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Syu YM, Lee IC, Lu JF, Hung PL, Hong SY, Yang MT, Liang JS. Insights into clinical phenotypes and treatment responses in a Small cohort of Taiwanese patients with SCN1A variants: A Preliminary study. Pediatr Neonatol 2024:S1875-9572(24)00134-7. [PMID: 39181834 DOI: 10.1016/j.pedneo.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND SCN1A channelopathy is the most well-known cause for epileptic encephalopathies and contributes to a wide phenotypic spectrum. The variable expressivity is troublesome for the interpretation of clinical significance and prognoses. To investigate the clinical manifestations, medications and outcomes of patients with SCN1A channelopathies, we conducted this observation retrospective study in Taiwan. METHODS A cohort consisting of 16 patients (5 males and 11 females) from multiple centers with identified SCN1A variants was investigated and phenotypically relevant factors were recorded. The variants were identified using NGS and confirmed by Sanger sequencing. A panel of 90 epileptic-related genes was used to identify SCN1A variants and to evaluate some of the potential SCN1A modifier genes. RESULTS The mean age of seizure onset was 10.4 months. Twelve of the sixteen patients (75%) had different degrees of neurocognitive sequela and psychobehavioral comorbidity in our cohort. Cognitive impairment was noted in all ten patients with Dravet syndrome (DS) and in two of the patients with non-DS phenotypes. A lower response rate to medications was also noted in patients with DS. Notably, a medication-specific tendency towards valproic acid (VPA), clobazam (CLB), and levetiracetam (LEV) was observed, revealing the effective pharmacotherapies for SCN1A-related seizures. An asymptomatic carrier with a reported pathogenic SCN1A variant was reviewed along with her monozygotic twin sister with DS. Nine novel SCN1A mutations are herein reported, eight of which being classified as pathogenic. CONCLUSION Our study revealed unfavorable outcomes for patients with SCN1A variants. Some patients with SCN1A channelopathy showed specific responsiveness to the pharmacotherapies previously either recommended or contraindicated for these patients. Our study also expands the genotype and provides valuable prognostic insights in patients with SCN1A channelopathy.
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Affiliation(s)
- Yu Min Syu
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City, 22021, Taiwan; Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei, 10449, Taiwan
| | - Inn-Chi Lee
- Division of Pediatric Neurology, Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, 40201, Taiwan; Institute of Medicine, School of Medicine, Chung Shan Medical University, Taichung, 40201, Taiwan
| | - Jyh-Feng Lu
- School of Medicine, Fu Jen Catholic University, New Taipei City, 24206, Taiwan
| | - Pi-Lien Hung
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, 83301, Taiwan
| | - Syuan-Yu Hong
- Division of Pediatric Neurology, Department of Pediatrics, Children's Hospital, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Ming-Tao Yang
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City, 22021, Taiwan
| | - Jao-Shwann Liang
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City, 22021, Taiwan; Department of Nursing, Asia Eastern University of Science and Technology, New Taipei City, 22030, Taiwan.
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Zeng K, Du J, Chen YZ, Wang DY, Sun ML, Li YZ, Wang DY, Liu SH, Zhu XM, Lv P, Du Z, Liu K, Yao J. Metabolomics efficiently discriminates monozygotic twins in peripheral blood. Int J Legal Med 2024:10.1007/s00414-024-03269-1. [PMID: 38858273 DOI: 10.1007/s00414-024-03269-1] [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: 11/15/2023] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Monozygotic (MZ) twins cannot be distinguished using conventional forensic STR typing because they present identical STR genotypings. However, MZ twins do not always live in the same environment and often have different dietary and other lifestyle habits. Metabolic profiles are deyermined by individual characteristics and are also influenced by the environment in which they live. Therefore, they are potential markers capable of identifying MZ twins. Moreover, the production of proteins varies from organism to organism and is influenced by both the physiological state of the body and the external environment. Hence, we used metabolomics and proteomics to identify metabolites and proteins in peripheral blood to discriminate MZ twins. We identified 1749 known metabolites and 622 proteins in proteomic analysis. The metabolic profiles of four pairs of MZ twins revealed minor differences in intra-MZ twins and major differences in inter-MZ twins. Each pair of MZ twins exhibited distinct characteristics, and four metabolites-methyl picolinate, acesulfame, paraxanthine, and phenylbenzimidazole sulfonic acid-were observed in all four MZ twin pairs. These four differential exogenous metabolites conincidently show that the different external environments and life styles can be well distinguished by metabolites, considering that twins do not all have the same eating habits and living environments. Moreover, MZ twins showed different protein profiles in serum but not in whole blood. Thus, our results indicate that differential metabolites provide potential biomarkers for the personal identification of MZ twins in forensic medicine.
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Affiliation(s)
- Kuo Zeng
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Jiang Du
- Department of Pathology, School of Basic Medicine, China Medical University, Shenyang, P.R. China
| | - Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Dan-Yang Wang
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Mao-Ling Sun
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Dong-Yi Wang
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Shu-Han Liu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Kun Liu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, P.R. China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China.
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China.
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China.
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Lourenço CM, Sallum JMF, Pereira AM, Girotto PN, Kok F, Vilela DRF, Barron E, Pessoa A, Oliveira BMD. A needle in a haystack? The impact of a targeted epilepsy gene panel in the identification of a treatable but rapidly progressive metabolic epilepsy: CLN2 disease. ARQUIVOS DE NEURO-PSIQUIATRIA 2024; 82:1-8. [PMID: 38763144 PMCID: PMC11102811 DOI: 10.1055/s-0044-1786854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/30/2024] [Indexed: 05/21/2024]
Abstract
BACKGROUND Neuronal ceroid lipofuscinoses (NCL) are a group of autosomal recessive, inherited, lysosomal, and neurodegenerative diseases that causes progressive dementia, seizures, movement disorders, language delay/regression, progressive visual failure, and early death. Neuronal ceroid lipofuscinosis type 2 (CLN2), caused by biallelic pathogenic variants of the TPP1 gene, is the only NCL with an approved targeted therapy. The laboratory diagnosis of CLN2 is established through highly specific tests, leading to diagnostic delays and eventually hampering the provision of specific treatment for patients with CLN2. Epilepsy is a common and clinically-identifiable feature among NCLs, and seizure onset is the main driver for families to seek medical care. OBJECTIVE To evaluate the results of the Latin America Epilepsy and Genetics Program, an epilepsy gene panel, as a comprehensive tool for the investigation of CLN2 among other genetic causes of epilepsy. METHODS A total of 1,284 patients with epilepsy without a specific cause who had at least 1 symptom associated with CLN2 were screened for variants in 160 genes associated with epilepsy or metabolic disorders presenting with epilepsy through an epilepsy gene panel. RESULTS Variants of the TPP1 gene were identified in 25 individuals (1.9%), 21 of them with 2 variants. The 2 most frequently reported variants were p.Arg208* and p.Asp276Val, and 2 novel variants were detected in the present study: p.Leu308Pro and c.89 + 3G > C Intron 2. CONCLUSION The results suggest that these genetic panels can be very useful tools to confirm or exclude CLN2 diagnosis and, if confirmed, provide disease-specific treatment for the patients.
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Affiliation(s)
| | - Juliana Maria Ferraz Sallum
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Oftalmologia e Ciências Visuais, São Paulo SP, Brazil.
| | | | | | - Fernando Kok
- Mendelics Análise Genômica, São Paulo SP, Brazil.
| | | | - Erika Barron
- BioMarin Brasil Farmacêutica Ltda., São Paulo SP, Brazil.
| | - André Pessoa
- Hospital Albert Sabin, Fortaleza CE, Brazil.
- Universidade Estadual do Ceará, Fortaleza CE, Brazil.
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Dessie EY, Ding L, Mersha TB. Integrative analysis identifies gene signatures mediating the effect of DNA methylation on asthma severity and lung function. Clin Epigenetics 2024; 16:15. [PMID: 38245772 PMCID: PMC10800055 DOI: 10.1186/s13148-023-01611-9] [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: 03/22/2023] [Accepted: 12/02/2023] [Indexed: 01/22/2024] Open
Abstract
DNA methylation (DNAm) changes play a key role in regulating gene expression in asthma. To investigate the role of epigenetics and transcriptomics change in asthma, we used publicly available DNAm (asthmatics, n = 96 and controls, n = 46) and gene expression (asthmatics, n = 79 and controls, n = 39) data derived from bronchial epithelial cells (BECs). We performed differential methylation/expression and weighted co-methylation/co-expression network analyses to identify co-methylated and co-expressed modules associated with asthma severity and lung function. For subjects with both DNAm and gene expression data (asthmatics, n = 79 and controls, n = 39), machine-learning technique was used to prioritize CpGs and differentially expressed genes (DEGs) for asthma risk prediction, and mediation analysis was used to uncover DEGs that mediate the effect of DNAm on asthma severity and lung function in BECs. Finally, we validated CpGs and their associated DEGs and the asthma risk prediction model in airway epithelial cells (AECs) dataset. The asthma risk prediction model based on 18 CpGs and 28 DEGs showed high accuracy in both the discovery BEC dataset with area under the receiver operating characteristic curve (AUC) = 0.99 and the validation AEC dataset (AUC = 0.82). Genes in the three co-methylated and six co-expressed modules were enriched in multiple pathways including WNT/beta-catenin signaling and notch signaling. Moreover, we identified 35 CpGs correlated with DEGs in BECs, of which 17 CpGs including cg01975495 (SERPINE1), cg10528482 (SLC9A3), cg25477769 (HNF1A) and cg26639146 (CD9), cg17945560 (TINAGL1) and cg10290200 (FLNC) were replicated in AECs. These DEGs mediate the association between DNAm and asthma severity and lung function. Overall, our study investigated the role of DNAm and gene expression change in asthma and provided an insight into the mechanisms underlying the effects of DNA methylation on asthma, asthma severity and lung function.
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Affiliation(s)
- Eskezeia Y Dessie
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lili Ding
- Division of Biostatistics and Epidemiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Dunn SE, Correale J, Gommerman JL, Horwitz MS. Editorial: Environmental factors in autoimmunity. Front Immunol 2024; 14:1361884. [PMID: 38292480 PMCID: PMC10824893 DOI: 10.3389/fimmu.2023.1361884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Affiliation(s)
- Shannon E. Dunn
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Jorge Correale
- Institute of Biological Chemistry and Physiocochemistry, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Marc S. Horwitz
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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Schulte S, Eberhardt N, Roedig T, Schreiner F, Plamper M, Bartmann P, Holterhus PM, Kulle AE, Gohlke B. Salivary Diurnal Glucocorticoid Profiles in Monozygotic Twins With Intratwin Birthweight Differences. J Clin Endocrinol Metab 2023; 109:e40-e50. [PMID: 37610251 DOI: 10.1210/clinem/dgad492] [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: 06/02/2023] [Revised: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
CONTEXT Low birthweight (bw) and unfavorable intrauterine conditions have been associated with metabolic sequelae in later life, but little is known about their impact on glucocorticoid metabolism. OBJECTIVE We studied monozygotic twins with intratwin bw differences to analyze the long-term impact of bw on glucocorticoid metabolism. METHODS 46 monozygotic twin pairs with bw differences of <1 SDS (concordant; n = 29) and ≥1 SDS (discordant; n = 17) were recruited. At 6.9 years (mean age), saliva samples were collected (at 7 hours, 13 hours, 18 hours and 21 hour) and analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS We found significant or highly significant intratwin correlations in all twin pairs at 3 of 4 (cortisol), and 4 of 4 (cortisone) time points. Graphic evaluation of the diurnal cortisol patterns for each twin pair showed a distinct alignment in all groups. Analyses of the change of intratwin differences over the day by mixed linear modeling showed no intratwin differences in diurnal patterns. Regression analyses of intratwin differences at 7:00 hours showed a significant influence of catch-up growth, indicating lower cortisol concentrations in smaller twins with more catch-up growth (adj. R2 = 0.159, P = .014, ß = -3.71, F(1,42) = 9.15, f2 = 0.19). CONCLUSION In monozygotic twins with intratwin bw differences, intratwin catch-up growth showed a moderate influence on intratwin differences in morning cortisol concentrations. We observed no differences regarding diurnal patterns. In contrast, in all groups, we found significant intratwin correlations for cortisol and cortisone over the day and a pronounced graphic alignment of cortisol diurnal patterns. We therefore suggest a predominant significance of the genetic background compared with bw differences on cortisol metabolism.
