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Estupiñán-Moreno E, Hernández-Rodríguez J, Li T, Ciudad L, Andrés-León E, Terron-Camero LC, Prieto-González S, Espígol-Frigolé G, Cid MC, Márquez A, Martin J, Ballestar E, Ortiz-Fernández L. Decoding CD4 + T cell transcriptome in giant cell arteritis: Novel pathways and altered cross-talk with monocytes. J Autoimmun 2024; 146:103240. [PMID: 38754238 DOI: 10.1016/j.jaut.2024.103240] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/16/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Giant cell arteritis (GCA) is an immune-mediated large-vessels vasculitis with complex etiology. Although the pathogenic mechanisms remain poorly understood, a central role for CD4+ T cells has been demonstrated. In this context, understanding the transcriptome dysregulation in GCA CD4+ T cells will yield new insights into its pathogenesis. METHODS Transcriptome analysis was conducted on CD4+ T cells from 70 patients with GCA with different disease activity and treatment status (active patients before treatment and patients in remission with and without glucocorticoid treatment), and 28 healthy controls. The study also evaluated potential impacts of DNA methylation on gene expression alterations and assessed cross-talk with CD14+ monocytes. RESULTS This study has uncovered a substantial number of genes and pathways potentially contributing to the pathogenicity of CD4+ T cells in GCA. Specifically, CD4+ T cells from GCA patients with active disease exhibited altered expression levels of genes involved in multiple immune-related processes, including various interleukins (IL) signaling pathways. Notably, IL-2, a decisive interleukin for regulatory T cells homeostasis, was among the most significant. Additionally, impaired apoptotic pathways appear crucial in GCA development. Our findings also suggest that histone-related epigenetic pathways may be implicated in promoting an inflammatory phenotype in GCA active patients. Finally, our study observed altered signaling communication, such as the Jagged-Notch signaling, between CD4+ T cells and monocytes that could have pathogenic relevance in GCA. CONCLUSIONS Our study suggests the participation of novel cytokines and pathways and the occurrence of a disruption of monocyte-T cell crosstalk driving GCA pathogenesis.
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Affiliation(s)
- Elkyn Estupiñán-Moreno
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - José Hernández-Rodríguez
- Vasculitis Research Unit. Department of Autoimmune Diseases, Hospital Clinic, Universitat de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Eduardo Andrés-León
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Laura Carmen Terron-Camero
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Sergio Prieto-González
- Vasculitis Research Unit. Department of Autoimmune Diseases, Hospital Clinic, Universitat de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Georgina Espígol-Frigolé
- Vasculitis Research Unit. Department of Autoimmune Diseases, Hospital Clinic, Universitat de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria C Cid
- Vasculitis Research Unit. Department of Autoimmune Diseases, Hospital Clinic, Universitat de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Ana Márquez
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Javier Martin
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain.
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain.
| | - Lourdes Ortiz-Fernández
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain.
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Díaz-Tejedor A, Rodríguez-Ubreva J, Ciudad L, Lorenzo-Mohamed M, González-Rodríguez M, Castellanos B, Sotolongo-Ravelo J, San-Segundo L, Corchete LA, González-Méndez L, Martín-Sánchez M, Mateos MV, Ocio EM, Garayoa M, Paíno T. Tinostamustine (EDO-S101), an Alkylating Deacetylase Inhibitor, Enhances the Efficacy of Daratumumab in Multiple Myeloma by Upregulation of CD38 and NKG2D Ligands. Int J Mol Sci 2024; 25:4718. [PMID: 38731936 PMCID: PMC11083018 DOI: 10.3390/ijms25094718] [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: 03/14/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Multiple myeloma is a malignancy characterized by the accumulation of malignant plasma cells in bone marrow and the production of monoclonal immunoglobulin. A hallmark of cancer is the evasion of immune surveillance. Histone deacetylase inhibitors have been shown to promote the expression of silenced molecules and hold potential to increase the anti-MM efficacy of immunotherapy. The aim of the present work was to assess the potential effect of tinostamustine (EDO-S101), a first-in-class alkylating deacetylase inhibitor, in combination with daratumumab, an anti-CD38 monoclonal antibody (mAb), through different preclinical studies. Tinostamustine increases CD38 expression in myeloma cell lines, an effect that occurs in parallel with an increment in CD38 histone H3 acetylation levels. Also, the expression of MICA and MICB, ligands for the NK cell activating receptor NKG2D, augments after tinostamustine treatment in myeloma cell lines and primary myeloma cells. Pretreatment of myeloma cell lines with tinostamustine increased the sensitivity of these cells to daratumumab through its different cytotoxic mechanisms, and the combination of these two drugs showed a higher anti-myeloma effect than individual treatments in ex vivo cultures of myeloma patients' samples. In vivo data confirmed that tinostamustine pretreatment followed by daratumumab administration significantly delayed tumor growth and improved the survival of mice compared to individual treatments. In summary, our results suggest that tinostamustine could be a potential candidate to improve the efficacy of anti-CD38 mAbs.
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Affiliation(s)
- Andrea Díaz-Tejedor
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Spain; (J.R.-U.); (L.C.)
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Spain; (J.R.-U.); (L.C.)
| | - Mauro Lorenzo-Mohamed
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Marta González-Rodríguez
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Bárbara Castellanos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Janet Sotolongo-Ravelo
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Laura San-Segundo
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Luis A. Corchete
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
- Centro de Investigación Biomédica En Red de Cáncer (CIBERONC, CB16/12/00233), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Lorena González-Méndez
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Montserrat Martín-Sánchez
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - María-Victoria Mateos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
- Centro de Investigación Biomédica En Red de Cáncer (CIBERONC, CB16/12/00233), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Enrique M. Ocio
- Hospital Universitario Marqués de Valdecilla (IDIVAL), Universidad de Cantabria, 39008 Santander, Spain;
| | - Mercedes Garayoa
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Teresa Paíno
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca, Consejo Superior de Investigaciones Científicas (CSIC), 37007 Salamanca, Spain; (A.D.-T.); (M.L.-M.); (M.G.-R.); (B.C.); (J.S.-R.); (L.S.-S.); (L.A.C.); (L.G.-M.); (M.M.-S.); (M.-V.M.); (M.G.)
