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Medina TS, Murison A, Smith M, Kinker GS, Chakravarthy A, Vitiello GAF, Turpin W, Shen SY, Yau HL, Sarmento OF, Faubion W, Lupien M, Silverberg MS, Arrowsmith CH, De Carvalho DD. The chromatin and single-cell transcriptional landscapes of CD4 T cells in inflammatory bowel disease link risk loci with a proinflammatory Th17 cell population. Front Immunol 2023; 14:1161901. [PMID: 37600767 PMCID: PMC10436103 DOI: 10.3389/fimmu.2023.1161901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The imbalance between Th17 and regulatory T cells in inflammatory bowel diseases (IBD) promotes intestinal epithelial cell damage. In this scenario, T helper cell lineage commitment is accompanied by dynamic changes to the chromatin that facilitate or repress gene expression. Methods Here, we characterized the chromatin landscape and heterogeneity of intestinal and peripheral CD4 T cellsfrom IBD patients using in house ATAC-Seq and single cell RNA-Seq libraries. Results We show that chromatin accessibility profiles of CD4 T cells from inflamed intestinal biopsies relate to genes associated with a network of inflammatory processes. After integrating the chromatin profiles of tissue-derived CD4 T cells and in-vitro polarized CD4 T cell subpopulations, we found that the chromatin accessibility changes of CD4 T cells were associated with a higher predominance of pathogenic Th17 cells (pTh17 cells) in inflamed biopsies. In addition, IBD risk loci in CD4 T cells were colocalized with accessible chromatin changes near pTh17-related genes, as shown in intronic STAT3 and IL23R regions enriched in areas of active intestinal inflammation. Moreover, single cell RNA-Seq analysis revealed a population of pTh17 cells that co-expresses Th1 and cytotoxic transcriptional programs associated with IBD severity. Discussion Altogether, we show that cytotoxic pTh17 cells were specifically associated with IBD genetic variants and linked to intestinal inflammation of IBD patients.
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Affiliation(s)
- Tiago S. Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michelle Smith
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Gabriela S. Kinker
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Williams Turpin
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Helen L. Yau
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Olga F. Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - William Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mark S. Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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Braga-Neto MB, Gaballa JM, Bamidele AO, Sarmento OF, Svingen P, Gonzalez M, Ramos GP, Sagstetter MR, Aseem SO, Sun Z, Faubion WA. Deregulation of Long Intergenic Non-coding RNAs in CD4+ T Cells of Lamina Propria in Crohn's Disease Through Transcriptome Profiling. J Crohns Colitis 2020; 14:96-109. [PMID: 31158273 PMCID: PMC6930003 DOI: 10.1093/ecco-jcc/jjz109] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The aetiology of Crohn's disease [CD] involves immune dysregulation in a genetically susceptible individual. Genome-wide association studies [GWAS] have identified 200 loci associated with CD, ulcerative colitis, or both, most of which fall within non-coding DNA regions. Long non-coding RNAs [lncRNAs] regulate gene expression by diverse mechanisms and have been associated with disease activity in inflammatory bowel disease. However, disease-associated lncRNAs have not been characterised in pathogenic immune cell populations. METHODS Terminal ileal samples were obtained from 22 CD patients and 13 controls. RNA from lamina propria CD4+ T cells was sequenced and long intergenic non-coding RNAs [lincRNAs] were detected. Overall expression patterns, differential expression [DE], and pathway and gene enrichment analyses were performed. Knockdown of novel lincRNAs XLOC_000261 and XLOC_000014 was performed. Expression of Th1 or Th17-associated transcription factors, T-bet and RORγt, respectively, was assessed by flow cytometry. RESULTS A total of 6402 lincRNAs were expressed, 960 of which were novel. Unsupervised clustering and principal component analysis showed that the lincRNA expression discriminated patients from controls. A total of 1792 lincRNAs were DE, and 295 [79 novel; 216 known] mapped to 267 of 5727 DE protein-coding genes. The novel lincRNAs were enriched in inflammatory and Notch signalling pathways [p <0.05]. Furthermore, DE lincRNAs in CD patients were more frequently found in DNA regions with known inflammatory bowel disease [IBD]-associated loci. The novel lincRNA XLOC_000261 negatively regulated RORγt expression in Th17 cells. CONCLUSIONS We describe a novel set of DE lincRNAs in CD-associated CD4+ cells and demonstrate that novel lincRNA XLOC_000261 appears to negatively regulate RORγt protein expression in Th17 cells.
