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Shi L, Lim JY, Kam LC. Improving regulatory T cell production through mechanosensing. J Biomed Mater Res A 2024; 112:1138-1148. [PMID: 38450935 PMCID: PMC11065567 DOI: 10.1002/jbm.a.37702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Induced Tregs (iTregs) have great promise in adoptive immunotherapy for treatment of autoimmune diseases. This report investigates the impacts of substrate stiffness on human Treg induction, providing a powerful yet simple approach to improving production of these cells. Conventional CD4+ human T cells were activated on materials of different elastic modulus and cultured under suppressive conditions. Enhanced Treg induction was observed on softer materials as early as 3 days following activation and persisted for multiple weeks. Substrate stiffness also affected epigenetic modification of Treg specific genes and Treg suppressive capacity. Tregs induced on substrates of an optimal stiffness balance quantity and suppressive quality.
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Affiliation(s)
- Lingting Shi
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jee Yoon Lim
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Lance C. Kam
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
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2
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Gootjes C, Zwaginga JJ, Roep BO, Nikolic T. Defining Human Regulatory T Cells beyond FOXP3: The Need to Combine Phenotype with Function. Cells 2024; 13:941. [PMID: 38891073 PMCID: PMC11172350 DOI: 10.3390/cells13110941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/18/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Regulatory T cells (Tregs) are essential to maintain immune homeostasis by promoting self-tolerance. Reduced Treg numbers or functionality can lead to a loss of tolerance, increasing the risk of developing autoimmune diseases. An overwhelming variety of human Tregs has been described, based on either specific phenotype, tissue compartment, or pathological condition, yet the bulk of the literature only addresses CD25-positive and CD127-negative cells, coined by naturally occurring Tregs (nTregs), most of which express the transcription factor Forkhead box protein 3 (FOXP3). While the discovery of FOXP3 was seminal to understanding the origin and biology of nTregs, there is evidence in humans that not all T cells expressing FOXP3 are regulatory, and that not all Tregs express FOXP3. Namely, the activation of human T cells induces the transient expression of FOXP3, irrespective of whether they are regulatory or inflammatory effectors, while some induced T cells that may be broadly defined as Tregs (e.g., Tr1 cells) typically lack demethylation and do not express FOXP3. Furthermore, it is unknown whether and how many nTregs exist without FOXP3 expression. Several other candidate regulatory molecules, such as GITR, Lag-3, GARP, GPA33, Helios, and Neuropilin, have been identified but subsequently discarded as Treg-specific markers. Multiparametric analyses have uncovered a plethora of Treg phenotypes, and neither single markers nor combinations thereof can define all and only Tregs. To date, only the functional capacity to inhibit immune responses defines a Treg and distinguishes Tregs from inflammatory T cells (Teffs) in humans. This review revisits current knowledge of the Treg universe with respect to their heterogeneity in phenotype and function. We propose that it is unavoidable to characterize human Tregs by their phenotype in combination with their function, since phenotype alone does not unambiguously define Tregs. There is an unmet need to align the expression of specific markers or combinations thereof with a particular suppressive function to coin functional Treg entities and categorize Treg diversity.
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Affiliation(s)
- Chelsea Gootjes
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (J.J.Z.); (T.N.)
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3
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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4
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Powell J, Talenti A, Fisch A, Hemmink JD, Paxton E, Toye P, Santos I, Ferreira BR, Connelley TK, Morrison LJ, Prendergast JGD. Profiling the immune epigenome across global cattle breeds. Genome Biol 2023; 24:127. [PMID: 37218021 DOI: 10.1186/s13059-023-02964-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences between breeds, variation at the epigenetic and chromatin levels remains poorly characterized. Here, we generate, sequence and analyse over 150 libraries at base-pair resolution to explore the dynamics of DNA methylation and chromatin accessibility of the bovine immune system across three distinct cattle lineages. RESULTS We find extensive epigenetic divergence between the taurine and indicine cattle breeds across immune cell types, which is linked to the levels of local DNA sequence divergence between the two cattle sub-species. The unique cell type profiles enable the deconvolution of complex cellular mixtures using digital cytometry approaches. Finally, we show distinct sub-categories of CpG islands based on their chromatin and methylation profiles that discriminate between classes of distal and gene proximal islands linked to discrete transcriptional states. CONCLUSIONS Our study provides a comprehensive resource of DNA methylation, chromatin accessibility and RNA expression profiles of three diverse cattle populations. The findings have important implications, from understanding how genetic editing across breeds, and consequently regulatory backgrounds, may have distinct impacts to designing effective cattle epigenome-wide association studies in non-European breeds.
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Affiliation(s)
- Jessica Powell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - Andrea Talenti
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Johanneke D Hemmink
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
| | - Edith Paxton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Philip Toye
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
- Centre for Tropical Livestock Genetics and Health, ILRI Kenya, PO Box 30709, Nairobi, 00100, Kenya
| | - Isabel Santos
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Beatriz R Ferreira
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Tim K Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Liam J Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
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5
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Zheng Y, Jun J, Brennan K, Gevaert O. EpiMix: an integrative tool for epigenomic subtyping using DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522660. [PMID: 36711917 PMCID: PMC9881910 DOI: 10.1101/2023.01.03.522660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DNA methylation (DNAme) is a major epigenetic factor influencing gene expression with alterations leading to cancer, immunological, and cardiovascular diseases. Recent technological advances enable genome-wide quantification of DNAme in large human cohorts. So far, existing methods have not been evaluated to identify differential DNAme present in large and heterogeneous patient cohorts. We developed an end-to-end analytical framework named "EpiMix" for population-level analysis of DNAme and gene expression. Compared to existing methods, EpiMix showed higher sensitivity in detecting abnormal DNAme that was present in only small patient subsets. We extended the model-based analyses of EpiMix to cis-regulatory elements within protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs. Using cell-type specific data from two separate studies, we discovered novel epigenetic mechanisms underlying childhood food allergy and survival-associated, methylation-driven non-coding RNAs in non-small cell lung cancer.
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Affiliation(s)
- Yuanning Zheng
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - John Jun
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Kevin Brennan
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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6
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Bock SL, Smaga CR, McCoy JA, Parrott BB. Genome-wide DNA methylation patterns harbour signatures of hatchling sex and past incubation temperature in a species with environmental sex determination. Mol Ecol 2022; 31:5487-5505. [PMID: 35997618 PMCID: PMC9826120 DOI: 10.1111/mec.16670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic data sets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulphite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligators (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and four test samples) and past incubation temperature with a mean absolute error of 1.2°C (in four test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as nonlethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity.
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Affiliation(s)
- Samantha L. Bock
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
| | - Christopher R. Smaga
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
| | - Jessica A. McCoy
- Department of BiologyCollege of CharlestonCharlestonSouth CarolinaUSA
| | - Benjamin B. Parrott
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
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7
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Wang X, Hong Y, Meng S, Gong W, Ren T, Zhang T, Liu X, Li L, Qiu L, Qian Z, Zhou S, Zhao M, Zhai Q, Meng B, Ren X, Zhang H, Wang X. A novel immune-related epigenetic signature based on the transcriptome for predicting the prognosis and therapeutic response of patients with diffuse large B-cell lymphoma. Clin Immunol 2022; 243:109105. [DOI: 10.1016/j.clim.2022.109105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/03/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022]
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8
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Aristin Revilla S, Kranenburg O, Coffer PJ. Colorectal Cancer-Infiltrating Regulatory T Cells: Functional Heterogeneity, Metabolic Adaptation, and Therapeutic Targeting. Front Immunol 2022; 13:903564. [PMID: 35874729 PMCID: PMC9304750 DOI: 10.3389/fimmu.2022.903564] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with one of the highest rates of incidence and mortality among cancers worldwide. Understanding the CRC tumor microenvironment (TME) is essential to improve diagnosis and treatment. Within the CRC TME, tumor-infiltrating lymphocytes (TILs) consist of a heterogeneous mixture of adaptive immune cells composed of mainly anti-tumor effector T cells (CD4+ and CD8+ subpopulations), and suppressive regulatory CD4+ T (Treg) cells. The balance between these two populations is critical in anti-tumor immunity. In general, while tumor antigen-specific T cell responses are observed, tumor clearance frequently does not occur. Treg cells are considered to play an important role in tumor immune escape by hampering effective anti-tumor immune responses. Therefore, CRC-tumors with increased numbers of Treg cells have been associated with promoting tumor development, immunotherapy failure, and a poorer prognosis. Enrichment of Treg cells in CRC can have multiple causes including their differentiation, recruitment, and preferential transcriptional and metabolic adaptation to the TME. Targeting tumor-associated Treg cell may be an effective addition to current immunotherapy approaches. Strategies for depleting Treg cells, such as low-dose cyclophosphamide treatment, or targeting one or more checkpoint receptors such as CTLA-4 with PD-1 with monoclonal antibodies, have been explored. These have resulted in activation of anti-tumor immune responses in CRC-patients. Overall, it seems likely that CRC-associated Treg cells play an important role in determining the success of such therapeutic approaches. Here, we review our understanding of the role of Treg cells in CRC, the possible mechanisms that support their homeostasis in the tumor microenvironment, and current approaches for manipulating Treg cells function in cancer.
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Affiliation(s)
- Sonia Aristin Revilla
- Center Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands
- Laboratory Translational Oncology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Onno Kranenburg
- Laboratory Translational Oncology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Paul J. Coffer
- Center Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands
- *Correspondence: Paul J. Coffer,
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9
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Smiline Girija AS. Protean role of epigenetic mechanisms and their impact in regulating the Tregs in TME. Cancer Gene Ther 2022; 29:661-664. [PMID: 34321625 DOI: 10.1038/s41417-021-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/28/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023]
Abstract
Constitutive expression of Foxp3+ Tregs in the tumor microenvironment (TME) specifically renders immune suppression in the tumor tissues. Being highly stable and self-tolerant, Tregs may be influenced by various epigenetic-associated mechanisms while exhibiting their functions. DNA methylation, histone acetylation, epigenetic silencing, alteration in chromatin networks, etc., are some of the main factors underlying the epigenetic-based Treg cell functional modulations in the TME. The possible reasons on why these epigenetic modulations should be specifically targeted are thus discussed, so that enhanced anti-tumor immunity in TME can be achieved.
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Affiliation(s)
- A S Smiline Girija
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, 600 077, India.
