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Schraw JM, Sok P, Desrosiers TA, Janitz AE, Langlois PH, Canfield MA, Frazier AL, Plon SE, Lupo PJ, Poynter JN. Associations between birth defects and childhood and adolescent germ cell tumors according to sex, histologic subtype, and site. Cancer 2023; 129:3300-3308. [PMID: 37366624 DOI: 10.1002/cncr.34906] [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: 01/19/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Studies have reported increased rates of birth defects among children with germ cell tumors (GCTs). However, few studies have evaluated associations by sex, type of defect, or tumor characteristics. METHODS Birth defect-GCT associations were evaluated among pediatric patients (N = 552) with GCTs enrolled in the Germ Cell Tumor Epidemiology Study and population-based controls (N = 6380) without cancer from the Genetic Overlap Between Anomalies and Cancer in Kids Study. The odds ratio (OR) and 95% confidence interval (CI) of GCTs according to birth defects status were estimated by using unconditional logistic regression. All defects were considered collectively and by genetic and chromosomal syndromes and nonsyndromic defects. Stratification was by sex, tumor histology (yolk sac tumor, teratoma, germinoma, and mixed/other), and location (gonadal, extragonadal, and intracranial). RESULTS Birth defects and syndromic defects were more common among GCT cases than controls (6.9% vs. 4.0% and 2.7% vs. 0.2%, respectively; both p < .001). In multivariable models, GCT risk was increased among children with birth defects (OR, 1.7; 95% CI, 1.3-2.4) and syndromic defects (OR, 10.4; 95% CI, 4.9-22.1). When stratified by tumor characteristics, birth defects were associated with yolk sac tumors (OR, 2.7; 95% CI, 1.3-5.0) and mixed/other histologies (OR, 2.1; 95% CI, 1.2-3.5) and both gonadal tumors (OR, 1.7; 95% CI, 1.0-2.7) and extragonadal tumors (OR, 3.8; 95% CI, 2.1-6.5). Nonsyndromic defects specifically were not associated with GCTs. In sex-stratified analyses, associations were observed among males but not females. CONCLUSIONS These data suggest that males with syndromic birth defects are at an increased risk of pediatric GCTs, whereas males with nonsyndromic defects and females are not at an increased risk. PLAIN LANGUAGE SUMMARY We investigated whether birth defects (such as congenital heart disease or Down syndrome) are linked to childhood germ cell tumors (GCTs), cancers that mainly develop in the ovaries or testes. We studied different types of birth defects (defects that were caused by chromosome changes such as Down syndrome or Klinefelter syndrome and defects that were not) and different types of GCTs. Only chromosome changes such as Down syndrome or Klinefelter syndrome were linked to GCTs. Our study suggests that most children with birth defects are not at an increased risk of GCTs because most birth defects are not caused by chromosome changes.
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Affiliation(s)
- Jeremy M Schraw
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Pagna Sok
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Tania A Desrosiers
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amanda E Janitz
- Department of Biostatistics and Epidemiology, Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Peter H Langlois
- Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Austin, Texas, USA
| | - Mark A Canfield
- Birth Defects Epidemiology and Surveillance Branch, Texas Department of State Health Services, Austin, Texas, USA
| | - A Lindsay Frazier
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sharon E Plon
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Philip J Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Jenny N Poynter
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
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2
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Merrill SM, Gladish N, Fu MP, Moore SR, Konwar C, Giesbrecht GF, MacIssac JL, Kobor MS, Letourneau NL. Associations of peripheral blood DNA methylation and estimated monocyte proportion differences during infancy with toddler attachment style. Attach Hum Dev 2023; 25:132-161. [PMID: 34196256 DOI: 10.1080/14616734.2021.1938872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Attachment is a motivational system promoting felt security to a caregiver resulting in a persistent internal working model of interpersonal behavior. Attachment styles are developed in early social environments and predict future health and development outcomes with potential biological signatures, such as epigenetic modifications like DNA methylation (DNAm). Thus, we hypothesized infant DNAm would associate with toddler attachment styles. An epigenome-wide association study (EWAS) of blood DNAm from 3-month-old infants was regressed onto children's attachment style from the Strange Situation Procedure at 22-months at multiple DNAm Cytosine-phosphate-Guanine (CpG) sites. The 26 identified CpGs associated with proinflammatory immune phenotypes and cognitive development. In post-hoc analyses, only maternal cognitive-growth fostering, encouraging intellectual exploration, contributed. For disorganized children, DNAm-derived cell-type proportions estimated higher monocytes -cells in immune responses hypothesized to increase with early adversity. Collectively, these findings suggested the potential biological embedding of both adverse and advantageous social environments as early as 3-months-old.
