scholarly journals Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges

2017 ◽  
Vol 115 (3) ◽  
pp. E488-E497 ◽  
Author(s):  
Barbara Piasecka ◽  
Darragh Duffy ◽  
Alejandra Urrutia ◽  
Hélène Quach ◽  
Etienne Patin ◽  
...  
Keyword(s):  
T Cells ◽  
Immune Responses ◽  
Disease Risk ◽  
Transcriptional Response ◽  
Cellular Heterogeneity ◽  
Specific Cell ◽  
Immune Gene ◽  
Immune Genes ◽  
Regulatory Variants ◽  
Age And Sex

The contribution of host genetic and nongenetic factors to immunological differences in humans remains largely undefined. Here, we generated bacterial-, fungal-, and viral-induced immune transcriptional profiles in an age- and sex-balanced cohort of 1,000 healthy individuals and searched for the determinants of immune response variation. We found that age and sex affected the transcriptional response of most immune-related genes, with age effects being more stimulus-specific relative to sex effects, which were largely shared across conditions. Although specific cell populations mediated the effects of age and sex on gene expression, including CD8+T cells for age and CD4+T cells and monocytes for sex, we detected a direct effect of these intrinsic factors for the majority of immune genes. The mapping of expression quantitative trait loci (eQTLs) revealed that genetic factors had a stronger effect on immune gene regulation than age and sex, yet they affected a smaller number of genes. Importantly, we identified numerous genetic variants that manifested their regulatory effects exclusively on immune stimulation, including aCandida albicans-specific master regulator at theCR1locus. These response eQTLs were enriched in disease-associated variants, particularly for autoimmune and inflammatory disorders, indicating that differences in disease risk may result from regulatory variants exerting their effects only in the presence of immune stress. Together, this study quantifies the respective effects of age, sex, genetics, and cellular heterogeneity on the interindividual variability of immune responses and constitutes a valuable resource for further exploration in the context of different infection risks or disease outcomes.

scholarly journals Increased NFATC4 Correlates With Poor Prognosis of AML Through Recruiting Regulatory T Cells

2020 ◽  
Vol 11 ◽  
Author(s):  
Chong Zhao ◽  
Shaoxin Yang ◽  
Wei Lu ◽  
Jiali Liu ◽  
Yanyu Wei ◽  
...  
Keyword(s):  
T Cells ◽  
Immune Responses ◽  
Poor Prognosis ◽  
Risk Group ◽  
Pearson Correlation ◽  
Differentially Expressed ◽  
Immune Gene ◽  
Gene Set ◽  
Immune Genes ◽  
Pearson Correlation Analysis

Despite that immune responses play important roles in acute myeloid leukemia (AML), immunotherapy is still not widely used in AML due to lack of an ideal target. Therefore, we identified key immune genes and cellular components in AML by an integrated bioinformatics analysis, trying to find potential targets for AML. Eighty-six differentially expressed immune genes (DEIGs) were identified from 751 differentially expressed genes (DEGs) between AML patients with fair prognosis and poor prognosis from the TCGA database. Among them, nine prognostic immune genes, including NCR2, NPDC1, KIR2DL4, KLC3, TWIST1, SNORD3B-1, NFATC4, XCR1, and LEFTY1, were identified by univariate Cox regression analysis. A multivariable prediction model was established based on prognostic immune genes. Kaplan–Meier survival curve analysis indicated that patients in the high-risk group had a shorter survival rate and higher mortality than those in the low-risk group (P < 0.001), indicating good effectiveness of the model. Furthermore, nuclear factors of activated T cells-4 (NFATC4) was recognized as the key immune gene identified by co-expression of differentially expressed transcription factors (DETFs) and prognostic immune genes. ATP-binding cassette transporters (ABC transporters) were the downstream KEGG pathway of NFATC4, identified by gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA). To explore the immune responses NFATC4 was involved in, an immune gene set of T cell co-stimulation was identified by single-cell GSEA (ssGSEA) and Pearson correlation analysis, positively associated with NFATC4 in AML (R = 0.323, P < 0.001, positive). In order to find out the immune cell types affected by NFATC4, the CIBERSORT algorithm and Pearson correlation analysis were applied, and it was revealed that regulatory T cells (Tregs) have the highest correlation with NFATC4 (R = 0.526, P < 0.001, positive) in AML from 22 subsets of tumor-infiltrating immune cells. The results of this study were supported by multi-omics database validation. In all, our study indicated that NFATC4 was the key immune gene in AML poor prognosis through recruiting Tregs, suggesting that NFATC4 might serve as a new therapy target for AML.