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10
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Pregnolato S, Sabir H, Luyt K, Rienecker KDA, Isles AR, Chakkarapani E. Regulation of glutamate transport and neuroinflammation in a term newborn rat model of hypoxic–ischaemic brain injury. Brain Neurosci Adv 2022; 6:23982128221097568. [PMID: 35615059 PMCID: PMC9125068 DOI: 10.1177/23982128221097568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/12/2022] [Indexed: 11/17/2022] Open
Abstract
In the newborn brain, moderate-severe hypoxia–ischaemia induces glutamate excitotoxicity and inflammation, possibly via dysregulation of candidate astrocytic glutamate transporter ( Glt1) and pro-inflammatory cytokines (e.g. Tnfα, Il1β, Il6). Epigenetic mechanisms may mediate dysregulation. Hypotheses: (1) hypoxia–ischaemia dysregulates mRNA expression of these candidate genes; (2) expression changes in Glt1 are mediated by DNA methylation changes; and (3) methylation values in brain and blood are correlated. Seven-day-old rat pups ( n = 42) were assigned to nine groups based on treatment (for each timepoint: naïve ( n = 3), sham ( n = 3), hypoxia–ischaemia ( n = 8) and timepoint for tissue collection (6, 12 and 24 h post-hypoxia). Moderate hypoxic–ischemic brain injury was induced via ligation of the left common carotid artery followed by 100 min hypoxia (8% O2, 36°C). mRNA was quantified in cortex and hippocampus for the candidate genes, myelin ( Mbp), astrocytic ( Gfap) and neuronal ( Map2) markers (qPCR). DNA methylation was measured for Glt1 in cortex and blood (bisulphite pyrosequencing). Hypoxia–ischaemia induced pro-inflammatory cytokine upregulation in both brain regions at 6 h. This was accompanied by gene expression changes potentially indicating onset of astrogliosis and myelin injury. There were no significant changes in expression or promoter DNA methylation of Glt1. This pilot study supports accumulating evidence that hypoxia–ischaemia causes neuroinflammation in the newborn brain and prioritises further expression and DNA methylation analyses focusing on this pathway. Epigenetic blood biomarkers may facilitate identification of high-risk newborns at birth, maximising chances of neuroprotective interventions.
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Affiliation(s)
- Silvia Pregnolato
- Department of Neonatal Neurology, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hemmen Sabir
- Department of Neonatology and Pediatric Intensive Care, Children’s Hospital, University of Bonn, Bonn, Germany
- Department of Pediatrics I/Neonatology, University Hospital Essen, University Duisburg Essen, Essen, Germany
| | - Karen Luyt
- Department of Neonatal Neurology, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kira DA Rienecker
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, CA, USA
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Anthony R Isles
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
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11
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Silva TC, Young JI, Martin ER, Chen XS, Wang L. MethReg: estimating the regulatory potential of DNA methylation in gene transcription. Nucleic Acids Res 2022; 50:e51. [PMID: 35100398 PMCID: PMC9122535 DOI: 10.1093/nar/gkac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/17/2021] [Accepted: 01/11/2022] [Indexed: 01/02/2023] Open
Abstract
Epigenome-wide association studies often detect many differentially methylated sites, and many are located in distal regulatory regions. To further prioritize these significant sites, there is a critical need to better understand the functional impact of CpG methylation. Recent studies demonstrated that CpG methylation-dependent transcriptional regulation is a widespread phenomenon. Here, we present MethReg, an R/Bioconductor package that analyzes matched DNA methylation and gene expression data, along with external transcription factor (TF) binding information, to evaluate, prioritize and annotate CpG sites with high regulatory potential. At these CpG sites, TF-target gene associations are often only present in a subset of samples with high (or low) methylation levels, so they can be missed by analyses that use all samples. Using colorectal cancer and Alzheimer's disease datasets, we show MethReg significantly enhances our understanding of the regulatory roles of DNA methylation in complex diseases.
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Affiliation(s)
- Tiago C Silva
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I Young
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R Martin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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12
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Dubey R, Prabhakar PK, Gupta J. Epigenetics: key to improve delayed wound healing in type 2 diabetes. Mol Cell Biochem 2022; 477:371-383. [PMID: 34739665 DOI: 10.1007/s11010-021-04285-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/23/2021] [Indexed: 12/13/2022]
Abstract
Diabetes-related delayed wound healing is a multifactorial, nuanced, and intertwined complication that causes substantial clinical morbidity. The etiology of diabetes and its related microvascular complications is affected by genes, diet, and lifestyle factors. Epigenetic modifications such as DNA methylation, histone modifications, and post-transcriptional RNA regulation (microRNAs) are subsequently recognized as key facilitators of the complicated interaction between genes and the environment. Current research suggests that diabetes-persuaded dysfunction of epigenetic pathways, which results in changed expression of genes in target cells and cause diabetes-related complications including cardiomyopathy, nephropathy, retinopathy, delayed wound healing, etc., which are foremost drivers to diabetes-related adverse outcomes. In this paper, we discuss the role of epigenetic mechanisms in controlling tissue repair, angiogenesis, and expression of growth factors, as well as recent findings that show the alteration of epigenetic events during diabetic wound healing.
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Affiliation(s)
- Rupal Dubey
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University (LPU), Jalandhar-Delhi G.T. Road, 144411, Phagwara, Punjab, India
| | - Pranav Kumar Prabhakar
- Department of Medical Laboratory Sciences, School of Physiotherapy and Paramedical Sciences, Lovely Professional University, 144411, Phagwara, Punjab, India
| | - Jeena Gupta
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University (LPU), Jalandhar-Delhi G.T. Road, 144411, Phagwara, Punjab, India.
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13
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Matos C, Renner K, Peuker A, Schoenhammer G, Schreiber L, Bruss C, Eder R, Bruns H, Flamann C, Hoffmann P, Gebhard C, Herr W, Rehli M, Peter K, Kreutz M. Physiological levels of 25-hydroxyvitamin D 3 induce a suppressive CD4 + T cell phenotype not reflected in the epigenetic landscape. Scand J Immunol 2022; 95:e13146. [PMID: 35073416 DOI: 10.1111/sji.13146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
1,25-dihydroxyvitamin D3 (1,25(OH)2 D3 ), the active metabolite of vitamin D3 has a strong impact on the differentiation and function of immune cells. Here we analyzed the influence of its precursor 25-hydroxyvitamin D3 (25(OH)D3 ) on the differentiation of human CD4+ T cells applying physiological concentrations in vitro. Our data show that 25(OH)D3 is converted to its active form 1,25(OH)2 D3 by T cells, which in turn supports FOXP3, CD25 and CTLA-4 expression and inhibits IFN-γ production. These changes were not reflected in the demethylation of the respective promoters. Furthermore, we investigated the impact of vitamin D3 metabolites under induced Treg polarization conditions using TGF-β. Surprisingly, no additive effect but a decreased percentage of FOXP3 expressing cells was observed. However, the combination of 25(OH)D3 or 1,25(OH)2 D3 together with TGF-β further upregulated CD25 and CTLA-4 and significantly increased soluble CTLA-4 and IL-10 secretion whereas IFN-γ expression of iTreg was decreased. Our data suggest that physiological levels of 25(OH)D3 act as potent modulator of human CD4+ T cells and autocrine or paracrine production of 1,25(OH)2 D3 by T cells might be crucial for the local regulation of an adaptive immune response. However, since no epigenetic changes are detected by 25(OH)D3 a rather transient phenotype is induced.
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Affiliation(s)
- Carina Matos
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Kathrin Renner
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Alice Peuker
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Gabriele Schoenhammer
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Laura Schreiber
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Christina Bruss
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Ruediger Eder
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Heiko Bruns
- Department of Internal Medicine 5 - Hematology/Oncology, University Hospital of Erlangen, Germany
| | - Cindy Flamann
- Department of Internal Medicine 5 - Hematology/Oncology, University Hospital of Erlangen, Germany
| | - Petra Hoffmann
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany.,Regensburg Centre for Interventional Immunology, University Hospital Regensburg, 93053, Regensburg, Germany
| | - Claudia Gebhard
- Regensburg Centre for Interventional Immunology, University Hospital Regensburg, 93053, Regensburg, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Michael Rehli
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany.,Regensburg Centre for Interventional Immunology, University Hospital Regensburg, 93053, Regensburg, Germany
| | - Katrin Peter
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany
| | - Marina Kreutz
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center of Regensburg, Germany.,Regensburg Centre for Interventional Immunology, University Hospital Regensburg, 93053, Regensburg, Germany
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14
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Wu ZH, Yang DL, Wang L, Liu J. Epigenetic and Immune-Cell Infiltration Changes in the Tumor Microenvironment in Hepatocellular Carcinoma. Front Immunol 2021; 12:793343. [PMID: 34925377 PMCID: PMC8674919 DOI: 10.3389/fimmu.2021.793343] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/17/2021] [Indexed: 01/02/2023] Open
Abstract
Background Epigenetics regulate gene expression without altering the DNA sequence. Epigenetics targeted chemotherapeutic approach can be used to overcome treatment resistance and low response rate in HCC. However, a comprehensive review of genomic data was carried out to determine the role of epigenesis in the tumor microenvironment (TME), immune cell-infiltration characteristics in HCC is still insufficient. Methods The association between epigenetic-related genes (ERGs), inflammatory response-related genes (IRRGs) and CRISPR genes was determined by merging genomic and CRISPR data. Further, characteristics of immune-cell infiltration in the tumor microenvironment was evaluated. Results Nine differentially expressed genes (ANP32B, ASF1A, BCORL1, BMI1, BUB1, CBX2, CBX3, CDK1, and CDK5) were shown to be independent prognostic factors based on lasso regression in the TCGA-LIHC and ICGC databases. In addition, the results showed significant differences in expression of PDCD-1 (PD-1) and CTLA4 between the high- and low-epigenetic score groups. The CTRP and PRISM-derived drug response data yielded four CTRP-derived compounds (SB-743921, GSK461364, gemcitabine, and paclitaxel) and two PRISM-derived compounds (dolastatin-10 and LY2606368). Patients with high ERGs benefited more from immune checkpoint inhibitor (ICI) therapy than patients with low ERGs. In addition, the high ERGs subgroup had a higher T cell exclusion score, while the low ERGs subgroup had a higher T cell dysfunction. However, there was no difference in microsatellite instability (MSI) score among the two subgroups. Further, genome-wide CRISPR-based loss-of function screening derived from DepMap was conducted to determine key genes leading to HCC development and progression. In total, 640 genes were identified to be essential for survival in HCC cell lines. The protein-protein interaction (PPI) network demonstrated that IRRGs PSEN1 was linked to most ERGs and CRISPR genes such as CDK1, TOP2A, CBX2 and CBX3. Conclusion Epigenetic alterations of cancer-related genes in the tumor microenvironment play a major role in carcinogenesis. This study showed that epigenetic-related novel biomarkers could be useful in predicting prognosis, clinical diagnosis, and management in HCC.
