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Franco Acevedo A, Mack JJ, Valenzuela NM. The transcriptional repressor BCL6 regulates CXCR3 chemokine and HLA II expression in endothelial cells. Am J Transplant 2024:S1600-6135(24)00449-0. [PMID: 39074669 DOI: 10.1016/j.ajt.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/08/2024] [Accepted: 07/23/2024] [Indexed: 07/31/2024]
Abstract
IFNγ induces an endothelial pro-immunogenic phenotype through the JAK/STAT1 pathway, which can shape the activation of alloreactive leukocytes in transplant rejection. In immune cells, the DNA binding protein BCL6 controls transcription of inflammatory genes. This study tested if BCL6 modulates IFNγ-induced gene expression in endothelial cells (EC). In vitro, BCL6 was IFNγ-inducible in primary human endothelium, along with CXCR3 chemokines and HLA. BCL6 was also increased in human cardiac transplants during acute rejection, as were HLA II and CXCL9. Knockdown of BCL6 augmented, while overexpression and BTB domain inhibitors (BCL6-BTBi) suppressed, HLA II and CXCR3 chemokine expression but not HLA I. Further, BCL6 had a greater effect on HLA-DR and DP, but was less involved in regulating HLA-DQ expression. The effect correlated with BCL6 binding motifs in or near affected genes. The BCL6 DNA recognition sequence was highly similar to that of STAT1, and BTBi reduced STAT1's transcriptional activity in vitro. Our results show for the first time that BCL6 selectively controls IFNγ-induced endothelial gene expression, advancing our understanding of the endogenous mechanisms regulating donor immunogenicity.
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Affiliation(s)
- Adriana Franco Acevedo
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, USA
| | - Julia J Mack
- Department of Cardiology, University of California, Los Angeles, USA
| | - Nicole M Valenzuela
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, USA.
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2
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Baba T, Koyama A, Uotani R, Miyake H, Inata K, Sasaki SI, Shimizu Y, Inoue Y, Adachi K, Nanba E, Miyazaki D. Association of IL-4 with pachychoroid neovasculopathy. Sci Rep 2023; 13:1152. [PMID: 36670145 PMCID: PMC9860019 DOI: 10.1038/s41598-023-28108-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
The purpose of this study was to identify the inflammatory cytokines that were associated with pachychoroid neovasculopathy (PNV). Seventy-five eyes of 75 patients with PNV, 145 eyes of 145 patients with neovascular age-related macular degeneration without pachyvessels, and 150 eyes of 150 normal subjects were examined for the levels of intraocular cytokines. In eyes with PNV, the levels of IL-1α, IL-1β, IL-2, IL-4, IL-10, and VEGF were significantly higher than that of the controls. Logistic regression analysis showed that the highest association with the pachyvessels was found for IL-4, IL-2, and IL-1α. In eyes with PNV, the levels of IL-4, IL-2, IL-5, IL-13, IL-1α, and IL-1β were significantly higher in eyes with both increased choroidal thickness and choroidal vessel diameter. The strongest correlation with the choroidal thickness and vessel diameter was observed for IL-4. In PNV eyes with polypoidal lesions, the levels of IL-4, IL-17, and TNFβ were significantly correlated with the number of polypoidal lesions. Of these cytokines, IL-4 was especially associated with the thickness of the choroidal vessels and the formation of polypoidal lesions. We conclude that IL-4 is most likely involved in establishing the clinical characteristics of PNV and polypoidal vascular remodeling.
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Affiliation(s)
- Takashi Baba
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan.
| | - Ayumi Koyama
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Ryu Uotani
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Hitomi Miyake
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Kodai Inata
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Shin-Ichi Sasaki
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Yumiko Shimizu
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Yoshitsugu Inoue
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Kaori Adachi
- Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, Yonago, Tottori, Japan
| | - Eiji Nanba
- Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, Yonago, Tottori, Japan
- Otani Hospital, Tsuyama, Okayama, Japan
| | - Dai Miyazaki
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
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3
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Zaazouee MS, Alwarraqi AG, Mohammed YA, Badheeb MA, Farhat AM, Eleyan M, Morad A, Zeid MAA, Mohamed AS, AbuEl-Enien H, Abdelalim A, Elsnhory AB, Hrizat YSM, Altahir NT, Atef D, Elshanbary AA, Alsharif KF, Alzahrani KJ, Algahtani M, Theyab A, Hawsawi YM, Aldarmahi AA, Abdel-Daim MM. Dupilumab efficacy and safety in patients with moderate to severe asthma: A systematic review and meta-analysis. Front Pharmacol 2022; 13:992731. [PMID: 36263132 PMCID: PMC9574251 DOI: 10.3389/fphar.2022.992731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
Background: Dupilumab is a human monoclonal antibody directed against the alpha subunit of the interleukin-4 receptor and inhibits the signaling of IL-4 and IL-13. It is approved for treating asthma and other type-2 inflammatory diseases. There is a conflict in the literature regarding the safety and efficacy of dupilumab. Thus, we aimed to assess the safety and efficacy of dupilumab in patients with moderate to severe asthma. Methods: Six databases (PubMed, Embase, Scopus, Web of Science, Cochrane library, and clinicaltrials.gov registry) were searched until January 2022. We included randomized controlled trials that compared dupilumab with the placebo in moderate to severe asthma patients. We extracted the data at 12 and 24 weeks and analyzed them using review manager 5.4. Findings: Thirteen trials were included. Dupilumab significantly improved the forced expiratory volume in 1 s, asthma control questionnaire score, the fraction of exhaled nitric oxide level, and immunoglobulin E level at 12 and 24 weeks (p < 0.05). However, it was associated with increased blood eosinophils at 12 and 24 weeks. Dupilumab was generally a safe agent for asthmatic patients. It showed no significant difference compared with the placebo regarding most adverse events. Conclusion: Dupilumab improves pulmonary function and reduces local and systemic inflammatory markers with minimal adverse events in patients with moderate to severe asthma.
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Affiliation(s)
- Mohamed Sayed Zaazouee
- Faculty of Medicine, Al‐Azhar University, Assiut, Egypt
- *Correspondence: Mohamed Sayed Zaazouee, , orcid.org/0000-0003-0904-9153
| | | | | | | | | | - Mohammed Eleyan
- Department of Laboratory Medical Sciences, Alaqsa University, Gaza, Palestine
- Faculty of Medicine, Al-Azhar University, Gaza, Palestine
| | - Afnan Morad
- Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Marwa Abdel-Aziz Zeid
- Clinical Pharmacist, Pediatrics Department, Ministry of Health, Qalyubia, Egypt
- Faculty of Pharmacy, October 6 University, Giza, Egypt
| | - Aya Shaban Mohamed
- Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Hazem AbuEl-Enien
- Faculty of Pharmacy and Drug Manufacturing, Pharos University, Alexandria, Egypt
| | | | | | | | | | - Doaa Atef
- Department of Emergency Medicine, Assiut University, Assiut, Egypt
| | | | - Khalaf F. Alsharif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mohammad Algahtani
- Department of Laboratory and Blood Bank, Security Forces Hospital, Mecca, Saudi Arabia
| | - Abdulrahman Theyab
- Department of Laboratory and Blood Bank, Security Forces Hospital, Mecca, Saudi Arabia
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
| | - Yousef M. Hawsawi
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Ahmed A. Aldarmahi
- Basic Science Department, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
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4
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Sofia C, Simonetti J, Boccabella C, Bonini M. When one plus one means more than two: the blockade of both IL-4 and IL-13 inflammatory pathways with dupilumab in a case of severe refractory T2-high asthma. BMJ Case Rep 2022; 15:e244503. [PMID: 35039340 PMCID: PMC8767963 DOI: 10.1136/bcr-2021-244503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2021] [Indexed: 11/04/2022] Open
Abstract
Novel approach of asthma includes personalised therapy involving specific immune pathways. We describe here a case of T2-high asthma in a 66-year-old woman treated with maximal inhaled therapy and inappropriate usage of oral corticosteroids showing poor symptoms control. Both anti-IgE and (omalizumab) and anti-interleukin (IL)-5 (mepolizumab) monoclonal antibodies treatments were prescribed without significant benefit. Add-on subcutaneous dupilumab, a monoclonal antibody directed against the IL-4 receptor subunit alpha, inhibiting signalling from both IL-4 and IL-13, proved to be an effective and safe medication to obtain rapid asthma control. Considering the previous lack of response to both anti-IgE and anti-eosinophilic strategies, we hypothesise that dupilumab upstream activity could exert different and more relevant effects than the simple inhibition of the two single downstream pathways. The current case highlights the need for a deeper analysis of biomolecular interactions in the framework of different asthma endotypes, to identify peculiar profiles associated with specific treatment responses.
