Jiang Feng, Wu Chuyan, Wang Ming, Wei Ke, Zhou Guoping, Wang Jimei
Neonatal Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China.
Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
Clin Chim Acta. 2020 Dec;511:306-318. doi: 10.1016/j.cca.2020.10.030. Epub 2020 Oct 24.
In multiple malignancies, whether tumor mutation burden (TMB) correlated with increased survival or promotion of immunotherapy remained a debate. Our aim was to analyze the prognosis of TMB and the possible connection with immune infiltration of the skin cutaneous melanoma (SKCM).
We gathered somatic mutation data from the 472 SKCM patients using the Cancer Genome Atlas (TCGA) database and analyzed the mutation profiles using ""maftools" package. TMB was determined and samples were divided into high and low TMB groups. We undertook differential analysis to determine the profiles of expression between two groups using the "limma" package and established the 10 Hub TMB signature from a batch survival study. Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Set Enrichment Analysis (GSEA) were performed in order to test considerably enriched pathways between the two groups. The connections of 10 TMB-related signature mutants with immune infiltration in SKCM were further assessed based on the TIMER database. We used the CIBERSORT package to measure the amount of 22 immune fractions between low and high TMB groups, and Wilcoxon's rank-sum amounts estimated the significant difference. In addition, the Cox regression model and survival analysis were used to determine the prognostic importance of immune cells. Finally, we estabilished a multivaried Cox results Tumor Mutation Burden Prognostic Index (TMBPI) and built a Receiver Operating Characteristic (ROC) curve to check the predictive accuracy.
Single nucleotide polymorphism (SNP) was more frequent than insertion or deletion and C > T was SKCM's most frequently single nucleotide variants (SNV). Higher TMB levels provided poor survival outcomes, associated with tumor stage, age, and gender. In addition, 224 differentially expressed genes were obtained and Venn diagram established the top 25 immune-related genes. GSEA observed that patients in high TMB groups associated with nucleotide excision repair, pyrimidine metabolism, basal transcription factors, spliceosome, RNA polymerase, and RNA degradation in cancers. 10 hub TMB-related immune genes were also established and 10 signature mutants were correlated with lower immune infiltrates. In addition, the infiltration levels of macrophages M1 and macrophages M2 in the low-TMB group were lower. Eventually, the TMBPI was developed and the AUC of ROC curve was 0.604.
High TMB contributed to low survival outcomes and may prevent SKCM immune infiltration. The 10 hub immune signature TMB-related mutants conferred lower immune cell infiltration that required further confirmation.
在多种恶性肿瘤中，肿瘤突变负荷（TMB）是否与生存率提高或免疫治疗的促进相关仍存在争议。我们的目的是分析TMB对皮肤黑色素瘤（SKCM）的预后影响以及与免疫浸润的可能联系。
我们使用癌症基因组图谱（TCGA）数据库收集了472例SKCM患者的体细胞突变数据，并使用“maftools”软件包分析突变谱。确定TMB并将样本分为高TMB组和低TMB组。我们使用“limma”软件包进行差异分析以确定两组之间的表达谱，并通过批量生存研究建立了10个核心TMB特征。进行基因本体（GO）分析、京都基因与基因组百科全书（KEGG）分析和基因集富集分析（GSEA），以检测两组之间显著富集的通路。基于TIMER数据库进一步评估10个与TMB相关的特征突变体与SKCM免疫浸润的联系。我们使用CIBERSORT软件包测量低TMB组和高TMB组之间22种免疫细胞成分的数量，Wilcoxon秩和检验估计显著差异。此外，使用Cox回归模型和生存分析来确定免疫细胞的预后重要性。最后，我们建立了多变量Cox结果肿瘤突变负荷预后指数（TMBPI）并构建了受试者工作特征（ROC）曲线以检验预测准确性。
单核苷酸多态性（SNP）比插入或缺失更频繁，C>T是SKCM最常见的单核苷酸变异（SNV）。较高的TMB水平导致较差的生存结果，与肿瘤分期、年龄和性别相关。此外，获得了224个差异表达基因，维恩图确定了前25个免疫相关基因。GSEA观察到高TMB组患者与癌症中的核苷酸切除修复、嘧啶代谢、基础转录因子、剪接体、RNA聚合酶和RNA降解相关。还建立了10个核心TMB相关免疫基因，10个特征突变体与较低的免疫浸润相关。此外，低TMB组中M1巨噬细胞和M2巨噬细胞的浸润水平较低。最终，开发了TMBPI，ROC曲线的AUC为0.604。
高TMB导致低生存结果，并可能阻止SKCM免疫浸润。10个核心TMB相关免疫特征突变体导致较低的免疫细胞浸润，这需要进一步证实。