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Affiliation(s)
- Manuel B Braga-Neto
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Joseph M Gaballa
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Adebowale O Bamidele
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Olga F Sarmento
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Phyllis Svingen
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michelle Gonzalez
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Guilherme Piovezani Ramos
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mary R Sagstetter
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
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Gaballa JM, Braga Neto MB, Ramos GP, Bamidele AO, Gonzalez MM, Sagstetter MR, Sarmento OF, Faubion WA. The Role of Histone Methyltransferases and Long Non-coding RNAs in the Regulation of T Cell Fate Decisions. Front Immunol 2018; 9:2955. [PMID: 30619315 PMCID: PMC6300512 DOI: 10.3389/fimmu.2018.02955] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/30/2018] [Indexed: 12/13/2022] Open
Abstract
T cell lineage decisions are critical for the development of proper immune responses to pathogens as well as important for the resolution of inflammatory responses. This differentiation process relies on a combination of intrinsic and extrinsic factors converging upon epigenetic regulation of transcriptional networks relevant to specific T cell lineages. As these biochemical modifications represent therapeutic opportunities in cancer biology and autoimmunity, implications of writers and readers of epigenetic marks to immune cell differentiation and function are highly relevant. Given the ready adoption of histone methyltransferase inhibitors in the clinic, we focus this review on the role of three histone modifying complexes: PRC-1, PRC-2, and G9A in modulating T cell fate decisions. Furthermore, we explore the role of long non-coding RNAs in regulating these processes, and discuss recent advances and challenges of implementing epigenetic therapies into clinical practice.
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Affiliation(s)
- Joseph M Gaballa
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | | | | | - Adebowale O Bamidele
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Michelle M Gonzalez
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Olga F Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
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Bamidele AO, Svingen PA, Sagstetter MR, Sarmento OF, Gonzalez M, Braga Neto MB, Kugathasan S, Lomberk G, Urrutia RA, Faubion WA. Disruption of FOXP3-EZH2 Interaction Represents a Pathobiological Mechanism in Intestinal Inflammation. Cell Mol Gastroenterol Hepatol 2018; 7:55-71. [PMID: 30510991 PMCID: PMC6260395 DOI: 10.1016/j.jcmgh.2018.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023]
Abstract
Background & Aims Forkhead box protein 3 (FOXP3)+ regulatory T cell (Treg) dysfunction is associated with autoimmune diseases; however, the mechanisms responsible for inflammatory bowel disease pathophysiology are poorly understood. Here, we tested the hypothesis that a physical interaction between transcription factor FOXP3 and the epigenetic enzyme enhancer of zeste homolog 2 (EZH2) is essential for gene co-repressive function. Methods Human FOXP3 mutations clinically relevant to intestinal inflammation were generated by site-directed mutagenesis. T lymphocytes were isolated from mice, human blood, and lamina propria of Crohn's disease (CD) patients and non-CD controls. We performed proximity ligation or a co-immunoprecipitation assay in FOXP3-mutant+, interleukin 6 (IL6)-treated or CD-CD4+ T cells to assess FOXP3-EZH2 protein interaction. We studied IL2 promoter activity and chromatin state of the interferon γ locus via luciferase reporter and chromatin-immunoprecipitation assays, respectively, in cells expressing FOXP3 mutants. Results EZH2 binding was abrogated by inflammatory bowel disease-associated FOXP3 cysteine 232 (C232) mutation. The C232 mutant showed impaired repression of IL2 and diminished EZH2-mediated trimethylation of histone 3 at lysine 27 on interferon γ, indicative of compromised Treg physiologic function. Generalizing this mechanism, IL6 impaired FOXP3-EZH2 interaction. IL6-induced effects were reversed by Janus kinase 1/2 inhibition. In lamina propria-derived CD4+T cells from CD patients, we observed decreased FOXP3-EZH2 interaction. Conclusions FOXP3-C232 mutation disrupts EZH2 recruitment and gene co-repressive function. The proinflammatory cytokine IL6 abrogates FOXP3-EZH2 interaction. Studies in lesion-derived CD4+ T cells have shown that reduced FOXP3-EZH2 interaction is a molecular feature of CD patients. Destabilized FOXP3-EZH2 protein interaction via diverse mechanisms and consequent Treg abnormality may drive gastrointestinal inflammation.
