Identification of a Prognostic Transcriptome Signature for Hepatocellular Carcinoma with Lymph Node Metastasis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35847584", "kind": "science-record", "revision": 4, "content_hash": "sha256:40a71ef78292c52b4aad7596a0fa7085dd014add759927a9bffff04291193d9d", "created_at": "2026-11-01T18:14:55Z", "updated_at": "2026-11-01T22:07:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a Prognostic Transcriptome Signature for Hepatocellular Carcinoma with Lymph Node Metastasis.", "doi": "10.1155/2022/7291406", "pmid": "35847584", "authors": ["Jie Ma", "Xue-Qin Chen", "Zuo-Lin Xiang"], "journal": "Oxidative medicine and cellular longevity", "year": 2022, "abstract": "Hepatocellular carcinoma (HCC) is one of the most aggressive malignant tumors, and the prognosis of HCC patients with lymph node metastasis (LNM) is poor. However, robust biomarkers for predicting the prognosis of HCC LNM are still lacking. This study used weighted gene coexpression network analysis of GSE28248 (N = 80) microarray data to identify gene modules associated with HCC LNM and validated in GSE40367 dataset (N = 18). The prognosis-related genes in the HCC LNM module were further screened based on the prognostic curves of 371 HCC samples from TCGA. We finally developed a prognostic signature, PSG-30, as a prognostic-related biomarker in HCC LNM. The HCC subtypes identified by PSG-30-based consensus clustering analysis showed significant differences in prognosis, clinicopathological stage, m6A modification, ferroptosis activation, and immune characteristics. In addition, RAD54B was selected by regression model as an independent risk factor affecting the prognosis of HCC patients with LNM, and its expression was significantly positively correlated with tumor mutational burden and microsatellite instability in high-risk subtypes. Patients with high RAD54B expression had a better prognosis in the immune checkpoint inhibitor-treated cohorts but had a poor prognosis in the HCC sorafenib-treated group. The association of high RAD54B expression with LNM in breast cancer (BRCA) and cholangiocarcinoma and its prognostic effect in BRCA LNM cases suggest the value of RAD54B at the pancancer level. In conclusion, PSG-30 can effectively identify HCC LNM population with poor prognosis, and high-risk patients with high RAD54B expression may be more suitable for immunotherapy.", "claims": [{"id": "claim-method", "statement": "Specifically, the Pearson correlation matrix and average linkage method were first used for paired genes, and the power function a|mn = |C|mn^β (c | mn = Pearson correlation between gene m and gene n; a | mn = adjacency between gene m and gene n) was then used for weighted adjacency matrix construction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35847584", "locator": "sections[5] \"2.3. 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All data relevant to the study are included in the article or uploaded as supplementary information."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Weighted gene coexpression network analysis of GSE28248 (N = 80) identified HCC LNM-associated gene modules and was validated with GSE40367 (N = 18), ultimately yielding PSG-30.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35847584", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study used weighted gene coexpression network analysis of GSE28248 (N = 80) microarray data to identify gene modules associated with HCC LNM and validated in GSE40367 dataset (N = 18)."}, {"asset": "source:pmid:35847584", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We finally developed a prognostic signature, PSG-30, as a prognostic-related biomarker in HCC LNM."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Weighted gene coexpression network analysis of GSE28248 (N = 80) identified HCC LNM-associated gene modules and was validated with GSE40367 (N = 18), ultimately yielding PSG-30.", "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:35847584"], "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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