MIP-1α and MIP-1β differentially mediate mucosal and systemic adaptive immunity

Blood ◽  
2003 ◽  
Vol 101 (3) ◽  
pp. 807-814 ◽  
Author(s):  
James W. Lillard ◽  
Udai P. Singh ◽  
Prosper N. Boyaka ◽  
Shailesh Singh ◽  
Dennis D. Taub ◽  
...  
Keyword(s):  
T Cells ◽  
Immune Responses ◽  
Adaptive Immunity ◽  
Cd8 T Cells ◽  
Host Cells ◽  
Secretory Iga ◽  
Specific Cell ◽  
Cellular Immune Responses ◽  
Cc Chemokines ◽  
Cellular Immune

AbstractMacrophage inflammatory protein-1α (MIP-1α) and MIP-1β are distinct but highly homologous CC chemokines produced by a variety of host cells in response to various external stimuli and share affinity for CCR5. To better elucidate the role of these CC chemokines in adaptive immunity, we have characterized the affects of MIP-1α and MIP-1β on cellular and humoral immune responses. MIP-1α stimulated strong antigen (Ag)–specific serum immunoglobulin G (IgG) and IgM responses, while MIP-1β promoted lower IgG and IgM but higher serum IgA and IgE antibody (Ab) responses. MIP-1α elevated Ag-specific IgG1 and IgG2b followed by IgG2a and IgG3 subclass responses, while MIP-1β only stimulated IgG1 and IgG2b subclasses. Correspondingly, MIP-1β produced higher titers of Ag-specific mucosal secretory IgA Ab levels when compared with MIP-1α. Splenic T cells from MIP-1α– or MIP-1β–treated mice displayed higher Ag-specific Th1 (interferon-γ [IFN-γ]) as well as selective Th2 (interleukin-5 [IL-5] and IL-6) cytokine responses than did T cells from control groups. Interestingly, mucosally derived T cells from MIP-1β–treated mice displayed higher levels of IL-4 and IL-6 compared with MIP-1α–treated mice. However, MIP-1α effectively enhanced Ag-specific cell-mediated immune responses. In correlation with their selective effects on humoral and cellular immune responses, these chemokines also differentially attract CD4+ versus CD8+ T cells and modulate CD40, CD80, and CD86 expressed by B220+ cells as well as CD28, 4-1BB, and gp39 expression by CD4+ and CD8+ T cells in a dose-dependent fashion. Taken together, these studies suggest that these CC chemokines differentially enhance mucosal and serum humoral as well as cellular immune responses.

scholarly journals Immunization with Ehrlichia P28 Outer Membrane Proteins Confers Protection in a Mouse Model of Ehrlichiosis

2011 ◽  
Vol 18 (12) ◽  
pp. 2018-2025 ◽  
Author(s):  
Patricia A. Crocquet-Valdes ◽  
Nagaraja R. Thirumalapura ◽  
Nahed Ismail ◽  
Xuejie Yu ◽  
Tais B. Saito ◽  
...  
Keyword(s):  
T Cells ◽  
Membrane Proteins ◽  
Immune Responses ◽  
Outer Membrane ◽  
Outer Membrane Proteins ◽  
The United States ◽  
Mononuclear Phagocytes ◽  
Specific Cell ◽  
Content Type ◽  
Ifn Γ