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Affiliation(s)
- Carmelo Sofia
- Department of Cardiovascular and Thoracic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Lazio, Italy
| | - Jacopo Simonetti
- Department of Cardiovascular and Thoracic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Lazio, Italy
| | - Cristina Boccabella
- Department of Cardiovascular and Thoracic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Lazio, Italy
| | - Matteo Bonini
- Department of Cardiovascular and Thoracic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Lazio, Italy
- National Heart and Lung Institute (NHLI), Imperial College London, London, UK
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5
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Bacharier LB, Maspero JF, Katelaris CH, Fiocchi AG, Gagnon R, de Mir I, Jain N, Sher LD, Mao X, Liu D, Zhang Y, Khan AH, Kapoor U, Khokhar FA, Rowe PJ, Deniz Y, Ruddy M, Laws E, Patel N, Weinreich DM, Yancopoulos GD, Amin N, Mannent LP, Lederer DJ, Hardin M. Dupilumab in Children with Uncontrolled Moderate-to-Severe Asthma. N Engl J Med 2021; 385:2230-2240. [PMID: 34879449 DOI: 10.1056/nejmoa2106567] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Children with moderate-to-severe asthma continue to have disease complications despite the receipt of standard-of-care therapy. The monoclonal antibody dupilumab has been approved for the treatment of adults and adolescents with asthma as well as with other type 2 inflammatory diseases. METHODS In this 52-week phase 3, randomized, double-blind, placebo-controlled trial, we assigned 408 children between the ages of 6 and 11 years who had uncontrolled moderate-to-severe asthma to receive a subcutaneous injection of dupilumab (at a dose of 100 mg for those weighing ≤30 kg and 200 mg for those weighing >30 kg) or matched placebo every 2 weeks. All the children continued to receive a stable dose of standard background therapy. The primary end point was the annualized rate of severe asthma exacerbations. Secondary end points included the change from baseline in the percentage of predicted prebronchodilator forced expiratory volume in 1 second (ppFEV1) at week 12 and in the score on the Asthma Control Questionnaire 7 Interviewer-Administered (ACQ-7-IA) at week 24. End points were evaluated in the two primary efficacy populations who had either a type 2 inflammatory asthma phenotype (≥150 blood eosinophils per cubic millimeter or a fraction of exhaled nitric oxide of ≥20 ppb at baseline) or a blood eosinophil count of at least 300 cells per cubic millimeter at baseline. RESULTS In patients with the type 2 inflammatory phenotype, the annualized rate of severe asthma exacerbations was 0.31 (95% confidence interval [CI], 0.22 to 0.42) with dupilumab and 0.75 (95% CI, 0.54 to 1.03) with placebo (relative risk reduction in the dupilumab group, 59.3%; 95% CI, 39.5 to 72.6; P<0.001). The mean (±SE) change from baseline in the ppFEV1 was 10.5±1.0 percentage points with dupilumab and 5.3±1.4 percentage points with placebo (mean difference, 5.2 percentage points; 95% CI, 2.1 to 8.3; P<0.001). Dupilumab also resulted in significantly better asthma control than placebo (P<0.001). Similar results were observed in the patients with an eosinophil count of at least 300 cells per cubic millimeter at baseline. The incidence of serious adverse events was similar in the two groups. CONCLUSIONS Among children with uncontrolled moderate-to-severe asthma, those who received add-on dupilumab had fewer asthma exacerbations and better lung function and asthma control than those who received placebo. (Funded by Sanofi and Regeneron Pharmaceuticals; Liberty Asthma VOYAGE ClinicalTrials.gov number, NCT02948959.).
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Affiliation(s)
- Leonard B Bacharier
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Jorge F Maspero
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Constance H Katelaris
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Alessandro G Fiocchi
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Remi Gagnon
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Ines de Mir
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Neal Jain
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Lawrence D Sher
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Xuezhou Mao
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Dongfang Liu
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Yi Zhang
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Asif H Khan
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Upender Kapoor
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Faisal A Khokhar
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Paul J Rowe
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Yamo Deniz
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Marcella Ruddy
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Elizabeth Laws
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Naimish Patel
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - David M Weinreich
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - George D Yancopoulos
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Nikhil Amin
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Leda P Mannent
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - David J Lederer
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
| | - Megan Hardin
- From Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville (L.B.B.); Fundación CIDEA, Buenos Aires (J.F.M.); Campbelltown Hospital, Campbelltown, NSW, and Western Sydney University, Sydney (C.H.K.) - both in Australia; Bambino Gesù Children's Hospital IRCCS, Rome (A.G.F.); Clinique Spécialisée en Allergie de la Capitale, Quebec, QC, Canada (R.G.); Hospital Vall d'Hebron, Barcelona (I.M.); Arizona Allergy and Immunology Research, Gilbert (N.J.); Peninsula Research Associates, Rolling Hills Estates, CA (L.D.S.); Sanofi, Bridgewater, NJ (X.M., U.K., P.J.R., E.L.); Sanofi, Beijing (D.L.); Regeneron Pharmaceuticals, Tarrytown, NY (Y.Z., F.A.K., Y.D., M.R., D.M.W., G.D.Y., N.A., D.J.L.); Sanofi, Chilly-Mazarin, France (A.H.K., L.P.M.); and Sanofi Genzyme, Cambridge, MA (N.P., M.H.)
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6
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Pandey N, Omkar Chandra, Mishra S, Kumar V. Improving Chromatin-Interaction Prediction Using Single-Cell Open-Chromatin Profiles and Making Insight Into the Cis-Regulatory Landscape of the Human Brain. Front Genet 2021; 12:738194. [PMID: 34691152 PMCID: PMC8533004 DOI: 10.3389/fgene.2021.738194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Single-cell open-chromatin profiles have the potential to reveal the pattern of chromatin-interaction in a cell type. However, currently available cis-regulatory network prediction methods using single-cell open-chromatin profiles focus more on local chromatin interactions despite the fact that long-range interactions among genomic sites play a significant role in gene regulation. Here, we propose a method that predicts both short and long-range interactions among genomic sites using single-cell open chromatin profiles. Our method, termed as single-cell epigenome based chromatin-interaction analysis (scEChIA) exploits signal imputation and refined L1 regularization. For a few single-cell open-chromatin profiles, scEChIA outperformed other tools even in terms of accuracy of prediction. Using scEChIA, we predicted almost 0.7 million interactions among genomic sites across seven cell types in the human brain. Further analysis revealed cell type for connection between genes and expression quantitative trait locus (eQTL) in the human brain and making insight about target genes of human-accelerated-elements and disease-associated mutations. Our analysis enabled by scEChIA also hints about the possible action of a few transcription factors (TFs), especially through long-range interaction in brain endothelial cells.
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Affiliation(s)
- Neetesh Pandey
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Omkar Chandra
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Shreya Mishra
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Vibhor Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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7
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Higashijima Y, Matsui Y, Shimamura T, Nakaki R, Nagai N, Tsutsumi S, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Ruan X, Li G, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Ruan Y, Glass CK, Kanki Y. Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells. EMBO J 2020; 39:e103949. [PMID: 32125007 DOI: 10.15252/embj.2019103949] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022] Open
Abstract
Histone H3 lysine-9 di-methylation (H3K9me2) and lysine-27 tri-methylation (H3K27me3) are linked to repression of gene expression, but the functions of repressive histone methylation dynamics during inflammatory responses remain enigmatic. Here, we report that lysine demethylases 7A (KDM7A) and 6A (UTX) play crucial roles in tumor necrosis factor (TNF)-α signaling in endothelial cells (ECs), where they are regulated by a novel TNF-α-responsive microRNA, miR-3679-5p. TNF-α rapidly induces co-occupancy of KDM7A and UTX at nuclear factor kappa-B (NF-κB)-associated elements in human ECs. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and are both required for activation of NF-κB-dependent inflammatory genes. Chromosome conformation capture-based methods furthermore uncover increased interactions between TNF-α-induced super enhancers at NF-κB-relevant loci, coinciding with KDM7A and UTX recruitments. Simultaneous pharmacological inhibition of KDM7A and UTX significantly reduces leukocyte adhesion in mice, establishing the biological and potential translational relevance of this mechanism. Collectively, these findings suggest that rapid erasure of repressive histone marks by KDM7A and UTX is essential for NF-κB-dependent regulation of genes that control inflammatory responses of ECs.
