Prognosis and Immunotherapy Response With a Novel Golgi Apparatus Signature-Based Formula in Lung Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35127727", "kind": "science-record", "revision": 5, "content_hash": "sha256:41c9ceef02996fcf29bff130da2c3ffad157f581bcecbdaea82ca1455690b861", "created_at": "2026-11-01T17:36:52Z", "updated_at": "2026-11-01T22:48:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognosis and Immunotherapy Response With a Novel Golgi Apparatus Signature-Based Formula in Lung Adenocarcinoma.", "doi": "10.3389/fcell.2021.817085", "pmid": "35127727", "authors": ["Yupeng Jiang", "Wenhao Ouyang", "Chenzi Zhang", "Yunfang Yu", "Herui Yao"], "journal": "Frontiers in cell and developmental biology", "year": 2021, "abstract": "The Golgi apparatus (GA) is a cellular organelle that participates in the packaging, modification, and transport of proteins and lipids from the endoplasmic reticulum to be further fabricated before being presented to other cellular components. Recent studies have demonstrated that GA facilitates numerous cellular processes in cancer development. Therefore, this study aimed to establish a novel lung adenocarcinoma (LUAD) risk evaluation model based on GA gene signatures. In this study, we used TCGA-LUAD (n = 500) as the training cohort and GSE50081 (n = 127), GSE68465 (442), and GSE72094 (398) as the validation cohorts. Two immunotherapy datasets (GSE135222 and GSE126044) were also obtained from a previous study. Based on machine algorithms and bioinformatics methods, a GA gene-related risk score (GARS) was established. We found that the GARS independently predicted the prognosis of LUAD patients and remained effective across stages IA to IIIA. Then, we identified that the GARS was highly correlated with mutations in P53 and TTN. Further, this study identified that GARS is related to multiple immune microenvironmental characteristics. Furthermore, we investigated GSE135222 and GSE126044 and found that a lower GARS may be indicative of an improved therapeutic effect of PD-1/PD-L1 therapy. We also found that high GARS may lead to a better response to multiple anticancer drugs. Finally, we established a nomogram to better guide clinical application. To our knowledge, this is the first study to demonstrate a novel GA signature-based risk score formula to predict clinical prognosis and guide the treatment of LUAD patients.", "claims": [{"id": "claim-method", "statement": "Consequently, univariate Cox analysis of overall survival (OS) was applied to screen for GA-related genes with prognostic value. Subsequently, least absolute shrinkage and selection operator (LASSO) regression with 10-fold cross-validation was performed, 1,000 cycles of the “glmnet” package were run using the R software, and 1,000 random stimulations were set.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35127727", "locator": "sections[6] \"Construction and Verification of the Golgi Apparatus Gene-Related Risk Score Formula\" paragraph 2", "quote": "Consequently, univariate Cox analysis of overall survival (OS) was applied to screen for GA-related genes with prognostic value. Subsequently, least absolute shrinkage and selection operator (LASSO) regression with 10-fold cross-validation was performed, 1,000 cycles of the “glmnet” package were run using the R software, and 1,000 random stimulations were set."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA-LUAD from TCGA database (https://portal.gdc.cancer.gov/); GSE68465, GSE72094, GSE50081, GSE135222 and GSE126044 cohort from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35127727", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA-LUAD from TCGA database (https://portal.gdc.cancer.gov/); GSE68465, GSE72094, GSE50081, GSE135222 and GSE126044 cohort from GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The Golgi apparatus gene-related risk score independently predicted overall survival in lung adenocarcinoma patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35127727", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found that the GARS independently predicted the prognosis of LUAD patients and remained effective across stages IA to IIIA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The Golgi apparatus gene-related risk score independently predicted overall survival in lung adenocarcinoma 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:35127727"], "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:GSE126044"], "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:GSE126044"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35127727", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2021.817085", "sha256": "sha256:56e3de76529f47f7a93f49d7ef8d8bfc2f85c95c602946c23c89f77a4af40237", "bytes": 46833, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcell.2021.817085", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8811463", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE126044", "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=GSE126044", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE126044", "version": null, "note": "Publicly available datasets were analyzed in this study. 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Subsequently, least absolute shrinkage and selection operator (LASSO) regression with 10-fold cross-validation was performed, 1,000 cycles of the “glmnet” package were run using the R software, and 1,000 random stimulations were set."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "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": ["GSE50081", "GSE68465", "GSE72094", "GSE135222", "GSE126044"], "resolved_accessions": ["GSE50081", "GSE68465", "GSE72094", "GSE135222", "GSE126044"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: TCGA-LUAD from TCGA database (https://portal.gdc.cancer.gov/); GSE68465, GSE72094, GSE50081, GSE135222 and GSE126044 cohort from GEO database (https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE50081, GSE68465, GSE72094, GSE135222, GSE126044 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:35127727", "data:geo:GSE126044"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE126044"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:33:05Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14276, "completion_tokens": 2196, "cached_tokens": 264}}, "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:35127727", "type": "paper", "label": "pmid:35127727"}, {"id": "source:pmid:35127727", "type": "manuscript", "label": "PMID 35127727 full text"}, {"id": "data:geo:GSE126044", "type": "dataset", "label": "GEO GSE126044"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35127727", "type": "paper", "label": "pmid:35127727"}, {"id": "source:pmid:35127727", "type": "manuscript", "label": "PMID 35127727 full text"}, {"id": "data:geo:GSE126044", "type": "dataset", "label": "GEO GSE126044"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35127727", "type": "extraction", "used": ["source:pmid:35127727"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE126044", "type": "accession_resolution", "used": ["data:geo:GSE126044"], "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:35127727", "parent_hash": "sha256:1f349745f3e359e798ee387855ab1b305fec938fbfe9c6726039c10b528ddaa4", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE126044 licence not read", "asset:data:geo:GSE126044 not downloaded", "asset:data:geo:GSE135222 licence not read", "asset:data:geo:GSE135222 not downloaded", "asset:data:geo:GSE50081 licence not read", "asset:data:geo:GSE50081 not downloaded", "asset:data:geo:GSE68465 licence not read", "asset:data:geo:GSE68465 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE72094 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": "methylation_array", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["CIBERSORT, QUANTISEQ, Timer, CIBERSORT-ABS, EPIC, and XCELL algorithms. The “gsva” R package"], "order_basis": "paper_text_order:2017", "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": ["Consequently, univariate Cox analysis of overall survival (OS) was applied to screen for GA-related genes with prognostic value. Subsequently, least absolute shrinkage and selection operator (LASSO) regression with 10-fold cross-validation was performed, 1,000 cycles of the “glmnet” package were run using the R software, and 1,000 random stimulations were set."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}