scholarly journals 953 Transcriptional analysis of leukocytes from COVID convalescent donors reveals persistent activation of the innate and adaptive immune system

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A1002-A1003
Author(s):  
Mallikarjuna Gedda ◽  
Patrick Danaher ◽  
Lipei Saho ◽  
Martin Ongkeko ◽  
Leonard Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
T Cell ◽  
T Cell Receptor ◽  
Time Windows ◽  
Cell Receptor ◽  
Differentially Expressed ◽  
Tcr Diversity ◽  
The Mean ◽  
Over Time

BackgroundCoronavirus disease 2019 (COVID-19) results in robust but dysregulated acute immune response characterized by pro-inflammatory cytokine production and T-cell exhaustion, but little is known concerning immune response following recovery. We assessed immune function in convalescent plasma donors (CCD) who had recovered from COVID-19.MethodsThe cellular immune response and T-cell receptor (TCR) diversity in CCD was investigated using the nCounter host response and TCR diversity panels. 270 CCD and 40 healthy donor (HD) blood samples collected 11 to 193 days after diagnosis were analyzed. The CCD samples were from 162 donors, 69 donated more than once. All HD donated only once.ResultsMany genes were differentially expressed for months following infection. Analysis of samples collected 0 to 90 days post-diagnosis found that 19 of 773 genes were differentially expressed among CCD and HD (FDR < 0.05) (figure 1a). At 90 to 120 days, 120 to 150 and >150 post-diagnosis, 13, 58 and 4 genes were differentially expressed respectively (FDR < 0.05) (figures 1b-d). At 120 to 150 days the differentially expressed genes included those in Treg differentiation, type III interferon signaling and chemokine signaling pathways. 76 genes were differently expressed at least once during the time windows described above. (Figure 1e). Among CCD, the expression of CTLA-4, ICOS, ICOSLG, OSM and CXCR4 were initially elevated but fell to HD levels at the end of the study period. The expression of LILRA6, CCR2 and CX3CR1 increased or remained elevated throughout (figure 1f).A subset of samples departed notably from the average trend. The transcriptome of each CCD sample was scored by its similarity to the mean transcriptome of HD samples. This analysis revealed 21 CCD samples from 19 unique donors were highly perturbed from HD samples (figure 2a). Among these highly perturbed samples 80% were collected > 90 days post-diagnosis. The perturbed samples clustered into two groups, labelled P1 and P2 (figure 2b) and displayed dysregulation of distinct gene sets (figures 2c, 2d). The P1 were characterized by increased expression of genes in myeloid inflammation, type 1 interferon and innate immune signaling pathways, lower COVID antibody levels and increased T-cell receptor diversity. P2 were characterized by highly up-regulated CD44, BCL2, TGFB1, IL18BP, IL27RA, and IL11RA.Abstract 953 Figure 1Longitudinal trends in CCD gene expression. a-d: Differential expression results in HD vs. 4 time windows of CCD. Genes with FDR <0.1 are labeled; e: average CCD log2 fold-changes from HD over time. Color is only given for times where the Loess regression is different from the mean HD with p < 0.05; f: longitudinal results for selected genes. Orange lines connect CCD samples over time. Blue lines show inner 95% quantiles of HD samplesAbstract 953 Figure 2CCD with more severe departure from HD gene expression. a: CCD samples (in orange) were scored for perturbation from the mean HD (in blue), and 21 highly perturbed sample subsets emerged; b: clustering of the 21 highly perturbed patients. The dendrogram was cut to define two groups. c: volcano plots comparing expression in P1 (left) and P2 (right) vs. CCD; d: longitudinal trends of selected genes perturbed in P1 and P2ConclusionsImmune dysregulation in CCD continues at least 6 months post-infection. Some CCDs experienced marked transcriptional changes which may be the result of COVID-19 reactivation and could be responsible for long-haul syndrome.AcknowledgementsN/ATrial RegistrationNCT04360278ReferencesN/A Ethics ApprovalN/AConsentN/A

scholarly journals Comparative gene expression profiling of T-cell acute lymphoblastic leukemias (T-ALL) expressing the T-cell receptor 𝛂β or γδ (T-ALL𝛂β / T-ALLγδ)