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Affiliation(s)
- Yoshiki Higashijima
- Department of Bioinformational Pharmacology, Tokyo Medical and Dental University, Tokyo, Japan.,Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Yusuke Matsui
- Division of Biomedical and Health Informatics, Graduate school of medicine, Nagoya university, Nagoya, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Nao Nagai
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Shuichi Tsutsumi
- Division of Genome Sciences, RCAST, The University of Tokyo, Tokyo, Japan
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany.,Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mizuko Osaka
- Department of Nutrition in Cardiovascular Disease, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Life Sciences and Bioethics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masayuki Yoshida
- Department of Life Sciences and Bioethics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryo Watanabe
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akashi Taguchi
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Mai Miura
- Isotope Science Center, The University of Tokyo, Tokyo, Japan.,Laboratory for Systems Biology and Medicine, RCAST, The University of Tokyo, Tokyo, Japan
| | - Xiaoan Ruan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Guoliang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Tsuyoshi Inoue
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsushi Furukawa
- Department of Bioinformational Pharmacology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Aburatani
- Division of Genome Sciences, RCAST, The University of Tokyo, Tokyo, Japan
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Yijun Ruan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
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8
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Nakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, Senbonmatsu T, Homma Y, Nishimura S, Mitsuyama T, Aburatani H, Kimura H, Shirahige K. Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells. Epigenetics Chromatin 2019; 12:77. [PMID: 31856914 PMCID: PMC6921469 DOI: 10.1186/s13072-019-0319-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/03/2019] [Indexed: 01/19/2023] Open
Abstract
Background Endothelial cells (ECs) make up the innermost layer throughout the entire vasculature. Their phenotypes and physiological functions are initially regulated by developmental signals and extracellular stimuli. The underlying molecular mechanisms responsible for the diverse phenotypes of ECs from different organs are not well understood. Results To characterize the transcriptomic and epigenomic landscape in the vascular system, we cataloged gene expression and active histone marks in nine types of human ECs (generating 148 genome-wide datasets) and carried out a comprehensive analysis with chromatin interaction data. We developed a robust procedure for comparative epigenome analysis that circumvents variations at the level of the individual and technical noise derived from sample preparation under various conditions. Through this approach, we identified 3765 EC-specific enhancers, some of which were associated with disease-associated genetic variations. We also identified various candidate marker genes for each EC type. We found that the nine EC types can be divided into two subgroups, corresponding to those with upper-body origins and lower-body origins, based on their epigenomic landscape. Epigenomic variations were highly correlated with gene expression patterns, but also provided unique information. Most of the deferentially expressed genes and enhancers were cooperatively enriched in more than one EC type, suggesting that the distinct combinations of multiple genes play key roles in the diverse phenotypes across EC types. Notably, many homeobox genes were differentially expressed across EC types, and their expression was correlated with the relative position of each organ in the body. This reflects the developmental origins of ECs and their roles in angiogenesis, vasculogenesis and wound healing. Conclusions This comprehensive analysis of epigenome characterization of EC types reveals diverse transcriptional regulation across human vascular systems. These datasets provide a valuable resource for understanding the vascular system and associated diseases.
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Affiliation(s)
- Ryuichiro Nakato
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Youichiro Wada
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan. .,Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Ryo Nakaki
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Genta Nagae
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.,Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Yuki Katou
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Natsu Nakajima
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Hiroshi Fukuhara
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Atsushi Iguchi
- Department of Cardiovascular Surgery, Saitama Medical University International Medical Center, Saitama, 350-1298, Japan
| | - Takahide Kohro
- Department of Clinical Informatics, Jichi Medical University School of Medicine, Shimotsuke, 329-0498, Japan
| | - Yasuharu Kanki
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.,Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yutaka Saito
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.,Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Mika Kobayashi
- Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan
| | | | - Naoki Osato
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.,Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Kenji Tatsuno
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Asuka Kamio
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Yoko Hayashi-Takanaka
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hiromi Wada
- Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan.,Brain Attack Center, Ohta Memorial Hospital, Fukuyama, 720-0825, Japan
| | - Shinzo Ohta
- Brain Attack Center, Ohta Memorial Hospital, Fukuyama, 720-0825, Japan
| | - Masanori Aikawa
- The Center for Excellence in Vascular Biology and the Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division and Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hiroyuki Nakajima
- Department of Cardiovascular Surgery, Saitama Medical University International Medical Center, Saitama, 350-1298, Japan
| | - Masaki Nakamura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | | | | | - Tatsuo Kawakatsu
- Bio-Medical Department, Kurabo Industries Ltd., Neyagawa, Osaka, 572-0823, Japan
| | - Michiru Genno
- Bio-Medical Department, Kurabo Industries Ltd., Neyagawa, Osaka, 572-0823, Japan
| | - Hiroshi Yanase
- Bio-Medical Department, Kurabo Industries Ltd., Neyagawa, Osaka, 572-0823, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Takaaki Senbonmatsu
- Department of Cardiology, Saitama Medical University International Medical Center, Saitama, 350-1298, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Shigeyuki Nishimura
- Department of Cardiology, Saitama Medical University International Medical Center, Saitama, 350-1298, Japan
| | - Toutai Mitsuyama
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.,Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hiroyuki Aburatani
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.,Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Hiroshi Kimura
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan. .,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan. .,Laboratory of Functional Nuclear Imaging, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Katsuhiko Shirahige
- Japan Agency for Medical Research and Development (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan. .,Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
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9
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Rabe KF, Nair P, Brusselle G, Maspero JF, Castro M, Sher L, Zhu H, Hamilton JD, Swanson BN, Khan A, Chao J, Staudinger H, Pirozzi G, Antoni C, Amin N, Ruddy M, Akinlade B, Graham NMH, Stahl N, Yancopoulos GD, Teper A. Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma. N Engl J Med 2018; 378:2475-2485. [PMID: 29782224 DOI: 10.1056/nejmoa1804093] [Citation(s) in RCA: 710] [Impact Index Per Article: 118.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Dupilumab is a fully human anti-interleukin-4 receptor α monoclonal antibody that blocks both interleukin-4 and interleukin-13 signaling. Its effectiveness in reducing oral glucocorticoid use in patients with severe asthma while maintaining asthma control is unknown. METHODS We randomly assigned 210 patients with oral glucocorticoid-treated asthma to receive add-on dupilumab (at a dose of 300 mg) or placebo every 2 weeks for 24 weeks. After a glucocorticoid dose-adjustment period before randomization, glucocorticoid doses were adjusted in a downward trend from week 4 to week 20 and then maintained at a stable dose for 4 weeks. The primary end point was the percentage reduction in the glucocorticoid dose at week 24. Key secondary end points were the proportion of patients at week 24 with a reduction of at least 50% in the glucocorticoid dose and the proportion of patients with a reduction to a glucocorticoid dose of less than 5 mg per day. Severe exacerbation rates and the forced expiratory volume in 1 second (FEV1) before bronchodilator use were also assessed. RESULTS The percentage change in the glucocorticoid dose was -70.1% in the dupilumab group, as compared with -41.9% in the placebo group (P<0.001); 80% versus 50% of the patients had a dose reduction of at least 50%, 69% versus 33% had a dose reduction to less than 5 mg per day, and 48% versus 25% completely discontinued oral glucocorticoid use. Despite reductions in the glucocorticoid dose, in the overall population, dupilumab treatment resulted in a severe exacerbation rate that was 59% (95% confidence interval [CI], 37 to 74) lower than that in the placebo group and resulted in an FEV1 that was 0.22 liters (95% CI, 0.09 to 0.34) higher. Injection-site reactions were more common with dupilumab than with placebo (9% vs. 4%). Transient blood eosinophilia was observed in more patients in the dupilumab group than in the placebo group (14% vs. 1%). CONCLUSIONS In patients with glucocorticoid-dependent severe asthma, dupilumab treatment reduced oral glucocorticoid use while decreasing the rate of severe exacerbations and increasing the FEV1. Transient eosinophilia was observed in approximately 1 in 7 dupilumab-treated patients. (Funded by Sanofi and Regeneron Pharmaceuticals; LIBERTY ASTHMA VENTURE ClinicalTrials.gov number, NCT02528214 .).
