Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33628633", "kind": "science-record", "revision": 8, "content_hash": "sha256:3609f8b5198bf47cf1870362586acb00258a4aebf11c6000c72d2d5791c7f8f4", "created_at": "2026-11-01T15:41:26Z", "updated_at": "2026-11-01T22:46:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma.", "doi": "10.7717/peerj.10680", "pmid": "33628633", "authors": ["Shaopeng Zheng", "Lintong Yao", "Fasheng Li", "Luyu Huang", "Yunfang Yu", "Zenan Lin", "Hao Li", "Jin Xia", "Michael Lanuti", "Haiyu Zhou"], "journal": "PeerJ", "year": 2021, "abstract": "OBJECTIVE: The current study aims to identify the dysregulated pathway involved in carcinogenesis and the essential survival-related dysregulated genes among this pathway in the early stage of lung adenocarcinoma (LUAD).\nPATIENTS AND METHODS: Data from The Cancer Genome Atlas (TCGA) including 526 tumor tissues of LUAD and 59 healthy lung tissues were analyzed to gain differentially expressed genes (DEGs). Gene ontology (GO) analysis was conducted with DAVID, while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs was performed, followed by gene set enrichment analysis (GSEA) methods. Survival analysis was implemented in TCGA dataset and validated in Gene Expression Omnibus (GEO) cohort GSE50081, which includes 127 patients with stage I LUAD.\nRESULTS: GSEA enrichment analysis suggested that homologous recombination repair (HRR) pathway was significantly enriched. Subsequent KEGG pathway enrichment analysis indicated the significant up-regulation of HRR pathway in patients with T1 stage LUAD. Retrieved in Gene database, RAD54L is involved in HRR pathway and were recognized to be significantly differentially expressed in T1 stage LUAD in our study. The survival analysis indicated that high expression of RAD54L was significantly related to worse overall survival in patients with T1 stage LUAD (TCGA cohort: HR=2.10, 95% CI [1.47-2.98], P = 0.001; GSE50081 validation cohort: HR = 2.61, 95% CI [1.51-4.52], P = 0.002). Multivariate cox regression analysis indicated that RAD54L is an independent prognostic factor in the early-stage LUAD.\nCONCLUSION: HRR pathway is up-regulated in LUAD, among which the expression of RAD54L was found to be significantly differentially expressed in T1 stage tumor tissue. Patients with high expression of RAD54L were associated with worse overall survival in the TCGA cohort and validation cohort. This study suggests a potential mechanism of lung cancer progression and provide a budding prognostic factor and treatment target in early-stage LUAD.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes are extracted by limma package with the standard of the absolute value of log2 fold change more than 1, and the adjusted P value less than 0.05. Benjamini–Hochberg false discovery rate method was applied to adjust P value and decrease the false positive rate.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33628633", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Differentially expressed genes are extracted by limma package with the standard of the absolute value of log2 fold change more than 1, and the adjusted P value less than 0.05. Benjamini–Hochberg false discovery rate method was applied to adjust P value and decrease the false positive rate."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nRaw data are available at The Cancer Genome Atlas (TCGA-LUAD: https://portal.gdc.cancer.gov/projects/TCGA-LUAD) and at NCBI GEO (GSE50081).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33628633", "locator": "sections[25] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nRaw data are available at The Cancer Genome Atlas (TCGA-LUAD: https://portal.gdc.cancer.gov/projects/TCGA-LUAD) and at NCBI GEO (GSE50081)."}], "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:33628633"], "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:GSE50081"], "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": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate adjustment"}, "inputs": ["data:geo:GSE50081"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33628633", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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