64 research outputs found
Epitranscriptomic regulation in immunity and autoimmune disease: Unraveling novel implications of RNA modification m6A
No full textThe immune system protects the human body against pathogens such as viruses, bacteria, and parasites. It has innate and acquired components, which together recognize and eliminate these threats. When the immune system mistakes the body's own materials for pathogens, autoimmune diseases can occur. Immune cells, including T-helper cells (CD4+ T cells) and monocytes, play crucial roles in pathogen recognition, immune activation, and signaling molecule production. T-helper cells activate other immune cells through co-activation molecules like ICOS, CD28, and CD40L, while monocytes are involved in phagocytosis and regulating immune responses. RNA molecules labeled with m6A modification are key in regulating immune cell function. Proteins such as FTO and METTL3 modulate the presence of m6A on RNA, influencing gene expression and immune activation. m6A modifications impact the production and secretion of signaling molecules like TNF, which are critical in immune responses and autoimmune diseases. Research detailed in this thesis highlights the importance of m6A in: - Activating T-helper cells by regulating CD40L expression. - Modulating TNF production in T-helper cells and monocytes. - Controlling immune cell activation and antiviral responses against respiratory syncytial virus (RSV). - Influencing autoimmune diseases like juvenile idiopathic arthritis through altered expression of FTO and m6A labeling. These findings offer potential therapeutic targets for treating immune-related diseases and viral infections by manipulating m6A-regulating proteins
Get Spliced: Uniting Alternative Splicing and Arthritis
No full textImmune responses demand the rapid and precise regulation of gene protein expression. Splicing is a crucial step in this process; ~95% of protein-coding gene transcripts are spliced during mRNA maturation. Alternative splicing allows for distinct functional regulation, as it can affect transcript degradation and can lead to alternative functional protein isoforms. There is increasing evidence that splicing can directly regulate immune responses. For several genes, immune cells display dramatic changes in isoform-level transcript expression patterns upon activation. Recent advances in long-read RNA sequencing assays have enabled an unbiased and complete description of transcript isoform expression patterns. With an increasing amount of cell types and conditions that have been analyzed with such assays, thousands of novel transcript isoforms have been identified. Alternative splicing has been associated with autoimmune diseases, including arthritis. Here, GWASs revealed that SNPs associated with arthritis are enriched in splice sites. In this review, we will discuss how alternative splicing is involved in immune responses and how the dysregulation of alternative splicing can contribute to arthritis pathogenesis. In addition, we will discuss the therapeutic potential of modulating alternative splicing, which includes examples of spliceform-based biomarkers for disease severity or disease subtype, splicing manipulation using antisense oligonucleotides, and the targeting of specific immune-related spliceforms using antibodies
Cytosim codebase extensions for a 2D T cell model
No full textCode is used in "Kinesin-4 KIF21B limits microtubule growth to allow rapid centrosome polarization in T cells", by Peter Jan Hooikaas, Hugo G.J. Damstra, Oane J. Gros, Wilhelmina E. van Riel, Maud Martin, Yesper T.H. Smits, Jorg van Loosdregt, Lukas C. Kapitein, Florian Berger, Anna Akhmanova. The code is an extended form of Cytosim, made by François Nedelec (https://gitlab.com/f.nedelec/cytosim). Only the minor extensions outside of the base code, listed in the README.txt file, can be attributed to author O.J.Gros, other authors are taken from the registered contributors on the cytosim gitlab, as having worked on the code base that was extended
Restoring T Cell Tolerance, Exploring the Potential of Histone Deacetylase Inhibitors for the Treatment of Juvenile Idiopathic Arthritis
No full textJuvenile Idiopathic Arthritis (JIA) is characterized by a loss of immune tolerance. Here, the balance between the activity of effector T (Teff) cells and regulatory T (Treg) cells is disturbed resulting in chronic inflammation in the joints. Presently, therapeutic strategies are predominantly aimed at suppressing immune activation and pro-inflammatory effector mechanisms, ignoring the opportunity to also promote tolerance by boosting the regulatory side of the immune balance. Histone deacetylases (HDACs) can deacetylate both histone and non-histone proteins and have been demonstrated to modulate epigenetic regulation as well as cellular signaling in various cell types. Importantly, HDACs are potent regulators of both Teff cell and Treg cell function and can thus be regarded as attractive therapeutic targets in chronic inflammatory arthritis. HDAC inhibitors (HDACi) have proven therapeutic potential in the cancer field, and are presently being explored for their potential in the treatment of autoimmune diseases. Specific HDACi have already been demonstrated to reduce the secretion of pro-inflammatory cytokines by Teff cells, and promote Treg numbers and suppressive capacity in vitro and in vivo. In this review, we outline the role of the different classes of HDACs in both Teff cell and Treg cell function. Furthermore, we will review the effect of different HDACi on T cell tolerance and explore their potential as a therapeutic strategy for the treatment of oligoarticular and polyarticular JIA
Tissue-Resident Memory T Cells in Chronic Inflammation-Local Cells with Systemic Effects?