2019 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Acute Lymphoblastic Leukemia ◽  
T Cell ◽  
T Cell Receptor ◽  
Expression Profiling ◽  
Lymphoblastic Leukemia ◽  
Cell Receptor ◽  
Differentially Expressed ◽  
Aggressive Form ◽  
Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive form of leukemia with inferior treatment outcomes. The T-cell receptor (TCR) exists in two major forms: the 𝛂βTCR or the γδTCR, and 20-35% of T-ALL cases express either the 𝛂βTCR or the γδTCR (T-ALL𝛂β or T-ALLγδ). Using a published dataset from a cohort of 14 TCR+ T-ALL patients, I found a series of genes that are differentially expressed among patients T-ALL𝛂β or T-ALLγδ. Any number of these differentially expressed genes may be a scientifically and/or clinically actionable target in TCR+ T-ALL.

scholarly journals T-Cell Receptor Engagement Confers Resistance to Chemotherapy in T-Cell Lymphoproliferative Disorders

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2959-2959
Author(s):  
Tianjiao Wang ◽  
Avery Polk ◽  
Ye Lu ◽  
Ryan A Wilcox
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
B Cell ◽  
Signaling Pathways ◽  
T Cell Receptor ◽  
Antigen Receptor ◽  
Cell Receptor ◽  
Differentially Expressed ◽  
Receptor Signaling ◽  
Antigen Receptor Signaling

Abstract Background: Chemotherapy resistance and primary refractory disease are common among patients with the more common peripheral T-cell lymphomas (TCL) treated with anthracycline-based chemotherapy. Antigen-receptor signaling activates a number of proliferation and survival pathways in normal lymphocytes. When activated in lymphomas, antigen-receptor signaling might confer resistance to chemotherapy. Until recently, the role of antigen-receptor signaling in B-cell malignancies was poorly understood. It is now appreciated that B-cell receptor (BCR) signaling is an important driver of B-cell lymphoma growth and survival, and represents an attractive therapeutic target in these lymphomas. In contrast, the potential role of T-cell receptor (TCR) signaling in T-cell lymphomagenesis is poorly understood. The observation that most (≈95%) TCLs express an intact TCR suggests that malignant T cells, like their B-cell counterparts, may benefit from antigen-receptor signaling. Methods: TCL cell lines and primary patient specimens were subjected to TCR activation by CD3/CD28 beads. Gene expression profiling was performed by Affymetrix human gene 2.1 ST array at different time points (4, 8, 24 hours) following TCR engagement. Results were further validated by immunophenotyping by flow cytometry, western blot and cytokine measurement by enzyme-linked immunosorbent assay (ELISA). The proliferation and chemoresistance of the TCL cells following TCR engagement were determined by MTT assay. Results: Microarray gene expression profiling of TCLs showed differential gene expression upon TCR engagement by CD3/CD28 beads at different time points. A total of 1274 genes were differentially expressed commonly in the patient specimens. Some of the differentially expressed genes were confirmed in independent samples by immunophenotyping (CD25, CD30, CD69, CD137, CCR4, GITR) and cytokine (IL2, IL13, IL10, IFNγ) release. Gene enrichment analysis of the common differentially expressed genes showed that pro-proliferation and pro-survival signaling pathways, including TCR (FDR: 0.05%), MAPK (FDR: 2.8%), NFκB (FDR: 0.1%) and cytokines (FDR: 0.03%) were enriched in TCR-engaged TCL cells. The activation of TCR and NFκB signaling in TCR-engaged TCLs was also confirmed by western blot and flow cytometry. More importantly, the proliferation of TCLs increased by 2-4 fold when cocultured with CD3/CD28 beads for 72 hours (p<0.01). In the presence of either vincristine or romidepsin, the viability of TCLs increased by 1.5-4 fold by CD3/CD28 bead treatment (p<0.01). TCR-dependent proliferation and chemoresistance in TCLs was significantly inhibited by agents targeting TCR and NFκB signaling pathways. Conclusions: T-cell receptor dependent signaling pathways are rational therapeutic targets in the T-cell lymphomas. Disclosures No relevant conflicts of interest to declare.

