Dataset Information

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

ABSTRACT: Chromosomal instability (CIN) is closely associated to the early detection of several clinical tumours. 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.

SUBMITTER: Liu N

PROVIDER: S-EPMC10280610 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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

Liu Ning N Liu Guangjing G Ma Qian Q Li Xiaobing X

IET systems biology 20230425 3

Chromosomal instability (CIN) is closely associated to the early detection of several clinical tumours. 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 fact ...[more]

PMID: 37186446

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Project description:BackgroundSkin cutaneous melanoma (SKCM) is the deadliest dermatology tumor. Ongoing researches have confirmed that the NOD-like receptors (NLRs) family are crucial in driving carcinogenesis. However, the function of NLRs signaling pathway-related genes in SKCM remains unclear.ObjectiveTo establish and identify an NLRs-related prognostic signature and to explore its predictive power for heterogeneous immune response in SKCM patients.MethodsEstablishment of the predictive signature using the NLRs-related genes by least absolute shrinkage and selection operator-Cox regression analysis (LASSO-COX algorithm). Through univariate and multivariate COX analyses, NLRs signature's independent predictive effectiveness was proven. CIBERSORT examined the comparative infiltration ratios of 22 distinct types of immune cells. RT-qPCR and immunohistochemistry implemented expression validation for critical NLRs-related prognostic genes in clinical samples.ResultsThe prognostic signature, including 7 genes, was obtained by the LASSO-Cox algorithm. In TCGA and validation cohorts, SKCM patients with higher risk scores had remarkably poorer overall survival. The independent predictive role of this signature was confirmed by multivariate Cox analysis. Additionally, a graphic nomogram demonstrated that the risk score of the NLRs signature has high predictive accuracy. SKCM patients in the low-risk group revealed a distinct immune microenvironment characterized by the significantly activated inflammatory response, interferon-α/γ response, and complement pathways. Indeed, several anti-tumor immune cell types were significantly accumulated in the low-risk group, including M1 macrophage, CD8 T cell, and activated NK cell. It is worth noting that our NLRs prognostic signature could serve as one of the promising biomarkers for predicting response rates to immune checkpoint blockade (ICB) therapy. Furthermore, the results of expression validation (RT-qPCR and IHC) were consistent with the previous analysis.ConclusionA promising NLRs signature with excellent predictive efficacy for SKCM was developed.

Dataset Information

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

Publications

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

Similar Datasets

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