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Affiliation(s)
- Zeng-Hong Wu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dong-Liang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Liu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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15
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Guerin LN, Barnett KR, Hodges E. Dual detection of chromatin accessibility and DNA methylation using ATAC-Me. Nat Protoc 2021; 16:5377-5397. [PMID: 34663963 PMCID: PMC11057009 DOI: 10.1038/s41596-021-00608-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/02/2021] [Indexed: 01/05/2023]
Abstract
The epigenome is multidimensional, with individual molecular components operating on different levels to control transcriptional output. Techniques that combine measurements of these features can reveal their precise correspondence in genomic space, or temporal connectivity, to better understand how they jointly regulate genes. ATAC-Me is an integrated method to probe DNA methylation and chromatin accessibility from a single DNA fragment library. Intact nuclei undergo Tn5 transposition to isolate DNA fragments within nucleosome-free regions. Isolated fragments are exposed to sodium bisulfite before library amplification and sequencing. A typical ATAC-Me experiment detects ~60,000-75,000 peak regions (P < 0.05), covering ~3-4 million CpG sites with at least 5× coverage. These sites display a range of methylation values depending on the cellular and genomic context. The approach is well suited for time course studies that aim to capture chromatin and DNA methylation dynamics in tandem during cellular differentiation. The protocol is completed in 2 d with standard molecular biology equipment and expertise. Analysis of resulting data uses publicly available software requiring basic bioinformatics skills to interpret results.
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Affiliation(s)
- Lindsey N. Guerin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kelly R. Barnett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
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16
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Diedrich JD, Dong Q, Ferguson DC, Bergeron BP, Autry RJ, Qian M, Yang W, Smith C, Papizan JB, Connelly JP, Hagiwara K, Crews KR, Pruett-Miller SM, Pui CH, Yang JJ, Relling MV, Evans WE, Savic D. Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks. Leukemia 2021; 35:3078-3091. [PMID: 33714976 PMCID: PMC8435544 DOI: 10.1038/s41375-021-01209-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/03/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a hematopoietic malignancy comprised of molecular subtypes largely characterized by aneuploidy or recurring chromosomal rearrangements. Despite extensive information on the ALL transcriptome and methylome, there is limited understanding of the ALL chromatin landscape. We therefore mapped accessible chromatin in 24 primary ALL cell biospecimens comprising three common molecular subtypes (DUX4/ERG, ETV6-RUNX1 and hyperdiploid) from patients treated at St. Jude Children's Research Hospital. Our findings highlight extensive chromatin reprogramming in ALL, including the identification ALL subtype-specific chromatin landscapes that are additionally modulated by genetic variation. Chromatin accessibility differences between ALL and normal B-cells implicate the activation of B-cell repressed chromatin domains and detail the disruption of normal B-cell development in ALL. Among ALL subtypes, we uncovered roles for basic helix-loop-helix, homeodomain and activator protein 1 transcription factors in promoting subtype-specific chromatin accessibility and distinct gene regulatory networks. In addition to chromatin subtype-specificity, we further identified over 3500 DNA sequence variants that alter the ALL chromatin landscape and contribute to inter-individual variability in chromatin accessibility. Collectively, our data suggest that subtype-specific chromatin landscapes and gene regulatory networks impact ALL biology and contribute to transcriptomic differences among ALL subtypes.
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Affiliation(s)
- Jonathan D Diedrich
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qian Dong
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brennan P Bergeron
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Maoxiang Qian
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colton Smith
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James B Papizan
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA.
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17
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Lam AJ, Lin DTS, Gillies JK, Uday P, Pesenacker AM, Kobor MS, Levings MK. Optimized CRISPR-mediated gene knockin reveals FOXP3-independent maintenance of human Treg identity. Cell Rep 2021; 36:109494. [PMID: 34348163 DOI: 10.1016/j.celrep.2021.109494] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/28/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022] Open
Abstract
Regulatory T cell (Treg) therapy is a promising curative approach for a variety of immune-mediated conditions. CRISPR-based genome editing allows precise insertion of transgenes through homology-directed repair, but its use in human Tregs has been limited. We report an optimized protocol for CRISPR-mediated gene knockin in human Tregs with high-yield expansion. To establish a benchmark of human Treg dysfunction, we target the master transcription factor FOXP3 in naive and memory Tregs. Although FOXP3-ablated Tregs upregulate cytokine expression, effects on suppressive capacity in vitro manifest slowly and primarily in memory Tregs. Moreover, FOXP3-ablated Tregs retain their characteristic protein, transcriptional, and DNA methylation profile. Instead, FOXP3 maintains DNA methylation at regions enriched for AP-1 binding sites. Thus, although FOXP3 is important for human Treg development, it has a limited role in maintaining mature Treg identity. Optimized gene knockin with human Tregs will enable mechanistic studies and the development of tailored, next-generation Treg cell therapies.
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Affiliation(s)
- Avery J Lam
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - David T S Lin
- BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Jana K Gillies
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Prakruti Uday
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Anne M Pesenacker
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Michael S Kobor
- BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Megan K Levings
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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18
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Piotrowska M, Gliwiński M, Trzonkowski P, Iwaszkiewicz-Grzes D. Regulatory T Cells-Related Genes Are under DNA Methylation Influence. Int J Mol Sci 2021; 22:7144. [PMID: 34281195 PMCID: PMC8267835 DOI: 10.3390/ijms22137144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
Regulatory T cells (Tregs) exert a highly suppressive function in the immune system. Disturbances in their function predispose an individual to autoimmune dysregulation, with a predominance of the pro-inflammatory environment. Besides Foxp3, which is a master regulator of these cells, other genes (e.g., Il2ra, Ctla4, Tnfrsf18, Ikzf2, and Ikzf4) are also involved in Tregs development and function. Multidimensional Tregs suppression is determined by factors that are believed to be crucial in the action of Tregs-related genes. Among them, epigenetic changes, such as DNA methylation, tend to be widely studied over the past few years. DNA methylation acts as a repressive mark, leading to diminished gene expression. Given the role of increased CpG methylation upon Tregs imprinting and functional stability, alterations in the methylation pattern can cause an imbalance in the immune response. Due to the fact that epigenetic changes can be reversible, so-called epigenetic modifiers are broadly used in order to improve Tregs performance. In this review, we place emphasis on the role of DNA methylation of the genes that are key regulators of Tregs function. We also discuss disease settings that have an impact on the methylation status of Tregs and systematize the usefulness of epigenetic drugs as factors able to influence Tregs functions.
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Affiliation(s)
| | | | | | - Dorota Iwaszkiewicz-Grzes
- Department of Medical Immunology, Medical University of Gdansk, 80-210 Gdańsk, Poland; (M.P.); (M.G.); (P.T.)
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19
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Renaude E, Kroemer M, Borg C, Peixoto P, Hervouet E, Loyon R, Adotévi O. Epigenetic Reprogramming of CD4 + Helper T Cells as a Strategy to Improve Anticancer Immunotherapy. Front Immunol 2021; 12:669992. [PMID: 34262562 PMCID: PMC8273698 DOI: 10.3389/fimmu.2021.669992] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/15/2021] [Indexed: 01/22/2023] Open
Abstract
Evidences highlight the role of various CD4+ helper T cells (CD4+ Th) subpopulations in orchestrating the immune responses against cancers. Epigenetics takes an important part in the regulation of CD4+ Th polarization and plasticity. In this review, we described the epigenetic factors that govern CD4+ T cells differentiation and recruitment in the tumor microenvironment and their subsequent involvement in the antitumor immunity. Finally, we discussed how to manipulate tumor reactive CD4+ Th responses by epigenetic drugs to improve anticancer immunotherapy.
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Affiliation(s)
- Elodie Renaude
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Centre Hospitalier Universitaire de Besançon, Centre d'Investigation Clinique, INSERM CIC 1431, Besançon, France
| | - Marie Kroemer
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Department of Pharmacy, University Hospital of Besançon, Besançon, France
| | - Christophe Borg
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Centre Hospitalier Universitaire de Besançon, Centre d'Investigation Clinique, INSERM CIC 1431, Besançon, France.,Department of Medical Oncology, University Hospital of Besançon, Besançon, France
| | - Paul Peixoto
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,EPIGENEXP Platform, University of Bourgogne Franche-Comté, Besançon, France
| | - Eric Hervouet
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,EPIGENEXP Platform, University of Bourgogne Franche-Comté, Besançon, France.,DImaCell Platform, University of Bourgogne Franche-Comté, Besançon, France
| | - Romain Loyon
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Olivier Adotévi
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Centre Hospitalier Universitaire de Besançon, Centre d'Investigation Clinique, INSERM CIC 1431, Besançon, France.,Department of Medical Oncology, University Hospital of Besançon, Besançon, France
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20
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Sinclair AJ. Could Changing the DNA Methylation Landscape Promote the Destruction of Epstein-Barr Virus-Associated Cancers? Front Cell Infect Microbiol 2021; 11:695093. [PMID: 34123880 PMCID: PMC8194487 DOI: 10.3389/fcimb.2021.695093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
DNA methylation at CpG motifs provides an epigenetic route to regulate gene expression. In general, an inverse correlation between DNA hypermethylation at CpG motifs and gene expression is observed. Epstein Barr-virus (EBV) infects people and the EBV genome resides in the nucleus where either its replication cycle initiates or it enters a long-term latency state where the viral genome becomes hypermethylated at CpG motifs. Viral gene expression shows a largely inverse correlation with DNA hypermethylation. DNA methylation occurs through the action of DNA methyl transferase enzymes: writer DNA methyl transferases add methyl groups to specific regions of unmethylated DNA; maintenance DNA methyl transferases reproduce the pattern of DNA methylation during genome replication. The impact of DNA methylation is achieved through the association of various proteins specifically with methylated DNA and their influence on gene regulation. DNA methylation can be changed through altering DNA methyl transferase activity or through the action of enzymes that further modify methylated CpG motifs. Azacytidine prodrugs that are incorporated into CpG motifs during DNA replication are recognized by DNA methyl transferases and block their function resulting in hypomethylation of DNA. EBV-associated cancers have hypermethylated viral genomes and many carcinomas also have highly hypermethylated cellular genomes. Decitabine, a member of the azacytidine prodrug family, reactivates viral gene expression and promotes the recognition of lymphoma cells by virus-specific cytotoxic T-cells. For EBV-associated cancers, the impact of decitabine on the cellular genome and the prospect of combining decitabine with other therapeutic approaches is currently unknown but exciting.
