Exploration of the relationships between tumor mutation burden with immune infiltrates in clear cell renal cell carcinoma.

Whether tumor mutation burden (TMB) correlated with improved survival outcomes or promotion of immunotherapies remained controversy in various malignancies. We aimed to investigate the prognosis of TMB and the potential association with immune infiltrates in clear cell renal cell carcinoma (ccRCC). We downloaded the somatic mutation data of 336 ccRCC patients from the Cancer Genome Atlas (TCGA) database, and analyzed the mutation profiles with "maftools" package. TMB was calculated and we classified the samples into high-TMB and low-TMB group. Differential analysis was conducted to compare the expression profiles between two groups using "limma" package, and we identified the 9 hub TMB-related signature from batch survival analysis. Gene ontology (GO) analysis and Gene Set Enrichment Analysis (GSEA) were performed to screen significantly enriched pathways between two groups. Based on the TIMER database, we further assessed the relationships of the mutants of 9 TMB-related signature with immune infiltration levels in ccRCC. Besides, we utilized the "CIBERSORT" package to estimate the abundance of 22 immune fractions between low- and high-TMB groups, and the significant difference were determined by Wilcoxon rank-sum test. Furthermore, Cox regression model combined with survival analysis were used to evaluate the prognostic value of immune cells. Last, we constructed a Tumor Mutation Burden Prognostic Index (TMBPI) from multivariate Cox results and Receiver Operating Characteristic (ROC) curve was drawn to assess the predictive accuracy. Single nucleotide polymorphism (SNP) occurred more frequently than insertion or deletion, and C>T was the most common of SNV in ccRCC. Higher TMB levels conferred poor survival outcomes, associated with higher tumor grades and advanced pathological stages. A total of 1,265 differentially expressed genes were obtained and top 19 immune-related genes were identified in Venn diagram. GSEA revealed that patients in higher TMB groups correlated with MAPK signaling pathway, Wnt signaling pathway and pathway in cancers. Moreover, we identified 9 hub TMB-related immune genes related with survival and mutants of 9 signature were associated with lower immune infiltrates. In addition, infiltration levels of CD8+ T cell, CD4+ memory resting T cell, M1 and M2 macrophages, as well as dendritic resting cells in high-TMB group were lower than that in low-TMB group, especially the level of CD8+ T cell and macrophage correlated negatively with prognosis of ccRCC. Last, the TMBPI was constructed and the AUC of ROC curve was 0.666. Higher TMB correlated with poor survival outcomes and might inhibit the immune infiltrates in ccRCC. The mutants of 9 hub TMB-related immune signature conferred lower immune cells infiltration which deserved further validation.

Zhang C ，Li Z ，Qi F ，Hu X ，Luo J ... -  《-》

Multi-omics analysis of tumor mutation burden combined with immune infiltrates in melanoma.

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.

Jiang F ，Wu C ，Wang M ，Wei K ，Zhou G ，Wang J ... -  《-》

Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis.

Tumor mutation burden (TMB) and tumor infiltrating lymphocytes have been well-recognized as molecular determinants of immunotherapeutic responsiveness in many types of cancer. However, the relationship between TMB with immune infiltrates and their prognostic role are reported occasionally in skin cutaneous melanoma (SKCM). We obtained the somatic mutation data and transcriptome profiles of 454 SKCM patients from The Cancer Genome Atlas (TCGA) database, and analyzed the mutation profiles using "maftools" package. Correlation analysis revealed that lower TMB levels conferred poor survival outcomes, associated with lower age and advanced pathological stage. Differential analysis was conducted to the genome expression between two TMB groups using "limma" package, and we identified four hub TMB-related immune genes including CNTFR, CRABP2, GAL, and PAEP. We further analyzed the underlying relationships of the copy number variations (CNVs) of four hub genes with immune infiltrates in SKCM microenvironment through TIMER database. The results indicated that diverse forms of CNVs carried by hub genes could commonly inhibit immune infiltrates. Based on the CIBERSORT method, we compared the proportions of 22 immune cells in two TMB groups and assessed their prognostic value. The data revealed that infiltrations levels of regulatory T (Treg) cell and dendritic activated cells in high-TMB group were lower than that in low-TMB group, while M1 and M2 macrophages showed the opposite trend, especially the levels of neutrophil and macrophage correlated positively with prognosis of SKCM. Finally, we constructed a TMB Prognostic Index (TMBPI) to evaluate the predictive accuracy of the four hub TMB-related immune genes. The ROC curve was drawn to assess the predictive accuracy with AUC = 0.664 and higher TMBPI conferred poor survival outcomes, which warranted further investigation and larger samples to validate.

Yan J ，Wu X ，Yu J ，Zhu Y ，Cang S ... -  《Frontiers in Oncology》

Identifying CD1c as a potential biomarker by the comprehensive exploration of tumor mutational burden and immune infiltration in diffuse large B cell lymphoma.

Xiang X ，Gao LM ，Zhang Y ，Zhu Q ，Zhao S ，Liu W ，Ye Y ，Tang Y ，Zhang W ... -  《PeerJ》

Integrated analysis of tumor mutation burden and immune infiltrates in endometrial cancer.

To explore the prognostic value of tumor mutation burden (TMB) and its correlation with immune infiltrates in endometrial cancer. Transcriptome and somatic mutation profiles of Uterine Corpus Endometrial Carcinoma (UCEC) were downloaded from TCGA database. Somatic mutations were analyzed by "maftools" and visualized in waterfall plot. We calculated TMB of each patients and divided all patients into the high-TMB group and the low-TMB group by the median threshold. Survival analysis and Wilcoxon test were used to investigate the prognostic value of TMB and its association with clinical variables. Differentially expressed genes (DEGs) were identified in 2 TMN groups and functional analysis was performed to find out significant biological pathways. A TMB-related signature was conducted by multivariate analysis, receiver operating characteristic (ROC) curve was performed to predict accuracy of the model, meanwhile, a validation cohort from Fudan University Shanghai Cancer Center (FUSCC) was obtained to verify the signature. Then we estimated association between TMB and immune infiltrates by CIBERSORT algorithm and figured out prognostic immune cells of UCEC in TIMER database. Total 575 samples including 25 normal tissues and 552 tumor samples were enrolled from TCGA database. PTEN mutations accounted for the most and single nucleotide polymorphism and C>T transitions were most frequent forms of somatic mutations in UCEC. The low-TMB group possessed worse survival than the high-TMB group (P = 0.004). DEGs in 2 TMB groups were mostly enriched in adaptive immune response and immunoglobulin/immune receptor component. A TMB-related signature consisting of GFAP, EDN3, CXCR3, PLXNA4, SST presented good predictability with area under the curve (AUC) = 0.686. In FUSCC validation cohort, the high-risk group possessed worse survival outcome than the low-risk group (P = 0.015). Immune infiltrates was correlated to survival in UCEC and low TMB were associated with less immune infiltrates, which suggested poor immune response. TMB was not only related to overall survival but also immune infiltrates in UCEC. The TMB-related signature (GFAP, EDN3, CXCR3, PLXNA4, SST) had good predictability for overall survival in endometrial cancer. Our study might have some merits in elucidating potential mechanism of TMB and immune infiltrates in UCEC and providing guidance of immunotherapy for endometrial cancer.

Zhou H ，Chen L ，Lei Y ，Li T ，Li H ，Cheng X ... -  《-》