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Affiliation(s)
- Sarah M Merrill
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Nicole Gladish
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Maggie P Fu
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Sarah R Moore
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Chaini Konwar
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Gerald F Giesbrecht
- Department of Pediatrics, University of Calgary, Calgary, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Julia L MacIssac
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Michael S Kobor
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.,Program in Child and Brain Development, CIFAR, Toronto, Canada
| | - Nicole L Letourneau
- Department of Pediatrics, University of Calgary, Calgary, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada.,Department of Psychiatry, University of Calgary, Calgary, Canada.,Faculty of Nursing, University of Calgary, Calgary, Canada
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3
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Gensous N, Sala C, Pirazzini C, Ravaioli F, Milazzo M, Kwiatkowska KM, Marasco E, De Fanti S, Giuliani C, Pellegrini C, Santoro A, Capri M, Salvioli S, Monti D, Castellani G, Franceschi C, Bacalini MG, Garagnani P. A Targeted Epigenetic Clock for the Prediction of Biological Age. Cells 2022; 11:cells11244044. [PMID: 36552808 PMCID: PMC9777448 DOI: 10.3390/cells11244044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks were initially developed to track chronological age, but accumulating evidence indicates that they can also predict biological age. They are usually based on the analysis of DNA methylation by genome-wide methods, but targeted approaches, based on the assessment of a small number of CpG sites, are advisable in several settings. In this study, we developed a targeted epigenetic clock purposely optimized for the measurement of biological age. The clock includes six genomic regions mapping in ELOVL2, NHLRC1, AIM2, EDARADD, SIRT7 and TFAP2E genes, selected from a re-analysis of existing microarray data, whose DNA methylation is measured by EpiTYPER assay. In healthy subjects (n = 278), epigenetic age calculated using the targeted clock was highly correlated with chronological age (Spearman correlation = 0.89). Most importantly, and in agreement with previous results from genome-wide clocks, epigenetic age was significantly higher and lower than expected in models of increased (persons with Down syndrome, n = 62) and decreased (centenarians, n = 106; centenarians' offspring, n = 143; nutritional intervention in elderly, n = 233) biological age, respectively. These results support the potential of our targeted epigenetic clock as a new marker of biological age and open its evaluation in large cohorts to further promote the assessment of biological age in healthcare practice.
