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Branch MC, Weber M, Li MY, Flora P, Ezhkova E. Overview of chromatin regulatory processes during surface ectodermal development and homeostasis. Dev Biol 2024; 515:30-45. [PMID: 38971398 DOI: 10.1016/j.ydbio.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/02/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The ectoderm is the outermost of the three germ layers of the early embryo that arise during gastrulation. Once the germ layers are established, the complex interplay of cellular proliferation, differentiation, and migration results in organogenesis. The ectoderm is the progenitor of both the surface ectoderm and the neural ectoderm. Notably, the surface ectoderm develops into the epidermis and its associated appendages, nails, external exocrine glands, olfactory epithelium, and the anterior pituitary. Specification, development, and homeostasis of these organs demand a tightly orchestrated gene expression program that is often dictated by epigenetic regulation. In this review, we discuss the recent discoveries that have highlighted the importance of chromatin regulatory mechanisms mediated by transcription factors, histone and DNA modifications that aid in the development of surface ectodermal organs and maintain their homeostasis post-development.
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Affiliation(s)
- Meagan C Branch
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madison Weber
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng-Yen Li
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pooja Flora
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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2
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Ren L, Chang YF, Jiang SH, Li XH, Cheng HP. DNA methylation modification in Idiopathic pulmonary fibrosis. Front Cell Dev Biol 2024; 12:1416325. [PMID: 38915445 PMCID: PMC11194555 DOI: 10.3389/fcell.2024.1416325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/22/2024] [Indexed: 06/26/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and irreversible interstitial lung disease with a prognosis worse than lung cancer. It is a fatal lung disease with largely unknown etiology and pathogenesis, and no effective therapeutic drugs render its treatment largely unsuccessful. With continuous in-depth research efforts, the epigenetic mechanisms in IPF pathogenesis have been further discovered and concerned. As a widely studied mechanism of epigenetic modification, DNA methylation is primarily facilitated by DNA methyltransferases (DNMTs), resulting in the addition of a methyl group to the fifth carbon position of the cytosine base, leading to the formation of 5-methylcytosine (5-mC). Dysregulation of DNA methylation is intricately associated with the advancement of respiratory disorders. Recently, the role of DNA methylation in IPF pathogenesis has also received considerable attention. DNA methylation patterns include methylation modification and demethylation modification and regulate a range of essential biological functions through gene expression regulation. The Ten-Eleven-Translocation (TET) family of DNA dioxygenases is crucial in facilitating active DNA demethylation through the enzymatic conversion of the modified genomic base 5-mC to 5-hydroxymethylcytosine (5-hmC). TET2, a member of TET proteins, is involved in lung inflammation, and its protein expression is downregulated in the lungs and alveolar epithelial type II cells of IPF patients. This review summarizes the current knowledge of pathologic features and DNA methylation mechanisms of pulmonary fibrosis, focusing on the critical roles of abnormal DNA methylation patterns, DNMTs, and TET proteins in impacting IPF pathogenesis. Researching DNA methylation will enchance comprehension of the fundamental mechanisms involved in IPF pathology and provide novel diagnostic biomarkers and therapeutic targets for pulmonary fibrosis based on the studies involving epigenetic mechanisms.
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Affiliation(s)
- Lu Ren
- Clinical Nursing Teaching and Research Section, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yan-Fen Chang
- Medicine School, Zhengzhou University of Industrial Technology, Zhengzhou, China
| | - Shi-He Jiang
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao-Hong Li
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hai-Peng Cheng
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
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3
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Miculinić A, Mrkić Kobal I, Kušan T, Turkalj M, Plavec D. Current Challenges in Pediatric Asthma. CHILDREN (BASEL, SWITZERLAND) 2024; 11:632. [PMID: 38929213 PMCID: PMC11201822 DOI: 10.3390/children11060632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
Asthma is a chronic lung disease characterized by reversible bronchoconstriction and inflammation of the bronchi. Its increasing prevalence in childhood as well as different triggers make asthma a challenging disease in several ways: defining its phenotype/endotype, the diagnostic approach (especially in younger children), therapeutic options, and systematic follow-up. Considering these problems, this review approaches the current status and limitations of guidelines used for asthma management in children. It also emphasizes the key points which could lead to a better understanding and the direction to take in future studies.
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Affiliation(s)
- Andrija Miculinić
- Children’s Hospital Srebrnjak, Srebrnjak 100, 10000 Zagreb, Croatia (M.T.)
| | - Iva Mrkić Kobal
- Clinic for Pediatric Medicine Helena, Ulica Kneza Branimira 71, 10000 Zagreb, Croatia;
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
| | - Tin Kušan
- Children’s Hospital Srebrnjak, Srebrnjak 100, 10000 Zagreb, Croatia (M.T.)
| | - Mirjana Turkalj
- Children’s Hospital Srebrnjak, Srebrnjak 100, 10000 Zagreb, Croatia (M.T.)
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
- Faculty of Medicine, Catholic University of Croatia, 10000 Zagreb, Croatia
| | - Davor Plavec
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
- Prima Nova, Healthcare Institution, Zagrebačka Cesta 132A, 10000 Zagreb, Croatia
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4
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Connett GJ. Asthma, classical conditioning, and the autonomic nervous system - a hypothesis for why children wheeze. Arch Dis Child 2024; 109:462-467. [PMID: 37648401 PMCID: PMC11103287 DOI: 10.1136/archdischild-2023-325441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
Paediatric asthma is an increasing global healthcare problem for which current treatments are not always effective. This review explores how abnormal triggering of the autonomic diving reflex might be important in explaining research findings and the real-world experience of asthma. It hypothesises that the way in which stress during pregnancy is associated with childhood asthma could be through effects on the developing nervous system. This results in increased parasympathetic responsiveness and specifically, excessive triggering of the diving reflex in response to wetting and cooling of the face and nose as occurs with upper airway infections and allergic rhinitis. In aquatic mammals the reflex importantly includes the contraction of airway smooth muscle to minimise lung volume and prevent nitrogen narcosis from diving at depth. Misfiring of this reflex in humans could result in the pathological airway narrowing that occurs in asthma. The diving reflex, and possibly also smooth muscle, is a vestigial remnant of our aquatic past. The hypothesis further suggests that classically conditioned reflex responses to neutral cues and contexts that were present at the same time as the stimuli that initially caused symptoms, become of themselves ongoing triggers of recurrent wheeze. Symptoms occurring in this way, irrespective of the presence of allergens and ongoing airway sensitisation, explain why allergen avoidance is poorly effective in alleviating wheeze and why asthma is made worse by stress. Interventions to suppress the diving reflex and to prevent reflex conditioned wheezing could result in more effective asthma management.
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Affiliation(s)
- Gary James Connett
- National Institute for Health Research, Southampton Biomedical Research Centre, Southampton Chldren's Hospital, Southampton, UK
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5
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Diaconu ID, Gheorman V, Grigorie GA, Gheonea C, Tenea-Cojan TS, Mahler B, Voropanov IA, Firoiu MC, Pîrvu AS, Popescu AB, Văruț R. A Comprehensive Look at the Development of Asthma in Children. CHILDREN (BASEL, SWITZERLAND) 2024; 11:581. [PMID: 38790577 PMCID: PMC11120211 DOI: 10.3390/children11050581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/01/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Asthma, a prevalent chronic respiratory condition affecting millions of children globally, presents a significant health challenge. This review critically examines the developmental pathways of asthma in children, focusing on genetic, environmental, and early-life determinants. Specifically, we explore the impact of prenatal and postnatal factors such as maternal smoking, nutrition, respiratory infections, and allergen exposure on asthma development. Our analysis highlights the intricate interplay of these influences and their contribution to childhood asthma. Moreover, we emphasize targeted strategies and interventions to mitigate its burden, including genetic counseling for at-risk families, environmental modifications to reduce triggers, and early-life immunomodulation. By delving into these preventive measures and interventions, our review aims to provide actionable insights for healthcare professionals in developing tailored strategies to address the complexities of childhood asthma. In summary, this article offers a detailed examination of asthma development in children, aiming to enhance understanding and inform efforts to reduce its burden through targeted interventions.