- Servicio de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
- Centro de Investigación Biomédica En Red de Cáncer (CIBERONC, CB16/12/00233), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
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3
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Barmada A, Handfield LF, Godoy-Tena G, de la Calle-Fabregat C, Ciudad L, Arutyunyan A, Andrés-León E, Hoo R, Porter T, Oszlanczi A, Richardson L, Calero-Nieto FJ, Wilson NK, Marchese D, Sancho-Serra C, Carrillo J, Presas-Rodríguez S, Ramo-Tello C, Ruiz-Sanmartin A, Ferrer R, Ruiz-Rodriguez JC, Martínez-Gallo M, Munera-Campos M, Carrascosa JM, Göttgens B, Heyn H, Prigmore E, Casafont-Solé I, Solanich X, Sánchez-Cerrillo I, González-Álvaro I, Raimondo MG, Ramming A, Martin J, Martínez-Cáceres E, Ballestar E, Vento-Tormo R, Rodríguez-Ubreva J. Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases shows aberrant immune responses to infection. Eur J Immunol 2024; 54:e2350633. [PMID: 37799110 DOI: 10.1002/eji.202350633] [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: 06/28/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
In COVID-19, hyperinflammatory and dysregulated immune responses contribute to severity. Patients with pre-existing autoimmune conditions can therefore be at increased risk of severe COVID-19 and/or associated sequelae, yet SARS-CoV-2 infection in this group has been little studied. Here, we performed single-cell analysis of peripheral blood mononuclear cells from patients with three major autoimmune diseases (rheumatoid arthritis, psoriasis, or multiple sclerosis) during SARS-CoV-2 infection. We observed compositional differences between the autoimmune disease groups coupled with altered patterns of gene expression, transcription factor activity, and cell-cell communication that substantially shape the immune response under SARS-CoV-2 infection. While enrichment of HLA-DRlow CD14+ monocytes was observed in all three autoimmune disease groups, type-I interferon signaling as well as inflammatory T cell and monocyte responses varied widely between the three groups of patients. Our results reveal disturbed immune responses to SARS-CoV-2 in patients with pre-existing autoimmunity, highlighting important considerations for disease treatment and follow-up.
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Affiliation(s)
- Anis Barmada
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | | | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Anna Arutyunyan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Regina Hoo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Tarryn Porter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Agnes Oszlanczi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Fernando J Calero-Nieto
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nicola K Wilson
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Carmen Sancho-Serra
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Silvia Presas-Rodríguez
- MS Unit, Department of Neurology, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Cristina Ramo-Tello
- MS Unit, Department of Neurology, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Adolfo Ruiz-Sanmartin
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Ricard Ferrer
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Martínez-Gallo
- Division of Immunology, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Munera-Campos
- Dermatology Service, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Jose Manuel Carrascosa
- Dermatology Service, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Berthold Göttgens
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Ivette Casafont-Solé
- Department of Rheumatology, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Department of Infectious Diseases, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Xavier Solanich
- Department of Internal Medicine, Hospital Universitari de Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Maria Gabriella Raimondo
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Ramming
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eva Martínez-Cáceres
- Division of Immunology, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
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Suárez-de-la-Rica A, Croes B, Ciudad L, Vallejo I, Mújica J, Díaz-Almirón M, Maseda E. Vitamin C and thiamine for the treatment of refractory septic shock in surgical critically ill patients: a retrospective before-and-after study. Rev Esp Quimioter 2023; 36:187-192. [PMID: 36440551 PMCID: PMC10066916 DOI: 10.37201/req/107.2022] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE This study aimed to evaluate whether early vitamin C and thiamine administration was associated with a lower 28-day and in-hospital mortality in surgical critically ill patients with refractory septic shock. METHODS We performed a retrospective before-and-after study on patients with refractory septic shock. According to local protocol, hydrocortisone is initiated in case of refractory septic shock. In January 2017, the protocol was changed and vitamin C and thiamine were included. Patients who were admitted in 2015-2016 and 2017-2018 were included in the control and treatment groups, respectively. The primary end point was 28-day and in-hospital mortality. Secondary end points were ICU mortality, ICU and hospital length of stay, duration of vasopressors and mechanical ventilation, use of renal replacement therapy (RRT), and the modification in serum procalcitonin and SOFA score during the first 72 h. RESULTS A total of 120 patients were included (58 in the treatment group and 62 in the control group). Log-rank test in Kaplan-Meier curves showed lower 28-day and in-hospital mortality over time in the treatment group (p=0.021 and p=0.035, respectively) but it not reached statistical significance in ICU mortality over time (p=0.100). The need of RRT was less frequent in treatment group (17.2% vs. 37.1%, p=0.024). There were no differences in other secondary outcomes. CONCLUSIONS Intravenous vitamin C and thiamine administration in surgical patients with refractory septic shock may be associated with a lower 28-day and in-hospital mortality. Further prospective studies are needed in refractory septic shock.
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Affiliation(s)
| | | | | | | | | | | | - E Maseda
- Emilio Maseda, Department of Anesthesiology and Surgical Critical Care. Hospital Univer-sitario La Paz. Madrid. Spain.
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5
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Martins-Ferreira R, Leal B, Chaves J, Ciudad L, Samões R, Martins da Silva A, Pinho Costa P, Ballestar E. Circulating cell-free DNA methylation mirrors alterations in cerebral patterns in epilepsy. Clin Epigenetics 2022; 14:188. [PMID: 36575526 PMCID: PMC9795776 DOI: 10.1186/s13148-022-01416-2] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND DNA methylation profiling of circulating cell-free DNA (cfDNA) has rapidly become a promising strategy for biomarker identification and development. The cell-type-specific nature of DNA methylation patterns and the direct relationship between cfDNA and apoptosis can potentially be used non-invasively to predict local alterations. In addition, direct detection of altered DNA methylation patterns performs well as a biomarker. In a previous study, we demonstrated marked DNA methylation alterations in brain tissue from patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS). RESULTS We performed DNA methylation profiling in cfDNA isolated from the serum of MTLE patients and healthy controls using BeadChip arrays followed by systematic bioinformatic analysis including deconvolution analysis and integration with DNase accessibility data sets. Differential cfDNA methylation analysis showed an overrepresentation of gene ontology terms and transcription factors related to central nervous system function and regulation. Deconvolution analysis of the DNA methylation data sets ruled out the possibility that the observed differences were due to changes in the proportional contribution of cortical neurons in cfDNA. Moreover, we found no overrepresentation of neuron- or glia-specific patterns in the described cfDNA methylation patterns. However, the MTLE-HS cfDNA methylation patterns featured a significant overrepresentation of the epileptic DNA methylation alterations previously observed in the hippocampus. CONCLUSIONS Our results support the use of cfDNA methylation profiling as a rational approach to seeking non-invasive and reproducible epilepsy biomarkers.