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Affiliation(s)
- Sandra Schulte
- Department of Paediatric Endocrinology and Diabetology, Children's University Hospital Bonn, 53127 Bonn, Germany
| | - Nora Eberhardt
- Department of Paediatric Endocrinology and Diabetology, Children's University Hospital Bonn, 53127 Bonn, Germany
| | - Thea Roedig
- Department of Paediatric Endocrinology and Diabetology, Children's University Hospital Bonn, 53127 Bonn, Germany
| | - Felix Schreiner
- Department of Paediatric Endocrinology and Diabetology, Children's University Hospital Bonn, 53127 Bonn, Germany
| | - Michaela Plamper
- Department of Paediatric Endocrinology and Diabetology, Children's University Hospital Bonn, 53127 Bonn, Germany
| | - Peter Bartmann
- Department of Neonatology and Paediatric Intensive Care, Children's University Hospital Bonn, 53127 Bonn, Germany
| | - Paul-Martin Holterhus
- Department of Paediatrics and Adolescent Medicine I, Paediatric Endocrinology and Diabetes, University Hospital of Schleswig - Holstein, Campus Kiel/Christian-Albrechts University of Kiel, 24105 Kiel, Germany
| | - Alexandra E Kulle
- Department of Paediatrics and Adolescent Medicine I, Paediatric Endocrinology and Diabetes, University Hospital of Schleswig - Holstein, Campus Kiel/Christian-Albrechts University of Kiel, 24105 Kiel, Germany
| | - Bettina Gohlke
- Department of Paediatric Endocrinology and Diabetology, Children's University Hospital Bonn, 53127 Bonn, Germany
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Boer LL, Winter E, Gorissen B, Oostra RJ. Phenotypically Discordant Anomalies in Conjoined Twins: Quirks of Nature Governed by Molecular Pathways? Diagnostics (Basel) 2023; 13:3427. [PMID: 37998563 PMCID: PMC10669976 DOI: 10.3390/diagnostics13223427] [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: 10/03/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
A multitude of additional anomalies can be observed in virtually all types of symmetrical conjoined twins. These concomitant defects can be divided into different dysmorphological patterns. Some of these patterns reveal their etiological origin through their topographical location. The so-called shared anomalies are traceable to embryological adjustments and directly linked to the conjoined-twinning mechanism itself, inherently located within the boundaries of the coalescence area. In contrast, discordant patterns are anomalies present in only one of the twin members, intrinsically distant from the area of union. These dysmorphological entities are much more difficult to place in a developmental perspective, as it is presumed that conjoined twins share identical intra-uterine environments and intra-embryonic molecular and genetic footprints. However, their existence testifies that certain developmental fields and their respective developmental pathways take different routes in members of conjoined twins. This observation remains a poorly understood phenomenon. This article describes 69 cases of external discordant patterns within different types of otherwise symmetrical mono-umbilical conjoined twins and places them in a developmental perspective and a molecular framework. Gaining insights into the phenotypes and underlying (biochemical) mechanisms could potentially pave the way and generate novel etiological visions in the formation of conjoined twins itself.
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Affiliation(s)
- Lucas L. Boer
- Department of Medical Imaging, Section Anatomy and Museum for Anatomy and Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Eduard Winter
- Pathologisch-Anatomische Sammlung im Narrenturm-NHM, 1090 Vienna, Austria
| | - Ben Gorissen
- Department of Medical Imaging, Section Anatomy and Museum for Anatomy and Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Roelof-Jan Oostra
- Department of Medical Biology, Sections Clinical Anatomy & Embryology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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Hammi Y, Ferjani M, Meddeb R, Kacem R, Sayari T, Mrad R, Gargah T. Phenotype Spectrum in Tunisian Population with NPHP1 Deletion. Indian J Nephrol 2023; 33:426-431. [PMID: 38174310 PMCID: PMC10752411 DOI: 10.4103/ijn.ijn_248_22] [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: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 01/05/2024] Open
Abstract
Introduction Nephronophthisis (NPHP) is a tubulointerstitial kidney disorder with an autosomal recessive inheritance pattern. Its genetic heterogeneity contributes to phenotype variability. The most frequent etiology of juvenile nephronophthisis is a mutation in the nephronophthisis type 1 (NPHP1) gene. This study aimed to evaluate the genotype-phenotype correlation in NPHP1 gene mutation. Methods A multicenter retrospective study was performed over 20 years from 1998 to 2018 to describe the clinical, biological, and radiological features associated with the large deletion NPHP1 gene in 32 patients. Results The incidence of NPHP1 was 1.6/204041. Eighty-one percent of our patients were born out of consanguineous marriages. The mean age at diagnosis was 14 ± 7 years. The patients were divided into three groups: isolated nephronophthisis (72%), syndromic nephronophthisis (19%), and patients without recognizable syndrome (9%). Intrafamilial and geographical variability was observed in syndrome diagnoses and in age at the onset of CKD stage 5. Genotype frequency varied between 50% and 100% in genealogical data. Juvenile (47%), adolescent (37%), and adult (13%) clinical forms have been distinguished by the onset of CKD stage 5. The five-year survival rate of renal transplantation was 80%. Conclusion Given the broad clinical spectrum of NPHP1 associated with the large deletion of the NPHP1 gene, no genotype-phenotype correlation could be established.
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Affiliation(s)
- Yousra Hammi
- Department of Pediatric, Charles Nicolle Hospital, Tunis, Tunisia
- Department of Community Health Department A, Medecine Faculty of Tunis, University of Tunis El Manar, Tunisia
| | - Maryem Ferjani
- Department of Pediatric, Charles Nicolle Hospital, Tunis, Tunisia
- Department of Community Health Department A, Medecine Faculty of Tunis, University of Tunis El Manar, Tunisia
| | - Rym Meddeb
- Department of Community Health Department A, Medecine Faculty of Tunis, University of Tunis El Manar, Tunisia
- Department of Genetic, Charles Nicolle Hospital, Tunis, Tunisia
| | - Rania Kacem
- Department of Pediatric, CHI Frejus, Saint Raphaël, Tunisia
| | - Taha Sayari
- Department of Pediatric, Charles Nicolle Hospital, Tunis, Tunisia
- Department of Community Health Department A, Medecine Faculty of Tunis, University of Tunis El Manar, Tunisia
| | - Ridha Mrad
- Department of Community Health Department A, Medecine Faculty of Tunis, University of Tunis El Manar, Tunisia
- Department of Genetic, Charles Nicolle Hospital, Tunis, Tunisia
| | - Tahar Gargah
- Department of Pediatric, Charles Nicolle Hospital, Tunis, Tunisia
- Department of Community Health Department A, Medecine Faculty of Tunis, University of Tunis El Manar, Tunisia
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Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Chih-Hsiang Y, Bergsma A, Drougard A, Dror E, Chandler D, Schramek D, Triche TJ, Pospisilik JA. Developmental priming of cancer susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557446. [PMID: 37745326 PMCID: PMC10515831 DOI: 10.1101/2023.09.12.557446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity (Trim28+/D9) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility 'states' in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.
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Affiliation(s)
- Ilaria Panzeri
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Luca Fagnocchi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Stefanos Apostle
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Megan Tompkins
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Kristen Schaefer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Genetics and Genome Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yang Chih-Hsiang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Alexis Bergsma
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Parkinson’s Disease Center, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Anne Drougard
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Erez Dror
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Darrell Chandler
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Timothy J. Triche
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - J. Andrew Pospisilik
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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Si W, Ni Y, Jiang Q, Tan L, Sparagano O, Li R, Yang G. Nanopore sequencing identifies differentially methylated genes in the central nervous system in experimental autoimmune encephalomyelitis. J Neuroimmunol 2023; 381:578134. [PMID: 37364516 DOI: 10.1016/j.jneuroim.2023.578134] [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: 04/25/2023] [Revised: 05/31/2023] [Accepted: 06/18/2023] [Indexed: 06/28/2023]
Abstract
Multiple Sclerosis (MS) is a chronic autoimmune-mediated demyelinating disease of the central nervous system (CNS) that might be triggered by aberrant epigenetic changes in the genome. DNA methylation is the most studied epigenetic mechanism that participates in MS pathogenesis. However, the overall methylation level in the CNS of MS patients remains elusive. We used direct long-read nanopore DNA sequencing and characterized the differentially methylated genes in the brain from mice with experimental autoimmune encephalomyelitis (EAE), an animal model of MS. We identified 163 hypomethylated promoters and 327 hypermethylated promoters. These genomic alterations were linked to various biological processes including metabolism, immune responses, neural activities, and mitochondrial dynamics, all of which are vital for EAE development. Our results indicate a great potential of nanopore sequencing in identifying genomic DNA methylation in EAE and provide important guidance for future studies investigating the MS/EAE pathology.
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Affiliation(s)
- Wen Si
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR 999077, China
| | - Ying Ni
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR 999077, China
| | - Qianling Jiang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR 999077, China
| | - Lu Tan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR 999077, China
| | - Olivier Sparagano
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR 999077, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR 999077, China.
| | - Guan Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR 999077, China.
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Hefter H, Kruschel TS, Novak M, Rosenthal D, Luedde T, Meuth SG, Albrecht P, Hartmann CJ, Samadzadeh S. Differences in the Time Course of Recovery from Brain and Liver Dysfunction in Conventional Long-Term Treatment of Wilson Disease. J Clin Med 2023; 12:4861. [PMID: 37510976 PMCID: PMC10381896 DOI: 10.3390/jcm12144861] [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: 05/03/2023] [Revised: 06/30/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The aim of this study was to demonstrate that both neurological and hepatic symptoms respond to copper chelation therapy in Wilson disease (WD). However, the time course of their recovery is different. METHODS Eighteen patients with neurological WD from a single specialized center who had been listed for liver transplantation during the last ten years and two newly diagnosed homozygous twins were recruited for this retrospective study. The mean duration of conventional treatment was 7.3 years (range: 0.25 to 36.2 years). A custom Wilson disease score with seven motor items, three non-motor items, and 33 biochemical parameters of the blood and urine, as well as the MELD score, was determined at various checkup visits during treatment. These data were extracted from the charts of the patients. RESULTS Treatment was initiated with severity-dependent doses (≥900 mg) of D-penicillamine (DPA) or triethylene-tetramin-dihydrochloride (TRIEN). The motor score improved in 10 and remained constant in 8 patients. Worsening of neurological symptoms was observed only in two patients who developed comorbidities (myasthenia gravis or hemispheric stroke). The neurological symptoms continuously improved over the years until the majority of patients became only mildly affected. In contrast to this slow recovery of the neurological symptoms, the MELD score and liver enzymes had already started to improve after 1 month and rapidly improved over the next 6 months in 19 patients. The cholinesterase levels continued to increase significantly (p < 0.0074) even further. One patient whose MELD score indicated further progression of liver disease received an orthotopic liver transplantation 3 months after the diagnosis of WD and the onset of DPA treatment. CONCLUSIONS Neurological and hepatic symptoms both respond to copper chelation therapy. For patients with acute liver failure, the first 4 months are critical. This is the time span in which patients have to wait either for a donor organ or until significant improvement has occurred under conventional therapy. For patients with severe neurological symptoms, it is important that they are treated with fairly high doses over several years.