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Affiliation(s)
- Alison J Sinclair
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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21
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A Role for Folate in Microbiome-Linked Control of Autoimmunity. J Immunol Res 2021; 2021:9998200. [PMID: 34104654 PMCID: PMC8159645 DOI: 10.1155/2021/9998200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/04/2021] [Indexed: 02/03/2023] Open
Abstract
The microbiome exerts considerable control over immune homeostasis and influences susceptibility to autoimmune and autoinflammatory disease (AD/AID) such as inflammatory bowel disease (IBD), multiple sclerosis (MS), type 1 diabetes (T1D), psoriasis, and uveitis. In part, this is due to direct effects of the microbiome on gastrointestinal (GI) physiology and nutrient transport, but also to indirect effects on immunoregulatory controls, including induction and stabilization of T regulatory cells (T reg). Secreted bacterial metabolites such as short-chain fatty acids (SCFA) are under intense investigation as mediators of these effects. In contrast, folate (vitamin B9), an essential micronutrient, has attracted less attention, possibly because it exerts global physiological effects which are difficult to differentiate from specific effects on the immune system. Here, we review the role of folate in AD/AID with some emphasis on sight-threatening autoimmune uveitis. Since folate is required for the generation and maintenance of T reg , we propose that one mechanism for microbiome-based control of AD/AID is via folate-dependent induction of GI tract T reg , particularly colonic T reg, via anergic T cells (T an). Hence, folate supplementation has potential prophylactic and/or therapeutic benefit in AID/AD.
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22
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Bam M, Chintala S, Fetcko K, Williamsen BC, Siraj S, Liu S, Wan J, Xuei X, Liu Y, Leibold AT, Dey M. Genome wide DNA methylation landscape reveals glioblastoma's influence on epigenetic changes in tumor infiltrating CD4+ T cells. Oncotarget 2021; 12:967-981. [PMID: 34012510 PMCID: PMC8121608 DOI: 10.18632/oncotarget.27955] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
CD4+ helper T (Th) cells play a critical role in shaping anti-tumor immunity by virtue of their ability to differentiate into multiple lineages in response to environmental cues. Various CD4+ lineages can orchestrate a broad range of effector activities during the initiation, expansion, and memory phase of endogenous anti-tumor immune response. In this clinical corelative study, we found that Glioblastoma (GBM) induces multi- and mixed-lineage immune response in the tumor microenvironment. Whole-genome bisulfite sequencing of tumor infiltrating and blood CD4+ T-cell from GBM patients showed 13571 differentially methylated regions and a distinct methylation pattern of methylation of tumor infiltrating CD4+ T-cells with significant inter-patient variability. The methylation changes also resulted in transcriptomic changes with 341 differentially expressed genes in CD4+ tumor infiltrating T-cells compared to blood. Analysis of specific genes involved in CD4+ differentiation and function revealed differential methylation status of TBX21, GATA3, RORC, FOXP3, IL10 and IFNG in tumor CD4+ T-cells. Analysis of lineage specific genes revealed differential methylation and gene expression in tumor CD4+ T-cells. Interestingly, we observed dysregulation of several ligands of T cell function genes in GBM tissue corresponding to the T-cell receptors that were dysregulated in tumor infiltrating CD4+ T-cells. Our results suggest that GBM might induce epigenetic alterations in tumor infiltrating CD4+ T-cells there by influencing anti-tumor immune response by manipulating differentiation and function of tumor infiltrating CD4+ T-cells. Thus, further research is warranted to understand the role of tumor induced epigenetic modification of tumor infiltrating T-cells to develop effective anti-GBM immunotherapy.
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Affiliation(s)
- Marpe Bam
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- These authors contributed equally to this work
| | - Sreenivasulu Chintala
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN, USA
- These authors contributed equally to this work
| | - Kaleigh Fetcko
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Brooke Carmen Williamsen
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Seema Siraj
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Sheng Liu
- Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jun Wan
- Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiaoling Xuei
- Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Adam T. Leibold
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mahua Dey
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN, USA
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23
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Zhang C, Zhang X, Huang L, Guan Y, Huang X, Tian X, Zhang L, Tao W. ATF3 drives senescence by reconstructing accessible chromatin profiles. Aging Cell 2021; 20:e13315. [PMID: 33539668 PMCID: PMC7963335 DOI: 10.1111/acel.13315] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/11/2022] Open
Abstract
Chromatin organization and transcriptional profiles undergo tremendous reordering during senescence. However, uncovering the regulatory mechanisms between chromatin reconstruction and gene expression in senescence has been elusive. Here, we depicted the landscapes of both chromatin accessibility and gene expression to reveal gene regulatory networks in human umbilical vein endothelial cell (HUVEC) senescence and found that chromatin accessibilities are redistributed during senescence. Particularly, the intergenic chromatin was massively shifted with the increased accessibility regions (IARs) or decreased accessibility regions (DARs), which were mainly enhancer elements. We defined AP‐1 transcription factor family as being responsible for driving chromatin accessibility reconstruction in IARs, where low DNA methylation improved binding affinity of AP‐1 and further increased the chromatin accessibility. Among AP‐1 transcription factors, we confirmed ATF3 was critical to reconstruct chromatin accessibility to promote cellular senescence. Our results described a dynamic landscape of chromatin accessibility whose remodeling contributes to the senescence program, we identified that AP‐1 was capable of reorganizing the chromatin accessibility profile to regulate senescence.
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Affiliation(s)
- Chao Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
- PKU‐Tsinghua‐NIBS Graduate Program School of Life Sciences Peking University Beijing China
| | - Xuebin Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Li Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Yiting Guan
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Xiaoke Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Xiao‐Li Tian
- Department of Human Population Genetics Human Aging Research Institute (HARI) and School of Life Sciences Nanchang University Nanchang China
| | - Lijun Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Wei Tao
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
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24
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Camacho-Ordonez N, Ballestar E, Timmers HTM, Grimbacher B. What can clinical immunology learn from inborn errors of epigenetic regulators? J Allergy Clin Immunol 2021; 147:1602-1618. [PMID: 33609625 DOI: 10.1016/j.jaci.2021.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/20/2022]
Abstract
The epigenome is at the interface between environmental factors and the genome, regulating gene transcription, DNA repair, and replication. Epigenetic modifications play a crucial role in establishing and maintaining cell identity and are especially crucial for neurology, musculoskeletal integrity, and the function of the immune system. Mutations in genes encoding for the components of the epigenetic machinery lead to the development of distinct disorders, especially involving the central nervous system and host defense. In this review, we focus on the role of epigenetic modifications for the function of the immune system. By studying the immune phenotype of patients with monogenic mutations in components of the epigenetic machinery (inborn errors of epigenetic regulators), we demonstrate the importance of DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and mRNA processing for immunity. Moreover, we give a short overview on therapeutic strategies targeting the epigenome.
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Affiliation(s)
- Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - H Th Marc Timmers
- German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Urology, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST- Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany.
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25
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Kressler C, Gasparoni G, Nordström K, Hamo D, Salhab A, Dimitropoulos C, Tierling S, Reinke P, Volk HD, Walter J, Hamann A, Polansky JK. Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype. Front Immunol 2021; 11:609891. [PMID: 33488615 PMCID: PMC7817622 DOI: 10.3389/fimmu.2020.609891] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/20/2020] [Indexed: 12/22/2022] Open
Abstract
CD4+ regulatory T cells (Tregs) are key mediators of immunological tolerance and promising effector cells for immuno-suppressive adoptive cellular therapy to fight autoimmunity and chronic inflammation. Their functional stability is critical for their clinical utility and has been correlated to the demethylated state of the TSDR/CNS2 enhancer element in the Treg lineage transcription factor FOXP3. However, proof for a causal contribution of the TSDR de-methylation to FOXP3 stability and Treg induction is so far lacking. We here established a powerful transient-transfection CRISPR-Cas9-based epigenetic editing method for the selective de-methylation of the TSDR within the endogenous chromatin environment of a living cell. The induced de-methylated state was stable over weeks in clonal T cell proliferation cultures even after expression of the editing complex had ceased. Epigenetic editing of the TSDR resulted in FOXP3 expression, even in its physiological isoform distribution, proving a causal role for the de-methylated TSDR in FOXP3 regulation. However, successful FOXP3 induction was not associated with a switch towards a functional Treg phenotype, in contrast to what has been reported from FOXP3 overexpression approaches. Thus, TSDR de-methylation is required, but not sufficient for a stable Treg phenotype induction. Therefore, targeted demethylation of the TSDR may be a critical addition to published in vitro Treg induction protocols which so far lack FOXP3 stability.
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Affiliation(s)
- Christopher Kressler
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | | | - Karl Nordström
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Dania Hamo
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | | | | | - Sascha Tierling
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Petra Reinke
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hans-Dieter Volk
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jörn Walter
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Alf Hamann
- Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | - Julia K Polansky
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
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26
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Nussbaum L, Chen YL, Ogg GS. Role of regulatory T cells in psoriasis pathogenesis and treatment. Br J Dermatol 2021; 184:14-24. [PMID: 32628773 DOI: 10.1111/bjd.19380] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2020] [Indexed: 12/14/2022]
Abstract
Psoriasis is a chronic inflammatory disease with a strong genetic component that can be triggered by environmental factors. Disease pathogenesis is mainly driven by type 1 and type 17 cytokine-producing cells which, in healthy individuals, are modulated by regulatory T cells (Tregs). Tregs play a fundamental role in immune homeostasis and contribute to the prevention of autoimmune disease by suppressing immune responses. In psoriasis, Tregs are impaired in their suppressive function leading to an altered T-helper 17/Treg balance. Although Treg dysfunction in patients with psoriasis is associated with disease exacerbation, it is unknown how they are functionally regulated. In this review, we discuss recent insights into Tregs in the setting of psoriasis with an emphasis on the effect of current treatments on Tregs and how already available therapeutics that modulate Treg frequency or functionality could be exploited for treatment of psoriasis.