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Affiliation(s)
- Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain ,grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - Bárbara Leal
- grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - João Chaves
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,grid.413438.90000 0004 0574 5247Neurology Service, Hospital de Santo António - Centro Hospitalar Universitário do Porto (HSA-CHUP), Porto, Portugal
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain
| | - Raquel Samões
- grid.413438.90000 0004 0574 5247Neurology Service, Hospital de Santo António - Centro Hospitalar Universitário do Porto (HSA-CHUP), Porto, Portugal
| | - António Martins da Silva
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,Neurophysiology Service, HSA-CHUP, Porto, Portugal
| | - Paulo Pinho Costa
- grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,grid.422270.10000 0001 2287 695XDepartment of Human Genetics, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain ,grid.22069.3f0000 0004 0369 6365Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241 China
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6
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Morante-Palacios O, Godoy-Tena G, Calafell-Segura J, Ciudad L, Martínez-Cáceres EM, Sardina JL, Ballestar E. Vitamin C enhances NF-κB-driven epigenomic reprogramming and boosts the immunogenic properties of dendritic cells. Nucleic Acids Res 2022; 50:10981-10994. [PMID: 36305821 PMCID: PMC9638940 DOI: 10.1093/nar/gkac941] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/23/2022] [Accepted: 10/10/2022] [Indexed: 11/19/2022] Open
Abstract
Dendritic cells (DCs), the most potent antigen-presenting cells, are necessary for effective activation of naïve T cells. DCs’ immunological properties are modulated in response to various stimuli. Active DNA demethylation is crucial for DC differentiation and function. Vitamin C, a known cofactor of ten-eleven translocation (TET) enzymes, drives active demethylation. Vitamin C has recently emerged as a promising adjuvant for several types of cancer; however, its effects on human immune cells are poorly understood. In this study, we investigate the epigenomic and transcriptomic reprogramming orchestrated by vitamin C in monocyte-derived DC differentiation and maturation. Vitamin C triggers extensive demethylation at NF-κB/p65 binding sites, together with concordant upregulation of antigen-presentation and immune response-related genes during DC maturation. p65 interacts with TET2 and mediates the aforementioned vitamin C-mediated changes, as demonstrated by pharmacological inhibition. Moreover, vitamin C increases TNFβ production in DCs through NF-κB, in concordance with the upregulation of its coding gene and the demethylation of adjacent CpGs. Finally, vitamin C enhances DC’s ability to stimulate the proliferation of autologous antigen-specific T cells. We propose that vitamin C could potentially improve monocyte-derived DC-based cell therapies.
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Affiliation(s)
- Octavio Morante-Palacios
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
- Germans Trias i Pujol Research Institute (IGTP), 08916, Badalona, Barcelona, Spain
| | - Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Eva M Martínez-Cáceres
- Division of Immunology, Germans Trias i Pujol Hospital, LCMN, Germans Trias iPujol Research Institute (IGTP), 08916, Badalona, Barcelona, Spain
- Department of Cell Biology, Physiology, Immunology, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - José Luis Sardina
- Epigenetic Control of Haematopoiesis Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Esteban Ballestar
- To whom correspondence should be addressed. Tel: +34 935572800; Fax: +34 934651472;
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7
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Estupiñán-Moreno E, Ortiz-Fernández L, Li T, Hernández-Rodríguez J, Ciudad L, Andrés-León E, Terron-Camero LC, Prieto-González S, Espígol-Frigolé G, Cid MC, Márquez A, Ballestar E, Martín J. Methylome and transcriptome profiling of giant cell arteritis monocytes reveals novel pathways involved in disease pathogenesis and molecular response to glucocorticoids. Ann Rheum Dis 2022; 81:1290-1300. [PMID: 35705375 PMCID: PMC9380516 DOI: 10.1136/annrheumdis-2022-222156] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/17/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Giant cell arteritis (GCA) is a complex systemic vasculitis mediated by the interplay between both genetic and epigenetic factors. Monocytes are crucial players of the inflammation occurring in GCA. Therefore, characterisation of the monocyte methylome and transcriptome in GCA would be helpful to better understand disease pathogenesis. METHODS We performed an integrated epigenome-and transcriptome-wide association study in CD14+ monocytes from 82 patients with GCA, cross-sectionally classified into three different clinical statuses (active, in remission with or without glucocorticoid (GC) treatment), and 31 healthy controls. RESULTS We identified a global methylation and gene expression dysregulation in GCA monocytes. Specifically, monocytes from active patients showed a more proinflammatory phenotype compared with healthy controls and patients in remission. In addition to inflammatory pathways known to be involved in active GCA, such as response to IL-6 and IL-1, we identified response to IL-11 as a new pathway potentially implicated in GCA. Furthermore, monocytes from patients in remission with treatment showed downregulation of genes involved in inflammatory processes as well as overexpression of GC receptor-target genes. Finally, we identified changes in DNA methylation correlating with alterations in expression levels of genes with a potential role in GCA pathogenesis, such as ITGA7 and CD63, as well as genes mediating the molecular response to GC, including FKBP5, ETS2, ZBTB16 and ADAMTS2. CONCLUSION Our results revealed profound alterations in the methylation and transcriptomic profiles of monocytes from GCA patients, uncovering novel genes and pathways involved in GCA pathogenesis and in the molecular response to GC treatment.
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Affiliation(s)
- Elkyn Estupiñán-Moreno
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Lourdes Ortiz-Fernández
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - Jose Hernández-Rodríguez
- Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - Eduardo Andrés-León
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Laura Carmen Terron-Camero
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Sergio Prieto-González
- Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Georgina Espígol-Frigolé
- Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria Cinta Cid
- Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ana Márquez
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
- Systemic Autoimmune Diseases Unit, Hospital Clinico San Cecilio, Instituto de Investigación Biosanitaria de Granada ibs.GRANADA, Granada, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
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8
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de la Calle-Fabregat C, Rodríguez-Ubreva J, Ciudad L, Ramírez J, Celis R, Azuaga AB, Cuervo A, Graell E, Pérez-García C, Díaz-Torné C, Salvador G, Gómez-Puerta JA, Haro I, Sanmartí R, Cañete JD, Ballestar E. The synovial and blood monocyte DNA methylomes mirror prognosis, evolution and treatment in early arthritis. JCI Insight 2022; 7:158783. [PMID: 35324478 PMCID: PMC9090240 DOI: 10.1172/jci.insight.158783] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 01/25/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Identifying predictive biomarkers at early stages of inflammatory arthritis is crucial for starting appropriate therapies to avoid poor outcomes. Monocytes (MOs) and macrophages, largely associated with arthritis, are contributors and sensors of inflammation through epigenetic modifications. In this study, we investigated associations between clinical features and DNA methylation in blood and synovial fluid (SF) MOs in a prospective cohort of patients with early inflammatory arthritis. DNA methylation profiles of undifferentiated arthritis (UA) blood MOs exhibited marked alterations in comparison with those from healthy donors. We identified additional differences both in blood and SF MOs after comparing patients with UA grouped by their future outcomes, i.e., good versus poor. Patient profiles in subsequent visits revealed a reversion toward a healthy level in both groups, those requiring disease-modifying antirheumatic drugs and those who remitted spontaneously. Changes in disease activity between visits also affected DNA methylation, which was partially concomitant in the SF of UA and in blood MOs of patients with rheumatoid arthritis. Epigenetic similarities between arthritis types allow a common prediction of disease activity. Our results constitute a resource of DNA methylation–based biomarkers of poor prognosis, disease activity, and treatment efficacy for the personalized clinical management of early inflammatory arthritis.
