scholarly journals A 12-chemokine Gene Signature Is Associated With an Enhanced Cancer-immunity Cycle and Is Relevant for Precision Immunotherapy

2021 ◽  
Author(s):  
Xingchen Li ◽  
Zhiyi Wan ◽  
Xiu Liu ◽  
Kai Ou ◽  
Lin Yang
Keyword(s):  
Bladder Cancer ◽  
Immune Cell ◽  
Predictive Biomarkers ◽  
Gene Signature ◽  
Cytolytic Activity ◽  
The Cancer Genome Atlas ◽  
Cancer Immunity ◽  
Lymphoid Structures ◽  
Tcga Dataset ◽  
Predictive And Prognostic Biomarker

Abstract Background: Advances in the understanding of checkpoint blockade immunotherapy have suggested that boosting the cancer-immunity cycle (CIC) can help induce regression of tumors. However, good efficacy only occurs in a subset of patients. Predictive biomarkers that can reflect the tumor microenvironment (TME) and CIC may have great potential. More recently, the presence of intratumoral tertiary lymphoid structures (TLSs) has also been correlated with clinical benefit in patients.Methods: In this study, we comprehensively measured the immunogram scores (IGSs) for the CIC and explored the associations between immunological and mutational features and a 12-chemokine metagene TLS signature in data from The Cancer Genome Atlas (TCGA). Three immunotherapy datasets were further applied for validation.Results: In the TCGA dataset, we observed that the 12-chemokine TLS signature score was positively associated with a boosted CIC, as represented by increased tumor mutational burden (TMB) and neoantigen burden (TNB), enriched immune cell infiltration, and elevated cytolytic activity and checkpoint expression. Specifically, in bladder cancer and melanoma, a high 12-chemokine TLS signature score was found to potentially reflect an expanded CIC phenotype characterized by high TNB and an immune-inflamed feature. The predictive and prognostic value of the 12-chemokine TLS signature was further validated in several immunotherapy datasets.Conclusion: The score of a 12-chemokine metagene signature may serve as a pancancer marker of the immune-active phenotype. The 12-chemokine TLS signature showed promise as a predictive and prognostic biomarker for ICB efficacy, especially in melanoma and bladder cancer.

scholarly journals Association of PD-1/PD-L axis expression with cytolytic activity, mutational load, and prognosis in melanoma and other solid tumors

2016 ◽  
Vol 113 (48) ◽  
pp. E7769-E7777 ◽  
Author(s):  
Ludmila Danilova ◽  
Hao Wang ◽  
Joel Sunshine ◽  
Genevieve J. Kaunitz ◽  
Tricia R. Cottrell ◽  
...  
Keyword(s):  
Predictive Biomarkers ◽  
Gene Signature ◽  
Cytolytic Activity ◽  
The Cancer Genome Atlas ◽  
Conditional Inference ◽  
Tumor Type ◽  
Mutational Load ◽  
Prognostic Features ◽  
Cancer Genome Atlas ◽  
Tumor Types

Programmed cell death protein-1 (PD-1)/programmed death ligand-1 (PD-L1) checkpoint blockade has led to remarkable and durable objective responses in a number of different tumor types. A better understanding of factors associated with the PD-1/PD-L axis expression is desirable, as it informs their potential role as prognostic and predictive biomarkers and may suggest rational treatment combinations. In the current study, we analyzedPD-L1,PD-L2,PD-1, and cytolytic activity (CYT) expression, as well as mutational density from melanoma and eight other solid tumor types using The Cancer Genome Atlas database. We found that in some tumor types,PD-L2expression is more closely linked toTh1/IFNGexpression and PD-1 and CD8 signaling thanPD-L1. In contrast, mutational load was not correlated with aTh1/IFNGgene signature in any tumor type.PD-L1,PD-L2,PD-1,CYTexpression, and mutational density are all positive prognostic features in melanoma, and conditional inference modeling revealedPD-1/CYTexpression (i.e., an inflamed tumor microenvironment) as the most impactful feature, followed by mutational density. This study elucidates the highly interdependent nature of these parameters, and also indicates that future biomarkers for anti–PD-1/PD-L1 will benefit from tumor-type–specific, integrated, mRNA, protein, and genomic approaches.

