LAMP5, One of Four Genes Related to Oxidative Stress That Predict Biochemical Recurrence-Free Survival, Promotes Proliferation and Invasion in Prostate Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39634037", "kind": "science-record", "revision": 3, "content_hash": "sha256:c1338506d5f86ef6767c67af1d9e22a7a7ad7acc3547c7fc35902c38bcc27ae0", "created_at": "2026-11-01T20:29:54Z", "updated_at": "2026-11-01T22:13:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "LAMP5, One of Four Genes Related to Oxidative Stress That Predict Biochemical Recurrence-Free Survival, Promotes Proliferation and Invasion in Prostate Cancer.", "doi": "10.2147/AABC.S489131", "pmid": "39634037", "authors": ["Peiqiang Wu", "Jianlei Zhang", "Li Guo", "Bohong Chen", "Lingxiao Xiong", "Yuefeng Du"], "journal": "Advances and applications in bioinformatics and chemistry : AABC", "year": 2024, "abstract": "Background: Prostate cancer (PCa) development largely depends on increased levels of oxidative stress (OS) and a deficient anti-oxidative system. Identifying genes associated with oxidative stress is critical in order to direct PCa therapy and future research.\nMethods: The TCGA and GTEx databases provided the bulk RNA-seq data, and the GEO database provided the single-cell data GSE141445. Utilizing reactive oxygen species (ROS) markers, single-cell analysis and cluster identification related to oxidative stress were conducted using the R packages \"Seurat\" and \"AUCell\". The differentially expressed genes (DEGs) in normal and PCa samples were identified with the \"limma\" R package. LASSO regression analysis was used to build a recurrence score (RS) model. The R packages \"maftools\" and the CIBERSORT method were employed to explore genetic mutation and the infiltrating immune cell, respectively. LAMP5 was chosen for further investigation after random forest analysis was performed.\nResults: The RS model for PCa was found to be an independent predictor. The tumor immune microenvironment and the frequency of gene mutations differed significantly between the high- and low-risk score groups. Further investigation revealed that downregulation of LAMP5 in PC-3 and DU145 cell lines suppressed cell proliferation and invasion, as demonstrated by the results of in vitro experiments.\nConclusion: We successfully created a robust RS model. The result of the study indicates that LAMP5 could contribute to cell proliferation and invasion in PCa.", "claims": [{"id": "claim-method", "statement": "LASSO regression analysis was used to build a recurrence score (RS) model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39634037", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "LASSO regression analysis was used to build a recurrence score (RS) model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Any interested party could obtain access to the datasets used in this work by contacting the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39634037", "locator": "sections[34] \"Data Sharing Statement\" paragraph 2", "quote": "Any interested party could obtain access to the datasets used in this work by contacting the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The RS model for PCa was found to be an independent predictor.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39634037", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The RS model for PCa was found to be an independent predictor."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The RS model for PCa was found to be an independent predictor.", "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:39634037"], "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:GSE141445"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE141445"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39634037", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/AABC.S489131", "sha256": "sha256:1d051ada7433abb3d3dc603bf1ac6c8c32be6aa7a6b56621aefceb6d7004e1b4", "bytes": 49655, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/AABC.S489131", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11616484", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE141445", "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=GSE141445", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE141445", "version": null, "note": "Any interested party could obtain access to the datasets used in this work by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Any interested party could obtain access to the datasets used in this work