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Bamidele AO, Mishra SK, Piovezani Ramos G, Hirsova P, Klatt EE, Abdelrahman LM, Sagstetter MR, Davidson HM, Fehrenbach PJ, Valenzuela-Pérez L, Kim Lee HS, Zhang S, Aguirre Lopez A, Kurdi AT, Westphal MS, Gonzalez MM, Gaballa JM, Kosinsky RL, Lee HE, Smyrk TC, Bantug G, Gades NM, Faubion WA. Interleukin 21 Drives a Hypermetabolic State and CD4 + T-Cell-Associated Pathogenicity in Chronic Intestinal Inflammation. Gastroenterology 2024; 166:826-841.e19. [PMID: 38266738 PMCID: PMC11034723 DOI: 10.1053/j.gastro.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/09/2023] [Revised: 11/23/2023] [Accepted: 01/15/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND & AIMS Incapacitated regulatory T cells (Tregs) contribute to immune-mediated diseases. Inflammatory Tregs are evident during human inflammatory bowel disease; however, mechanisms driving the development of these cells and their function are not well understood. Therefore, we investigated the role of cellular metabolism in Tregs relevant to gut homeostasis. METHODS Using human Tregs, we performed mitochondrial ultrastructural studies via electron microscopy and confocal imaging, biochemical and protein analyses using proximity ligation assay, immunoblotting, mass cytometry and fluorescence-activated cell sorting, metabolomics, gene expression analysis, and real-time metabolic profiling utilizing the Seahorse XF analyzer. We used a Crohn's disease single-cell RNA sequencing dataset to infer the therapeutic relevance of targeting metabolic pathways in inflammatory Tregs. We examined the superior functionality of genetically modified Tregs in CD4+ T-cell-induced murine colitis models. RESULTS Mitochondria-endoplasmic reticulum appositions, known to mediate pyruvate entry into mitochondria via voltage-dependent anion channel 1 (VDAC1), are abundant in Tregs. VDAC1 inhibition perturbed pyruvate metabolism, eliciting sensitization to other inflammatory signals reversible by membrane-permeable methyl pyruvate supplementation. Notably, interleukin (IL) 21 diminished mitochondria-endoplasmic reticulum appositions, resulting in enhanced enzymatic function of glycogen synthase kinase 3 β, a putative negative regulator of VDAC1, and a hypermetabolic state that amplified Treg inflammatory response. Methyl pyruvate and glycogen synthase kinase 3 β pharmacologic inhibitor (LY2090314) reversed IL21-induced metabolic rewiring and inflammatory state. Moreover, IL21-induced metabolic genes in Tregs in vitro were enriched in human Crohn's disease intestinal Tregs. Adoptively transferred Il21r-/- Tregs efficiently rescued murine colitis in contrast to wild-type Tregs. CONCLUSIONS IL21 triggers metabolic dysfunction associated with Treg inflammatory response. Inhibiting IL21-induced metabolism in Tregs may mitigate CD4+ T-cell-driven chronic intestinal inflammation.
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Affiliation(s)
- Adebowale O Bamidele
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Immunology, Mayo Clinic, Rochester, Minnesota.