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Key Words
- C232, cysteine 232
- CD, Crohn’s disease
- ChIP, chromatin-immunoprecipitation
- Crohn’s Disease
- EED, embryonic ectoderm development
- EZH2, enhancer of zeste homolog 2
- Epigenetics
- FCS, fetal calf serum
- FOXP3, forkhead domain-containing X-chromosome–encoded protein
- H3K27me3, trimethylated histone H3 at lysine 27
- IBD, inflammatory bowel disease
- IL, interleukin
- IPEX, immune dysregulation, polyendocrinopathy, enteropathy, X-linked
- JAK, Janus kinase
- LZ, leucine zipper
- PBMC, peripheral blood mononuclear cell
- PBS, phosphate-buffered saline
- PLA, proximity ligation assay
- PMA, phorbol 12-myristate 13-acetate
- PRC2, polycomb repressive complex 2
- Proinflammatory Cytokine
- Regulatory T Cells
- STAT, signal transducer and activator of transcription
- SUZ12, suppressor of zeste
- Th, T helper
- Treg, regulatory T cell
- WT, wild-type
- co-IP, co-immunoprecipitation
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Affiliation(s)
- Adebowale O Bamidele
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Phyllis A Svingen
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mary R Sagstetter
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Olga F Sarmento
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Michelle Gonzalez
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Manuel B Braga Neto
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, School of Medicine, Atlanta, Georgia
| | - Gwen Lomberk
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Raul A Urrutia
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - William A Faubion
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.
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Sarmento OF, Svingen PA, Xiong Y, Sun Z, Bamidele AO, Mathison AJ, Smyrk TC, Nair AA, Gonzalez MM, Sagstetter MR, Baheti S, McGovern DPB, Friton JJ, Papadakis KA, Gautam G, Xavier RJ, Urrutia RA, Faubion WA. The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD). J Biol Chem 2016; 292:706-722. [PMID: 27909059 DOI: 10.1074/jbc.m116.749663] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/21/2016] [Indexed: 12/14/2022] Open
Abstract
Regulatory T (Treg) cells expressing the transcription factor FOXP3 play a pivotal role in maintaining immunologic self-tolerance. We and others have shown previously that EZH2 is recruited to the FOXP3 promoter and its targets in Treg cells. To further address the role for EZH2 in Treg cellular function, we have now generated mice that lack EZH2 specifically in Treg cells (EZH2Δ/ΔFOXP3+). We find that EZH2 deficiency in FOXP3+ T cells results in lethal multiorgan autoimmunity. We further demonstrate that EZH2Δ/ΔFOXP3+ T cells lack a regulatory phenotype in vitro and secrete proinflammatory cytokines. Of special interest, EZH2Δ/ΔFOXP3+ mice develop spontaneous inflammatory bowel disease. Guided by these results, we assessed the FOXP3 and EZH2 gene networks by RNA sequencing in isolated intestinal CD4+ T cells from patients with Crohn's disease. Gene network analysis demonstrates that these CD4+ T cells display a Th1/Th17-like phenotype with an enrichment of gene targets shared by FOXP3 and EZH2. Combined, these results suggest that the inflammatory milieu found in Crohn's disease could lead to or result from deregulation of FOXP3/EZH2-enforced T cell gene networks contributing to the underlying intestinal inflammation.