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Affiliation(s)
- Klaus F Rabe
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Parameswaran Nair
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Guy Brusselle
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Jorge F Maspero
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Mario Castro
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Lawrence Sher
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Hongjie Zhu
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Jennifer D Hamilton
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Brian N Swanson
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Asif Khan
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Jingdong Chao
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Heribert Staudinger
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Gianluca Pirozzi
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Christian Antoni
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Nikhil Amin
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Marcella Ruddy
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Bolanle Akinlade
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Neil M H Graham
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Neil Stahl
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - George D Yancopoulos
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
| | - Ariel Teper
- From LungenClinic Grosshansdorf, Grosshansdorf, and Christian Albrechts University Kiel, Kiel - both in Germany (K.F.R.); McMaster University and St. Joseph's Healthcare, Hamilton, ON, Canada (P.N.); Ghent University Hospital, Ghent, Belgium (G.B.); Fundación CIDEA (Centro de Investigación de Enfermedades Alérgicas y Respiratorias), Buenos Aires (J.F.M.); Washington University School of Medicine, St. Louis (M.C.); Peninsula Research Associates, Rolling Hills Estates, CA (L.S.); Sanofi, Bridgewater, NJ (H.Z., B.N.S., H.S., G.P., C.A., A.T.); Regeneron Pharmaceuticals, Tarrytown, NY (J.D.H., J.C., N.A., M.R., B.A., N.M.H.G., N.S., G.D.Y.); and Sanofi, Chilly Mazarin, France (A.K.)
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10
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Zhao Y, Shi D, Cao K, Wu F, Zhu X, Wen S, You Q, Zhang K, Liu L, Zhou H. Fingolimod targets cerebral endothelial activation to block leukocyte recruitment in the central nervous system. J Leukoc Biol 2017; 103:107-118. [PMID: 29345065 DOI: 10.1002/jlb.3a0717-287r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/05/2017] [Indexed: 12/16/2022] Open
Abstract
Fingolimod (FTY720), an immunomodulator, is approved as an oral treatment for patients with relapsing forms of multiple sclerosis. Its effects are largely attributed to its mechanism of selectively retaining lymphocytes in the lymph nodes to reduce autoreactive T-cell recruitment in the CNS. In this study, we investigated the therapeutic effect of FTY720 on an animal model of CNS inflammation induced by intracerebral ventricle LPS injection. We found that FTY720 treatment significantly prevented LPS-induced neutrophil recruitment in the CNS by inhibiting leukocyte recruitment in cerebral microvessels. Furthermore, FTY720 also inhibited the expressions of adhesion molecules on the cerebral endothelium, but did not affect the expression levels of pro-inflammatory cytokines (TNF-α and IL-6) and chemokines (CXCL1 and CXCL2) in the CNS parenchyma. The inhibition of endothelial activation was accompanied by reduced phosphorylation of signaling molecules, including serine/threonine-specific protein kinase (Akt), STAT6, and nuclear factor-κB. This FTY720-attenuated inhibition of leukocyte recruitment and endothelial activation was reversed by blocking the functions of sphingosine kinase 2 or sphingosine-1-phosphate receptor 1. Our study demonstrated, for the first time, that FTY720 directly inhibits the phosphorylation of multiple signaling molecules in endothelial cells, thereby effectively blocking leukocyte recruitment in the CNS.
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Affiliation(s)
- Yawei Zhao
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Dongyan Shi
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Kelei Cao
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Fengjiao Wu
- Department of Immunology, Anhui Provincial Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Xingxing Zhu
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Shuang Wen
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Qiang You
- Department of Biotherapy, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Keqi Zhang
- Ningbo Yongxin Optics Co., Ltd, Ningbo, China
| | - Lixin Liu
- Department of Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Hong Zhou
- Department of Immunology, Nanjing Medical University, Nanjing, China
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11
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Ko YE, Yoon SY, Ly SY, Kim JH, Sohn KY, Kim JW. 1-palmitoyl-2-linoleoyl-3-acetyl-rac-glycerol (PLAG) reduces hepatic injury in concanavalin A-treated mice. J Cell Biochem 2017; 119:1392-1405. [PMID: 28749086 DOI: 10.1002/jcb.26299] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 07/18/2017] [Indexed: 11/10/2022]
Abstract
1-palmitoyl-2-linoleoyl-3-acetyl-rac-glycerol (PLAG), a chemically synthesized monoacetyldiaglyceride, is one of the constituents in Sika deer antlers and has been known traditionally as having immunomodulatory effects. However, the mechanism by which PLAG controls neutrophil migration, which evokes liver injury in the hepatitis animal model, remains largely unknown. This study was designed to evaluate the immunomodulatory effects of PLAG on cytokine secretion and neutrophil migration in vivo and in vitro. Concanavalin A (Con A) induced leukocyte infiltration in the liver and increased plasma cytokine levels. Pretreatment with PLAG reduced the levels of interleukin (IL)-4, IL-6, IL-10, and CXCL2, but maintained interferon (IFN)-γ levels and modulated neutrophil recruitment toward the liver. Furthermore, the mRNA and protein levels of IL-4 and CXCL2 in liver tissue were also decreased in the Con A-treated mice. Liver histology analyses showed that PLAG reduced Con A-induced hepatic necrosis, which was accompanied by leukocyte infiltration. The in vitro studies revealed that PLAG reduced IL-4 secretion in Con A stimulated T cell and blocked signal transducer and activator of transcription 6 (STAT6) Con A induced hepatocyte. PLAG attenuated IL-4 induced activation of atypical protein kinase C (PKC)/STAT6 in hepatocytes and inhibited neutrophil migration toward the liver tissue through suppression of IL-8/vascular cell adhesion molecule (VCAM) expression. These results suggest that PLAG could mitigate excess neutrophil migration into liver tissue and potentially have a therapeutic effect on immune-mediated liver injury.
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Affiliation(s)
- Young E Ko
- Cell Factory Research Center, Division of Systems Biology and Bioengineering, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.,Department of Food and Nutrition, Chungnam National University, Daejeon, Republic of Korea
| | - Sun Y Yoon
- Division of Global New Drug Development, ENZYCHEM Lifesciences, Daejeon, Korea
| | - Sun Y Ly
- Department of Food and Nutrition, Chungnam National University, Daejeon, Republic of Korea
| | - Joo H Kim
- Department of Pathology, EulJi University School of Medicine, Daejeon, Republic of Korea
| | - Ki Y Sohn
- Division of Global New Drug Development, ENZYCHEM Lifesciences, Daejeon, Korea
| | - Jae W Kim
- Cell Factory Research Center, Division of Systems Biology and Bioengineering, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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12
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Kanki Y, Nakaki R, Shimamura T, Matsunaga T, Yamamizu K, Katayama S, Suehiro JI, Osawa T, Aburatani H, Kodama T, Wada Y, Yamashita JK, Minami T. Dynamically and epigenetically coordinated GATA/ETS/SOX transcription factor expression is indispensable for endothelial cell differentiation. Nucleic Acids Res 2017; 45:4344-4358. [PMID: 28334937 PMCID: PMC5416769 DOI: 10.1093/nar/gkx159] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 02/25/2017] [Indexed: 12/29/2022] Open
Abstract
Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analysed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs. We determined that Gata2, Fli1, Sox7 and Sox18 are master regulators of EC that are induced following expression of the haemangioblast commitment pioneer factor, Etv2. These master regulator gene loci were repressed by H3K27me3 throughout the mesoderm period but rapidly transitioned to histone modification switching from H3K27me3 to H3K4me3 after treatment with vascular endothelial growth factor. SiRNA knockdown experiments indicated that these regulators are indispensable not only for proper EC differentiation but also for blocking the commitment to other closely aligned lineages. Collectively, our detailed epigenetic analysis may provide an advanced model for understanding temporal regulation of chromatin signatures and resulting gene expression profiles during EC commitment. These studies may inform the future development of methods to stimulate the vascular endothelium for regenerative medicine.
