scholarly journals Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Muhammad Munir Iqbal ◽  
Michael Serralha ◽  
Parwinder Kaur ◽  
David Martino
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
T Cells ◽  
T Cell ◽  
Chromatin Remodeling ◽  
T Cell Activation ◽  
Cell Activation ◽  
Specific Gene ◽  
Gene Promoters ◽  
Time Points

AbstractT-cell activation induces context-specific gene expression programs that promote energy generation and biosynthesis, progression through the cell cycle and ultimately cell differentiation. The aim of this study was to apply the omni ATAC-seq method to characterize the landscape of chromatin changes induced by T-cell activation in mature naïve CD4+ T-cells. Using a well-established ex vivo protocol of canonical T-cell receptor signaling, we generated genome-wide chromatin maps of naïve T-cells from pediatric donors in quiescent or recently activated states. We identified thousands of individual chromatin accessibility peaks that are associated with T-cell activation, the majority of which were annotated intronic and intergenic enhancer regions. A core set of 3268 gene promoters underwent chromatin remodeling and concomitant changes in gene expression in response to activation, and were enriched in multiple pathways controlling cell cycle regulation, metabolism, inflammatory response genes and cell survival. Leukemia inhibitory factor (LIF) was among those factors that gained the highest accessibility and expression, in addition to IL2-STAT5 dependent chromatin remodeling in the T-cell activation response. Using publicly available data we found the chromatin response was far more dynamic at 24-h compared with 72-h post-activation. In total 546 associations were reproduced at both time-points with similar strength of evidence and directionality of effect. At the pathways level, the IL2-STAT5, KRAS signalling and UV response pathways were replicable at both time-points, although differentially modulated from 24 to 72 h post-activation.

scholarly journals Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation

2021 ◽  
Author(s):  
Blagoje Soskic ◽  
Eddie Cano-Gamez ◽  
Deborah J. Smyth ◽  
Kirsty Ambridge ◽  
Ziying Ke ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
T Cell Activation ◽  
Cell Activation ◽  
Memory T Cells ◽  
Disease Risk ◽  
Effector Memory ◽  
Immune Disease ◽  
Time Points

AbstractDuring activation, T cells undergo extensive changes in gene expression which shape the properties of cells to exert their effector function. Therefore, understanding the genetic regulation of gene expression during T cell activation provides essential insights into how genetic variants influence the response to infections and immune diseases. We generated a single-cell map of expression quantitative trait loci (eQTL) across a T cell activation time-course. We profiled 655,349 CD4+ naive and memory T cells, capturing transcriptional states of unstimulated cells and three time points of cell activation in 119 healthy individuals. We identified 38 cell clusters, including stable clusters such as central and effector memory T cells and transient clusters that were only present at individual time points of activation, such as interferon-responding cells. We mapped eQTLs using a T cell activation trajectory and identified 6,407 eQTL genes, of which a third (2,265 genes) were dynamically regulated during T cell activation. We integrated this information with GWAS variants for immune-mediated diseases and observed 127 colocalizations, with significant enrichment in dynamic eQTLs. Immune disease loci colocalized with genes that are involved in the regulation of T cell activation, and genes with similar functions tended to be perturbed in the same direction by disease risk alleles. Our results emphasize the importance of mapping context-specific gene expression regulation, provide insights into the mechanisms of genetic susceptibility of immune diseases, and help prioritize new therapeutic targets.

scholarly journals Nanoconfinement of Microvilli Alters Gene Expression and Boosts T cell Activation

2021 ◽  
Author(s):  
Morteza Aramesh ◽  
Diana Stoycheva ◽  
Ioana Sandu ◽  
Stephan J. Ihle ◽  
Tamara Zund ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Cell Signaling ◽  
T Cell Activation ◽  
Cell Activation ◽  
Local Environment ◽  
T Cell Signaling ◽  
Sense And Respond ◽  
Altered Gene

