scholarly journals Catenin Alpha-2 Mutation Changes the Immune Microenvironment in Lung Adenocarcinoma Patients Receiving Immune Checkpoint Inhibitors

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Wen ◽  
Anqi Lin ◽  
Weiliang Zhu ◽  
Ting Wei ◽  
Peng Luo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Checkpoint ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Immune Microenvironment ◽  
Gene Set Enrichment ◽  
Cancer Genome Atlas

Background: Lung cancer has always been the most prevalent cancer. Lung adenocarcinoma (LUAD) is the most common lung cancer subtype and has a high tumor mutation rate. In addition to KRAS, EGFR, ALK, HER2, ROS1, and BRAF, which are known to have high mutation rates, we discovered some new mutated genes, such as catenin alpha-2 (CTNNA2), in LUAD patients treated with immune checkpoint inhibitors (ICIs). These mutant genes are potential therapeutic targets for LUAD.Methods: We analyzed a cohort of LUAD patients with somatic mutation and survival data in the Cancer Genome Atlas (TCGA) database and a cohort of LUAD patients receiving immune checkpoint inhibitors with clinical data and whole-exome sequencing (WES) mutation data to evaluate the role of CTNNA2 gene mutation in LUAD. In addition, CIBERSORT was used to analyze the immune characteristics of CTNNA2 wild-type patients and CTNNA2 mutant-type patients, and gene set enrichment analysis (GSEA) was employed for pathway enrichment analysis. The results were verified by downloading data regarding the drug sensitivity of LUAD cell lines from the Genomics of Drug Sensitivity in Cancer (GDSC) database.Results: We found that CTNNA2 mutation was associated with longer overall survival (OS) in LUAD patients. Analysis of the cohort from the Cancer Genome Atlas showed that patients with CTNNA2 mutation had more tumor neoantigens and a greater tumor mutation burden (TMB). Through further analysis of the tumor immune microenvironment, we found that in LUAD patients with CTNNA2 mutations, the gene expression levels of chemokine C-X-C motif chemokine 9 (CXCL9) and granzyme B (GZMB) were elevated, and the gene expression level of inhibitory receptor killer cell immunoglobulin-like receptor 2DL1 (KIR2DL1) was significantly reduced. These alterations might affect gene expression in macrophages, NK cells, and mast cell markers. In addition, LUAD patients with CTNNA2 mutation had a significantly increased number of mutations in DNA damage response (DDR) genes. The drug susceptibility results and gene set enrichment analysis showed that after CTNNA2 mutation occurred, changes were found in the DNA damage response pathway, the phosphoinositide 3-kinase (PI3K) pathway and others, indicating that CTNNA2 mutation can regulate the activation of PI3K and DDR pathways.Conclusion: Our findings provide novel insights into the underlying pathogenesis of LUAD. CTNNA2 mutation can change the immune microenvironment, thereby improving patient prognosis. The results also suggest that CTNNA2 may become a new biomarker and therapeutic target for LUAD in the future.

scholarly journals Association Between FSIP2 Mutation and an Improved Efficacy of Immune Checkpoint Inhibitors in Patients With Skin Cutaneous Melanoma

2021 ◽  
Vol 8 ◽  
Author(s):  
Haoxuan Ying ◽  
Anqi Lin ◽  
Junyi Liang ◽  
Jian Zhang ◽  
Peng Luo
Keyword(s):  
Immune Checkpoint ◽  
Cutaneous Melanoma ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Response To Treatment ◽  
Interacting Protein ◽  
Tumor Immunogenicity