scholarly journals Transgenic Technology and the Study of Hepatitis Viruses: A Review of What We Have Learned

2000 ◽  
Vol 14 (9) ◽  
pp. 781-787 ◽  
Author(s):  
David R Milich
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Immune Response ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Transgenic Technology ◽  
Gene Expression And Regulation ◽  
Hepatitis Viruses ◽  
Hbv Replication ◽  
Viral Genes

Because of the absence of inbred animal models susceptible to infection by the hepatitis B (HBV), C (HCV) and delta (HDV) viruses, and the inability to culture these viruses, a number of investigators have produced transgenic (Tg) mice that express one or all the viral genes. This review attempts to catalogue and characterize the Tg mice produced to date. The topics addressed are HBV, HCV and HDV gene expression and regulation; HBV replication models and factors that inhibit replication; HBV pathogenesis models; HBV tolerance and persistence models; modulation of the immune response to HBV proteins in Tg mice; T cell receptor Tg mice; and models of hepatocellular carcinoma.

scholarly journals The ht beta gene encodes a novel CACCC box-binding protein that regulates T-cell receptor gene expression

1993 ◽  
Vol 13 (9) ◽  
pp. 5691-5701
Author(s):  
Y Wang ◽  
J A Kobori ◽  
L Hood
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
T Cell Receptor ◽  
Binding Protein ◽  
Cell Receptor ◽  
Regulatory Function ◽  
Human T Cell ◽  
Alpha Gene ◽  
Beta Gene

A gene encoding a novel CACCC box-binding protein that binds to the promoter region of the human T-cell receptor (TCR) V beta 8.1 gene and the mouse TCR alpha gene silencer has been cloned. This gene, termed ht beta, contains four zinc fingers of the class Cys2-X12-His2 that may be responsible for DNA binding and a highly negatively charged region that defines a putative transcriptional activation domain. Analysis of the expression of ht beta mRNA revealed similar expression levels and patterns in various cell lines. The bacterially expressed ht beta protein can bind to the CACCC box in both the human TCR V beta 8.1 gene promoter and the mouse TCR alpha gene silencer. The CACCC box is essential for efficient transcription of the V beta 8.1 promoter. Cotransfection with an ht beta expression plasmid and a reporter vector indicated that ht beta can activate human TCR V beta 8.1 gene transcription. ht beta also is able to counteract the silencing effect of the mouse TCR alpha gene silencer. The CACCC box has been found in almost all V beta 8.1 gene subfamily members and in both TCR alpha and beta gene enhancers in humans and mice. These results suggest that the CACCC box-binding protein may have an important regulatory function for TCR gene expression in alpha beta T cells versus gamma delta T cells.

Analysis of immunoglobulin and T-cell receptor gene deficiency in graft rejection by gene expression profiles1

2004 ◽  
Vol 77 (4) ◽  
pp. 580-586 ◽  
Author(s):  
Rachel A. DeFina ◽  
Yurong Liang ◽  
Hongzhen He ◽  
Kathleen J. Haley ◽  
Kenneth Christopher ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
T Cell Receptor ◽  
Graft Rejection ◽  
Receptor Gene ◽  
Cell Receptor ◽  
Gene Deficiency ◽  
T Cell Receptor Gene ◽  
Cell Receptor Gene

scholarly journals RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease

2017 ◽  
Vol 64 (4) ◽  
pp. 476-481 ◽  
Author(s):  
Jerome Bouquet ◽  
Jennifer L. Gardy ◽  
Scott Brown ◽  
Jacob Pfeil ◽  
Ruth R. Miller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Disease ◽  
T Cell ◽  
B Cell ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Rna Seq ◽  
Viral Pathogen ◽  
Complex Chronic Disease

scholarly journals Functional Reprogramming of the Primary Immune Response by T Cell Receptor Antagonism