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Affiliation(s)
- Yasuharu Kanki
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan.,Division of Vascular Biology, RCAST, The University of Tokyo, Tokyo 153-8904, Japan.,Division of Systems Biology, RCAST, The University of Tokyo, Tokyo 153-8904, Japan
| | - Ryo Nakaki
- Division of Genome Sciences, RCAST, The University of Tokyo, Tokyo 153-8904, Japan
| | - Teppei Shimamura
- Department of Systems Biology, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan
| | - Taichi Matsunaga
- Department of Stem Cell Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Deparment of Cell Growth and Differentiation, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Kohei Yamamizu
- Department of Stem Cell Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Deparment of Cell Growth and Differentiation, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Shiori Katayama
- Department of Stem Cell Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Deparment of Cell Growth and Differentiation, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Jun-Ichi Suehiro
- Division of Vascular Biology, RCAST, The University of Tokyo, Tokyo 153-8904, Japan.,Department of Pharmacology and Toxicology, Kyorin University School of Medicine, Tokyo 181-8611, Japan
| | - Tsuyoshi Osawa
- Division of Vascular Biology, RCAST, The University of Tokyo, Tokyo 153-8904, Japan.,Division of Systems Biology, RCAST, The University of Tokyo, Tokyo 153-8904, Japan
| | - Hiroyuki Aburatani
- Division of Genome Sciences, RCAST, The University of Tokyo, Tokyo 153-8904, Japan
| | - Tatsuhiko Kodama
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan.,Division of Systems Biology, RCAST, The University of Tokyo, Tokyo 153-8904, Japan
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan
| | - Jun K Yamashita
- Department of Stem Cell Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Deparment of Cell Growth and Differentiation, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Takashi Minami
- Division of Vascular Biology, RCAST, The University of Tokyo, Tokyo 153-8904, Japan.,Division of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, Japan
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13
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Xu S. Transcriptome Profiling in Systems Vascular Medicine. Front Pharmacol 2017; 8:563. [PMID: 28970795 PMCID: PMC5609594 DOI: 10.3389/fphar.2017.00563] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/08/2017] [Indexed: 02/06/2023] Open
Abstract
In the post-genomic, big data era, our understanding of vascular diseases has been deepened by multiple state-of-the-art “–omics” approaches, including genomics, epigenomics, transcriptomics, proteomics, lipidomics and metabolomics. Genome-wide transcriptomic profiling, such as gene microarray and RNA-sequencing, emerges as powerful research tools in systems medicine and revolutionizes transcriptomic analysis of the pathological mechanisms and therapeutics of vascular diseases. In this article, I will highlight the workflow of transcriptomic profiling, outline basic bioinformatics analysis, and summarize recent gene profiling studies performed in vascular cells as well as in human and mice diseased samples. Further mining of these public repository datasets will shed new light on our understanding of the cellular basis of vascular diseases and offer novel potential targets for therapeutic intervention.
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Affiliation(s)
- Suowen Xu
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, RochesterNY, United States
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14
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Fu M, Fu S, Ni S, Zou L, Liu Y, Hong T. Anti-inflammatory effect of epigallocatechin gallate in a mouse model of ovalbumin-induced allergic rhinitis. Int Immunopharmacol 2017; 49:102-108. [DOI: 10.1016/j.intimp.2017.05.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/09/2017] [Accepted: 05/23/2017] [Indexed: 12/14/2022]
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15
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Day DS, Zhang B, Stevens SM, Ferrari F, Larschan EN, Park PJ, Pu WT. Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types. Genome Biol 2016; 17:120. [PMID: 27259512 PMCID: PMC4893286 DOI: 10.1186/s13059-016-0984-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/12/2016] [Indexed: 01/02/2023] Open
Abstract
Background For many genes, RNA polymerase II stably pauses before transitioning to productive elongation. Although polymerase II pausing has been shown to be a mechanism for regulating transcriptional activation, the extent to which it is involved in control of mammalian gene expression and its relationship to chromatin structure remain poorly understood. Results Here, we analyze 85 RNA polymerase II chromatin immunoprecipitation (ChIP)-sequencing experiments from 35 different murine and human samples, as well as related genome-wide datasets, to gain new insights into the relationship between polymerase II pausing and gene regulation. Across cell and tissue types, paused genes (pausing index > 2) comprise approximately 60 % of expressed genes and are repeatedly associated with specific biological functions. Paused genes also have lower cell-to-cell expression variability. Increased pausing has a non-linear effect on gene expression levels, with moderately paused genes being expressed more highly than other paused genes. The highest gene expression levels are often achieved through a novel pause-release mechanism driven by high polymerase II initiation. In three datasets examining the impact of extracellular signals, genes responsive to stimulus have slightly lower pausing index on average than non-responsive genes, and rapid gene activation is linked to conditional pause-release. Both chromatin structure and local sequence composition near the transcription start site influence pausing, with divergent features between mammals and Drosophila. Most notably, in mammals pausing is positively correlated with histone H2A.Z occupancy at promoters. Conclusions Our results provide new insights into the contribution of RNA polymerase II pausing in mammalian gene regulation and chromatin structure. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0984-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel S Day
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.,Harvard/MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA
| | - Bing Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA. .,Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Sean M Stevens
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Francesco Ferrari
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Erica N Larschan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA. .,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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16
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Olenscki Gilli SC, Pericole FV, Benites BD, Sippert EÂ, Castilho LM, Addas-Carvalho M, Olalla Saad ST. Cytokine polymorphisms in sickle cell disease and the relationship with cytokine expression. Exp Hematol 2016; 44:583-9. [PMID: 27026283 DOI: 10.1016/j.exphem.2016.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 03/02/2016] [Accepted: 03/20/2016] [Indexed: 01/21/2023]
Abstract
Sickle cell disease is a chronic inflammatory condition characterized by elevated levels of inflammatory cytokines, which may be regulated by genetic polymorphisms and could be associated with diverse disease presentations and alloimmunization. The aim of this study was to evaluate Treg and Th17 cell frequencies, cytokine gene polymorphisms, and their association with cytokine expression profile in patients with sickle cell disease. For that purpose, we evaluated the IL intron 3 variable number tandem repeat (VNTR, genotypes 1.1, 1.2, 2.2, and 2.3), IL4-T590C>T, IL6-174G>C, TNFα-308G>A, IL10-819T>C, IL10-592A>C, and IL10-1082A>G polymorphisms and their correlation with TGFβ, IL4, IL6, and IL10 gene expression in sickle cell patients. We observed a significant decrease in Treg frequency together with a substantial increase in Th17 response in patients with sickle cell disease compared with healthy controls (p < 0.001 and p = 0.014, respectively). There was also a higher prevalence of the IL4-590T/T genotype in patients with sickle cell disease than in Afro-Brazilian descendent controls (p < 0.001) and higher expression of IL4 in patients with the 1.1 genotype of IL4 intron 3 VNTR (p = 0.06). Significantly greater gene expression of TGFβ, IL6, and IL10 was observed in sickle cell patients when compared with controls (p = 0.01, 0.03, and <0.001, respectively). Moreover, higher levels of interleukin-6 and -10 were observed in the group of alloimmunized patients. These new data bring insights into the deregulation in the immune system affecting sickle cell patients and must be further investigated in larger cohorts to better characterize individual variations in immune responses and new markers for disease morbidity.
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Affiliation(s)
- Simone Cristina Olenscki Gilli
- Hematology and Hemotherapy Center, University of Campinas, HEMOCENTRO- UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, São Paulo, Brazil
| | - Fernando Vieira Pericole
- Hematology and Hemotherapy Center, University of Campinas, HEMOCENTRO- UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, São Paulo, Brazil
| | - Bruno Deltreggia Benites
- Hematology and Hemotherapy Center, University of Campinas, HEMOCENTRO- UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, São Paulo, Brazil.
| | - Emilia Ângela Sippert
- Hematology and Hemotherapy Center, University of Campinas, HEMOCENTRO- UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, São Paulo, Brazil
| | - Lilian Maria Castilho
- Hematology and Hemotherapy Center, University of Campinas, HEMOCENTRO- UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, São Paulo, Brazil
| | - Marcelo Addas-Carvalho
- Hematology and Hemotherapy Center, University of Campinas, HEMOCENTRO- UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, São Paulo, Brazil
| | - Sara Teresinha Olalla Saad
- Hematology and Hemotherapy Center, University of Campinas, HEMOCENTRO- UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, São Paulo, Brazil
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17
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Li CP, Yang BH. A hypothesis-effect of T cell epitope fusion peptide specific immunotherapy on signal transduction. Int J Clin Exp Med 2015; 8:19632-19634. [PMID: 26770626 PMCID: PMC4694526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/28/2015] [Indexed: 06/05/2023]
Abstract
Asthma is a chronic nonspecific inflammatory disease of the airway primarily mediated by different inflammatory cells, including mast cells, eosinophils and T cells. We hereby specially focused on a signal pathway for Janus kinase-signal transducer and activators of transduction (JAK-STATs), which has been the interest of study in asthma since it more likely regulates cellular proliferation and differentiation, and consequently modulates immune system. In our consideration, knowledge on this signal pathway may provide an avenue for rational options in treatment of asthma on control of immune response basis.