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Affiliation(s)
- Harald Hefter
- Departments of Neurology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
| | - Theodor S Kruschel
- Departments of Neurology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
| | - Max Novak
- Departments of Neurology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
| | - Dietmar Rosenthal
- Departments of Neurology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
| | - Tom Luedde
- Departments of Gastroenterology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
| | - Sven G Meuth
- Departments of Neurology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
| | - Philipp Albrecht
- Departments of Neurology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
- Department of Neurology, Kliniken Maria Hilf GmbH Mönchengladbach, 41063 Mönchengladbach, Germany
| | - Christian J Hartmann
- Departments of Neurology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
| | - Sara Samadzadeh
- Departments of Neurology, University of Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Unverstät zu Berlin, Experimental and Clinical Research Center, 13125 Berlin, Germany
- Department of Regional Health Research and Molecular Medicine, University of Southern Denmark, 5230 Odense, Denmark
- Department of Neurology, Slagelse Hospital, 4200 Slagelse, Denmark
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12
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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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Truong BT, Shull LC, Lencer E, Bend EG, Field M, Blue EE, Bamshad MJ, Skinner C, Everman D, Schwartz CE, Flanagan-Steet H, Artinger KB. PRDM1 DNA-binding zinc finger domain is required for normal limb development and is disrupted in split hand/foot malformation. Dis Model Mech 2023; 16:dmm049977. [PMID: 37083955 PMCID: PMC10151829 DOI: 10.1242/dmm.049977] [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: 11/10/2022] [Accepted: 03/09/2023] [Indexed: 04/22/2023] Open
Abstract
Split hand/foot malformation (SHFM) is a rare limb abnormality with clefting of the fingers and/or toes. For many individuals, the genetic etiology is unknown. Through whole-exome and targeted sequencing, we detected three novel variants in a gene encoding a transcription factor, PRDM1, that arose de novo in families with SHFM or segregated with the phenotype. PRDM1 is required for limb development; however, its role is not well understood and it is unclear how the PRDM1 variants affect protein function. Using transient and stable overexpression rescue experiments in zebrafish, we show that the variants disrupt the proline/serine-rich and DNA-binding zinc finger domains, resulting in a dominant-negative effect. Through gene expression assays, RNA sequencing, and CUT&RUN in isolated pectoral fin cells, we demonstrate that Prdm1a directly binds to and regulates genes required for fin induction, outgrowth and anterior/posterior patterning, such as fgfr1a, dlx5a, dlx6a and smo. Taken together, these results improve our understanding of the role of PRDM1 in the limb gene regulatory network and identified novel PRDM1 variants that link to SHFM in humans.
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Affiliation(s)
- Brittany T. Truong
- Human Medical Genetics & Genomics Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lomeli C. Shull
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ezra Lencer
- Biology Department, Lafayette College, Easton, PA 18042, USA
| | - Eric G. Bend
- Greenwood Genetics Center, Greenwood, SC 29646, USA
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, AUS
| | - Elizabeth E. Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | - Kristin B. Artinger
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
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Tovo PA, Marozio L, Abbona G, Calvi C, Frezet F, Gambarino S, Dini M, Benedetto C, Galliano I, Bergallo M. Pregnancy Is Associated with Impaired Transcription of Human Endogenous Retroviruses and of TRIM28 and SETDB1, Particularly in Mothers Affected by Multiple Sclerosis. Viruses 2023; 15:v15030710. [PMID: 36992419 PMCID: PMC10051116 DOI: 10.3390/v15030710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Accumulating evidence highlights the pathogenetic role of human endogenous retroviruses (HERVs) in eliciting and maintaining multiple sclerosis (MS). Epigenetic mechanisms, such as those regulated by TRIM 28 and SETDB1, are implicated in HERV activation and in neuroinflammatory disorders, including MS. Pregnancy markedly improves the course of MS, but no study explored the expressions of HERVs and of TRIM28 and SETDB1 during gestation. Using a polymerase chain reaction real-time Taqman amplification assay, we assessed and compared the transcriptional levels of pol genes of HERV-H, HERV-K, HERV-W; of env genes of Syncytin (SYN)1, SYN2, and multiple sclerosis associated retrovirus (MSRV); and of TRIM28 and SETDB1 in peripheral blood and placenta from 20 mothers affected by MS; from 27 healthy mothers, in cord blood from their neonates; and in blood from healthy women of child-bearing age. The HERV mRNA levels were significantly lower in pregnant than in nonpregnant women. Expressions of all HERVs were downregulated in the chorion and in the decidua basalis of MS mothers compared to healthy mothers. The former also showed lower mRNA levels of HERV-K-pol and of SYN1, SYN2, and MSRV in peripheral blood. Significantly lower expressions of TRIM28 and SETDB1 also emerged in pregnant vs. nonpregnant women and in blood, chorion, and decidua of mothers with MS vs. healthy mothers. In contrast, HERV and TRIM28/SETDB1 expressions were comparable between their neonates. These results show that gestation is characterized by impaired expressions of HERVs and TRIM28/SETDB1, particularly in mothers with MS. Given the beneficial effects of pregnancy on MS and the wealth of data suggesting the putative contribution of HERVs and epigenetic processes in the pathogenesis of the disease, our findings may further support innovative therapeutic interventions to block HERV activation and to control aberrant epigenetic pathways in MS-affected patients.
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Affiliation(s)
- Pier-Angelo Tovo
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Correspondence: (P.-A.T.); (M.B.)
| | - Luca Marozio
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, 10126 Turin, Italy
| | - Giancarlo Abbona
- Pathology Unit, Department Laboratory Medicine, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Federica Frezet
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, 10126 Turin, Italy
| | - Stefano Gambarino
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Maddalena Dini
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Chiara Benedetto
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, 10126 Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Correspondence: (P.-A.T.); (M.B.)
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15
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Yuan X, Huang J, Wen L, Novakovic B, Kilby MD, Tong C, Qi H, Saffery R, Baker PN. Genome-wide DNA methylation analysis of discordant monozygotic twins reveals consistent sites of differential methylation associated with congenital heart disease. Genomics 2023; 115:110565. [PMID: 36690264 DOI: 10.1016/j.ygeno.2023.110565] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/04/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND Despite being essentially genetically identical, monozygotic (MZ) twins can be discordant for congenital heart disease (CHD), thus highlighting the importance of in utero environmental factors for CHD pathogenesis. This study aimed to identify the epigenetic variations between discordant MZ twin pairs that are associated with CHD at birth. METHODS Cord blood of CHD-discordant MZ twins from the Chongqing Longitudinal Twin Study Cohort was subjected to whole-genome bisulfite sequencing, then validated by MeDIP-qPCR and qRT-PCR. RESULTS 379 DMRs mapped to 175 differentially methylated genes (DMGs) were associated with CHD. Functional enrichment analysis identified these DMGs are involved in histone methylation, actin cytoskeleton organization, the regulation of cell differentiation, and adrenergic signaling in cardiomyocytes. Of note, SPESP1 and NOX5 were hypermethylated in CHD, and associated with lower gene expression levels. CONCLUSIONS Specific DNA methy (DNAm) variations in cord blood were associated with CHD, thus illustrating new biomarkers and potential interventional targets for CHD. TRIAL REGISTRATION ChiCTR-OOC-16008203, registered on 1 April 2016 at the Chinese Clinical Trial Registry.
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Affiliation(s)
- Xi Yuan
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jiayu Huang
- Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Wen
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Boris Novakovic
- Molecular Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Mark D Kilby
- Fetal Medicine Centre, Birmingham Women's & Children's Foundation Trust, Birmingham B15 2TG, UK; Institute of Metabolism & Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chao Tong
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Hongbo Qi
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China.
| | - Richard Saffery
- Molecular Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Parkville, VIC, Australia.
| | - Philip N Baker
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; College of Life Sciences, University of Leicester, Leicester LE1 7RH, UK.
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16
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Hong X, Miao K, Cao W, Lv J, Yu C, Huang T, Sun D, Liao C, Pang Y, Pang Z, Yu M, Wang H, Wu X, Liu Y, Gao W, Li L. Association Between DNA Methylation and Blood Pressure: A 5-Year Longitudinal Twin Study. Hypertension 2023; 80:169-181. [PMID: 36345830 DOI: 10.1161/hypertensionaha.122.19953] [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: 11/10/2022]
Abstract
BACKGROUND Previous EWASs (Epigenome-Wide Association Studies) have reported hundreds of blood pressure (BP) associated 5'-cytosine-phosphate-guanine-3' (CpG) sites. However, their results were inconsistent. Longitudinal observations on the temporal relationship between DNA methylation and BP are lacking. METHODS A candidate CpG site association study for BP was conducted on 1072 twins in the Chinese National Twin Registry. PubMed and EMBASE were searched for candidate CpG sites. Cross-lagged models were used to assess the temporal relationship between BP and DNA methylation in 308 twins who completed 2 surveys in 2013 and 2018. Then, the significant cross-lagged associations were validated by adopting the Inference About Causation From Examination of Familial Confounding approach. Finally, to evaluate the cumulative effects of DNA methylation on the progression of hypertension, we established methylation risk scores based on BP-associated CpG sites and performed Markov multistate models. RESULTS 16 and 20 CpG sites were validated to be associated with systolic BP and diastolic BP, respectively. In the cross-lagged analysis, we detected that methylation of 2 CpG sites could predict subsequent systolic BP, and systolic BP predicted methylation at another 3 CpG sites. For diastolic BP, methylation at 3 CpG sites had significant cross-lagged effects for predicting diastolic BP levels, while the prediction from the opposite direction was observed at one site. Among these, 3 associations were validated in the Inference About Causation From Examination of Familial Confounding analysis. Using the Markov multistate model, we observed that methylation risk scores were associated with the development of hypertension. CONCLUSIONS Our findings suggest the significance of DNA methylation in the development of hypertension.
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Affiliation(s)
- Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Ke Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, China (Z.P.)
| | - Min Yu
- Zhejiang Center for Disease Control and Prevention, Hangzhou, China (M.Y.)
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, China (H.W.)
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, China (X.W.)
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, China (Y.L.)
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
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Ting Y, Ting Z, Fei Z, Chun-Fang L, Zhen H. Prenatal Diagnosis of Structural Anomaly Among Singletons and Twins: Eight-Year Experience in a Chinese Tertiary Center. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2023; 42:185-192. [PMID: 35942928 DOI: 10.1002/jum.16069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/04/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES This study was designed to reveal structural abnormalities in singleton and twin pregnancies in the Chinese population. METHODS This retrospective study spanned 8 years and included 1228 singleton pregnancies (112,919 examinees) and 49 twin pregnancies (1865 examinees) with structural anomalies diagnosed by ultrasound. Detailed descriptions of anomalies, gestational weeks at diagnosis, and maternal age were recorded. The odds ratio was evaluated in twin pregnancies with detectable structural anomalies. RESULTS The annual average "ultrasound prevalence of fetal anomalies" among singleton and twin pregnancies were 1.09 and 3.06%, respectively. Mothers with twin anomalies were older (P < .001), and twin pregnancies were diagnosed with anomalies in earlier gestational weeks than singleton (P = .011). No differences were found in the types of anomalies between singleton and twin pregnancies. Central nervous system anomaly was the most common type in singleton and twin pregnancies. Twin pregnancies had higher rates of major anomalies than singleton (total OR 2.45), especially cardiovascular, central nervous, and gastrointestinal systems and ear/eye/face/neck disorders. CONCLUSIONS Compared with singleton, twin pregnancies had higher odds of detectable structural anomalies. Twin pregnancies with structural anomalies were diagnosed at earlier gestational age and associated with older maternal age. Central nervous system anomaly was the most common type in singleton and twin pregnancies.
