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Wang L, Xiao J, Zhang B, Hou A. Epigenetic modifications in the development of bronchopulmonary dysplasia: a review. Pediatr Res 2024:10.1038/s41390-024-03167-7. [PMID: 38570557 DOI: 10.1038/s41390-024-03167-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/25/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
While perinatal medicine advancements have bolstered survival outcomes for premature infants, bronchopulmonary dysplasia (BPD) continues to threaten their long-term health. Gene-environment interactions, mediated by epigenetic modifications such as DNA methylation, histone modification, and non-coding RNA regulation, take center stage in BPD pathogenesis. Recent discoveries link methylation variations across biological pathways with BPD. Also, the potential reversibility of histone modifications fuels new treatment avenues. The review also highlights the promise of utilizing mesenchymal stem cells and their exosomes as BPD therapies, given their ability to modulate non-coding RNA, opening novel research and intervention possibilities. IMPACT: The complexity and universality of epigenetic modifications in the occurrence and development of bronchopulmonary dysplasia were thoroughly discussed. Both molecular and cellular mechanisms contribute to the diverse nature of epigenetic changes, suggesting the need for deeper biochemical techniques to explore these molecular alterations. The utilization of innovative cell-specific drug delivery methods like exosomes and extracellular vesicles holds promise in achieving precise epigenetic regulation.
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Affiliation(s)
- Lichuan Wang
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Jun Xiao
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Bohan Zhang
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Ana Hou
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China.
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2
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Frazer LC, Yamaguchi Y, Singh DK, Akopyants NS, Good M. DNA methylation in necrotizing enterocolitis. Expert Rev Mol Med 2024; 26:e16. [PMID: 38557638 DOI: 10.1017/erm.2024.16] [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: 04/04/2024]
Abstract
Epigenetic modifications, such as DNA methylation, are enzymatically regulated processes that directly impact gene expression patterns. In early life, they are central to developmental programming and have also been implicated in regulating inflammatory responses. Research into the role of epigenetics in neonatal health is limited, but there is a growing body of literature related to the role of DNA methylation patterns and diseases of prematurity, such as the intestinal disease necrotizing enterocolitis (NEC). NEC is a severe intestinal inflammatory disease, but the key factors that precede disease development remain to be determined. This knowledge gap has led to a failure to design effective targeted therapies and identify specific biomarkers of disease. Recent literature has identified altered DNA methylation patterns in the stool and intestinal tissue of neonates with NEC. These findings provide the foundation for a new avenue in NEC research. In this review, we will provide a general overview of DNA methylation and then specifically discuss the recent literature related to methylation patterns in neonates with NEC. We will also discuss how DNA methylation is used as a biomarker for other disease states and how, with further research, methylation patterns may serve as potential biomarkers for NEC.
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Affiliation(s)
- Lauren C Frazer
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yukihiro Yamaguchi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dhirendra K Singh
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalia S Akopyants
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Misty Good
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Yaremenko AV, Pechnikova NA, Porpodis K, Damdoumis S, Aggeli A, Theodora P, Domvri K. Association of Fetal Lung Development Disorders with Adult Diseases: A Comprehensive Review. J Pers Med 2024; 14:368. [PMID: 38672994 PMCID: PMC11051200 DOI: 10.3390/jpm14040368] [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: 02/22/2024] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Fetal lung development is a crucial and complex process that lays the groundwork for postnatal respiratory health. However, disruptions in this delicate developmental journey can lead to fetal lung development disorders, impacting neonatal outcomes and potentially influencing health outcomes well into adulthood. Recent research has shed light on the intriguing association between fetal lung development disorders and the development of adult diseases. Understanding these links can provide valuable insights into the developmental origins of health and disease, paving the way for targeted preventive measures and clinical interventions. This review article aims to comprehensively explore the association of fetal lung development disorders with adult diseases. We delve into the stages of fetal lung development, examining key factors influencing fetal lung maturation. Subsequently, we investigate specific fetal lung development disorders, such as respiratory distress syndrome (RDS), bronchopulmonary dysplasia (BPD), congenital diaphragmatic hernia (CDH), and other abnormalities. Furthermore, we explore the potential mechanisms underlying these associations, considering the role of epigenetic modifications, transgenerational effects, and intrauterine environmental factors. Additionally, we examine the epidemiological evidence and clinical findings linking fetal lung development disorders to adult respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), and other respiratory ailments. This review provides valuable insights for healthcare professionals and researchers, guiding future investigations and shaping strategies for preventive interventions and long-term care.