BackgroundImmune checkpoint inhibitors (ICIs) have shown remarkable success in treating skin cutaneous melanoma (SKCM); however, the response to treatment varies greatly between patients. Considering that the efficacy of ICI treatment is influenced by many factors, we selected the Fibrosheath interacting protein 2 (FSIP2) gene and systematically analyzed its potential to predict the efficacy of ICI treatment.MethodsPatient data were collected from an ICI treatment cohort (n = 120) and a The Cancer Genome Atlas (TCGA)-SKCM cohort (n = 467). The data were divided into an FSIP2-mutant (MT) group and FSIP2-wild-type (WT) group according to FSIP2 mutation status. In this study, we analyzed the patients’ overall survival rate, tumor mutational burden (TMB), neoantigen load (NAL), copy number variation (CNV), cell infiltration data and immune-related genes. We used gene set enrichment analysis (GSEA) to delineate biological pathways and processes associated with the efficacy of immunotherapy.ResultsThe efficacy of ICI treatment of SKCM patients with FSIP2 mutation was significantly better than that of patients without FSIP2 mutation. The patients in the FSIP2-MT group had higher tumor immunogenicity and lower regulatory T cell (Treg) infiltration. Results of GSEA showed that pathways related to tumor progression (MAPK and FGFR), immunomodulation, and IL-2 synthesis inhibition were significantly downregulated in the FSIP2-MT group.ConclusionOur research suggests that the FSIP2 gene has the potential to predict the efficacy of ICI treatment. The high tumor immunogenicity and low Treg levels observed may be closely related to the fact that patients with FSIP2-MT can benefit from ICI treatment.

scholarly journals Association Between FSIP2 Mutation and an Improved Prognosis in Patients With Skin Cutaneous Melanoma Treated With Immune Checkpoint Inhibitors

2020 ◽  
Author(s):  
Haoxuan Ying ◽  
Anqi Lin ◽  
Jian Zhang ◽  
Peng Luo
Keyword(s):  
Immune Checkpoint ◽  
Cutaneous Melanoma ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Response To Treatment ◽  
Interacting Protein ◽  
Tumor Immunogenicity

Abstract Background Immune checkpoint inhibitors (ICIs) have been remarkably successful in skin cutaneous melanoma (SKCM), however the response to treatment varies greatly among different patients. Considering that the efficacy of ICI treatment is affected by many factors, we selected the Fibrosheath interacting protein 2 (FSIP2) gene and systematically analyzed its potential as a predictor of ICI treatment prognosis. Methods Patient data were collected from an ICI treatment cohort (n = 120) and The Cancer Genome Atlas (TCGA)-SKCM cohort (n = 467). The data was divided into an FSIP2-mutant (MT) group and FSIP2-wild-type (WT) group according to the FSIP2 mutation status. In this study we analyzed the patients’ overall survival rate, tumor mutational burden (TMB), neoantigen load (NAL), copy number variation (CNV), cell infiltration data and immune-related genes. We used gene set enrichment analysis (GSEA) to delineate biological pathways and processes associated with the prognosis of immunotherapy. Results The prognosis of SKCM patients with FSIP2-MT receiving ICIs was significantly better than that of those with FSIP2-WT. The patients in the FSIP2-MT group had higher tumor immunogenicity and lower regulatory T cell (Treg) infiltration. Results of GSEA showed that pathways related to tumor progression (MAPK and FGFR), immunomodulation, and IL-2 synthesis inhibition were significantly downregulated in the FSIP2-MT group. Conclusion Our research suggests that the FSIP2 gene has the potential to predict the prognosis of ICI treatment. The higher tumor immunogenicity and lower Treg levels may be closely related to the fact that patients with FSIP2-MT can benefit more from ICI treatment.

PTPRD/PTPRT mutations as potential positive predictor for response of immune checkpoint inhibitors in non-small cell lung cancer (NSCLC).

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15112-e15112
Author(s):  
Jian Zeng ◽  
Guoqiang Wang ◽  
Zhengqing Yan ◽  
Hao Zheng ◽  
Jianqiang Li ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Overall Survival ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Enrichment Analysis ◽  
Small Cell ◽  
Gene Set Enrichment Analysis ◽  
Small Cell Lung ◽  
Gene Set Enrichment ◽  
Nsclc Patients

