Identification of Ubiquitin-Related Gene-Pair Signatures for Predicting Tumor Microenvironment Infiltration and Drug Sensitivity of Lung Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35884544", "kind": "science-record", "revision": 3, "content_hash": "sha256:e818bd6b539594a6b62802a243724d45e343b102b18f458578d252b49ffbf9b8", "created_at": "2026-11-01T18:14:58Z", "updated_at": "2026-11-01T21:28:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Ubiquitin-Related Gene-Pair Signatures for Predicting Tumor Microenvironment Infiltration and Drug Sensitivity of Lung Adenocarcinoma.", "doi": "10.3390/cancers14143478", "pmid": "35884544", "authors": ["Yumei Li", "Lanfen An", "Zhe Jia", "Jingxia Li", "E Zhou", "Feng Wu", "Zhengrong Yin", "Wei Geng", "Tingting Liao", "Wenjing Xiao", "Jingjing Deng", "Wenjuan Chen", "Minglei Li", "Yang Jin"], "journal": "Cancers", "year": 2022, "abstract": "Lung adenocarcinoma (LUAD) is a common pathological type of lung cancer worldwide, and new biomarkers are urgently required to guide more effective individualized therapy for patients. Ubiquitin-related genes (UbRGs) partially participate in the initiation and progression of lung cancer. In this study, we used ubiquitin-related gene pairs (UbRGPs) in tumor tissues to access the function of UbRGs in overall survival, immunocyte infiltration, and tumor mutation burden (TMB) of patients with LUAD from The Cancer Genome Atlas (TCGA) database. In addition, we constructed a prognostic signature based on six UbRGPs and evaluated its performance in an internal (TCGA testing set) and an external validation set (GSE13213). The prognostic signature revealed that risk scores were negatively correlated with the overall survival, immunocyte infiltration, and expression of immune checkpoint inhibitor-related genes and positively correlated with the TMB. Patients in the high-risk group showed higher sensitivity to partially targeted and chemotherapeutic drugs than those in the low-risk group. This study contributes to the understanding of the characteristics of UbRGPs in LUAD and provides guidance for effective immuno-, chemo-, and targeted therapy.", "claims": [{"id": "claim-method", "statement": "Subsequently, the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm and stepwise multivariate Cox proportional hazard regression analysis were used to construct the UbRGP-based prognostic signature in the training cohort.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35884544", "locator": "sections[8] \"2.6. Establishment and Evaluation of UbRGPs-Related Prognostic Signature\" paragraph 2", "quote": "Subsequently, the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm and stepwise multivariate Cox proportional hazard regression analysis were used to construct the UbRGP-based prognostic signature in the training cohort."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data are available from the public databases, including the TCGA database (https://portal.gdc.cancer.gov/, last accessed on 30 January 2022), GEO database (https://www.ncbi.nlm.nih.gov/geo/, last accessed on 20 December 2021), and iUUCD 2.0 database (http://iuucd.biocuckoo.org/, last accessed on 10 October 2021), and GSEA analysis (http://www.broadinstitute.org/gsea, last accessed on 24 March 2022).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35884544", "locator": "sections[30] \"notes\" paragraph 1", "quote": "All the data are available from the public databases, including the TCGA database (https://portal.gdc.cancer.gov/, last accessed on 30 January 2022), GEO database (https://www.ncbi.nlm.nih.gov/geo/, last accessed on 20 December 2021), and iUUCD 2.0 database (http://iuucd.biocuckoo.org/, last accessed on 10 October 2021), and GSEA analysis (http://www.broadinstitute.org/gsea, last accessed on 24 March 2022)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A prognostic signature based on six UbRGPs was established, which performed well in predicting the immune infiltration and tumor mutation burden (TMB) in the TME and the response of LUAD to immuno-, chemo-, and targeted therapy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35884544", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A prognostic signature based on six UbRGPs was established, which performed well in predicting the immune infiltration and tumor mutation burden (TMB) in the TME and the response of LUAD to immuno-, chemo-, and targeted therapy."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A prognostic signature based on six UbRGPs was established, which performed well in predicting the immune infiltration and tumor mutation burden (TMB) in the TME and the response of LUAD to immuno-, chemo-, and targeted therapy.", "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:35884544"], "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. 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