scholarly journals Molecular Characteristics, Clinical Implication, and Cancer Immunity Interactions of Pyroptosis-Related Genes in Breast Cancer

2021 ◽  
Vol 8 ◽  
Author(s):  
Dandan Xu ◽  
Zhipeng Ji ◽  
Ling Qiang
Keyword(s):  
Breast Cancer ◽  
Immune Cell ◽  
Cox Regression ◽  
Gene Signature ◽  
Immune Checkpoints ◽  
Molecular Characteristics ◽  
Predictive Index ◽  
Cox Regression Analysis ◽  
Cancer Immunity ◽  
Tcga Dataset

Objective: Pyroptosis represents an emerging inflammatory form of programmed cell death. Herein, specific functions and clinical implications of pyroptosis-related genes were systematically characterized in breast cancer.Methods: Expression, somatic mutation and copy number variation of 33 pyroptosis-related genes were assessed in breast cancer from TCGA dataset. Their interactions, biological functions and prognostic values were then observed. By stepwise Cox regression analysis, a pyroptosis-related gene signature was generated. The predictive efficacy in survival was examined by survival analyses, ROCs, univariate and multivariate analyses and subgroup analyses. Associations between risk score (RS) and cancer immunity cycle, HLA, immune cell infiltrations, and immune checkpoints were analyzed.Results: Most of pyroptosis-related genes were abnormally expressed in breast cancer. CASP8, NLRC4, NLRP3, NLRP2, PLCG1, NLRP1, NLRP7, SCAF11, GSDMC, and NOD1 occurred somatic mutations as well as most of them had high frequency of CNV. There were closely interactions between them. These genes were distinctly enriched in immune-related processes. A three-gene signature was generated, containing IL-18, GSDMC, and TIRAP. High RS predicted poorer overall survival, progression, and recurrence. After verification, this RS was an independent and sensitive predictive index. This RS was negatively correlated to cancer immunity cycle. Also, low RS was characterized by high HLA, immune cell infiltrations and immune checkpoints. A nomogram including age and RS was generated for accurately predicting 5-, 8-, and 10-year survival probabilities.Conclusion: Pyroptosis-related genes exert key roles in cancer immunity and might be applied as a prognostic factor of breast cancer.

scholarly journals A 17-Gene Signature Predicted Prognosis in Renal Cell Carcinoma

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Fan Li ◽  
Weifeng Hu ◽  
Wei Zhang ◽  
Guohao Li ◽  
Yonglian Guo
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Malignant Tumors ◽  
Prognostic Significance ◽  
Gene Signature ◽  
The Cancer Genome Atlas ◽  
Prognostic Indicators ◽  
Incidence And Mortality ◽  
Tcga Dataset

Renal cell carcinoma (RCC), which was one of the most common malignant tumors in urinary system, had gradually increased incidence and mortality in recent years. Although significant advances had been made in molecular and biology research on the pathogenesis of RCC, effective treatments and prognostic indicators were still lacking. In order to predict the prognosis of RCC better, we identified 17 genes that were associated with the overall survival (OS) of RCC patients from The Cancer Genome Atlas (TCGA) dataset and a 17-gene signature was developed. Through SurvExpress, we analyzed the expression differences of the 17 genes and their correlation with the survival of RCC patients in five datasets (ZHAO, TCGA, KIPAN, KIRC, and KIRP), and then evaluated the survival prognostic significance of the 17-gene signature for RCC. Our results showed that the 17-gene signature had a predictive prognostic value not only in single pathologic RCC, but also in multiple pathologic types of RCC. In conclusion, the 17-gene signature model was related to the survival of RCC patients and could help predict the prognosis with significant clinical implications.

scholarly journals An Immune-Related Gene Signature for Predicting Survival and Immunotherapy Efficacy in Hepatocellular Carcinoma

2020 ◽  
Author(s):  
Yifei Dai ◽  
Weijie Qiang ◽  
Kequan Lin ◽  
Yu Gui ◽  
Xun Lan ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Immune Cell ◽  
Prognostic Index ◽  
Gene Signature ◽  
The Cancer Genome Atlas ◽  
Lasso Regression ◽  
Related Gene ◽  
Immune Related Gene ◽  
Clinicopathologic Factors ◽  
Immune Related Genes