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Affiliation(s)
- Ileana Diana Diaconu
- Department of Pediatric Pneumology, University of Medicine and Pharmacy of Craiova, Petru Rareș 2 Str., 200349 Craiova, Romania;
| | - Veronica Gheorman
- Department of Medical Semiology, University of Medicine and Pharmacy of Craiova, Petru Rareș 2 Str., 200349 Craiova, Romania
| | - Gabriela Adriana Grigorie
- Department of Pneumology, University of Medicine and Pharmacy of Craiova, Petru Rareș 2 Str., 200349 Craiova, Romania;
| | - Cristian Gheonea
- Department of Pediatrics, University of Medicine and Pharmacy of Craiova, Petru Rareș 2 Str., 200349 Craiova, Romania;
| | - Tiberiu-Stefanita Tenea-Cojan
- Department of Surgery, University of Medicine and Pharmacy of Craiova, CFR Hospital of Craiova, Stirbei-Voda Str., 200374 Craiova, Romania;
| | - Beatrice Mahler
- Department of Pneumology, Faculty of Medicine “Carol Davila”, “Marius Nasta” Institute of Pneumoftiziology, 050159 Bucharest, Romania;
| | - Ion Alexandru Voropanov
- Department of Pediatric Pneumology, Carol Davila University of Medicine and Pharmacy, “Marius Nasta” Institute of Pneumoftiziology, 050159 Bucharest, Romania;
| | - Mihnea Cristian Firoiu
- Department of Urology, Fundeni Clinical Institute, Carol Davila University of Medicine and Pharmacy, Sos. Fundeni nr. 258, 022328 Bucharest, Romania;
| | - Andreea Silvia Pîrvu
- Department of Biochemistry, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Alexandru Bogdan Popescu
- Radiology Department, Targoviste County Emergency Hospital, Tudor Vladimirescu 48 Str., 130083 Targoviste, Romania;
| | - Renata Văruț
- Department of Pharmacology, University of Medicine and Pharmacy, Petru Rareş Street 2-4, 200349 Craiova, Romania;
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Varricchi G, Brightling CE, Grainge C, Lambrecht BN, Chanez P. Airway remodelling in asthma and the epithelium: on the edge of a new era. Eur Respir J 2024; 63:2301619. [PMID: 38609094 PMCID: PMC11024394 DOI: 10.1183/13993003.01619-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/15/2024] [Indexed: 04/14/2024]
Abstract
Asthma is a chronic, heterogeneous disease of the airways, often characterised by structural changes known collectively as airway remodelling. In response to environmental insults, including pathogens, allergens and pollutants, the epithelium can initiate remodelling via an inflammatory cascade involving a variety of mediators that have downstream effects on both structural and immune cells. These mediators include the epithelial cytokines thymic stromal lymphopoietin, interleukin (IL)-33 and IL-25, which facilitate airway remodelling through cross-talk between epithelial cells and fibroblasts, and between mast cells and airway smooth muscle cells, as well as through signalling with immune cells such as macrophages. The epithelium can also initiate airway remodelling independently of inflammation in response to the mechanical stress present during bronchoconstriction. Furthermore, genetic and epigenetic alterations to epithelial components are believed to influence remodelling. Here, we review recent advances in our understanding of the roles of the epithelium and epithelial cytokines in driving airway remodelling, facilitated by developments in genetic sequencing and imaging techniques. We also explore how new and existing therapeutics that target the epithelium and epithelial cytokines could modify airway remodelling.
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Affiliation(s)
- Gilda Varricchi
- Department of Translational Medical Sciences and Center for Basic and Clinical Immunology Research (CISI), School of Medicine, University of Naples Federico II, WAO Center of Excellence, Naples, Italy
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
- G. Varricchi and C.E. Brightling contributed equally
| | - Christopher E. Brightling
- Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
- G. Varricchi and C.E. Brightling contributed equally
| | - Christopher Grainge
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia
| | - Bart N. Lambrecht
- Center for Inflammation Research, Laboratory of Immunoregulation and Mucosal Immunology, VIB Center for Inflammation Research, Ghent, Belgium
| | - Pascal Chanez
- Department of Respiratory Diseases, Aix-Marseille University, Marseille, France
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7
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Zhou X, Sampath V, Nadeau KC. Effect of air pollution on asthma. Ann Allergy Asthma Immunol 2024; 132:426-432. [PMID: 38253122 PMCID: PMC10990824 DOI: 10.1016/j.anai.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
Asthma is a chronic inflammatory airway disease characterized by respiratory symptoms, variable airflow obstruction, bronchial hyperresponsiveness, and airway inflammation. Exposure to air pollution has been linked to an increased risk of asthma development and exacerbation. This review aims to comprehensively summarize recent data on the impact of air pollution on asthma development and exacerbation. Specifically, we reviewed the effects of air pollution on the pathogenic pathways of asthma, including type 2 and non-type 2 inflammatory responses, and airway epithelial barrier dysfunction. Air pollution promotes the release of epithelial cytokines, driving TH2 responses, and induces oxidative stress and the production of proinflammatory cytokines. The enhanced type 2 inflammation, furthered by air pollution-induced dysfunction of the airway epithelial barrier, may be associated with the exacerbation of asthma. Disruption of the TH17/regulatory T cell balance by air pollutants is also related to asthma exacerbation. As the effects of air pollution exposure may accumulate over time, with potentially stronger impacts in the development of asthma during certain sensitive life periods, we also reviewed the effects of air pollution on asthma across the lifespan. Future research is needed to better characterize the sensitive period contributing to the development of air pollution-induced asthma and to map air pollution-associated epigenetic biomarkers contributing to the epigenetic ages onto asthma-related genes.
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Affiliation(s)
- Xiaoying Zhou
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Vanitha Sampath
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Kari C Nadeau
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.