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Affiliation(s)
- Alexey V. Yaremenko
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Oncology Unit, Pulmonary Department, George Papanikolaou Hospital, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (K.P.); (S.D.)
| | - Nadezhda A. Pechnikova
- Laboratory of Chemical Engineering A’, School of Chemical Engineering, Faculty of Engineering, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (N.A.P.); (A.A.)
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | - Konstantinos Porpodis
- Oncology Unit, Pulmonary Department, George Papanikolaou Hospital, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (K.P.); (S.D.)
| | - Savvas Damdoumis
- Oncology Unit, Pulmonary Department, George Papanikolaou Hospital, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (K.P.); (S.D.)
| | - Amalia Aggeli
- Laboratory of Chemical Engineering A’, School of Chemical Engineering, Faculty of Engineering, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (N.A.P.); (A.A.)
| | - Papamitsou Theodora
- Laboratory of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
| | - Kalliopi Domvri
- Oncology Unit, Pulmonary Department, George Papanikolaou Hospital, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (K.P.); (S.D.)
- Laboratory of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
- Pathology Department, George Papanikolaou Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
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Hodge KM, Zhabotynsky V, Burt AA, Carter BS, Fry RC, Helderman J, Hofheimer JA, McGowan EC, Neal CR, Pastyrnak SL, Smith LM, DellaGrotta SA, Dansereau LM, Lester BM, Marsit CJ, O'Shea TM, Everson TM. Epigenetic associations in HPA axis genes related to bronchopulmonary dysplasia and antenatal steroids. Pediatr Res 2024:10.1038/s41390-024-03116-4. [PMID: 38480856 DOI: 10.1038/s41390-024-03116-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/26/2024] [Accepted: 02/17/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD), a common morbidity among very preterm infants, is associated with chronic disease and neurodevelopmental impairments. A hypothesized mechanism for these outcomes lies in altered glucocorticoid (GC) activity. We hypothesized that BPD and its treatments may result in epigenetic differences in the hypothalamic-pituitary-adrenal (HPA) axis, which is modulated by GC, and could be ascertained using an established GC risk score and DNA methylation (DNAm) of HPA axis genes. METHODS DNAm was quantified from buccal tissue (ECHO-NOVI) and from neonatal blood spots (ELGAN ECHO) via the EPIC microarray. Prenatal maternal characteristics, pregnancy complication, and neonatal medical complication data were collected from medical record review and maternal interviews. RESULTS The GC score was not associated with steroid exposure or BPD. However, six HPA genes involved in stress response regulation demonstrated differential methylation with antenatal steroid exposure; two CpGs within FKBP5 and POMC were differentially methylated with BPD severity. These findings were sex-specific in both cohorts; males had greater magnitude of differential methylation within these genes. CONCLUSIONS These findings suggest that BPD severity and antenatal steroids are associated with DNAm at some HPA genes in very preterm infants and the effects appear to be sex-, tissue-, and age-specific. IMPACT This study addresses bronchopulmonary dysplasia (BPD), an important health outcome among preterm neonates, and interrogates a commonly studied pathway, the hypothalamic-pituitary-adrenal (HPA) axis. The combination of BPD, the HPA axis, and epigenetic markers has not been previously reported. In this study, we found that BPD itself was not associated with epigenetic responses in the HPA axis in infants born very preterm; however, antenatal treatment with steroids was associated with epigenetic responses.
