High CDCP1 Expression Reflects Immune and Stromal Remodeling and Oncogenic Signaling in Pancreatic Ductal Adenocarcinoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41488282", "kind": "science-record", "revision": 1, "content_hash": "sha256:9d6378ac8f6f4bc81c8bed6dc55477439af8cbd2e0e00bf10adf43cfd4fe189d", "created_at": "2026-11-01T10:25:54Z", "updated_at": "2026-11-01T10:25:54Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "High CDCP1 Expression Reflects Immune and Stromal Remodeling and Oncogenic Signaling in Pancreatic Ductal Adenocarcinoma.", "doi": "10.14740/wjon2682", "pmid": "41488282", "authors": null, "journal": "World journal of oncology", "year": 2026, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41488282"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], 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"source:pmid:41488282", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.14740/wjon2682", "sha256": "sha256:bc556844a77f071eedc83aff1a2c59e203bc940c018de6a909fc4531208f26c7", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.14740/wjon2682", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:41488282 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41488282"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41488282"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "200d072ffd70835817506a1e4195a7616a093b62da0741e69a1539d9d40aec88", "source_hash": "bc556844a77f071eedc83aff1a2c59e203bc940c018de6a909fc4531208f26c7", "raw_response_sha256": "sha256:78f22047b8c4ed502ff9103fd36159b09771d15d8befdf9649ce3c237c48a0b3", "raw_response_chars": 5054}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "4b9ddfbe59c0b04ee5b02ab9731799c8a579b2eab157263f12d9f334669db1ec", "source_hash": "bc556844a77f071eedc83aff1a2c59e203bc940c018de6a909fc4531208f26c7", "raw_response_sha256": "sha256:eb7ee4f2609b4d3409c90f52d4fbf19843df95d3509490635297f865df330f50", "raw_response_chars": 65421}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "d85584682e0d8dafb257e65534d5916850a7270c953fbcdfac41290655cec2a5", "source_hash": "bc556844a77f071eedc83aff1a2c59e203bc940c018de6a909fc4531208f26c7", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that high CDCP1 expression in PDAC is associated with poor patient survival, reduced CD8+ T-cell infiltration, decreased stromal cellular fractions, increased genomic instability, and activation of multiple oncogenic signaling pathways; it does not state a headline numerical result for the main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that high CDCP1 expression in PDAC is associated with poor patient survival, reduced CD8+ T-cell infiltration, decreased stromal cellular fractions, increased genomic instability, and activation of multiple oncogenic signaling pathways; it does not state a headline numerical result for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:15:52.343697+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "4486b63402fd382065d70fff9f74d4d0385d960cfc752c3c86eb6a60dafcbb4a", "source_hash": "bc556844a77f071eedc83aff1a2c59e203bc940c018de6a909fc4531208f26c7", "raw_response": "<think>We need respond JSON object schema. Need interpret registered target headline numerical result paper states main finding. Source has no headline numerical result? We need examine. Paper text provides n=214 cases etc but main finding high CDCP1 associated with TME remodeling, genomic instability, pathway enrichments no reported effect sizes/p-values except thresholds, 64 cell types, data cohort counts. No number stated for \"headline numerical result\" main finding. Likely answer number_stated false, parent_value 0, unit \"\", evidence \"\", target_result describe no numerical result for registered target; text states qualitative findings: high CDCP1 associated with poor survival etc. Need ensure exact quote? User says if no number for registered target false etc. Need output pure JSON. Could target_result be \"No headline numerical result is stated; the paper reports qualitative associations...\" no evidence requirement for false. Need distinguish n=214 maybe headline number? Target \"the headline numerical result the paper states for its main finding\". Could be sample size? They might expect 214? We must reason deeply.\n\nThe paper supplied is abstract etc. It says analyzed transcriptomic and clinical data from 214 PDAC cases (TCGA n=145; GSE62452 n=69). Headline numerical result could be 214 cases? But not result, cohort size. No hazard ratio, odds ratio, survival etc. They ask single numerical result replication registered target has to reproduce. Registered target generic \"headline numerical result the paper states for its main finding\". Main finding high CDCP1 expression associated etc with no numeric effect reported. Therefore false. Need target_result mention qualitative statements and counts maybe \"The text states that high CDCP1 expression is associated with poor patient survival, reduced CD8+ T-cell infiltration, decreased stromal cellular fractions, increased genomic instability, and activation of multiple oncogenic signaling pathways, but provides no headline numerical result.\" Need no evidence? empty exact. parent 0. number false.