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8
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Abrar MNF, Jiang Y, Zhang H, Li L, Arshad H. Epigenetic Features in Newborns Associated with Preadolescence Lung Function and Asthma Acquisition during Adolescence. EPIGENOMES 2024; 8:12. [PMID: 38525738 PMCID: PMC10961756 DOI: 10.3390/epigenomes8020012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024] Open
Abstract
The association between newborn DNA methylation (DNAm) and asthma acquisition (AA) during adolescence has been suggested. Lung function (LF) has been shown to be associated with asthma risk and its severity. However, the role of LF in the associations between DNAm and AA is unclear, and it is also unknown whether the association between DNAm and AA is consistent with that between DNAm and LF. We address this question through assessing newborn epigenetic features of preadolescence LF and of AA during adolescence, along with their biological pathways and processes. Our study's primary medical significance lies in advancing the understanding of asthma's early life origins. By investigating epigenetic markers in newborns and their association with lung function in preadolescence, we aim to uncover potential early biomarkers of asthma risk. This could facilitate earlier detection and intervention strategies. Additionally, exploring biological pathways linking early lung function to later asthma development can offer insights into the disease's pathogenesis, potentially leading to novel therapeutic targets. METHODS The study was based on the Isle of Wight Birth cohort (IOWBC). Female subjects with DNAm data at birth and with no asthma at age 10 years were included (n = 249). The R package ttScreening was applied to identify CpGs potentially associated with AA from 10 to 18 years and with LF at age 10 (FEV1, FVC, and FEV1/FVC), respectively. Agreement in identified CpGs between AA and LF was examined, along with their biological pathways and processes via the R function gometh. We tested the findings in an independent cohort, the Avon Longitudinal Study of Parents and Children (ALSPAC), to examine overall replicability. RESULTS In IOWBC, 292 CpGs were detected with DNAm associated with AA and 1517 unique CpGs for LF (514 for FEV1, 436 for FVC, 408 for FEV1/FVC), with one overlapping CpG, cg23642632 (NCKAP1) between AA and LF. Among the IOWBC-identified CpGs, we further tested in ALSPAC and observed the highest agreement between the two cohorts in FVC with respect to the direction of association and statistical significance. Epigenetic enrichment analyses indicated non-specific connections in the biological pathways and processes between AA and LF. CONCLUSIONS The present study suggests that FEV1, FVC, and FEV1/FVC (as objective measures of LF) and AA (incidence of asthma) are likely to have their own specific epigenetic features and biological pathways at birth. More replications are desirable to fully understand the complexity between DNAm, lung function, and asthma acquisition.
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Affiliation(s)
- Mohammad Nahian Ferdous Abrar
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA; (M.N.F.A.); (Y.J.); (L.L.)
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA; (M.N.F.A.); (Y.J.); (L.L.)
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA; (M.N.F.A.); (Y.J.); (L.L.)
| | - Liang Li
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA; (M.N.F.A.); (Y.J.); (L.L.)
| | - Hasan Arshad
- David Hide Asthma and Allergy Research Centre, Isle of Wight P030 5TG, UK;
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton S017 1BJ, UK
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9
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Potaczek DP, Bazan-Socha S, Wypasek E, Wygrecka M, Garn H. Recent Developments in the Role of Histone Acetylation in Asthma. Int Arch Allergy Immunol 2024; 185:641-651. [PMID: 38522416 DOI: 10.1159/000536460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/22/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Epigenetic modifications are known to mediate both beneficial and unfavorable effects of environmental exposures on the development and clinical course of asthma. On the molecular level, epigenetic mechanisms participate in multiple aspects of the emerging and ongoing asthma pathology. SUMMARY Studies performed in the last several years expand our knowledge on the role of histone acetylation, a classical epigenetic mark, in the regulation of (patho)physiological processes of diverse cells playing a central role in asthma, including those belonging to the immune system (e.g., CD4+ T cells, macrophages) and lung structure (e.g., airway epithelial cells, pulmonary fibroblasts). Those studies demonstrate a number of specific histone acetylation-associated mechanisms and pathways underlying pathological processes characteristic for asthma, as well as report their modification modalities. KEY MESSAGES Dietary modulation of histone acetylation levels in the immune system might protect against the development of asthma and other allergies. Interfering with the enzymes controlling the histone acetylation status of structural lung and (local) immune cells might provide future therapeutic options for asthmatics. Despite some methodological obstacles, analysis of the histone acetylation levels might improve asthma diagnostics.
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Affiliation(s)
- Daniel P Potaczek
- Translational Inflammation Research Division and Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University of Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Marburg, Germany
- Center for Infection and Genomics of the Lung (CIGL), Member of the Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Bioscientia MVZ Labor Mittelhessen GmbH, Giessen, Germany
| | - Stanisława Bazan-Socha
- Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Ewa Wypasek
- Krakow Center for Medical Research and Technology, John Paul II Hospital, Krakow, Poland
- Faculty of Medicine and Health Sciences, Andrzej Frycz Modrzewski Krakow University, Krakow, Poland
| | - Małgorzata Wygrecka
- Center for Infection and Genomics of the Lung (CIGL), Member of the Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Institute of Lung Health, Member of the German Center for Lung Research (DZL), Giessen, Germany
- CSL Behring Innovation GmbH, Marburg, Germany
| | - Holger Garn
- Translational Inflammation Research Division and Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University of Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Marburg, Germany
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10
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Yang T, Wan R, Tu W, Avvaru SN, Gao P. Aryl hydrocarbon receptor: Linking environment to aging process in elderly patients with asthma. Chin Med J (Engl) 2024; 137:382-393. [PMID: 38238253 PMCID: PMC10876263 DOI: 10.1097/cm9.0000000000002960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Indexed: 02/12/2024] Open
Abstract
ABSTRACT Aging is a significant risk factor for various diseases, including asthma, and it often leads to poorer clinical outcomes, particularly in elderly individuals. It is recognized that age-related diseases are due to a time-dependent accumulation of cellular damage, resulting in a progressive decline in cellular and physiological functions and an increased susceptibility to chronic diseases. The effects of aging affect not only the elderly but also those of younger ages, posing significant challenges to global healthcare. Thus, understanding the molecular mechanisms associated with aging in different diseases is essential. One intriguing factor is the aryl hydrocarbon receptor (AhR), which serves as a cytoplasmic receptor and ligand-activated transcription factor and has been linked to the aging process. Here, we review the literature on several major hallmarks of aging, including mitochondrial dysfunction, cellular senescence, autophagy, mitophagy, epigenetic alterations, and microbiome disturbances. Moreover, we provide an overview of the impact of AhR on these hallmarks by mediating responses to environmental exposures, particularly in relation to the immune system. Furthermore, we explore how aging hallmarks affect clinical characteristics, inflammatory features, exacerbations, and the treatment of asthma. It is suggested that AhR signaling may potentially play a role in regulating asthma phenotypes in elderly populations as part of the aging process.
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Affiliation(s)
- Tianrui Yang
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
- Department of Geriatric Medicine, The First People’s Hospital of Yunnan Province, Kunming, Yunnan 650032, China
| | - Rongjun Wan
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wei Tu
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
- The State Key Laboratory of Respiratory Disease for Allergy, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518055, China
| | - Sai Nithin Avvaru
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Peisong Gao
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
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11
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Elrebehy MA, Abulsoud AI, El-Dakroury WA, Abdel Mageed SS, Elshaer SS, Fathi D, Rizk NI, Moustafa YM, Elballal MS, Mohammed OA, Abdel-Reheim MA, Zaki MB, Mahmoud AMA, Rashad AA, Sawan ES, Al-Noshokaty TM, Saber S, Doghish AS. Tuning into miRNAs: A comprehensive analysis of their impact on diagnosis, and progression in asthma. Pathol Res Pract 2024; 254:155147. [PMID: 38246033 DOI: 10.1016/j.prp.2024.155147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Asthma is a diverse inflammatory illness affecting the respiratory passages, leading to breathing challenges, bouts of coughing and wheezing, and, in severe instances, significant deterioration in quality of life. Epigenetic regulation, which involves the control of gene expression through processes such as post-transcriptional modulation of microRNAs (miRNAs), plays a role in the evolution of various asthma subtypes. In immune-mediated diseases, miRNAs play a regulatory role in the behavior of cells that form the airway structure and those responsible for defense mechanisms in the bronchi and lungs. They control various cellular processes such as survival, growth, proliferation, and the production of chemokines and immune mediators. miRNAs possess chemical and biological characteristics that qualify them as suitable biomarkers for diseases. They allow for the categorization of patients to optimize drug selection, thus streamlining clinical management and decreasing both the economic burden and the necessity for critical care related to the disease. This study provides a concise overview of the functions of miRNAs in asthma and elucidates their regulatory effects on the underlying processes of the disease. We provide a detailed account of the present status of miRNAs as biomarkers for categorizing asthma, identifying specific asthma subtypes, and selecting appropriate treatment options.
