Identification of an immune prognostic 11-gene signature for lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33552736", "kind": "science-record", "revision": 7, "content_hash": "sha256:a273dd0db74e1bf8d2da93cee537aec8ba5f18f008dcdd8d825b4d98bd77ae70", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:03:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of an immune prognostic 11-gene signature for lung adenocarcinoma.", "doi": "10.7717/peerj.10749", "pmid": "33552736", "authors": ["Tao Yang", "Lizheng Hao", "Renyun Cui", "Huanyu Liu", "Jian Chen", "Jiongjun An", "Shuo Qi", "Zhong Li"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: The immunological tumour microenvironment (TME) has occupied a very important position in the beginning and progression of non-small cell lung cancer (NSCLC). Prognosis of lung adenocarcinoma (LUAD) remains poor for the local progression and widely metastases at the time of clinical diagnosis. Our objective is to identify a potential signature model to improve prognosis of LUAD.\nMETHODS: With the aim to identify a novel immune prognostic signature associated with overall survival (OS), we analysed LUADs extracted from The Cancer Genome Atlas (TCGA). Immune scores and stromal scores of TCGA-LUAD were downloaded from Estimation of STromal and Immune cells in MAlignant Tumour tissues Expression using data (ESTIMATE). LASSO COX regression was applied to build the prediction model. Then, the prognostic gene signature was validated in the GSE68465 dataset.\nRESULTS: The data from TCGA datasets showed patients in stage I and stage II had higher stromal scores than patients in stage IV (P < 0.05), and for immune score patients in stage I were higher than patients in stage III and stage IV (P < 0.05). The improved overall survivals were observed in high stromal score and immune score groups. Patients in the high-risk group exhibited the inferior OS (P = 2.501e - 05). By validating the 397 LUAD patients from GSE68465, we observed a better OS in the low-risk group compared to the high-risk group, which is consistent with the results from the TCGA cohort. Nomogram results showed that practical and predicted survival coincided very well, especially for 3-year survival.\nCONCLUSION: We obtained an 11 immune score related gene signature model as an independent element to effectively classify LUADs into different risk groups, which might provide a support for precision treatments. Moreover, immune score may play a potential valuable sole for estimating OS in LUADs.", "claims": [{"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.\nTCGA-LUAD mRNA FPKM data is available at Figshare:\nHao, Lizheng (2021): dat2.zip. figshare. Dataset. https://doi.org/10.6084/m9.figshare.13515998.v1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33552736", "locator": "sections[31] \"Data Availability Statement\" paragraphs 1-5", "quote": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.\nTCGA-LUAD mRNA FPKM data is available at Figshare:\nHao, Lizheng (2021): dat2.zip. figshare. Dataset. https://doi.org/10.6084/m9.figshare.13515998.v1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33552736"], "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:GSE68465"], "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:GSE68465"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33552736", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.10749", "sha256": "sha256:947602c3d90a6344f50235df8bbfc00e7373a60e69ee97e1b2662656e3506739", "bytes": 50598, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.10749", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7825366", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE68465", "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=GSE68465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68465", "version": null, "note": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.\nTCGA-LUAD mRNA FPKM data is available at Figshare:\nHao, Lizheng (2021): dat2.zip. figshare. Dataset. https://doi.org/10.6084/m9.figshare.13515998.v1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.\nTCGA-LUAD mRNA FPKM data is available at Figshare:\nHao, Lizheng (2021): dat2.zip. figshare. 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"section[12]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:33552736:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c8b2d1bd0c01fdc1215291a253152792a6450ca17076cae5f6efb9b50f4f1360", "bytes": 1839, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#table-2", "version": null, "note": "The biological functions of the coding genes.", "structure": {"pmcid": "PMC7825366", "section_index": 18, "section_title": "Discussion", "row_count": 12, "column_count": 2}, "table": {"label": "Table 2", "caption": "The biological functions of the coding genes.", "rows": [["Gene", "Immune-related functions"], ["CD70", "CD70 belongs to TNF ligand family and can enhance the generation of cytolytic T cells and induce proliferation of co-stimulated T cells (Keller et al., 2007; Kuka et al., 2013). The regulatory mechanisms for the CD70-CD27 pathway is critical for prognosis of cancer patients."], ["CXorf21", "CXorf21 is a mediator of the X-chromosome gene of systemic lupus erythematosus in female (Bentham et al., 2015; Harris et al., 2019b) and is expressed only in immune cell (Harris et al., 2019a)."], ["CD74", "CD74 expression serves as a prognostic factor in many cancers (Ekmekcioglu et al., 2016; Otterstrom et al., 2014; Ruvolo et al., 2019; Zeiner et al., 2015; Zeiner et al., 2018; Zhang et al., 2014)."], ["RUBCNL", "RUBCNL is a vertebrate-specific autophagy regulator (Cheng et al., 2017), and involves autophagy in NSCLC (Levy, Towers & Thorburn, 2017)."], ["BIRC3", "BIRC3 involves in the prognostication system in Chronic Lymphocytic Leukemia (Alhourani et al., 2016) and hepatocellular carcinoma patients undergoing curative resection (Fu et al., 2019)."], ["TESC", "TESC can reinforce the radio-resistant properties of NSCLC (Lee et al., 2018)."], ["INSL4", "Abnormal INSL4 signaling may act as a promising therapeutic target for LKB1-deficient NSCLC (Yang et al., 2018)."], ["HLA-DOB", "HLA-DOB are expressed in antigen presenting cells which is tightly linked with the immunity."], ["CIITA", "The vaccination with CIITA-tumour cells is constructed to facilitate anti-tumour cells to enhance the immune system (Accolla et al., 2019)."], ["STAP1", "No relevant report yet."], ["OBP2A", "No relevant report yet."]], "row_count": 12, "column_count": 2, "numeric_cells": 11, "header_rows": 1, "locator": "section[18]/table-wrap[1]#table-2"}}], "gaps": ["asset:data:geo:GSE68465 not downloaded", "asset:data:geo:GSE68465 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": "reordered", "quote": "“LASSO COX regression was applied to build the prediction model.”"}}, {"id": "method-2", "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"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}], "targets": [], "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. 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