Immune gene signatures and integrative spatially-resolved digital profiling of prognostic biomarkers for mesothelioma.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e20071-e20071
Author(s):  
Sarah Elizabeth Church ◽  
Carmen Ballesteros-Merino ◽  
Amy H Sullivan ◽  
Andrew M White ◽  
Michael D Bailey ◽  
...  
Keyword(s):  
T Cell ◽  
Protein Expression ◽  
Immune Cell ◽  
Uv Light ◽  
Expression Profiles ◽  
Dna Barcode ◽  
Lymphocyte Activation ◽  
Immune Gene ◽  
Gene Signatures ◽  
Two Samples

e20071 Background: Malignant mesothelioma has been an incurable disease with few effective therapies. While PD-1 targeted therapies have elicited some patient responses, the overall response rate for mesothelioma is low. Since mesothelioma is derived from the mesothelium of the lung, we hypothesize that immune cells in the tumor microenvironment (TME) may behave differently than other solid tumors that are responsive to immunotherapy. Here we characterize prognostic immune gene signatures and spatial protein expression in the mesothelioma TME. Methods: 50 FFPE mesothelioma samples were analyzed using the NanoString PanCancer IO360 assay which measures expression of 770 genes, including the abundance of 14 immune cell types and of 32 IO signatures. All genes and signatures were correlated with overall survival (OS). GeoMx digital spatial profiling (DSP) was performed on 40 samples assessing the protein expression along 12 geometric circular regions-of-interest (ROI). Tissue slides were stained with a combination of fluorescent-labeled antibodies (pan-cytokeratin, CD3, CD68) and a panel of 38-antibodies each conjugated to a unique UV-photocleavable DNA barcode. UV light was applied to the defined ROI, which releases the DNA barcodes for quantitation on the nCounter platform. Results: Unsupervised clustering of samples based on gene signatures showed two distinct groups; one, with low expression of lymphocyte activation/exhaustion signatures and the second, with moderate expression of immune signatures. Two samples had high expression of all immune gene signatures, also confirmed by DSP had increased expression of T cell markers. Tumor proliferation (p < 0.001), hypoxia (p = 0.04), glycolysis (p < 0.001), B7-H3 (p = 0.007) and TGF-β (p = 0.001) signatures were significantly associated with shorter OS. Additional DSP profiling of these mesothelioma samples showed both T cell excluded and desert TMEs. Conclusions: We show that the mesothelioma TME has distinct immune biology associated with OS. Tumors from patients with poor survival had expression profiles previously described to be associated with immune excluded and desert phenotypes. We show that gene expression and DSP identifies unique targets for immunotherapy and we hypothesize that these findings may guide the development of combination trials that will be effective against mesothelioma.

scholarly journals EPEN-22. SINGLE-CELL RNA SEQUENCING IDENTIFIES UPREGULATION OF IKZF1 IN PFA2 MYELOID SUBPOPULATION DRIVING AN ANTI-TUMOR PHENOTYPE

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii312-iii312
Author(s):  
Andrea Griesinger ◽  
Eric Prince ◽  
Andrew Donson ◽  
Kent Riemondy ◽  
Timothy Ritzman ◽  
...  
Keyword(s):  
T Cell ◽  
Single Cell ◽  
T Cell Activation ◽  
Expression Profiles ◽  
Myeloid Cells ◽  
Cell Subset ◽  
Lineage Tracing ◽  
Machine Learning Techniques ◽  
Cell Subpopulation ◽  
Immune Gene

