Exploring the molecular mechanisms and shared gene signatures between rheumatoid arthritis and diffuse large B cell lymphoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36389761", "kind": "science-record", "revision": 2, "content_hash": "sha256:2a1115a561584c183d57079e27119e435b33199f592f5555115e2c0fb8cf633f", "created_at": "2026-11-01T19:00:51Z", "updated_at": "2026-11-01T21:29:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the molecular mechanisms and shared gene signatures between rheumatoid arthritis and diffuse large B cell lymphoma.", "doi": "10.3389/fimmu.2022.1036239", "pmid": "36389761", "authors": ["Haoguang Li", "Le Yu", "Xiuling Zhang", "Jingjing Shang", "Xinwang Duan"], "journal": "Frontiers in immunology", "year": 2022, "abstract": "The relationship between rheumatoid arthritis (RA) and diffuse large B-cell lymphoma (DLBCL) is well characterized, but the molecular mechanisms underlying this association have not been clearly investigated. Our study aimed to identify shared gene signatures and molecular mechanisms between RA and DLBCL. We selected multiple Gene Expression Omnibus (GEO) datasets (GSE93272, GSE83632, GSE12453, GSE1919) to obtain gene expression levels and clinical information about patients with RA and DLBCL. Weighted gene co-expression network analysis (WGCNA) was used to research co-expression networks associated with RA and DLBCL. Subsequently, we performed enrichment analysis of shared genes and screened the most significant core genes. We observed expression of the screened target gene, galectin 2 (LGALS2), in DLBCL patients and its impact on patient prognosis. Finally, we analyzed the molecular functional mechanism of LGALS2 and observed its relationship with the immune response in DLBCL using single-sample Gene Set Enrichment Analysis (ssGSEA). WGCNA recognized two major modules for RA and DLBCL, respectively. Shared genes (551) were identified for RA and DLBCL by observing the intersection. In addition, a critical shared gene, LGALS2, was acquired in the validation tests. Next, we found that the expression level of LGALS2 gradually decreased with tumor progression in DLBCL and that increased expression of LGALS2 predicted a better prognosis for DLBCL patients. ssGSEA revealed that LGALS2 is involved in immune-related pathways and has a significant regulatory effect on human immune responses. Additionally, we observed that LGALS2 is closely related to the sensitivity of multiple chemotherapeutic drugs. There is extremely little research on the molecular mechanism of correlation between RA and DLBCL. Our study identified that LGALS2 is a potential therapeutic target and an immune-related biomarker for patients with RA and DLBCL.", "claims": [{"id": "claim-method", "statement": "Weighted gene co-expression network analysis (WGCNA) was used to research co-expression networks associated with RA and DLBCL.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36389761", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Weighted gene co-expression network analysis (WGCNA) was used to research co-expression networks associated with RA and DLBCL."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36389761", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our study identified that LGALS2 is a potential therapeutic target and an immune-related biomarker for patients with RA and DLBCL.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36389761", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our study identified that LGALS2 is a potential therapeutic target and an immune-related biomarker for patients with RA and DLBCL."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our study identified that LGALS2 is a potential therapeutic target and an immune-related biomarker for patients with RA and DLBCL.", "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:36389761"], "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:GSE12453"], "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:GSE12453"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36389761", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2022.1036239", "sha256": "sha256:194ad0d6fb767942c392a0fceaccb03270bc10e007295977b9a05643f0d522f5", "bytes": 40962, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2022.1036239", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9659608", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12453", "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=GSE12453", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12453", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36389761", "data:geo:GSE12453"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12453"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:15:55Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12049, "completion_tokens": 2812, "cached_tokens": 256}}, "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:36389761", "type": "paper", "label": "pmid:36389761"}, {"id": "source:pmid:36389761", "type": "manuscript", "label": "PMID 36389761 full text"}, {"id": "data:geo:GSE12453", "type": "dataset", "label": "GEO GSE12453"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36389761", "type": "paper", "label": "pmid:36389761"}, {"id": "source:pmid:36389761", "type": "manuscript", "label": "PMID 36389761 full text"}, {"id": "data:geo:GSE12453", "type": "dataset", "label": "GEO GSE12453"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36389761", "type": "extraction", "used": ["source:pmid:36389761"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12453", "type": "accession_resolution", "used": ["data:geo:GSE12453"], "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:36389761", "parent_hash": "sha256:3a78fa95d7bf123053a95a272e4776bfa9257b00643646690ee4d1728c405a51", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE12453 licence not read", "asset:data:geo:GSE12453 not downloaded", "asset:data:geo:GSE1919 licence not read", "asset:data:geo:GSE1919 not downloaded", "asset:data:geo:GSE83632 licence not read", "asset:data:geo:GSE83632 not downloaded", "asset:data:geo:GSE93272 licence not read", "asset:data:geo:GSE93272 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}