Identification of SLC31A1 as a prognostic biomarker and a target for therapeutics in breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39448672", "kind": "science-record", "revision": 3, "content_hash": "sha256:0aebe399fb13d1ea88cc0ce1b720d211d7b0584cd076b30372cf2c503fd300fb", "created_at": "2026-11-01T20:29:42Z", "updated_at": "2026-11-01T22:55:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of SLC31A1 as a prognostic biomarker and a target for therapeutics in breast cancer.", "doi": "10.1038/s41598-024-76162-x", "pmid": "39448672", "authors": ["Hongtao Fu", "Shanshan Dong", "Kun Li"], "journal": "Scientific reports", "year": 2024, "abstract": "Copper-induced cell death is regulated through protein lipoylation, which is critical for gene expression and phenotypic regulation. Neverless, the role of Cuproptosis-related genes in breast cancer (BC) remains unknown. This study aimed to construct a prognostic signature based on the expression of Cuproptosis-related genes in order to guide the diagnosis and treatment for BC. Cuproptosis-related genes prognostic signature has ata of 1250 BC tissues and 583 normal breast tissues were obtained from The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), and GEO GSE65212. The prognostic signature was established and evaluated with nineteen Cuproptosis-related genes. A series of in silico analyses based on SLC31A1, included expression analysis, independent prognostic analysis, correlation analysis, immune-related analysis and survival analysis. Finally, a series of cell experiments (including quantitative real-time polymerase chain reaction and western blot), and mice experiments were applied to evaluate the impact of SLC31A1 on BC. Cuproptosis-related genes prognostic signature has good predictive promising for survival in BC patients. We discovered that SLC31A1SLC31A1 was overexpressed in BC and was its independent prognostic factor. High expression of the SLC31A1 was correlated with poor prognosis and immune infiltrating of BC. SLC31A1 expression is associated with immune, chemotherapeutic and targeted therapy outcomes in BC. The proliferation, migration, and invasiveness of Her2 + enriched BC cells were decreased by SLC31A1 knockdown, also resulting in a decrease in tumor volume in mouse model. SLC31A1 is a candidate biomarker or therapeutic target in precision oncology, with diagnostic and prognostic significance in BC.", "claims": [{"id": "claim-method", "statement": "We performed through multivariate cox regression analysis and then iterative analysis through step function to obtain the prognosis model. We used log rank and univariate Cox regression to compare the difference in survival between two or more groups, and performed timeROC (v 0.4) analysis to determine the accuracy of the discriminant prediction model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39448672", "locator": "sections[5] \"Cuproptosis-related genes prognostic model\" paragraph 2", "quote": "We performed through multivariate cox regression analysis and then iterative analysis through step function to obtain the prognosis model. We used log rank and univariate Cox regression to compare the difference in survival between two or more groups, and performed timeROC (v 0.4) analysis to determine the accuracy of the discriminant prediction model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analysed during the current study are available in the TCGA repository (https://portal.gdc.cancer.gov/), GEO (GSE65212, http://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39448672", "locator": "sections[42] \"notes\" paragraph 1", "quote": "The datasets generated and analysed during the current study are available in the TCGA repository (https://portal.gdc.cancer.gov/), GEO (GSE65212, http://www.ncbi.nlm.nih.gov/geo)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The low-risk subgroup had better survival outcomes than the high-risk subgroup (p = 7.84e-06).", "kind": "quantitative", "target": {"value": 7.0, "unit": "p-value", "tolerance": null, "source": "K-M survival curves showed that the outcomes of BC cases in the low-risk subgroup were better than those with high-risk (p = 7.84e-06) (Fig. 1B, d)."