Pyroptosis-Related Gene Signature Predicts the Prognosis of ccRCC Using TCGA and Single-Cell RNA Seq Database.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36349258", "kind": "science-record", "revision": 3, "content_hash": "sha256:309e437abb63b0d73e1cc5d7a23a8e5ffd8bd51000257e2a3b3cf0e8418adb49", "created_at": "2026-11-01T18:15:47Z", "updated_at": "2026-11-01T21:29:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Pyroptosis-Related Gene Signature Predicts the Prognosis of ccRCC Using TCGA and Single-Cell RNA Seq Database.", "doi": "10.1155/2022/8224618", "pmid": "36349258", "authors": ["Ying Gan", "Zhenan Zhang", "Xiaofei Wang", "Aolin Li", "Yu Fan", "Qian Zhang"], "journal": "Journal of healthcare engineering", "year": 2022, "abstract": "Clear cell renal cell carcinoma (ccRCC) is the most prevalent type of renal carcinoma, which is not sensitive to both radiotherapy and chemotherapy. The objective response rate of metastatic renal cancer to targeted drugs and immunotherapy is unsatisfactory. Pyroptosis, proven as an inflammatory form of programmed cell death, could be activated by some inflammasomes, while could create a tumor-suppressing environment by releasing inflammatory factors in the tumor. To explore indicators predicting the prognosis of ccRCC and the effect of antitumor therapy, we constructed a pyroptosis risk model containing 4 genes after 11 pyroptosis-related genes of 516 ccRCC cases in the TCGA database were scanned. Based on the risk score, 516 ccRCC cases were divided into two groups for functional enrichment analysis and immune profile to seek functional pathways and potential therapeutic targets. Besides, those results were verified in GSE29609 and single-cell transcriptomic data. The study suggests that the conducted pyroptosis model could predict the prognosis of ccRCC and reflect the immune microenvironment, which may help in immune checkpoint inhibitor treatment.", "claims": [{"id": "claim-method", "statement": "Multivariate Cox regression analyses were used for the pyroptosis risk model establishment (Supplementary Table S1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36349258", "locator": "sections[11] \"3.2. Construction and Evaluation of the Pyroptosis Risk Model\" paragraph 2", "quote": "Multivariate Cox regression analyses were used for the pyroptosis risk model establishment (Supplementary Table S1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36349258", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The risk model had an accuracy of 0.674 (95% CI: 0.624–0.724) in the TCGA cohort (Figure 4(b)).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The risk model had an accuracy of 0.674 (95% CI: 0.624–0.724) in the TCGA cohort (Figure 4(b))."}, "evidence": [{"asset": "source:pmid:36349258", "locator": "sections[11] \"3.2. Construction and Evaluation of the Pyroptosis Risk Model\" paragraph 3", "quote": "The risk model had an accuracy of 0.674 (95% CI: 0.624–0.724) in the TCGA cohort (Figure 4(b))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The risk model had an accuracy of 0.674 (95% CI: 0.624–0.724) in the TCGA cohort (Figure 4(b)).", "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:36349258"], "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:GSE29609"], "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:GSE29609"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36349258", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/8224618", "sha256": "sha256:f9bf8f68d2c869d9a5f7735b596a19e259da531800dc8d752152dc7c0d3c4cb9", "bytes": 23810, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/8224618", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9637477", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29609", "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=GSE29609", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29609", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM733579", "GSM733580", "GSM733581", "GSM733582", "GSM733583", "GSM733584", "GSM733585", "GSM733586", "GSM733587", "GSM733588", "GSM733589", "GSM733590", "GSM733591", "GSM733592", "GSM733593", "GSM733594", "GSM733595", "GSM733596", "GSM733597", "GSM733598", "GSM733599", "GSM733600", "GSM733601", "GSM733602", "GSM733603", "GSM733604", "GSM733605", "GSM733606", "GSM733607", "GSM733608", "GSM733609", "GSM733610", "GSM733611", "GSM733612", "GSM733613", "GSM733614", "GSM733615", "GSM733616", "GSM733617"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "1708", "taxon": "Homo sapiens", "title": "Clear-cell renal cell carcinomas tumors", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE29609 not downloaded", "asset:data:geo:GSE29609 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": "Multivariate Cox regression analyses were used for the pyroptosis risk model establishment (Supplementary Table S1)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": ["GSE29609"], "resolved_accessions": ["GSE29609"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author upon request."], "basis": "The paper names GSE29609 in Gene Expression Omnibus (GEO) database 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:36349258", "data:geo:GSE29609"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29609"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:15:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7775, "completion_tokens": 1469, "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:36349258", "type": "paper", "label": "pmid:36349258"}, {"id": "source:pmid:36349258", "type": "manuscript", "label": "PMID 36349258 full text"}, {"id": "data:geo:GSE29609", "type": "dataset", "label": "GEO GSE29609"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36349258", "type": "paper", "label": "pmid:36349258"}, {"id": "source:pmid:36349258", "type": "manuscript", "label": "PMID 36349258 full text"}, {"id": "data:geo:GSE29609", "type": "dataset", "label": "GEO GSE29609"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36349258", "type": "extraction", "used": ["source:pmid:36349258"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29609", "type": "accession_resolution", "used": ["data:geo:GSE29609"], "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:36349258", "parent_hash": "sha256:a7fd441374b3a19e352066701c2b4e07293939ee14eee5ee22d579f239b52691", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE29609 licence not read", "asset:data:geo:GSE29609 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Multivariate Cox regression analyses were used for the pyroptosis risk model establishment (Supplementary Table S1)."], "order_basis": "analysis_only", "id": "assay:1"}]}