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Affiliation(s)
- Noémie Gensous
- Department of Internal Medicine and Clinical Immunology, CHU Bordeaux (Groupe Hospitalier Saint-André), 33077 Bordeaux, France
- UMR/CNRS 5164, ImmunoConcEpT, CNRS, University of Bordeaux, 33076 Bordeaux, France
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Maddalena Milazzo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | | | - Elena Marasco
- Personal Genomics S.R.L., Via Roveggia, 43/B, 37134 Verona, Italy
| | - Sara De Fanti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology, Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Camilla Pellegrini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50139 Florence, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Department of Applied Mathematics, Lobachevsky University, 603105 Nizhny Novgorod, Russia
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
- Correspondence: ; Tel.: +39-051-6225977
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, 14152 Huddinge, Sweden
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4
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Henneman P, Mul AN, Li Yim AY, Krzyzewska IM, Alders M, Adelia A, Mizee MR, Mannens MM. Prenatal NeuN+ neurons of Down syndrome display aberrant integrative DNA methylation and gene expression profiles. Epigenomics 2022; 14:375-390. [PMID: 35232286 DOI: 10.2217/epi-2021-0523] [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: 11/21/2022] Open
Abstract
Aim: To detect expression quantitative trait methylation (eQTM) loci within the cerebrum of prenatal Down syndrome (DS) and controls. Material & methods: DNA methylation gene expression profiles were acquired from NeuN+ nuclei, obtained from cerebrum sections of DS and controls. Linear regression models were applied to both datasets and were subsequently applied in an integrative analysis model to detect DS-associated eQTM loci. Results & conclusion: Widespread aberrant DNA methylation and gene expression were observed in DS. A substantial number of differentially methylated loci were replicated according to a previously reported study. Subsequent integrative analyses (eQTM) yielded numerous associated DS loci. the authors associated DNA methylation, gene expression and eQTM loci with DS that may underlie particular DS phenotypical characteristics.
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Affiliation(s)
- Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Adri N Mul
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Andrew Yf Li Yim
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Izabela M Krzyzewska
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Adelia Adelia
- Neuroimmunology Research Group & Netherlands Brain Bank, Netherlands Institute for Neuroscience, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Mark R Mizee
- Neuroimmunology Research Group & Netherlands Brain Bank, Netherlands Institute for Neuroscience, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Marcel M Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
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5
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Naumova OY, Lipschutz R, Rychkov SY, Zhukova OV, Grigorenko EL. DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome. Genes (Basel) 2021; 12:genes12081115. [PMID: 34440289 PMCID: PMC8391316 DOI: 10.3390/genes12081115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
Recent research has provided evidence on genome-wide alterations in DNA methylation patterns due to trisomy 21, which have been detected in various tissues of individuals with Down syndrome (DS) across different developmental stages. Here, we report new data on the systematic genome-wide DNA methylation perturbations in blood cells of individuals with DS from a previously understudied age group—young children. We show that the study findings are highly consistent with those from the prior literature. In addition, utilizing relevant published data from two other developmental stages, neonatal and adult, we track a quasi-longitudinal trend in the DS-associated DNA methylation patterns as a systematic epigenomic destabilization with age.
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Affiliation(s)
- Oxana Yu. Naumova
- Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia; (S.Y.R.); (O.V.Z.)
- Department of Psychology, University of Houston, Houston, TX 77204, USA;
- Correspondence: or (O.Y.N.); (E.L.G.)
| | - Rebecca Lipschutz
- Department of Psychology, University of Houston, Houston, TX 77204, USA;
| | - Sergey Yu. Rychkov
- Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia; (S.Y.R.); (O.V.Z.)
| | - Olga V. Zhukova
- Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia; (S.Y.R.); (O.V.Z.)
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, TX 77204, USA;
- Department of Psychology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: or (O.Y.N.); (E.L.G.)
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6
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Abstract
Children show a higher incidence of leukaemia compared with young adolescents, yet their cells are less damaged because of their young age. Children with Down syndrome (DS) have an even higher risk of developing leukaemia during the first years of life. The presence of a constitutive trisomy of chromosome 21 (T21) in DS acts as a genetic driver for leukaemia development, however, additional oncogenic mutations are required. Therefore, T21 provides the opportunity to better understand leukaemogenesis in children. Here, we describe the increased risk of leukaemia in DS during childhood from a somatic evolutionary view. According to this idea, cancer is caused by a variation in inheritable phenotypes within cell populations that are subjected to selective forces within the tissue context. We propose a model in which the increased risk of leukaemia in DS children derives from higher rates of mutation accumulation, already present during fetal development, which is further enhanced by changes in selection dynamics within the fetal liver niche. This model could possibly be used to understand the rate-limiting steps of leukaemogenesis early in life.