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Affiliation(s)
- Chao-Pin Li
- Department of Medical Parasitology, Wannan Medical College Wuhu 241002, Anhui, P. R. China
| | - Bang-He Yang
- Department of Medical Parasitology, Wannan Medical College Wuhu 241002, Anhui, P. R. China
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18
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Cheng LE, Sullivan BM, Retana LE, Allen CDC, Liang HE, Locksley RM. IgE-activated basophils regulate eosinophil tissue entry by modulating endothelial function. ACTA ACUST UNITED AC 2015; 212:513-24. [PMID: 25779634 PMCID: PMC4387286 DOI: 10.1084/jem.20141671] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 02/11/2015] [Indexed: 01/22/2023]
Abstract
Basophils orchestrate eosinophil recruitment during IgE-dependent dermatitis by interacting with inflamed endothelium and producing IL-4. IL-4 in turn induces endothelial VCAM-1 expression, which is required for subsequent eosinophil accumulation. Vertebrate immunity has evolved a modular architecture in response to perturbations. Allergic inflammation represents such a module, with signature features of antigen-specific IgE and tissue eosinophilia, although the cellular and molecular circuitry coupling these responses remains unclear. Here, we use genetic and imaging approaches in models of IgE-dependent eosinophilic dermatitis to demonstrate a requisite role for basophils. After antigenic inflammation, basophils initiate transmigration like other granulocytes but, upon activation via their high-affinity IgE receptor, alter their migratory kinetics to persist at the endothelium. Prolonged basophil–endothelial interactions, in part dependent on activation of focal adhesion kinases, promote delivery of basophil-derived IL-4 to the endothelium and subsequent induction of endothelial vascular cell adhesion molecule-1 (VCAM-1), which is required for eosinophil accumulation. Thus, basophils are gatekeepers that link adaptive immunity with innate effector programs by altering access to tissue sites by activation-induced interactions with the endothelium.
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Affiliation(s)
- Laurence E Cheng
- Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143 Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143
| | - Brandon M Sullivan
- Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143
| | - Lizett E Retana
- Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143
| | - Christopher D C Allen
- Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143 Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143 Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143
| | - Hong-Erh Liang
- Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143
| | - Richard M Locksley
- Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143 Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143 Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143 Department of Pediatrics, Department of Medicine, Department of Anatomy, Sandler Asthma Basic Research Center, Cardiovascular Research Institute, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143
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19
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Sharma R, Colarusso P, Zhang H, Stevens KM, Patel KD. FRNK negatively regulates IL-4-mediated inflammation. J Cell Sci 2014; 128:695-705. [PMID: 25501808 DOI: 10.1242/jcs.156588] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Focal adhesion kinase (FAK)-related nonkinase (PTK2 isoform 6 in humans, hereafter referred to as FRNK) is a cytoskeletal regulatory protein that has recently been shown to dampen lung fibrosis, yet its role in inflammation is unknown. Here, we show for the first time that expression of FRNK negatively regulates IL-4-mediated inflammation in a human model of eosinophil recruitment. Mechanistically, FRNK blocks eosinophil accumulation, firm adhesion and transmigration by preventing transcription and protein expression of VCAM-1 and CCL26. IL-4 activates STAT6 to induce VCAM-1 and CCL26 transcription. We now show that IL-4 also increases GATA6 to induce VCAM-1 expression. FRNK blocks IL-4-induced GATA6 transcription but has little effect on GATA6 protein expression and no effect on STAT6 activation. FRNK can block FAK or Pyk2 signaling and we, thus, downregulated these proteins using siRNA to determine whether signaling from either protein is involved in the regulation of VCAM-1 and CCL26. Knockdown of FAK, Pyk2 or both had no effect on VCAM-1 or CCL26 expression, which suggests that FRNK acts independently of FAK and Pyk2 signaling. Finally, we found that IL-4 induces the late expression of endogenous FRNK. In summary, FRNK represents a novel mechanism to negatively regulate IL-4-mediated inflammation.
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Affiliation(s)
- Ritu Sharma
- Department of Physiology and Pharmacology, University of Calgary; Calgary, AB T2N 4N1, Canada
| | - Pina Colarusso
- Department of Physiology and Pharmacology, University of Calgary; Calgary, AB T2N 4N1, Canada The Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Hong Zhang
- Department of Physiology and Pharmacology, University of Calgary; Calgary, AB T2N 4N1, Canada
| | - Katarzyna M Stevens
- Department of Physiology and Pharmacology, University of Calgary; Calgary, AB T2N 4N1, Canada The Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Kamala D Patel
- Department of Physiology and Pharmacology, University of Calgary; Calgary, AB T2N 4N1, Canada The Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
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20
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Langhanki J, Rudolph K, Erkel G, Opatz T. Total synthesis and biological evaluation of the natural product (-)-cyclonerodiol, a new inhibitor of IL-4 signaling. Org Biomol Chem 2014; 12:9707-15. [PMID: 25350537 DOI: 10.1039/c4ob02021a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In a screening program of natural compounds from fungi, the known cyclopentanoid sesquiterpene (-)-cyclonerodiol was identified as a specific inhibitor of the IL-4 induced STAT6 signaling pathway (IC50 = 9.7 μM) which is required for the differentiation of naive CD4 T cells to T helper type 2 (Th2) lymphocytes. As many allergic conditions, including allergic asthma and atopic diseases, are driven by an excessive Th2 response, STAT6 is a promising target for the development of new therapeutics. The compound was synthesized in six steps from (-)-linalool using an epoxide radical cyclization as the key step.
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Affiliation(s)
- Jens Langhanki
- Institute of Organic Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany.
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21
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Toellner KM. Cognate interactions: extrafollicular IL-4 drives germinal-center reactions, a new role for an old cytokine. Eur J Immunol 2014; 44:1917-20. [PMID: 24965782 PMCID: PMC4140537 DOI: 10.1002/eji.201444825] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/02/2014] [Accepted: 06/24/2014] [Indexed: 01/26/2023]
Abstract
Over the past 25 years it has become clear that B and T lymphocytes go through a range of interactions and migratory events when B cells differentiate to become high-affinity, antibody-secreting cells. This B-cell differentiation is associated with multiple sequential cognate interactions. In this issue of the European Journal of Immunology, Turqueti-Neves et al. [Eur. J. Immunol. 2014. 44: 2130–2138] show that IL-4, a cytokine well known as a regulator of Ig class switch recombination, has another as-yet-unappreciated role. The authors show that IL-4 produced by T-helper cells outside germinal centers has a major effect on the early stages of germinal-center B-cell differentiation. This Commentary will summarize their findings and relate them to what we know on the sequence of cognate interactions and migratory events B cells undergo during T-dependent immune responses.
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Affiliation(s)
- Kai-Michael Toellner
- School of Immunity and Infection, Medical School IBR, University of Birmingham, Birmingham, United Kingdom
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22
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Suehiro JI, Kanki Y, Makihara C, Schadler K, Miura M, Manabe Y, Aburatani H, Kodama T, Minami T. Genome-wide approaches reveal functional vascular endothelial growth factor (VEGF)-inducible nuclear factor of activated T cells (NFAT) c1 binding to angiogenesis-related genes in the endothelium. J Biol Chem 2014; 289:29044-59. [PMID: 25157100 DOI: 10.1074/jbc.m114.555235] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
VEGF is a key regulator of endothelial cell migration, proliferation, and inflammation, which leads to activation of several signaling cascades, including the calcineurin-nuclear factor of activated T cells (NFAT) pathway. NFAT is not only important for immune responses but also for cardiovascular development and the pathogenesis of Down syndrome. By using Down syndrome model mice and clinical patient samples, we showed recently that the VEGF-calcineurin-NFAT signaling axis regulates tumor angiogenesis and tumor metastasis. However, the connection between genome-wide views of NFAT-mediated gene regulation and downstream gene function in the endothelium has not been studied extensively. Here we performed comprehensive mapping of genome-wide NFATc1 binding in VEGF-stimulated primary cultured endothelial cells and elucidated the functional consequences of VEGF-NFATc1-mediated phenotypic changes. A comparison of the NFATc1 ChIP sequence profile and epigenetic histone marks revealed that predominant NFATc1-occupied peaks overlapped with promoter-associated histone marks. Moreover, we identified two novel NFATc1 regulated genes, CXCR7 and RND1. CXCR7 knockdown abrogated SDF-1- and VEGF-mediated cell migration and tube formation. siRNA treatment of RND1 impaired vascular barrier function, caused RhoA hyperactivation, and further stimulated VEGF-mediated vascular outgrowth from aortic rings. Taken together, these findings suggest that dynamic NFATc1 binding to target genes is critical for VEGF-mediated endothelial cell activation. CXCR7 and RND1 are NFATc1 target genes with multiple functions, including regulation of cell migration, tube formation, and barrier formation in endothelial cells.