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Affiliation(s)
- Yuan Ting
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Zhang Ting
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Zhao Fei
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Li Chun-Fang
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Han Zhen
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
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18
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Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to understand cellular responses to environmental influences in diseases. PLoS Genet 2023; 19:e1010567. [PMID: 36656803 PMCID: PMC9851565 DOI: 10.1371/journal.pgen.1010567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.
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Affiliation(s)
- Julia J. Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York, United States of America
| | - Srilakshmi Raj
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David A. Knowles
- New York Genome Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - John M. Greally
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
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Suseelan S, Pinna G. Heterogeneity in major depressive disorder: The need for biomarker-based personalized treatments. Adv Clin Chem 2022; 112:1-67. [PMID: 36642481 DOI: 10.1016/bs.acc.2022.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Major Depressive Disorder (MDD) or depression is a pathological mental condition affecting millions of people worldwide. Identification of objective biological markers of depression can provide for a better diagnostic and intervention criteria; ultimately aiding to reduce its socioeconomic health burden. This review provides a comprehensive insight into the major biomarker candidates that have been implicated in depression neurobiology. The key biomarker categories are covered across all the "omics" levels. At the epigenomic level, DNA-methylation, non-coding RNA and histone-modifications have been discussed in relation to depression. The proteomics system shows great promise with inflammatory markers as well as growth factors and neurobiological alterations within the endocannabinoid system. Characteristic lipids implicated in depression together with the endocrine system are reviewed under the metabolomics section. The chapter also examines the novel biomarkers for depression that have been proposed by studies in the microbiome. Depression affects individuals differentially and explicit biomarkers identified by robust research criteria may pave the way for better diagnosis, intervention, treatment, and prediction of treatment response.
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Affiliation(s)
- Shayam Suseelan
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States
| | - Graziano Pinna
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States; UI Center on Depression and Resilience (UICDR), Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States; Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States.
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20
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Hong X, Wu Z, Cao W, Lv J, Yu C, Huang T, Sun D, Liao C, Pang Y, Pang Z, Cong L, Wang H, Wu X, Liu Y, Gao W, Li L. Longitudinal Association of DNA Methylation With Type 2 Diabetes and Glycemic Traits: A 5-Year Cross-Lagged Twin Study. Diabetes 2022; 71:2804-2817. [PMID: 36170668 DOI: 10.2337/db22-0513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Investigators of previous cross-sectional epigenome-wide association studies (EWAS) in adults have reported hundreds of 5'-cytosine-phosphate-guanine-3' (CpG) sites associated with type 2 diabetes mellitus (T2DM) and glycemic traits. However, the results from EWAS have been inconsistent, and longitudinal observations of these associations are scarce. Furthermore, few studies have investigated whether DNA methylation (DNAm) could be modified by smoking, drinking, and glycemic traits, which have broad impacts on genome-wide DNAm and result in altering the risk of T2DM. Twin studies provide a valuable tool for epigenetic studies, as twins are naturally matched for genetic information. In this study, we conducted a systematic literature search in PubMed and Embase for EWAS, and 214, 33, and 117 candidate CpG sites were selected for T2DM, HbA1c, and fasting blood glucose (FBG). Based on 1,070 twins from the Chinese National Twin Registry, 67, 17, and 16 CpG sites from previous studies were validated for T2DM, HbA1c, and FBG. Longitudinal review and blood sampling for phenotypic information and DNAm were conducted twice in 2013 and 2018 for 308 twins. A cross-lagged analysis was performed to examine the temporal relationship between DNAm and T2DM or glycemic traits in the longitudinal data. A total of 11 significant paths from T2DM to subsequent DNAm and 15 paths from DNAm to subsequent T2DM were detected, suggesting both directions of associations. For glycemic traits, we detected 17 cross-lagged associations from baseline glycemic traits to subsequent DNAm, and none were from the other cross-lagged direction, indicating that CpG sites may be the consequences, not the causes, of glycemic traits. Finally, a longitudinal mediation analysis was performed to explore the mediation effects of DNAm on the associations of smoking, drinking, and glycemic traits with T2DM. No significant mediations of DNAm in the associations linking smoking and drinking with T2DM were found. In contrast, our study suggested a potential role of DNAm of cg19693031, cg00574958, and cg04816311 in mediating the effect of altered glycemic traits on T2DM.
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Affiliation(s)
- Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhiyu Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Liming Cong
- Zhejiang Center for Disease Control and Prevention, Hangzhou, China
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, China
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
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21
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DNA methylation at birth in monozygotic twins discordant for pediatric acute lymphoblastic leukemia. Nat Commun 2022; 13:6077. [PMID: 36241624 PMCID: PMC9568651 DOI: 10.1038/s41467-022-33677-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 09/28/2022] [Indexed: 01/11/2023] Open
Abstract
Aberrant DNA methylation constitutes a key feature of pediatric acute lymphoblastic leukemia at diagnosis, however its role as a predisposing or early contributor to leukemia development remains unknown. Here, we evaluate DNA methylation at birth in 41 leukemia-discordant monozygotic twin pairs using the Illumina EPIC array on archived neonatal blood spots to identify epigenetic variation associated with development of pediatric acute lymphoblastic leukemia, independent of genetic influence. Through conditional logistic regression we identify 240 significant probes and 10 regions associated with the discordant onset of leukemia. We identify a significant negative coefficient bias, indicating DNA hypomethylation in cases, across the array and enhanced in open sea, shelf/shore, and gene body regions compared to promoter and CpG island regions. Here, we show an association between global DNA hypomethylation and future development of pediatric acute lymphoblastic leukemia across disease-discordant genetically identical twins, implying DNA hypomethylation may contribute more generally to leukemia risk.
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22
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Migliore L, Coppedè F. Gene-environment interactions in Alzheimer disease: the emerging role of epigenetics. Nat Rev Neurol 2022; 18:643-660. [PMID: 36180553 DOI: 10.1038/s41582-022-00714-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2022] [Indexed: 12/15/2022]
Abstract
With the exception of a few monogenic forms, Alzheimer disease (AD) has a complex aetiology that is likely to involve multiple susceptibility genes and environmental factors. The role of environmental factors is difficult to determine and, until a few years ago, the molecular mechanisms underlying gene-environment (G × E) interactions in AD were largely unknown. Here, we review evidence that has emerged over the past two decades to explain how environmental factors, such as diet, lifestyle, alcohol, smoking and pollutants, might interact with the human genome. In particular, we discuss how various environmental AD risk factors can induce epigenetic modifications of key AD-related genes and pathways and consider how epigenetic mechanisms could contribute to the effects of oxidative stress on AD onset. Studies on early-life exposures are helping to uncover critical time windows of sensitivity to epigenetic influences from environmental factors, thereby laying the foundations for future primary preventative approaches. We conclude that epigenetic modifications need to be considered when assessing G × E interactions in AD.
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Affiliation(s)
- Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy. .,Department of Laboratory Medicine, Pisa University Hospital, Pisa, Italy.
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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23
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Yang CH, Fagnocchi L, Apostle S, Wegert V, Casaní-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Bras J, Thomasen M, Grunnet LG, Vaag AA, Gillberg L, Grundberg E, Conesa A, Körner A, Pospisilik JA. Independent phenotypic plasticity axes define distinct obesity sub-types. Nat Metab 2022; 4:1150-1165. [PMID: 36097183 PMCID: PMC9499872 DOI: 10.1038/s42255-022-00629-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023]
Abstract
Studies in genetically 'identical' individuals indicate that as much as 50% of complex trait variation cannot be traced to genetics or to the environment. The mechanisms that generate this 'unexplained' phenotypic variation (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) as a conserved factor that buffers against UPV. We find that Nnat deficiency in isogenic mice triggers the emergence of a bi-stable polyphenism, where littermates emerge into adulthood either 'normal' or 'overgrown'. Mechanistically, this is mediated by an insulin-dependent overgrowth that arises from histone deacetylase (HDAC)-dependent β-cell hyperproliferation. A multi-dimensional analysis of monozygotic twin discordance reveals the existence of two patterns of human UPV, one of which (Type B) phenocopies the NNAT-buffered polyphenism identified in mice. Specifically, Type-B monozygotic co-twins exhibit coordinated increases in fat and lean mass across the body; decreased NNAT expression; increased HDAC-responsive gene signatures; and clinical outcomes linked to insulinemia. Critically, the Type-B UPV signature stratifies both childhood and adult cohorts into four metabolic states, including two phenotypically and molecularly distinct types of obesity.
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Affiliation(s)
- Chih-Hsiang Yang
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | | | - Vanessa Wegert
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Kathrin Landgraf
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
| | - Ilaria Panzeri
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erez Dror
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Roche Diagnostics Deutschland, Mannheim, Germany
| | - Till Wörpel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Di Lu
- Van Andel Institute, Grand Rapids, MI, USA
| | - Tao Yang
- Van Andel Institute, Grand Rapids, MI, USA
| | - Elizabeth Gibbons
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Martin Thomasen
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Louise G Grunnet
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Allan A Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Linn Gillberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, MO, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, USA
| | - Antje Körner
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - J Andrew Pospisilik
- Van Andel Institute, Grand Rapids, MI, USA.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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24
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Transcriptome Profiling Reveals Differential Expression of Circadian Behavior Genes in Peripheral Blood of Monozygotic Twins Discordant for Parkinson's Disease. Cells 2022; 11:cells11162599. [PMID: 36010675 PMCID: PMC9406852 DOI: 10.3390/cells11162599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Parkinson’s disease (PD) is one of the most common neurodegenerative diseases. Investigating individuals with the most identical genetic background is optimal for minimizing the genetic contribution to gene expression. These individuals include monozygotic twins discordant for PD. Monozygotic twins have the same genetic background, age, sex, and often similar environmental conditions. The aim of this study was to carry out a transcriptome analysis of the peripheral blood of three pairs of monozygotic twins discordant for PD. We identified the metabolic process “circadian behavior” as a priority process for further study. Different expression of genes included in the term “circadian behavior” confirms that this process is involved in PD pathogenesis. We found increased expression of three genes associated with circadian behavior, i.e., PTGDS, ADORA2A, and MTA1, in twins with PD. These genes can be considered as potential candidate genes for this disease.
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25
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Yang X, Li L, Chai X, Liu J. The association between ST8SIA2 gene and behavioral phenotypes in children with autism spectrum disorder. Front Behav Neurosci 2022; 16:929878. [PMID: 35957920 PMCID: PMC9359136 DOI: 10.3389/fnbeh.2022.929878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 (ST8SIA2) encodes a type II membrane protein that is thought to catalyze the transfer of sialic acid (SA) from CMP-SA to N-linked oligosaccharides and glycoproteins. Some population and animal studies have indicated an association between the ST8SIA2 gene and autism spectrum disorder (ASD). However, there is limited information on the correlation between ST8SIA2 and autistic behavioral symptoms.MethodsIn this study, 69 ASD and 76 normal control children who were age- and sex-matched were recruited. ST8SIA2 expression and methylation levels were measured by reverse transcription quantitative real-time PCR and pyrosequencing, respectively, and the behavioral phenotypes of ASD children were assessed.ResultsThe ASD group had lower ST8SIA2 gene expression levels than the control group [t(0.05/2,143) = 2.582, p = 0.011]. Moreover, ST8SIA2 expression levels were positively correlated with daily life skills (rs = 0.381, p = 0.008) and negatively associated with stereotyped behaviors in the ASD group (rs = -0.510, p = 0.004). The methylation levels of the Chr. 15: 92984625 and Chr. 15: 92998561 sites of the ST8SIA2 gene in ASD children were higher than those of controls. The Chr. 15: 92984625 site was positively correlated with the stereotyped behaviors of ASD children (rs = 0.41, p = 0.039).ConclusionThis study provides a scientific basis to elucidate the relationship between the ST8SIA2 gene and behavioral phenotypes of ASD.