Abstract Background: Hepatocellular carcinoma (HCC) ranks the fourth in terms of cancer-related mortality globally. Herein, in this research, we attempted to develop a novel immune-related gene signature that could predict survival and efficacy of immunotherapy for HCC patients.Methods: The transcriptomic and clinical data of HCC samples were downloaded from The Cancer Genome Atlas (TCGA) and GSE14520 datasets, followed by acquisition of immune-related genes from the ImmPort database. Afterwards, an immune-related gene-based prognostic index (IRGPI) was constructed using the Least Absolute Shrinkage and Selection Operator (LASSO) regression model. Kaplan-Meier survival curves as well as time-dependent receiver operating characteristic (ROC) curve were performed to evaluate its predictive capability. Besides, both univariate and multivariate analysis on overall survival for the IRGPI and multiple clinicopathologic factors were carried out, followed by the construction of nomogram. Finally, we explored the possible correlation of IRGPI with immune cell infiltration or immunotherapy efficacy. Results: Analysis of 365 HCC samples identified 11 differentially expressed genes, which were selected to establish the IRGPI. Notably, it can predict survival of HCC patients more accurately than published biomarkers. Furthermore, IRGPI can predict the infiltration of immune cells in the tumor microenvironment of HCC, as well as the response of immunotherapy.Conclusion: Collectively, the currently established IRGPI can accurately predict survival, reflect the immune microenvironment, and predict the efficacy of immunotherapy among HCC patients.

scholarly journals Prognostic Significance of Gene Signature of Tertiary Lymphoid Structures in Patients With Lung Adenocarcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Hong Feng ◽  
Fujun Yang ◽  
Lihong Qiao ◽  
Kai Zhou ◽  
Junfei Wang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Lung Adenocarcinoma ◽  
Immune Cell ◽  
Prognostic Significance ◽  
Gene Signature ◽  
Driver Gene ◽  
Immune Microenvironment ◽  
High Group ◽  
Tertiary Lymphoid Structures ◽  
Lymphoid Structures

BackgroundLung adenocarcinoma (LUAD) is a highly mortal cancer. Tertiary lymphoid structures (TLS) are ectopic lymphoid organs with similar morphological and molecular characters to secondary lymphoid organ. The aim of this study is to investigate the prognostic effect of a gene signature associated with TLSs, including B-cell-specific genes.MethodsClinical data of 515 LUAD patients in the TGCA cohort were used to examine the relationship of TLS signature with immune microenvironment, tumor mutational burden (TMB), and driver gene mutations. Patients were divided into the TLS signature high group and TLS signature low group, and comparative analysis of survival and its influencing factors between the two groups was performed. The resulting data were then validated in the GSE37745 cohort.ResultsTLS signature high group had significantly better overall survival (OS) and progression-free interval (PFI) as well as significantly higher infiltration of immune cell subsets, cancer immune cycle (CIC) signature except for immunogram score2 (IGS2), and expression of major checkpoint genes than the TLS signature low group. Notably, while TLS signature was not markedly associated with TMB and mutation frequencies of driver genes, there were significant differences in overall survival of patients with given mutation status of EGFR, KRAS, BRAF and TP53 genes between the TLS signature high and low groups.ConclusionThis study provided evidence that LUAD patients with high TLS signature had a favorable immune microenvironment and better prognosis, suggesting that TLS signature is an independent positive prognostic factor for LUAD patients.

scholarly journals Development of a Novel Immune Infiltration-Based Gene Signature to Predict Prognosis and Immunotherapy Response of Patients With Cervical Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Sihui Yu ◽  
Xi Li ◽  
Jiawen Zhang ◽  
Sufang Wu
Keyword(s):  
Cervical Cancer ◽  
Immune Cell ◽  
Cox Regression ◽  
Patient Survival ◽  
Checkpoint Inhibitors ◽  
Cell Types ◽  
Gene Signature ◽  
The Cancer Genome Atlas ◽  
Cervical Lesions ◽  
Immune Infiltration

