Bakr Mohamed Nabil, Takahashi Haruko, Kikuchi Yutaka
Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
National Institute of Oceanography and Fisheries (NIOF), Cairo 11516, Egypt.
Biomedicines. 2022 Jun 22;10(7):1478. doi: 10.3390/biomedicines10071478.
Since the current melanoma clinicopathological staging system remains restricted to predicting survival outcomes, establishing precise prognostic targets is needed. Here, we used gene expression signature (GES) classification and Cox regression analyses to biologically characterize melanoma cells at the single-cell level and construct a prognosis-related gene signature for melanoma. By analyzing publicly available scRNA-seq data, we identified six distinct GESs (named: "Anti-apoptosis", "Immune cell interactions", "Melanogenesis", "Ribosomal biogenesis", "Extracellular structure organization", and "Epithelial-Mesenchymal Transition (EMT)"). We verified these GESs in the bulk RNA-seq data of patients with skin cutaneous melanoma (SKCM) from The Cancer Genome Atlas (TCGA). Four GESs ("Immune cell interactions", "Melanogenesis", "Ribosomal biogenesis", and "Extracellular structure organization") were significantly correlated with prognosis ( = 1.08 × 10, = 0.042, = 0.001, and = 0.031, respectively). We identified a prognostic signature of melanoma composed of 45 genes (MPS_45). MPS_45 was validated in TCGA-SKCM (HR = 1.82, = 9.08 × 10) and three other melanoma datasets (GSE65904: HR = 1.73, = 0.006; GSE19234: HR = 3.83, = 0.002; and GSE53118: HR = 1.85, = 0.037). MPS_45 was independently associated with survival ( = 0.002) and was proved to have a high potential for predicting prognosis in melanoma patients.
由于当前的黑色素瘤临床病理分期系统仍局限于预测生存结果，因此需要建立精确的预后指标。在此，我们使用基因表达特征（GES）分类和Cox回归分析，在单细胞水平对黑色素瘤细胞进行生物学特征分析，并构建黑色素瘤的预后相关基因特征。通过分析公开可用的scRNA-seq数据，我们鉴定出六种不同的GES（命名为：“抗凋亡”、“免疫细胞相互作用”、“黑色素生成”、“核糖体生物发生”、“细胞外结构组织”和“上皮-间质转化（EMT）”）。我们在来自癌症基因组图谱（TCGA）的皮肤黑色素瘤（SKCM）患者的批量RNA-seq数据中验证了这些GES。四种GES（“免疫细胞相互作用”、“黑色素生成”、“核糖体生物发生”和“细胞外结构组织”）与预后显著相关（分别为 = 1.08 × 10， = 0.042， = 0.001和 = 0.031）。我们鉴定出一个由45个基因组成的黑色素瘤预后特征（MPS_45）。MPS_45在TCGA-SKCM（HR = 1.82， = 9.08 × 10）和其他三个黑色素瘤数据集（GSE65904：HR = 1.73， = 0.006；GSE19234：HR = 3.83， = 0.002；和GSE53118：HR = 1.85， = 0.037）中得到验证。MPS_45与生存独立相关（ = 0.002），并被证明在预测黑色素瘤患者预后方面具有很高的潜力。