}, "evidence": [{"asset": "source:pmid:39448672", "locator": "sections[25] \"Construction of a prognostic signature in cuproptosis-related genes\" paragraph 2", "quote": "K-M survival curves showed that the outcomes of BC cases in the low-risk subgroup were better than those with high-risk (p = 7.84e-06) (Fig. 1B, d)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The low-risk subgroup had better survival outcomes than the high-risk subgroup (p = 7.84e-06).", "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:39448672"], "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:GSE65212"], "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:GSE65212"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39448672", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-76162-x", "sha256": "sha256:2e7fdb7a5c788dabf7e655c32a641853b9fc32a09c194f758b9cf8cea6059135", "bytes": 48883, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-76162-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11502855", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65212", "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=GSE65212", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65212", "version": null, "note": "The datasets generated and analysed during the current study are available in the TCGA repository (https://portal.gdc.cancer.gov/), GEO (GSE65212, http://www.ncbi.nlm.nih.gov/geo).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and analysed during the current study are available in the TCGA repository (https://portal.gdc.cancer.gov/), GEO (GSE65212, http://www.ncbi.nlm.nih.gov/geo).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1589620", "GSM1589621", "GSM1589622", "GSM1589623", "GSM1589624", "GSM1589625", "GSM1589626", "GSM1589627", "GSM1589628", "GSM1589629", "GSM1589630", "GSM1589631", "GSM1589632", "GSM1589633", "GSM1589634", "GSM1589635", "GSM1589636", "GSM1589637", "GSM1589638", "GSM1589639", "GSM1589640", "GSM1589641", "GSM1589642", "GSM1589643", "GSM1589644", "GSM1589645", "GSM1589646", "GSM1589647", "GSM1589648", "GSM1589649", "GSM1589650", "GSM1589651", "GSM1589652", "GSM1589653", "GSM1589654", "GSM1589655", "GSM1589656", "GSM1589657", "GSM1589658", "GSM1589659", "GSM1589660", "GSM1589661", "GSM1589662", "GSM1589663", "GSM1589664", "GSM1589665", "GSM1589666", "GSM1589667", "GSM1589668", "GSM1589669", "GSM1589670", "GSM1589671", "GSM1589672", "GSM1589673", "GSM1589674", "GSM1589675", "GSM1589676", "GSM1589677", "GSM1589678", "GSM1589679", "GSM1589680", "GSM1589681", "GSM1589682", "GSM1589683", "GSM1589684", "GSM1589685", "GSM1589686", "GSM1589687", "GSM1589688", "GSM1589689", "GSM1589690", "GSM1589691", "GSM1589692", "GSM1589693", "GSM1589694", "GSM1589695", "GSM1589696", "GSM1589697", "GSM1589698", "GSM1589699", "GSM1589700", "GSM1589701", "GSM1589702", "GSM1589703", "GSM1589704", "GSM1589705", "GSM1589706", "GSM1589707", "GSM1589708", "GSM1589709", "GSM1589710", "GSM1589711", "GSM1589712", "GSM1589713", "GSM1589714", "GSM1589715", "GSM1589716", "GSM1589717", "GSM1589718", "GSM1589719", "GSM1589720", "GSM1589721", "GSM1589722", "GSM1589723", "GSM1589724", "GSM1589725", "GSM1589726", "GSM1589727", "GSM1589728", "GSM1589729", "GSM1589730", "GSM1589731", "GSM1589732", "GSM1589733", "GSM1589734", "GSM1589735", "GSM1589736", "GSM1589737", "GSM1589738", "GSM1589739", "GSM1589740", "GSM1589741", "GSM1589742", "GSM1589743", "GSM1589744", "GSM1589745", "GSM1589746", "GSM1589747", "GSM1589748", "GSM1589749", "GSM1589750", "GSM1589751", "GSM1589752", "GSM1589753", "GSM1589754", "GSM1589755", "GSM1589756", "GSM1589757", "GSM1589758", "GSM1589759", "GSM1589760", "GSM1589761", "GSM1589762", "GSM1589763", "GSM1589764", "GSM1589765", "GSM1589766", "GSM1589767", "GSM1589768", "GSM1589769", "GSM1589770", "GSM1589771", "GSM1589772", "GSM1589773", "GSM1589774", "GSM1589775", "GSM1589776", "GSM1589777", "GSM1589778", "GSM1589779", "GSM1589780", "GSM1589781", "GSM1589782", "GSM1589783", "GSM1589784", "GSM1589785", "GSM1589786", "GSM1589787", "GSM1589788", "GSM1589789", "GSM1589790", "GSM1589791", "GSM1589792", "GSM1589793", "GSM1589794", "GSM1589795", "GSM1589796", "GSM1589797"], "sample_count": 178, "group_sizes": null, "group_sizes_basis": null, "platform": "14877", "taxon": "Homo sapiens", "title": "Expression profiling of breast cancer samples from Institut Curie (Maire cohort) -- BrainArray CDF", "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:GSE65212 not downloaded", "asset:data:geo:GSE65212 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": "We performed through multivariate cox regression analysis and then iterative analysis through step function to obtain the prognosis model. We used log rank and univariate Cox regression to compare the difference in survival between two or more groups, and performed timeROC (v 0.4) analysis to determine the accuracy of the discriminant prediction model."