e15112 Background: Immune checkpoint inhibitors (ICIs) have demonstrated positive results in non-small cell lung cancer (NSCLC) patients, with durable responses and prolonged overall survival (OS). Nevertheless, the response rate to immunotherapy is still limited. It is necessary to identify clinically useful biomarkers that can distinguish patients who can respond to ICIs. PTPRD/PTPRT are the phosphatases of JAK-STAT signaling, which may be associated with response to ICIs. Here we aimed to demonstrate the association between PTPRD/PTPRT and ICIs. Methods: Genomic and survival data of NSCLC patients administrated with anti–PD-1/PD-L1 or anti–CTLA-4 antibodies (Rizvi2015; Hellmann2018; Rizvi2018 Samstein2019) were retrieved from publicly accessible data. Genomic, survival and mRNA data of 1007 patients with NSCLC was obtained from The Cancer Genome Atlas (TCGA). Association between PTPRD/PTPRT mutation and progression-free survival (PFS) and overall survival (OS) were analyzed. Gene set enrichment analysis (GSEA) was used to determine potentially relevant gene expression signatures between specific subgroups. Results: PTPRD/PTPRT mutations were significantly associated with better PFS in Rizvi2015 cohort (HR = 0.16; 95% CI, 0.02-1.17; P = 0.03), Hellmann2018 cohort (HR, 0.49; 95% CI, 0.26-0.94; P = 0.03) and Rizvi2018 cohort (HR = 0.64; 95% CI, 0.44-0.92; P = 0.01). PTPRD/PTPRT mutation was also significantly associated with better OS in Samstein2019 cohort (HR, 0.66; 95% CI, 0.45-0.97; P = 0.03). In TCGA, no association between PTPRD/PTPRT mutations and OS was observed (P = 0.91), suggesting that PTPRD/PTPRT mutations were not prognostic factor. PTPRD/PTPRT mutations were associated with increased TMB (P < 0.0001). The mRNA expression of STAT1 and CD4 was higher in patients with PTPRD/PTPRT mutant type than PTPRD/PTPRT wild type. Gene Set Enrichment Analysis revealed prominent enrichment of signatures related to inflammatory response, interferon gamma response and antigen processing and presentation in patients with PTPRD/PTPRT mutation. Conclusions: Our results suggest that PTPRD/PTPRT mutation is associated with better PFS and OS in NSCLC patients receiving ICIs by increasing immune-related gene signatures. The role of PTPRD/PTPRT in immunotherapy is needed to be further studied.

scholarly journals CXCL5 Has Potential to Be a Marker for Hepatocellular Carcinoma Prognosis and Was Correlating With Immune Infiltrates

2021 ◽  
Vol 11 ◽  
Author(s):  
Yuan Nie ◽  
Mei-chun Jiang ◽  
Cong Liu ◽  
Qi Liu ◽  
Xuan Zhu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cox Regression ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Hospital Data ◽  
Gene Set Enrichment ◽  
Local Hospital ◽  
High Expression Group ◽  
Cancer Genome Atlas

BackgroundsTumor microenvironment (TME) plays a crucial role in the initiation and progression of Hepatocellular Carcinoma (HCC), especially immune infiltrates. However, there is still a challenge in understanding the modulation of the immune and stromal components in TME, especially TME related genes.MethodsThe proportion of tumor-infiltrating immune cells (TICs) and the immune and stromal scores in 374 HCC patients from The Cancer Genome Atlas (TCGA) database were determined using CIBERSORT and ESTIMATE computational methods. The final screened genes were confirmed by the PPI network and univariate Cox regression of the differentially expressed genes based on different immune or stromal scores. The correlation between the expression levels of the final gene interactions and the clinical characteristics was based on TCGA database and local hospital data. Gene set enrichment analysis (GSEA) and the effect of CXCL5 expression on TICs were conducted.ResultsThere were correlations between the expression of CXCL5 and survival of HCC patients and TMN classification both in TCGA database and local hospital data. The immune-related activities were enriched in the high-expression group; however, the metabolic pathways were enriched in the low-expression group. The result of CIBERSORT analyzing had indicated that CXCL5 expression were correlated with the proportion of NK cells activated, macrophages M0, Mast cells resting, Neutrophils.ConclusionsCXCL5 was a potential prognostic marker for HCC and provides clues regarding immune infiltrates, which offers extra insight for therapeutics of HCC, however, more independent cohorts and functional experiments of CXCL5 are warranted.

scholarly journals Prognostic Biomarker SYK and its Correlation with Immune Infiltrates in Glioma

