Differences in the Tumor Immunity-related Gene Expression Profile Between Acral lentiginous and Non-acral Melanoma

Supplement table Ⅰ. Clinicopathological features of patients in our study Supplement table Ⅱ. Materials and methods of gene expression analysis Supplement table Ⅲ. Lists of differentially expressed genes in acral lentiginous melanoma compared to non-acral cutaneous melanoma Supplement table Ⅳ. Undirected and directed global significance scores of 18 pathways Supplement figure 1. Tumor immune-related gene expression profile of acral lentiginous melanoma (ALM) and non-acral cutaneous melanoma (NACM). Heatmap of unsupervised hierarchical clustering of total genes, MA plot, and principal component analysis plot showed that tumor immune-related genes were differently expressed between ALM and NACM, but ALM and NACM were not classified into separate clusters. Supplement figure 2. Volcano plots of each pathway that was significantly different in gene set enrichment analysis between acral lentiginous melanoma (ALM) and non-acral cutaneous melanoma (NACM). Whole genes are described as gray dots, while genes within the selected gene set are highlighted in yellow squares. Supplement figure 3. Immune cell profile analysis of acral lentiginous melanoma (ALM) and non-acral cutaneous melanoma (NACM). Pairwise box plots of immune-cell abundance scores obtained from the NanoString nSolver program and total score of tumor-infiltrating lymphocytes (TILs) according to melanoma subtype revealed that neutrophils were more abundant while total TILs were lowered in ALM. Supplement figure 4. Immune cell profile analysis using Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) of acral lentiginous melanoma (ALM) and non-acral cutaneous melanoma (NACM). Pairwise box plots of immune-cell scores revealed resting dendritic cells, neutrophils, and M2 macrophage subtypes were abundant in ALM than NACM. Supplement figure 5. Immunohistochemistry of acral lentiginous melanoma (ALM) and non-acral cutaneous melanoma (NACM). Representative histograms of ALM and positivity ratio of CXCL-5 /ENA-78, Cartilage oligometric matrix protein (COMP), LAG-3, and CD163 according to the melanoma subtype. (CXCL-5 /ENA-78, ×200; COMP, ×200; LAG3, ×100, CD163, ×200). ns: not significant Supplement figure 6. Gene expression profiles of normal human skin dataset (gene expression omnibus (GEO) accession number GSE5591, platform number GPL4213) according to anatomical site (acral versus non-acral). Volcano plot, adjusted p-value histogram, uniform manifold approximation and projection (UMAP), and MA plot revealed that there was no statistically significant difference (adjusted p-value <0.05) between acral and non-acral sites.补充表Ⅰ. 本研究纳入患者的临床病理特征 补充表Ⅱ. 基因表达分析的材料与方法 补充表Ⅲ. 肢端雀斑样黑色素瘤（acral lentiginous melanoma, ALM）与非肢端皮肤黑色素瘤（non-acral cutaneous melanoma, NACM）相比的差异表达基因列表 补充表Ⅳ. 18条通路的无向与有向全局显著性评分 补充图1. 肢端雀斑样黑色素瘤（ALM）与非肢端皮肤黑色素瘤（NACM）的肿瘤免疫相关基因表达谱。对全部基因进行无监督层次聚类的热图、MA图以及主成分分析图结果显示，两类黑色素瘤的肿瘤免疫相关基因表达存在差异，但ALM与NACM并未被划分为独立聚类簇。 补充图2. 肢端雀斑样黑色素瘤（ALM）与非肢端皮肤黑色素瘤（NACM）间基因集富集分析中显著差异的每条通路的火山图。全部基因以灰色圆点表示，所选基因集中的基因以黄色方块高亮标注。 补充图3. 肢端雀斑样黑色素瘤（ALM）与非肢端皮肤黑色素瘤（NACM）的免疫细胞谱分析。根据黑色素瘤亚型，通过NanoString nSolver程序获得的免疫细胞丰度评分以及肿瘤浸润淋巴细胞（TILs）总评分的成对箱线图结果显示，ALM中中性粒细胞丰度更高，而总TILs水平更低。 补充图4. 基于相对RNA转录本子集估算细胞类型（Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts, CIBERSORT）的肢端雀斑样黑色素瘤（ALM）与非肢端皮肤黑色素瘤（NACM）免疫细胞谱分析。免疫细胞评分的成对箱线图结果显示，ALM中静息树突状细胞、中性粒细胞以及M2巨噬细胞亚型的丰度高于NACM。 补充图5. 肢端雀斑样黑色素瘤（ALM）与非肢端皮肤黑色素瘤（NACM）的免疫组化分析。展示了ALM的代表性免疫组化图像，以及不同黑色素瘤亚型中CXCL-5/ENA-78、软骨寡聚基质蛋白（COMP）、淋巴细胞活化基因3（LAG-3）以及CD163的阳性比例。（CXCL-5/ENA-78：×200；COMP：×200；LAG3：×100；CD163：×200）。ns：无统计学意义 补充图6. 基于解剖部位（肢端vs非肢端）的正常人体皮肤数据集基因表达谱（基因表达综合（Gene Expression Omnibus, GEO）登录号GSE5591，平台编号GPL4213）。火山图、校正后p值直方图、统一流形近似与投影（Uniform Manifold Approximation and Projection, UMAP）以及MA图结果显示，肢端与非肢端部位间无统计学显著差异（校正后p值<0.05）。