| | - Shravan K Mishra
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Petra Hirsova
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Emily E Klatt
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Leena M Abdelrahman
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Heidi M Davidson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Patrick J Fehrenbach
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Hyun Se Kim Lee
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Song Zhang
- Mayo Clinic Metabolomics Core, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Abner Aguirre Lopez
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Ahmed T Kurdi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Maria S Westphal
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Michelle M Gonzalez
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Joseph M Gaballa
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Hee Eun Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Glenn Bantug
- Immunobiology Laboratory, Department of Biomedicine, University Hospital of Basel, Basel, Switzerland
| | - Naomi M Gades
- Department of Comparative Medicine, Mayo Clinic, Scottsdale, Arizona
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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Gaballa JM, Højen JF, De Graaf DM, Amo-Aparicio J, Marchetti C, Cavalli G, Dinarello A, Li S, Corbisiero MF, Tengesdal IW, Redzic JS, Azam T, Webber WS, Pankratz KA, May MJ, Cominelli F, Eisenmesser EZ, Kim S, Dinarello CA, Boraschi D. International nomenclature guidelines for the IL-1 family of cytokines and receptors. Nat Immunol 2024; 25:581-582. [PMID: 38499798 DOI: 10.1038/s41590-024-01777-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Affiliation(s)
- Joseph M Gaballa
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Jesper Falkesgaard Højen
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Dennis M De Graaf
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jesus Amo-Aparicio
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carlo Marchetti
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Alberto Dinarello
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Suzhao Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Isak W Tengesdal
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Tania Azam
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - William S Webber
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Karl A Pankratz
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Makenna J May
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Elan Z Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Soohyun Kim
- College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Charles A Dinarello
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Diana Boraschi
- Shenzhen Institute of Advanced Technology (SIAT) of the Chinese Academy of Science (CAS), and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen, China
- National Research Council, Napoli, Italy
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3
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Dinarello A, May M, Amo-Aparicio J, Azam T, Gaballa JM, Marchetti C, Tesoriere A, Ghirardo R, Redzic JS, Webber WS, Atif SM, Li S, Eisenmesser EZ, de Graaf DM, Dinarello CA. IL-38 regulates intestinal stem cell homeostasis by inducing WNT signaling and beneficial IL-1β secretion. Proc Natl Acad Sci U S A 2023; 120:e2306476120. [PMID: 37906644 PMCID: PMC10636342 DOI: 10.1073/pnas.2306476120] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/02/2023] [Accepted: 09/13/2023] [Indexed: 11/02/2023] Open
Abstract
The IL-1 Family member IL-38 has been characterized primarily as an antiinflammatory cytokine in human and mouse models of systemic diseases. Here, we examined the role of IL-38 in the murine small intestine (SI). Immunostaining of SI revealed that IL-38 expression partially confines to intestinal stem cells. Cultures of intestinal organoids reveal IL-38 functions as a growth factor by increasing organoid size via inducing WNT3a. In contrast, organoids from IL-38-deficient mice develop more slowly. This reduction in size is likely due to the downregulation of intestinal stemness markers (i.e., Fzd5, Ephb2, and Olfm4) expression compared with wild-type organoids. The IL-38 binding to IL-1R6 and IL-1R9 is still a matter of debate. Therefore, to analyze the molecular mechanisms of IL-38 signaling, we also examined organoids from IL-1R9-deficient mice. Unexpectedly, these organoids, although significantly smaller than wild type, respond to IL-38, suggesting that IL-1R9 is not involved in IL-38 signaling in the stem cell crypt. Nevertheless, silencing of IL-1R6 disabled the organoid response to the growth property of IL-38, thus suggesting IL-1R6 as the main receptor used by IL-38 in the crypt compartment. In organoids from wild-type mice, IL-38 stimulation induced low concentrations of IL-1β which contribute to organoid growth. However, high concentrations of IL-1β have detrimental effects on the cultures that were prevented by treatment with recombinant IL-38. Overall, our data demonstrate an important regulatory function of IL-38 as a growth factor, and as an antiinflammatory molecule in the SI, maintaining homeostasis.
