PAQR6 as a prognostic biomarker and potential therapeutic target in kidney renal clear cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39742277", "kind": "science-record", "revision": 4, "content_hash": "sha256:db736427dd95199c1a06b9619c29a6126ffaa424df5c087c050fe8b5518117f6", "created_at": "2026-11-01T20:30:04Z", "updated_at": "2026-11-01T22:55:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PAQR6 as a prognostic biomarker and potential therapeutic target in kidney renal clear cell carcinoma.", "doi": "10.3389/fimmu.2024.1521629", "pmid": "39742277", "authors": ["Tao Zou", "Zongming Jia", "Jixiang Wu", "Xuxu Liu", "Minghao Deng", "Xuefeng Zhang", "Yuxin Lin", "Jigen Ping"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Background: Progestin And AdipoQ Receptor Family Member VI (PAQR6) plays a significant role in the non-genomic effects of rapid steroid responses and is abnormally expressed in various tumors. However, its biological function in kidney renal clear cell carcinoma (KIRC) and its potential as a therapeutic target remain underexplored.\nMethods: In this study, PAQR6 was identified as a critical oncogene by WGCNA algorithm and differential gene expression analysis using TCGA - KIRC and GSE15641 data. The differences in PAQR6 expression and its association with KIRC survival outcomes were investigated, and transcriptomic data were used to further elucidate PAQR6's biological functions. Moreover, XCELL and single - cell analysis assessed the correlation between PAQR6 expression and immune infiltration. TIDE algorithm was used to assess how well various patient cohorts responded to immune checkpoint therapy. Finally, the role of PAQR6 in the development of KIRC was verified through EdU, scratch assays, and Transwell assays.\nResults: Our findings suggest that elevated expression of PAQR6 is linked to a poor prognosis for KIRC patients. Functional enrichment analysis demonstrated that PAQR6 is primarily involved in angiogenesis and pluripotent stem cell differentiation, which are crucial in mediating the development of KIRC. Additionally, we established a ceRNA network that is directly related to overall prognosis, further supporting the role of PAQR6 as a prognostic biomarker for KIRC.\nConclusion: Using both computational and experimental methods, this study leads the charge in discovering and verifying PAQR6 as a prognostic biomarker and possible therapeutic target for KIRC. In the future, to determine its molecular mechanism in KIRC carcinogenesis, more in vivo research will be carried out.", "claims": [{"id": "claim-method", "statement": "The expression of PAQR6 in KIRC and normal kidney tissues was detected by the Wilcoxon rank-sum test. The log-rank test was used for prognostic analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39742277", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "The expression of PAQR6 in KIRC and normal kidney tissues was detected by the Wilcoxon rank-sum test. The log-rank test was used for prognostic analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA-TCGA: https://portal.gdc.cancer.gov/GEO (GSE15641,GSE29609): https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39742277", "locator": "sections[25] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA-TCGA: https://portal.gdc.cancer.gov/GEO (GSE15641,GSE29609): https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Elevated PAQR6 expression is linked to a poor prognosis for KIRC patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39742277", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our findings suggest that elevated expression of PAQR6 is linked to a poor prognosis for KIRC patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Elevated PAQR6 expression is linked to a poor prognosis for KIRC patients.", "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:39742277"], "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:GSE111360"], "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:GSE111360"], "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:39742277", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2024.1521629", "sha256": "sha256:5618247b85459f0227a41da133a9f8a317365811fa4d61fe18b76b1f9091d0cb", "bytes": 51655, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2024.1521629", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11685228", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE111360", "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=GSE111360", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE111360", "version": null, "note": "Publicly available datasets were analyzed in this study. 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PAQ", "l bovine serum (Gibco, USA) and the cell was cultured in a 37°C cell incubator containing 5% CO2."], "order_basis": "paper_text_order:2929", "id": "assay:2"}, {"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": ["37°C cell incubator containing 5% CO2. PAQR6 knockdown lentivirus were purchased from Shanghai Gene", "re the role of PAQR6 in KIRC phenotypes. The knockdown treatment was performed using three differen", "of PAQR6 on tumor cell proliferation. In the knockdown group, the decreased PAQR6 significantly inh", "D ). The scratch assay demonstrated that the knockdown of PAQR6 evidently inhibited the migration o"], "order_basis": "paper_text_order:3094", "id": "assay:3"}, {"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": ["e-based therapies. Experimental verification Western blot was performed to evaluate the protein level", "ntibodies: Information on antibodies used in Western Blot experiments. Flowchart: The bioinformatics a"], "order_basis": "paper_text_order:8738", "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": 1.0, "evidence": ["The expression of PAQR6 in KIRC and normal kidney tissues was detected by the Wilcoxon rank-sum test. The log-rank test was used for prognostic analysis."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}