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Affiliation(s)
- Kenyaita M Hodge
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Vasyl Zhabotynsky
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amber A Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brian S Carter
- Department of Pediatrics-Neonatology, Children's Mercy Hospital, Kansas City, MO, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jennifer Helderman
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Julie A Hofheimer
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Elisabeth C McGowan
- Department of Pediatrics, Warren Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
| | - Charles R Neal
- Department of Pediatrics, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Steven L Pastyrnak
- Department of Pediatrics, Spectrum Health-Helen Devos Hospital, Grand Rapids, MI, USA
| | - Lynne M Smith
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sheri A DellaGrotta
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
| | - Lynne M Dansereau
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
| | - Barry M Lester
- Department of Pediatrics, Warren Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Todd M Everson
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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Zhang Z, Reynolds SR, Stolrow HG, Chen JQ, Christensen BC, Salas LA. Deciphering the role of immune cell composition in epigenetic age acceleration: Insights from cell-type deconvolution applied to human blood epigenetic clocks. Aging Cell 2024; 23:e14071. [PMID: 38146185 DOI: 10.1111/acel.14071] [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: 08/17/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/27/2023] Open
Abstract
Aging is a significant risk factor for various human disorders, and DNA methylation clocks have emerged as powerful tools for estimating biological age and predicting health-related outcomes. Methylation data from blood DNA has been a focus of more recently developed DNA methylation clocks. However, the impact of immune cell composition on epigenetic age acceleration (EAA) remains unclear as only some clocks incorporate partial cell type composition information when analyzing EAA. We investigated associations of 12 immune cell types measured by cell-type deconvolution with EAA predicted by six widely-used DNA methylation clocks in data from >10,000 blood samples. We observed significant associations of immune cell composition with EAA for all six clocks tested. Across the clocks, nine or more of the 12 cell types tested exhibited significant associations with EAA. Higher memory lymphocyte subtype proportions were associated with increased EAA, and naïve lymphocyte subtypes were associated with decreased EAA. To demonstrate the potential confounding of EAA by immune cell composition, we applied EAA in rheumatoid arthritis. Our research maps immune cell type contributions to EAA in human blood and offers opportunities to adjust for immune cell composition in EAA studies to a significantly more granular level. Understanding associations of EAA with immune profiles has implications for the interpretation of epigenetic age and its relevance in aging and disease research. Our detailed map of immune cell type contributions serves as a resource for studies utilizing epigenetic clocks across diverse research fields, including aging-related diseases, precision medicine, and therapeutic interventions.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
| | - Samuel R Reynolds
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Hannah G Stolrow
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Ji-Qing Chen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Molecular and Cellular Biology Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
- Molecular and Cellular Biology Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
- Molecular and Cellular Biology Program, Guarini School of Graduate and Advanced Studies, Hanover, New Hampshire, USA
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Bao T, Zhu H, Ma M, Sun T, Hu J, Li J, Cao L, Cheng H, Tian Z. Implication of m6A Methylation Regulators in the Immune Microenvironment of Bronchopulmonary Dysplasia. Biochem Genet 2024:10.1007/s10528-024-10664-1. [PMID: 38393623 DOI: 10.1007/s10528-024-10664-1] [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: 09/09/2022] [Accepted: 01/01/2024] [Indexed: 02/25/2024]
Abstract
N6-methyladenosine (m6A) regulates gene expression and governs many important biological processes. However, the function of m6A in the development of bronchopulmonary dysplasia (BPD) remains poorly characterized. Thus, the purpose of this investigation was to evaluate the effects of m6A RNA methylation regulators on the development of BPD. BPD-related transcriptome data were downloaded from the GEO database. Differentially expressed m6A methylation regulators between BPD and control group were identified. Consensus clustering was conducted for the classification of BPD and association between clusters and BPD phenotypes were explored. Analysis of differentially expressed genes (DEGs) and immune-related DEGs was performed. The GSEA, GO and KEGG analyses were used to interpret the functional enrichments. The composition of immune cell subtypes in BPD subsets was predicted by CIBERSORT analysis. Compared with the control group, expression of most m6A regulators showed significant alteration, especially for IGF2BP1/2/3. BPD was classified into 2 subsets, and cluster 1 was correlated with severe BPD. Furthermore, the results of functional enrichment analyses showed a disturbed immune-related signaling pathway. Based on CIBERSORT analysis, we found that the proportion of immune cell subsets changed between cluster 1 and cluster 2. Our study revealed the implication of m6A methylation regulators in the development of BPD, which might provide a novel insight for the diagnosis and treatment of BPD.
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Affiliation(s)
- Tianping Bao
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Haiyan Zhu
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Mengmeng Ma
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Tingting Sun
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Jingjing Hu
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - JingYan Li
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Linxia Cao
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Huaiping Cheng
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Zhaofang Tian
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China.