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Affiliation(s)
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - Julio Ramírez
- Rheumatology Department, Hospital Clinic and IDIBAPS, Barcelona, Spain
| | - Raquel Celis
- Rheumatology Department, Hospital Clinic and IDIBAPS, Barcelona, Spain
| | - Ana B Azuaga
- Rheumatology Department, Hospital Clinic and IDIBAPS, Barcelona, Spain
| | - Andrea Cuervo
- Rheumatology Department, Hospital Clinic and IDIBAPS, Barcelona, Spain
| | - Eduard Graell
- Rheumatology Department, Hospital Universitari Parc Taulí, Sabadell, Spain
| | | | - César Díaz-Torné
- Servei de Reumatologia, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Georgina Salvador
- Rheumatology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | | | - Isabel Haro
- Unit of Synthesis and Biomedical Applications of Peptides, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
| | - Raimon Sanmartí
- Rheumatology Department, Hospital Clinic and IDIBAPS, Barcelona, Spain
| | - Juan D Cañete
- Rheumatology Department, Hospital Clinic and IDIBAPS, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
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9
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Martins-Ferreira R, Leal B, Chaves J, Li T, Ciudad L, Rangel R, Santos A, Martins da Silva A, Pinho Costa P, Ballestar E. Epilepsy progression is associated with cumulative DNA methylation changes in inflammatory genes. Prog Neurobiol 2022; 209:102207. [DOI: 10.1016/j.pneurobio.2021.102207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 01/09/2023]
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10
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Català-Moll F, Ferreté-Bonastre AG, Godoy-Tena G, Morante-Palacios O, Ciudad L, Barberà L, Fondelli F, Martínez-Cáceres EM, Rodríguez-Ubreva J, Li T, Ballestar E. Vitamin D receptor, STAT3, and TET2 cooperate to establish tolerogenesis. Cell Rep 2022; 38:110244. [DOI: 10.1016/j.celrep.2021.110244] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/27/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022] Open
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11
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Morante-Palacios O, Ciudad L, Micheroli R, de la Calle-Fabregat C, Li T, Barbisan G, Houtman M, Edalat SG, Frank-Bertoncelj M, Ospelt C, Ballestar E. Coordinated glucocorticoid receptor and MAFB action induces tolerogenesis and epigenome remodeling in dendritic cells. Nucleic Acids Res 2021; 50:108-126. [PMID: 34893889 PMCID: PMC8754638 DOI: 10.1093/nar/gkab1182] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Glucocorticoids (GCs) exert potent anti-inflammatory effects in immune cells through the glucocorticoid receptor (GR). Dendritic cells (DCs), central actors for coordinating immune responses, acquire tolerogenic properties in response to GCs. Tolerogenic DCs (tolDCs) have emerged as a potential treatment for various inflammatory diseases. To date, the underlying cell type-specific regulatory mechanisms orchestrating GC-mediated acquisition of immunosuppressive properties remain poorly understood. In this study, we investigated the transcriptomic and epigenomic remodeling associated with differentiation to DCs in the presence of GCs. Our analysis demonstrates a major role of MAFB in this process, in synergy with GR. GR and MAFB both interact with methylcytosine dioxygenase TET2 and bind to genomic loci that undergo specific demethylation in tolDCs. We also show that the role of MAFB is more extensive, binding to thousands of genomic loci in tolDCs. Finally, MAFB knockdown erases the tolerogenic properties of tolDCs and reverts the specific DNA demethylation and gene upregulation. The preeminent role of MAFB is also demonstrated in vivo for myeloid cells from synovium in rheumatoid arthritis following GC treatment. Our results imply that, once directly activated by GR, MAFB plays a critical role in orchestrating the epigenomic and transcriptomic remodeling that define the tolerogenic phenotype.
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Affiliation(s)
- Octavio Morante-Palacios
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Raphael Micheroli
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Carlos de la Calle-Fabregat
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Gisela Barbisan
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Miranda Houtman
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sam G Edalat
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mojca Frank-Bertoncelj
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Barcelona, Spain
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12
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Morante-Palacios O, Lorente-Sorolla C, Ciudad L, Calafell-Segura J, Garcia-Gomez A, Català-Moll F, Ruiz-Sanmartín A, Martínez-Gallo M, Ferrer R, Ruiz-Rodriguez JC, Álvarez-Errico D, Ballestar E. JAK2-STAT Epigenetically Regulates Tolerized Genes in Monocytes in the First Encounter With Gram-Negative Bacterial Endotoxins in Sepsis. Front Immunol 2021; 12:734652. [PMID: 34867954 PMCID: PMC8635809 DOI: 10.3389/fimmu.2021.734652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/01/2021] [Accepted: 10/21/2021] [Indexed: 01/03/2023] Open
Abstract
Microbial challenges, such as widespread bacterial infection in sepsis, induce endotoxin tolerance, a state of hyporesponsiveness to subsequent infections. The participation of DNA methylation in this process is poorly known. In this study, we perform integrated analysis of DNA methylation and transcriptional changes following in vitro exposure to gram-negative bacterial lipopolysaccharide, together with analysis of ex vivo monocytes from septic patients. We identify TET2-mediated demethylation and transcriptional activation of inflammation-related genes that is specific to toll-like receptor stimulation. Changes also involve phosphorylation of STAT1, STAT3 and STAT5, elements of the JAK2 pathway. JAK2 pathway inhibition impairs the activation of tolerized genes on the first encounter with lipopolysaccharide. We then confirm the implication of the JAK2-STAT pathway in the aberrant DNA methylome of patients with sepsis caused by gram-negative bacteria. Finally, JAK2 inhibition in monocytes partially recapitulates the expression changes produced in the immunosuppressive cellular state acquired by monocytes from gram-negative sepsis, as described by single cell-RNA-sequencing. Our study evidences both the crucial role the JAK2-STAT pathway in epigenetic regulation and initial response of the tolerized genes to gram-negative bacterial endotoxins and provides a pharmacological target to prevent exacerbated responses.