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Affiliation(s)
- Alberto Dinarello
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Makenna May
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Jesus Amo-Aparicio
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Tania Azam
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Joseph M. Gaballa
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Carlo Marchetti
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | | | | | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO80045
| | - William S. Webber
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Shaikh M. Atif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Suzhao Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Elan Z. Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO80045
| | - Dennis M. de Graaf
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Charles A. Dinarello
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
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4
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Ramos GP, Bamidele AO, Klatt EE, Sagstetter MR, Kurdi AT, Hamdan FH, Kosinsky RL, Gaballa JM, Nair A, Sun Z, Dasari S, Lanza IR, Rozeveld CN, Schott MB, Urrutia G, Westphal MS, Clarkson BD, Howe CL, Marietta EV, Luckey DH, Murray JA, Gonzalez M, Braga Neto MB, Gibbons HR, Smyrk TC, Johnsen S, Lomberk G, Faubion WA. G9a Modulates Lipid Metabolism in CD4 T Cells to Regulate Intestinal Inflammation. Gastroenterology 2023; 164:256-271.e10. [PMID: 36272457 PMCID: PMC9892272 DOI: 10.1053/j.gastro.2022.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 02/24/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND & AIMS Although T-cell intrinsic expression of G9a has been associated with murine intestinal inflammation, mechanistic insight into the role of this methyltransferase in human T-cell differentiation is ill defined, and manipulation of G9a function for therapeutic use against inflammatory disorders is unexplored. METHODS Human naive T cells were isolated from peripheral blood and differentiated in vitro in the presence of a G9a inhibitor (UNC0642) before being characterized via the transcriptome (RNA sequencing), chromatin accessibility (assay for transposase-accessible chromatin by sequencing), protein expression (cytometry by time of flight, flow cytometry), metabolism (mitochondrial stress test, ultrahigh performance liquid chromatography-tandem mas spectroscopy) and function (T-cell suppression assay). The in vivo role of G9a was assessed using 3 murine models. RESULTS We discovered that pharmacologic inhibition of G9a enzymatic function in human CD4 T cells led to spontaneous generation of FOXP3+ T cells (G9a-inibitors-T regulatory cells [Tregs]) in vitro that faithfully reproduce human Tregs, functionally and phenotypically. Mechanistically, G9a inhibition altered the transcriptional regulation of genes involved in lipid biosynthesis in T cells, resulting in increased intracellular cholesterol. Metabolomic profiling of G9a-inibitors-Tregs confirmed elevated lipid pathways that support Treg development through oxidative phosphorylation and enhanced lipid membrane composition. Pharmacologic G9a inhibition promoted Treg expansion in vivo upon antigen (gliadin) stimulation and ameliorated acute trinitrobenzene sulfonic acid-induced colitis secondary to tissue-specific Treg development. Finally, Tregs lacking G9a expression (G9a-knockout Tregs) remain functional chronically and can rescue T-cell transfer-induced colitis. CONCLUSION G9a inhibition promotes cholesterol metabolism in T cells, favoring a metabolic profile that facilitates Treg development in vitro and in vivo. Our data support the potential use of G9a inhibitors in the treatment of immune-mediated conditions including inflammatory bowel disease.
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Affiliation(s)
- Guilherme Piovezani Ramos
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Adebowale O Bamidele
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Emily E Klatt
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Mary R Sagstetter
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Ahmed T Kurdi
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Feda H Hamdan
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Robyn Laura Kosinsky
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Joseph M Gaballa
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Asha Nair
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | - Ian R Lanza
- Metabolomics Core, Mayo Clinic, Rochester, Minnesota
| | - Cody N Rozeveld
- Department of Biology, Northwestern College, Orange City, Iowa
| | - Micah B Schott
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Guillermo Urrutia
- Genomic Sciences and Precision Medicine Center, Milwaukee, Wisconsin; Division of Research Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Maria S Westphal
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Charles L Howe
- Department of Immunology, Mayo Clinic, Rochester, Minnesota; Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | - Eric V Marietta
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - David H Luckey
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Joseph A Murray
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Michelle Gonzalez
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Manuel B Braga Neto
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Hunter R Gibbons
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Steven Johnsen
- Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center, Milwaukee, Wisconsin; Division of Research Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - William A Faubion
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Immunology, Mayo Clinic, Rochester, Minnesota.
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5
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Gonzalez MM, Bamidele AO, Svingen PA, Sagstetter MR, Smyrk TC, Gaballa JM, Hamdan FH, Kosinsky RL, Gibbons HR, Sun Z, Ye Z, Nair A, Ramos GP, Braga Neto MB, Wixom AQ, Mathison AJ, Johnsen SA, Urrutia R, Faubion WA. BMI1 maintains the Treg epigenomic landscape to prevent inflammatory bowel disease. J Clin Invest 2021; 131:e140755. [PMID: 34128475 DOI: 10.1172/jci140755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/04/2020] [Accepted: 04/15/2021] [Indexed: 12/13/2022] Open
Abstract
FOXP3+ Tregs are expanded within the inflamed intestine of human Crohn's disease, yet FOXP3-mediated gene repression within these cells is lost. The polycomb repressive complexes play a role in FOXP3 target gene regulation, but deeper mechanistic insight is incomplete. We have now specifically identified the polycomb-repressive complex 1 (PRC1) family member, BMI1 in the regulation of a proinflammatory enhancer network in both human and murine Tregs. Using human Tregs and lamina propria T cells, we inferred PRC1 to regulate Crohn's associated gene networks through assays of chromatin accessibility. Conditional deletion of BMI1 in murine FOXP3+ cells led to systemic inflammation. BMI1-deficient Tregs beared a TH1/TH17-like phenotype as assessed by assays of genome wide transcription, chromatin accessibility and proteomic techniques. Finally, BMI1 mutant FOXP3+ cells did not suppress colitis in the adoptive transfer model of human inflammatory bowel disease. We propose that BMI1 plays an important role in enforcing Treg identity in vitro and in vivo. Loss of Treg identity via genetic or transient BMI1 depletion perturbs the epigenome and converts Tregs into Th1/Th17-like proinflammatory cells, a transition relevant to human Crohn's disease associated CD4+ T cells.
