Development of a novel autophagy-related gene prognostic signature for gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35116589", "kind": "science-record", "revision": 4, "content_hash": "sha256:83480593cbb37e0d0eb01e251bb5c0842332740bc30ce5ab91ea2218fd1a5405", "created_at": "2026-11-01T17:36:51Z", "updated_at": "2026-11-01T22:48:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of a novel autophagy-related gene prognostic signature for gastric cancer.", "doi": "10.21037/tcr-21-191", "pmid": "35116589", "authors": ["Fanni Li", "Yukui Shang", "Haowei Zhang", "Junjun She", "Guanghui Wang", "Qi Sun"], "journal": "Translational cancer research", "year": 2021, "abstract": "BACKGROUND: A growing number of evidence has revealed the vital role of autophagy in pathological processes of cancer, including gastric cancer (GC). However, many previous studies only focused on exploring single pathway or limited genes of interest in GC, which only reflected partial functions of autophagy. The present study aimed to construct an autophagy-related risk signature for GC.\nMETHODS: Differentially expressed autophagy-related genes (ARGs) in GC and non-tumor samples were screened through The Cancer Genome Atlas (TCGA) database, followed by bioinformatics analysis using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) platforms. Prognosis-related ARGs were generated by univariate and multivariate Cox regression test.\nRESULTS: A total of seven prognosis-related ARGs (HSPB8, NRG2, GABARAPL1, TMEM74, DLC1, MAP1LC3C and NRG3) were determined to establish a prognostic index (PI) model, which was demonstrated to be an independent prognostic indicator for patients with GC. More importantly, it was successfully validated in an external cohort of patients from the GSE15460 dataset, indicating the useful reproducibility of this signature. In addition, the PI model was associated with immune cell infiltration estimates in GC.\nCONCLUSIONS: Taken together, the present study suggested that the seven ARGs-related signature could serve as an independent prognostic indicator for patients with GC.", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression analyses were performed to examine the relationship between each differentially expressed ARG and the overall survival (OS) of patients with GC. Only those OS-related ARGs were subsequently analyzed using multivariate Cox regression analysis in order to discover the ARGs that act as independent indicators of poor prognosis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116589", "locator": "sections[5] \"Establishment and evaluation of the ARGs-based PI model\" paragraph 2", "quote": "Univariate Cox regression analyses were performed to examine the relationship between each differentially expressed ARG and the overall survival (OS) of patients with GC. Only those OS-related ARGs were subsequently analyzed using multivariate Cox regression analysis in order to discover the ARGs that act as independent indicators of poor prognosis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "A variety of ARGs were obtained through the Human Autophagy Database (HADb, http://www.autophagy.lu/index.html).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116589", "locator": "sections[3] \"Data and information extraction\" paragraph 2", "quote": "A variety of ARGs were obtained through the Human Autophagy Database (HADb, http://www.autophagy.lu/index.html)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A seven-ARG prognostic index model was established as an independent prognostic indicator for patients with gastric cancer and was validated in the external GSE15460 cohort.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35116589", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of seven prognosis-related ARGs (HSPB8, NRG2, GABARAPL1, TMEM74, DLC1, MAP1LC3C and NRG3) were determined to establish a prognostic index (PI) model, which was demonstrated to be an independent prognostic indicator for patients with GC."}, {"asset": "source:pmid:35116589", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "More importantly, it was successfully validated in an external cohort of patients from the GSE15460 dataset, indicating the useful reproducibility of this signature."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A seven-ARG prognostic index model was established as an independent prognostic indicator for patients with gastric cancer and was validated in the external GSE15460 cohort.", "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:35116589"], "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:GSE15460"], "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:GSE15460"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35116589", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-21-191", "sha256": "sha256:ab04cff7134d88e83452758414715e3f557cc1ad4a01bd7cb0aa45fc710e10f0", "bytes": 23024, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-21-191", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8797385", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15460", "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=GSE15460", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15460", "version": null, "note": "A variety of ARGs were obtained through the Human Autophagy Database (HADb, http://www.autophagy.lu/index.html).", 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