LncRNA weighted gene co-expression network analysis reveals novel biomarkers related to prostate cancer metastasis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36514044", "kind": "science-record", "revision": 2, "content_hash": "sha256:23044013553554497c4c61298f3ada492fae532ff170c45692148fc080ec2b7f", "created_at": "2026-11-01T19:01:01Z", "updated_at": "2026-11-01T21:29:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "LncRNA weighted gene co-expression network analysis reveals novel biomarkers related to prostate cancer metastasis.", "doi": "10.1186/s12920-022-01410-w", "pmid": "36514044", "authors": ["Miao Liu", "Man-Yun Chen", "Jia-Meng Huang", "Qian Liu", "Lin Wang", "Rong Liu", "Nian Yang", "Wei-Hua Huang", "Wei Zhang"], "journal": "BMC medical genomics", "year": 2022, "abstract": "BACKGROUND: Most prostate cancer patients die from metastasis and lack accurate efficacious biomarkers to monitor the disease behavior, optimize treatment and assess prognosis. Herein, we aimed to identify meaningful lncRNA biomarkers associated with prostate cancer metastatic progression.\nMETHODS: By repurposing microarray probes, 11,624 lncRNAs in prostate cancer were obtained from Gene Expression Omnibus database (GSE46691, N = 545; GSE29079, N = 235; GSE94767, N = 130). Weighted gene co-expression network analysis was applied to determine the co-expression lncRNA network pertinent to metastasis. Hub lncRNAs were screened. RNA-seq and clinical data from the Cancer Genome Atlas prostate cancer (TCGA-PRAD) cohort (N = 531) were analyzed. Transwell assay and bioinformatic analysis were performed for mechanism research.\nRESULTS: The high expression levels of nine hub lncRNAs (FTX, AC005261.1, NORAD, LINC01578, AC004542.2, ZFAS1, EBLN3P, THUMPD3-AS1, GAS5) were significantly associated with Gleason score and increased probability of metastatic progression. Among these lncRNAs, ZFAS1 had the consistent trends of expression in all of the analysis from different cohorts, and the Kaplan-Meier survival analyses showed higher expression of ZFAS1 was associated with shorter relapse free survival. In-vitro studies confirmed that downregulation of ZFAS1 decreased prostate cancer cell migration.\nCONCLUSION: We offered some new insights into discovering lncRNA markers correlated with metastatic progression of prostate cancer using the WGCNA. Some may serve as potential prognostic biomarkers and therapeutic targets for advanced metastatic prostate cancer.", "claims": [{"id": "claim-method", "statement": "Weighted gene co-expression network analysis was applied to determine the co-expression lncRNA network pertinent to metastasis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36514044", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Weighted gene co-expression network analysis was applied to determine the co-expression lncRNA network pertinent to metastasis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. All datasets for this study are included in the article. The authors acknowledge the efforts of all of the researchers who have contributed the data to the public databases of GEO (https://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE46691; GSE29079 and GSE94767, and the cancer genome database TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). The interpretation and reporting of these data are the sole responsibility of the authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36514044", "locator": "sections[26] \"Availability of data and materials\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. All datasets for this study are included in the article. The authors acknowledge the efforts of all of the researchers who have contributed the data to the public databases of GEO (https://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE46691; GSE29079 and GSE94767, and the cancer genome database TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). The interpretation and reporting of these data are the sole responsibility of the authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The high expression levels of nine hub lncRNAs (FTX, AC005261.1, NORAD, LINC01578, AC004542.2, ZFAS1, EBLN3P, THUMPD3-AS1, GAS5) were significantly associated with Gleason score and increased probability of metastatic progression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36514044", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The high expression levels of nine hub lncRNAs (FTX, AC005261.1, NORAD, LINC01578, AC004542.2, ZFAS1, EBLN3P, THUMPD3-AS1, GAS5) were significantly associated with Gleason score and increased probability of metastatic progression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The high expression levels of nine hub lncRNAs (FTX, AC005261.1, NORAD, LINC01578, AC004542.2, ZFAS1, EBLN3P, THUMPD3-AS1, GAS5) were significantly associated with Gleason score and increased probability of metastatic progression.", "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:36514044"], "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:GSE29079"], "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:GSE29079"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36514044", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-022-01410-w", "sha256": "sha256:9ebca3e2ab8a75ffb8299aa52c77382b6ceda271147216d46186b6c19603f67e", "bytes": 