Chromosome instability-associated prognostic signature and cluster investigation for cutaneous melanoma cases.

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In this study, the authors first established a novel prognostic model of melanoma using the hub genes of CIN, based on the datasets of The cancer genome atlas-skin cutaneous melanoma (TCGA-SKCM) and GSE65904 cohorts. Based on the risk scores of our model, the disease-specific survival (DSS) prognosis was worse in the high-risk group. Combining risk score, stage, age, ulceration, and clark factors, a Nomogram was generated to predict 1, 3, 5-year survival rates, which indicated a good clinical validity. Our finding also showed a correlation between high/low risk and tumour infiltration levels of 'activated CD8 T cells' and 'effector memory CD8 T cells'. Moreover, the authors first performed a CIN-based tumour clustering analysis using TCGA-SKCM cases, and identified two melanoma clusters, which exhibit the distinct DSS prognosis and the tumour-infiltrating levels of CD8 T cells. Taken together, a promising CIN-related prognostic signature and clustering for melanoma cases were first established in our study.", "claims": [{"id": "claim-method", "statement": "After training on TCGA‐SKCM, the lasso regression modelling analysis (Figure 2d–e) was performed to determine the correlation coefficients for four hub genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37186446", "locator": "sections[11] \"Lasso regression model\" paragraph 2", "quote": "After training on TCGA‐SKCM, the lasso regression modelling analysis (Figure 2d–e) was performed to determine the correlation coefficients for four hub genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained the data from the datasets of TCGA, GEO, and UCSC XENA. All data could be available upon reasonable request to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37186446", "locator": "sections[21] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "We obtained the data from the datasets of TCGA, GEO, and UCSC XENA. All data could be available upon reasonable request to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "There were higher tumour‐infiltrating levels of overall tumour purity (Figure 6a, p = 1.8e–09), stromal cell (p = 1.8e–05), immune cell (p = 5.8e–11), ‘T cell CD8’ (Figure 6b–c, p = 0.00055), ‘activated CD8 T cells’ (Figure 6d–e, p = 2.3e–10) and ‘effector memory CD8 T cells’ (p = 2.5e–14) in low‐risk group, compared with those in the high‐risk group.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37186446", "locator": "sections[14] \"Prognostic risk‐related immune cell infiltration\" paragraph 2", "quote": "There were higher tumour‐infiltrating levels of overall tumour purity (Figure 6a, p = 1.8e–09), stromal cell (p = 1.8e–05), immune cell (p = 5.8e–11), ‘T cell CD8’ (Figure 6b–c, p = 0.00055), ‘activated CD8 T cells’ (Figure 6d–e, p = 2.3e–10) and ‘effector memory CD8 T cells’ (p = 2.5e–14) in low‐risk group, compared with those in the high‐risk group."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "There were higher tumour‐infiltrating levels of overall tumour purity (Figure 6a, p = 1.8e–09), stromal cell (p = 1.8e–05), immune cell (p = 5.8e–11), ‘T cell CD8’ (Figure 6b–c, p = 0.00055), ‘activated CD8 T cells’ (Figure 6d–e, p = 2.3e–10) and ‘effector memory CD8 T cells’ (p = 2.5e–14) in low‐risk group, compared with those in the high‐risk group.", "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:37186446"], "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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