The prognostic value and potential mechanism of Matrix Metalloproteinases among Prostate Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32669958", "kind": "science-record", "revision": 8, "content_hash": "sha256:9f997dbae61b4376c097c11dfeec51e2ac3b382b6f99231bf1c4979ac75fd836", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:01:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The prognostic value and potential mechanism of Matrix Metalloproteinases among Prostate Cancer.", "doi": "10.7150/ijms.46780", "pmid": "32669958", "authors": ["Xinyu Geng", "Chunyang Chen", "Yuhua Huang", "Jianquan Hou"], "journal": "International journal of medical sciences", "year": 2020, "abstract": "Background: Matrix Metalloproteinases (MMPs) play an indispensable role in the initial alteration and development of PCa. We tried to generate an MMP-related prognostic signature (MMPS) in prostate cancer (PCa). Methods: TCGA-PRAD, MSKCC/GSE21032, GSE116918, GSE70769 cohorts were enrolled to assess the prognostic value of MMPs. The least absolute shrinkage and selection operator (LASSO) Cox regression was employed to generate the MMPS signature. The log-rank test and Kaplan-Meier (K-M) survival curve were applied to show the difference RFS, The receiver operating characteristic (ROC) curve and area under the ROC curve (AUC) was plotted to predict the accuracy of signature. CIBERSORT was conducted to analyze the different immune infiltration in MMPS-H and MMPS-L groups. Potential signaling pathways activated in the MMPS-H groups by Metascape. Results: MMP1, MMP7, MMP11, MMP24 and MMP26 were selected by LASSO regression and established the MMPS predict signature. The MMPS showed the high prognostic value in TCGA-PRAD training cohort (AUC=0.714) and validation cohorts (GSE116918: AUC=0.976, GSE70769: AUC=0.738, MSKCC: AUC=0.793). Pid integrin1 pathway, G2M checkpoint, and response to growth factor signaling pathways were activated in MMPS-H group, patients with the high MMPS risk score and low M2 macrophage showed the worst recurrence-free survival (RFS). Conclusion: MMPs involved and played an essential role in the tumorigenesis and biochemical recurrence in PCa patients. The MMPS signature could accurately predict the recurrence of PCa patients and validated in several cohorts.", "claims": [{"id": "claim-method", "statement": "The least absolute shrinkage and selection operator (LASSO) Cox regression was employed to generate the MMPS signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32669958", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The least absolute shrinkage and selection operator (LASSO) Cox regression was employed to generate the MMPS signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In the current study, we concerned the TCGA-PRAD cohort with the RNA sequence data from the platform based on the Illumina system and clinical characteristics download from UCSC (https://gdc.xenahubs.net/download/TCGA-PRAD.htseq_fpkm.tsv.gz)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32669958", "locator": "sections[3] \"Data acquirement from enrolled cohorts\" paragraph 2", "quote": "In the current study, we concerned the TCGA-PRAD cohort with the RNA sequence data from the platform based on the Illumina system and clinical characteristics download from UCSC (https://gdc.xenahubs.net/download/TCGA-PRAD.htseq_fpkm.tsv.gz)"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32669958"], "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:GSE116918"], "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:GSE116918"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32669958", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/ijms.46780", "sha256": "sha256:69be84022f227cfd796153359a8445f92f76300b2cd9c56bb34a885b2b2a7a5a", "bytes": 22049, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/ijms.46780", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7359399", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116918", "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=GSE116918", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116918", "version": null, "note": "In the current study, we concerned the TCGA-PRAD cohort with the RNA sequence data from the platform based on the Illumina system and clinical characteristics download from UCSC (https://gdc.xenahubs.net/download/TCGA-PRAD.htseq_fpkm.tsv.gz)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In the current