T cells sense and respond to their local environment at the nanoscale by forming small actin-rich protrusions, called microvilli, which play critical roles in signaling and antigen recognition, particularly at the interface with the antigen presenting cells. However, the mechanisms by which microvilli contribute to cell signaling and activation is largely unknown. Here, we present a tunable engineered system that promotes microvilli formation and T cell signaling via physical stimuli. We discovered that nanoporous surfaces favored microvilli formation, and markedly altered gene expression in T cells and promoted their activation. Mechanistically, confinement of microvilli inside of nanopores leads to size-dependent sorting of membrane-anchored proteins, specifically segregating CD45 phosphatases and T cell receptors (TCR) from the tip of the protrusions when microvilli are confined in 200 nm pores, but not in 400 nm pores. Consequently, formation of TCR nanoclustered hotspots within 200 nm pores, allows sustained and augmented signaling that prompts T cell activation even in the absence of TCR agonists. The synergistic combination of mechanical and biochemical signals on porous surfaces presents a straightforward strategy to investigate the role of microvilli in T cell signaling as well as to boost T cell activation and expansion for application in the growing field of adoptive immunotherapy.

Lysophosphatidic acid enhances interleukin-13 gene expression and promoter activity in T cells

2006 ◽  
Vol 290 (1) ◽  
pp. L66-L74 ◽  
Author(s):  
Joshua Rubenfeld ◽  
Jia Guo ◽  
Nitat Sookrung ◽  
Rongbing Chen ◽  
Wanpen Chaicumpa ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Signaling Pathways ◽  
T Cell Activation ◽  
Lysophosphatidic Acid ◽  
Cell Activation ◽  
Human Peripheral Blood ◽  
Regulatory Elements ◽  
Jurkat Cells

Lysophosphatidic acid (LPA) is a membrane-derived lysophospholipid with wide-ranging effects on multiple lung cells including airway epithelial and smooth muscle cells. LPA can augment migration and cytokine synthesis in lymphocytes, but its potential effects on Th2 cytokines have not been well studied. We examined the effects of physiological concentrations of LPA on IL-13 gene expression in human T cells. The Jurkat T cell line and human peripheral blood CD4+ T cells were incubated with LPA alone or with 1) pharmacological agonists of different signaling pathways, or 2) antibodies directed against the T cell receptor complex and costimulatory molecules. Luciferase-based reporter constructs driven by different lengths of the human IL-13 promoter were transfected by electroporation in Jurkat cells treated with and without LPA. The effects of LPA on IL-13 mRNA stability were examined using actinomycin D to halt ongoing transcription. Expression of mRNA encoding LPA2and LPP-1 increased with T cell activation. LPA augmented IL-13 secretion under conditions of submaximal T cell activation. This was observed using pharmacological agonists activating intracellular calcium-, PKC-, and cAMP-dependent signaling pathways, as well as antibodies directed against CD3 and CD28. LPA only slightly prolonged IL-13 mRNA half-life in submaximally stimulated Jurkat cells. In contrast, LPA significantly enhanced transcriptional activation of the IL-13 promoter via regulatory elements contained within proximal 312 bp. The effects of LPA on IL-13 promoter activation appeared to be distinct from those mediated by GATA-3. LPA can augment IL-13 gene expression in T cells, especially under conditions of submaximal activation.

scholarly journals Interleukin-2-dependent phosphorylation of the retinoblastoma-susceptibility-gene product p110-115RB in human T-cells

1992 ◽  
Vol 282 (3) ◽  
pp. 759-764 ◽  
Author(s):  
G A Evans ◽  
L M Wahl ◽  
W L Farrar
Keyword(s):  
Cell Cycle ◽  
T Cells ◽  
T Cell ◽  
Gene Transcription ◽  
T Cell Activation ◽  
Cell Activation ◽  
Susceptibility Gene ◽  
Interleukin 2 ◽  
Human T Cells ◽  
Rb Phosphorylation

