Single-cell and bulk RNA sequencing data jointly reveals VDAC2's impacts on prognosis and immune landscape of NSCLC.

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In present study, NSCLC cell clusters were extracted from single cell-sequencing dataset GSE131907, which were combined with hypoxia-related genes to group clusters. qRT-PCR and western blot were used to validate the expression of target gene. Nine NSCLC clusters were extracted, which were divided into two hypoxia-related subgroups, C1 and C2. Totally 101 differentially expressed prognostic genes were identified between subgroups. Of which, VDAC2 showed excellent prognostic value for NSCLC and was selected for further analysis. VDAC2 was upregulated in tumor samples in TCGA and was correlated with advanced stages. In vitro experiments validated this trend. Five crucial immune cells showed differential infiltration proportions between high and low VDAC2 expression groups. VDAC2 knockdown significantly inhibited the proliferation and invasion ability of NSCLC cells. Integrating single cell and bulk sequencing data as well as wet lab experiments, hypoxia-related VDAC2 exhibited important prognostic value and showed the promise of becoming immune-therapy target in NSCLC.", "claims": [{"id": "claim-method", "statement": "Among the marker genes in the hypoxia-related heterogeneous NSCLC subpopulations, C1 and C2, 101 genes were identified to be associated with prognosis of patients by univariate Cox regression analysis (Supplementary Table 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38382091", "locator": "sections[5] \"Hypoxia heterogeneous NSCLC subpopulation related VDAC2 showed important prognostic value in NSCLC\" paragraph 2", "quote": "Among the marker genes in the hypoxia-related heterogeneous NSCLC subpopulations, C1 and C2, 101 genes were identified to be associated with prognosis of patients by univariate Cox regression analysis (Supplementary Table 1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analyzed during the current study are available from the Gene Expression Omnibus (GEO) datasets (http://www.ncbi.nlm.nih.gov/geo) and The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38382091", "locator": "sections[28] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated and analyzed during the current study are available from the Gene Expression Omnibus (GEO) datasets (http://www.ncbi.nlm.nih.gov/geo) and The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Integrating single cell and bulk sequencing data as well as wet lab experiments, hypoxia-related VDAC2 exhibited important prognostic value and showed the promise of becoming immune-therapy target in NSCLC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38382091", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Integrating single cell and bulk sequencing data as well as wet lab experiments, hypoxia-related VDAC2 exhibited important prognostic value and showed the promise of becoming immune-therapy target in NSCLC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Integrating single cell and bulk sequencing data as well as wet lab experiments, hypoxia-related VDAC2 exhibited important prognostic value and showed the promise of becoming immune-therapy target in NSCLC.", "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:38382091"], "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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