Abstract We have previously shown immune gene phenotype variations between posterior fossa ependymoma subgroups. PFA1 tumors chronically secrete IL-6, which pushes the infiltrating myeloid cells to an immune suppressive function. In contrast, PFA2 tumors have a more immune activated phenotype and have a better prognosis. The objective of this study was to use single-cell(sc) RNAseq to descriptively characterize the infiltrating myeloid cells. We analyzed approximately 8500 cells from 21 PFA patient samples and used advanced machine learning techniques to identify distinct myeloid and lymphoid subpopulations. The myeloid compartment was difficult to interrupt as the data shows a continuum of gene expression profiles exist within PFA1 and PFA2. Through lineage tracing, we were able to tease out that PFA2 myeloid cells expressed more genes associated with an anti-viral response (MHC II, TNF-a, interferon-gamma signaling); while PFA1 myeloid cells had genes associated with an immune suppressive phenotype (angiogenesis, wound healing, IL-10). Specifically, we found expression of IKZF1 was upregulated in PFA2 myeloid cells. IKZF1 regulates differentiation of myeloid cells toward M1 or M2 phenotype through upregulation of either IRF5 or IRF4 respectively. IRF5 expression correlated with IKZF1, being predominately expressed in the PFA2 myeloid cell subset. IKZF1 is also involved in T-cell activation. While we have not completed our characterization of the T-cell subpopulation, we did find significantly more T-cell infiltration in PFA2 than PFA1. Moving forward these studies will provide us with valuable information regarding the molecular switches involved in the tumor-immune microenvironment and to better develop immunotherapy for PFA ependymoma.

scholarly journals The Effects of Simulated Microgravity on Macrophage Phenotype

Biomedicines ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 1205
Author(s):  
Christopher Ludtka ◽  
Erika Moore ◽  
Josephine B. Allen
Keyword(s):  
Protein Expression ◽  
Simulated Microgravity ◽  
Prolonged Exposure ◽  
Cell Function ◽  
Immune Cell ◽  
Expression Profiles ◽  
Microgravity Environment ◽  
M2 Macrophage ◽  
Macrophage Function ◽  
Gene And Protein Expression

The effects of spaceflight, including prolonged exposure to microgravity, can have significant effects on the immune system and human health. Altered immune cell function can lead to adverse health events, though precisely how and to what extent a microgravity environment impacts these cells remains uncertain. Macrophages, a key immune cell, effect the inflammatory response as well as tissue remodeling and repair. Specifically, macrophage function can be dictated by phenotype that can exist between spectrums of M0 macrophage: the classically activated, pro-inflammatory M1, and the alternatively activated, pro-healing M2 phenotypes. This work assesses the effects of simulated microgravity via clinorotation on M0, M1, and M2 macrophage phenotypes. We focus on phenotypic, inflammatory, and angiogenic gene and protein expression. Our results show that across all three phenotypes, microgravity results in a decrease in TNF-α expression and an increase in IL-12 and VEGF expression. IL-10 was also significantly increased in M1 and M2, but not M0 macrophages. The phenotypic cytokine expression profiles observed may be related to specific gravisensitive signal transduction pathways previously implicated in microgravity regulation of macrophage gene and protein expression. Our results highlight the far-reaching effects that simulated microgravity has on macrophage function and provides insight into macrophage phenotypic function in microgravity.

scholarly journals PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy

2020 ◽  
Vol 8 (2) ◽  
pp. e001631
Author(s):  
Sylvain Simon ◽  
Valentin Voillet ◽  
Virginie Vignard ◽  
Zhong Wu ◽  
Camille Dabrowski ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cell Population ◽  
Therapeutic Response ◽  
Immune Cell ◽  
Expression Profiles ◽  
Cell Subset ◽  
Phenotypic Characterization ◽  
Multiparameter Flow Cytometry ◽  
Specific Gene