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Affiliation(s)
- L Nussbaum
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Oxford National Institute for Health Research Biomedical Research Centre, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Y L Chen
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Oxford National Institute for Health Research Biomedical Research Centre, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - G S Ogg
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Oxford National Institute for Health Research Biomedical Research Centre, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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27
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Targeting the epigenetic regulation of antitumour immunity. Nat Rev Drug Discov 2020; 19:776-800. [PMID: 32929243 DOI: 10.1038/s41573-020-0077-5] [Citation(s) in RCA: 262] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 01/10/2023]
Abstract
Dysregulation of the epigenome drives aberrant transcriptional programmes that promote cancer onset and progression. Although defective gene regulation often affects oncogenic and tumour-suppressor networks, tumour immunogenicity and immune cells involved in antitumour responses may also be affected by epigenomic alterations. This could have important implications for the development and application of both epigenetic therapies and cancer immunotherapies, and combinations thereof. Here, we review the role of key aberrant epigenetic processes - DNA methylation and post-translational modification of histones - in tumour immunogenicity, as well as the effects of epigenetic modulation on antitumour immune cell function. We emphasize opportunities for small-molecule inhibitors of epigenetic regulators to enhance antitumour immune responses, and discuss the challenges of exploiting the complex interplay between cancer epigenetics and cancer immunology to develop treatment regimens combining epigenetic therapies with immunotherapies.
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28
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Ibragimov AN, Bylino OV, Shidlovskii YV. Molecular Basis of the Function of Transcriptional Enhancers. Cells 2020; 9:E1620. [PMID: 32635644 PMCID: PMC7407508 DOI: 10.3390/cells9071620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
Transcriptional enhancers are major genomic elements that control gene activity in eukaryotes. Recent studies provided deeper insight into the temporal and spatial organization of transcription in the nucleus, the role of non-coding RNAs in the process, and the epigenetic control of gene expression. Thus, multiple molecular details of enhancer functioning were revealed. Here, we describe the recent data and models of molecular organization of enhancer-driven transcription.
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Affiliation(s)
- Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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29
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Ohkura N, Sakaguchi S. Transcriptional and epigenetic basis of Treg cell development and function: its genetic anomalies or variations in autoimmune diseases. Cell Res 2020; 30:465-474. [PMID: 32367041 PMCID: PMC7264322 DOI: 10.1038/s41422-020-0324-7] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/08/2020] [Indexed: 01/01/2023] Open
Abstract
Naturally arising regulatory CD4+ T (Treg) cells, which specifically express the transcription factor FoxP3 in the nucleus and CD25 and CTLA-4 on the cell surface, are a T-cell subpopulation specialized for immune suppression, playing a key role in maintaining immunological self-tolerance and homeostasis. FoxP3 is required for Treg function, especially for its suppressive activity. However, FoxP3 expression per se is not necessary for Treg cell lineage commitment in the thymus and insufficient for full Treg-type gene expression in mature Treg cells. It is Treg-specific epigenetic changes such as CpG demethylation and histone modification that can confer a stable and heritable pattern of Treg type gene expression on developing Treg cells in a FoxP3-independent manner. Anomalies in the formation of Treg-specific epigenome, in particular, Treg-specific super-enhancers, which largely include Treg-specific DNA demethylated regions, are indeed able to cause autoimmune diseases in rodents. Furthermore, in humans, single nucleotide polymorphisms in Treg-specific DNA demethylated regions associated with Treg signature genes, such as IL2RA (CD25) and CTLA4, can affect the development and function of naïve Treg cells rather than effector T cells. Such genetic variations are therefore causative of polygenic common autoimmune diseases including type 1 diabetes and rheumatoid arthritis via affecting endogenous natural Treg cells. These findings on the transcription factor network with FoxP3 at a key position as well as Treg-specific epigenetic landscape facilitate our understanding of Treg cell development and function, and can be exploited to prepare functionally stable FoxP3-expressing Treg cells from antigen-specific conventional T cells to treat autoimmune diseases.
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Affiliation(s)
- Naganari Ohkura
- Experimental immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shimon Sakaguchi
- Experimental immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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30
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Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs. Mamm Genome 2020; 31:157-169. [PMID: 32285146 PMCID: PMC7369130 DOI: 10.1007/s00335-020-09832-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/19/2020] [Indexed: 12/28/2022]
Abstract
External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 °C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.
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31
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Colamatteo A, Carbone F, Bruzzaniti S, Galgani M, Fusco C, Maniscalco GT, Di Rella F, de Candia P, De Rosa V. Molecular Mechanisms Controlling Foxp3 Expression in Health and Autoimmunity: From Epigenetic to Post-translational Regulation. Front Immunol 2020; 10:3136. [PMID: 32117202 PMCID: PMC7008726 DOI: 10.3389/fimmu.2019.03136] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
The discovery of the transcription factor Forkhead box-p3 (Foxp3) has shed fundamental insights into the understanding of the molecular determinants leading to generation and maintenance of T regulatory (Treg) cells, a cell population with a key immunoregulatory role. Work over the past few years has shown that fine-tuned transcriptional and epigenetic events are required to ensure stable expression of Foxp3 in Treg cells. The equilibrium between phenotypic plasticity and stability of Treg cells is controlled at the molecular level by networks of transcription factors that bind regulatory sequences, such as enhancers and promoters, to regulate Foxp3 expression. Recent reports have suggested that specific modifications of DNA and histones are required for the establishment of the chromatin structure in conventional CD4+ T (Tconv) cells for their future differentiation into the Treg cell lineage. In this review, we discuss the molecular events that control Foxp3 gene expression and address the associated alterations observed in human diseases. Also, we explore how Foxp3 influences the gene expression programs in Treg cells and how unique properties of Treg cell subsets are defined by other transcription factors.
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Affiliation(s)
- Alessandra Colamatteo
- Treg Cell Laboratory, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Fortunata Carbone
- Laboratorio di Immunologia, Istituto per L'Endocrinologia e L'Oncologia Sperimentale, Consiglio Nazionale Delle Ricerche (IEOS-CNR), Naples, Italy.,Unità di NeuroImmunologia, Fondazione Santa Lucia, Rome, Italy
| | - Sara Bruzzaniti
- Laboratorio di Immunologia, Istituto per L'Endocrinologia e L'Oncologia Sperimentale, Consiglio Nazionale Delle Ricerche (IEOS-CNR), Naples, Italy.,Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Mario Galgani
- Treg Cell Laboratory, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy.,Laboratorio di Immunologia, Istituto per L'Endocrinologia e L'Oncologia Sperimentale, Consiglio Nazionale Delle Ricerche (IEOS-CNR), Naples, Italy
| | - Clorinda Fusco
- Treg Cell Laboratory, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Giorgia Teresa Maniscalco
- Dipartimento di Neurologia, Centro Regionale Sclerosi Multipla, Azienda Ospedaliera "A. Cardarelli", Naples, Italy
| | - Francesca Di Rella
- Clinical and Experimental Senology, Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Naples, Italy
| | | | - Veronica De Rosa
- Laboratorio di Immunologia, Istituto per L'Endocrinologia e L'Oncologia Sperimentale, Consiglio Nazionale Delle Ricerche (IEOS-CNR), Naples, Italy.,Unità di NeuroImmunologia, Fondazione Santa Lucia, Rome, Italy
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32
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Sambucci M, Gargano F, Guerrera G, Battistini L, Borsellino G. One, No One, and One Hundred Thousand: T Regulatory Cells' Multiple Identities in Neuroimmunity. Front Immunol 2019; 10:2947. [PMID: 31956323 PMCID: PMC6955595 DOI: 10.3389/fimmu.2019.02947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022] Open
Abstract
As the Nobel laureate Luigi Pirandello wrote in his novels, identities can be evanescent. Although a quarter of a century has passed since regulatory T cells (Treg) were first described, new studies continue to reveal surprising and contradictory features of this lymphocyte subset. Treg cells are the core of the immunological workforce engaged in the restraint of autoimmune or inflammatory reactions, and their characterization has revealed substantial heterogeneity and complexity in the phenotype and gene expression profiles, proving them to be a most versatile and adaptive cell type, as exemplified by their plasticity in fine-tuning immune responses. Defects in Treg function are associated with several autoimmune diseases, including multiple sclerosis, which is caused by an inappropriate immune reaction toward brain components; conversely, the beneficial effects of immunomodulating therapies on disease progression have been shown to partly act upon the biology of these cells. Both in animals and in humans the pool of circulating Treg cells is a mixture of natural (nTregs) and peripherally-induced Treg (pTregs). Particularly in humans, circulating Treg cells can be phenotypically subdivided into different subpopulations, which so far are not well-characterized, particularly in the context of autoimmunity. Recently, Treg cells have been rediscovered as mediators of tissue healing, and have also shown to be involved in organ homeostasis. Moreover, stability of the Treg lineage has recently been addressed by several conflicting reports, and immune-suppressive abilities of these cells have been shown to be dynamically regulated, particularly in inflammatory conditions, adding further levels of complexity to the study of this cell subset. Finally, Treg cells exert their suppressive function through different mechanisms, some of which—such as their ectoenzymatic activity—are particularly relevant in CNS autoimmunity. Here, we will review the phenotypically and functionally discernible Treg cell subpopulations in health and in multiple sclerosis, touching also upon the effects on this cell type of immunomodulatory drugs used for the treatment of this disease.
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Affiliation(s)
- Manolo Sambucci
- Neuroimmunology Unit, Santa Lucia Foundation IRCCS, Rome, Italy
| | | | | | - Luca Battistini
- Neuroimmunology Unit, Santa Lucia Foundation IRCCS, Rome, Italy
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33
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Epigenetic mechanisms regulating T-cell responses. J Allergy Clin Immunol 2019; 142:728-743. [PMID: 30195378 DOI: 10.1016/j.jaci.2018.07.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022]
Abstract
During the last decade, advances in sequencing technologies allowed production of a wealth of information on epigenetic modifications in T cells. Epigenome maps, in combination with mechanistic studies, have demonstrated that T cells undergo extensive epigenome remodeling in response to signals, which has a strong effect on phenotypic stability and function of lymphocytes. In this review we focus on DNA methylation, histone modifications, and chromatin structure as important epigenetic mechanisms involved in controlling T-cell responses. In particular, we discuss epigenetic processes in light of the development, activation, and differentiation of CD4+ T helper (TH), regulatory T, and CD8+ T cells. As central aspects of the adaptive immune system, we review mechanisms that ensure molecular memory, stability, plasticity, and exhaustion of T cells. We further discuss the effect of the tissue environment on imprinting T-cell epigenomes with potential implications for immunotherapy.