2021 ◽  
Author(s):  
Pei Liu ◽  
Jiamin Guo ◽  
Xiaoxiao Xu ◽  
Haixin Sun ◽  
Zheng Gong
Keyword(s):  
Development Process ◽  
Prognostic Biomarker ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Ppi Network ◽  
Glioma Patient ◽  
Gene Set Enrichment ◽  
Protein Protein Interaction ◽  
Cancer Genome Atlas

Abstract Background: Tumor microenvironment (TME) has great effects on the development process of glioma, and we sought to identify effective prognostic factors by analyzing data from patients with glioma. In this paper, CIBERSORT and ESTIMATE calculations were employed to figure up the ratio of tumor-infiltrating immune cells (TICs) and the quantity of immune and stromal components in 698 glioma dates from The Cancer Genome Atlas (TCGA) database. In addition, differentially expressed genes (DEGs) were studied by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and single genes associated with prognosis were identified by PPI network and COX combined analysis. Results: Immune and stromal scores of TME were significantly correlated with glioma patient survival. Through protein–protein interaction (PPI) network and regression analysis of COX, we finally determined that SYK was the best prognostic factor for patients with glioma. Gene Set Enrichment Analysis (GSEA) and CIBERSORT analysis were also employed, with the former showed that high-expression SYK group’s genes are principally enriched immune-related activities and the latter revealed that SYK expression was positively associated with T cells CD4 memory resting and Monocytes. All the above experimental analyses provided the theoretical basis for the biological prediction of SYK.Conclusions: SYK contributes to immune predictors in glioma patients by facilitating the shift of TME from immune dominance to metabolic activity, which provides promising insights into the treatment of glioma.

scholarly journals Comprehensive Analysis of Immune Correlation of KIF20A in Pan-cancer

2020 ◽  
Author(s):  
Xiao-Han Cui ◽  
Qiu-Ju Peng ◽  
Peng Gao ◽  
Xu-Dong Zhang ◽  
Ren-Zhi Li ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Immune Checkpoints ◽  
Rna Seq ◽  
Gene Set Enrichment ◽  
Related Information ◽  
Common Causes ◽  
Cancer Genome Atlas ◽  
Pan Cancer

Abstract Background: Cancer is one of the most common causes of death, and the morbidity and mortality are gradually increasing in the world. KIF20A plays an important role in tumors, but its immune relevance in pan-cancer needs to be further studied.Methods: KIF20A-related information was download from The Cancer Genome Atlas (TCGA). Collecting RNA-seq data is fragments per kilobase million (FPKM) style data. The ESTIMATE algorithm was used for estimating the stromal and immune scores for 33 tumors. Then, we analyzed the correlation between KIF20A in pan-cancer and immune checkpoints and performed gene set enrichment analysis (GSEA) analysis on the co-expressed genes of KIF20A in pan-cancer.Results: We have confirmed that the expression of KIF20A has a intensive correlation with prognosis in 33 kinds of tumors. Its expression of KIF20A was related to a variety of immune cells and immune checkpoints. Based on the results of GSEA for further analysis, in multiple tumors, KIF20A is related to immune-related pathways.Conclusion: We have demonstrated that KIF20A played an important role in pan-cancer and could affect the occurrence or development of a variety of tumors. Moreover, KIF20A was related to immunity, and KIF20A- related immune research in pan-cancer also needs to be further demonstrate.

scholarly journals Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes

2014 ◽  
Vol 13s3 ◽  
pp. CIN.S14027 ◽  
Author(s):  
Serdar Bozdag ◽  
Aiguo Li ◽  
Mehmet Baysan ◽  
Howard A. Fine
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Gene Set Enrichment ◽  
Master Regulators ◽  
Cancer Genome Atlas ◽  
Gene Regulatory ◽  
Comprehensive Study