2004 ◽  
Vol 200 (11) ◽  
pp. 1371-1382 ◽  
Author(s):  
Dipica Haribhai ◽  
Brandon Edwards ◽  
Mary L. Williams ◽  
Calvin B. Williams
Keyword(s):  
Immune Response ◽  
T Cell ◽  
Cell Fate ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Effector Function ◽  
Primary Immune Response ◽  
Cell Homing ◽  
T Cell Homing ◽  
Cell Receptor Antagonism

The T cell receptor must translate modest, quantitative differences in ligand binding kinetics into the qualitatively distinct signals used to determine cell fate. Here, we use mice that express an endogenous T cell receptor (TCR) antagonist and an adoptive transfer system to examine the influence of TCR signal quality on the development of effector function. We show that activation of antigen-specific T cells in the presence of an antagonist results in a functional reprogramming of the primary immune response, marked by altered T cell homing, a failure to develop effector function, and ultimately clonal elimination by apoptosis. Importantly, antagonism does not block cell division, implying that the signals promoting clonal expansion and effector differentiation are distinct.

Identification and functional characterization of the human T-cell receptor beta gene transcriptional enhancer: common nuclear proteins interact with the transcriptional regulatory elements of the T-cell receptor alpha and beta genes

1990 ◽  
Vol 10 (10) ◽  
pp. 5486-5495
Author(s):  
L R Gottschalk ◽  
J M Leiden
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
T Cell Receptor ◽  
Binding Sites ◽  
Cell Receptor ◽  
Nuclear Proteins ◽  
Transcriptional Enhancer ◽  
Enhancer Element ◽  
Beta 2 ◽  
Beta Gene

A transcriptional enhancer has been mapped to a region 5.5 kilobases 3' of the C beta 2 gene in the human T-cell receptor (TCR) beta-chain locus. Transient transfections allowed localization of enhancer activity to a 480-base-pair HincII-XbaI restriction enzyme fragment. The TCR beta enhancer was active on both the minimal simian virus 40 promoter and a TCR beta variable gene promoter in both TCR alpha/beta + and TCR gamma/delta + T cells. It displayed significantly less activity in Epstein-Barr virus-transformed B cells and K562 chronic myelogenous leukemia cells and no activity in HeLa fibroblasts. DNA sequence analysis revealed that the enhancer contains a consensus immunoglobulin kappa E2 motif, as well as an AP-1-binding site and a cyclic AMP response element. DNase I footprint analyses using Jurkat T-cell nuclear extracts allowed the identification of five nuclear protein-binding sites, T beta 1 to T beta 5, within the enhancer element. Deletion and in vitro mutagenesis studies demonstrated that the T beta 2- and T beta 3- and T beta 4-binding sites are each required for full transcriptional enhancer activity. In contrast, deletion of the T beta 1- and T beta 5-binding sites had essentially no effect on enhancer function. Electrophoretic mobility shift assays demonstrated that TCR alpha/beta + and TCR gamma/delta + T cells expressed T beta 2-, T beta 3-, and T beta 4-binding activities. In contrast, non-T-cell lines, in which the enhancer was inactive, each lacked expression of at least one of these binding activities. TCR alpha and beta gene expression may be regulated by a common set of T-cell nuclear proteins in that the T beta 2 element binding a set of cyclic AMP response element-binding proteins that are also bound by the T alpha 1 element of the human TCR alpha enhancer and the decamer element present in a large number of human and murine TCR beta promoters. Similarly, the T beta 5 TCR beta-enhancer element and the T alpha 2 TCR alpha-enhancer element bind at least one common T-cell nuclear protein. Taken together, these results suggest that TCR beta gene expression is regulated by the interaction of multiple T cell nuclear proteins with a transcriptional enhancer element located 3' of the C beta 2 gene and that some of these proteins may be involved in the coordinate regulation of TCR alpha and beta gene expression.

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