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Affiliation(s)
| | - Clara Lorente-Sorolla
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Antonio Garcia-Gomez
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Adolfo Ruiz-Sanmartín
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Ricard Ferrer
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Damiana Álvarez-Errico
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
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13
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Martins-Ferreira R, Leal BG, Chaves J, Fabregat C, Li T, Ciudad L, Samões R, Da Silva A, Costa P, Ballestar E. DNA methylation screening suggests brain origin of cell-free DNA in epilepsy. J Neurol Sci 2021. [DOI: 10.1016/j.jns.2021.119143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Català-Moll F, Ferreté-Bonastre AG, Li T, Weichenhan D, Lutsik P, Ciudad L, Álvarez-Prado ÁF, Rodríguez-Ubreva J, Klemann C, Speckmann C, Vilas-Zornoza A, Abolhassani H, Martínez-Gallo M, Dieli-Crimi R, Rivière JG, Martín-Nalda A, Colobran R, Soler-Palacín P, Kracker S, Hammarström L, Prosper F, Durandy A, Grimbacher B, Plass C, Ballestar E. Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction. Nucleic Acids Res 2021; 49:5057-5073. [PMID: 33950194 PMCID: PMC8136777 DOI: 10.1093/nar/gkab322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated deamination has been proposed as leading to active demethylation of 5-methycytosines in the DNA, although evidence both supports and casts doubt on such a role. In this study, using whole-genome bisulfite sequencing of HIGM2 B cells, we investigated direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation alterations, of which ∼25% are attributable to active DNA demethylation. For genes that undergo active demethylation that is impaired in HIGM2 individuals, our analysis indicates that AID is not directly involved. We demonstrate that the widespread alterations in the DNA methylation and expression profiles of HIGM2 naïve B cells result from premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data support a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns.
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Affiliation(s)
- Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Anna G Ferreté-Bonastre
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Ángel F Álvarez-Prado
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Christian Klemann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Medicine, Center for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Germany
| | - Amaya Vilas-Zornoza
- Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE 14186 Stockholm , Sweden
| | - Mónica Martínez-Gallo
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Romina Dieli-Crimi
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Jacques G Rivière
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Sven Kracker
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE 14186 Stockholm , Sweden
| | - Felipe Prosper
- Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Anne Durandy
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- German Center for Infection Research (DZIF), Satellite Center Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs University, Freiburg, Germany
- RESIST, Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
- Institute of Immunity & Transplantation, Royal Free Hospital, University College London, UK
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
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15
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Garcia-Gomez A, Li T, de la Calle-Fabregat C, Rodríguez-Ubreva J, Ciudad L, Català-Moll F, Godoy-Tena G, Martín-Sánchez M, San-Segundo L, Muntión S, Morales X, Ortiz-de-Solórzano C, Oyarzabal J, San José-Enériz E, Esteller M, Agirre X, Prosper F, Garayoa M, Ballestar E. Targeting aberrant DNA methylation in mesenchymal stromal cells as a treatment for myeloma bone disease. Nat Commun 2021; 12:421. [PMID: 33462210 PMCID: PMC7813865 DOI: 10.1038/s41467-020-20715-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Multiple myeloma (MM) progression and myeloma-associated bone disease (MBD) are highly dependent on bone marrow mesenchymal stromal cells (MSCs). MM-MSCs exhibit abnormal transcriptomes, suggesting the involvement of epigenetic mechanisms governing their tumor-promoting functions and prolonged osteoblast suppression. Here, we identify widespread DNA methylation alterations of bone marrow-isolated MSCs from distinct MM stages, particularly in Homeobox genes involved in osteogenic differentiation that associate with their aberrant expression. Moreover, these DNA methylation changes are recapitulated in vitro by exposing MSCs from healthy individuals to MM cells. Pharmacological targeting of DNMTs and G9a with dual inhibitor CM-272 reverts the expression of hypermethylated osteogenic regulators and promotes osteoblast differentiation of myeloma MSCs. Most importantly, CM-272 treatment prevents tumor-associated bone loss and reduces tumor burden in a murine myeloma model. Our results demonstrate that epigenetic aberrancies mediate the impairment of bone formation in MM, and its targeting by CM-272 is able to reverse MBD. Mesenchymal stromal cells (MSCs) have been shown to support multiple myeloma (MM) development. Here, MSCs isolated from the bone marrow of MM patients are shown to have altered DNA methylation patterns and a methyltransferase inhibitor reverts MM-associated bone loss and reduces tumour burden in MM murine models.
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Affiliation(s)
- Antonio Garcia-Gomez
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Badalona, Barcelona, Spain. .,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Carlos de la Calle-Fabregat
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Badalona, Barcelona, Spain
| | - Montserrat Martín-Sánchez
- Centro de Investigación del Cáncer, IBMCC (Universidad de Salamanca-CSIC) and Hospital Universitario de Salamanca-IBSAL, 37007, Salamanca, Spain
| | - Laura San-Segundo
- Centro de Investigación del Cáncer, IBMCC (Universidad de Salamanca-CSIC) and Hospital Universitario de Salamanca-IBSAL, 37007, Salamanca, Spain
| | - Sandra Muntión
- Centro de Investigación del Cáncer, IBMCC (Universidad de Salamanca-CSIC) and Hospital Universitario de Salamanca-IBSAL, 37007, Salamanca, Spain
| | - Xabier Morales
- Imaging Platform, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, 31008, Pamplona, Spain
| | - Carlos Ortiz-de-Solórzano
- Imaging Platform, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, 31008, Pamplona, Spain
| | - Julen Oyarzabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Edurne San José-Enériz
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, 31008, Pamplona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Xabier Agirre
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, 31008, Pamplona, Spain
| | - Felipe Prosper
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, 31008, Pamplona, Spain
| | - Mercedes Garayoa
- Centro de Investigación del Cáncer, IBMCC (Universidad de Salamanca-CSIC) and Hospital Universitario de Salamanca-IBSAL, 37007, Salamanca, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Badalona, Barcelona, Spain. .,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llobregat, Barcelona, Spain.