The state of phosphorylation of the retinoblastoma-susceptibility gene product, p110-115RB, is thought to have fundamental importance in controlling the progression of the cell through the cell cycle. We have studied RB phosphorylation in human T-cells in the context of T-cell activation, stimulated by phytohaemagglutinin (PHA) and interleukin-2 (IL-2). We show that, of the signals associated with T-cell activation, only signals that directly lead to movement into S phase of the cell cycle are capable of stimulating RB phosphorylation. Cyclosporin A (CsA), a potent inhibitor of IL-2 synthesis and cellular proliferation, blocked RB phosphorylation, and this was recovered with exogenous IL-2, indicating a direct involvement of IL-2 in controlling RB phosphorylation. We found that PHA did not stimulate RB phosphorylation within 10 h of treatment, but IL-2 could effectively stimulate RB phosphorylation within 2 h, and this approached a maximum within 8-10 h of IL-2 treatment. Further, by using actinomycin D to inhibit new gene transcription following IL-2 stimulation, we found that early-cell-cycle phosphorylation of RB required IL-2-stimulated gene transcription. From these data we conclude that, in human T-cells, RB phosphorylation is not directly associated with T-cell receptor-mediated events, but requires the interaction of IL-2 and new gene transcription following IL-2 stimulation.

Mechanism of Interleukin-10 Inhibition of T-Helper Cell Activation by Superantigen at the Level of the Cell Cycle

Blood ◽  
1999 ◽  
Vol 93 (1) ◽  
pp. 208-216 ◽  
Author(s):  
George Q. Perrin ◽  
Howard M. Johnson ◽  
Prem S. Subramaniam
Keyword(s):  
Cell Cycle ◽  
T Cells ◽  
T Cell ◽  
T Cell Activation ◽  
Cd4 T Cells ◽  
Cell Activation ◽  
Interleukin 2 ◽  
Interleukin 10 ◽  
Inhibitory Protein ◽  
Cell Functions

Abstract We have analyzed the effects of interleukin-10 (IL-10) on the entry of quiescent CD4+ T cells into the cell cycle upon stimulation with the superantigen staphylococcal enterotoxin B (SEB). IL-10 arrested cells at G0/G1. IL-10 treatment prevented the downregulation of p27Kip1, an inhibitory protein that controls progression out of the G0 phase of the cell cycle. IL-10 also prevented the upregulation of the G1 cyclins D2 and D3, proteins necessary for entry and progression through the G1 phase of the cell cycle. Associated with the inhibition of the cell cycle, IL-10 suppressed SEB induction of interleukin-2 (IL-2). Addition of exogenous IL-2 to IL-10–treated cells significantly reversed the antiproliferative effects of IL-10. Moreover, IL-10 effects on the early G1proteins p27Kip1 and cyclin D2 were similarly reversed by exogenous IL-2. Although this reversal by IL-2 was pronounced, it was not complete, suggesting that IL-10 may have some effects not directly related to the suppression of IL-2 production. Cell separation experiments suggest that IL-10 can effect purified CD4+ T cells directly, providing functional evidence for the presence of IL-10 receptors on CD4+ T cells. IL-10 also inhibited expression of IL-2 transcriptional regulators c-fos and c-jun, which also inhibit other cell functions. Our studies show that the mechanism of IL-10 regulation of quiescent CD4+ T-cell activation is mainly by blocking induction of IL-2 that is critical to downregulation of p27Kip1 and upregulation of D cyclins in T-cell activation and entry into the cell cycle.

DNA mismatch repair deficiency and benefit from adjuvant bevacizumab in NSABP C-08: Molecular profiling results.