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34
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Ordoñez R, Martínez-Calle N, Agirre X, Prosper F. DNA Methylation of Enhancer Elements in Myeloid Neoplasms: Think Outside the Promoters? Cancers (Basel) 2019; 11:cancers11101424. [PMID: 31554341 PMCID: PMC6827153 DOI: 10.3390/cancers11101424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/15/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022] Open
Abstract
Gene regulation through DNA methylation is a well described phenomenon that has a prominent role in physiological and pathological cell-states. This epigenetic modification is usually grouped in regions denominated CpG islands, which frequently co-localize with gene promoters, silencing the transcription of those genes. Recent genome-wide DNA methylation studies have challenged this paradigm, demonstrating that DNA methylation of regulatory regions outside promoters is able to influence cell-type specific gene expression programs under physiologic or pathologic conditions. Coupling genome-wide DNA methylation assays with histone mark annotation has allowed for the identification of specific epigenomic changes that affect enhancer regulatory regions, revealing an additional layer of complexity to the epigenetic regulation of gene expression. In this review, we summarize the novel evidence for the molecular and biological regulation of DNA methylation in enhancer regions and the dynamism of these changes contributing to the fine-tuning of gene expression. We also analyze the contribution of enhancer DNA methylation on the expression of relevant genes in acute myeloid leukemia and chronic myeloproliferative neoplasms. The characterization of the aberrant enhancer DNA methylation provides not only a novel pathogenic mechanism for different tumors but also highlights novel potential therapeutic targets for myeloid derived neoplasms.
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Affiliation(s)
- Raquel Ordoñez
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Nicolás Martínez-Calle
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Xabier Agirre
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain.
| | - Felipe Prosper
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain.
- Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Avenida Pío XII-36, 31008 Pamplona, Spain.
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35
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Loi E, Moi L, Fadda A, Satta G, Zucca M, Sanna S, Amini Nia S, Cabras G, Padoan M, Magnani C, Miligi L, Piro S, Gentilini D, Ennas MG, Southey MC, Giles GG, Wong Doo N, Cocco P, Zavattari P. Methylation alteration of SHANK1 as a predictive, diagnostic and prognostic biomarker for chronic lymphocytic leukemia. Oncotarget 2019; 10:4987-5002. [PMID: 31452839 PMCID: PMC6697638 DOI: 10.18632/oncotarget.27080] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/21/2019] [Indexed: 12/22/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease characterized by the clonal expansion of malignant B cells. To predict the clinical course of the disease, the identification of diagnostic biomarkers is urgently needed. Aberrant methylation patterns may predict CLL development and its course, being very early changes during carcinogenesis. Our aim was to identify CLL specific methylation patterns and to evaluate whether methylation aberrations in selected genes are associated with changes in gene expression. Here, by performing a genome-wide methylation analysis, we identified several CLL-specific methylation alterations. We focused on the most altered one, at a CpG island located in the body of SHANK1 gene, in our CLL cases compared to healthy controls. This methylation alteration was successfully validated in a larger cohort including 139 CLL and 20 control in silico samples. We also found a positive correlation between SHANK1 methylation level and absolute lymphocyte count, in particular CD19+ B cells, in CLL patients. Moreover, we were able to detect gains of methylation at SHANK1 in blood samples collected years prior to diagnosis. Overall, our results suggest methylation alteration at this SHANK1 CpG island as a biomarker for risk and diagnosis of CLL, and also in the personalized quantification of tumor aggressiveness.
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Affiliation(s)
- Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Antonio Fadda
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Giannina Satta
- Department of Medical Sciences and Public Health, Occupational Health Unit, University of Cagliari, Cagliari, Italy
| | - Mariagrazia Zucca
- Department of Biomedical Sciences, Cytomorphology Unit, University of Cagliari, Cagliari, Italy
| | - Sonia Sanna
- Department of Biomedical Sciences, Cytomorphology Unit, University of Cagliari, Cagliari, Italy
| | - Shadi Amini Nia
- Department of Medical Sciences and Public Health, Occupational Health Unit, University of Cagliari, Cagliari, Italy
| | | | - Marina Padoan
- Department of Medical Sciences, Unit of Medical Statistics and Cancer Epidemiology, University of Eastern Piedmont, Novara, Italy
| | - Corrado Magnani
- Department of Medical Sciences, Unit of Medical Statistics and Cancer Epidemiology, University of Eastern Piedmont, Novara, Italy
| | - Lucia Miligi
- Institute of Oncology Studies and Prevention, Florence, Italy
| | - Sara Piro
- Institute of Oncology Studies and Prevention, Florence, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Maria Grazia Ennas
- Department of Biomedical Sciences, Cytomorphology Unit, University of Cagliari, Cagliari, Italy
| | - Melissa C Southey
- Precision Medicine, Monash University, Melbourne, Melbourne, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Melbourne, Australia
| | - Nicole Wong Doo
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia.,Concord Hospital Clinical School, The University of Sydney, Sydney, Australia
| | - Pierluigi Cocco
- Department of Medical Sciences and Public Health, Occupational Health Unit, University of Cagliari, Cagliari, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
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36
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Delacher M, Schmidl C, Herzig Y, Breloer M, Hartmann W, Brunk F, Kägebein D, Träger U, Hofer AC, Bittner S, Weichenhan D, Imbusch CD, Hotz-Wagenblatt A, Hielscher T, Breiling A, Federico G, Gröne HJ, Schmid RM, Rehli M, Abramson J, Feuerer M. Rbpj expression in regulatory T cells is critical for restraining T H2 responses. Nat Commun 2019; 10:1621. [PMID: 30962454 PMCID: PMC6453958 DOI: 10.1038/s41467-019-09276-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
The transcriptional regulator Rbpj is involved in T-helper (TH) subset polarization, but its function in Treg cells remains unclear. Here we show that Treg-specific Rbpj deletion leads to splenomegaly and lymphadenopathy despite increased numbers of Treg cells with a polyclonal TCR repertoire. A specific defect of Rbpj-deficient Treg cells in controlling TH2 polarization and B cell responses is observed, leading to the spontaneous formation of germinal centers and a TH2-associated immunoglobulin class switch. The observed phenotype is environment-dependent and can be induced by infection with parasitic nematodes. Rbpj-deficient Treg cells adopt open chromatin landscapes and gene expression profiles reminiscent of tissue-derived TH2-polarized Treg cells, with a prevailing signature of the transcription factor Gata-3. Taken together, our study suggests that Treg cells require Rbpj to specifically restrain TH2 responses, including their own excessive TH2-like differentiation potential.
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Affiliation(s)
- Michael Delacher
- Chair for Immunology, University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Christian Schmidl
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
| | - Yonatan Herzig
- Department of Immunology, Weizmann Institute of Science, 234 Herzl Street, 76100, Rehovot, Israel
| | - Minka Breloer
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359, Hamburg, Germany
| | - Wiebke Hartmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359, Hamburg, Germany
| | - Fabian Brunk
- Division of Developmental Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Danny Kägebein
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ulrike Träger
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ann-Cathrin Hofer
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Sebastian Bittner
- Chair for Immunology, University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Achim Breiling
- Division of Epigenetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Giuseppina Federico
- Division of Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Hermann-Josef Gröne
- Division of Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Roland M Schmid
- Department of Internal Medicine, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - Michael Rehli
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
| | - Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, 234 Herzl Street, 76100, Rehovot, Israel
| | - Markus Feuerer
- Chair for Immunology, University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany.
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany.
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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Ntranos A, Ntranos V, Bonnefil V, Liu J, Kim-Schulze S, He Y, Zhu Y, Brandstadter R, Watson CT, Sharp AJ, Katz Sand I, Casaccia P. Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis. Brain 2019; 142:647-661. [PMID: 30698680 PMCID: PMC6821213 DOI: 10.1093/brain/awy344] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023] Open
Abstract
Cell-permeable formulations of metabolites, such as fumaric acid esters, have been used as highly effective immunomodulators in patients with multiple sclerosis and yet their mechanism of action remains elusive. Since fumaric acid esters are metabolites, and cell metabolism is highly intertwined with the epigenetic regulation of gene expression, we investigated whether this metabolic-epigenetic interplay could be leveraged for therapeutic purposes. To this end we recruited 47 treatment-naïve and 35 fumaric acid ester-treated patients with multiple sclerosis, as well as 16 glatiramer acetate-treated patients as a non-metabolite treatment control. Here we identify a significant immunomodulatory effect of fumaric acid esters on the expression of the brain-homing chemokine receptor CCR6 in CD4 and CD8 T cells of patients with multiple sclerosis, which include T helper-17 and T cytotoxic-17 cells. We report differences in DNA methylation of CD4 T cells isolated from untreated and treated patients with multiple sclerosis, using the Illumina EPIC 850K BeadChip. We first demonstrate that Krebs cycle intermediates, such as fumaric acid esters, have a significantly higher impact on epigenome-wide DNA methylation changes in CD4 T cells compared to amino-acid polymers such as glatiramer acetate. We then define a fumaric acid ester treatment-specific hypermethylation effect on microRNA MIR-21, which is critical for the differentiation of T helper-17 cells. This hypermethylation effect was attributed to the subpopulation of T helper-17 cells using a decomposition analysis and was further validated in an independent prospective cohort of seven patients before and after treatment with fumaric acid esters. In vitro treatment of CD4 and CD8 T cells with fumaric acid esters supported a direct and dose-dependent effect on DNA methylation at the MIR-21 promoter. Finally, the upregulation of miR-21 transcripts and CCR6 expression was inhibited if CD4 or CD8 T cells stimulated under T helper-17 or T cytotoxic-17 polarizing conditions were treated with fumaric acid esters in vitro. These data collectively define a direct link between fumaric acid ester treatment and hypermethylation of the MIR-21 locus in both CD4 and CD8 T cells and suggest that the immunomodulatory effect of fumaric acid esters in multiple sclerosis is at least in part due to the epigenetic regulation of the brain-homing CCR6+ CD4 and CD8 T cells.