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16
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Li T, Ortiz-Fernández L, Andrés-León E, Ciudad L, Javierre BM, López-Isac E, Guillén-Del-Castillo A, Simeón-Aznar CP, Ballestar E, Martin J. Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci. Genome Med 2020; 12:81. [PMID: 32977850 PMCID: PMC7519528 DOI: 10.1186/s13073-020-00779-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 03/24/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. METHODS DNA samples exacted from CD4+ T cells of 48 SSc patients and 16 healthy controls were hybridized on MethylationEPIC BeadChip array. In parallel, gene expression was interrogated by hybridizing total RNA on Clariom™ S array. Downstream bioinformatics analyses were performed to identify correlating differentially methylated CpG positions (DMPs) and differentially expressed genes (DEGs), which were then confirmed utilizing previously published promoter capture Hi-C (PCHi-C) data. RESULTS We identified 9112 and 3929 DMPs and DEGs, respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing PCHi-C data, we observed that 212 CD4+ T cell-specific pairs of DMP-DEG also formed part of three-dimensional promoter-enhancer networks, potentially involving CTCF. Finally, combining PCHi-C data with SSc GWAS data, we identified four important SSc-associated susceptibility loci, TNIP1 (rs3792783), GSDMB (rs9303277), IL12RB1 (rs2305743), and CSK (rs1378942), that could potentially interact with DMP-DEG pairs cg17239269-ANXA6, cg19458020-CCR7, cg10808810-JUND, and cg11062629-ULK3, respectively. CONCLUSION Our study unveils a potential link between genetic, epigenetic, and transcriptional deregulation in CD4+ T cells of SSc patients, providing a novel integrated view of molecular components driving SSc pathogenesis.
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Affiliation(s)
- Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Lourdes Ortiz-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Elena López-Isac
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Alfredo Guillén-Del-Castillo
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Carmen Pilar Simeón-Aznar
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain.
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain.
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17
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Li T, Garcia-Gomez A, Morante-Palacios O, Ciudad L, Özkaramehmet S, Van Dijck E, Rodríguez-Ubreva J, Vaquero A, Ballestar E. SIRT1/2 orchestrate acquisition of DNA methylation and loss of histone H3 activating marks to prevent premature activation of inflammatory genes in macrophages. Nucleic Acids Res 2020; 48:665-681. [PMID: 31799621 PMCID: PMC6954413 DOI: 10.1093/nar/gkz1127] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022] Open
Abstract
Sirtuins 1 and 2 (SIRT1/2) are two NAD-dependent deacetylases with major roles in inflammation. In addition to deacetylating histones and other proteins, SIRT1/2-mediated regulation is coupled with other epigenetic enzymes. Here, we investigate the links between SIRT1/2 activity and DNA methylation in macrophage differentiation due to their relevance in myeloid cells. SIRT1/2 display drastic upregulation during macrophage differentiation and their inhibition impacts the expression of many inflammation-related genes. In this context, SIRT1/2 inhibition abrogates DNA methylation gains, but does not affect demethylation. Inhibition of hypermethylation occurs at many inflammatory loci, which results in more drastic upregulation of their expression upon macrophage polarization following bacterial lipopolysaccharide (LPS) challenge. SIRT1/2-mediated gains of methylation concur with decreases in activating histone marks, and their inhibition revert these histone marks to resemble an open chromatin. Remarkably, specific inhibition of DNA methyltransferases is sufficient to upregulate inflammatory genes that are maintained in a silent state by SIRT1/2. Both SIRT1 and SIRT2 directly interact with DNMT3B, and their binding to proinflammatory genes is lost upon exposure to LPS or through pharmacological inhibition of their activity. In all, we describe a novel role for SIRT1/2 to restrict premature activation of proinflammatory genes.
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Affiliation(s)
- Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Garcia-Gomez
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Octavio Morante-Palacios
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sevgi Özkaramehmet
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Evelien Van Dijck
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alejandro Vaquero
- Chromatin Biology Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
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18
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Lorente-Sorolla C, Garcia-Gomez A, Català-Moll F, Toledano V, Ciudad L, Avendaño-Ortiz J, Maroun-Eid C, Martín-Quirós A, Martínez-Gallo M, Ruiz-Sanmartín A, Del Campo ÁG, Ferrer-Roca R, Ruiz-Rodriguez JC, Álvarez-Errico D, López-Collazo E, Ballestar E. Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis. Genome Med 2019; 11:66. [PMID: 31665078 PMCID: PMC6820973 DOI: 10.1186/s13073-019-0674-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [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: 07/18/2019] [Accepted: 10/07/2019] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Sepsis, a life-threatening organ dysfunction caused by a dysregulated systemic immune response to infection, associates with reduced responsiveness to subsequent infections. How such tolerance is acquired is not well understood but is known to involve epigenetic and transcriptional dysregulation. METHODS Bead arrays were used to compare global DNA methylation changes in patients with sepsis, non-infectious systemic inflammatory response syndrome, and healthy controls. Bioinformatic analyses were performed to dissect functional reprogramming and signaling pathways related to the acquisition of these specific DNA methylation alterations. Finally, in vitro experiments using human monocytes were performed to test the induction of similar DNA methylation reprogramming. RESULTS Here, we focused on DNA methylation changes associated with sepsis, given their potential role in stabilizing altered phenotypes. Tolerized monocytes from patients with sepsis display changes in their DNA methylomes with respect to those from healthy controls, affecting critical monocyte-related genes. DNA methylation profiles correlate with IL-10 and IL-6 levels, significantly increased in monocytes in sepsis, as well as with the Sequential Organ Failure Assessment score; the observed changes associate with TFs and pathways downstream to toll-like receptors and inflammatory cytokines. In fact, in vitro stimulation of toll-like receptors in monocytes results in similar gains and losses of methylation together with the acquisition of tolerance. CONCLUSION We have identified a DNA methylation signature associated with sepsis that is downstream to the response of monocytes to inflammatory signals associated with the acquisition of a tolerized phenotype and organic dysfunction.