2012 ◽  
Vol 30 (30_suppl) ◽  
pp. 55-55
Author(s):  
Katherine L. Pogue-Geile ◽  
Noriko Tanaka ◽  
Patrick Gavin ◽  
Greg Yothers ◽  
Linda H. Colangelo ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Mismatch Repair ◽  
T Cell Activation ◽  
Cell Activation ◽  
Statistical Tests ◽  
Differentially Expressed ◽  
Braf Mutations ◽  
Study Gene Expression

55 Background: The purpose of this study was to identify biomarkers that define a subset of patients who received benefit from bevacizumab (bev) in NSABP trial C-08, even though bev did not improve outcomes over standard adjuvant chemotherapy (CT) in the treatment of stage II and III colon cancer. Methods: A randomly selected cohort of C-08 cases (N=500) were profiled for whole genome expression (N=445) and for mutations (N=463) in KRAS, NRAS, PIK3CA, and MET. BRAF mutations and mismatch repair (MMR) status were profiled on the available cases (N=1,764 and 1,993, respectively). Cox proportional hazard models were used to assess prognosis and prediction for the value of bev using overall survival (0S) and time to recurrence (TTR) as end points. Results: The effect of bev was different for MMR deficient (MMR-d) and proficient tumors for OS (interaction p=.035) but not TTR (interaction p=.08). Patients with MMR-d (N=252) tumors showed a significant benefit from the addition of bev to CT for OS (hazard ratio =0.52 (95% CI: 0.29-0.94, p=0.028). KRAS, NRAS, PIK3CA, and MET were not significant for interaction with bev in the discovery cohort. BRAF mutations were associated with MMR status (p<.0001) and the prognostic value of MMR depended on BRAF for TTR (interaction p=.027) but not OS (interaction p=.31). The effect of bev was independent of BRAF (interaction p=.28 TTR and .37 OS). Three-factor interaction tests for bev, MMR, and BRAF were not significant for either endpoint. Gene expression analysis with BRB array tools identified 5 BioCarta pathways (p<0.05) which differentially expressed in 4 statistical tests; 4 of these pathways were directly or indirectly involved in T cell activation and one was involved in the activation of VEGF. Conclusions: Patients in C-08 with MMR-d tumors received benefit from bev treatment but these results need to be validated in a separate study. Gene expression data suggest that T-cells may be differentially expressed based on MMR status. Activation of VEGF has been shown to suppress T-cell development (Ohm et al. Blood. 2003:10;4878). A speculative possibility for the benefit of bev in MMR-d tumors may be due to blocking of VEGF, releasing T cells from VEGF suppression.

Regulation of T Cell Homeostasis and Cell Cycling in Patients with Acute Myeloid Leukemia.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2767-2767
Author(s):  
J. Katrin Hunger ◽  
Susanne Pfoertner ◽  
Philipp Ivanyi ◽  
Juergen Krauter ◽  
Arnold Ganser ◽  
...  
Keyword(s):  
Cell Cycle ◽  
T Cells ◽  
T Cell ◽  
T Cell Activation ◽  
Cd4 T Cells ◽  
Myeloid Leukemia ◽  
Cell Activation ◽  
Leukemic Cell ◽  
Soluble Factors ◽  
A Cell