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Affiliation(s)
- Achilles Ntranos
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Valentina Bonnefil
- Neuroscience, Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA
| | - Jia Liu
- Neuroscience, Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ye He
- Neuroscience, Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA
| | - Yunjiao Zhu
- Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Brandstadter
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Corey T Watson
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Andrew J Sharp
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilana Katz Sand
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrizia Casaccia
- Neuroscience, Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA
- Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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38
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Jiang H, Sun L, Hu C, Wang Y. Hypermethylated WNT10A and its clinical significance in colorectal cancer. Am J Transl Res 2018; 10:4290-4301. [PMID: 30662671 PMCID: PMC6325495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/02/2018] [Indexed: 06/09/2023]
Abstract
Colorectal cancer (CRC) is a heterogeneous disease in which unique subtypes are characterized by distinct genetic and epigenetic alterations. DNA methylation, a well-documented epigenetic modification, is a promising biomarker for the diagnosis and prognosis of cancers, including CRC. WNT10A is a member of the Wnt family. It belongs to the Wnt signaling pathway and is involved in CRC. However, studies regarding the methylation and expression of WNT10A in CRC are limited. In the current study, we analyzed the methylation status of WNT10A in 146 patients with CRC and normal controls. These samples were classified into two groups. The first group was an initial discovery set (i.e., fresh tissue samples from 40 patients with CRC and adjacent normal control samples). The second group was an independent validation set (i.e., formalin-fixed and paraffin-embeded [FFPE] samples from 106 patients with CRC and cutting edge tissues). The results showed a higher level of WNT10A hypermethylation of in CRC samples than in controls (Fresh tissue cohort: P = 2.8E-5; FFPE cohort: P = 3.6E-4).This finding was verified by WNT10A methylation data from The Cancer Genome Atlas portal (TCGA) (P = 1.9E-83). Subgroup analysis of clinical characteristics showed a higher WNT10A methylation level in elder patients (aged > 60 y) (P = 0.037) and, patients with distant metastasis (P = 0.033), rectal cancer (P = 0.03), and mucinous adenocarcinoma (P = 0.02). Furthermore, TCGA RNAseq data demonstrated lower WNT10A expression in patients with CRC than in controls (P = 4.0E-3) and showed a negative correlation between expression and methylation (r = -0.37, P = 5.7E-13). Moreover, the efficiency of WNT10A methylation for CRC diagnosis was analyzed in both cohorts of the present study and the TCGA cohorts, which indicated the potential use of WNT10A methylation as a tool for diagnosis of CRC.
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Affiliation(s)
- Haizhong Jiang
- Department of Gastroenterology, Ningbo First Hospital59 Liuting Street, Ningbo 315010, People’s Republic of China
| | - Linyin Sun
- Department of Gastroenterology, Ningbo First Hospital59 Liuting Street, Ningbo 315010, People’s Republic of China
| | - Chunyan Hu
- Department of Gastroenterology, Ningbo First Hospital59 Liuting Street, Ningbo 315010, People’s Republic of China
| | - Yaqing Wang
- Laboratory of Molecular Medicine, Ningbo First Hospital59 Liuting Street, Ningbo 315010, People’s Republic of China
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39
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Barros-Silva D, Marques CJ, Henrique R, Jerónimo C. Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications. Genes (Basel) 2018; 9:genes9090429. [PMID: 30142958 PMCID: PMC6162482 DOI: 10.3390/genes9090429] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/28/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022] Open
Abstract
DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.
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Affiliation(s)
- Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua António Bernardino Almeida, 4200-072 Porto, Portugal.
| | - C Joana Marques
- Genetics, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal.
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua António Bernardino Almeida, 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, 4050-313 Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua António Bernardino Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, 4050-313 Porto, Portugal.
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40
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Belot MP, Castell AL, Le Fur S, Bougnères P. Dynamic demethylation of the IL2RA promoter during in vitro CD4+ T cell activation in association with IL2RA expression. Epigenetics 2018; 13:459-472. [PMID: 30096258 DOI: 10.1080/15592294.2018.1469893] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
IL2RA, a subunit of the high affinity receptor for interleukin-2 (IL2), plays a crucial role in immune homeostasis. Notably, IL2RA expression is induced in CD4+ T cells in response to various stimuli and is constitutive in regulatory T cells (Tregs). We selected for our study 18 CpGs located within cognate regulatory regions of the IL2RA locus and characterized their methylation in naive, regulatory, and memory CD4+ T cells. We found that 5/18 CpGs (notably CpG + 3502) show dynamic, active demethylation during the in vitro activation of naive CD4+ T cells. Demethylation of these CpGs correlates with appearance of IL2RA protein at the cell surface. We found no influence of cis located SNP alleles upon CpG methylation. Treg cells show constitutive demethylation at all studied CpGs. Methylation of 9/18 CpGs, including CpG +3502, decreases with age. Our data thus identify CpG +3502 and a few other CpGs at the IL2RA locus as coordinated epigenetic regulators of IL2RA expression in CD4+ T cells. This may contribute to unravel how the IL2RA locus can be involved in immune physiology and pathology.
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Affiliation(s)
- Marie-Pierre Belot
- a Institut National de la Santé et de la Recherche Médicale UMR1169 , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France.,b Fondation de l'AP-HP pour la Recherche , Paris , France
| | - Anne-Laure Castell
- c Service de Médecine des Adolescents , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France
| | - Sophie Le Fur
- a Institut National de la Santé et de la Recherche Médicale UMR1169 , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France
| | - Pierre Bougnères
- a Institut National de la Santé et de la Recherche Médicale UMR1169 , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France.,c Service de Médecine des Adolescents , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France
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41
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Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM. Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Res 2018; 28:1364-1371. [PMID: 30093547 PMCID: PMC6120621 DOI: 10.1101/gr.232587.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 07/14/2018] [Indexed: 12/17/2022]
Abstract
DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopulations of cells, whereas genome-wide chromatin studies lack the same quantitative capacity. Testing DNA methylation throughout the genome is possible using whole-genome bisulfite sequencing (WGBS), but the high costs associated with the assay have made it impractical for studies involving more than limited numbers of samples. We have optimized a new transposase-based library preparation assay for the Illumina HiSeq X platform suitable for limited amounts of DNA and providing a major cost reduction for WGBS. By incorporating methylated cytosines during fragment end repair, we reveal an end-repair artifact affecting 1%-2% of reads that we can remove analytically. We show that the use of a high (G + C) content spike-in performs better than PhiX in terms of bisulfite sequencing quality. As expected, the loci with transposase-accessible chromatin are DNA hypomethylated and enriched in flanking regions by post-translational modifications of histones usually associated with positive effects on gene expression. Using these transposase-accessible loci to represent the cis-regulatory loci in the genome, we compared the representation of these loci between WGBS and other genome-wide DNA methylation assays, showing WGBS to outperform substantially all of the alternatives. We conclude that it is now technologically and financially feasible to perform WGBS in larger numbers of samples with greater accuracy than previously possible.
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Affiliation(s)
- Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Will Liao
- New York Genome Center, New York, New York 10013, USA
| | - Frank Wos
- New York Genome Center, New York, New York 10013, USA
| | - Andrew D Johnston
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | - Toby Bloom
- New York Genome Center, New York, New York 10013, USA
| | | | - Soren Germer
- New York Genome Center, New York, New York 10013, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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42
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Russell‐Hallinan A, Watson CJ, Baugh JA. Epigenetics of Aberrant Cardiac Wound Healing. Compr Physiol 2018; 8:451-491. [DOI: 10.1002/cphy.c170029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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43
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Nowak A, Lock D, Bacher P, Hohnstein T, Vogt K, Gottfreund J, Giehr P, Polansky JK, Sawitzki B, Kaiser A, Walter J, Scheffold A. CD137+CD154- Expression As a Regulatory T Cell (Treg)-Specific Activation Signature for Identification and Sorting of Stable Human Tregs from In Vitro Expansion Cultures. Front Immunol 2018; 9:199. [PMID: 29467769 PMCID: PMC5808295 DOI: 10.3389/fimmu.2018.00199] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/23/2018] [Indexed: 01/30/2023] Open
Abstract
Regulatory T cells (Tregs) are an attractive therapeutic tool for several different immune pathologies. Therapeutic Treg application often requires prolonged in vitro culture to generate sufficient Treg numbers or to optimize their functionality, e.g., via genetic engineering of their antigen receptors. However, purity of clinical Treg expansion cultures is highly variable, and currently, it is impossible to identify and separate stable Tregs from contaminating effector T cells, either ex vivo or after prior expansion. This represents a major obstacle for quality assurance of expanded Tregs and raises significant safety concerns. Here, we describe a Treg activation signature that allows identification and sorting of epigenetically imprinted Tregs even after prolonged in vitro culture. We show that short-term reactivation resulted in expression of CD137 but not CD154 on stable FoxP3+ Tregs that displayed a demethylated Treg-specific demethylated region, high suppressive potential, and lack of inflammatory cytokine expression. We also applied this Treg activation signature for rapid testing of chimeric antigen receptor functionality in human Tregs and identified major differences in the signaling requirements regarding CD137 versus CD28 costimulation. Taken together, CD137+CD154- expression emerges as a universal Treg activation signature ex vivo and upon in vitro expansion allowing the identification and isolation of epigenetically stable antigen-activated Tregs and providing a means for their rapid functional testing in vitro.
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Affiliation(s)
- Anna Nowak
- German Rheumatism Research Centre (DRFZ) Berlin, Leibniz Association, Berlin, Germany
| | - Dominik Lock
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Petra Bacher
- Department of Cellular Immunology, Clinic for Rheumatology and Clinical Immunology, Charité - University Medicine, Berlin, Germany
| | - Thordis Hohnstein
- Department of Cellular Immunology, Clinic for Rheumatology and Clinical Immunology, Charité - University Medicine, Berlin, Germany
| | - Katrin Vogt
- Institute for Medical Immunology, Charité - University Medicine, Berlin, Germany
| | - Judith Gottfreund
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Pascal Giehr
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Julia K Polansky
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - University Medicine, Berlin, Germany
| | - Birgit Sawitzki
- Institute for Medical Immunology, Charité - University Medicine, Berlin, Germany
| | | | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Alexander Scheffold
- German Rheumatism Research Centre (DRFZ) Berlin, Leibniz Association, Berlin, Germany.,Department of Cellular Immunology, Clinic for Rheumatology and Clinical Immunology, Charité - University Medicine, Berlin, Germany
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44
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Abstract
Zinc-finger and homeodomain transcription factors have been shown in vitro to bind to recognition motifs containing a methylated CpG. However, accessing these motifs in vivo might be seriously impeded by the inclusion of DNA in nucleosomes and by the condensed structure adopted by chromatin formed on methylated DNA. Here, we discuss how oxidation of 5-methylcytosine into 5-hydroxymethylcytosine could provide the initial destabilizing clue for such transcription factors to get access to nucleosomal DNA and read epigenetic information.