study, we concerned the TCGA-PRAD cohort with the RNA sequence data from the platform based on the Illumina system and clinical characteristics download from UCSC (https://gdc.xenahubs.net/download/TCGA-PRAD.htseq_fpkm.tsv.gz)", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3263664", "GSM3263665", "GSM3263666", "GSM3263667", "GSM3263668", "GSM3263669", "GSM3263670", "GSM3263671", "GSM3263672", "GSM3263673", "GSM3263674", "GSM3263675", "GSM3263676", "GSM3263677", "GSM3263678", "GSM3263679", "GSM3263680", "GSM3263681", "GSM3263682", "GSM3263683", "GSM3263684", "GSM3263685", "GSM3263686", "GSM3263687", "GSM3263688", "GSM3263689", "GSM3263690", "GSM3263691", "GSM3263692", "GSM3263693", "GSM3263694", "GSM3263695", "GSM3263696", "GSM3263697", "GSM3263698", "GSM3263699", "GSM3263700", "GSM3263701", "GSM3263702", "GSM3263703", "GSM3263704", "GSM3263705", "GSM3263706", "GSM3263707", "GSM3263708", "GSM3263709", "GSM3263710", "GSM3263711", "GSM3263712", "GSM3263713", "GSM3263714", "GSM3263715", "GSM3263716", "GSM3263717", "GSM3263718", "GSM3263719", "GSM3263720", "GSM3263721", "GSM3263722", "GSM3263723", "GSM3263724", "GSM3263725", "GSM3263726", "GSM3263727", "GSM3263728", "GSM3263729", "GSM3263730", "GSM3263731", "GSM3263732", "GSM3263733", "GSM3263734", "GSM3263735", "GSM3263736", "GSM3263737", "GSM3263738", "GSM3263739", "GSM3263740", "GSM3263741", "GSM3263742", "GSM3263743", "GSM3263744", "GSM3263745", "GSM3263746", "GSM3263747", "GSM3263748", "GSM3263749", "GSM3263750", "GSM3263751", "GSM3263752", "GSM3263753", "GSM3263754", "GSM3263755", "GSM3263756", "GSM3263757", "GSM3263758", "GSM3263759", "GSM3263760", "GSM3263761", "GSM3263762", "GSM3263763", "GSM3263764", "GSM3263765", "GSM3263766", "GSM3263767", "GSM3263768", "GSM3263769", "GSM3263770", "GSM3263771", "GSM3263772", "GSM3263773", "GSM3263774", "GSM3263775", "GSM3263776", "GSM3263777", "GSM3263778", "GSM3263779", "GSM3263780", "GSM3263781", "GSM3263782", "GSM3263783", "GSM3263784", "GSM3263785", "GSM3263786", "GSM3263787", "GSM3263788", "GSM3263789", "GSM3263790", "GSM3263791", "GSM3263792", "GSM3263793", "GSM3263794", "GSM3263795", "GSM3263796", "GSM3263797", "GSM3263798", "GSM3263799", "GSM3263800", "GSM3263801", "GSM3263802", "GSM3263803", "GSM3263804", "GSM3263805", "GSM3263806", "GSM3263807", "GSM3263808", "GSM3263809", "GSM3263810", "GSM3263811", "GSM3263812", "GSM3263813", "GSM3263814", "GSM3263815", "GSM3263816", "GSM3263817", "GSM3263818", "GSM3263819", "GSM3263820", "GSM3263821", "GSM3263822", "GSM3263823", "GSM3263824", "GSM3263825", "GSM3263826", "GSM3263827", "GSM3263828", "GSM3263829", "GSM3263830", "GSM3263831", "GSM3263832", "GSM3263833", "GSM3263834", "GSM3263835", "GSM3263836", "GSM3263837", "GSM3263838", "GSM3263839", "GSM3263840", "GSM3263841", "GSM3263842", "GSM3263843", "GSM3263844", "GSM3263845", "GSM3263846", "GSM3263847", "GSM3263848", "GSM3263849", "GSM3263850", "GSM3263851", "GSM3263852", "GSM3263853", "GSM3263854", "GSM3263855", "GSM3263856", "GSM3263857", "GSM3263858", "GSM3263859", "GSM3263860", "GSM3263861", "GSM3263862", "GSM3263863", "GSM3263864", "GSM3263865", "GSM3263866", "GSM3263867", "GSM3263868", "GSM3263869", "GSM3263870", "GSM3263871", "GSM3263872", "GSM3263873", "GSM3263874", "GSM3263875", "GSM3263876", "GSM3263877", "GSM3263878", "GSM3263879", "GSM3263880", "GSM3263881", "GSM3263882", "GSM3263883", "GSM3263884", "GSM3263885", "GSM3263886", "GSM3263887", "GSM3263888", "GSM3263889", "GSM3263890", "GSM3263891", "GSM3263892", "GSM3263893", "GSM3263894", "GSM3263895", "GSM3263896", "GSM3263897", "GSM3263898", "GSM3263899", "GSM3263900", "GSM3263901", "GSM3263902", "GSM3263903", "GSM3263904", "GSM3263905", "GSM3263906", "GSM3263907", "GSM3263908", "GSM3263909", "GSM3263910", "GSM3263911"], "sample_count": 248, "group_sizes": null, "group_sizes_basis": null, "platform": "25318", "taxon": "Homo sapiens", "title": "Using biopsies to improve risk stratification in patients with prostate cancer treated with radical radiation therapy", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE70769", "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=GSE70769", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70769", "version": null, "note": "In the current study, we concerned the TCGA-PRAD cohort with the RNA sequence data from the platform based on the Illumina system and clinical characteristics download from UCSC (https://gdc.xenahubs.net/download/TCGA-PRAD.htseq_fpkm.tsv.gz)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In