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Affiliation(s)
- Xiaolei Yang
- Postdoctoral Workstation, Research Institute of Medical and Pharmacy, Qiqihar Medical University, Qiqihar, China
- Department of Preventive Medicine, School of Public Health, Qiqihar Medical University, Qiqihar, China
| | - Lin Li
- Center for Prevention of Disease, Hospital of Traditional Chinese Medicine of Qiqihar, Qiqihar, China
| | - Xuejiao Chai
- Department of Preventive Medicine, School of Public Health, Qiqihar Medical University, Qiqihar, China
| | - Jicheng Liu
- Postdoctoral Workstation, Research Institute of Medical and Pharmacy, Qiqihar Medical University, Qiqihar, China
- *Correspondence: Jicheng Liu,
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
| | - Caroline F. Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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27
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Different Response Behavior to Therapeutic Approaches in Homozygotic Wilson's Disease Twins with Clinical Phenotypic Variability: Case Report and Literature Review. Genes (Basel) 2022; 13:genes13071217. [PMID: 35885998 PMCID: PMC9318625 DOI: 10.3390/genes13071217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 12/17/2022] Open
Abstract
Background: Wilson’s disease (WD) is an autosomal-recessive disorder of copper deposition caused by pathogenic variants in the copper-transporting ATP7B gene. There is not a clear correlation between genotype and phenotype in WD regarding symptom manifestations. This is supported by the presentation of genetically identical WD twins with phenotypic discordance and different response behavior to WD-specific therapy. Case Presentation: One of the female homozygous twins (age: 26 yrs) developed writing, speaking, swallowing and walking deficits which led to in-patient examination without conclusive results but recommended genetic testing. Both sisters were tested and were heterozygous for the C.2304dupC;p(Met769Hisf*26) and the C.3207C>A;p(His1069Gln) mutation. Self-medication of the affected sibling with 450 mg D-penicillamine (DPA) did not prevent further deterioration. She developed a juvenile parkinsonian syndrome and became wheelchair-bound and anarthric. A percutaneous endoscopic gastrostomy was applied. Her asymptomatic sister helped her with her daily life. Despite the immediate increase of the DPA dose (up to 1800 mg within 3 weeks) in the severely affected patient and the initiation of DPA therapy (up to 600 mg within 2 weeks) in the asymptomatic patient after the first visit in our institution, liver function tests further deteriorated in both patients. After 2 months, the parkinsonian patient started to improve and walk again, but experienced several falls, broke her right shoulder and underwent two necessary surgical interventions. With further consequent copper elimination therapy, liver dysfunction improved in both patients, without need for orthotopic liver transplantation (LTX) in the severely affected patient. Her excellent recovery of liver and brain dysfunction was only transiently interrupted by the development of a nephrotic syndrome which disappeared after switching to Cuprior®. Unfortunately, she died from fulminant pneumonia. Conclusion: Despite identical genetic disposition, WD symptom presentations may develop differently in monozygotic twins, and they may need to be placed on a very different therapeutical regimen. The underlying gene-environment interaction is unclear so far.
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28
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Ebert T, Tran N, Schurgers L, Stenvinkel P, Shiels PG. Ageing - Oxidative stress, PTMs and disease. Mol Aspects Med 2022; 86:101099. [PMID: 35689974 DOI: 10.1016/j.mam.2022.101099] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications (PTMs) have been proposed as a link between the oxidative stress-inflammation-ageing trinity, thereby affecting several hallmarks of ageing. Phosphorylation, acetylation, and ubiquitination cover >90% of all the reported PTMs. Several of the main PTMs are involved in normal "healthy" ageing and in different age-related diseases, for instance neurodegenerative, metabolic, cardiovascular, and bone diseases, as well as cancer and chronic kidney disease. Ultimately, data from human rare progeroid syndromes, but also from long-living animal species, imply that PTMs are critical regulators of the ageing process. Mechanistically, PTMs target epigenetic and non-epigenetic pathways during ageing. In particular, epigenetic histone modification has critical implications for the ageing process and can modulate lifespan. Therefore, PTM-based therapeutics appear to be attractive pharmaceutical candidates to reduce the burden of ageing-related diseases. Several phosphorylation and acetylation inhibitors have already been FDA-approved for the treatment of other diseases and offer a unique potential to investigate both beneficial effects and possible side-effects. As an example, the most well-studied senolytic compounds dasatinib and quercetin, which have already been tested in Phase 1 pilot studies, also act as kinase inhibitors, targeting cellular senescence and increasing lifespan. Future studies need to carefully determine the best PTM-based candidates for the treatment of the "diseasome of ageing".
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Affiliation(s)
- Thomas Ebert
- Karolinska Institute, Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Stockholm, Sweden; University of Leipzig Medical Center, Medical Department III - Endocrinology, Nephrology, Rheumatology, Leipzig, Germany.
| | - Ngoc Tran
- University of Glasgow, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary & Life Sciences, Institute of Cancer Sciences, Glasgow, UK
| | - Leon Schurgers
- Department of Biochemistry, Cardiovascular Research School Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Peter Stenvinkel
- Karolinska Institute, Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Stockholm, Sweden
| | - Paul G Shiels
- University of Glasgow, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary & Life Sciences, Institute of Cancer Sciences, Glasgow, UK
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29
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Moore SS, Mukherji P, Leung M, Vrentas CE, Mwanja MM, Dai J. Methylation at CpG sites related to growth differentiation factor-15 was not prospectively associated with cardiovascular death in discordant monozygotic twins. Sci Rep 2022; 12:4410. [PMID: 35292700 PMCID: PMC8924170 DOI: 10.1038/s41598-022-08369-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Myocardial infarction patients had decreased methylation at four growth differentiating factor-15 (GDF-15) related CpG sites (cg13033858, cg16936953, cg17150809, and cg18608055). These sites had not been studied for their association with cardiovascular disease (CVD) deaths. Thus, we aimed to assess the associations independent of genes, shared environment, and traditional CVD risk factors. Nineteen white, male, monozygotic twin pairs discordant for CVD deaths were included from the National Heart, Lung and Blood Institute Twin Study (NHLBI) initiated in 1969. Data on vital status was collected through December 31, 2014. Methylation of buffy coat DNA at exam 3 (1986-87) was measured using the Illumina HumanMethylation450 BeadChip. Principal component analysis was used to generate a score representing blood leukocyte composition and baseline CVD risk factors and predominated with natural killer cells, CD4+ T cells, and Framingham risk score. Conditional logistic regression demonstrated that methylation at the four CpG sites was not associated with CVD deaths before (all p > 0.05, bootstrapped p > 0.05) and after adjustment for the score (all p > 0.05). Joint influences of cg16936953 and the score were statistically significant (p < 0.05). In conclusion, joint influences of methylation at the site cg16936953 and the score are prospectively associated with CVD deaths independent of germline and common environment.ClinicalTrials.gov Identifier for NHLBI Twin Study: NCT00005124.
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Affiliation(s)
- Spencer Shawn Moore
- Doctoral Program of Osteopathic Medicine, College of Osteopathic Medicine, Des Moines University, Des Moines, IA, 50312, USA
| | - Pallavi Mukherji
- Emergency Medicine Residency Program, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Ming Leung
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Catherine E Vrentas
- Master Program of Public Health, Des Moines University, Des Moines, IA, 50312, USA
| | - Melsa M Mwanja
- Oregon State Department of Human Services, Salem, OR, 97303, USA
| | - Jun Dai
- Department of Public Health, College of Health Sciences, Des Moines University, 3200 Grand Avenue, Des Moines, IA, 50312, USA.
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30
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Walker RF. A Mechanistic Theory of Development-Aging Continuity in Humans and Other Mammals. Cells 2022; 11:cells11050917. [PMID: 35269539 PMCID: PMC8909351 DOI: 10.3390/cells11050917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 12/29/2022] Open
Abstract
There is consensus among biogerontologists that aging occurs either as the result of a purposeful genome-based, evolved program or due to spontaneous, randomly occurring, maladaptive events. Neither concept has yet identified a specific mechanism to explain aging’s emergence and acceleration during mid-life and beyond. Presented herein is a novel, unifying mechanism with empirical evidence that describes how aging becomes continuous with development. It assumes that aging emerges from deterioration of a regulatory process that directs morphogenesis and morphostasis. The regulatory system consists of a genome-wide “backbone” within which its specific genes are differentially expressed by the local epigenetic landscapes of cells and tissues within which they reside, thereby explaining its holistic nature. Morphostasis evolved in humans to ensure the nurturing of dependent offspring during the first decade of young adulthood when peak parental vitality prevails in the absence of aging. The strict redundancy of each morphostasis regulatory cycle requires sensitive dependence upon initial conditions to avoid initiating deterministic chaos behavior. However, when natural selection declines as midlife approaches, persistent, progressive, and specific DNA damage and misrepair changes the initial conditions of the regulatory process, thereby compromising morphostasis regulatory redundancy, instigating chaos, initiating senescence, and accelerating aging thereafter.
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Khan K, Ahram DF, Liu YP, Westland R, Sampogna RV, Katsanis N, Davis EE, Sanna-Cherchi S. Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations. Kidney Int 2022; 101:473-484. [PMID: 34780871 PMCID: PMC8934530 DOI: 10.1016/j.kint.2021.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development.
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Affiliation(s)
- Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address)
| | - Dina F. Ahram
- Division of Nephrology, Columbia University, New York, USA
| | - Yangfan P. Liu
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, USA.,Department of Pediatric Nephrology, Amsterdam UMC- Emma Children’s Hospital, Amsterdam, NL
| | | | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA (current address); Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
| | - Erica E. Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address).,Department of Pediatrics and Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,To whom correspondence should be addressed: ADDRESS CORRESPONDENCE TO: Simone Sanna-Cherchi, MD, Division of Nephrology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA; Phone: 212-851-4925; Fax: 212-851-5461; . Erica E. Davis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7662; Fax: 312-503-7343; , Nicholas Katsanis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7339; Fax: 312-503-7343;
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA.
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Krishna M, Engevik M, Queliza K, Britto S, Shah R, Ruan W, Wang H, Versalovic J, Kellermayer R. Maternal Lactobacillus reuteri supplementation shifts the intestinal microbiome in mice and provides protection from experimental colitis in female offspring. FASEB Bioadv 2022; 4:109-120. [PMID: 35141475 PMCID: PMC8814561 DOI: 10.1096/fba.2021-00078] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022] Open
Abstract
The purpose of our experiment was to explore how stochastic (inter-individual variation) gut microbiome composition may link to inflammatory bowel disease (IBD) susceptibility and guide the development of a perinatal preventative probiotic. Dextran sodium sulfate (DSS) was introduced to C57BL/BJ mice to induce acute colitis as a model of IBD. Potentially protective bacteria were identified using a discovery-validation cohort approach toward stochastic DSS susceptibility. Lactobacilli (two different cocktails of L. reuteri and L. johnsonii strains) or control media were supplemented by mouth to dams prior to delivery and during lactation (i.e., perinatal probiotic). The pups were evaluated for DSS susceptibility at young adulthood. Fecal Lactobacillus was increased in the DSS-resistant mice in both the discovery and validation cohorts. Maternal supplementation of female offspring with an L. reuteri cocktail (strains 6798-1, 6798-jm, and 6798-cm) induced progressive microbiome separation and protection against colitis by young adulthood. Maternal supplementation of L. reuteri could confer protection against DSS colitis in young adult female mice. This work is the first to exploit stochastic mammalian microbiome variation to guide microbial therapeutic identification. Our findings underscore neonatal microbiome plasticity and set the stage for the potential development of perinatally deliverable protective probiotics against human IBD.