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Affiliation(s)
- Michelle M Gonzalez
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Adebowale O Bamidele
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Phyllis A Svingen
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Mary R Sagstetter
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | | | - Joseph M Gaballa
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Feda H Hamdan
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Robyn Laura Kosinsky
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Hunter R Gibbons
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Zhifu Sun
- Department of Genetics and Bioinformatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Zhenqing Ye
- Department of Genetics and Bioinformatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Asha Nair
- Department of Genetics and Bioinformatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Guilherme P Ramos
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Manuel B Braga Neto
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Alexander Q Wixom
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Steven A Johnsen
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - William A Faubion
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine (CIM)
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6
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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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7
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Gaballa JM, Dabrian K, Desai R, Ngo R, Park D, Sakaji E, Sun Y, Tan B, Brinck M, Brobst O, Fernando R, Kim H, McCarthy S, Murphy M, Sarkis A, Sevier P, Singh A, Wu D, Wu MY, Ennis HA, Luhar R, Miller JE, Orchanian SB, Salbato AN, Alam S, Brenner L, Kailani Z, Laskow J, Ma X, Miikeda A, Nol-Bernardino P, Sukhina A, Walas N, Wei W, Do NP, Fournier CT, Kim CJ, Mosier SF, Pierson C, Romero IG, Sanchez M, Sawyerr O, Wang J, Watanabe R, Wu S, Chen A, Kazane K, Kettoola Y, Goodwin EC, Lund AJ, Villella W, Williams D, Freise A, Moberg Parker J. Genome Sequences of Cluster K Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley. Microbiol Resour Announc 2019; 8:e01481-18. [PMID: 30643892 PMCID: PMC6328665 DOI: 10.1128/mra.01481-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 11/27/2018] [Indexed: 12/03/2022] Open
Abstract
Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley were isolated from soil using Mycobacterium smegmatis mc2155. Genomic analysis indicated that they belong to subclusters K1 and K5. Their genomic architectures are typical of cluster K mycobacteriophages, with most variability occurring on the right end of the genome sequence.
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Affiliation(s)
- Joseph M. Gaballa
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Keeyon Dabrian
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Rachel Desai
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Ryan Ngo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Diane Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Erin Sakaji
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Yiwei Sun
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Boon Tan
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Marcia Brinck
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Olivia Brobst
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Rebecca Fernando
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Hannah Kim
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Siobhan McCarthy
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Michael Murphy
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Alexandra Sarkis
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Parker Sevier
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Amitoj Singh
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Darwin Wu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Min-Ying Wu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Hayley A. Ennis
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Rohan Luhar
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Justin E. Miller
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Stephanie B. Orchanian
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Alysha N. Salbato
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Sai Alam
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Lauren Brenner
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Zilla Kailani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Joel Laskow
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Xinyu Ma
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Aika Miikeda
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Paola Nol-Bernardino
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Alisa Sukhina
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Nikolina Walas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Wenyuan Wei
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Nam Phuong Do
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Christina T. Fournier
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Christy J. Kim
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Samantha F. Mosier
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Carly Pierson
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Ivonne G. Romero
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Mikael Sanchez
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Oyinlola Sawyerr
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Joyce Wang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Rina Watanabe
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Samuel Wu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Annie Chen
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Katelynn Kazane
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Yousif Kettoola
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Emma C. Goodwin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Andrew J. Lund
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - William Villella
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Drake Williams
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Amanda Freise
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
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8
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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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