Predictive models could indicate the clinical outcome of patients with carcinoma. Cervical cancer is one of the most frequently diagnosed female malignancies. Herein, we proposed an immune infiltration-related gene signature that predicts prognosis of patients with cervical cancer and depicts the immune landscape as well. We utilized the transcriptome data of The Cancer Genome Atlas (TCGA) and estimated the infiltration level of 28 immune cell types. We screened out four immune cell types conducive to patient survival and recognized their shared differentially expressed genes (DEGs). Four core genes (CHIT1, GTSF1L, PLA2G2D, and GNG8) that composed the ultimate signature were identified via univariate and multivariate Cox regression. The optimal model we built up could distinguish patients with cervical cancer into high-score and low-score subgroups. These two subgroups showed disparity in aspects of patient survival, immune infiltration landscape, and response to immune checkpoint inhibitors. Additionally, we found that GTSF1L was decreased gradually along with the severity of cervical lesions, and its potential role in immune contexture and clinical practice were also demonstrated. Our results suggested that the Immunoscore based on four immune-related genes could serve as a supplementary criterion to effectively foresee the survival outcome, tumor infiltration status, and immunotherapy efficacy of cervical cancer patients.

NT5E expression and the immune landscape of prostate cancer (PC): An analysis from The Cancer Genome Atlas database.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e16591-e16591
Author(s):  
Abhishek Tripathi ◽  
Edwin Lin ◽  
Roberto Nussenzveig ◽  
Mark Yandell ◽  
Sumanta K. Pal ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Immune Cell ◽  
Checkpoint Inhibitors ◽  
The Cancer Genome Atlas ◽  
Effector Memory ◽  
Marker Genes ◽  
Promote Tumor Growth ◽  
Tumor Phenotype ◽  
Tcga Dataset ◽  
Tumor Expression

e16591 Background: Immune checkpoint inhibitors targeting PD-1/L1 and CTLA-4 pathway have shown modest activity in patients with advanced PC. Additional immunosuppressive mechanisms in the PC tumor microenvironment need to be investigated. Increased CD73 (encoded by NT5E) expression results in generation of immunosuppressive adenosine in the tumor microenvironment and has been associated with metastasis and poor survival in PC. Utilizing the TCGA dataset, we investigated the association of NT5E expression with the immune landscape of PC. Methods: RNA-seq data for 331 PC tumor samples and 51 normal adjacent tissue (NAT) samples was downloaded and log2 transformed. Patients were split into low, intermediate, and high expression groups based on NT5E expression (≤ -1, -1 to 1 and ≥1 standard deviation from the overall mean) in tumor and NAT. A tumor inflammation signature (TIS) reflecting an inflamed tumor phenotype was calculated based on the averaged tumor expression of 18 previously validated genes (Ayers et al, 2017). Abundance of infiltrating immune cell subsets was estimated based on expression of previously identified 782 immune metagenes (Charoentong et al, 2017). Immune cell abundance scores and TIS were compared between NT5E expression groups using the Mann-Whitney U test and the Bonferroni correction was used to control for false discovery rate. Results: NT5E expression in NAT was not associated with the TIS or expression of immune cell marker genes. In contrast, NT5E expression in tumor tissue correlated positively with TIS (P < 0.001). Compared to tumors with low NT5E expression, those in high NT5E expression group had higher expression of central memory CD4+, effector memory CD8+, type 1 helper, NK and regulatory T (Treg) cell markers. Conclusions: In our analysis, NT5E expression correlated with markers of inflamed tumor phenotype in PC. Although NT5E expression was associated with higher CD8+and CD4+ T cells, concurrent increase in Tregs could inhibit the infiltrating lymphocytes and promote tumor growth. Our findings indicate a possible role for the adenosine pathway as a mediator of immunosuppression in PC and a potential therapeutic target. AT and EL: Equal contribution

Identification of ncRNA-mediated prognostic Value and Immune Infiltration of MTHFD2 in Bladder Cancer