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Affiliation(s)
- Mahesh Krishna
- Johns Hopkins School of MedicineBaltimoreMarylandUSA
- Section of Pediatric GastroenterologyBaylor College of MedicineHoustonTexasUSA
| | - Melinda Engevik
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTexasUSA
| | - Karen Queliza
- Pediatric Gastroenterology, Hepatology and NutritionMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Savini Britto
- Section of Pediatric GastroenterologyBaylor College of MedicineHoustonTexasUSA
| | - Rajesh Shah
- Department of MedicineBaylor Scott and WhiteAustinTexasUSA
| | - Wenly Ruan
- Section of Pediatric GastroenterologyBaylor College of MedicineHoustonTexasUSA
| | - Hongtao Wang
- Section of Pediatric GastroenterologyBaylor College of MedicineHoustonTexasUSA
| | - James Versalovic
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTexasUSA
| | - Richard Kellermayer
- Section of Pediatric GastroenterologyBaylor College of MedicineHoustonTexasUSA
- USDA/ARS Children's Nutrition Research CenterTexas Children's HospitalHoustonTexasUSA
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Iranzo-Tatay C, Hervas-Marin D, Rojo-Bofill LM, Garcia D, Vaz-Leal FJ, Calabria I, Beato-Fernandez L, Oltra S, Sandoval J, Rojo-Moreno L. Genome-wide DNA methylation profiling in anorexia nervosa discordant identical twins. Transl Psychiatry 2022; 12:15. [PMID: 35013117 PMCID: PMC8748827 DOI: 10.1038/s41398-021-01776-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/18/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
Up until now, no study has looked specifically at epigenomic landscapes throughout twin samples, discordant for Anorexia nervosa (AN). Our goal was to find evidence to confirm the hypothesis that epigenetic variations play a key role in the aetiology of AN. In this study, we quantified genome-wide patterns of DNA methylation using the Infinium Human DNA Methylation EPIC BeadChip array ("850 K") in DNA samples isolated from whole blood collected from a group of 7 monozygotic twin pairs discordant for AN. Results were then validated performing a genome-wide DNA methylation profiling using DNA extracted from whole blood of a group of non-family-related AN patients and a group of healthy controls. Our first analysis using the twin sample revealed 9 CpGs associated to a gene. The validation analysis showed two statistically significant CpGs with the rank regression method related to two genes associated to metabolic traits, PPP2R2C and CHST1. When doing beta regression, 6 of them showed statistically significant differences, including 3 CpGs associated to genes JAM3, UBAP2L and SYNJ2. Finally, the overall pattern of results shows genetic links to phenotypes which the literature has constantly related to AN, including metabolic and psychological traits. The genes PPP2R2C and CHST1 have both been linked to the metabolic traits type 2 diabetes through GWAS studies. The genes UBAP2L and SYNJ2 have been related to other psychiatric comorbidity.
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Affiliation(s)
- C Iranzo-Tatay
- Psychiatry Service, Hospital la Fe, Valencia, Spain
- Department of Psychiatry, Medicine School, University of Valencia, Valencia, Spain
| | - D Hervas-Marin
- Department of Applied Statistics and Operational Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | | | - D Garcia
- Epigenomics Unit, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - F J Vaz-Leal
- Department of Psychiatry, Medicine School, University of Extremadura, Badajoz, Spain
| | - I Calabria
- Epigenomics Unit, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - L Beato-Fernandez
- Eating Disorders and Children's Psychiatry Department, Hospital General, Ciudad Real, Spain
| | - S Oltra
- Genetics and Prenatal Diagnosis Unit, Hospital La fe, Valencia, Spain
| | - J Sandoval
- Epigenomics Unit, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.
- Biomarkers and Precision Medicine Unit (UByMP), Instituto de Investigación Sanitaria La Fe, Valencia, Spain.
| | - L Rojo-Moreno
- Psychiatry Service, Hospital la Fe, Valencia, Spain
- Department of Psychiatry, Medicine School, University of Valencia, Valencia, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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34
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Ogunmwonyi I, Adebajo A, Wilkinson JM. The genetic and epigenetic contributions to the development of nutritional rickets. Front Endocrinol (Lausanne) 2022; 13:1059034. [PMID: 36619587 PMCID: PMC9815715 DOI: 10.3389/fendo.2022.1059034] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Nutritional rickets is an important disease in global health. Although nutritional rickets commonly manifests as bony deformities, there is an increased risk of life-threatening seizures secondary to hypocalcaemia. Dietary vitamin D deficiency is associated with the development of nutritional rickets among children and infants. This is especially true in populations of darker skinned individuals in high-latitude environments due to decreased ultraviolet light exposure, and in populations in tropical and subtropical climates due to cultural practices. A growing body of evidence has demonstrated that genetic factors might influence the likelihood of developing nutritional rickets by influencing an individual's susceptibility to develop deficiencies in vitamin D and/or calcium. This evidence has been drawn from a variety of different techniques ranging from traditional twin studies to next generation sequencing techniques. Additionally, the role of the epigenome in the development of rickets, although poorly understood, may be related to the effects of DNA methylation and non-coding RNAs on genes involved in bone metabolism. This review aims to provide an overview of the current evidence that investigates the genetic and epigenetic determinants of nutritional rickets.
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35
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Arumugam T, Ramphal U, Adimulam T, Chinniah R, Ramsuran V. Deciphering DNA Methylation in HIV Infection. Front Immunol 2021; 12:795121. [PMID: 34925380 PMCID: PMC8674454 DOI: 10.3389/fimmu.2021.795121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
With approximately 38 million people living with HIV/AIDS globally, and a further 1.5 million new global infections per year, it is imperative that we advance our understanding of all factors contributing to HIV infection. While most studies have focused on the influence of host genetic factors on HIV pathogenesis, epigenetic factors are gaining attention. Epigenetics involves alterations in gene expression without altering the DNA sequence. DNA methylation is a critical epigenetic mechanism that influences both viral and host factors. This review has five focal points, which examines (i) fluctuations in the expression of methylation modifying factors upon HIV infection (ii) the effect of DNA methylation on HIV viral genes and (iii) host genome (iv) inferences from other infectious and non-communicable diseases, we provide a list of HIV-associated host genes that are regulated by methylation in other disease models (v) the potential of DNA methylation as an epi-therapeutic strategy and biomarker. DNA methylation has also been shown to serve as a robust therapeutic strategy and precision medicine biomarker against diseases such as cancer and autoimmune conditions. Despite new drugs being discovered for HIV, drug resistance is a problem in high disease burden settings such as Sub-Saharan Africa. Furthermore, genetic therapies that are under investigation are irreversible and may have off target effects. Alternative therapies that are nongenetic are essential. In this review, we discuss the potential role of DNA methylation as a novel therapeutic intervention against HIV.
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Affiliation(s)
- Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Romona Chinniah
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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Marion MC, Ramos PS, Bachali P, Labonte AC, Zimmerman KD, Ainsworth HC, Heuer SE, Robl RD, Catalina MD, Kelly JA, Howard TD, Lipsky PE, Grammer AC, Langefeld CD. Nucleic Acid-Sensing and Interferon-Inducible Pathways Show Differential Methylation in MZ Twins Discordant for Lupus and Overexpression in Independent Lupus Samples: Implications for Pathogenic Mechanism and Drug Targeting. Genes (Basel) 2021; 12:genes12121898. [PMID: 34946847 PMCID: PMC8701117 DOI: 10.3390/genes12121898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/27/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic, multisystem, autoimmune inflammatory disease with genomic and non-genomic contributions to risk. We hypothesize that epigenetic factors are a significant contributor to SLE risk and may be informative for identifying pathogenic mechanisms and therapeutic targets. To test this hypothesis while controlling for genetic background, we performed an epigenome-wide analysis of DNA methylation in genomic DNA from whole blood in three pairs of female monozygotic (MZ) twins of European ancestry, discordant for SLE. Results were replicated on the same array in four cell types from a set of four Danish female MZ twin pairs discordant for SLE. Genes implicated by the epigenetic analyses were then evaluated in 10 independent SLE gene expression datasets from the Gene Expression Omnibus (GEO). There were 59 differentially methylated loci between unaffected and affected MZ twins in whole blood, including 11 novel loci. All but two of these loci were hypomethylated in the SLE twins relative to the unaffected twins. The genes harboring these hypomethylated loci exhibited increased expression in multiple independent datasets of SLE patients. This pattern was largely consistent regardless of disease activity, cell type, or renal tissue type. The genes proximal to CpGs exhibiting differential methylation (DM) in the SLE-discordant MZ twins and exhibiting differential expression (DE) in independent SLE GEO cohorts (DM-DE genes) clustered into two pathways: the nucleic acid-sensing pathway and the type I interferon pathway. The DM-DE genes were also informatically queried for potential gene–drug interactions, yielding a list of 41 drugs including a known SLE therapy. The DM-DE genes delineate two important biologic pathways that are not only reflective of the heterogeneity of SLE but may also correlate with distinct IFN responses that depend on the source, type, and location of nucleic acid molecules and the activated receptors in individual patients. Cell- and tissue-specific analyses will be critical to the understanding of genetic factors dysregulating the nucleic acid-sensing and IFN pathways and whether these factors could be appropriate targets for therapeutic intervention.
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Affiliation(s)
- Miranda C. Marion
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Paula S. Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Prathyusha Bachali
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Adam C. Labonte
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Hannah C. Ainsworth
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Sarah E. Heuer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
- The Jackson Laboratory, Tufts Graduate School of Biomedical Sciences, Bar Harbor, ME 04609, USA
| | - Robert D. Robl
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Michelle D. Catalina
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Peter E. Lipsky
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Amrie C. Grammer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
- Correspondence:
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Schmitz L, Schulte S, Stoffel-Wagner B, Bartmann P, Plamper M, Schreiner F, Woelfle J, Gohlke B. Birthweight Differences in Adolescent Monozygotic Twins Influence Androgens, Psychological Morbidity, and Health-Related Quality of Life. Horm Res Paediatr 2021; 93:433-441. [PMID: 33567430 DOI: 10.1159/000512653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/23/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Adverse prenatal conditions can exert a long-lasting impact in later life. PATIENTS AND METHODS Thirty-eight post-pubertal monozygotic twin pairs (16 female pairs) with divergent birthweight (bw) due to twin-to-twin transfusion syndrome were examined at a median of 15.1 years. Auxological and endocrine parameters were measured. To evaluate effects of intra-twin bw and hormone differences on mental health, adolescents and their parents completed the Strengths and Difficulties Questionnaire (SDQ), identifying psychological problems. Twins answered the questionnaire on health-related quality of life (HrQoL, KIDSCREEN-52). RESULTS Parents attributed a higher number of psychological challenges to the formerly smaller twins, for example, total difficulties (8.8 vs. 6.5, p = 0.009). Differences in bw were associated with differences in parental evaluation of problems, for example, peer relationship problems (r = -0.57 and p = 0.0001). In contrast, bw differences did not affect subjects' self-assessment of psychological factors but on physical well-being (r = 0.42, p = 0.017). The formerly smaller discordant twins showed significantly lower HrQoL regarding psychological well-being (24.9 vs. 26.6, T1,15 = -2.2, and p = 0.043) and moods and emotions (29.8 vs. 32.0, T1,15 = -2.3, p = 0.039). Higher concentrations of androstenedione were linked to greater psychological well-being (r = 0.39 and p = 0.036) in all twin pairs. CONCLUSION Our results show that the prenatal environment leading to bw differences exerts a long-lasting impact on diverging parental evaluation of mental health. Formerly smaller discordant twins showed significantly lower HrQoL regarding psychological well-being and moods and emotions. Higher androstenedione concentrations were linked to greater psychological well-being.