No full textChronic inflammatory diseases such as rheumatoid arthritis (RA), Juvenile Idiopathic Arthritis (JIA), psoriasis, and inflammatory bowel disease (IBD) are characterized by systemic as well as local tissue inflammation, often with a relapsing-remitting course. Tissue-resident memory T cells (TRM) enter non-lymphoid tissue (NLT) as part of the anamnestic immune response, especially in barrier tissues, and have been proposed to fuel chronic inflammation. TRM display a distinct gene expression profile, including upregulation of CD69 and downregulation of CD62L, CCR7, and S1PR1. However, not all TRM are consistent with this profile, and it is now more evident that the TRM compartment comprises a heterogeneous population, with differences in their function and activation state. Interestingly, the paradigm of TRM remaining resident in NLT has also been challenged. T cells with TRM characteristics were identified in both lymph and circulation in murine and human studies, displaying similarities with circulating memory T cells. This suggests that re-activated TRM are capable of retrograde migration from NLT via differential gene expression, mediating tissue egress and circulation. Circulating 'ex-TRM' retain a propensity for return to NLT, especially to their tissue of origin. Additionally, memory T cells with TRM characteristics have been identified in blood from patients with chronic inflammatory disease, leading to the hypothesis that TRM egress from inflamed tissue as well. The presence of TRM in both tissue and circulation has important implications for the development of novel therapies targeting chronic inflammation, and circulating 'ex-TRM' may provide a vital diagnostic tool in the form of biomarkers. This review elaborates on the recent developments in the field of TRM in the context of chronic inflammatory diseases
The role of WNT signaling in mature T cells: T cell factor is coming home
No full textT cell factor, the effector transcription factor of the WNT signaling pathway, was so named because of the primary observation that it is indispensable for T cell development in the thymus. Since this discovery, the role of this signaling pathway has been extensively studied in T cell development, hematopoiesis, and stem cells; however, its functional role in mature T cells has remained relatively underinvestigated. Over the last few years, various studies have demonstrated that T cell factor can directly influence T cell function and the differentiation of Th1, Th2, Th17, regulatory T cell, follicular helper CD4+ T cell subsets, and CD8+ memory T cells. In this paper, we discuss the molecular mechanisms underlying these observations and place them in the general context of immune responses. Furthermore, we explore the implications and limitations of these findings for WNT manipulation as a therapeutic approach for treating immune-related diseases
Human regulatory T cells locally differentiate and are functionally heterogeneous within the inflamed arthritic joint
No full textOBJECTIVE: Tregs are crucial for immune regulation, and environment‐driven adaptation of effector (e)Tregs is essential for local functioning. However, the extent of human Treg heterogeneity in inflammatory settings is unclear. METHODS: We combined single‐cell RNA‐ and TCR‐sequencing on Tregs derived from three to six patients with juvenile idiopathic arthritis (JIA) to investigate the functional heterogeneity of human synovial fluid (SF)‐derived Tregs from inflamed joints. Confirmation and suppressive function of the identified Treg clusters was assessed by flow cytometry. RESULTS: Four Treg clusters were identified; incoming, activated eTregs with either a dominant suppressive or cytotoxic profile, and GPR56(+)CD161(+)CXCL13(+) Tregs. Pseudotime analysis showed differentiation towards either classical eTreg profiles or GPR56(+)CD161(+)CXCL13(+) Tregs supported by TCR data. Despite its most differentiated