the current study, we concerned the TCGA-PRAD cohort with the RNA sequence data from the platform based on the Illumina system and clinical characteristics download from UCSC (https://gdc.xenahubs.net/download/TCGA-PRAD.htseq_fpkm.tsv.gz)", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1817906", "GSM1817907", "GSM1817908", "GSM1817909", "GSM1817910", "GSM1817911", "GSM1817912", "GSM1817913", "GSM1817914", "GSM1817915", "GSM1817916", "GSM1817917", "GSM1817918", "GSM1817919", "GSM1817920", "GSM1817921", "GSM1817922", "GSM1817923", "GSM1817924", "GSM1817925", "GSM1817926", "GSM1817927", "GSM1817928", "GSM1817929", "GSM1817930", "GSM1817931", "GSM1817932", "GSM1817933", "GSM1817934", "GSM1817935", "GSM1817936", "GSM1817937", "GSM1817938", "GSM1817939", "GSM1817940", "GSM1817941", "GSM1817942", "GSM1817943", "GSM1817944", "GSM1817945", "GSM1817946", "GSM1817947", "GSM1817948", "GSM1817949", "GSM1817950", "GSM1817951", "GSM1817952", "GSM1817953", "GSM1817954", "GSM1817955", "GSM1817956", "GSM1817957", "GSM1817958", "GSM1817959", "GSM1817960", "GSM1817961", "GSM1817962", "GSM1817963", "GSM1817964", "GSM1817965", "GSM1817966", "GSM1817967", "GSM1817968", "GSM1817969", "GSM1817970", "GSM1817971", "GSM1817972", "GSM1817973", "GSM1817974", "GSM1817975", "GSM1817976", "GSM1817977", "GSM1817978", "GSM1817979", "GSM1817980", "GSM1817981", "GSM1817982", "GSM1817983", "GSM1817984", "GSM1817985", "GSM1817986", "GSM1817987", "GSM1817988", "GSM1817989", "GSM1817990", "GSM1817991", "GSM1817992", "GSM1817993", "GSM1817994", "GSM1817995", "GSM1817996", "GSM1817997", "GSM1817998", "GSM1817999"], "sample_count": 94, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Prostate cancer stratification using molecular profiles [Stockholm ExpressionArray]", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE116918 not downloaded", "asset:data:geo:GSE116918 licence not read", "asset:data:geo:GSE70769 not downloaded", "asset:data:geo:GSE70769 licence not read"]}, "analysis": {"state": "partial", "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": "The least absolute shrinkage and selection operator (LASSO) Cox regression was employed to generate the MMPS signature."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "log-rank"}}, {"id": "method-5", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-6", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["MSKCC/GSE21032", "GSE116918", "GSE70769"], "resolved_accessions": ["GSE116918", "GSE70769"], "statements": ["In the current study, we concerned the TCGA-PRAD cohort with the RNA sequence data from the platform based on the Illumina system and clinical characteristics download from UCSC (https://gdc.xenahubs.net/download/TCGA-PRAD.htseq_fpkm.tsv.gz)"], "basis": "The paper names GSE116918, GSE70769 in Gene Expression Omnibus (GEO) 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:32669958", "data:geo:GSE116918"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116918"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 18614, "completion_tokens": 2642, "cached_tokens": 792}}, "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:32669958", "type": "paper", "label": "pmid:32669958"}, {"id": "source:pmid:32669958", "type": "manuscript", "label": "PMID 32669958 full text"}, {"id": "data:geo:GSE116918", "type": "dataset", "label": "GEO GSE116918"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32669958", "type": "paper", "label": "pmid:32669958"}, {"id": "source:pmid:32669958", "type": "manuscript", "label": "PMID 32669958 full text"}, {"id": "data:geo:GSE116918", "type": "dataset", "label": "GEO GSE116918"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32669958", "type": "extraction", "used": ["source:pmid:32669958"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116918", "type": "accession_resolution", "used": ["data:geo:GSE116918"], "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:32669958", "parent_hash": "sha256:718727c6306979ae69119b81f4f0b21b71d9d7d7d80c750faeb98083f7aae013", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE116918 licence not read", "asset:data:geo:GSE116918 not downloaded", "asset:data:geo:GSE70769 licence not read", "asset:data:geo:GSE70769 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": ["The least absolute shrinkage and selection operator (LASSO) Cox regression was employed to generate the MMPS signature."], "order_basis": "analysis_only", "id": "assay:1"}]}