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Affiliation(s)
- Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt.
| | - Walaa A El-Dakroury
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Shereen Saeid Elshaer
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt; Department of Biochemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo 11823, Egypt
| | - Doaa Fathi
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Nehal I Rizk
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Yasser M Moustafa
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef 62521, Egypt.
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Menoufia 32897, Egypt
| | - Abdulla M A Mahmoud
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed A Rashad
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Eman S Sawan
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Tohada M Al-Noshokaty
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
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12
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Cardoso GC, Ganzella FADO, Miniskiskosky G, da Cunha RS, Ramos EADS. Digital methylation-specific PCR: New applications for liquid biopsy. Biomol Concepts 2024; 15:bmc-2022-0041. [PMID: 38345545 DOI: 10.1515/bmc-2022-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
Epigenetic analysis is a fundamental part of understanding pathophysiological processes with potential applications in diagnosis, prognosis, and assessment of disease susceptibility. Epigenetic changes have been widely studied in chronic obstructive pulmonary disease (COPD), but currently, there is no molecular marker used to improve the treatment of patients. Furthermore, this progressive disease is a risk factor for the development of more severe COVID-19. Methylation-specific polymerase chain reaction (MSP-PCR) plays an important role in the analysis of DNA methylation profiles, and it is one of the most widely used techniques. In this context, the combination of MSP-PCR with emerging PCR technologies, such as digital PCR (dPCR), results in more accurate analyses of the DNA methylation profile of the genes under study. In this study, we propose the application of the MSP-dPCR technique to evaluate the methylation profile of the ADAM33 gene from saliva samples and lung tissue biopsies of patients with COPD and COVID-19. MSP-dPCR generated a measurable prediction of gene methylation rate, with the potential application of this combined technology for diagnostic and prognostic purposes. It has also proven to be a powerful tool for liquid biopsy applications.
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Affiliation(s)
- Gabriela Casani Cardoso
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | | | - Guilherme Miniskiskosky
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | - Regiane Stafim da Cunha
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | - Edneia Amancio de Souza Ramos
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
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13
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Perez-Garcia J, Pino-Yanes M, Plender EG, Everman JL, Eng C, Jackson ND, Moore CM, Beckman KB, Medina V, Sharma S, Winnica DE, Holguin F, Rodríguez-Santana J, Villar J, Ziv E, Seibold MA, Burchard EG. Epigenomic response to albuterol treatment in asthma-relevant airway epithelial cells. Clin Epigenetics 2023; 15:156. [PMID: 37784136 PMCID: PMC10546710 DOI: 10.1186/s13148-023-01571-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Albuterol is the first-line asthma medication used in diverse populations. Although DNA methylation (DNAm) is an epigenetic mechanism involved in asthma and bronchodilator drug response (BDR), no study has assessed whether albuterol could induce changes in the airway epithelial methylome. We aimed to characterize albuterol-induced DNAm changes in airway epithelial cells, and assess potential functional consequences and the influence of genetic variation and asthma-related clinical variables. RESULTS We followed a discovery and validation study design to characterize albuterol-induced DNAm changes in paired airway epithelial cultures stimulated in vitro with albuterol. In the discovery phase, an epigenome-wide association study using paired nasal epithelial cultures from Puerto Rican children (n = 97) identified 22 CpGs genome-wide associated with repeated-use albuterol treatment (p < 9 × 10-8). Albuterol predominantly induced a hypomethylation effect on CpGs captured by the EPIC array across the genome (probability of hypomethylation: 76%, p value = 3.3 × 10-5). DNAm changes on the CpGs cg23032799 (CREB3L1), cg00483640 (MYLK4-LINC01600), and cg05673431 (KSR1) were validated in nasal epithelia from 10 independent donors (false discovery rate [FDR] < 0.05). The effect on the CpG cg23032799 (CREB3L1) was cross-tissue validated in bronchial epithelial cells at nominal level (p = 0.030). DNAm changes in these three CpGs were shown to be influenced by three independent genetic variants (FDR < 0.05). In silico analyses showed these polymorphisms regulated gene expression of nearby genes in lungs and/or fibroblasts including KSR1 and LINC01600 (6.30 × 10-14 ≤ p ≤ 6.60 × 10-5). Additionally, hypomethylation at the CpGs cg10290200 (FLNC) and cg05673431 (KSR1) was associated with increased gene expression of the genes where they are located (FDR < 0.05). Furthermore, while the epigenetic effect of albuterol was independent of the asthma status, severity, and use of medication, BDR was nominally associated with the effect on the CpG cg23032799 (CREB3L1) (p = 0.004). Gene-set enrichment analyses revealed that epigenomic modifications of albuterol could participate in asthma-relevant processes (e.g., IL-2, TNF-α, and NF-κB signaling pathways). Finally, nine differentially methylated regions were associated with albuterol treatment, including CREB3L1, MYLK4, and KSR1 (adjusted p value < 0.05). CONCLUSIONS This study revealed evidence of epigenetic modifications induced by albuterol in the mucociliary airway epithelium. The epigenomic response induced by albuterol might have potential clinical implications by affecting biological pathways relevant to asthma.
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Grants
- R01 ES015794 NIEHS NIH HHS
- R01 HL120393 NHLBI NIH HHS
- R01ES015794, R21ES24844 NIEHS NIH HHS
- UM1 HG008901 NHGRI NIH HHS
- R01MD010443, R56MD013312 NIMHD NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R21 ES024844 NIEHS NIH HHS
- R01 HL117626 NHLBI NIH HHS
- R56 MD013312 NIMHD NIH HHS
- R01 MD010443 NIMHD NIH HHS
- R01 HL155024 NHLBI NIH HHS
- R01HL155024-01, HHSN268201600032I, 3R01HL-117626-02S1, HHSN268201800002I, 3R01HL117004-02S3, 3R01HL-120393-02S1, R01HL117004, R01HL128439, R01HL135156, X01HL134589 NHLBI NIH HHS
- HHSN268201600032C NHLBI NIH HHS
- U24 HG008956 NHGRI NIH HHS
- Ministerio de Universidades
- Ministerio de Ciencia e Innovación
- Instituto de Salud Carlos III
- National Heart, Lung, and Blood Institute
- National Human Genome Research Institute
- National Institute of Environmental Health Sciences
- National Institute on Minority Health and Health Disparities
- The Centers for Common Disease Genomics of the Genome Sequencing Program
- Tobacco-Related Disease Research Program
- Sandler Family Foundation
- American Asthma Foundation
- Amos Medical Faculty Development Program from the Robert Wood Johnson Foundation
- Harry Wm. and Diana V. Hind Distinguished Professor in Pharmaceutical Sciences II
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Affiliation(s)
- Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Canary Islands, Spain.