ABSTRACTThe obligately intracellular bacteriumEhrlichia chaffeensisthat resides in mononuclear phagocytes is the etiologic agent of human monocytotropic ehrlichiosis (HME). HME is an emerging and often life-threatening, tick-transmitted infectious disease in the United States. Effective primary immune responses againstEhrlichiainfection involve generation ofEhrlichia-specific gamma interferon (IFN-γ)-producing CD4+T cells and cytotoxic CD8+T cells, activation of macrophages by IFN-γ, and production ofEhrlichia-specific antibodies of the Th1 isotype. Currently, there are no vaccines available against HME. We evaluated the ability of 28-kDa outer membrane proteins (P28-OMP-1) of the closely relatedEhrlichia muristo stimulate long-term protective memory T and B cell responses and confer protection in mice. The spleens of mice vaccinated withE. murisP28-9, P28-12, P28-19, or a mixture of these three P28 proteins (P28s) using a DNA prime-protein boost regimen and challenged withE. murishad significantly lower bacterial loads than the spleens of mock-vaccinated mice. Mice immunized with P28-9, P28-12, P28-19, or the mixture inducedEhrlichia-specific CD4+Th1 cells. Interestingly, mice immunized with P28-14, orthologs of which inE. chaffeensisandE. canisare primarily expressed in tick cells, failed to lower the ehrlichial burden in the spleen. Immunization with the recombinant P28-19 protein alone also significantly decreased the bacterial load in the spleen and liver compared to those of the controls. Our study reports, for the first time, the protective roles of theEhrlichiaP28-9 and P28-12 proteins in addition to confirming previous reports of the protective ability of P28-19. Partial protection induced by immunization with P28-9, P28-12, and P28-19 againstEhrlichiawas associated with the generation ofEhrlichia-specific cell-mediated and humoral immune responses.

scholarly journals Identification the prognostic value of immune gene signature and infiltrating immune cells of esophageal cancer patients

2020 ◽  
Author(s):  
Lin Wang ◽  
Qian Wei ◽  
Ming Zhang ◽  
Lianze Chen ◽  
Zinan Li ◽  
...  
Keyword(s):  
T Cells ◽  
Esophageal Cancer ◽  
Signaling Pathway ◽  
Immune Cells ◽  
Roc Curves ◽  
Survival Outcome ◽  
Immune Gene ◽  
Prognostic Signature ◽  
Immune Genes ◽  
Validation Set

Abstract Background Esophageal cancer (ESCA) is one of the deadliest solid malignancies with worse survival in the world. The poor prognosis of ESCA is not only related to malignant cells, but also affected by the microenvironment. We aimed to establish prognostic signature consisting of immune genes to predict the survival outcome of patients and estimate the prognosis value of infiltrating immune cells in tumor microenvironment (TME). Methods Based on integrated analysis of gene expression profiling and immune gene database, differentially immune-related genes were filtered out. Then, stepwise Cox regression analysis was applied to identify survival related immune genes and construct prognosis signature. Functional enrichment analysis was performed to explore biology function. Kaplan-Meier (K-M) curves and receiver operating characteristic (ROC) curves were performed to validate the predictive effect of predictive signature. We also verified the clinical value of prognostic signature under the influence of different clinical parameters. For deeper analysis, we evaluated the correlation between prognosis signature and infiltrating immune cells by Tumor Immune Estimation Resource (TIMER) and CIBERSORT. Results Finally, we identified 303 differentially immune genes as candidate and constructed immune prognosis signature composed of six immune genes. Furthermore, we observed that the prognosis signature was enriched in cytokine-mediated signaling pathway, lymphocyte activation, immune effector process, cancer pathway, NF-kappa B signaling pathway. K-M survival curves showed that the prognosis signature indeed have good predictive ability in entire ESCA set ( P =0.003), validation set 1 ( P =0.008) and validation set 2 ( P =0.036). The area under the curve (AUC) of ROC curves validated the predictive accuracy of immune signature in three cohorts (AUC=0.757, 0.800 and 0.701), respectively. In addition, we identified the prognosis value of infiltrating-immune cells including activated memory CD4 T cells, T cells follicular helper cells and monocytes and provided a landscape of TME. Conclusions The results indicated that immune prognosis signature can be a novel biomarker to predict survival outcome, which can provide new targets for immunotherapy and individualized therapies in ESCA and open up a new prospect for improving the prognosis of ESCA patients in the era of immunotherapy.