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Abstract
Bronchopulmonary dysplasia (BPD) remains the most common complication of premature birth, imposing a significant and potentially life-long burden on patients and their families. Despite advances in our understanding of the mechanisms that contribute to patterns of lung injury and dysfunctional repair, current therapeutic strategies remain non-specific with limited success. Contemporary definitions of BPD continue to rely on clinician prescribed respiratory support requirements at specific time points. While these criteria may be helpful in broadly identifying infants at higher risk of adverse outcomes, they do not offer any precise information regarding the degree to which each compartment of the lung is affected. In this review we will outline the different pulmonary phenotypes of BPD and discuss important features in the pathogenesis, clinical presentation, and management of these frequently overlapping scenarios.
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Affiliation(s)
- Margaret Gilfillan
- Division of Neonatology, St. Christopher's Hospital for Children/Drexel University College of Medicine, Philadelphia, PA, USA
| | - Vineet Bhandari
- Division of Neonatology, The Children's Regional Hospital at Cooper/Cooper Medical School of Rowan University, Camden, NJ 08103, USA.
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8
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Lavoie PM, Rayment JH. Genetics of bronchopulmonary dysplasia: An update. Semin Perinatol 2023; 47:151811. [PMID: 37775368 DOI: 10.1016/j.semperi.2023.151811] [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] [Indexed: 10/01/2023]
Abstract
Bronchopulmonary dysplasia (BPD) is a multi-factorial disease that results from multiple clinical factors, including lung immaturity, mechanical ventilation, oxidative stress, pulmonary congestion due to increasing cardiac blood shunting, nutritional and immunological factors. Twin studies have indicated that susceptibility to BPD can be strongly inherited in some settings. Studies have reported associations between common genetic variants and BPD in preterm infants. Recent genomic studies have highlighted a potential role for molecular pathways involved in inflammation and lung development in affected infants. Rare mutations in genes encoding the lipid transporter ATP-binding cassette, sub-family A, member 3 (ABCA3 gene) which is involved in surfactant synthesis in alveolar type II cells, as well as surfactant protein B (SFTPB) and C (SFTPC) can also result in severe form of neonatal-onset interstitial lung diseases and may also potentially affect the course of BPD. This chapter summarizes the current state of knowledge on the genetics of BPD.
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Affiliation(s)
- Pascal M Lavoie
- Division of Neonatology, Department of Pediatrics, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, Vancouver, Canada.
| | - Jonathan H Rayment
- BC Children's Hospital Research Institute, Vancouver, Canada; Division of Respiratory Medicine, Department of Pediatrics, University of British Columbia, Vancouver, Canada; Division of Respiratory Medicine, BC Children's Hospital, Vancouver, Canada
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9
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Fang F, Zhou L, Perng W, Marsit CJ, Knight AK, Cardenas A, Aung MT, Hivert MF, Aris IM, Goodrich JM, Smith AK, Gaylord A, Fry RC, Oken E, O'Connor G, Ruden DM, Trasande L, Herbstman JB, Camargo CA, Bush NR, Dunlop AL, Dabelea DM, Karagas MR, Breton CV, Ober C, Everson TM, Page GP, Ladd-Acosta C. Evaluation of pediatric epigenetic clocks across multiple tissues. Clin Epigenetics 2023; 15:142. [PMID: 37660147 PMCID: PMC10475199 DOI: 10.1186/s13148-023-01552-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/12/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND Epigenetic clocks are promising tools for assessing biological age. We assessed the accuracy of pediatric epigenetic clocks in gestational and chronological age determination. RESULTS Our study used data from seven tissue types on three DNA methylation profiling microarrays and found that the Knight and Bohlin clocks performed similarly for blood cells, while the Lee clock was superior for placental samples. The pediatric-buccal-epigenetic clock performed the best for pediatric buccal samples, while the Horvath clock is recommended for children's blood cell samples. The NeoAge clock stands out for its unique ability to predict post-menstrual age with high correlation with the observed age in infant buccal cell samples. CONCLUSIONS Our findings provide valuable guidance for future research and development of epigenetic clocks in pediatric samples, enabling more accurate assessments of biological age.