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Affiliation(s)
- Olga F Sarmento
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Phyllis A Svingen
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Yuning Xiong
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, and
| | - Adebowale O Bamidele
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Angela J Mathison
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Thomas C Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905
| | - Asha A Nair
- Division of Biomedical Statistics and Informatics, and
| | - Michelle M Gonzalez
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Mary R Sagstetter
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | | | - Dermot P B McGovern
- the F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Hospital, Los Angeles, California 90048
| | - Jessica J Friton
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Konstantinos A Papadakis
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Goel Gautam
- the Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, and.,the Center for Computational and Integrative Biology, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Ramnik J Xavier
- the Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, and.,the Center for Computational and Integrative Biology, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Raul A Urrutia
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - William A Faubion
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine,
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Papadakis KA, Krempski J, Svingen P, Xiong Y, Sarmento OF, Lomberk GA, Urrutia RA, Faubion WA. Krüppel-like factor KLF10 deficiency predisposes to colitis through colonic macrophage dysregulation. Am J Physiol Gastrointest Liver Physiol 2015; 309:G900-9. [PMID: 26472224 PMCID: PMC4669350 DOI: 10.1152/ajpgi.00309.2015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/13/2015] [Indexed: 01/31/2023]
Abstract
Krüppel-like factor (KLF)-10 is an important transcriptional regulator of TGF-β1 signaling in both CD8(+) and CD4(+) T lymphocytes. In the present study, we demonstrate a novel role for KLF10 in the regulation of TGFβRII expression with functional relevance in macrophage differentiation and activation. We first show that transfer of KLF10(-/-) bone marrow-derived macrophages into wild-type (WT) mice leads to exacerbation of experimental colitis. At the cell biological level, using two phenotypic strategies, we show that KLF10-deficient mice have an altered colonic macrophage phenotype with higher frequency of proinflammatory LyC6(+)MHCII(+) cells and a reciprocal decrease of the anti-inflammatory LyC6(-)MHCII(+) subset. Additionally, the anti-inflammatory CD11b(+)CX3CR1(hi) subset of colonic macrophages is significantly decreased in KLF10(-/-) compared with WT mice under inflammatory conditions. Molecularly, CD11b(+) colonic macrophages from KLF10(-/-) mice exhibit a proinflammatory cytokine profile with increased production of TNF-α and lower production of IL-10 in response to LPS stimulation. Because KLF10 is a transcription factor, we explored how this protein may regulate macrophage function. Consequently, we analyzed the expression of TGFβRII expression in colonic macrophages and found that, in the absence of KLF10, macrophages express lower levels of TGFβRII and display an attenuated Smad-2 phosphorylation following TGF-β1 stimulation. We further show that KLF10 directly binds to the TGFβRII promoter in macrophages, leading to enhanced gene expression through histone H3 acetylation. Collectively, our data reveal a critical role for KLF10 in the epigenetic regulation of TGFβRII expression in macrophages and the acquisition of a "regulatory" phenotype that contributes to intestinal mucosal homeostasis.