Abstract Background and Aims: Although leukemic cells express tumor-associated antigens, suppression of an effective T cell immune response is a well known phenomenon in acute myeloid leukemia (AML). In principle, the malignant cells may escape immune surveillance by (1) incomplete T cell activation due to the absence of costimulatory molecules on the leukemic cell types, (2) secretion of soluble immunosuppressive factors, which may lead among others to (3) induction of anergic and/or regulatory T cell phenotypes. A better understanding of the underlying mechanism would have important implications for the development of immunotherapeutic strategies. Methods: CD3+ T cells were analyzed for activation, proliferation and Th1 cytokine production after coculturing with primary AML cells or leukemic cell supernatant. In addition, self-developed human Treg microarrays were used to reveal a gene expression profile of CD4+ T cells isolated from untreated AML patients (n=7) in comparison to CD4+ T cells from healthy volunteers (n=6) and AML patients after achieving a complete remission (n=4). The specific regulation of selected canditate genes was confirmed by realtime RT-PCR. Based on microarray results cell-cycle analyses were performed in order to study the effect of primary AML cells on the cell-cycle progression of stimulated T-cells. Results: Our studies could show that primary AML cells suppress T cell activation, proliferation and Th1 cytokines production mainly in a cell-contact dependent manner and to a minor degree via soluble factors. Nevertheless, cell-cycle analyses demonstrated that soluble factors from leukemic cell supernatants may inhibit the cell-cycle entry of T cells after mitogenic stimulation with an arrest in G0/G1 phase. Interestingly, the molecular profile of CD4+ T cells isolated from untreated AML patients could identify a profound dysregulation of molecules involved in the regulation of cell-cycle (i.e., CDK4, Vav2, Egr-1, Id2) and apoptosis (i.e., Bcl-2, Bax). In addition, genes important for the immune response (i.e., IL2R, CTLA-4), especially various chemokines/-receptors (i.e., RANTES, CXCL10, CCR2) were dysregulated, whereas the expression pattern of genes specific for regulatory T cells (i.e., FoxP3, PD-1, GITR) were broadly unaffected. Conclusion: AML cells (in-)/directly modulate normal T cell function such as activation, proliferation, cytokine/chemokine production and cell-cycle regulation. One might speculate that the lack of an effective anti-tumor response is associated with a cell-cycle arrest resulting in T cell anergy. Cell-cycle regulators may serve as potential targets for novel immunotherapeutic strategies to eradicate minimal residual disease in patients with AML.

Mechanism of Interleukin-10 Inhibition of T-Helper Cell Activation by Superantigen at the Level of the Cell Cycle

Blood ◽  
1999 ◽  
Vol 93 (1) ◽  
pp. 208-216
Author(s):  
George Q. Perrin ◽  
Howard M. Johnson ◽  
Prem S. Subramaniam
Keyword(s):  
Cell Cycle ◽  
T Cells ◽  
T Cell ◽  
T Cell Activation ◽  
Cd4 T Cells ◽  
Cell Activation ◽  
Interleukin 2 ◽  
Interleukin 10 ◽  
Inhibitory Protein ◽  
Cell Functions

We have analyzed the effects of interleukin-10 (IL-10) on the entry of quiescent CD4+ T cells into the cell cycle upon stimulation with the superantigen staphylococcal enterotoxin B (SEB). IL-10 arrested cells at G0/G1. IL-10 treatment prevented the downregulation of p27Kip1, an inhibitory protein that controls progression out of the G0 phase of the cell cycle. IL-10 also prevented the upregulation of the G1 cyclins D2 and D3, proteins necessary for entry and progression through the G1 phase of the cell cycle. Associated with the inhibition of the cell cycle, IL-10 suppressed SEB induction of interleukin-2 (IL-2). Addition of exogenous IL-2 to IL-10–treated cells significantly reversed the antiproliferative effects of IL-10. Moreover, IL-10 effects on the early G1proteins p27Kip1 and cyclin D2 were similarly reversed by exogenous IL-2. Although this reversal by IL-2 was pronounced, it was not complete, suggesting that IL-10 may have some effects not directly related to the suppression of IL-2 production. Cell separation experiments suggest that IL-10 can effect purified CD4+ T cells directly, providing functional evidence for the presence of IL-10 receptors on CD4+ T cells. IL-10 also inhibited expression of IL-2 transcriptional regulators c-fos and c-jun, which also inhibit other cell functions. Our studies show that the mechanism of IL-10 regulation of quiescent CD4+ T-cell activation is mainly by blocking induction of IL-2 that is critical to downregulation of p27Kip1 and upregulation of D cyclins in T-cell activation and entry into the cell cycle.

scholarly journals CTLA-4 engagement inhibits IL-2 accumulation and cell cycle progression upon activation of resting T cells.