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Affiliation(s)
- Fang Fang
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, 3040 East Cornwallis Road, Durham, NC, 27709-2194, USA.
| | - Linran Zhou
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, 3040 East Cornwallis Road, Durham, NC, 27709-2194, USA
| | - Wei Perng
- Department of Epidemiology, Colorado School of Public Health, Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Anna K Knight
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford, CA, USA
| | - Max T Aung
- Division of Environmental Health, Department of Population and Populace Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Izzuddin M Aris
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Abigail Gaylord
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - George O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Douglas M Ruden
- Department of Obstetrics and Gynecology, Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Leonardo Trasande
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | - Julie B Herbstman
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicole R Bush
- Department of Psychiatry and Behavioral Sciences, Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Anne L Dunlop
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Dana M Dabelea
- Department of Epidemiology, Colorado School of Public Health, Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Carrie V Breton
- Division of Environmental Health, Department of Population and Populace Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Todd M Everson
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Grier P Page
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, 3040 East Cornwallis Road, Durham, NC, 27709-2194, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Liu W, Yang X, Mao Z, Du Y, Lassiter C, AlAkwaa FM, Benny PA, Garmire LX. Severe preeclampsia is not associated with significant DNA methylation changes but cell proportion changes in the cord blood - caution on the importance of confounding adjustment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.31.23294898. [PMID: 37693517 PMCID: PMC10491383 DOI: 10.1101/2023.08.31.23294898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Epigenome-wide DNA methylation analysis (EWAS) is an important approach to identify biomarkers for early disease detection and prognosis prediction, yet its results could be confounded by other factors such as cell-type heterogeneity and patient characteristics. In this study, we address the importance of confounding adjustment by examining DNA methylation patterns in cord blood exposed to severe preeclampsia (PE), a prevalent and potentially fatal pregnancy complication. Without such adjustment, a misleading global hypomethylation pattern is obtained. However, after adjusting cell type proportions and patient clinical characteristics, most of the so-called significant CpG methylation changes associated with severe PE disappear. Rather, the major effect of PE on cord blood is through the proportion changes in different cell types. These results are validated using a previously published cord blood DNA methylation dataset, where global hypomethylation pattern was also wrongfully obtained without confounding adjustment. Additionally, several cell types significantly change as gestation progress (eg. granulocyte, nRBC, CD4T, and B cells), further confirming the importance of cell type adjustment in EWAS study of cord blood tissues. Our study urges the community to perform confounding adjustments in EWAS studies, based on cell type heterogeneity and other patient characteristics.
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Affiliation(s)
- Wenting Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Xiaotong Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Zhixin Mao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Yuheng Du
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | | | - Fadhl M AlAkwaa
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Paula A Benny
- University of Hawaii Cancer Center, Epidemiology, Honolulu, HI
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
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Cho HY, Wang X, Campbell MR, Panduri V, Coviello S, Caballero MT, Bennett BD, Kleeberger SR, Polack FP, Ofman G, Bell DA. Prospective epigenome and transcriptome analyses of cord and peripheral blood from preterm infants at risk of bronchopulmonary dysplasia. Sci Rep 2023; 13:12262. [PMID: 37507442 PMCID: PMC10382533 DOI: 10.1038/s41598-023-39313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a prevalent chronic lung disease of prematurity with limited treatment options. To uncover biomarkers of BPD risk, this study investigated epigenetic and transcriptomic signatures of prematurity at birth and during the neonatal period at day 14 and 28. Peripheral blood DNAs from preterm infants were applied to methylation arrays and cell-type composition was estimated by deconvolution. Covariate-adjusted robust linear regression elucidated BPD- and prolonged oxygen (≥ 14 days) exposure-associated CpGs. RNAs from cord and peripheral blood were sequenced, and differentially expressed genes (DEGs) for BPD or oxygen exposure were determined. Estimated neutrophil-lymphocyte ratios in peripheral blood at day 14 in BPD infants were significantly higher than nonBPD infants, suggesting an heightened inflammatory response in developing BPD. BPD-DEGs in cord blood indicated lymphopoiesis inhibition, altered Th1/Th2 responses, DNA damage, and organ degeneration. On day 14, BPD-associated CpGs were highly enriched in neutrophil activation, infection, and CD4 + T cell quantity, and BPD-DEGs were involved in DNA damage, cellular senescence, T cell homeostasis, and hyper-cytokinesis. On day 28, BPD-associated CpGs along with BPD-DEGs were enriched for phagocytosis, neurological disorder, and nucleotide metabolism. Oxygen supplementation markedly downregulated mitochondrial biogenesis genes and altered CpGs annotated to developmental genes. Prematurity-altered DNA methylation could cause abnormal lymphopoiesis, cellular assembly and cell cycle progression to increase BPD risk. Similar pathways between epigenome and transcriptome networks suggest coordination of the two in dysregulating leukopoiesis, adaptive immunity, and innate immunity. The results provide molecular insights into biomarkers for early detection and prevention of BPD.