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Affiliation(s)
| | - James Krempski
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
| | - Phyllis Svingen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
| | - Olga F Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
| | - Gwen A Lomberk
- Epigenetics and Chromatin Dynamics Laboratory, Departments of Medicine and Biochemistry and Molecular Biology, Epigenetic Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Raul A Urrutia
- Epigenetics and Chromatin Dynamics Laboratory, Departments of Medicine and Biochemistry and Molecular Biology, Epigenetic Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
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Papadakis KA, Krempski J, Reiter J, Svingen P, Xiong Y, Sarmento OF, Huseby A, Johnson AJ, Lomberk GA, Urrutia RA, Faubion WA. Krüppel-like factor KLF10 regulates transforming growth factor receptor II expression and TGF-β signaling in CD8+ T lymphocytes. Am J Physiol Cell Physiol 2014; 308:C362-71. [PMID: 25472963 DOI: 10.1152/ajpcell.00262.2014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
KLF10 has recently elicited significant attention as a transcriptional regulator of transforming growth factor-β1 (TGF-β1) signaling in CD4(+) T cells. In the current study, we demonstrate a novel role for KLF10 in the regulation of TGF-β receptor II (TGF-βRII) expression with functional relevance in antiviral immune response. Specifically, we show that KLF10-deficient mice have an increased number of effector/memory CD8(+) T cells, display higher levels of the T helper type 1 cell-associated transcription factor T-bet, and produce more IFN-γ following in vitro stimulation. In addition, KLF10(-/-) CD8(+) T cells show enhanced proliferation in vitro and homeostatic proliferation in vivo. Freshly isolated CD8(+) T cells from the spleen of adult mice express lower levels of surface TGF-βRII (TβRII). Congruently, in vitro activation of KLF10-deficient CD8(+) T cells upregulate TGF-βRII to a lesser extent compared with wild-type (WT) CD8(+) T cells, which results in attenuated Smad2 phosphorylation following TGF-β1 stimulation compared with WT CD8(+) T cells. Moreover, we demonstrate that KLF10 directly binds to the TGF-βRII promoter in T cells, leading to enhanced gene expression. In vivo viral infection with Daniel's strain Theiler's murine encephalomyelitis virus (TMEV) also led to lower expression of TGF-βRII among viral-specific KLF10(-/-) CD8(+) T cells and a higher percentage of IFN-γ-producing CD8(+) T cells in the spleen. Collectively, our data reveal a critical role for KLF10 in the transcriptional activation of TGF-βRII in CD8(+) T cells. Thus, KLF10 regulation of TGF-βRII in this cell subset may likely play a critical role in viral and tumor immune responses for which the integrity of the TGF-β1/TGF-βRII signaling pathway is crucial.
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Affiliation(s)
| | - James Krempski
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Jesse Reiter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Phyllis Svingen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Olga F Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - April Huseby
- Division of Immunology and Neurology, Mayo Clinic, Rochester, Minnesota; and
| | - Aaron J Johnson
- Division of Immunology and Neurology, Mayo Clinic, Rochester, Minnesota; and
| | - Gwen A Lomberk
- Epigenetics and Chromatin Dynamics Laboratory, Departments of Medicine and Biochemistry and Molecular Biology, Epigenetic Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Raul A Urrutia
- Epigenetics and Chromatin Dynamics Laboratory, Departments of Medicine and Biochemistry and Molecular Biology, Epigenetic Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota;
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8
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Xiong Y, Khanna S, Grzenda AL, Sarmento OF, Svingen PA, Lomberk GA, Urrutia RA, Faubion WA. Polycomb antagonizes p300/CREB-binding protein-associated factor to silence FOXP3 in a Kruppel-like factor-dependent manner. J Biol Chem 2012; 287:34372-85. [PMID: 22896699 PMCID: PMC3464543 DOI: 10.1074/jbc.m111.325332] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 08/14/2012] [Indexed: 01/10/2023] Open
Abstract
Inducible gene expression underlies the epigenetically inherited differentiation program of most immune cells. We report that the promoter of the FOXP3 gene possesses two distinct functional states: an "off state" mediated by the polycomb histone methyltransferase complex and a histone acetyltransferase-dependent "on state." Regulating these states is the presence of a Kruppel-like factor (KLF)-containing Polycomb response element. In the KLF10(-/-) mouse, the FOXP3 promoter is epigenetically silenced by EZH2 (Enhancer of Zeste 2)-mediated trimethylation of Histone 3 K27; thus, impaired FOXP3 induction and inappropriate adaptive T regulatory cell differentiation results in vitro and in vivo. The epigenetic transmittance of adaptive T regulatory cell deficiency is demonstrated throughout more than 40 generations of mice. These results provide insight into chromatin remodeling events key to phenotypic features of distinct T cell populations.
