Systematic Analyses of a Chemokine Family-Based Risk Model Predicting Clinical Outcome and Immunotherapy Response in Lung Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34705571", "kind": "science-record", "revision": 4, "content_hash": "sha256:365beb365f8fc5cec0d47f67c6c6e41291717df53a209564f8ae37b06a7a857d", "created_at": "2026-11-01T17:36:22Z", "updated_at": "2026-11-01T22:05:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Systematic Analyses of a Chemokine Family-Based Risk Model Predicting Clinical Outcome and Immunotherapy Response in Lung Adenocarcinoma.", "doi": "10.1177/09636897211055046", "pmid": "34705571", "authors": ["Jiarui Chen", "Xingyu Liu", "Qiuji Wu", "Xueping Jiang", "Zihang Zeng", "Jiali Li", "Yanping Gao", "Yan Gong", "Conghua Xie"], "journal": "Cell transplantation", "year": 2021, "abstract": "Chemokines exhibited complicated functions in antitumor immunity, with their expression profile and clinical importance of lung adenocarcinoma (LUAD) patients remaining largely undetermined. This study aimed to explore the expression patterns of chemokine family in LUAD and construct a predictive chemokine family-based signature. A total of 497 samples were downloaded from the Cancer Genome Atlas (TCGA) data portal as the training set, and the combination of 4 representative Gene Expression Omnibus (GEO) datasets, including GSE30219, GSE50081, GSE37745, and GSE31210, were utilized as the validation set. A three gene-based signature was constructed using univariate and stepwise multivariate Cox regression analysis, classifying patients into high and low risk groups according to the overall survival. The independent GEO datasets were utilized to validate this signature. Another multivariate analysis revealed that this signature remained an independent prognostic factor in LUAD patients. Furthermore, patients in the low risk group featured immunoactive tumor microenvironment (TME), higher IPS scores and lower TIDE scores, and was regarded as the potential beneficiaries of immunotherapy. Finally, the role of risky CCL20 was validated by immunohistochemistry (IHC), and patients possessed higher CCL20 expression presented shorter overall survival (P = 0.011).", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression model and a subsequent stepwise multivariate Cox regression were employed to screen the most significant survival-related genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34705571", "locator": "sections[10] \"Statistical Analysis\" paragraph 2", "quote": "Univariate Cox regression model and a subsequent stepwise multivariate Cox regression were employed to screen the most significant survival-related genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Availability of Data and Materials: The datasets analyzed in this study can be found in TCGA portal (https://portal.gdc.cancer.gov/) and GEO portal (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210). Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34705571", "locator": "sections[23] \"fn-group\" paragraph 1", "quote": "Availability of Data and Materials: The datasets analyzed in this study can be found in TCGA portal (https://portal.gdc.cancer.gov/) and GEO portal (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210). Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Finally, the role of risky CCL20 was validated by immunohistochemistry (IHC), and patients possessed higher CCL20 expression presented shorter overall survival (P = 0.011).", "kind": "quantitative", "target": {"value": 0.011, "unit": "p-value", "tolerance": null, "source": "Finally, the role of risky CCL20 was validated by immunohistochemistry (IHC), and patients possessed higher CCL20 expression presented shorter overall survival (P = 0.011)."}, "evidence": [{"asset": "source:pmid:34705571", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Finally, the role of risky CCL20 was validated by immunohistochemistry (IHC), and patients possessed higher CCL20 expression presented shorter overall survival (P = 0.011)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Finally, the role of risky CCL20 was validated by immunohistochemistry (IHC), and patients possessed higher CCL20 expression presented shorter overall survival (P = 0.011).", "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:34705571"], "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:GSE30219"], "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:GSE30219"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34705571", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/09636897211055046", "sha256": "sha256:520dec8138af394f85cedb011625d0b9b071740c620474201f7ce2144af766e2", "bytes": 33073, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/09636897211055046", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8554550", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30219", "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=GSE30219", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30219", "version": null, "note": "Availability of Data and Materials: The datasets analyzed in this study can be found in TCGA portal (https://portal.gdc.cancer.gov/) and GEO portal (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210). Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of Data and Materials: The datasets analyzed in this study can be found in TCGA portal (https://portal.gdc.cancer.gov/) and GEO portal (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210). Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1465989", "GSM1465990", "GSM1465991", "GSM1465992", "GSM1465993", "GSM1465994", "GSM1465995", "GSM1465996", "GSM1465997", "GSM1465998", "GSM1465999", "GSM748053", "GSM748054", "GSM748055", "GSM748056", "GSM748057", "GSM748058", "GSM748059", "GSM748060", "GSM748061", "GSM748062", "GSM748063", "GSM748064", "GSM748065", "GSM748066", "GSM748067", "GSM748068", "GSM748069", "GSM748070", "GSM748071", "GSM748072", "GSM748073", "GSM748074", "GSM748075", "GSM748076", "GSM748077", "GSM748078", "GSM748079", "GSM748080", "GSM748081", "GSM748083", "GSM748084", "GSM748085", "GSM748086", "GSM748087", "GSM748088", "GSM748089", "GSM748090", "GSM748091", "GSM748092", "GSM748093", "GSM748094", "GSM748095", "GSM748096", "GSM748097", "GSM748098", "GSM748099", "GSM748100", "GSM748101", "GSM748102", "GSM748103", "GSM748104", "GSM748105", "GSM748106", "GSM748107", 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(https://portal.gdc.cancer.gov/) and GEO portal (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210). Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of Data and Materials: The datasets analyzed in this study can be found in TCGA portal (https://portal.gdc.cancer.gov/) and GEO portal (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210). 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Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of Data and Materials: The datasets analyzed in this study can be found in TCGA portal (https://portal.gdc.cancer.gov/) and GEO portal (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210). 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A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE30219", "GSE50081", "GSE37745", "GSE31210"], "resolved_accessions": ["GSE30219", "GSE50081", "GSE37745", "GSE31210"], "statements": ["Availability of Data and Materials: The datasets analyzed in this study can be found in TCGA portal (https://portal.gdc.cancer.gov/) and GEO portal (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745& https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210). Further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE30219, GSE50081, GSE37745, GSE31210 in Gene Expression Omnibus (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:34705571", "data:geo:GSE30219"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30219"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:05:07Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9327, "completion_tokens": 2630, "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:34705571", "type": "paper", "label": "pmid:34705571"}, {"id": "source:pmid:34705571", "type": "manuscript", "label": "PMID 34705571 full text"}, {"id": "data:geo:GSE30219", "type": "dataset", "label": "GEO GSE30219"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34705571", "type": "paper", "label": "pmid:34705571"}, {"id": "source:pmid:34705571", "type": "manuscript", "label": "PMID 34705571 full text"}, {"id": "data:geo:GSE30219", "type": "dataset", "label": "GEO GSE30219"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34705571", "type": "extraction", "used": ["source:pmid:34705571"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30219", "type": "accession_resolution", "used": ["data:geo:GSE30219"], "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:34705571", "parent_hash": "sha256:d1291ccfbf73b08bc38c264ed4f5f08306c51da8408a276a67708e67a85190da", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE31210 licence not read", "asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE37745 licence not read", "asset:data:geo:GSE37745 not downloaded", "asset:data:geo:GSE50081 licence not read", "asset:data:geo:GSE50081 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ly, the role of risky CCL20 was validated by immunohistochemistry (IHC), and patients possessed higher CCL20 e", "CCL20 was validated by immunohistochemistry (IHC), and patients possessed higher CCL20 expres"], "order_basis": "paper_text_order:1346", "id": "assay:1"}, {"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": ["Univariate Cox regression model and a subsequent stepwise multivariate Cox regression were employed to screen the most significant survival-related genes."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}