1996 ◽  
Vol 183 (6) ◽  
pp. 2533-2540 ◽  
Author(s):  
M F Krummel ◽  
J P Allison
Keyword(s):  
Cell Cycle ◽  
T Cells ◽  
Cell Death ◽  
T Cell ◽  
T Cell Activation ◽  
Cell Cycle Progression ◽  
Cell Activation ◽  
Apoptotic Cell ◽  
Activated T Cells ◽  
Activated State

While interactions between CD28 and members of the B7 family costimulate and enhance T cell responses, recent evidence indicates that the CD28 homologue CTLA-4 plays a downregulatory role. The mechanism by which this occurs is not clear, but it has been suggested that CTLA-4 terminates ongoing responses of activated T cells, perhaps by induction of apoptosis. Here we demonstrate that CTLA-4 engagement by antibody cross-linking or binding to B7 inhibits proliferation and accumulation of the primary T cell growth factor, IL-2, by cells stimulated with anti-CD3 and anti-CD28. This inhibition is not a result of enhanced cell death. Rather it appears to result from restriction of transition from the G1 to the S phase of the cell cycle. Our observation that upregulation of both the IL-2R alpha chain and the CD69 activation antigen are inhibited by CTLA-4 engagement supplies further evidence that CTLA-4 restricts the progression of T cells to an activated state. Together this data demonstrates that CTLA-4 can regulate T cell activation in the absence of induction of apoptotic cell death.

scholarly journals Simian Immunodeficiency Virus Nef Protein Delays the Progression of CD4+ T Cells through G1/S Phase of the Cell Cycle

2002 ◽  
Vol 76 (8) ◽  
pp. 3587-3595 ◽  
Author(s):  
Thomas Ndolo ◽  
Navdeep K. Dhillon ◽  
Hau Nguyen ◽  
Moraima Guadalupe ◽  
Maria Mudryj ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Proliferation ◽  
T Cells ◽  
T Cell ◽  
Simian Immunodeficiency Virus ◽  
T Cell Activation ◽  
Cell Activation ◽  
Apoptotic Cell ◽  
S Phase ◽  
Immunodeficiency Virus

ABSTRACT Human and simian immunodeficiency virus (HIV and SIV, respectively) infections are characterized by gradual depletion of CD4+ T cells. The underlying mechanisms of CD4+ T-cell depletion and HIV and SIV persistence are not fully determined. The Nef protein is expressed early in infection and is necessary for pathogenesis. Nef can cause T-cell activation and downmodulates cell surface signaling molecules. However, the effect of Nef on the cell cycle has not been well characterized. To determine the role of Nef in the cell cycle, we investigated whether the SIV Nef protein can modulate cell proliferation and apoptosis in CD4+ Jurkat T cells. We developed a CD4+ Jurkat T-cell line that stably expresses SIV Nef under the control of an inducible promoter. Alterations in cell proliferation were determined by flow cytometry using stable intracytoplasmic fluorescent dye 5- and 6-carboxyfluorescein diacetate succinimidyl ester and bromodeoxyuridine incorporation. Apoptotic cell death was measured by annexin V and propidium iodide staining. Our results demonstrated that SIV Nef inhibited Fas-induced apoptosis in these cells and that the mechanism involved upregulation of the Bcl-2 protein. SIV Nef suppressed CD4+ T-cell proliferation by inhibiting the progression of cells into S phase of the cell cycle. Suppression involved an upregulation of cyclin-dependent kinase inhibitors p21 and p27 and the downregulation of cyclin D1 and cyclin A. In summary, inhibition of apoptosis by Nef can lead to persistence of infected cells and can support viral replication. In addition, a Nef-mediated delay in cell cycle progression may contribute to CD4+ T-cell anergy/depletion seen in HIV and SIV disease.

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