scholarly journals The Virulence of Different Vaccinia Virus Strains Is Directly Proportional to Their Ability To Downmodulate Specific Cell-Mediated Immune CompartmentsIn Vivo

2018 ◽  
Vol 93 (6) ◽  
Author(s):  
Lorena F. D. de Freitas ◽  
Rafael P. Oliveira ◽  
Mariana C. G. Miranda ◽  
Raíssa P. Rocha ◽  
Edel F. Barbosa-Stancioli ◽  
...  
Keyword(s):  
T Cells ◽  
Immune Responses ◽  
Vaccinia Virus ◽  
Viral Vector ◽  
Smallpox Vaccination ◽  
Direct Result ◽  
Cell Mediated Immunity ◽  
Specific Cell ◽  
Cell Responses ◽  
Virus Strains

ABSTRACTVaccinia virus (VACV) is a notorious virus for a number of scientific reasons; however, most of its notoriety comes from the fact that it was used as a vaccine against smallpox, being ultimately responsible for the eradication of that disease. Nonetheless, many different vaccinia virus strains have been obtained over the years; some are suitable to be used as vaccines, whereas others are virulent and unsuitable for this purpose. Interestingly, different vaccinia virus strains elicit different immune responsesin vivo, and this is a direct result of the genomic differences among strains. In order to evaluate the net result of virus-encoded immune evasion strategies of vaccinia viruses, we compared antiviral immune responses in mice intranasally infected by the highly attenuated and nonreplicative MVA strain, the attenuated and replicative Lister strain, or the virulent WR strain. Overall, cell responses elicited upon WR infections are downmodulated compared to those elicited by MVA and Lister infections, especially in determined cell compartments such as macrophages/monocytes and CD4+T cells. CD4+T cells are not only diminished in WR-infected mice but also less activated, as evaluated by the expression of costimulatory molecules such as CD25, CD212, and CD28 and by the production of cytokines, including tumor necrosis factor alpha (TNF-α), gamma interferon (IFN-γ), interleukin-4 (IL-4), and IL-10. On the other hand, MVA infections are able to induce strong T-cell responses in mice, whereas Lister infections consistently induced responses that were intermediary between those induced by WR and MVA. Together, our results support a model in which the virulence of a VACV strain is proportional to its potential to downmodulate the host’s immune responses.IMPORTANCEVaccinia virus was used as vaccine against smallpox and was instrumental in the successful eradication of that disease. Although smallpox vaccination is no longer in place in the overall population, the use of vaccinia virus in the development of viral vector-based vaccines has become popular. Nonetheless, different vaccinia virus strains are known and induce different immune responses. To look into this, we compared immune responses triggered by mouse infections with the nonreplicative MVA strain, the attenuated Lister strain, or the virulent WR strain. We observed that the WR strain was capable of downmodulating mouse cell responses, whereas the highly attenuated MVA strain induced high levels of cell-mediated immunity. Infections by the intermediately attenuated Lister strain induced cell responses that were intermediary between those induced by WR and MVA. We propose that the virulence of a vaccinia virus strain is directly proportional to its ability to downmodulate specific compartments of antiviral cell responses.

scholarly journals Genetic Variants in Immune Related Genes as Predictors of Responsiveness to BCG Immunotherapy in Metastatic Melanoma Patients

Cancers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 91
Author(s):  
Romela Irene Ramos ◽  
Misa A. Shaw ◽  
Leland Foshag ◽  
Stacey L. Stern ◽  
Negin Rahimzadeh ◽  
...  
Keyword(s):  
Immune Responses ◽  
Disease Free Survival ◽  
Phase Iii ◽  
Stage Iii ◽  
Immune Gene ◽  
Nucleotide Polymorphisms ◽  
Predictive Tool ◽  
Immune Genes ◽  
Ajcc Stage ◽  
Melanoma Patients