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Affiliation(s)
- Lioba Schmitz
- Paediatric Endocrinology Division, Children's University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Sandra Schulte
- Paediatric Endocrinology Division, Children's University Hospital Bonn, University of Bonn, Bonn, Germany,
| | - Birgit Stoffel-Wagner
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Peter Bartmann
- Department of Neonatology, Children's University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Michaela Plamper
- Paediatric Endocrinology Division, Children's University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Felix Schreiner
- Paediatric Endocrinology Division, Children's University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Joachim Woelfle
- Paediatric Endocrinology Division, Children's University Hospital Bonn, University of Bonn, Bonn, Germany.,Children's University Hospital Erlangen, University of Erlangen, Erlangen, Germany
| | - Bettina Gohlke
- Paediatric Endocrinology Division, Children's University Hospital Bonn, University of Bonn, Bonn, Germany
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Heritability of musculoskeletal pain and pain sensitivity phenotypes: two generations of the Raine Study. Pain 2021; 163:e580-e587. [PMID: 34686644 DOI: 10.1097/j.pain.0000000000002411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
ABSTRACT There is a need to better understand biological factors that increase the risk of persistent musculoskeletal pain and heightened pain sensitivity. Knowing the heritability (how genes account for differences in people's traits) can enhance the understanding of genetic versus environmental influences of pain and pain sensitivity. However, there are gaps in current knowledge, including the need for intergenerational studies to broaden our understanding of the genetic basis of pain. Data from Gen1 and Gen2 of the Raine Study were used to investigate the heritability of musculoskeletal pain, and pressure and cold pain sensitivity. Participants included parents (Gen 1, n=1092) and their offspring (Gen 2, n=688) who underwent a battery of testing and questionnaires including pressure and cold pain threshold testing and assessments of physical activity, sleep, musculoskeletal pain, mental health and adiposity. Heritability estimates were derived using the Sequential Oliogenic Linkage Analysis Routines (SOLAR) software. Heritability estimates for musculoskeletal pain and pressure pain sensitivity were significant, accounting for between 0.190 and 0.289 of the variation in the phenotype. In contrast, heritability of cold pain sensitivity was not significant. This is the largest intergenerational study to date to comprehensively investigate the heritability of both musculoskeletal pain and pain sensitivity, using robust statistical analysis. This study provides support for the heritability of musculoskeletal pain and pain sensitivity to pressure, suggesting the need for further convergence of genetic and environmental factors in models for the development and/or maintenance of these pain disorders.
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Abtahi H, Gholamzadeh M, Shahmoradi L, Shariat M. An information-based framework for development national twin registry: Scoping review and focus group discussion. Int J Health Plann Manage 2021; 36:1423-1444. [PMID: 34519094 DOI: 10.1002/hpm.3256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Registries in various clinical domains have been established in the last decades. The specific genetic structure of twins has enabled researchers to find answers to the role of genetics and the environment in medical sciences. Thus, twin registries were developed across the world to support twin studies. Our main objective was to devise a conceptual model for developing the national twin registry to ensure the success of this registry. METHODS In this descriptive and qualitative study, the combination of literature review and focus group discussions was applied to achieve suitable models for developing a national twin registry based on lessons learned from founded registries. The qualitative synthesis and reporting results were conducted based on the COREQ checklist. RESULTS According to a systematic literature review, the characteristics and employed strategies employed by established twin registries were recognized. Moreover, based on our objectives, suitable models for registry development were defined. The source of information, the different levels of data, and the information flow were determined based on this model. CONCLUSION Suggesting a conceptual framework for twin registry development at the national level based on the experiences of other countries could contribute to a greater understanding of twin registry implementation efficiently.
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Affiliation(s)
- Hamidreza Abtahi
- Associate Professor of Pulmonary and Critical Care Department, Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Marsa Gholamzadeh
- Ph.D. Student in Medical Informatics, Health Information Management Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Shahmoradi
- Associate Professor of Health Information Management, Health Information Management Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Mamak Shariat
- Family Health Research Institute, Maternal-Fetal and Neonatal Research Center, Tehran University of Medical Science, Tehran, Iran
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40
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Nofal H, AlAkad R, Nofal A, Rabie E, Chaikul T, Chiu FPC, Pramanik R, Alabdulkareem A, Onoufriadis A. H syndrome: A review of treatment options and a hypothesis of phenotypic variability. Dermatol Ther 2021; 34:e15082. [PMID: 34351669 DOI: 10.1111/dth.15082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/25/2021] [Accepted: 08/01/2021] [Indexed: 11/30/2022]
Abstract
H syndrome is a rare autosomal recessive disorder with clinical features comprising: hyperpigmentation, hypertrichosis, hearing loss, heart anomalies, low height, hypogonadism and hepatosplenomegaly. H syndrome results from loss-of-function mutations in SLC29A3 which leads to abnormal proliferation and function of histiocytes. Herein, we discuss the considerable phenotypic heterogeneity detected in a consanguineous Egyptian family comprising of four affected siblings, two of which are monozygotic twin and the possible therapeutics. The phenotypic variability may be attributed to the role of histiocytes in the tissue response to injury. Such variable expressivity of H syndrome renders the diagnosis challenging and delays the management. The different treatment approaches used for this rare entity are reviewed.
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Affiliation(s)
- Hagar Nofal
- Dermatology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Rania AlAkad
- Dermatology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmad Nofal
- Dermatology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Eman Rabie
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre (NRC), Cairo, Egypt.,Biotechnology Program, School of Sciences and Engineering, The American University in Cairo (AUC), Cairo, Egypt
| | - Thithiwat Chaikul
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Frank Po-Chao Chiu
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Rashida Pramanik
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Ahmad Alabdulkareem
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Alexandros Onoufriadis
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
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41
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Abstract
Epigenetics has enriched human disease studies by adding new interpretations to disease features that cannot be explained by genetic and environmental factors. However, identifying causal mechanisms of epigenetic origin has been challenging. New opportunities have risen from recent findings in intra-individual and cyclical epigenetic variation, which includes circadian epigenetic oscillations. Cytosine modifications display deterministic temporal rhythms, which may drive ageing and complex disease. Temporality in the epigenome, or the 'chrono' dimension, may help the integration of epigenetic, environmental and genetic disease studies, and reconcile several disparities stemming from the arbitrarily delimited research fields. The ultimate goal of chrono-epigenetics is to predict disease risk, age of onset and disease dynamics from within individual-specific temporal dynamics of epigenomes.
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42
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Combined healthy lifestyle score and risk of epigenetic aging: a discordant monozygotic twin study. Aging (Albany NY) 2021; 13:14039-14052. [PMID: 34032609 PMCID: PMC8202852 DOI: 10.18632/aging.203022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/02/2021] [Indexed: 01/24/2023]
Abstract
We investigated whether lifestyle influences epigenetic aging in 143 monozygotic twin pairs discordant for the combined healthy lifestyle score. Twins were scored for four lifestyle factors as unhealthy or healthy; non-smoker, moderate drinker, adequate fruit and vegetable intake, and sufficient physical activity. The combined healthy lifestyle score was calculated for each participant by summing the binary score for each factor. Individual and co-twin analyses were used to assess the relationship between single or combined lifestyle scores, along with DNA methylation age acceleration (AA) calculated using Horvath’s and Li’s epigenetic clocks, focusing on AA and intrinsic epigenetic age acceleration (IEAA) measures. Compared with the twins that scored no or one healthy lifestyle point, those who scored four healthy lifestyle points had lower Li_IEAA with similar results observed in the co-twin analysis. No significant relationships were found in analyses based on Horvath’s clock, although the direction of correlations was consistent with that determined using Li’s clock. Smoking and drinking did not significantly affect DNA methylation AA; however, physical activity and intake of vegetables and fruits did, although the influence varied depending on the epigenetic clock. Our findings suggest that a healthy lifestyle may be an important way to delay aging and prevent age-related diseases.
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43
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Lu M, Xueying Q, Hexiang P, Wenjing G, Hägg S, Weihua C, Chunxiao L, Canqing Y, Jun L, Zengchang P, Liming C, Hua W, Xianping W, Yunzhang W, Liming L. Genome-wide associations between alcohol consumption and blood DNA methylation: evidence from twin study. Epigenomics 2021; 13:939-951. [PMID: 33993705 DOI: 10.2217/epi-2021-0039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Alcohol intake alters DNA methylation profiles and methylation might mediate the association between alcohol and disease, but limited number of positive CpG sites repeatedly replicated. Materials & methods: In total, 57 monozygotic (MZ) twin pairs discordant for alcohol drinking from the Chinese National Twin Registry and 158 MZ and dizygotic twin pairs in the Swedish Adoption/Twin Study of Aging were evaluated. DNA methylation was detected using the Infinium HumanMethylation450 BeadChip. Results: Among candidate CpG sites, cg07326074 was significantly correlated with drinking after adjusting for covariates in MZ twins in both datasets but not in the entire sample or dizygotic twins. Conclusion: The hypermethylation of cg07326074, located in the tumor-promoting gene C16orf59, was associated with alcohol consumption.
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Affiliation(s)
- Meng Lu
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Qin Xueying
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China.,Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Peng Hexiang
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Gao Wenjing
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Cao Weihua
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Li Chunxiao
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Yu Canqing
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Lv Jun
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Pang Zengchang
- Qingdao Center for Disease Control & Prevention, Qingdao 266033, PR China
| | - Cong Liming
- Zhejiang Center for Disease Control & Prevention, Hangzhou 310051, PR China
| | - Wang Hua
- Jiangsu Center for Disease Control & Prevention, Nanjing 210009, PR China
| | - Wu Xianping
- Sichuan Center for Disease Control & Prevention, Chengdu 610041, PR China
| | - Wang Yunzhang
- Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Li Liming
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
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44
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Yukina MY, Larina AA, Vasilyev EV, Troshina EA, Dimitrova DA. Search for Genetic Predictors of Adult Autoimmune Polyendocrine Syndrome in Monozygotic Twins. CLINICAL MEDICINE INSIGHTS-ENDOCRINOLOGY AND DIABETES 2021; 14:11795514211009796. [PMID: 33953634 PMCID: PMC8058797 DOI: 10.1177/11795514211009796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 11/20/2022]
Abstract
Autoimmune polyendocrine syndromes (APS) are a heterogeneous group of diseases characterized by the presence of autoimmune dysfunction of 2 or more endocrine glands and other non-endocrine organs. The components of the syndrome can manifest throughout life: in childhood—APS type 1 (the juvenile type) and in adulthood—APS type 2, 3, and 4 (the adult types). Adult types of APS are more common in clinical practice. It is a polygenic disease associated with abnormalities in genes encoding key regulatory proteins of the major histocompatibility complex (MHC). The search of for candidate genes responsible for mutations in adult APS is continuing. Genetic predisposition is insufficient for the manifestation of the APS of adults, since the penetrance of the disease, even among monozygotic twins, does not approach 100% (30–70%). The article presents the case of isolated Addison’s disease and APS type 2 in monozygotic twins with a revealed compound heterozygosity in the candidate gene VTCN1.