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7
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Moccia C, Popovic M, Isaevska E, Fiano V, Trevisan M, Rusconi F, Polidoro S, Richiardi L. Birthweight DNA methylation signatures in infant saliva. Clin Epigenetics 2021; 13:57. [PMID: 33741061 PMCID: PMC7980592 DOI: 10.1186/s13148-021-01053-1] [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: 11/23/2020] [Accepted: 03/09/2021] [Indexed: 11/17/2022] Open
Abstract
Background Low birthweight has been repeatedly associated with long-term adverse health outcomes and many non-communicable diseases. Our aim was to look-up cord blood birthweight-associated CpG sites identified by the PACE Consortium in infant saliva, and to explore saliva-specific DNA methylation signatures of birthweight. Methods DNA methylation was assessed using Infinium HumanMethylation450K array in 135 saliva samples collected from children of the NINFEA birth cohort at an average age of 10.8 (range 7–17) months. The association analyses between birthweight and DNA methylation variations were carried out using robust linear regression models both in the exploratory EWAS analyses and in the look-up of the PACE findings in infant saliva. Results None of the cord blood birthweight-associated CpGs identified by the PACE Consortium was associated with birthweight when analysed in infant saliva. In saliva EWAS analyses, considering a false discovery rate p-values < 0.05, birthweight as continuous variable was associated with DNA methylation in 44 CpG sites; being born small for gestational age (SGA, lower 10th percentile of birthweight for gestational age according to WHO reference charts) was associated with DNA methylation in 44 CpGs, with only one overlapping CpG between the two analyses. Despite no overlap with PACE results at the CpG level, two of the top saliva birthweight CpGs mapped at genes associated with birthweight with the same direction of the effect also in the PACE Consortium (MACROD1 and RPTOR). Conclusion Our study provides an indication of the birthweight and SGA epigenetic salivary signatures in children around 10 months of age. DNA methylation signatures in cord blood may not be comparable with saliva DNA methylation signatures at about 10 months of age, suggesting that the birthweight epigenetic marks are likely time and tissue specific. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01053-1.
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Affiliation(s)
- Chiara Moccia
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy.
| | - Maja Popovic
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| | - Morena Trevisan
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
| | - Franca Rusconi
- Unit of Epidemiology, 'Anna Meyer' Children's University Hospital, Florence, Italy
| | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.,MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO Piemonte, Via Santena 7, 10126, Turin, Italy
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8
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Laufer BI, Gomez JA, Jianu JM, LaSalle JM. Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature. Epigenetics Chromatin 2021; 14:13. [PMID: 33750431 PMCID: PMC7942011 DOI: 10.1186/s13072-021-00387-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated). Results DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development. Conclusions Taken together, these results support a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00387-7.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA. .,Genome Center, University of California, Davis, CA, 95616, USA. .,MIND Institute, University of California, Davis, CA, 95616, USA.
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9
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Muskens IS, Li S, Jackson T, Elliot N, Hansen HM, Myint SS, Pandey P, Schraw JM, Roy R, Anguiano J, Goudevenou K, Siegmund KD, Lupo PJ, de Bruijn MFTR, Walsh KM, Vyas P, Ma X, Roy A, Roberts I, Wiemels JL, de Smith AJ. The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis. Nat Commun 2021; 12:821. [PMID: 33547282 PMCID: PMC7865055 DOI: 10.1038/s41467-021-21064-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Down syndrome is associated with genome-wide perturbation of gene expression, which may be mediated by epigenetic changes. We perform an epigenome-wide association study on neonatal bloodspots comparing 196 newborns with Down syndrome and 439 newborns without Down syndrome, adjusting for cell-type heterogeneity, which identifies 652 epigenome-wide significant CpGs (P < 7.67 × 10-8) and 1,052 differentially methylated regions. Differential methylation at promoter/enhancer regions correlates with gene expression changes in Down syndrome versus non-Down syndrome fetal liver hematopoietic stem/progenitor cells (P < 0.0001). The top two differentially methylated regions overlap RUNX1 and FLI1, both important regulators of megakaryopoiesis and hematopoietic development, with significant hypermethylation at promoter regions of these two genes. Excluding Down syndrome newborns harboring preleukemic GATA1 mutations (N = 30), identified by targeted sequencing, has minimal impact on the epigenome-wide association study results. Down syndrome has profound, genome-wide effects on DNA methylation in hematopoietic cells in early life, which may contribute to the high frequency of hematological problems, including leukemia, in children with Down syndrome.
