Integrated analysis of multiple transcriptomic data identifies ST8SIA6‑AS1 and LINC01093 as potential biomarkers in HBV‑associated liver cancer.

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Therefore, the aim of the present study was to investigate the regulatory mechanisms of lncRNAs in this disease. HBV-liver cancer related transcriptome expression profile data (GSE121248 and GSE55092) from the Gene Expression Omnibus database and survival prognosis information from The Cancer Genome Atlas (TCGA) database were obtained for analysis. The limma package was used to identify the overlapped differentially expressed RNAs (DERs), including DElncRNAs and DEmRNAs, in the GSE121248 and GSE55092 datasets. The screened optimized lncRNA signatures were used to develop a nomogram model based on the GSE121248 dataset, which was validated using the GSE55092 and TCGA datasets. A competitive endogenous RNA (ceRNA) network was constructed based on the screened prognosis-associated lncRNA signatures from TCGA dataset. In addition, the levels of specific lncRNAs were evaluated in HBV-infected human liver cancer tissues and cells, and Cell Counting Kit-8, ELISA and Transwell assays were performed to evaluate the effects of the lncRNAs in HBV-expressing liver cancer cells. A total of 535 overlapped DERs, including 30 DElncRNAs and 505 DEmRNAs, were identified in the GSE121248 and GSE55092 datasets. An optimized DElncRNA signature comprising 10 lncRNAs was used to establish a nomogram. ST8SIA6-AS1 and LINC01093 were identified as lncRNAs associated with HBV-liver cancer prognosis in TCGA dataset, and were applied to construct a ceRNA network. Reverse transcription-quantitative PCR analysis showed that ST8SIA6-AS1 was upregulated and LINC01093 was downregulated in HBV-infected human liver cancer tissues and HBV-expressing liver cancer cells compared with non-HBV-infected controls. ST8SIA6-AS1 knockdown and LINC01093 overexpression independently reduced the number of copies of HBV DNA, the levels of hepatitis B surface antigen and hepatitis B e antigen, as well as cell proliferation, migration and invasion. In summary, the present study identified ST8SIA6-AS1 and LINC01093 as two potential biomarkers that may be effective therapeutic targets for HBV-associated liver cancer.", "claims": [{"id": "claim-method", "statement": "The limma package of R3.6.1 version 3.34.7 (20) was utilized to screen the DERs, including DElncRNAs and DEmRNAs, between the HBV-liver cancer and normal control groups in GSE121248 and GSE55092.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37065781", "locator": "sections[4] \"Screening of overlapped differentially expressed RNAs (DERs)\" paragraph 2", "quote": "The limma package of R3.6.1 version 3.34.7 (20) was utilized to screen the DERs, including DElncRNAs and DEmRNAs, between the HBV-liver cancer and normal control groups in GSE121248 and GSE55092."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37065781", "locator": "sections[27] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The limma package was used to screen differentially expressed RNAs between HBV-liver cancer and normal control groups in the GSE121248 and GSE55092 datasets.", "kind": "quantitative", "target": {"value": 3.6, "unit": "correlation coefficient", "tolerance": null, "source": "The limma package of R3.6.1 version 3.34.7 (20) was utilized to screen the DERs, including DElncRNAs and DEmRNAs, between the HBV-liver cancer and normal control groups in GSE121248 and GSE55092."}, "evidence": [{"asset": "source:pmid:37065781", "locator": "sections[4] \"Screening of overlapped differentially expressed RNAs (DERs)\" paragraph 2", "quote": "The limma package of R3.6.1 version 3.34.7 (20) was utilized to screen the DERs, including DElncRNAs and DEmRNAs, between the HBV-liver cancer and normal control groups in GSE121248 and GSE55092."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The limma package was used to screen differentially expressed RNAs between HBV-liver cancer and normal control groups in the GSE121248 and GSE55092 datasets.", "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:37065781"], "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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