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Canary Islands, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Spain.
| | - Elizabeth G Plender
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Camille M Moore
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Biomedical Research, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Denver, CO, USA
| | - Kenneth B Beckman
- University of Minnesota Genomics Center (UMNGC), Minneapolis, MN, USA
| | | | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daniel Efrain Winnica
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Fernando Holguin
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Multidisciplinary Organ Dysfunction Evaluation Research Network (MODERN), Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
- Li Ka Shing Knowledge Institute at the St. Michael's Hospital, Toronto, ON, Canada
| | - Elad Ziv
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco (UCSF), San Francisco, CA, USA
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14
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Cardenas A, Fadadu RP, Koppelman GH. Epigenome-wide association studies of allergic disease and the environment. J Allergy Clin Immunol 2023; 152:582-590. [PMID: 37295475 PMCID: PMC10564109 DOI: 10.1016/j.jaci.2023.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The epigenome is at the intersection of the environment, genotype, and cellular response. DNA methylation of cytosine nucleotides, the most studied epigenetic modification, has been systematically evaluated in human studies by using untargeted epigenome-wide association studies (EWASs) and shown to be both sensitive to environmental exposures and associated with allergic diseases. In this narrative review, we summarize findings from key EWASs previously conducted on this topic; interpret results from recent studies; and discuss the strengths, challenges, and opportunities regarding epigenetics research on the environment-allergy relationship. The majority of these EWASs have systematically investigated select environmental exposures during the prenatal and early childhood periods and allergy-associated epigenetic changes in leukocyte-isolated DNA and more recently in nasal cells. Overall, many studies have found consistent DNA methylation associations across cohorts for certain exposures, such as smoking (eg, aryl hydrocarbon receptor repressor gene [AHRR] gene), and allergic diseases (eg, EPX gene). We recommend the integration of both environmental exposures and allergy or asthma within long-term prospective designs to strengthen causality as well as biomarker development. Future studies should collect paired target tissues to examine compartment-specific epigenetic responses, incorporate genetic influences in DNA methylation (methylation quantitative trait locus), replicate findings across diverse populations, and carefully interpret epigenetic signatures from bulk, target tissue or isolated cells.
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Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford University, Stanford, Calif
| | - Raj P Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen, The Netherlands; Groningen Research Institute of Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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15
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Vasileva D, Greenwood CMT, Daley D. A Review of the Epigenetic Clock: Emerging Biomarkers for Asthma and Allergic Disease. Genes (Basel) 2023; 14:1724. [PMID: 37761864 PMCID: PMC10531327 DOI: 10.3390/genes14091724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
DNA methylation (DNAm) is a dynamic, age-dependent epigenetic modification that can be used to study interactions between genetic and environmental factors. Environmental exposures during critical periods of growth and development may alter DNAm patterns, leading to increased susceptibility to diseases such as asthma and allergies. One method to study the role of DNAm is the epigenetic clock-an algorithm that uses DNAm levels at select age-informative Cytosine-phosphate-Guanine (CpG) dinucleotides to predict epigenetic age (EA). The difference between EA and calendar age (CA) is termed epigenetic age acceleration (EAA) and reveals information about the biological capacity of an individual. Associations between EAA and disease susceptibility have been demonstrated for a variety of age-related conditions and, more recently, phenotypes such as asthma and allergic diseases, which often begin in childhood and progress throughout the lifespan. In this review, we explore different epigenetic clocks and how they have been applied, particularly as related to childhood asthma. We delve into how in utero and early life exposures (e.g., smoking, air pollution, maternal BMI) result in methylation changes. Furthermore, we explore the potential for EAA to be used as a biomarker for asthma and allergic diseases and identify areas for further study.
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Affiliation(s)
- Denitsa Vasileva
- Centre for Heart Lung Innovation, University of British Columbia and Saint Paul’s Hospital, Vancouver, BC V6Z 1Y6, Canada;
| | - Celia M. T. Greenwood
- Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada;
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC H3A 0G4, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada
| | - Denise Daley
- Centre for Heart Lung Innovation, University of British Columbia and Saint Paul’s Hospital, Vancouver, BC V6Z 1Y6, Canada;
- Department of Medicine, Respiratory Division, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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16
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Romero-Tapia SDJ, Becerril-Negrete JR, Castro-Rodriguez JA, Del-Río-Navarro BE. Early Prediction of Asthma. J Clin Med 2023; 12:5404. [PMID: 37629446 PMCID: PMC10455492 DOI: 10.3390/jcm12165404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
The clinical manifestations of asthma in children are highly variable, are associated with different molecular and cellular mechanisms, and are characterized by common symptoms that may diversify in frequency and intensity throughout life. It is a disease that generally begins in the first five years of life, and it is essential to promptly identify patients at high risk of developing asthma by using different prediction models. The aim of this review regarding the early prediction of asthma is to summarize predictive factors for the course of asthma, including lung function, allergic comorbidity, and relevant data from the patient's medical history, among other factors. This review also highlights the epigenetic factors that are involved, such as DNA methylation and asthma risk, microRNA expression, and histone modification. The different tools that have been developed in recent years for use in asthma prediction, including machine learning approaches, are presented and compared. In this review, emphasis is placed on molecular mechanisms and biomarkers that can be used as predictors of asthma in children.
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Affiliation(s)
- Sergio de Jesus Romero-Tapia
- Health Sciences Academic Division (DACS), Juarez Autonomous University of Tabasco (UJAT), Villahermosa 86040, Mexico
| | - José Raúl Becerril-Negrete
- Department of Clinical Immunopathology, Universidad Autónoma del Estado de México, Toluca 50000, Mexico;
| | - Jose A. Castro-Rodriguez
- Department of Pediatric Pulmonology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330077, Chile;
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17
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Lajiness JD, Cook-Mills JM. Catching Our Breath: Updates on the Role of Dendritic Cell Subsets in Asthma. Adv Biol (Weinh) 2023; 7:e2200296. [PMID: 36755197 PMCID: PMC10293089 DOI: 10.1002/adbi.202200296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/04/2023] [Indexed: 02/10/2023]
Abstract
Dendritic cells (DCs), as potent antigen presenting cells, are known to play a central role in the pathophysiology of asthma. The understanding of DC biology has evolved over the years to include multiple subsets of DCs with distinct functions in the initiation and maintenance of asthma. Furthermore, asthma is increasingly recognized as a heterogeneous disease with potentially diverse underlying mechanisms. The goal of this review is to summarize the role of DCs and the various subsets therein in the pathophysiology of asthma and highlight some of the crucial animal models shaping the field today. Potential future avenues of investigation to address existing gaps in knowledge are discussed.
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Affiliation(s)
- Jacquelyn D Lajiness
- Department of Pediatrics, Division of Neonatology, Indiana University School of Medicine, 1030 West Michigan Street, Suite C 4600, Indianapolis, IN, 46202-5201, USA
| | - Joan M Cook-Mills
- Department of Pediatrics, Department of Microbiology and Immunology, Pediatric Pulmonary, Asthma, and Allergy Basic Research Program, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W. Walnut Street, R4-202A, Indianapolis, IN, 46202, USA
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18
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Herrera-Luis E, Forno E, Celedón JC, Pino-Yanes M. Asthma Exacerbations: The Genes Behind the Scenes. J Investig Allergol Clin Immunol 2023; 33:76-94. [PMID: 36420738 PMCID: PMC10638677 DOI: 10.18176/jiaci.0878] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The clinical and socioeconomic burden of asthma exacerbations (AEs) constitutes a major public health problem. In the last 4 years, there has been an increase in ethnic diversity in candidate-gene and genome-wide association studies of AEs, which in the latter case led to the identification of novel genes and underlying pathobiological processes. Pharmacogenomics, admixture mapping analyses, and the combination of multiple "omics" layers have helped to prioritize genomic regions of interest and/or facilitated our understanding of the functional consequences of genetic variation. Nevertheless, the field still lags behind the genomics of asthma, where a vast compendium of genetic approaches has been used (eg, gene-environment nteractions, next-generation sequencing, and polygenic risk scores). Furthermore, the roles of the DNA methylome and histone modifications in AEs have received little attention, and microRNA findings remain to be validated in independent studies. Likewise, the most recent transcriptomic studies highlight the importance of the host-airway microbiome interaction in the modulation of risk of AEs. Leveraging -omics and deep-phenotyping data from subtypes or homogenous subgroups of patients will be crucial if we are to overcome the inherent heterogeneity of AEs, boost the identification of potential therapeutic targets, and implement precision medicine approaches to AEs in clinical practice.