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Affiliation(s)
- Clara Lorente-Sorolla
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Antonio Garcia-Gomez
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Víctor Toledano
- Innate Immunity Group, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain.,Emergency Department, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - José Avendaño-Ortiz
- Innate Immunity Group, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain.,Emergency Department, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain
| | - Charbel Maroun-Eid
- Innate Immunity Group, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain
| | | | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group Vall d'Hebron Research Institute (VHIR), 08035, Barcelona, Spain
| | - Adolfo Ruiz-Sanmartín
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Álvaro García Del Campo
- Cardiac Post-Surgery Unit (UPCC), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Ricard Ferrer-Roca
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Damiana Álvarez-Errico
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain
| | - Eduardo López-Collazo
- Innate Immunity Group, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain.,Tumor Immunology Lab, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain.,Center for Biomedical Research Network, CIBEres, Madrid, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain. .,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
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19
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Rodríguez-Ubreva J, de la Calle-Fabregat C, Li T, Ciudad L, Ballestar ML, Català-Moll F, Morante-Palacios O, Garcia-Gomez A, Celis R, Humby F, Nerviani A, Martin J, Pitzalis C, Cañete JD, Ballestar E. Inflammatory cytokines shape a changing DNA methylome in monocytes mirroring disease activity in rheumatoid arthritis. Ann Rheum Dis 2019; 78:1505-1516. [DOI: 10.1136/annrheumdis-2019-215355] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 01/16/2023]
Abstract
ObjectiveRheumatoid arthritis (RA) is a chronic systemic autoimmune disease that mainly targets joints. Monocytes and macrophages are critical in RA pathogenesis and contribute to inflammatory lesions. These extremely plastic cells respond to extracellular signals which cause epigenomic changes that define their pathogenic phenotype. Here, we interrogated how DNA methylation alterations in RA monocytes are determined by extracellular signals.MethodsHigh-throughput DNA methylation analyses of patients with RA and controls and in vitro cytokine stimulation were used to investigate the underlying mechanisms behind DNA methylation alterations in RA as well as their relationship with clinical parameters, including RA disease activity.ResultsThe DNA methylomes of peripheral blood monocytes displayed significant changes and increased variability in patients with RA with respect to healthy controls. Changes in the monocyte methylome correlate with DAS28, in which high-activity patients are divergent from healthy controls in contrast to remission patients whose methylome is virtually identical to healthy controls. Indeed, the notion of a changing monocyte methylome is supported after comparing the profiles of same individuals at different stages of activity. We show how these changes are mediated by an increase in disease activity-associated cytokines, such as tumour necrosis factor alpha and interferons, as they recapitulate the DNA methylation changes observed in patients in vitro.ConclusionWe demonstrate a direct link between RA disease activity and the monocyte methylome through the action of inflammation-associated cytokines. Finally, we have obtained a DNA methylation-based mathematical formula that predicts inflammation-mediated disease activity for RA and other chronic immune-mediated inflammatory diseases.
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de la Rica L, García-Gómez A, Comet NR, Rodríguez-Ubreva J, Ciudad L, Vento-Tormo R, Company C, Álvarez-Errico D, García M, Gómez-Vaquero C, Ballestar E. NF-κB-direct activation of microRNAs with repressive effects on monocyte-specific genes is critical for osteoclast differentiation. Genome Biol 2015; 16:2. [PMID: 25601191 PMCID: PMC4290566 DOI: 10.1186/s13059-014-0561-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/04/2014] [Indexed: 12/12/2022] Open
Abstract
Background Monocyte-to-osteoclast conversion is a unique terminal differentiation process that is exacerbated in rheumatoid arthritis and bone metastasis. The mechanisms implicated in upregulating osteoclast-specific genes involve transcription factors, epigenetic regulators and microRNAs (miRNAs). It is less well known how downregulation of osteoclast-inappropriate genes is achieved. Results In this study, analysis of miRNA expression changes in osteoclast differentiation from human primary monocytes revealed the rapid upregulation of two miRNA clusters, miR-212/132 and miR-99b/let-7e/125a. We demonstrate that they negatively target monocyte-specific and immunomodulatory genes like TNFAIP3, IGF1R and IL15. Depletion of these miRNAs inhibits osteoclast differentiation and upregulates their targets. These miRNAs are also upregulated in other inflammatory monocytic differentiation processes. Most importantly, we demonstrate for the first time the direct involvement of Nuclear Factor kappa B (NF-κB) in the regulation of these miRNAs, as well as with their targets, whereby NF-κB p65 binds the promoters of these two miRNA clusters and NF-κB inhibition or depletion results in impaired upregulation of their expression. Conclusions Our results reveal the direct involvement of NF-κB in shutting down certain monocyte-specific genes, including some anti-inflammatory activities, through a miRNA-dependent mechanism for proper osteoclast differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0561-5) contains supplementary material, which is available to authorized users.
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Hernando H, Islam ABMMK, Rodríguez-Ubreva J, Forné I, Ciudad L, Imhof A, Shannon-Lowe C, Ballestar E. Epstein-Barr virus-mediated transformation of B cells induces global chromatin changes independent to the acquisition of proliferation. Nucleic Acids Res 2013; 42:249-63. [PMID: 24097438 PMCID: PMC3874198 DOI: 10.1093/nar/gkt886] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Epstein–Barr virus (EBV) infects and transforms human primary B cells inducing indefinite proliferation. To investigate the potential participation of chromatin mechanisms during the EBV-mediated transformation of resting B cells we performed an analysis of global changes in histone modifications. We observed a remarkable decrease and redistribution of heterochromatin marks including H4K20me3, H3K27me3 and H3K9me3. Loss of H4K20me3 and H3K9me3 occurred at constitutive heterochromatin repeats. For H3K27me3 and H3K9me3, comparison of ChIP-seq data revealed a decrease in these marks in thousands of genes, including clusters of HOX and ZNF genes, respectively. Moreover, DNase-seq data comparison between resting and EBV-transformed B cells revealed increased endonuclease accessibility in thousands of genomic sites. We observed that both loss of H3K27me3 and increased accessibility are associated with transcriptional activation. These changes only occurred in B cells transformed with EBV and not in those stimulated to proliferate with CD40L/IL-4, despite their similarities in the cell pathways involved and proliferation rates. In fact, B cells infected with EBNA-2 deficient EBV, which have much lower proliferation rates, displayed similar decreases for heterochromatic histone marks. Our study describes a novel phenomenon related to transformation of B cells, and highlights its independence of the pure acquisition of proliferation.
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Affiliation(s)
- Henar Hernando
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avda. Gran Via 199-203, 08908 L'Hospitalet de Llobregat, Barcelona, Spain, Department of Experimental and Health Sciences, Barcelona Biomedical Research Park, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh, Center for Integrated Protein Science and Adolf-Butenandt Institute, Ludwig Maximilians University of Munich, 80336 Munich, Germany and CR-UK Institute for Cancer Studies, University of Birmingham, Birmingham B15 2TT, UK
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Gutierrez-Cosío S, de la Rica L, Ballestar E, Santamaría C, Sánchez-Abarca LI, Caballero-Velazquez T, Blanco B, Calderón C, Herrero-Sánchez C, Carrancio S, Ciudad L, Cañizo C, San Miguel JF, Pérez-Simón JA. Epigenetic regulation of PRAME in acute myeloid leukemia is different compared to CD34+ cells from healthy donors: effect of 5-AZA treatment. Leuk Res 2012; 36:895-9. [PMID: 22503131 DOI: 10.1016/j.leukres.2012.02.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 02/21/2012] [Accepted: 02/27/2012] [Indexed: 12/20/2022]
Abstract
PRAME is a tumor associated antigen (TAA) of particular interest since it is widely expressed by lymphoid and myeloid malignancies. Several studies have associated high PRAME RNA levels with good prognosis in acute myeloid leukemia (AML). PRAME expression is regulated at the epigenetic level. For this reason inhibitors of DNA methylation, such as 5-azacytidine, can modulate the expression of this TAAs. In the current study we analyzed the effect of 5-azaC on the expression of PRAME in blasts versus CD34+ cells from healthy donors in an attempt to increase its expression, thus inducing a potential target for therapeutic strategies.
