Prognostic value of tripartite motif (TRIM) family gene signature from bronchoalveolar lavage cells in idiopathic pulmonary fibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36474231", "kind": "science-record", "revision": 2, "content_hash": "sha256:aa269528db14b2bd78337159dc2c1fabdf5f46d1a9a58df2159cdd0787d3f4f0", "created_at": "2026-11-01T19:00:57Z", "updated_at": "2026-11-01T21:29:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic value of tripartite motif (TRIM) family gene signature from bronchoalveolar lavage cells in idiopathic pulmonary fibrosis.", "doi": "10.1186/s12890-022-02269-4", "pmid": "36474231", "authors": ["Mi Zhou", "Jie Ouyang", "Guoqing Zhang", "Xin Zhu"], "journal": "BMC pulmonary medicine", "year": 2022, "abstract": "BACKGROUND: Tripartite motif (TRIM) family genes get involved in the pathogenesis and development of various biological processes; however, the prognostic value of TRIM genes for idiopathic pulmonary fibrosis (IPF) needs to be explored.\nMETHODS: We acquired gene expression based on bronchoalveolar lavage (BAL) cells and clinical data of three independent IPF cohorts in the GSE70866 dataset from the Gene expression omnibus (GEO) database. Differentially expressed TRIM genes (DETGs) between IPF patients and healthy donors were identified and used to establish a risk signature by univariate and multivariate Cox regression analysis in the training cohort. The risk signature was further validated in other IPF cohorts, and compared with previously published signatures. Moreover, we performed functional enrichment analysis to explore the potential mechanisms. Eventually, the quantitative real time PCR was conducted to validate the expressions of the key genes in BAL from 12 IPF patients and 12 non-IPF controls from our institution.\nRESULTS: We identified 4 DETGs including TRIM7, MEFV, TRIM45 and TRIM47 significantly associated with overall survival (OS) of IPF patients (P < 0.05). A multiple stepwise Cox regression analysis was performed to construct a 4-TRIM-gene prognostic signature. We categorized IPF patients into one low-risk group and the other high-risk group as per the average risk value of the TRIM prognostic signature in the training and validation cohorts. The IPF individuals in the low-risk group demonstrated an obvious OS advantage compared with the high-risk one (P < 0.01). The time-dependent receiver operating characteristic approach facilitated the verification of the predictive value of the TRIM prognostic signature in the training and validation cohorts, compared with other published signatures. A further investigation of immune cells and IPF survival displayed that higher proportion of resting memory CD4+ T cells and resting mast cells harbored OS advantage over lower proportion, however lower proportion of neutrophils, activated dendritic cells and activated NK cells indicated worse prognosis.\nCONCLUSION: The TRIM family genes are significant for the prognosis of IPF and our signature could serve as a robust model to predict OS.", "claims": [{"id": "claim-method", "statement": "Differentially expressed TRIM genes (DETGs) between IPF patients and healthy donors were identified and used to establish a risk signature by univariate and multivariate Cox regression analysis in the training cohort.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36474231", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed TRIM genes (DETGs) between IPF patients and healthy donors were identified and used to establish a risk signature by univariate and multivariate Cox regression analysis in the training cohort."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The Data used in the current study was obtained from publicly available repository. The datasets generated or analyzed during the current study are available in the GEO database (GSE70866) repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36474231", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The Data used in the current study was obtained from publicly available repository. The datasets generated or analyzed during the current study are available in the GEO database (GSE70866) repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper established a four-TRIM-gene prognostic signature for overall survival in IPF using univariate and multivariate Cox regression analysis of BAL-cell gene expression from three independent IPF cohorts in GSE70866.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36474231", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We acquired gene expression based on bronchoalveolar lavage (BAL) cells and clinical data of three independent IPF cohorts in the GSE70866 dataset from the Gene expression omnibus (GEO) database."}, {"asset": "source:pmid:36474231", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed TRIM genes (DETGs) between IPF patients and healthy donors were identified and used to establish a risk signature by univariate and multivariate Cox regression analysis in the training cohort."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper established a four-TRIM-gene prognostic signature for overall survival in IPF using univariate and multivariate Cox regression analysis of BAL-cell gene expression from three independent IPF cohorts in GSE70866.", "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:36474231"], "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:GSE70866"], "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:GSE70866"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36474231", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12890-022-02269-4", "sha256": "sha256:944be18b46878a48eaaad534829f27670d359fe6d23aa820d0d9998f463cf9a7", "bytes": 36363, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12890-022-02269-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9724366", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE70866", "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=GSE70866", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70866", "version": null, "note": "The