Glioblastoma multiforme (GBM) is the most common malignant brain tumor. GBM samples are classified into subtypes based on their transcriptomic and epigenetic profiles. Despite numerous studies to better characterize GBM biology, a comprehensive study to identify GBM subtype-specific master regulators, gene regulatory networks, and pathways is missing. Here, we used FastMEDUSA to compute master regulators and gene regulatory networks for each GBM subtype. We also ran Gene Set Enrichment Analysis and Ingenuity Pathway Analysis on GBM expression dataset from The Cancer Genome Atlas Project to compute GBM- and GBM subtype-specific pathways. Our analysis was able to recover some of the known master regulators and pathways in GBM as well as some putative novel regulators and pathways, which will aide in our understanding of the unique biology of GBM subtypes.

scholarly journals A four-gene signature predicts survival and anti-CTLA4 immunotherapeutic responses based on immune classification of melanoma

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ying Mei ◽  
Mei-Ju May Chen ◽  
Han Liang ◽  
Li Ma
Keyword(s):  
Enrichment Analysis ◽  
Gene Signature ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Gene Set Enrichment ◽  
Malignant Skin ◽  
Cancer Genome Atlas ◽  
Melanoma Patients ◽  
Potential Use

AbstractCutaneous melanoma is the most malignant skin cancer. Biomarkers for stratifying patients at initial diagnosis and informing clinical decisions are highly sought after. Here we classified melanoma patients into three immune subtypes by single-sample gene-set enrichment analysis. We further identified a four-gene tumor immune-relevant (TIR) signature that was significantly associated with the overall survival of melanoma patients in The Cancer Genome Atlas cohort and in an independent validation cohort. Moreover, when applied to melanoma patients treated with the CTLA4 antibody, ipilimumab, the TIR signature could predict the response to ipilimumab and the survival. Notably, the predictive power of the TIR signature was higher than that of other biomarkers. The genes in this signature, SEL1L3, HAPLN3, BST2, and IFITM1, may be functionally involved in melanoma progression and immune response. These findings suggest that this four-gene signature has potential use in prognosis, risk assessment, and prediction of anti-CTLA4 response in melanoma patients.

scholarly journals High expression of PIMREG predicts poor survival outcomes and is correlated with immune infiltrates in lung adenocarcinoma

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11697
Author(s):  
Feng Jiang ◽  
Min Liang ◽  
Xiaolu Huang ◽  
Wenjing Shi ◽  
Yumin Wang
Keyword(s):  
Prognostic Value ◽  
Cox Regression ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
High Expression ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Kaplan Meier ◽  
Cancer Genome Atlas

Background PIMREG is upregulated in multiple cancer types. However, the potential role of PIMREG in lung adenocarcinoma (LUAD) remains unclear. The present study aimed to explore its clinical significance in LUAD. Methods Using the Cancer Genome Atlas (TCGA) databases, we obtained 513 samples of LUAD and 59 normal samples from the Cancer Genome Atlas (TCGA) databases to analyze the relationship between PIMREG and LUAD. We used t and Chi-square tests to evaluate the level of expression of PIMREG and its clinical implication in LUAD. The prognostic value of PIMREG in LUAD was identified through the Kaplan–Meier method, Cox regression analysis, and nomogram. Gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA) were performed to screen biological pathways and analyze the correlation of the immune infiltrating level with the expression of PIMREG in LUAD. Results PIMREG was highly expressed in patients with LUAD. Specifically, the level of PIMREG gradually increased from pathological stage I to IV. Further, we validated the higher expression of PIMREG expressed in LUAD cell lines. Moreover, PIMREG had a high diagnostic value, with an -AUC of 0.955. Kaplan–Meier survival and Cox regression analyses revealed that the high expression of PIMREG was independently associated with poor clinical outcomes. In our prognostic nomogram, the expression of PIMREG implied a significant prognostic value. Gene set enrichment analysis (GSEA) identified that the high expression PIMREG phenotype was involved in the mitotic cell cycle, mRNA splicing, DNA repair, Rho GTPase signaling, TP53 transcriptional regulation, and translation pathways. Next, we also explored the correlation of PIMREG and tumor-immune interactions and found a negative correlation between PIMREG and the immune infiltrating level of T cells, macrophages, B cells, dendritic cells (DCs) , and CD8+ T cells in LUAD. Conclusions High levels of PIMREG correlated with poor prognosis and immune infiltrates in LUAD.

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