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Affiliation(s)
- Yuning Xiong
- From the Chromatin Dynamics and Epigenetics Laboratory
- the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905
| | - Sahil Khanna
- From the Chromatin Dynamics and Epigenetics Laboratory
- the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905
| | - Adrienne L. Grzenda
- From the Chromatin Dynamics and Epigenetics Laboratory
- the Departments of Molecular Biology and
- the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905
| | - Olga F. Sarmento
- From the Chromatin Dynamics and Epigenetics Laboratory
- the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905
| | - Phyllis A. Svingen
- From the Chromatin Dynamics and Epigenetics Laboratory
- the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905
| | - Gwen A. Lomberk
- From the Chromatin Dynamics and Epigenetics Laboratory
- the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905
| | - Raul A. Urrutia
- From the Chromatin Dynamics and Epigenetics Laboratory
- the Departments of Molecular Biology and
- the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905
| | - William A. Faubion
- From the Chromatin Dynamics and Epigenetics Laboratory
- Immunology, and
- the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905
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Cherepanova OA, Pidkovka NA, Sarmento OF, Yoshida T, Gan Q, Adiguzel E, Bendeck MP, Berliner J, Leitinger N, Owens GK. Oxidized phospholipids induce type VIII collagen expression and vascular smooth muscle cell migration. Circ Res 2009; 104:609-18. [PMID: 19168440 DOI: 10.1161/circresaha.108.186064] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Phenotypic switching of vascular smooth muscle cells (VSMCs) is known to play a critical role in the development of atherosclerosis. However, the factors present within lesions that mediate VSMC phenotypic switching are unclear. Oxidized phospholipids (OxPLs), including 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphorylcholine (POVPC), are active components of minimally modified low density lipoprotein and have been previously shown to induce multiple proatherogenic events in endothelial cells and macrophages, but their effects on VSMCs have been largely unexplored until recently. We previously showed that OxPLs induced phenotypic switching of VSMCs, including suppression of SMC differentiation marker genes. The goal of the present studies was to test the hypothesis that OxPLs alter extracellular matrix production and VSMC migration. Results showed that POVPC activated expression of several extracellular matrix proteins in VSMC. POVPC increased expression of type VIII collagen alpha1 chain (Col8a1) mRNA in cultured VSMCs and in vivo in rat carotid arteries by 9-fold and 4-fold, respectively. POVPC-induced activation of Col8a1 gene expression was reduced by small interfering RNA-mediated suppression of Krüppel-like factor 4 (Klf4) and Sp1, and was abolished in Klf4-knockout VSMCs. POVPC increased Klf4 binding to the Col8a1 gene promoter both in vivo in rat carotid arteries and in cultured VSMCs based on chromatin immunoprecipitation assays. Moreover, POVPC-induced VSMC migration was markedly reduced in Klf4- or type VIII collagen-knockout VSMCs. Given evidence that OxPLs are present within atherosclerotic lesions, it is interesting to suggest that OxPL-induced changes in VSMC phenotype may contribute to the pathogenesis of atherosclerosis at least in part through changes in extracellular matrix composition.