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Affiliation(s)
- E Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
| | - E Forno
- Division of Pediatric Pulmonary Medicine, UPMC Children´s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - J C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children´s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - M Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain 4 Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
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19
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Bhat S, Rotti H, Prasad K, Kabekkodu SP, Saadi AV, Shenoy SP, Joshi KS, Nesari TM, Shengule SA, Dedge AP, Gadgil MS, Dhumal VR, Salvi S, Satyamoorthy K. Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function. J Ayurveda Integr Med 2023; 14:100692. [PMID: 37018893 PMCID: PMC10122039 DOI: 10.1016/j.jaim.2023.100692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 10/13/2022] [Accepted: 02/01/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The Indian traditional medicinal system, Ayurveda, describes several lifestyle practices, processes and medicines as an intervention to treat asthma. Rasayana therapy is one of them and although these treatment modules show improvement in bronchial asthma, their mechanism of action, particularly the effect on DNA methylation, is largely understudied. OBJECTIVES Our study aimed at identifying the contribution of DNA methylation changes in modulating bronchial asthma phenotype upon Ayurveda intervention. MATERIALS AND METHODS In this study, genome-wide methylation profiling in peripheral blood DNA of healthy controls and bronchial asthmatics before (BT) and after (AT) Ayurveda treatment was performed using array-based profiling of reference-independent methylation status (aPRIMES) coupled to microarray technique. RESULTS We identified 4820 treatment-associated DNA methylation signatures (TADS) and 11,643 asthma-associated DNA methylation signatures (AADS), differentially methylated [FDR (≤0.1) adjusted p-values] in AT and HC groups respectively, compared to BT group. Neurotrophin TRK receptor signaling pathway was significantly enriched for differentially methylated genes in bronchial asthmatics, compared to AT and HC subjects. Additionally, we identified over 100 differentially methylated immune-related genes located in the promoter/5'-UTR regions of TADS and AADS. Various immediate-early response and immune regulatory genes with functions such as transcription factor activity (FOXD1, FOXD2, GATA6, HOXA3, HOXA5, MZF1, NFATC1, NKX2-2, NKX2-3, RUNX1, KLF11), G-protein coupled receptor activity (CXCR4, PTGER4), G-protein coupled receptor binding (UCN), DNA binding (JARID2, EBF2, SOX9), SNARE binding (CAPN10), transmembrane signaling receptor activity (GP1BB), integrin binding (ITGA6), calcium ion binding (PCDHGA12), actin binding (TRPM7, PANX1, TPM1), receptor tyrosine kinase binding (PIK3R2), receptor activity (GDNF), histone methyltransferase activity (MLL5), and catalytic activity (TSTA3) were found to show consistent methylation status between AT and HC group in microarray data. CONCLUSIONS Our study reports the DNA methylation-regulated genes in bronchial asthmatics showing improvement in symptoms after Ayurveda intervention. DNA methylation regulation in the identified genes and pathways represents the Ayurveda intervention responsive genes and may be further explored as diagnostic, prognostic, and therapeutic biomarkers for bronchial asthma in peripheral blood.
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Affiliation(s)
- Smitha Bhat
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Harish Rotti
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Keshava Prasad
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushma P Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Kalpana S Joshi
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Tanuja M Nesari
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sushant A Shengule
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Amrish P Dedge
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Maithili S Gadgil
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Vikram R Dhumal
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sundeep Salvi
- Department of Pulmonary Medicine, Chest Research Foundation, Pune, Maharashtra, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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20
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Miyake K, Kushima M, Shinohara R, Horiuchi S, Otawa S, Akiyama Y, Ooka T, Kojima R, Yokomichi H, Yamagata Z. Maternal smoking status before and during pregnancy and bronchial asthma at 3 years of age: a prospective cohort study. Sci Rep 2023; 13:3234. [PMID: 36828882 PMCID: PMC9958124 DOI: 10.1038/s41598-023-30304-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
The association between maternal pre-pregnancy smoking status and asthma risk is unclear. This study aimed to investigate the association between pre- and post-pregnancy maternal smoking status and bronchial asthma at 3 years of age in a large birth cohort. Data of 75,411 mother-child pairs from the Japan Environment and Children's Study (JECS) were analysed using multivariate logistic regression analysis. Overall, 7.2% of the children had bronchial asthma. The maternal smoking status before childbirth was as follows: Never = 60.0%, Quit before recognising current pregnancy = 24.1%, Quit after finding out about current pregnancy = 12.3%, and Still smoking = 3.6%. Children of mothers who sustained smoking during pregnancy had an increased risk of bronchial asthma at 3 years of age even after adjusting for pre- and postnatal covariates (adjusted odds ratio [aOR] 1.34, 95% confidence interval [CI] 1.15-1.56). Children of mothers who quit before (aOR 1.09, 95% CI 1.02-1.18) or after (aOR 1.11, 95% CI 1.01-1.23) recognising the current pregnancy had an increased risk of bronchial asthma at 3 years of age. Maternal smoking throughout pregnancy and smoking exposure pre-pregnancy or in early pregnancy increases the risk of bronchial asthma in children.
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Affiliation(s)
- Kunio Miyake
- Department of Health Sciences, School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
| | - Megumi Kushima
- grid.267500.60000 0001 0291 3581Center for Birth Cohort Studies, University of Yamanashi, Yamanashi, Japan
| | - Ryoji Shinohara
- grid.267500.60000 0001 0291 3581Center for Birth Cohort Studies, University of Yamanashi, Yamanashi, Japan
| | - Sayaka Horiuchi
- grid.267500.60000 0001 0291 3581Center for Birth Cohort Studies, University of Yamanashi, Yamanashi, Japan
| | - Sanae Otawa
- grid.267500.60000 0001 0291 3581Center for Birth Cohort Studies, University of Yamanashi, Yamanashi, Japan
| | - Yuka Akiyama
- grid.267500.60000 0001 0291 3581Department of Health Sciences, School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898 Japan
| | - Tadao Ooka
- grid.267500.60000 0001 0291 3581Department of Health Sciences, School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898 Japan
| | - Reiji Kojima
- grid.267500.60000 0001 0291 3581Department of Health Sciences, School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898 Japan
| | - Hiroshi Yokomichi
- grid.267500.60000 0001 0291 3581Department of Health Sciences, School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898 Japan
| | - Zentaro Yamagata
- grid.267500.60000 0001 0291 3581Department of Health Sciences, School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898 Japan ,grid.267500.60000 0001 0291 3581Center for Birth Cohort Studies, University of Yamanashi, Yamanashi, Japan
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21
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Gil-Martínez M, Lorente-Sorolla C, Rodrigo-Muñoz JM, Lendínez MÁ, Núñez-Moreno G, de la Fuente L, Mínguez P, Mahíllo-Fernández I, Sastre J, Valverde-Monge M, Quirce S, Caballero ML, González-Barcala FJ, Arismendi E, Bobolea I, Valero A, Muñoz X, Cruz MJ, Martínez-Rivera C, Plaza V, Olaguibel JM, del Pozo V. Analysis of Differentially Expressed MicroRNAs in Serum and Lung Tissues from Individuals with Severe Asthma Treated with Oral Glucocorticoids. Int J Mol Sci 2023; 24:1611. [PMID: 36675122 PMCID: PMC9864670 DOI: 10.3390/ijms24021611] [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: 12/19/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Nowadays, microRNAs (miRNAs) are increasingly used as biomarkers due to their potential contribution to the diagnosis and targeted treatment of a range of diseases. The aim of the study was to analyze the miRNA expression profiles in serum and lung tissue from patients with severe asthma treated with oral corticosteroids (OCS) and those without OCS treatment. For this purpose, serum and lung tissue miRNAs of OCS and non-OCS asthmatic individuals were evaluated by miRNAs-Seq, and subsequently miRNA validation was performed using RT-qPCR. Additionally, pathway enrichment analysis of deregulated miRNAs was conducted. We observed altered expression by the next-generation sequencing (NGS) of 11 miRNAs in serum, of which five (hsa-miR-148b-3p, hsa-miR-221-5p, hsa-miR-618, hsa-miR-941, and hsa-miR-769-5p) were validated by RT-qPCR, and three miRNAs in lung tissue (hsa-miR-144-3p, hsa-miR-144-5p, and hsa-miR-451a). The best multivariate logistic regression model to differentiate individuals with severe asthma, treated and untreated with OCS, was to combine the serum miRNAs hsa-miR-221-5p and hsa-miR-769-5p. Expression of hsa-miR-148b-3p and hsa-miR-221-5p correlated with FEV1/FVC (%) and these altered miRNAs act in key signaling pathways for asthma disease and the regulated expression of some genes (FOXO3, PTEN, and MAPK3) involved in these pathways. In conclusion, there are miRNA profiles differentially expressed in OCS-treated individuals with asthma and could be used as biomarkers of OCS treatment.