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Affiliation(s)
- S Gutierrez-Cosío
- Hematology Unit, Hospital Universitario de Salamanca, Salamanca, Spain
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Ballestar E, Javierre BM, de la Rica L, Gómez-Cabrero D, Tegnér J, Gomez-Vaquero C, Narvaez J, Hernando H, Rodriguez VC, Vento R, Ciudad L, Rodriguez-Ubreva J. Epigenetic alterations in autoimmune disease. Lab Invest 2011. [PMCID: PMC3242220 DOI: 10.1186/1479-5876-9-s2-i3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rodríguez-Ubreva J, Ciudad L, Gómez-Cabrero D, Parra M, Bussmann LH, di Tullio A, Kallin EM, Tegnér J, Graf T, Ballestar E. Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes. Nucleic Acids Res 2011; 40:1954-68. [PMID: 22086955 PMCID: PMC3299990 DOI: 10.1093/nar/gkr1015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transcription factor-induced lineage reprogramming or transdifferentiation experiments are essential for understanding the plasticity of differentiated cells. These experiments helped to define the specific role of transcription factors in conferring cell identity and played a key role in the development of the regenerative medicine field. We here investigated the acquisition of DNA methylation changes during C/EBPα-induced pre-B cell to macrophage transdifferentiation. Unexpectedly, cell lineage conversion occurred without significant changes in DNA methylation not only in key B cell- and macrophage-specific genes but also throughout the entire set of genes differentially methylated between the two parental cell types. In contrast, active and repressive histone modification marks changed according to the expression levels of these genes. We also demonstrated that C/EBPα and RNA Pol II are associated with the methylated promoters of macrophage-specific genes in reprogrammed macrophages without inducing methylation changes. Our findings not only provide insights about the extent and hierarchy of epigenetic events in pre-B cell to macrophage transdifferentiation but also show an important difference to reprogramming towards pluripotency where promoter DNA demethylation plays a pivotal role.
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Affiliation(s)
- Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08907 L'Hospitalet de Llobregat, Barcelona, Spain
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25
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Javierre BM, Rodriguez-Ubreva J, Al-Shahrour F, Corominas M, Graña O, Ciudad L, Agirre X, Pisano DG, Valencia A, Roman-Gomez J, Calasanz MJ, Prosper F, Esteller M, Gonzalez-Sarmiento R, Ballestar E. Long-range epigenetic silencing associates with deregulation of Ikaros targets in colorectal cancer cells. Mol Cancer Res 2011; 9:1139-51. [PMID: 21737484 DOI: 10.1158/1541-7786.mcr-10-0515] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Transcription factors are common targets of epigenetic inactivation in human cancer. Promoter hypermethylation and subsequent silencing of transcription factors can lead to further deregulation of their targets. In this study, we explored the potential epigenetic deregulation in cancer of Ikaros family genes, which code for essential transcription factors in cell differentiation and exhibit genetic defects in hematologic neoplasias. Unexpectedly, our analysis revealed that Ikaros undergoes very specific promoter hypermethylation in colorectal cancer, including in all the cell lines studied and around 64% of primary colorectal adenocarcinomas, with increasing proportions in advanced Duke's stages. Ikaros hypermethylation occurred in the context of a novel long-range epigenetic silencing (LRES) region. Reintroduction of Ikaros in colorectal cancer cells, ChIP-chip analysis, and validation in primary samples led us to identify a number of direct targets that are possibly related with colorectal cancer progression. Our results not only provide the first evidence that LRES can have functional specific effects in cancer but also identify several deregulated Ikaros targets that may contribute to progression in colorectal adenocarcinoma.
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Affiliation(s)
- Biola M Javierre
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, Barcelona, Spain
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Clynen E, Ciudad L, Bellés X, Piulachs MD. Conservation of fruitless' role as master regulator of male courtship behaviour from cockroaches to flies. Dev Genes Evol 2011; 221:43-8. [PMID: 21340608 DOI: 10.1007/s00427-011-0352-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 01/31/2011] [Indexed: 11/29/2022]
Abstract
In Drosophila melanogaster, male courtship behaviour is regulated by the fruitless gene. In D. melanogaster, fruitless encodes a set of putative transcription factors that are sex-specifically spliced. Male-specific variants are necessary and sufficient to elicit male courtship behaviour. Fruitless sequences have been reported in other insect species, but there are no data available on their functional role. In the present work, we cloned and sequenced fruitless in males of the German cockroach, Blattella germanica, and we studied its expression in male brain and testes. B. germanica fruitless encodes a 350-amino acid protein with BTB and Zinc finger domains typical of fruitless sequences. Upon RNAi-mediated knockdown of fruitless in B. germanica, males no longer exhibit courtship behaviour, thus implying that fruitless is necessary for male sexual behaviour in our cockroach model. This suggests that the role of fruitless as master regulator of male sexual behaviour has been conserved along insect evolution, at least from cockroaches to flies.
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Affiliation(s)
- Elke Clynen
- Institute of Evolutionary Biology (CSIC-UPF), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
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Abstract
During vitellogenesis, one of the most tightly regulated processes in oviparous reproduction, vitellogenins are incorporated into the oocyte through vitellogenin receptor (VgR)-mediated endocytosis. In this paper, we report the cloning of the VgR cDNA from Blattella germanica, as well as the first functional analysis of VgR following an RNA interference (RNAi) approach. We characterized the VgR, VgR mRNA and protein expression patterns in pre-adult and adult stages of this cockroach, as well as VgR immunolocalization in ovarioles, belonging to the panoistic type. We then specifically disrupted VgR gene function using RNAi techniques. Knockdown of VgR expression led to a phenotype characterized by low yolk content in the ovary and high vitellogenin concentration in the haemolymph. This phenotype is equivalent to that of the yolkless mutant of Drosophila melanogaster, which have the yl (VgR) gene disrupted. The results additionally open the perspective that development genes can be functionally analyzed via systemic RNAi in this basal species.
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Affiliation(s)
- Laura Ciudad
- Department of Physiology and Molecular Biodiversity. Institute of Molecular Biology of Barcelona, Barcelona, Spain
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