. The following datasets from NCBI GEO were used in this work and were analyzed: GSE12021, GSE55235, and GSE55457. The Supplementary Files contain the code."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 679 DEGs were identified, containing 270 downregulated genes and 409 upregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36699262", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 679 DEGs were identified, containing 270 downregulated genes and 409 upregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 679 DEGs were identified, containing 270 downregulated genes and 409 upregulated 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:36699262"], "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:GSE12021"], "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:GSE12021"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36699262", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2023.e12799", "sha256": "sha256:2c0dd7ec5952de605c7a4dff193776d09e50d0a5d1dc7ad5cde86fd3fd332651", "bytes": 48588, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2023.e12799", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9868484", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12021", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12021", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12021", "version": null, "note": "The datasets used and analyzed during the current study are available from NCBI GEO: GSE12021, GSE55235 and GSE55457. The following datasets from NCBI GEO were used in this work and were analyzed: GSE12021, GSE55235, and GSE55457. The Supplementary Files contain the code.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analyzed during the current study are available from NCBI GEO: GSE12021, GSE55235 and GSE55457. The following datasets from NCBI GEO were used in this work and were analyzed: GSE12021, GSE55235, and GSE55457. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE12021", "GSE55457", "GSE55235"], "resolved_accessions": ["GSE12021", "GSE55457", "GSE55235"], "statements": ["The datasets used and analyzed during the current study are available from NCBI GEO: GSE12021, GSE55235 and GSE55457. The following datasets from NCBI GEO were used in this work and were analyzed: GSE12021, GSE55235, and GSE55457. The Supplementary Files contain the code."], "basis": "The paper names GSE12021, GSE55457, GSE55235 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36699262", "data:geo:GSE12021"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12021"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:24:33Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13880, "completion_tokens": 1459, "cached_tokens": 128}}, "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:36699262", "type": "paper", "label": "pmid:36699262"}, {"id": "source:pmid:36699262", "type": "manuscript", "label": "PMID 36699262 full text"}, {"id": "data:geo:GSE12021", "type": "dataset", "label": "GEO GSE12021"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36699262", "type": "paper", "label": "pmid:36699262"}, {"id": "source:pmid:36699262", "type": "manuscript", "label": "PMID 36699262 full text"}, {"id": "data:geo:GSE12021", "type": "dataset", "label": "GEO GSE12021"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36699262", "type": "extraction", "used": ["source:pmid:36699262"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12021", "type": "accession_resolution", "used": ["data:geo:GSE12021"], "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:36699262", "parent_hash": "sha256:f2fd9b9aedc75cdd2920e410a9b3124e6c812389320b44cd5bcf7e0af385446a", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE12021 licence not read", "asset:data:geo:GSE12021 not downloaded", "asset:data:geo:GSE55235 licence not read", "asset:data:geo:GSE55235 not downloaded", "asset:data:geo:GSE55457 licence not read", "asset:data:geo:GSE55457 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["mune cell infiltration in RA. Methods: Three microarray datasets (GSE12021, GSE55457, and GSE55235),", "thods Data processing and technology roadmap Microarray datasets of RA were downloaded from the GEO", "e probe with GPL96 platform genes to perform microarray annotation, when a probe corresponds to mult", "version 5.30) according to GPL96 platform of Affymetrix Human Genome U133A Array, matched the probe"], "order_basis": "paper_text_order:624", "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": 0.93, "evidence": [". PCR amplification was performed by a CFX96 real-time PCR instrument (BIO-RAD, USA) with SYBR Premix ("], "order_basis": "paper_text_order:6730", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Limma package [12] (version: 3.5) of R software (version: 4.1.2) was utilized to identify the DEGs."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}