Table1_Data-driven analysis to identify prognostic immune-related biomarkers in BRAF mutated cutaneous melanoma microenvironment.DOC

Skin cutaneous melanoma is one of the deadly diseases, and more than 50% of the patients have BRAF gene mutations. Evidence suggests that oncogenic BRAF modulates the immune system’s ability to recognize SKCM cells. Due to the complexity of the tumor microenvironment (TME) and a lack of a rational mechanistic basis, it is urgent to investigate the immune infiltration and identify prognostic biomarkers in BRAF mutated SKCM patients. Multiple methods including ESTIMATE algorithm, differential gene analysis, prognostic analysis and immune infiltration analysis were performed to investigate the tumor microenvironment. Based on the patient’s immune score and stromal score, immune-related genes DEGs were identified. Functional analysis revealed that these genes were mainly enriched in biological processes such as immune response, defense response and positive regulation of immune system. Furthermore, we analyzed the immune infiltrating cell components of BRAF mutated patients and revealed 4 hub genes associated with overall survival time. Several cells (Monocyte, Macrophage and Gamma delta cells) have been found to be significantly decreased in immune-high BRAF mutated SKCM group. While CD4+T, CD8+T, CD4 naïve, Tr1, Th2 and many T cell subsets were significantly increased in immune-high group. These immune cells and genes were closely related to each other. This study revealed that the dysregulation of immune function and immune cells may contribute to the poor outcomes of BRAF mutated patients. It is of great significance to our further understanding of the TME and immune dysfunction in BRAF mutated SKCM.

皮肤黑色素瘤（cutaneous melanoma, SKCM）是致死性疾病之一，超过50%的患者存在BRAF基因突变。现有证据表明，致癌性BRAF可调控免疫系统识别皮肤黑色素瘤细胞的能力。由于肿瘤微环境（tumor microenvironment, TME）结构复杂且缺乏合理的机制阐释基础，探究BRAF突变型皮肤黑色素瘤患者的免疫浸润特征并识别预后生物标志物已成为当务之急。本研究采用包括ESTIMATE算法、差异基因分析、预后分析及免疫浸润分析在内的多种方法对肿瘤微环境展开研究。基于患者的免疫评分与基质评分，筛选得到免疫相关差异表达基因（differentially expressed genes, DEGs）。功能富集分析显示，上述基因主要富集于免疫应答、防御应答及免疫系统正向调控等生物学过程。此外，本研究分析了BRAF突变型患者的免疫浸润细胞组成，揭示了4个与总生存期相关的核心枢纽基因。研究发现，在免疫高分BRAF突变型皮肤黑色素瘤组中，单核细胞（Monocyte）、巨噬细胞（Macrophage）及γδ T细胞（Gamma delta cells）的浸润水平显著降低；而CD4+T细胞、CD8+T细胞、初始CD4+T细胞（CD4 naïve）、1型调节性T细胞（Tr1）、2型辅助性T细胞（Th2）等多种T细胞亚群的浸润水平在免疫高分组中显著升高。这些免疫细胞与基因之间存在紧密关联。本研究揭示，免疫功能与免疫细胞的失调可能是BRAF突变型患者预后不良的潜在诱因。该研究对于进一步理解BRAF突变型皮肤黑色素瘤的肿瘤微环境及免疫功能异常具有重要意义。