BackgroundClinical benefit from programmed cell death 1 receptor (PD-1) inhibitors relies on reinvigoration of endogenous antitumor immunity. Nonetheless, robust immunological markers, based on circulating immune cell subsets associated with therapeutic efficacy are yet to be validated.MethodsWe isolated peripheral blood mononuclear cell from three independent cohorts of melanoma and Merkel cell carcinoma patients treated with PD-1 inhibitor, at baseline and longitudinally after therapy. Using multiparameter flow cytometry and cell sorting, we isolated four subsets of CD8+ T cells, based on PD-1 and TIGIT expression profiles. We performed phenotypic characterization, T cell receptor sequencing, targeted transcriptomic analysis and antitumor reactivity assays to thoroughly characterize each of these subsets.ResultsWe documented that the frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T-cells after 1 month of anti-PD-1 therapy was associated with clinical response and overall survival. This DPOS T-cell population was enriched in highly activated T-cells, tumor-specific and emerging T-cell clonotypes and T lymphocytes overexpressing CXCR5, a key marker of the CD8 cytotoxic follicular T cell population. Additionally, transcriptomic profiling defined a specific gene signature for this population as well as the overexpression of specific pathways associated with the therapeutic response.ConclusionsOur results provide a convincing rationale for monitoring this PD-1+TIGIT+ circulating population as an early cellular-based marker of therapeutic response to anti-PD-1 therapy.

Association between cetuximab response and differential immunologic gene expression signatures in colorectal cancer metastases.

2016 ◽  
Vol 34 (4_suppl) ◽  
pp. 558-558 ◽  
Author(s):  
Michael Sangmin Lee ◽  
Benjamin Garrett Vincent ◽  
Autumn Jackson McRee ◽  
Hanna Kelly Sanoff
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
T Cells ◽  
T Cell ◽  
Immune Cell ◽  
Expression Profiles ◽  
Gene Set Enrichment Analysis ◽  
Activated T Cells ◽  
Gene Sets

558 Background: Different immune cell infiltrates into colorectal cancer (CRC) tumors are associated with different prognoses. Tumor-associated macrophages contribute to immune evasion and accelerated tumor progression. Conversely, tumor infiltrating lymphocytes at the invasive margin of CRC liver metastases are associated with improved outcomes with chemotherapy. Cetuximab is an IgG1 monoclonal antibody against epidermal growth factor receptor (EGFR) and stimulates antibody-dependent cellular cytotoxicity (ADCC) in vitro. However, it is unclear in humans if response to cetuximab is modulated by the immune response. We hypothesized that different immune patterns detected in gene expression profiles of CRC metastases are associated with different responses to cetuximab. Methods: We retrieved gene expression data from biopsies of metastases from 80 refractory CRC patients treated with cetuximab monotherapy (GEO GSE5851). Samples were dichotomized by cetuximab response as having either disease control (DC) or progressive disease (PD). We performed gene set enrichment analysis (GSEA) with GenePattern 3.9.4 using gene sets of immunologic signatures obtained from the Molecular Signatures Database v5.0. Results: Among the 68 patients with response annotated, 25 had DC and 43 had PD. In the PD cohort, 59/1910 immunologic gene sets had false discovery rate (FDR) < 0.1. Notably, multiple gene sets upregulated in monocyte signatures were associated with PD. Also, gene sets consistent with PD1-ligated T cells compared to control activated T cells (FDR = 0.052) or IL4-treated CD4 T cells compared to controls (FDR = 0.087) were associated with PD. Conclusions: Cetuximab-resistant patients tended to have baseline increased expression of gene signatures reflective of monocytic infiltrates, consistent with also having increased expression of the IL4-treated T-cell signature. Cetuximab resistance was also associated with increased expression of the PD1-ligated T cell signature. These preliminary findings support further evaluation of the effect of differential immune infiltrates in prognosis of metastatic CRC treated with cetuximab.

scholarly journals Aberrant Lymphocyte Activation Precedes Delayed Virus-Specific T-Cell Response after both Primary Infection and Secondary Exposure to Hepadnavirus in the Woodchuck Model of Hepatitis B Virus Infection

2008 ◽  
Vol 82 (14) ◽  
pp. 6992-7008 ◽  
Author(s):  
Shashi A. Gujar ◽  
Adam K. Jenkins ◽  
Clifford S. Guy ◽  
Jinguo Wang ◽  
Tomasz I. Michalak
Keyword(s):  
T Cell ◽  
Cell Response ◽  
Hepatitis Virus ◽  
Expression Profiles ◽  
Lymphocyte Activation ◽  
T Cell Response ◽  
Specific Response ◽  
Cell Reactivity ◽  
Necrosis Factor Alpha