phenotype, GPR56(+)CD161(+)CXCL13(+) Tregs were shown to be suppressive. Furthermore, BATF was identified as an overarching eTreg regulator, with the novel Treg‐associated regulon BHLHE40 driving differentiation towards GPR56(+)CD161(+)CXCL13(+) Tregs, and JAZF1 towards classical eTregs. CONCLUSION: Our study reveals a heterogeneous population of Tregs at the site of inflammation in JIA. SF Treg differentiate to a classical eTreg profile with a more dominant suppressive or cytotoxic profile that share a similar TCR repertoire, or towards GPR56(+)CD161(+)CXCL13(+) Tregs with a more distinct TCR repertoire. Genes characterising GPR56(+)CD161(+)CXCL13(+) Tregs were also mirrored in other T‐cell subsets in both the tumor and the autoimmune setting. Finally, the identified key regulators driving SF Treg adaptation may be interesting targets for autoimmunity or tumor interventions
CBP/P300 Inhibition Impairs CD4+ T Cell Activation: Implications for Autoimmune Disorders
No full textT cell activation is critical for an effective immune response against pathogens. However, dysregulation contributes to the pathogenesis of autoimmune diseases, including Juvenile Idiopathic Arthritis (JIA). The molecular mechanisms underlying T cell activation are still incompletely understood. T cell activation promotes the acetylation of histone 3 at Lysine 27 (H3K27ac) at enhancer and promoter regions of proinflammatory cytokines, thereby increasing the expression of these genes which is essential for T cell function. Co-activators E1A binding protein P300 (P300) and CREB binding protein (CBP), collectively known as P300/CBP, are essential to facilitate H3K27 acetylation. Presently, the role of P300/CBP in human CD4+ T cells activation remains incompletely understood. To assess the function of P300/CBP in T cell activation and autoimmune disease, we utilized iCBP112, a selective inhibitor of P300/CBP, in T cells obtained from healthy controls and JIA patients. Treatment with iCBP112 suppressed T cell activation and cytokine signaling pathways, leading to reduced expression of many proinflammatory cytokines, including IL-2, IFN-γ, IL-4, and IL-17A. Moreover, P300/CBP inhibition in T cells derived from the inflamed synovium of JIA patients resulted in decreased expression of similar pathways and preferentially suppressed the expression of disease-associated genes. This study underscores the regulatory role of P300/CBP in regulating gene expression during T cell activation while offering potential insights into the pathogenesis of autoimmune diseases. Our findings indicate that P300/CBP inhibition could potentially be leveraged for the treatment of autoimmune diseases such as JIA in the future
The Epigenetic and Epitranscriptomic Regulation of Immune Activation
No full textGene expression in immune cells is regulated by intricate mechanisms that contribute to the immune response. Precise control of this expression is crucial for achieving well-timed and finely tuned expression of genes and pathways associated with inflammation. Disruption of this delicate balance can lead to severe complications, such as infections, auto-inflammatory disorders, or autoimmune diseases. This thesis elucidates the role of histone regulation and post-transcriptional regulation via m6A modification in both the adaptive and innate immune systems. Chapter 1 provides a general introduction, setting the stage for the detailed investigations that follow. Chapter 2 delves into the impact of histone regulation on CD4+ T cell activation by inhibiting key co-activators and HAT proteins P300/CBP. The potential of targeted inhibition of P300/CBP through BET inhibition is explored as a therapeutic approach for treating Juvenile Idiopathic Arthritis (JIA). In Chapter 3, the focus shifts to the role of m6A modification in monocyte activation. Following monocyte activation, differential expression of multiple m6A-associated proteins is uncovered, leading to