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45
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The role of DNA methylation in syndromic and non-syndromic congenital heart disease. Clin Epigenetics 2021; 13:93. [PMID: 33902696 PMCID: PMC8077695 DOI: 10.1186/s13148-021-01077-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
Congenital heart disease (CHD) is a common structural birth defect worldwide, and defects typically occur in the walls and valves of the heart or enlarged blood vessels. Chromosomal abnormalities and genetic mutations only account for a small portion of the pathogenic mechanisms of CHD, and the etiology of most cases remains unknown. The role of epigenetics in various diseases, including CHD, has attracted increased attention. The contributions of DNA methylation, one of the most important epigenetic modifications, to CHD have not been illuminated. Increasing evidence suggests that aberrant DNA methylation is related to CHD. Here, we briefly introduce DNA methylation and CHD and then review the DNA methylation profiles during cardiac development and in CHD, abnormalities in maternal genome-wide DNA methylation patterns are also described. Whole genome methylation profile and important differentially methylated genes identified in recent years are summarized and clustered according to the sample type and methodologies. Finally, we discuss the novel technology for and prospects of CHD-related DNA methylation.
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46
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Varghaei P, Yoon G, Estiar MA, Veyron S, Leveille E, Dupré N, Trempe JF, Rouleau GA, Gan-Or Z. GCH1 mutations in hereditary spastic paraplegia. Clin Genet 2021; 100:51-58. [PMID: 33713342 DOI: 10.1111/cge.13955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 01/09/2023]
Abstract
GCH1 mutations have been associated with dopa-responsive dystonia (DRD), Parkinson's disease (PD) and tetrahydrobiopterin (BH4 )-deficient hyperphenylalaninemia B. Recently, GCH1 mutations have been reported in five patients with hereditary spastic paraplegia (HSP). Here, we analyzed a total of 400 HSP patients (291 families) from different centers across Canada by whole exome sequencing (WES). Three patients with heterozygous GCH1 variants were identified: monozygotic twins with a p.(Ser77_Leu82del) variant, and a patient with a p.(Val205Glu) variant. The former variant is predicted to be likely pathogenic and the latter is pathogenic. The three patients presented with childhood-onset lower limb spasticity, hyperreflexia and abnormal plantar responses. One of the patients had diurnal fluctuations, and none had parkinsonism or dystonia. Phenotypic differences between the monozygotic twins were observed, who responded well to levodopa treatment. Pathway enrichment analysis suggested that GCH1 shares processes and pathways with other HSP-associated genes, and structural analysis of the variants indicated a disruptive effect. In conclusion, GCH1 mutations may cause HSP; therefore, we suggest a levodopa trial in HSP patients and including GCH1 in the screening panels of HSP genes. Clinical differences between monozygotic twins suggest that environmental factors, epigenetics, and stochasticity could play a role in the clinical presentation.
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Affiliation(s)
- Parizad Varghaei
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Grace Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada
| | - Mehrdad A Estiar
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Simon Veyron
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montréal, Canada
| | - Etienne Leveille
- Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Nicolas Dupré
- Axe Neurosciences, CHU de Québec-Université Laval, Quebec City, Québec, Canada.,Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montréal, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Ziv Gan-Or
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
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47
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Wagner RN, Piñón Hofbauer J, Wally V, Kofler B, Schmuth M, De Rosa L, De Luca M, Bauer JW. Epigenetic and metabolic regulation of epidermal homeostasis. Exp Dermatol 2021; 30:1009-1022. [PMID: 33600038 PMCID: PMC8359218 DOI: 10.1111/exd.14305] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 02/06/2023]
Abstract
Continuous exposure of the skin to environmental, mechanical and chemical stress necessitates constant self‐renewal of the epidermis to maintain its barrier function. This self‐renewal ability is attributed to epidermal stem cells (EPSCs), which are long‐lived, multipotent cells located in the basal layer of the epidermis. Epidermal homeostasis – coordinated proliferation and differentiation of EPSCs – relies on fine‐tuned adaptations in gene expression which in turn are tightly associated with specific epigenetic signatures and metabolic requirements. In this review, we will briefly summarize basic concepts of EPSC biology and epigenetic regulation with relevance to epidermal homeostasis. We will highlight the intricate interplay between mitochondrial energy metabolism and epigenetic events – including miRNA‐mediated mechanisms – and discuss how the loss of epigenetic regulation and epidermal homeostasis manifests in skin disease. Discussion of inherited epidermolysis bullosa (EB) and disorders of cornification will focus on evidence for epigenetic deregulation and failure in epidermal homeostasis, including stem cell exhaustion and signs of premature ageing. We reason that the epigenetic and metabolic component of epidermal homeostasis is significant and warrants close attention. Charting epigenetic and metabolic complexities also represents an important step in the development of future systemic interventions aimed at restoring epidermal homeostasis and ameliorating disease burden in severe skin conditions.
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Affiliation(s)
- Roland N Wagner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Josefina Piñón Hofbauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Verena Wally
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Barbara Kofler
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Matthias Schmuth
- Department of Dermatology, Medical University Innsbruck, Innsbruck, Austria
| | - Laura De Rosa
- Holostem Terapie Avanzate S.r.l., Center for Regenerative Medicine "Stefano Ferrari", Modena, Italy
| | - Michele De Luca
- Center for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Johann W Bauer
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
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48
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Lim TB, Foo SYR, Chen CK. The Role of Epigenetics in Congenital Heart Disease. Genes (Basel) 2021; 12:genes12030390. [PMID: 33803261 PMCID: PMC7998561 DOI: 10.3390/genes12030390] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common birth defect among newborns worldwide and contributes to significant infant morbidity and mortality. Owing to major advances in medical and surgical management, as well as improved prenatal diagnosis, the outcomes for these children with CHD have improved tremendously so much so that there are now more adults living with CHD than children. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. For this reason, the complex process of cardiogenesis, which is governed by multiple interlinked and dose-dependent pathways, is a well investigated process. In addition to the sequence of the genome, the contribution of epigenetics to cardiogenesis is increasingly recognized. Significant progress has been made dissecting the epigenome of the heart and identified associations with cardiovascular diseases. The role of epigenetic regulation in cardiac development/cardiogenesis, using tissue and animal models, has been well reviewed. Here, we curate the current literature based on studies in humans, which have revealed associated and/or causative epigenetic factors implicated in CHD. We sought to summarize the current knowledge on the functional role of epigenetics in cardiogenesis as well as in distinct CHDs, with an aim to provide scientists and clinicians an overview of the abnormal cardiogenic pathways affected by epigenetic mechanisms, for a better understanding of their impact on the developing fetal heart, particularly for readers interested in CHD research.
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Affiliation(s)
- Tingsen Benson Lim
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Sik Yin Roger Foo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
- Correspondence:
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49
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Discordant phenotypes in twins with infantile nystagmus. Sci Rep 2021; 11:2826. [PMID: 33531592 PMCID: PMC7854608 DOI: 10.1038/s41598-021-82368-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/18/2021] [Indexed: 11/08/2022] Open
Abstract
Infantile nystagmus (IN) may result from aetiologies including albinism and FRMD7 mutations. IN has low prevalence, and twins with IN are rare. Whilst discordant presentation has been previously reported for IN, we present for the first time the comprehensive assessment of diagnostically discordant monozygotic twins. From a cohort of over 2000 patients, we identified twins and triplets discordant for nystagmus. Using next-generation sequencing, high-resolution infra-red pupil tracking and optical coherence tomography, we characterised differences in genotype and phenotype. Monozygotic twins (n = 1), dizygotic twins (n = 3) and triplets (n = 1) were included. The monozygotic twins had concordant TYR variants. No causative variants were identified in the triplets. Dizygotic twins had discordant variants in TYR, OCA2 and FRMD7. One unaffected co-twin demonstrated sub-clinical nystagmus. Foveal hypoplasia (FH) was noted in four of five probands. Both co-twins of the monozygotic pair and triplets displayed FH. In three families, at least one parent had FH without nystagmus. FH alone may be insufficient to develop nystagmus. Whilst arrested optokinetic reflex pathway development is implicated in IN, discordant twins raise questions regarding where differences in development have arisen. In unaffected monozygotes therefore, genetic variants may predispose to oculomotor instability, with variable expressivity possibly responsible for the discordance observed.
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50
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Brosens E, Peters NCJ, van Weelden KS, Bendixen C, Brouwer RWW, Sleutels F, Bruggenwirth HT, van Ijcken WFJ, Veenma DCM, Otter SCMCD, Wijnen RMH, Eggink AJ, van Dooren MF, Reutter HM, Rottier RJ, Schnater JM, Tibboel D, de Klein A. Unraveling the Genetics of Congenital Diaphragmatic Hernia: An Ongoing Challenge. Front Pediatr 2021; 9:800915. [PMID: 35186825 PMCID: PMC8852845 DOI: 10.3389/fped.2021.800915] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/28/2021] [Indexed: 12/16/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a congenital structural anomaly in which the diaphragm has not developed properly. It may occur either as an isolated anomaly or with additional anomalies. It is thought to be a multifactorial disease in which genetic factors could either substantially contribute to or directly result in the developmental defect. Patients with aneuploidies, pathogenic variants or de novo Copy Number Variations (CNVs) impacting specific genes and loci develop CDH typically in the form of a monogenetic syndrome. These patients often have other associated anatomical malformations. In patients without a known monogenetic syndrome, an increased genetic burden of de novo coding variants contributes to disease development. In early years, genetic evaluation was based on karyotyping and SNP-array. Today, genomes are commonly analyzed with next generation sequencing (NGS) based approaches. While more potential pathogenic variants are being detected, analysis of the data presents a bottleneck-largely due to the lack of full appreciation of the functional consequence and/or relevance of the detected variant. The exact heritability of CDH is still unknown. Damaging de novo alterations are associated with the more severe and complex phenotypes and worse clinical outcome. Phenotypic, genetic-and likely mechanistic-variability hampers individual patient diagnosis, short and long-term morbidity prediction and subsequent care strategies. Detailed phenotyping, clinical follow-up at regular intervals and detailed registries are needed to find associations between long-term morbidity, genetic alterations, and clinical parameters. Since CDH is a relatively rare disorder with only a few recurrent changes large cohorts of patients are needed to identify genetic associations. Retrospective whole genome sequencing of historical patient cohorts using will yield valuable data from which today's patients and parents will profit Trio whole genome sequencing has an excellent potential for future re-analysis and data-sharing increasing the chance to provide a genetic diagnosis and predict clinical prognosis. In this review, we explore the pitfalls and challenges in the analysis and interpretation of genetic information, present what is currently known and what still needs further study, and propose strategies to reap the benefits of genetic screening.
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Affiliation(s)
- Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Nina C J Peters
- Division of Obstetrics and Fetal Medicine, Department of Obstetrics and Gynecology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Kim S van Weelden
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Division of Obstetrics and Fetal Medicine, Department of Obstetrics and Gynecology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Charlotte Bendixen
- Unit of Pediatric Surgery, Department of General, Visceral, Vascular and Thoracic Surgery, University Hospital Bonn, Bonn, Germany
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Frank Sleutels
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Hennie T Bruggenwirth
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Wilfred F J van Ijcken
- Center for Biomics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Danielle C M Veenma
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Pediatrics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Suzan C M Cochius-Den Otter
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Rene M H Wijnen
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Alex J Eggink
- Division of Obstetrics and Fetal Medicine, Department of Obstetrics and Gynecology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Heiko Martin Reutter
- Institute of Human Genetics, University Hospital of Bonn, Bonn, Germany.,Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Robbert J Rottier
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - J Marco Schnater
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery and Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
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