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Affiliation(s)
- Olga A Cherepanova
- Department of Molecular Physiology and Biological Physics, University of Virginia, Robert M Berne Cardiovascular Research Center, Charlottesville, VA 22908, USA
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10
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Sarmento OF, Digilio LC, Wang Y, Perlin J, Herr JC, Allis CD, Coonrod SA. Dynamic alterations of specific histone modifications during early murine development. J Cell Sci 2004; 117:4449-59. [PMID: 15316069 DOI: 10.1242/jcs.01328] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In order to investigate whether covalent histone modifications may be involved in early embryonic reprogramming events, changes in global levels of a series of histone tail modifications were studied during oocyte maturation and pre-implantation mouse development using indirect immunofluorescence and scanning confocal microscopy. Results showed that histone modifications could be classified into two strikingly distinct categories. The first contains stable `epigenetic' marks such as histone H3 lysine 9 methylation [Me(Lys9)H3], histone H3 lysine 4 methylation [Me(Lys4)H3] and histone H4/H2A serine 1 phosphorylation [Ph(Ser1)H4/H2A]. The second group contains dynamic and reversible marks and includes hyperacetylated histone H4, histone H3 arginine 17 methylation [Me(Arg17)H3] and histone H4 arginine 3 methylation [Me(Arg3)H4]). Our results also showed that removal of these marks in eggs and early embryos occurs during metaphase suggesting that the enzymes responsible for the loss of these modifications are probably cytoplasmic in nature. Finally, we provide data demonstrating that treatment of cellular histones with peptidylarginine deiminase (PAD) results in loss of staining for the histone H4 arginine 3 methyl mark, suggesting that PADs can reverse histone arginine methyl modifications.
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Affiliation(s)
- Olga F Sarmento
- Department of Cell Biology, University of Virginia Health Science Center, PO Box 800732, Charlottesville, VA 22908, USA
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Wright PW, Bolling LC, Calvert ME, Sarmento OF, Berkeley EV, Shea MC, Hao Z, Jayes FC, Bush LA, Shetty J, Shore AN, Reddi PP, Tung KS, Samy E, Allietta MM, Sherman NE, Herr JC, Coonrod SA. ePAD, an oocyte and early embryo-abundant peptidylarginine deiminase-like protein that localizes to egg cytoplasmic sheets. Dev Biol 2003; 256:73-88. [PMID: 12654293 DOI: 10.1016/s0012-1606(02)00126-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Selected for its high relative abundance, a protein spot of MW approximately 75 kDa, pI 5.5 was cored from a Coomassie-stained two-dimensional gel of proteins from 2850 zona-free metaphase II mouse eggs and analyzed by tandem mass spectrometry (TMS), and novel microsequences were identified that indicated a previously uncharacterized egg protein. A 2.4-kb cDNA was then amplified from a mouse ovarian adapter-ligated cDNA library by RACE-PCR, and a unique 2043-bp open reading frame was defined encoding a 681-amino-acid protein. Comparison of the deduced amino acid sequence with the nonredundant database demonstrated that the protein was approximately 40% identical to the calcium-dependent peptidylarginine deiminase (PAD) enzyme family. Northern blotting, RT-PCR, and in situ hybridization analyses indicated that the protein was abundantly expressed in the ovary, weakly expressed in the testis, and absent from other tissues. Based on the homology with PADs and its oocyte-abundant expression pattern, the protein was designated ePAD, for egg and embryo-abundant peptidylarginine deiminase-like protein. Anti-recombinant ePAD monospecific antibodies localized the molecule to the cytoplasm of oocytes in primordial, primary, secondary, and Graafian follicles in ovarian sections, while no other ovarian cell type was stained. ePAD was also expressed in the immature oocyte, mature egg, and through the blastocyst stage of embryonic development, where expression levels began to decrease. Immunoelectron microscopy localized ePAD to egg cytoplasmic sheets, a unique keratin-containing intermediate filament structure found only in mammalian eggs and in early embryos, and known to undergo reorganization at critical stages of development. Previous reports that PAD-mediated deimination of epithelial cell keratin results in cytoskeletal remodeling suggest a possible role for ePAD in cytoskeletal reorganization in the egg and early embryo.
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Affiliation(s)
- Paul W Wright
- Department of Cell Biology and Center for Research in Contraceptive and Reproductive Health, University of Virginia, Charlottesville, VA 22908, USA
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