elevated m6A levels. m6A methylation is identified on numerous genes within the TNF signaling via the NFkB pathway, including TNF itself. The m6A reader YTHDC1 binds to m6A-modified TNF, promoting TNF protein expression by facilitating the nuclear export of TNF mRNA. Chapter 4 elaborates on the increased expression of WTAP observed in monocyte activation. An alternative WTAP promoter is identified, which increases expression of a specific WTAP mRNA isoform in monocyte activation under the regulation of NFkB. Chapter 5 returns to JIA, demonstrating expression differences of m6A-associated proteins and increased m6A levels in monocytes derived from the inflamed joint of JIA patients. Decreased expression of the m6A eraser FTO can be induced by environmental cues from the synovial fluid of the inflamed joint. Chapter 6 examines the role of m6A in host immunity against Respiratory Syncytial Virus (RSV) infection. m6A modifications are detected on respiratory viruses, including RSV, which enhances viral replication and immune evasion. On host transcripts, the m6A reader YTHDC1 negatively regulates RSV entry by reducing the expression of the RSV entry receptor CX3CR1. The role of m6A in adaptive immunity and CD4+ T cell activation is discussed in Chapter 7 and Chapter 8, particularly in regulating stability of CD40L and TNF mRNA via m6A reader protein YTHDF2. Chapter 9 provides a general discussion, summarizing the findings of the thesis. Both histone regulation and m6A modification emerge as critical mechanisms for precisely modulating gene expression in different components of the immune system. This chapter explores the intricate interplay between these mechanisms, highlighting factors such as timing, transcript specificity, and reader specificity for m6A modifications. Furthermore, the potential implications of BET inhibition and m6A protein inhibition are underscored as promising therapeutic strategies for addressing autoimmune diseases. Overall, this thesis provides novel insights into how distinct forms of gene regulation orchestrate the immune response. Epigenetic and epitranscriptomic mechanisms, such as histone regulation and m6A modifications, exhibit multifaceted roles in T cell and monocyte activation
NRF2/Itaconate Axis Regulates Metabolism and Inflammatory Properties of T Cells in Children with JIA
No full textBackground: CD4+ T cells critically contribute to the initiation and perturbation of inflammation. When CD4+ T cells enter inflamed tissues, they adapt to hypoxia and oxidative stress conditions, and to a reduction in nutrients. We aimed to investigate how this distinct environment regulates T cell responses within the inflamed joints of patients with childhood rheumatism (JIA) by analyzing the behavior of NRF2—the key regulator of the anti-oxidative stress response—and its signaling pathways. Methods: Flow cytometry and quantitative RT-PCR were used to perform metabolic profiling of T cells and to measure the production of inflammatory cytokines. Loss of function analyses were carried out by means of siRNA transfection experiments. NRF2 activation was induced by treatment with 4-octyl-Itaconate (4-OI). Results: Flow cytometry analyses revealed a high metabolic status in CD4+ T cells taken from synovial fluid (SF) with greater mitochondrial mass, and increased glucose and fatty acid uptake. This resulted in a heightened oxidative status of SF CD4+ T cells. Despite raised ROS levels, expression of NRF2 and its target gene NQO1 were lower in CD4+ T cells from SF than in those from blood. Indeed, NRF2 activation of CD4+ T cells downregulated oxidative stress markers, altered the metabolic phenotype and reduced secretion of IFN-γ. Conclusion: NRF2 could be a potential regulator in CD4+ T cells during chronic inflammation and could instigate a drift toward disease progression or regression, depending on the inflammatory environment
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