54155, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-022-01410-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9745985", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29079", "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=GSE29079", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29079", "version": null, "note": "Publicly available datasets were analyzed in this study. All datasets for this study are included in the article. The authors acknowledge the efforts of all of the researchers who have contributed the data to the public databases of GEO (https://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE46691; GSE29079 and GSE94767, and the cancer genome database TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). The interpretation and reporting of these data are the sole responsibility of the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. All datasets for this study are included in the article. The authors acknowledge the efforts of all of the researchers who have contributed the data to the public databases of GEO (https://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE46691; GSE29079 and GSE94767, and the cancer genome database TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). The interpretation and reporting of these data are the sole responsibility of the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM720503", "GSM720504", "GSM720505", "GSM720506", "GSM720507", "GSM720508", "GSM720509", "GSM720510", "GSM720511", "GSM720512", "GSM720513", "GSM720514", "GSM720515", "GSM720516", "GSM720517", "GSM720518", "GSM720519", "GSM720520", "GSM720521", "GSM720522", "GSM720523", "GSM720524", "GSM720525", "GSM720526", "GSM720527", "GSM720528", "GSM720529", "GSM720530", "GSM720531", "GSM720532", "GSM720533", "GSM720534", "GSM720535", "GSM720536", "GSM720537", "GSM720538", "GSM720539", "GSM720540", "GSM720541", "GSM720542", "GSM720543", "GSM720544", "GSM720545", "GSM720546", "GSM720547", "GSM720548", "GSM720549", "GSM720550", "GSM720551", "GSM720552", "GSM720553", "GSM720554", "GSM720555", "GSM720556", "GSM720557", "GSM720558", "GSM720559", "GSM720560", "GSM720561", "GSM720562", "GSM720563", "GSM720564", "GSM720565", "GSM720566", "GSM720567", "GSM720568", "GSM720569", "GSM720570", "GSM720571", "GSM720572", "GSM720573", "GSM720574", "GSM720575", "GSM720576", "GSM720577", "GSM720578", "GSM720579", "GSM720580", "GSM720581", "GSM720582", "GSM720583", "GSM720584", "GSM720585", "GSM720586", "GSM720587", "GSM720588", "GSM720589", "GSM720590", "GSM720591", "GSM720592", "GSM720593", "GSM720594", "GSM720595", "GSM720596", "GSM720597"], "sample_count": 95, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Gene expression profiles of 48 normal and 47 prostate tumor tissue samples", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE46691", "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=GSE46691", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46691", "version": null, "note": "Publicly available datasets were analyzed in this study. All datasets for this study are included in the article. The authors acknowledge the efforts of all of the researchers who have contributed the data to the public databases of GEO (https://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE46691; GSE29079 and GSE94767, and the cancer genome database TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). The interpretation and reporting of these data are the sole responsibility of the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. All datasets for this study are included in the article. The authors acknowledge the efforts of all of the researchers who have contributed the data to the public databases of GEO (https://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE46691; GSE29079 and GSE94767, and the cancer genome database TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). 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prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE94767", "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=GSE94767", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE94767", "version": null, "note": "Publicly available datasets were analyzed in this study. All datasets for this study are included in the article. The authors acknowledge the efforts of all of the researchers who have contributed the data to the public databases of GEO (https://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE46691; GSE29079 and GSE94767, and the cancer genome database TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). The interpretation and reporting of these data are the sole responsibility of the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. All datasets for this study are included in the article. The authors acknowledge the efforts of all of the researchers who have contributed the data to the public databases of GEO (https://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE46691; GSE29079 and GSE94767, and the cancer genome database TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). 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