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Affiliation(s)
- Hye-Youn Cho
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Xuting Wang
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Michelle R Campbell
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Vijayalakshmi Panduri
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | | | - Mauricio T Caballero
- Fundación INFANT, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Brian D Bennett
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Steven R Kleeberger
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Fernando P Polack
- Fundación INFANT, Buenos Aires, Argentina
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Gaston Ofman
- Fundación INFANT, Buenos Aires, Argentina
- Section of Neonatal-Perinatal Medicine, Center for Pregnancy and Newborn Research, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Douglas A Bell
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, Building 101, MD C3-03, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA.
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Pathogenesis of Bronchopulmonary Dysplasia: Role of Oxidative Stress from 'Omics' Studies. Antioxidants (Basel) 2022; 11:antiox11122380. [PMID: 36552588 PMCID: PMC9774798 DOI: 10.3390/antiox11122380] [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: 10/15/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD) remains the most common respiratory complication of prematurity as younger and smaller infants are surviving beyond the immediate neonatal period. The recognition that oxidative stress (OS) plays a key role in BPD pathogenesis has been widely accepted since at least the 1980s. In this article, we examine the interplay between OS and genetic regulation and review 'omics' data related to OS in BPD. Data from animal models (largely models of hyperoxic lung injury) and from human studies are presented. Epigenetic and transcriptomic analyses have demonstrated several genes related to OS to be differentially expressed in murine models that mimic BPD as well as in premature infants at risk of BPD development and infants with established lung disease. Alterations in the genetic regulation of antioxidant enzymes is a common theme in these studies. Data from metabolomics and proteomics have also demonstrated the potential involvement of OS-related pathways in BPD. A limitation of many studies includes the difficulty of obtaining timely and appropriate samples from human patients. Additional 'omics' studies could further our understanding of the role of OS in BPD pathogenesis, which may prove beneficial for prevention and timely diagnosis, and aid in the development of targeted therapies.
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Durward A, Macrae D. Long term outcome of babies with pulmonary hypertension. Semin Fetal Neonatal Med 2022; 27:101384. [PMID: 36031529 DOI: 10.1016/j.siny.2022.101384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Neonatal pulmonary hypertension (PH) is associated with many severe congenital abnormalities (congenital diaphragmatic hernia) or acquired cardiorespiratory diseases such as pneumonia, meconium aspiration and bronchopulmonary dysplasia (BPD). If no cause is found it may be labelled idiopathic persistent pulmonary hypertension of the newborn. Although PH may result in life threatening hypoxia and circulatory failure, in the majority of cases, it resolves in the neonatal period following treatment of the underlying cause. However, in some cases, neonatal PH progresses into infancy and childhood where symptoms include failure to thrive and eventually right heart failure or death if left untreated. This chronic condition is termed pulmonary vascular hypertensive disease (PHVD). Although classification and diagnostic criteria have only recently been proposed for pediatric PHVD, little is known about the pathophysiology of chronic neonatal PH, or why pulmonary vascular resistance may remain elevated well beyond infancy. This review explores the many factors involved in chronic PH and what implications this may have on long term outcome when the disease progresses beyond the neonatal period.
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Affiliation(s)
- Andrew Durward
- ECMO Service, Cardiac Intensive Care Unit, Sidra Medicine, Doha, Qatar.
| | - Duncan Macrae
- Cardiac Intensive Care, Sidra Medicine, Doha, Qatar; Paediatric Intensive Care Medicine, Imperial College, London, UK
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