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Affiliation(s)
| | - Yasuharu Kanki
- From the Division of Vascular Biology, Systems Biology, The Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904 Japan and
| | | | - Keri Schadler
- From the Division of Vascular Biology, the Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Mai Miura
- From the Division of Vascular Biology
| | | | | | - Tatsuhiko Kodama
- Systems Biology, The Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904 Japan and
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Shin JH, Xu L, Li RW, Gao Y, Bickhart D, Liu GE, Baldwin R, Li CJ. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Anim Genet 2014; 45 Suppl 1:40-50. [PMID: 24990294 DOI: 10.1111/age.12147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2014] [Indexed: 12/11/2022]
Abstract
This report presents a study utilizing next-generation sequencing technology, combined with chromatin immunoprecipitation (ChIP-seq) technology to analyze histone modification induced by butyrate and to construct a high-definition map of the epigenomic landscape with normal histone H3 and H4 and their variants in bovine cells at the whole-genome scale. A total of 10 variants of histone H3 and H4 modifications were mapped at the whole-genome scale (acetyl-H3K18-ChIP-seq, trimethy-H3K9, histone H4 ChIP-seq, acetyl-H4K5 ChIP-seq, acetyl-H4K12 ChIP-seq, acetyl-H4K16 ChIP-seq, histone H3 ChIP-seq, acetyl H3H9 ChIP-seq, acetyl H3K27 ChIP-seq and tetra-acetyl H4 ChIP-seq). Integrated experiential data and an analysis of histone and histone modification at a single base resolution across the entire genome are presented. We analyzed the enriched binding regions in the proximal promoter (within 5 kb upstream or at the 5'-untranslated region from the transcriptional start site (TSS)), and the exon, intron and intergenic regions (defined by regions 25 kb upstream and 10 kb downstream from the TSS). A de novo search for the binding motif of the 10 ChIP-seq datasets discovered numerous motifs from each of the ChIP-seq datasets. These consensus sequences indicated that histone modification at different locations changes the histone H3 and H4 binding preferences. Nevertheless, a high degree of conservation in histone binding also was presented in these motifs. This first extensive epigenomic landscape mapping in bovine cells offers a new framework and a great resource for testing the role of epigenomes in cell function and transcriptomic regulation.
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Affiliation(s)
- J H Shin
- Lieber Institute for Brain Development, Johns Hopkins University, 855 North Wolfe Street, Suite 102, Baltimore, MD, 21205, USA
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Direct evidence for pitavastatin induced chromatin structure change in the KLF4 gene in endothelial cells. PLoS One 2014; 9:e96005. [PMID: 24797675 PMCID: PMC4010393 DOI: 10.1371/journal.pone.0096005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 04/02/2014] [Indexed: 01/11/2023] Open
Abstract
Statins exert atheroprotective effects through the induction of specific transcriptional factors in multiple organs. In endothelial cells, statin-dependent atheroprotective gene up-regulation is mediated by Kruppel-like factor (KLF) family transcription factors. To dissect the mechanism of gene regulation, we sought to determine molecular targets by performing microarray analyses of human umbilical vein endothelial cells (HUVECs) treated with pitavastatin, and KLF4 was determined to be the most highly induced gene. In addition, it was revealed that the atheroprotective genes induced with pitavastatin, such as nitric oxide synthase 3 (NOS3) and thrombomodulin (THBD), were suppressed by KLF4 knockdown. Myocyte enhancer factor-2 (MEF2) family activation is reported to be involved in pitavastatin-dependent KLF4 induction. We focused on MEF2C among the MEF2 family members and identified a novel functional MEF2C binding site 148 kb upstream of the KLF4 gene by chromatin immunoprecipitation along with deep sequencing (ChIP-seq) followed by luciferase assay. By applying whole genome and quantitative chromatin conformation analysis {chromatin interaction analysis with paired end tag sequencing (ChIA-PET), and real time chromosome conformation capture (3C) assay}, we observed that the MEF2C-bound enhancer and transcription start site (TSS) of KLF4 came into closer spatial proximity by pitavastatin treatment. 3D-Fluorescence in situ hybridization (FISH) imaging supported the conformational change in individual cells. Taken together, dynamic chromatin conformation change was shown to mediate pitavastatin-responsive gene induction in endothelial cells.
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Minami T. Genome- and epigenome-wide analysis of endothelial cell activation and inflammation. Inflamm Regen 2014. [DOI: 10.2492/inflammregen.34.094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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26
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Lazarski CA, Ford J, Katzman SD, Rosenberg AF, Fowell DJ. IL-4 attenuates Th1-associated chemokine expression and Th1 trafficking to inflamed tissues and limits pathogen clearance. PLoS One 2013; 8:e71949. [PMID: 23991011 PMCID: PMC3753298 DOI: 10.1371/journal.pone.0071949] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/09/2013] [Indexed: 12/21/2022] Open
Abstract
Interleukin 4 (IL-4) plays a central role in the orchestration of Type 2 immunity. During T cell activation in the lymph node, IL-4 promotes Th2 differentiation and inhibits Th1 generation. In the inflamed tissue, IL-4 signals promote innate and adaptive Type-2 immune recruitment and effector function, positively amplifying the local Th2 response. In this study, we identify an additional negative regulatory role for IL-4 in limiting the recruitment of Th1 cells to inflamed tissues. To test IL-4 effects on inflammation subsequent to Th2 differentiation, we transiently blocked IL-4 during ongoing dermal inflammation (using anti-IL-4 mAb) and analyzed changes in gene expression. Neutralization of IL-4 led to the upregulation of a number of genes linked to Th1 trafficking, including CXCR3 chemokines, CCL5 and CCR5 and an associated increase in IFNγ, Tbet and TNFα genes. These gene expression changes correlated with increased numbers of IFNγ-producing CD4+ T cells in the inflamed dermis. Moreover, using an adoptive transfer approach to directly test the role of IL-4 in T cell trafficking to the inflamed tissues, we found IL-4 neutralization led to an early increase in Th1 cell recruitment to the inflamed dermis. These data support a model whereby IL-4 dampens Th1-chemokines at the site of inflammation limiting Th1 recruitment. To determine biological significance, we infected mice with Leishmania major, as pathogen clearance is highly dependent on IFNγ-producing CD4+ T cells at the infection site. Short-term IL-4 blockade in established L. major infection led to a significant increase in the number of IFNγ-producing CD4+ T cells in the infected ear dermis, with no change in the draining LN. Increased lymphocyte influx into the infected tissue correlated with a significant decrease in parasite number. Thus, independent of IL-4's role in the generation of immune effectors, IL-4 attenuates lymphocyte recruitment to the inflamed/infected dermis and limits pathogen clearance.
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Affiliation(s)
- Christopher A. Lazarski
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Jill Ford
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Shoshana D. Katzman
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Alexander F. Rosenberg
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Deborah J. Fowell
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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Garcia-Bassets I, Wang D. Cistrome plasticity and mechanisms of cistrome reprogramming. Cell Cycle 2012; 11:3199-210. [PMID: 22895178 DOI: 10.4161/cc.21281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mammalian genomes contain thousands of cis-regulatory elements for each transcription factor (TF), but TFs only occupy a relatively small subset referred to as cistrome. Recent studies demonstrate that a TF cistrome might differ among different organisms, tissue types and individuals. In a cell, a TF cistrome might differ among different physiological states, pathological stages and between physiological and pathological conditions. It is, therefore, remarkable how highly plastic these binding profiles are, and how massively they can be reprogrammed in rapid response to intra/extracellular variations and during cell identity transitions and evolution. Biologically, cistrome reprogramming events tend to be followed by changes in transcriptional outputs, thus serving as transformative mechanisms to synchronically alter the biology of the cell. In this review, we discuss the molecular basis of cistrome plasticity and attempt to integrate the different mechanisms and biological conditions associated with cistrome reprogramming. Emerging data suggest that, when altered, these reprogramming events might be linked to tumor development and/or progression, which is a radical conceptual change in our mechanistic understanding of cancer and, potentially, other diseases.