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Affiliation(s)
- Marta Gil-Martínez
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Clara Lorente-Sorolla
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain
| | - José M. Rodrigo-Muñoz
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Miguel Ángel Lendínez
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain
| | - Gonzalo Núñez-Moreno
- Department of Genetics, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Ignacio Mahíllo-Fernández
- Biostatistics and Epidemiology Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Joaquín Sastre
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Allergy Department, Hospital Universitario Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Marcela Valverde-Monge
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Allergy Department, Hospital Universitario Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Santiago Quirce
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Department of Allergy, Hospital Universitario La Paz, IdiPAZ, 28046 Madrid, Spain
| | - María L. Caballero
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Department of Allergy, Hospital Universitario La Paz, IdiPAZ, 28046 Madrid, Spain
| | - Francisco J. González-Barcala
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Pulmonology Department, Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
| | - Ebymar Arismendi
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Allergy Unit & Severe Asthma Unit, Pulmonology and Allergy Department, Hospital Clínic, 08036 Barcelona, Spain
| | - Irina Bobolea
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Allergy Unit & Severe Asthma Unit, Pulmonology and Allergy Department, Hospital Clínic, 08036 Barcelona, Spain
| | - Antonio Valero
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Allergy Unit & Severe Asthma Unit, Pulmonology and Allergy Department, Hospital Clínic, 08036 Barcelona, Spain
| | - Xavier Muñoz
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Pulmonology Department, Hospital Vall d’Hebron, 08035 Barcelona, Spain
| | - María Jesús Cruz
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Pulmonology Department, Hospital Vall d’Hebron, 08035 Barcelona, Spain
| | - Carlos Martínez-Rivera
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Pulmonology Department, Hospital Germans Trias i Pujol, 08916 Badalona, Spain
| | - Vicente Plaza
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Respiratory Medicine Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
| | - José M. Olaguibel
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Severe Asthma Unit, Department of Allergy, Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Victoria del Pozo
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Autónoma de Madrid, 28029 Madrid, Spain
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22
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Li J, Qiu CY, Tao YJ, Cheng L. Epigenetic modifications in chronic rhinosinusitis with and without nasal polyps. Front Genet 2023; 13:1089647. [PMID: 36699454 PMCID: PMC9868256 DOI: 10.3389/fgene.2022.1089647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023] Open
Abstract
Chronic rhinosinusitis (CRS) has brought a huge socioeconomic burden. However, its mechanism is still elusive, which may involve genetic, environmental and some other factors. Epigenetic analyses have been conducted to explore the mechanisms underlying CRS. Here, we reviewed the fruits in the epigenetic studies on DNA methylation, histone modification, and non-coding RNA regulation. We concluded that the epigenetic research on CRS has made great breakthroughs, especially in the past 5 years and the field of microRNAs. "Epigenetic therapies" are expected to be designed to treat CRS in the future.
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Affiliation(s)
- Jing Li
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China,Department of Otorhinolaryngology, The Affiliated Jiangning Hospital, Nanjing Medical University, Nanjing, China
| | - Chang-Yu Qiu
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China,International Centre for Allergy Research, Nanjing Medical University, Nanjing, China
| | - Yue-Jin Tao
- Department of Otorhinolaryngology, The Affiliated Jiangning Hospital, Nanjing Medical University, Nanjing, China,*Correspondence: Yue-Jin Tao, ; Lei Cheng,
| | - Lei Cheng
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China,International Centre for Allergy Research, Nanjing Medical University, Nanjing, China,*Correspondence: Yue-Jin Tao, ; Lei Cheng,
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23
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Clement K, McGill MR, Miousse IR, Young SG, Melnyk S, Koturbash I. Methylsulfonylmethane Serves as a Donor of Methyl Groups for Methylation of DNA in Human Liver HepaRG Cells. J Diet Suppl 2022; 20:950-962. [PMID: 36469606 PMCID: PMC10239780 DOI: 10.1080/19390211.2022.2153957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methylsulfonylmethane (MSM), a natural organosulfur compound, is a popular dietary supplement sold both as a single product and as a constituent of multi-ingredient products. It has been postulated that MSM may serve as a donor for methyl groups for various cellular processes; however, studies have yet to demonstrate this. Therefore, the goal of this study was to determine whether or not MSM, supplemented to fully differentiated human HepaRG cells at physiologically-relevant concentrations, can serve as a donor for methyl groups for DNA methylation. For this purpose, methyl groups in the MSM molecule were labeled with deuterium (deuterated) and incorporation of the labeled 5-methylcytosine into the HepaRG cell DNA was evaluated using liquid chromatography/mass spectrometry (LC-MS/MS). We report that MSM supplementation resulted in significant incorporation of deuterated product into DNA in a time- and dose-dependent fashion. These changes were not associated with increased 5-methylcytosine content, did not result in changes of DNA methylation or re-distribution of DNA methylation patterns between the retrotransposons LINE-1 and HERV18, and were not associated with cytotoxicity. In conclusion, short-term supplementation with MSM in vitro demonstrates that MSM can serve as a donor of methyl groups for methylation of DNA, but does not affect the levels of DNA methylation globally and does not lead to redistribution of the DNA methylation patterns within the most abundant repetitive elements. Future studies will be needed to validate these findings in vivo and to investigate whether or not MSM can restore normal DNA methylation patterns within the hypomethylated phenotype.
