Identification of a Metabolic Reprogramming-Associated Risk Model Related to Prognosis, Immune Microenvironment, and Immunotherapy of Stomach Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36185624", "kind": "science-record", "revision": 3, "content_hash": "sha256:d53d38a39ceae6afe931b78c0dfbb00371df9a22cf78214c7c50a05195932f1b", "created_at": "2026-11-01T18:15:28Z", "updated_at": "2026-11-01T21:29:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a Metabolic Reprogramming-Associated Risk Model Related to Prognosis, Immune Microenvironment, and Immunotherapy of Stomach Adenocarcinoma.", "doi": "10.1155/2022/7248572", "pmid": "36185624", "authors": ["Yan Zhao", "Dongsheng Zhang", "Yueming Sun"], "journal": "Journal of oncology", "year": 2022, "abstract": "Stomach adenocarcinoma (STAD) is one of the most common malignant digestive tumors. Metabolic reprogramming is an essential feature of tumorigenesis. The roles of metabolic reprogramming in STAD patients were investigated to explore the tumor immune microenvironment (TME) and potential therapeutic strategies. STAD samples' transcriptomic and clinical data were collected from The Cancer Genome Atlas (TCGA) set and the GSE84437 set. The signature based on the metabolism-related genes (MRGs) was built using the Cox regression model to predict prognosis in STAD. Notably, this MRG-based signature (MRGS) accurately predicted STAD patients' clinical survival in multiple datasets and could serve as an indicator independently. STAD patients with high scores on the MRGS were eligible for generating a type I/II interferon (IFN) response, according to a complete examination of the link between the MRGS and TME. Tumor Immune Dysfunction and Exclusion (TIDE) and immunophenoscore (IPS) analyses revealed that STAD patients with different MRGS scores had different reactions to immunotherapy. Consequently, assessing the pattern of these MRGs increases the understanding of TME features in STAD, hence directing the development of successful immunotherapy regimens.", "claims": [{"id": "claim-method", "statement": "The signature based on the metabolism-related genes (MRGs) was built using the Cox regression model to predict prognosis in STAD.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36185624", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The signature based on the metabolism-related genes (MRGs) was built using the Cox regression model to predict prognosis in STAD."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found in TCGA-STAD and GSE84437.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36185624", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found in TCGA-STAD and GSE84437."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The values of the area under the ROC curves performed in the TCGA training set were 0.659, 0.758, and 0.783, separately for 1-, 3-, and 5- year survival, suggesting that MRGS had a good performance in monitoring survival.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36185624", "locator": "sections[12] \"3.2. Valuation of the Predicting Ability of MRGS\" paragraph 2", "quote": "The values of the area under the ROC curves performed in the TCGA training set were 0.659, 0.758, and 0.783, separately for 1-, 3-, and 5- year survival, suggesting that MRGS had a good performance in monitoring survival."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The values of the area under the ROC curves performed in the TCGA training set were 0.659, 0.758, and 0.783, separately for 1-, 3-, and 5- year survival, suggesting that MRGS had a good performance in monitoring survival.", "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:36185624"], "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:GSE84437"], "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:GSE84437"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36185624", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/7248572", "sha256": "sha256:ba4b4752cf7153c66783907a0fcafc8a1e78c346b9ec34b421ce1fe6fcfc83a3", "bytes": 40224, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/7248572", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9519326", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84437", "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=GSE84437", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84437", "version": null, "note": "Publicly available datasets were analyzed in this study. 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