Data used in the current study was obtained from publicly available repository. The datasets generated or analyzed during the current study are available in the GEO database (GSE70866) repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Data used in the current study was obtained from publicly available repository. The datasets generated or analyzed during the current study are available in the GEO database (GSE70866) repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1820719", "GSM1820720", "GSM1820721", "GSM1820722", "GSM1820723", "GSM1820724", "GSM1820725", "GSM1820726", "GSM1820727", "GSM1820728", "GSM1820729", "GSM1820730", "GSM1820731", "GSM1820732", "GSM1820733", "GSM1820734", "GSM1820735", "GSM1820736", "GSM1820737", "GSM1820738", "GSM1820739", "GSM1820740", "GSM1820741", "GSM1820742", "GSM1820743", "GSM1820744", "GSM1820745", "GSM1820746", "GSM1820747", "GSM1820748", "GSM1820749", "GSM1820750", "GSM1820751", "GSM1820752", "GSM1820753", "GSM1820754", "GSM1820755", "GSM1820756", "GSM1820757", "GSM1820758", "GSM1820759", "GSM1820760", "GSM1820761", "GSM1820762", "GSM1820763", "GSM1820764", "GSM1820765", "GSM1820766", "GSM1820767", "GSM1820768", "GSM1820769", "GSM1820770", "GSM1820771", "GSM1820772", "GSM1820773", "GSM1820774", "GSM1820775", "GSM1820776", "GSM1820777", "GSM1820778", "GSM1820779", "GSM1820780", "GSM1820781", "GSM1820782", "GSM1820783", "GSM1820784", "GSM1820785", "GSM1820786", "GSM1820787", "GSM1820788", "GSM1820789", "GSM1820790", "GSM1820791", "GSM1820792", "GSM1820793", "GSM1820794", "GSM1820795", "GSM1820796", "GSM1820797", "GSM1820798", "GSM1820799", "GSM1820800", "GSM1820801", "GSM1820802", "GSM1820803", "GSM1820804", "GSM1820805", "GSM1820806", "GSM1820807", "GSM1820808", "GSM1820809", "GSM1820810", "GSM1820811", "GSM1820812", "GSM1820813", "GSM1820814", "GSM1820815", "GSM1820816", "GSM1820817", "GSM1820818", "GSM1820819", "GSM1820820", "GSM1820821", "GSM1820822", "GSM1820823", "GSM1820824", "GSM1820825", "GSM1820826", "GSM1820827", "GSM1820828", "GSM1820829", "GSM1820830", "GSM1820831", "GSM1820832", "GSM1820833", "GSM1820834", "GSM1820835", "GSM1820836", "GSM1820837", "GSM1820838", "GSM1820839", "GSM1820840", "GSM1820841", "GSM1820842", "GSM1820843", "GSM1820844", "GSM1820845", "GSM1820846", "GSM1820847", "GSM1820848", "GSM1820849", "GSM1820850", "GSM1820851", "GSM1820852", "GSM1820853", "GSM1820854", "GSM1820855", "GSM1820856", "GSM1820857", "GSM1820858", "GSM1820859", "GSM1820860", "GSM1820861", "GSM1820862", "GSM1820863", "GSM1820864", "GSM1820865", "GSM1820866", "GSM1820867", "GSM1820868", "GSM1820869", "GSM1820870", "GSM1820871", "GSM1820872", "GSM1820873", "GSM1820874", "GSM1820875", "GSM1820876", "GSM1820877", "GSM1820878", "GSM1820879", "GSM1820880", "GSM1820881", "GSM1820882", "GSM1820883", "GSM1820884", "GSM1820885", "GSM1820886", "GSM1820887", "GSM1820888", "GSM1820889", "GSM1820890", "GSM1820891", "GSM1820892", "GSM1820893", "GSM1820894", "GSM1820895", "GSM1820896", "GSM1820897", "GSM1820898", "GSM1820899", "GSM1820900", "GSM1820901", "GSM1820902", "GSM1820903", "GSM1820904", "GSM1820905", "GSM1820906", "GSM1820907", "GSM1820908", "GSM1820909", "GSM1820910", "GSM1820911", "GSM1820912", "GSM1820913", "GSM1820914"], "sample_count": 196, "group_sizes": null, "group_sizes_basis": null, "platform": "17077;14550", "taxon": "Homo sapiens", "title": "BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (II)", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE70866 not downloaded", "asset:data:geo:GSE70866 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed TRIM genes (DETGs) between IPF patients and healthy donors were identified and used to establish a risk signature by univariate and multivariate Cox regression analysis in the training cohort."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE70866"], "resolved_accessions": ["GSE70866"], "statements": ["The Data used in the current study was obtained from publicly available repository. The datasets generated or analyzed during the current study are available in the GEO database (GSE70866) repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866."], "basis": "The paper names GSE70866 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": ["cox_ph"], "assets": ["source:pmid:36474231", "data:geo:GSE70866"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE70866"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:18:50Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11273, "completion_tokens": 1582, "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:36474231", "type": "paper", "label": "pmid:36474231"}, {"id": "source:pmid:36474231", "type": "manuscript", "label": "PMID 36474231 full text"}, {"id": "data:geo:GSE70866", "type": "dataset", "label": "GEO GSE70866"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36474231", "type": "paper", "label": "pmid:36474231"}, {"id": "source:pmid:36474231", "type": "manuscript", "label": "PMID 36474231 full text"}, {"id": "data:geo:GSE70866", "type": "dataset", "label": "GEO GSE70866"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36474231", "type": "extraction", "used": ["source:pmid:36474231"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE70866", "type": "accession_resolution", "used": ["data:geo:GSE70866"], "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:36474231", "parent_hash": "sha256:a426245537afb438af2f6f7dc290a3c2a74d8f9a73c0be5f90994fff5203c8eb", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE70866 licence not read", "asset:data:geo:GSE70866 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed TRIM genes (DETGs) between IPF patients and healthy donors were identified and used to establish a risk signature by univariate and multivariate Cox regression analysis in the training cohort."], "order_basis": "analysis_only", "id": "assay:1"}]}