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Affiliation(s)
- Kirsten Clement
- Department of Environmental Health Sciences, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Center for Dietary Supplements Research, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Mitchell R. McGill
- Department of Environmental Health Sciences, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Center for Dietary Supplements Research, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Isabelle R. Miousse
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205 USA
| | - Sean G. Young
- Department of Environmental Health Sciences, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Stepan Melnyk
- Arkansas Children’s Research Institute, Little Rock, AR, 72205, USA
| | - Igor Koturbash
- Department of Environmental Health Sciences, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Center for Dietary Supplements Research, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
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24
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Maggi E, Parronchi P, Azzarone BG, Moretta L. A pathogenic integrated view explaining the different endotypes of asthma and allergic disorders. Allergy 2022; 77:3267-3292. [PMID: 35842745 DOI: 10.1111/all.15445] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 01/28/2023]
Abstract
The inflammation of allergic diseases is characterized by a complex interaction between type 2 and type 3 immune responses, explaining clinical symptoms and histopathological patterns. Airborne stimuli activate the mucosal epithelium to release a number of molecules impacting the activity of resident immune and environmental cells. Signals from the mucosal barrier, regulatory cells, and the inflamed tissue are crucial conditions able to modify innate and adaptive effector cells providing the selective homing of eosinophils or neutrophils. The high plasticity of resident T- and innate lymphoid cells responding to external signals is the prerequisite to explain the multiplicity of endotypes of allergic diseases. This notion paved the way for the huge use of specific biologic drugs interfering with pathogenic mechanisms of inflammation. Based on the response of the epithelial barrier, the activity of resident regulatory cells, and functions of structural non-lymphoid environmental cells, this review proposes some immunopathogenic scenarios characterizing the principal endotypes which can be associated with a precise phenotype of asthma. Recent literature indicates that similar concepts can also be applied to the inflammation of other non-respiratory allergic disorders. The next challenges will consist in defining specific biomarker(s) of each endotype allowing for a quick diagnosis and the most effective personalized therapy.
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Affiliation(s)
- Enrico Maggi
- Department of Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Paola Parronchi
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | | | - Lorenzo Moretta
- Department of Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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25
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Gautam Y, Johansson E, Mersha TB. Multi-Omics Profiling Approach to Asthma: An Evolving Paradigm. J Pers Med 2022; 12:jpm12010066. [PMID: 35055381 PMCID: PMC8778153 DOI: 10.3390/jpm12010066] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 02/04/2023] Open
Abstract
Asthma is a complex multifactorial and heterogeneous respiratory disease. Although genetics is a strong risk factor of asthma, external and internal exposures and their interactions with genetic factors also play important roles in the pathophysiology of asthma. Over the past decades, the application of high-throughput omics approaches has emerged and been applied to the field of asthma research for screening biomarkers such as genes, transcript, proteins, and metabolites in an unbiased fashion. Leveraging large-scale studies representative of diverse population-based omics data and integrating with clinical data has led to better profiling of asthma risk. Yet, to date, no omic-driven endotypes have been translated into clinical practice and management of asthma. In this article, we provide an overview of the current status of omics studies of asthma, namely, genomics, transcriptomics, epigenomics, proteomics, exposomics, and metabolomics. The current development of the multi-omics integrations of asthma is also briefly discussed. Biomarker discovery following multi-omics profiling could be challenging but useful for better disease phenotyping and endotyping that can translate into advances in asthma management and clinical care, ultimately leading to successful precision medicine approaches.
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26
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Wang C, Wang J, Zheng X, Zhang J, Zhang J, Qiao G, Liu H, Zhao H, Bai J, Zhang H, Zhang Z. Epigenetic regulation is involved in traffic-related PM 2.5 aggravating allergic airway inflammation in rats. Clin Immunol 2021; 234:108914. [PMID: 34954131 DOI: 10.1016/j.clim.2021.108914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/27/2021] [Accepted: 12/20/2021] [Indexed: 11/29/2022]
Abstract
Increasing fine particulate matter (PM2.5) and epigenetic modifications are closely associated with the pathogenesis of asthma, but the definite mechanism remains unclear. The traffic-related PM2.5 exposure aggravated pulmonary inflammation and changed the methylation level of interferon gamma (Ifng) and interleukin (Il)4 genes, and then altered levels of affiliated cytokines of IFN-γ and IL-4 in rats with allergic airway inflammation. It also increased the level of miR146a and decreased the level of miR31. In addition, transcription factors of nuclear factor kappa B (NF-κB) and signal transducer and activator of transcription 6 (Stat6) rose; forkhead box P3 (Foxp3) and signal transducer and activator of transcription 4 (Stat4) lowered. The traffic-related PM2.5 altered epigenetic modifications in allergic airway inflammation of rats leading to inflammation exacerbation through impaired regulatory T (Treg) cells function and T-helper type 1 (Th1)/Th2 cells imbalance, which provided a new target for the treatment and control of asthma.
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Affiliation(s)
- Caihong Wang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Jing Wang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Xin Zheng
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Jiaqi Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Jingwei Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Guoguo Qiao
- Teaching Experiment Center, School of Public Health, Shanxi Medical University, China
| | - Haifang Liu
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Huichao Zhao
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Jianying Bai
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Hongmei Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China
| | - Zhihong Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, China.
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27
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Dietary Fibers: Effects, Underlying Mechanisms and Possible Role in Allergic Asthma Management. Nutrients 2021; 13:nu13114153. [PMID: 34836408 PMCID: PMC8621630 DOI: 10.3390/nu13114153] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
Abstract
The prevalence of asthma is increasing, but the cause remains under debate. Research currently focuses on environmental and dietary factors that may impact the gut-lung axis. Dietary fibers are considered to play a crucial role in supporting diversity and activity of the microbiome, as well as immune homeostasis in the gut and lung. This review discusses the current state of knowledge on how dietary fibers and their bacterial fermentation products may affect the pathophysiology of allergic asthma. Moreover, the impact of dietary fibers on early type 2 asthma management, as shown in both pre-clinical and clinical studies, is described. Short-chain fatty acids, fiber metabolites, modulate host immunity and might reduce the risk of allergic asthma development. Underlying mechanisms include G protein-coupled receptor activation and histone deacetylase inhibition. These results are supported by studies in mice, children and adults with allergic asthma. Fibers might also exert direct effects on the immune system via yet to be elucidated mechanisms. However, the effects of specific types of fiber, dosages, duration of treatment, and combination with probiotics, need to be explored. There is an urgent need to further valorize the potential of specific dietary fibers in prevention and treatment of allergic asthma by conducting more large-scale dietary intervention trials.
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28
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Fang L, Roth M. Airway Wall Remodeling in Childhood Asthma-A Personalized Perspective from Cell Type-Specific Biology. J Pers Med 2021; 11:jpm11111229. [PMID: 34834581 PMCID: PMC8625708 DOI: 10.3390/jpm11111229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/16/2022] Open
Abstract
Airway wall remodeling is a pathology occurring in chronic inflammatory lung diseases including asthma, chronic obstructive pulmonary disease, and fibrosis. In 2017, the American Thoracic Society released a research statement highlighting the gaps in knowledge and understanding of airway wall remodeling. The four major challenges addressed in this statement were: (i) the lack of consensus to define “airway wall remodeling” in different diseases, (ii) methodologic limitations and inappropriate models, (iii) the lack of anti-remodeling therapies, and (iv) the difficulty to define endpoints and outcomes in relevant studies. This review focuses on the importance of cell-cell interaction, especially the bronchial epithelium, in asthma-associated airway wall remodeling. The pathology of “airway wall remodeling” summarizes all structural changes of the airway wall without differentiating between different pheno- or endo-types of asthma. Indicators of airway wall remodeling have been reported in childhood asthma in the absence of any sign of inflammation; thus, the initiation event remains unknown. Recent studies have implied that the interaction between the epithelium with immune cells and sub-epithelial mesenchymal cells is modified in asthma by a yet unknown epigenetic mechanism during early childhood.
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