by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4203181"], "sample_count": 1, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single cell analysis reveals onset of multiple progression associated transcriptomic remodellings in prostate cancer", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE46602", "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=GSE46602", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46602", "version": null, "note": "Any interested party could obtain access to the datasets used in this work by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Any interested party could obtain access to the datasets used in this work by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1133136", "GSM1133137", "GSM1133138", "GSM1133139", "GSM1133140", "GSM1133141", "GSM1133142", "GSM1133143", "GSM1133144", "GSM1133145", "GSM1133146", "GSM1133147", "GSM1133148", "GSM1133149", "GSM1133150", "GSM1133151", "GSM1133152", "GSM1133153", "GSM1133154", "GSM1133155", "GSM1133156", "GSM1133157", "GSM1133158", "GSM1133159", "GSM1133160", "GSM1133161", "GSM1133162", "GSM1133163", "GSM1133164", "GSM1133165", "GSM1133166", "GSM1133167", "GSM1133168", "GSM1133169", "GSM1133170", "GSM1133171", "GSM1133172", "GSM1133173", "GSM1133174", "GSM1133175", "GSM1133176", "GSM1133177", "GSM1133178", "GSM1133179", "GSM1133180", "GSM1133181", "GSM1133182", "GSM1133183", "GSM1133184", "GSM1133185"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from prostate cancer and benign prostate glands", "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:GSE70768", "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=GSE70768", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70768", "version": null, "note": "Any interested party could obtain access to the datasets used in this work by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Any interested party could obtain access to the datasets used in this work by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1817707", "GSM1817708", "GSM1817709", "GSM1817710", "GSM1817711", "GSM1817712", "GSM1817713", "GSM1817714", "GSM1817715", "GSM1817716", "GSM1817717", "GSM1817718", "GSM1817719", "GSM1817720", "GSM1817721", "GSM1817722", "GSM1817723", "GSM1817724", "GSM1817725", "GSM1817726", "GSM1817727", "GSM1817728", "GSM1817729", "GSM1817730", "GSM1817731", "GSM1817732", "GSM1817733", "GSM1817734", "GSM1817735", "GSM1817736", "GSM1817737", "GSM1817738", "GSM1817739", "GSM1817740", "GSM1817741", "GSM1817742", "GSM1817743", "GSM1817744", "GSM1817745", "GSM1817746", "GSM1817747", "GSM1817748", "GSM1817749", "GSM1817750", "GSM1817751", "GSM1817752", "GSM1817753", "GSM1817754", "GSM1817755", "GSM1817756", "GSM1817757", "GSM1817758", "GSM1817759", "GSM1817760", "GSM1817761", "GSM1817762", "GSM1817763", "GSM1817764", "GSM1817765", "GSM1817766", "GSM1817767", "GSM1817768", "GSM1817769", "GSM1817770", "GSM1817771", "GSM1817772", "GSM1817773", "GSM1817774", "GSM1817775", "GSM1817776", "GSM1817777", "GSM1817778", "GSM1817779", "GSM1817780", "GSM1817781", "GSM1817782", "GSM1817783", "GSM1817784", "GSM1817785", "GSM1817786", "GSM1817787", "GSM1817788", "GSM1817789", "GSM1817790", "GSM1817791", "GSM1817792", "GSM1817793", "GSM1817794", "GSM1817795", "GSM1817796", "GSM1817797", "GSM1817798", "GSM1817799", "GSM1817800", "GSM1817801", "GSM1817802", "GSM1817803", "GSM1817804", "GSM1817805", "GSM1817806", "GSM1817807", "GSM1817808", "GSM1817809", "GSM1817810", "GSM1817811", "GSM1817812", "GSM1817813", "GSM1817814", "GSM1817815", "GSM1817816", "GSM1817817", "GSM1817818", "GSM1817819", "GSM1817820", "GSM1817821", "GSM1817822", "GSM1817823", "GSM1817824", "GSM1817825", "GSM1817826", "GSM1817827", "GSM1817828", "GSM1817829", "GSM1817830", "GSM1817831", "GSM1817832", "GSM1817833", "GSM1817834", "GSM1817835", "GSM1817836", "GSM1817837", "GSM1817838", "GSM1817839", "GSM1817840", "GSM1817841", "GSM1817842", "GSM1817843", "GSM1817844", "GSM1817845", "GSM1817846", "GSM1817847", "GSM1817848", "GSM1817849", "GSM1817850", "GSM1817851", "GSM1817852", "GSM1817853", "GSM1817854", "GSM1817855", "GSM1817856", "GSM1817857", "GSM1817858", "GSM1817859", "GSM1817860", "GSM1817861", "GSM1817862", "GSM1817863", "GSM1817864", "GSM1817865", "GSM1817866", "GSM1817867", "GSM1817868", "GSM1817869", "GSM1817870", "GSM1817871", "GSM1817872", "GSM1817873", "GSM1817874", "GSM1817875", "GSM1817876", "GSM1817877", "GSM1817878", "GSM1817879", "GSM1817880", "GSM1817881", "GSM1817882", "GSM1817883", "GSM1817884", "GSM1817885", "GSM1817886", "GSM1817887", "GSM1817888", "GSM1817889", "GSM1817890", "GSM1817891", "GSM1817892", "GSM1817893", "GSM1817894", "GSM1817895", "GSM1817896", "GSM1817897", "GSM1817898", "GSM1817899", "GSM1817900", "GSM1817901", "GSM1817902", "GSM1817903", "GSM1817904", "GSM1817905"], "sample_count": 199, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Prostate cancer stratification using molecular profiles [CamCap 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:GSE141445 not downloaded", "asset:data:geo:GSE141445 licence not read", "asset:data:geo:GSE46602 not downloaded", "asset:data:geo:GSE46602 licence not read", "asset:data:geo:GSE70768 not downloaded", "asset:data:geo:GSE70768 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-3", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-5", "family": null, "specific": null, "label": "LASSO regression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "LASSO regression analysis was used to build a recurrence score (RS) model."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE141445", "GSE46602", "GSE70768"], "resolved_accessions": ["GSE141445", "GSE46602", "GSE70768"], "statements": ["Any interested party could obtain access to the datasets used in this work by contacting the corresponding author."], "basis": "The paper names GSE141445, GSE46602, GSE70768 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:39634037", "data:geo:GSE141445"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE141445"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:40:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13998, "completion_tokens": 1969, "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:39634037", "type": "paper", "label": "pmid:39634037"}, {"id": "source:pmid:39634037", "type": "manuscript", "label": "PMID 39634037 full text"}, {"id": "data:geo:GSE141445", "type": "dataset", "label": "GEO GSE141445"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39634037", "type": "paper", "label": "pmid:39634037"}, {"id": "source:pmid:39634037", "type": "manuscript", "label": "PMID 39634037 full text"}, {"id": "data:geo:GSE141445", "type": "dataset", "label": "GEO GSE141445"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39634037", "type": "extraction", "used": ["source:pmid:39634037"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE141445", "type": "accession_resolution", "used": ["data:geo:GSE141445"], "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:39634037", "parent_hash": "sha256:ac8021b8504d4d1ac19465844be4952a793ab1019d8827c1d601451f1631790f", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE141445 licence not read", "asset:data:geo:GSE141445 not downloaded", "asset:data:geo:GSE46602 licence not read", "asset:data:geo:GSE46602 not downloaded", "asset:data:geo:GSE70768 licence not read", "asset:data:geo:GSE70768 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Materials and Methods Cell Culture and Transfection The RWPE-1, PC3, DU145, and LNCaP human pros", "and LNCaP. In subsequent tests, si-LAMP5 was transfected into PC3 and DU145, and the two lines were c", "ed to the control cells, PC3 and DU145 cells transfected with si-LAMP5 exhibited significantly bigger", "blot analysis verified the efficacy of LAMP5 knockdown; Original blots/gels are presented in Supple"], "order_basis": "paper_text_order:1710", "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": 0.99, "evidence": ["through the loss of function experiment. The RT-qPCR showed the levels of LAMP5 expression in the", "pression in both lines were quantified using RT-qPCR and Western blotting techniques (Figure 9B a", "Experimental Validation of LAMP5 in PCa. (A) RT-qPCR of LAMP5 expression in PCa cell lines. (B an", "AMP5 expression in PCa cell lines. (B and C) RT-qPCR and Western blot analysis verified the effic"], "order_basis": "paper_text_order:3542", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["both lines were quantified using RT-qPCR and Western blotting techniques (Figure 9B and C). The original W", "g techniques (Figure 9B and C). The original Western blot is shown in Supplementary Figure 5. The CCK-", "ion in PCa cell lines. (B and C) RT-qPCR and Western blot analysis verified the efficacy of LAMP5 knoc"], "order_basis": "paper_text_order:4003", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["blot is shown in Supplementary Figure 5. The CCK-8 assay showed that when LAMP5 was downregulat", "are presented in Supplementary Figure 5. (D) CCK-8 assay detected the proliferative activity of"], "order_basis": "paper_text_order:4116", "id": "assay:4"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}