Adjuvant immunotherapy in melanoma patients improves clinical outcomes. However, success is unpredictable due to inherited heterogeneity of immune responses. Inherent immune genes associated with single nucleotide polymorphisms (SNPs) may influence anti-tumor immune responses. We assessed the predictive ability of 26 immune-gene SNPs genomic panels for a clinical response to adjuvant BCG (Bacillus Calmette-Guérin) immunotherapy, using melanoma patient cohorts derived from three phase III multicenter clinical trials: AJCC (American Joint Committee on Cancer) stage IV patients given adjuvant BCG (pilot cohort; n = 92), AJCC stage III patients given adjuvant BCG (verification cohort; n = 269), and AJCC stage III patients that are sentinel lymph node (SLN) positive receiving no immunotherapy (control cohort; n = 80). The SNP panel analysis demonstrated that the responder patient group had an improved disease-free survival (DFS) (hazard ratio [HR] 1.84, 95% CI 1.09–3.13, p = 0.021) in the pilot cohort. In the verification cohort, an improved overall survival (OS) (HR 1.67, 95% CI 1.07–2.67, p = 0.025) was observed. No significant differences of SNPs were observed in DFS or OS in the control patient cohort. This study demonstrates that SNP immune genes can be utilized as a predictive tool for identifying melanoma patients that are inherently responsive to BCG and potentially other immunotherapies in the future.

scholarly journals Development of an Individualized Immune Prognostic Signature for Clear Cell Renal Cell Carcinoma through the Identification of Differential Immune Genes

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Jianfeng Wang ◽  
Chaozhi Tang ◽  
Xiaowu Liu
Keyword(s):  
Renal Cell Carcinoma ◽  
T Cells ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Immune Gene ◽  
Cell Renal Cell Carcinoma ◽  
Immune Genes ◽  
Tumor Microenvironments ◽  
Prognosis Model

Increasing evidence has shown that tumor microenvironments are an important feature in clear cell renal cell carcinoma (ccRCC) carcinogenesis and therapeutic efficacy. In this study, two subtypes of ccRCC, high- and low-immune groups, were identified based on the immune gene datasets, of which the differential immune genes were identified accordingly. Furthermore, we constructed a risk prognosis model using five immune genes, specifically, AQP9, KIAA1429, HAMP, CCL13, and CCL21. This model was highly predictive of ccRCC clinical characteristics and showed potential for use in immunotherapy. Furthermore, the five identified genes were highly correlated with the abundance of B cells, CD4 T cells, CD8 T cells, macrophages, neutrophils, and dendritic cells in the tumor microenvironments. Among them, AQP9, KIAA1429, and HAMP exhibited significant prognostic potential. These findings indicate that monitoring and operating tumor microenvironments are of great significance for ccRCC prognosis and precise immunotherapy.

scholarly journals A Four-Immune Gene Prognostic Risk Model for Colorectal Adenocarcinoma Based on the TCGA and Immport Data Sets

2020 ◽  
Author(s):  
Boyang Xu ◽  
Ziqi Peng ◽  
Yue An ◽  
Xue Yao ◽  
Mingjun Sun
Keyword(s):  
T Cells ◽  
Colorectal Adenocarcinoma ◽  
Immune Cell ◽  
Risk Model ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Data Sets ◽  
Immune Gene ◽  
Immune Genes ◽  
Follicular Helper

Abstract BackgroundAs one of the hot spots in oncology field, immune research provides new ideas for the diagnosis and treatment of tumors. Different histological types of colorectal cancer are different. Adenocarcinoma, as the type with the highest proportion, has a high research value. This study aims to build an immune gene prognostic risk model for colorectal adenocarcinoma to improve the diagnosis and prognosis prediction of colorectal adenocarcinoma.MethodsThe differentially expressed immune genes could be obtained from the gene expression data downloaded from The Cancer Genome Atlas (TCGA) and the immune gene data downloaded from the ImmPort Database. Univariate COX and multivariate COX analyses were used to construct the immune gene prognostic risk model of and the clinical application potential of this model. The correlation between the model and the immune cells infiltration and the influence of each immune cell on the survival were analyzed.Results5975 differentially expressed genes were obtained, and 497 differentially expressed immune genes were selected by combining the information of immune genes. Among them, 36 immune genes were associated with prognosis, and 4 immune genes (THRB, IL1RL2, LGR6, LTB4R2) were included in the prognostic risk model of immune genes. Patients with higher Risk Score had shorter survival. Compared with gender, age and pathological stage, the model has better prediction potential. In addition, the model was correlated with Macrophages M0, Macrophages M1, T cells follicular helper and NK cells activated. Among them, T cells follicular helper and Macrophages M0 were related to the survival of patients.ConclusionWe developed a prognostic risk model containing four immune genes, THRB, IL1RL2, LGR6 and LTB4R2, which accurately described the prognosis of the patient, and affected the survival of patients by influencing the infiltration of Macrophages M0 and T cells follicular helper.