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "log rank"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 7.0, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["GSE65212"], "resolved_accessions": ["GSE65212"], "statements": ["The datasets generated and analysed during the current study are available in the TCGA repository (https://portal.gdc.cancer.gov/), GEO (GSE65212, http://www.ncbi.nlm.nih.gov/geo)."], "basis": "The paper names GSE65212 in 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:39448672", "data:geo:GSE65212"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65212"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:36:55Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14362, "completion_tokens": 2243, "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:39448672", "type": "paper", "label": "pmid:39448672"}, {"id": "source:pmid:39448672", "type": "manuscript", "label": "PMID 39448672 full text"}, {"id": "data:geo:GSE65212", "type": "dataset", "label": "GEO GSE65212"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39448672", "type": "paper", "label": "pmid:39448672"}, {"id": "source:pmid:39448672", "type": "manuscript", "label": "PMID 39448672 full text"}, {"id": "data:geo:GSE65212", "type": "dataset", "label": "GEO GSE65212"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39448672", "type": "extraction", "used": ["source:pmid:39448672"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65212", "type": "accession_resolution", "used": ["data:geo:GSE65212"], "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:39448672", "parent_hash": "sha256:3fe597eaba9930c1ed7c484fff2d7c752f25329e1e2a8a6b7526985a9bc99e6d", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE65212 licence not read", "asset:data:geo:GSE65212 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tive real-time polymerase chain reaction and western blot), and mice experiments were applied to evalu"], "order_basis": "paper_text_order:1023", "id": "assay:1"}, {"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": ["enriched BC cells were decreased by SLC31A1 knockdown, also resulting in a decrease in tumor volum", "Methods Cell culture and transfection Cell line were from the Chinese Academy of S", "GGAGAATT-3′, GeneChem, Shanghai, China) were transfected into the SKBR3 cell lines using Lipofectamin", "rding to the manufacturer’s protocols. After transfection, the SKBR3 cell lines were harvested for fur"], "order_basis": "paper_text_order:1619", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["o resulting in a decrease in tumor volume in mouse model. SLC31A1 is a candidate biomarker or therape", "o resulting in a decrease in tumor volume in mouse model. SLC31A1 is a candidate biomarker or t"], "order_basis": "paper_text_order:1677", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["se Academy of Science (Shanghai, China). The cell line was grown in a sterile and humidified cell culture inc", "d 5% CO2. MCF-7, BT474, SKBR3 and MDA-MB-231 cell lines was cultured using MEM (Procell, Wuhan, China) containing", "ntration of 10% FBS and 1% P/S. MCF-10 A was cultured with the following medium: DMEM + 5% HS + 20ng/ml", "cell culture incubator at 37 °C and 5% CO2. MCF-7, BT474, SKBR3 and MDA-MB-231 cell lines was"], "order_basis": "paper_text_order:1931", "id": "assay:4"}, {"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": ["We performed through multivariate cox regression analysis and then iterative analysis through step function to obtain the prognosis model. We used log rank and univariate Cox regression to compare the difference in survival between two or more groups, and performed timeROC (v 0.4) analysis to determine the accuracy of the discriminant prediction model."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}