\n\nWe should make sure do not identify thresholds NES>1.5 FDR<0.25 or top tertile 214 as headline. This is likely dataset question asking main result numerical but not present. Need simply false. Could use concise target_result with quoted text? They say \"say in target_result what the text does state instead.\" We can state qualitative conclusion and cohort n perhaps. No invention. We can quote exact conclusion for robustness: \"The paper states qualitatively that high CDCP1 expression in PDAC is associated with poor patient survival, reduced CD8+ T-cell infiltration, decreased stromal cellular fractions, increased genomic instability, and activation of multiple oncogenic signaling pathways; it gives no headline numerical result for this main finding.\" This is paraphrase but target_result no constraint beyond say what states; okay.\n\nNeed final valid JSON no markdown. Could parent_value 0, unit \"\", evidence \"\", target_result as above, number_stated false. Need avoid including numerical 214 in target result? Could mention \"The main finding is reported qualitatively ...; the numerical values given describe the cohort and analysis thresholds rather than a headline effect estimate.\" That is fine. But if target_result includes e.g. 214 it's not output field needed. I'd keep no numbers except no main finding numeric.\n\nWe have much tokens but no need. Need obey \"Reply with a JSON object\" exact. Final JSON fields order same schema.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states qualitatively that high CDCP1 expression in PDAC is associated with poor patient survival, reduced CD8+ T-cell infiltration, decreased stromal cellular fractions, increased genomic instability, and activation of multiple oncogenic signaling pathways. It does not state a headline numerical result for this main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states qualitatively that high CDCP1 expression in PDAC is associated with poor patient survival, reduced CD8+ T-cell infiltration, decreased stromal cellular fractions, increased genomic instability, and activation of multiple oncogenic signaling pathways. It does not state a headline numerical result for this main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:15:58.457785+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "No numerical effect estimate is reported for the headline finding. The stated main finding is that high CDCP1 expression was significantly associated with reduced infiltration of CD8+ T cells, adipocytes, and fibroblasts.", "minimax_alt": "unclear — no numerical effect estimate for the headline finding is reported. The stated headline result is that high CDCP1 expression defines a transcriptionally distinct PDAC subtype characterized by immune evasion, stromal depletion, and genomic instability.", "decisive": false}, "analysis_methods": {"minimax": ["xCell algorithm", "Gene Set Enrichment Analysis (GSEA) with Hallmark gene sets", "Gene Set Variation Analysis (GSVA)", "Kruskal-Wallis test", "Mann-Whitney U test", "Fisher’s exact test", "Log-rank test"], "minimax_alt": ["Patients were stratified into high CDCP1 and low CDCP1 groups based on tertile distribution within each cohort, with the top tertile defined as high and the remaining two tertiles combined as low.", "To estimate TME composition, the xCell algorithm was applied to bulk transcriptome data to infer the relative abundance of 64 immune and stromal cell types [14].", "To investigate pathway activity, we conducted Gene Set Enrichment Analysis (GSEA) using the Hallmark gene sets from the Molecular Signatures Database (MSigDB v7.5.1) [13].", "In addition, Gene Set Variation Analysis (GSVA) was performed using the GSVA package in R to calculate enrichment scores for selected hallmark pathways, including E2F targets, G2M checkpoint, MYC targets, mitotic spindle, mTORC1 signaling, p53 pathway, glycolysis, and hypoxia.", "Mutation data were used to calculate silent and non-silent mutation rates, single nucleotide variant (SNV) burden, and insertion/deletion (indel) neoantigen loads.", "We assessed the association between CDCP1 expression and mutation status of canonical PDAC driver genes (KRAS, TP53, CDKN2A, and SMAD4)."], "decisive": false}, "statistical_method": {"minimax": "Kruskal-Wallis test or the Mann-Whitney U test, as appropriate", "minimax_alt": "Kruskal-Wallis test or the Mann-Whitney U test for group comparisons; Fisher’s exact test for categorical variables; Log-rank test for survival analysis", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:6155466f634caf45385ae5d2e78a0243afb806e6a1b6b5282394d3610737d2b8", "type": "sep_package", "label": "SEP v1 package for pmid:41488282"}], "activities": [{"id": "activity:conversion:pmid:41488282", "type": "conversion", "used": ["package:6155466f634caf45385ae5d2e78a0243afb806e6a1b6b5282394d3610737d2b8"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "19315c9d-e9ad-4cf1-8d31-007d8a33b202", "parent_hash": "6155466f634caf45385ae5d2e78a0243afb806e6a1b6b5282394d3610737d2b8", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:41488282 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41488282' does not resolve to a declared asset", "targets"]}