ABSTRACT The contribution of virus-specific T lymphocytes to the outcome of acute hepadnaviral hepatitis is well recognized, but a reason behind the consistent postponement of this response remains unknown. Also, the characteristics of T-cell reactivity following reexposure to hepadnavirus are not thoroughly recognized. To investigate these issues, healthy woodchucks (Marmota monax) were infected with liver-pathogenic doses of woodchuck hepatitis virus (WHV) and investigated unchallenged or after challenge with the same virus. As expected, the WHV-specific T-cell response appeared late, 6 to 7 weeks postinfection, remained high during acute disease, and then declined but remained detectable long after the resolution of hepatitis. Interestingly, almost immediately after infection, lymphocytes acquired a heightened capacity to proliferate in response to mitogenic (nonspecific) stimuli. This reactivity subsided before the WHV-specific T-cell response appeared, and its decline coincided with the cells' augmented susceptibility to activation-induced death. The analysis of cytokine expression profiles confirmed early in vivo activation of immune cells and revealed their impairment of transcription of tumor necrosis factor alpha and gamma interferon. Strikingly, reexposure of the immune animals to WHV swiftly induced hyperresponsiveness to nonspecific stimuli, followed again by the delayed virus-specific response. Our data show that both primary and secondary exposures to hepadnavirus induce aberrant activation of lymphocytes preceding the virus-specific T-cell response. They suggest that this activation and the augmented death of the cells activated, accompanied by a defective expression of cytokines pivotal for effective T-cell priming, postpone the adaptive T-cell response. These impairments likely hamper the initial recognition and clearance of hepadnavirus, permitting its dissemination in the early phase of infection.

scholarly journals ImSig: A resource for the identification and quantification of immune signatures in blood and tissue transcriptomics data

2016 ◽  
Author(s):  
Ajit Johnson Nirmal ◽  
Tim Regan ◽  
Barbara Bo-Ju Shih ◽  
David Arthur Hume ◽  
Andrew Harvey Sims ◽  
...  
Keyword(s):  
Immune Cell ◽  
Cell Types ◽  
Clinical Samples ◽  
Marker Genes ◽  
Immune Gene ◽  
Gene Signatures ◽  
Transcriptomic Data ◽  
Prognostic Assessment ◽  
The Status ◽  
Transcriptomics Data

AbstractThe outcome of many diseases is commonly correlated with the immune response at the site of pathology. The ability to monitor the status of the immune system in situ provides a mechanistic understanding of disease progression, a prognostic assessment and a guide for therapeutic intervention. Global transcriptomic data can be deconvoluted to provide an indication of the cell types present and their activation state, but the gene signatures proposed to date are either disease-specific or have been derived from data generated from isolated cell populations. Here we describe an improved set of immune gene signatures, ImSig, derived based on their co-expression in blood and tissue datasets. ImSig includes validated lists of marker genes for the main immune cell types and a number of core pathways. When used in combination with network analysis, ImSig is an accurate and easy to use approach for monitoring immune phenotypes in transcriptomic data derived from clinical samples.

scholarly journals Immune gene expression profiles in high-grade urothelial carcinoma of the bladder: a NanoString study

2020 ◽  
Vol 74 (1) ◽  
pp. 53-57 ◽  
Author(s):  
Ekaterina Olkhov-Mitsel ◽  
Anjelica Hodgson ◽  
Stanley K Liu ◽  
Danny Vesprini ◽  
Jane Bayani ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Immune Evasion ◽  
Messenger Rna ◽  
Immune Cell ◽  
Expression Profiles ◽  
Differentially Expressed Gene ◽  
Immune Gene ◽  
High Grade ◽  
Predictive Values