scholarly journals Alu repeats at the boundaries of regulatory elements shape the epigenetic environment of immune genes in T cells

2021 ◽  
Author(s):  
Mickael COSTALLAT ◽  
Christophe Rachez ◽  
Christian MUCHARDT
Keyword(s):  
Dna Methylation ◽  
T Cells ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Average Length ◽  
Boundary Function ◽  
Regulatory Elements ◽  
Immune Gene ◽  
Alu Elements ◽  
Immune Genes

Promoters and enhancers are sites of transcription initiation (TSSs) and carry active histone modifications, including H3K4me1, H3K4me3, and H3K27ac. Yet, the principles governing the boundaries of such regulatory elements are still poorly characterized. Alu elements are good candidates for a boundary function, being highly abundant in gene-rich regions, while essentially excluded from regulatory elements. Here, we show that the interval from the TSS to the first upstream Alu accommodates essentially all H3K4me3 marks, while excluding DNA methylation. In contrast, enhancer-enriched H3K4me1 and H3K27ac marks eventually cross the first-Alu limit, consistent with enhancer-annotation occasionally overlapping with Alu elements. Remarkably, the average length of TSS-to-first Alu intervals greatly varies in-between tissues, being longer in stem- and shorter in immune-cells. Shortest TSS-to-Alu intervals were observed at promoters active in T cells, particularly at immune genes, correlating with serendipitous RNA polymerase II transcription and accumulation of H3K4me1 signal at the first-Alu. At several T-cell first-Alus, the DNA methylation was further found to evolved with age, regressing from young to middle-aged, then recovering later in life. Thus, the first-Alu upstream of TSSs functions as a dynamic boundary for regulatory elements, initiating the upstream DNA-methylation landscape, while also participating in the recording of immune gene transcriptional events.

scholarly journals Increasing a Robust Antigen-Specific Cytotoxic T Lymphocyte Response by FMDV DNA Vaccination with IL-9 Expressing Construct

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Qiang Zou ◽  
Bing Wu ◽  
Xiaodan He ◽  
Yizhi Zhang ◽  
Youmin Kang ◽  
...  
Keyword(s):  
T Cells ◽  
Immune Responses ◽  
Cytotoxic T Lymphocyte ◽  
Humoral Response ◽  
Cellular Responses ◽  
Dna Vaccination ◽  
Specific Cell ◽  
Lymphocyte Response ◽  
Molecular Adjuvant ◽  
Cytotoxic T Lymphocyte Response

Various chemokines and cytokines as adjuvants can be used to improve efficacy of DNA vaccination. In this study, we sought to investigate if a DNA construct expressing IL-9 (designed as proV-IL9) as a molecular adjuvant enhance antigen specific immune responses elicited by the pcD-VP1 DNA vaccination. Mice immunized with pcD-VP1 combined with proV-IL9 developed a strong humoral response. In addition, the coinoculation induced significant higher level of antigen-specific cell proliferation and cytotoxic response. This agreed well with higher expression level of IFN-γand perforin in CD8+T cells, but not with IL-17 in these T cells. The results indicate that IL-9 induces the development of IFN-γ-producing CD8+T cells (Tc1), but not the IL-17-producing CD8+T cells (Tc17). Up-regulated expressions of BCL-2 and BCL-XL were exhibited in these Tc1 cells, suggesting that IL-9 may trigger antiapoptosis mechanism in these cells. Together, these results demonstrated that IL-9 used as molecular adjuvant could enhance the immunogenicity of DNA vaccination, in augmenting humoral and cellular responses and particularly promoting Tc1 activations. Thus, the IL-9 may be utilized as a potent Tc1 adjuvant for DNA vaccines.

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