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Affiliation(s)
- Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
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28
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Yae T, Tsuchihashi K, Ishimoto T, Motohara T, Yoshikawa M, Yoshida GJ, Wada T, Masuko T, Mogushi K, Tanaka H, Osawa T, Kanki Y, Minami T, Aburatani H, Ohmura M, Kubo A, Suematsu M, Takahashi K, Saya H, Nagano O. Alternative splicing of CD44 mRNA by ESRP1 enhances lung colonization of metastatic cancer cell. Nat Commun 2012; 3:883. [PMID: 22673910 DOI: 10.1038/ncomms1892] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 05/08/2012] [Indexed: 12/15/2022] Open
Abstract
In cancer metastasis, various environmental stressors attack the disseminating cells. The successful colonization of cancer cells in secondary sites therefore requires the ability of the cells to avoid the consequences of such exposure to the stressors. Here we show that orthotopic transplantation of a CD44 variant isoform-expressing (CD44v(+)) subpopulation of 4T1 breast cancer cells, but not that of a CD44v(-) subpopulation, in mice results in efficient lung metastasis accompanied by expansion of stem-like cancer cells. Such metastasis is dependent on the activity of the cystine transporter xCT, and the stability of this protein is controlled by CD44v. We find that epithelial splicing regulatory protein 1 regulates the expression of CD44v, and knockdown of epithelial splicing regulatory protein 1 in CD44v(+) cells results in an isoform switch from CD44v to CD44 standard (CD44s), leading to reduced cell surface expression of xCT and suppression of lung colonization. The epithelial splicing regulatory protein 1-CD44v-xCT axis is thus a potential therapeutic target for the prevention of metastasis.
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Affiliation(s)
- Toshifumi Yae
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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Dynamic change of chromatin conformation in response to hypoxia enhances the expression of GLUT3 (SLC2A3) by cooperative interaction of hypoxia-inducible factor 1 and KDM3A. Mol Cell Biol 2012; 32:3018-32. [PMID: 22645302 DOI: 10.1128/mcb.06643-11] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Hypoxia-inducible factor 1 (HIF1) is a master regulator of adaptive gene expression under hypoxia. However, a role for HIF1 in the epigenetic regulation remains unknown. Genome-wide analysis of HIF1 binding sites (chromatin immunoprecipitation [ChIP] with deep sequencing) of endothelial cells clarified that HIF1 mainly binds to the intergenic regions distal from transcriptional starting sites under both normoxia and hypoxia. Next, we examined the temporal profile of gene expression under hypoxic conditions by using DNA microarrays. We clarified that early hypoxia-responsive genes are functionally associated with glycolysis, including GLUT3 (SLC2A3). Acetylated lysine 27 of histone 3 covered the HIF1 binding sites, and HIF1 functioned as an enhancer of SLC2A3 by interaction with lysine (K)-specific demethylase 3A (KDM3A). Knockdown of HIF1α and KDM3A showed that glycolytic genes are regulated by both HIF1 and KDM3A and respond to hypoxia in a manner independent of cell type specificity. We elucidated that both the chromatin conformational structure and histone modification change under hypoxic conditions and enhance the expression of SLC2A3 based on the combined results of chromatin conformation capture (3C) and ChIP assays. KDM3A is recruited to the SLC2A3 locus in an HIF1-dependent manner and demethylates H3K9me2 so as to upregulate its expression. These findings provide novel insights into the interaction between HIF1 and KDM3A and also the epigenetic regulation of HIF1.
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Black SM, Benson BA, Idossa D, Vercellotti GM, Dalmasso AP. Protection of porcine endothelial cells against apoptosis with interleukin-4. Xenotransplantation 2012; 18:343-54. [PMID: 22168141 DOI: 10.1111/j.1399-3089.2011.00678.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Apoptosis is crucial for tissue development and homeostasis, and insufficient apoptosis is pivotal in cancer pathogenesis. Apoptosis may also be important in tissue injury and in this case, it is of interest to induce protection against apoptosis. In organ transplantation, apoptosis has been implicated in acute vascular rejection (AVR); in xenotransplantation, the inducers of apoptosis of relevance in AVR, such as tumor necrosis factor-α (TNF-α), also cause endothelial cell (EC) activation. We have previously shown that interleukin (IL)-4 and IL-13 induced protection in porcine ECs against activation and apoptosis triggered by TNF-α. Now we define signaling processes activated by IL-4 in porcine ECs and mechanisms required for IL-4-induced protection against apoptosis. METHODS Porcine aortic ECs were used as primary cultures or as virus-induced immortalized cells derived from galactosyl transferase-deficient (Gal(-/-) ) or wild-type pigs. ECs were stimulated with porcine IL-4, either extrinsically or transduced with recombinant adenovirus (adeno) IL-4, and analyzed using immunoblotting. Apoptosis was induced with TNF-α plus cycloheximide and assessed using neutral red uptake or flow cytometry. The role of various signaling proteins in IL-4-induced protection was established using pharmacologic inhibitors and siRNA downregulation of protein expression. RESULTS IL-4 induced similar degrees of phosphorylation of STAT6 in all 3 types of ECs, and STAT6 was phosphorylated through Jak3. IL-4 induced phosphorylation of Bad through Jak3. Stimulation of ECs with IL-4 caused protection of ECs against apoptosis with an absolute requirement of Jak3/STAT6 activation and major participation of mammalian target of rapamycin complex 2 (mTORC2), Akt, and extracellular signal-regulated kinase 1/2. IL-4 caused no increase in EC levels of protective proteins hemoxygenase-1, inhibitor of apoptosis protein, heat shock protein 70, Bcl-2, and Bcl-xL. ECs transduced with adenoIL-4 exhibited strong and durable protection from apoptosis. Gal(-/-) ECs were as susceptible to induction of protection with IL-4 as wild-type ECs. CONCLUSIONS IL-4 induces activation of Jak3/STAT6 and phosphorylation of Bad in porcine ECs, ultimately resulting in effective protection of the ECs from apoptosis. Delineation of downstream signals activated by IL-4 that are required for induction of protection suggests possible sites of intervention to design effective therapeutic agents. This is of interest because substances such as IL-4 have pleiotropic effects and cannot be used directly due to potential deleterious effects. Inducing resistance to apoptosis in porcine vascular endothelium may be important to facilitate xenograft survival and accommodation.
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Affiliation(s)
- Sylvester M Black
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
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Shin JH, Li RW, Gao Y, Baldwin R, Li CJ. Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells. Funct Integr Genomics 2012; 12:119-30. [PMID: 22249597 DOI: 10.1007/s10142-012-0263-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/29/2011] [Accepted: 01/02/2012] [Indexed: 12/18/2022]
Abstract
Butyrate-induced histone acetylation plays an important role in the regulation of gene expression. However, the regulation mechanisms of histone modification remain largely unclear. To comprehensively analyze histone modification induced by butyrate, we utilized chromatin immunoprecipitation (ChIP) technology combined with next-generation sequencing technology (ChIP-seq) to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3 and acetylated histone H3K9 and H3K27 on a large scale. To determine the location of histone H3, acetyl-H3K9, and acetyl-H3K27 binding sites within the bovine genome, we analyzed the H3-, acetyl-H3K9-, and acetyl-H3K27-enriched binding regions in the proximal promoter within 5 kb upstream, or at the 5' untranslated region (UTR) from the transcriptional start site (TSS), exon, intron, and intergenic regions (defined as regions 25 kb upstream or 10 kb downstream from the TSS). Our analysis indicated that the distribution of histone H3, acetyl-H3K9, and acetyl-H3K27 correlated with transcription activity induced by butyrate. Using the GADEM algorithm, several motifs were generated for each of the ChIP-seq datasets. A de novo search for H3, acetyl-H3K9, and acetyl-H3K27 binding motifs indicated that histone modification (acetylation) at various locations changes the histone H3 binding preferences. Our results reveal that butyrate-induced acetylation in H3K9 and H3K27 changes the sequence-based binding preference of histone H3 and underlies the potential mechanisms of gene expression regulation induced by butyrate.
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Affiliation(s)
- Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins University, 855 North Wolfe Street, Suite 102, Baltimore, MD 21205, USA
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