AimsThe advent of immune checkpoint inhibitor therapy has proven beneficial in a subset of high-grade urothelial carcinomas (HGUC) of the bladder. Although treatment selection is currently largely determined by programmed death-ligand 1 (PD-L1) status, multiple factors in the immune system may modulate the host immune response to HGUC and immunotherapy. In this pilot study, we used a transcriptomic approach to identify the immune milieu associated with PD-L1 expression to enhance our understanding of the HGUC immune evasion network.MethodsThe immune transcriptome of 40 HGUC cystectomy cases was profiled using the NanoString nCounter Human V.1.1 PanCancer Panel. All cases were assessed for associated PD-L1 status (SP263) using whole tissue sections. PD-L1 status was determined as high or low using 25% tumour and/or immune cell staining.ResultsThe most significantly differentially expressed gene was PD-L1 messenger RNA (CD274), which strongly correlated with protein expression (r=0.720, p<0.001). The sensitivity, specificity, positive and negative predictive values of CD274 for PD-L1 expression were 85%, 96%, 92% and 93%, respectively. The PD-L1 associated gene signature also included complement components C1QA and CD46 and NOD2 (innate immune system), proinflammatory cytokines CXCL14, CXCL16, CCL3, CCL3L1 and OSM along with the immune response mediator SMAD3, among others. Pathway analysis determined enrichment of these genes in interleukin-10 production, lymphocyte chemotaxis and aberrant IFNγ, NF-κB and ERK signalling networks.ConclusionsWe report key genes and pathways in the immune transcriptome and their association with PD-L1 status, which may be involved in immune evasion of HGUC and warrants further investigation.

Proteomic Analysis Identifies Outcome-Predictive Clusters in Patients with Peripheral T-Cell Lymphoma, Not Otherwise Specified

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1623-1623
Author(s):  
Maja Ludvigsen ◽  
Martin Bjerregaard Pedersen ◽  
Stephen Jacques Hamilton-Dutoit ◽  
Knud Bendix ◽  
Michael Boe Møller ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
T Cell ◽  
Protein Expression ◽  
Proteomic Analysis ◽  
Cell Lymphoma ◽  
Expression Profiles ◽  
Peripheral T Cell Lymphoma ◽  
Not Otherwise Specified ◽  
Protein Expression Profiles ◽  
Unsupervised Cluster Analysis

Abstract Introduction: Peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) is a heterogeneous group of mature T-cell lymphomas, probably composed by different biologically related subsets that have not yet been conclusively identified. In the WHO classification, PTCL-NOS accounts for 25-30% of all mature T-/NK-cell malignancies. The clinical outcome is generally poor with a 5-yr overall survival of 30-35% after conventional treatment strategies. The aim of the study was to apply proteomic analysis in PTCL-NOS and to use the protein expression profiles to characterize clinically relevant subsets within this heterogeneous entity by means of unsupervised cluster analysis. Methods: Archival frozen tumor tissue samples from 20 patients diagnosed with PTCL-NOS from 1991 to 2010 were analyzed for protein expression by high-resolution two-dimensional gel electrophoresis. Individual protein spots were visualized with fluorescence staining and the expression profiles were identified. All patients were homogeneously treated with curatively intended anthracycline-containing combination regimens. Clinico-pathological features were obtained from the Danish Lymphoma Registry (LYFO) and from patient records. Hyperplastic tonsils from healthy adults were included as reference tissue (n=8). Principal component analysis and unsupervised hierarchical cluster analysis were performed on the basis of the protein expression profiles. Differentially expressed (two-fold or higher, Mann-Whitney U-test) proteins between the detected clusters were identified by liquid chromatography - tandem mass spectrometry. Results: Unsupervised cluster analysis defined three distinct clusters: one containing all reference samples and two additional ones further subdividing the PTCL-NOS cases in two separate subsets. Patients from these two PTCL-NOS subsets had significantly different responses to treatment and survival (p = 0.001). The differentially expressed proteins were primarily involved in (i) promotion of tumor growth, (ii) regulation of cellular metabolism, and (iii) immune responses. Conclusion : Proteomic analysis identified shared protein expression patterns and potential prognostic markers in subsets of PTCL-NOS. Disclosures No relevant conflicts of interest to declare.

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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