P2RY13+ dendritic cells correlate with enhanced antigen presentation and lymphocyte activation in lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41601785", "kind": "science-record", "revision": 3, "content_hash": "sha256:c6b6ad2eb7e3667126cc494d541f9347f7432dd9ddc85a29df6d7744fcd36c18", "created_at": "2026-11-01T20:31:34Z", "updated_at": "2026-11-01T22:57:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "P2RY13+ dendritic cells correlate with enhanced antigen presentation and lymphocyte activation in lung adenocarcinoma.", "doi": "10.3389/fmed.2025.1708670", "pmid": "41601785", "authors": ["Cong Lan", "Jian Zhong", "Siyao Che"], "journal": "Frontiers in medicine", "year": 2025, "abstract": "Background: Although P2RY13 has been implicated in immune regulation and prognosis in lung adenocarcinoma (LUAD), its specific cellular expression and functional mechanisms within the tumor microenvironment (TME) remain poorly understood.\nMethods: We integrated transcriptomic and clinical data from TCGA and GEO (GSE68465 and GSE31210), performed differential gene expression and functional enrichment analyses, and employed multiple algorithms including CIBERSORT, MCP-counter, quanTIseq, TIMER, and ESTIMATE to evaluate immune infiltration. Single-cell RNA sequencing data (GSE131907) was analyzed using Seurat to identify cell-type-specific expression, while CellChat was used to infer intercellular communication. Pathway activities were assessed with eight scoring methods (AUCell, UCell, AddModuleScore, GSVA, JASMINE, singscore, ssGSEA, viper) using MSigDB gene sets.\nResults: Our results demonstrated that P2RY13 was significantly downregulated in LUAD and predicted poor prognosis independently. It correlated positively with immune infiltration, particularly T cell markers. Single-cell analysis revealed specific enrichment in dendritic cells (DCs), with P2RY13(+) DCs more prevalent in normal tissues and exhibiting enhanced activity in antigen presentation and T cell activation.\nConclusion: P2RY13 is an independent prognostic biomarker in LUAD, linked to an immunologically active TME. Its specific expression in dendritic cells enhances antigen presentation and T cell activation, underscoring its role in promoting anti-tumor immunity.", "claims": [{"id": "claim-method", "statement": "Survival analysis was performed using the Kaplan–Meier method and compared with the log-rank test. Multivariate Cox regression models were applied to evaluate the prognostic value of P2RY13 expression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41601785", "locator": "sections[9] \"Survival and statistical analysis\" paragraph 2", "quote": "Survival analysis was performed using the Kaplan–Meier method and compared with the log-rank test. Multivariate Cox regression models were applied to evaluate the prognostic value of P2RY13 expression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets (GSE68465 and GSE31210) analyzed in the present study were derived from publicly accessible databases (TCGA: https://portal.gdc.cancer.gov/; GEO: https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41601785", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "The datasets (GSE68465 and GSE31210) analyzed in the present study were derived from publicly accessible databases (TCGA: https://portal.gdc.cancer.gov/; GEO: https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "P2RY13 was significantly downregulated in LUAD and predicted poor prognosis independently.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41601785", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our results demonstrated that P2RY13 was significantly downregulated in LUAD and predicted poor prognosis independently."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "P2RY13 was significantly downregulated in LUAD and predicted poor prognosis independently.", "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:41601785"], "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:GSE131907"], "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:GSE131907"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41601785", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2025.1708670", "sha256": 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