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Affiliation(s)
- Elise A Mahé
- a University of Rennes 1, UMR6290 CNRS , Institute of Genetics and Development of Rennes , Campus de Beaulieu, Rennes Cedex , France
| | - Thierry Madigou
- a University of Rennes 1, UMR6290 CNRS , Institute of Genetics and Development of Rennes , Campus de Beaulieu, Rennes Cedex , France
| | - Gilles Salbert
- a University of Rennes 1, UMR6290 CNRS , Institute of Genetics and Development of Rennes , Campus de Beaulieu, Rennes Cedex , France
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45
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Bocian K, Kiernozek E, Domagała-Kulawik J, Korczak-Kowalska G, Stelmaszczyk-Emmel A, Drela N. Expanding Diversity and Common Goal of Regulatory T and B Cells. I: Origin, Phenotype, Mechanisms. Arch Immunol Ther Exp (Warsz) 2017; 65:501-520. [PMID: 28477096 PMCID: PMC5688216 DOI: 10.1007/s00005-017-0469-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 03/14/2017] [Indexed: 12/21/2022]
Abstract
Immunosuppressive activity of regulatory T and B cells is critical to limit autoimmunity, excessive inflammation, and pathological immune response to conventional antigens or allergens. Both types of regulatory cells are intensively investigated, however, their development and mechanisms of action are still not completely understood. Both T and B regulatory cells represent highly differentiated populations in terms of phenotypes and origin, however, they use similar mechanisms of action. The most investigated CD4+CD25+ regulatory T cells are characterized by the expression of Foxp3+ transcription factor, which is not sufficient to maintain their lineage stability and suppressive function. Currently, it is considered that specific epigenetic changes are critical for defining regulatory T cell stability in the context of their suppressive function. It is not yet known if similar epigenetic regulation determines development, lineage stability, and function of regulatory B cells. Phenotype diversity, confirmed or hypothetical developmental pathways, multiple mechanisms of action, and role of epigenetic changes in these processes are the subject of this review.
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Affiliation(s)
- Katarzyna Bocian
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Ewelina Kiernozek
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | | | - Grażyna Korczak-Kowalska
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - Anna Stelmaszczyk-Emmel
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland
| | - Nadzieja Drela
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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46
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White N, Benton M, Kennedy D, Fox A, Griffiths L, Lea R, Mengersen K. Accounting for cell lineage and sex effects in the identification of cell-specific DNA methylation using a Bayesian model selection algorithm. PLoS One 2017; 12:e0182455. [PMID: 28957352 PMCID: PMC5619727 DOI: 10.1371/journal.pone.0182455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/18/2017] [Indexed: 01/22/2023] Open
Abstract
Cell- and sex-specific differences in DNA methylation are major sources of epigenetic variation in whole blood. Heterogeneity attributable to cell type has motivated the identification of cell-specific methylation at the CpG level, however statistical methods for this purpose have been limited to pairwise comparisons between cell types or between the cell type of interest and whole blood. We developed a Bayesian model selection algorithm for the identification of cell-specific methylation profiles that incorporates knowledge of shared cell lineage and allows for the identification of differential methylation profiles in one or more cell types simultaneously. Under the proposed methodology, sex-specific differences in methylation by cell type are also assessed. Using publicly available, cell-sorted methylation data, we show that 51.3% of female CpG markers and 61.4% of male CpG markers identified were associated with differential methylation in more than one cell type. The impact of cell lineage on differential methylation was also highlighted. An evaluation of sex-specific differences revealed differences in CD56+NK methylation, within both single and multi- cell dependent methylation patterns. Our findings demonstrate the need to account for cell lineage in studies of differential methylation and associated sex effects.
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Affiliation(s)
- Nicole White
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Miles Benton
- Genomics Research Center, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Daniel Kennedy
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Andrew Fox
- Florey Department of Neuroscience and Mental Health, Melbourne, Victoria, Australia
| | - Lyn Griffiths
- Genomics Research Center, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Rodney Lea
- Genomics Research Center, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kerrie Mengersen
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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47
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Arthur-Farraj PJ, Morgan CC, Adamowicz M, Gomez-Sanchez JA, Fazal SV, Beucher A, Razzaghi B, Mirsky R, Jessen KR, Aitman TJ. Changes in the Coding and Non-coding Transcriptome and DNA Methylome that Define the Schwann Cell Repair Phenotype after Nerve Injury. Cell Rep 2017; 20:2719-2734. [PMID: 28903050 PMCID: PMC5608958 DOI: 10.1016/j.celrep.2017.08.064] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/17/2017] [Accepted: 08/18/2017] [Indexed: 12/12/2022] Open
Abstract
Repair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34. Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair.
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Affiliation(s)
- Peter J Arthur-Farraj
- Department of Clinical Neurosciences, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Medicine, Imperial College, London W12 0NN, UK; Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK.
| | - Claire C Morgan
- Department of Medicine, Imperial College, London W12 0NN, UK
| | - Martyna Adamowicz
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH16 2XU, UK
| | - Jose A Gomez-Sanchez
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Shaline V Fazal
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Anthony Beucher
- Department of Medicine, Imperial College, London W12 0NN, UK
| | - Bonnie Razzaghi
- Department of Medicine, Imperial College, London W12 0NN, UK
| | - Rhona Mirsky
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Kristjan R Jessen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Timothy J Aitman
- Department of Medicine, Imperial College, London W12 0NN, UK; Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH16 2XU, UK.
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48
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He X, Koenen HJ, Slaats JH, Joosten I. Stabilizing human regulatory T cells for tolerance inducing immunotherapy. Immunotherapy 2017; 9:735-751. [PMID: 28771099 DOI: 10.2217/imt-2017-0017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Many autoimmune diseases develop as a consequence of an altered balance between autoreactive immune cells and suppressive FOXP3+ Treg. Restoring this balance through amplification of Treg represents a promising strategy to treat disease. However, FOXP3+ Treg might become unstable especially under certain inflammatory conditions, and might transform into proinflammatory cytokine-producing cells. The issue of heterogeneity and instability of Treg has caused considerable debate in the field and has important implications for Treg-based immunotherapy. In this review, we discuss how Treg stability is defined and what the molecular mechanisms underlying the maintenance of FOXP3 expression and the regulation of Treg stability are. Also, we elaborate on current strategies used to stabilize human Treg for clinical purposes. This review focuses on human Treg, but considering that cell-intrinsic mechanisms to regulate Treg stability in mice and in humans might be similar, data derived from mice studies are also discussed in this paper.
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Affiliation(s)
- Xuehui He
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,College of Computer Science, Qinghai Normal University, Xining, Qinghai, China
| | - Hans Jpm Koenen
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen Hr Slaats
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Irma Joosten
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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49
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Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol 2017; 18:137. [PMID: 28732548 PMCID: PMC5522596 DOI: 10.1186/s13059-017-1273-4] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling. Here we show that integration of chromatin characteristics can be applied to predict distal enhancer candidates in Zea mays, thereby providing a basis for a better understanding of gene regulation in this important crop plant. Result To predict transcriptional enhancers in the crop plant maize (Zea mays L. ssp. mays), we integrated available genome-wide DNA methylation data with newly generated maps for chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac) enrichment in young seedling and husk tissue. Approximately 1500 intergenic regions, displaying low DNA methylation, high chromatin accessibility and H3K9ac enrichment, were classified as enhancer candidates. Based on their chromatin profiles, candidate sequences can be classified into four subcategories. Tissue-specificity of enhancer candidates is defined based on the tissues in which they are identified and putative target genes are assigned based on tissue-specific expression patterns of flanking genes. Conclusions Our method identifies three previously identified distal enhancers in maize, validating the new set of enhancer candidates and enlarging the toolbox for the functional characterization of gene regulation in the highly repetitive maize genome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1273-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rurika Oka
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Johan Zicola
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Blaise Weber
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Sarah N Anderson
- Department of Plant Biology, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Charlie Hodgman
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Huub C J Hoefsloot
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Franziska Turck
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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50
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Yasuhiko Y, Hirabayashi Y, Ono R. LTRs of Endogenous Retroviruses as a Source of Tbx6 Binding Sites. Front Chem 2017; 5:34. [PMID: 28664156 PMCID: PMC5471307 DOI: 10.3389/fchem.2017.00034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/23/2017] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are abundant in mammalian genomes and can modulate the gene expression of surrounding genes by disrupting endogenous binding sites for transcription factors (TFs) or providing novel TFs binding sites within retrotransposon sequences. Here, we show that a (C/T)CACACCT sequence motif in ORR1A, ORR1B, ORR1C, and ORR1D, Long Terminal Repeats (LTRs) of MaLR endogenous retrovirus (ERV), is the direct target of Tbx6, an evolutionary conserved family of T-box TFs. Moreover, by comparing gene expression between control mice (Tbx6 +/−) and Tbx6-deficient mice (Tbx6 −/−), we demonstrate that at least four genes, Twist2, Pitx2, Oscp1, and Nfxl1, are down-regulated with Tbx6 deficiency. These results suggest that ORR1A, ORR1B, ORR1C and ORR1D may contribute to the evolution of mammalian embryogenesis.
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Affiliation(s)
- Yukuto Yasuhiko
- Division of Cellular and Molecular Toxicology, Biological Safety Research Centre, National Institute of Health SciencesTokyo, Japan
| | - Yoko Hirabayashi
- Division of Cellular and Molecular Toxicology, Biological Safety Research Centre, National Institute of Health SciencesTokyo, Japan
| | - Ryuichi Ono
- Division of Cellular and Molecular Toxicology, Biological Safety Research Centre, National Institute of Health SciencesTokyo, Japan
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