2021 ◽  
Author(s):  
Hao Zhang ◽  
Rui Li ◽  
Wanjun Deng ◽  
Huihua Xiong
Keyword(s):  
Bladder Cancer ◽  
Immune Cell ◽  
Tumor Development ◽  
Redox Balance ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Nucleic Acid Metabolism ◽  
Mitochondrial Enzymes ◽  
Immune Cell Infiltration ◽  
Cellular Mechanisms

Abstract Background: Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), one of mitochondrial enzymes, is involved in folate and nucleic acid metabolism and maintains the cellular redox balance. However, the function of MTHFD2 in bladder cancer is still poorly characterized. This study was designed to elucidate the effect and regulatory mechanism of MTHFD2 on bladder cancer cells and explore the relationships between MTHFD2 and immune cell infiltration in tumor microenvironment (TME). Methods: The data from Oncomine, TIMER, The Cancer Genome Atlas (TCGA) and The Human Protein Atlas (HPA) database were extracted to evaluate the expression of MTHFD2 and its prognostic role in pan-cancer, especially in bladder cancer. Enrichment analyses, were utilized to explore the underlying cellular mechanisms. The ncRNA regulatory axis was established by Starbase database, and the PPI network was constructed by Cytoscape software. Ultimately, the relations between the expression of MTHFD2 and immune cell infiltration in bladder cancer was indicated by TCGA and TIMER databases.Results: Our results demonstrated that MTHFD2 expression was generally up-regulated in pan-cancers and its high expression was correlated with poor prognosis of patients with bladder cancer. Specifically, our study revealed that MTHFD2 was a powerful risk factor and involved in the tumor development of bladder cancer. Furthermore, hsa_circ_0046140 and hsa_circ_0006769/miR-383-5p/MTHFD2 axis could also play a significant role in tumorigenesis. Ultimately, a strong correlation was observed between MTHFD2 expression and various immune cell infiltration, which implied that MTHFD2 might serve as an agent in tumor immunotherapy. Conclusion: MTHFD2 is widely overexpressed in pan-cancers, and its expression is related with the prognosis of patients and the multiple immune cell infiltrates in TME. Besides, hsa_circ_0046140 and hsa_circ_0006769/miR-383-5p/MTHFD2 axis are implicated with the proliferation and invasion of tumors.

scholarly journals Immune Gene Signature Delineates a Subclass of Papillary Thyroid Cancer with Unfavorable Clinical Outcomes

Cancers ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 494 ◽  
Author(s):  
Kyuryung Kim ◽  
Sora Jeon ◽  
Tae-Min Kim ◽  
Chan Jung
Keyword(s):  
Clinical Outcomes ◽  
Immune Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cytolytic Activity ◽  
The Cancer Genome Atlas ◽  
Immune Checkpoints ◽  
Immune Gene ◽  
Papillary Thyroid ◽  
Thyroid Cancers

Papillary thyroid carcinoma (PTC) represents a heterogeneous disease with diverse clinical outcomes highlighting a need to identify robust biomarkers with clinical relevance. We applied non-negative matrix factorization-based deconvolution to publicly available gene expression profiles of thyroid cancers in the Cancer Genome Atlas (TCGA) consortium. Among three metagene signatures identified, two signatures were enriched in canonical BRAF-like and RAS-like thyroid cancers with up-regulation of genes involved in oxidative phosphorylation and cell adhesions, respectively. The third metagene signature representing up-regulation of immune-related genes further segregated BRAF-like and RAS-like PTCs into their respective subgroups of immunoreactive (IR) and immunodeficient (ID), respectively. BRAF-IR PTCs showed enrichment of tumor infiltrating immune cells, tall cell variant PTC, and shorter recurrence-free survival compared to BRAF-ID PTCs. RAS-IR and RAS-ID PTC subtypes included majority of normal thyroid tissues and follicular variant PTC, respectively. Immunopathological features of PTC subtypes such as immune cell fraction, repertoire of T cell receptors, cytolytic activity, and expression level of immune checkpoints such as and PD-L1 and CTLA-4 were consistently observed in two different cohorts. Taken together, an immune-related metagene signature can classify PTCs into four molecular subtypes, featuring the distinct histologic type, genetic and transcriptional alterations, and potential clinical significance.

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