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Affiliation(s)
- Ivo S Muskens
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Thomas Jackson
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Natalina Elliot
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Priyatama Pandey
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Jeremy M Schraw
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Ritu Roy
- Computational Biology and Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Joaquin Anguiano
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Katerina Goudevenou
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Kimberly D Siegmund
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Kyle M Walsh
- Department of Neurosurgery, Duke University, Durham, NC, USA
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Anindita Roy
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Irene Roberts
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA.
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10
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Laufer BI, Hwang H, Jianu JM, Mordaunt CE, Korf IF, Hertz-Picciotto I, LaSalle JM. Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles. Hum Mol Genet 2020; 29:3465-3476. [PMID: 33001180 PMCID: PMC7788293 DOI: 10.1093/hmg/ddaa218] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Neonatal dried blood spots (NDBS) are a widely banked sample source that enables retrospective investigation into early life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early life Down syndrome (DS) DNA methylation profiles. DS represents an example of genetics shaping epigenetics, as multiple array-based studies have demonstrated that trisomy 21 is characterized by genome-wide alterations to DNA methylation. By assaying over 24 million CpG sites, thousands of genome-wide significant (q < 0.05) differentially methylated regions (DMRs) that distinguished DS from typical development and idiopathic developmental delay were identified. Machine learning feature selection refined these DMRs to 22 loci. The DS DMRs mapped to genes involved in neurodevelopment, metabolism, and transcriptional regulation. Based on comparisons with previous DS methylation studies and reference epigenomes, the hypermethylated DS DMRs were significantly (q < 0.05) enriched across tissues while the hypomethylated DS DMRs were significantly (q < 0.05) enriched for blood-specific chromatin states. A ~28 kb block of hypermethylation was observed on chromosome 21 in the RUNX1 locus, which encodes a hematopoietic transcription factor whose binding motif was the most significantly enriched (q < 0.05) overall and specifically within the hypomethylated DMRs. Finally, we also identified DMRs that distinguished DS NDBS based on the presence or absence of congenital heart disease (CHD). Together, these results not only demonstrate the utility of low-pass WGBS on NDBS samples for epigenome-wide association studies, but also provide new insights into the early life mechanisms of epigenomic dysregulation resulting from trisomy 21.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Ian F Korf
- Genome Center, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Irva Hertz-Picciotto
- MIND Institute, University of California, Davis, CA 95616, USA.,Department of Public Health Sciences, School of Medicine, University of California, Davis, CA 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
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11
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Laan L, Klar J, Sobol M, Hoeber J, Shahsavani M, Kele M, Fatima A, Zakaria M, Annerén G, Falk A, Schuster J, Dahl N. DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors. Clin Epigenetics 2020; 12:9. [PMID: 31915063 PMCID: PMC6950999 DOI: 10.1186/s13148-019-0803-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
Background Down syndrome (DS) is characterized by neurodevelopmental abnormalities caused by partial or complete trisomy of human chromosome 21 (T21). Analysis of Down syndrome brain specimens has shown global epigenetic and transcriptional changes but their interplay during early neurogenesis remains largely unknown. We differentiated induced pluripotent stem cells (iPSCs) established from two DS patients with complete T21 and matched euploid donors into two distinct neural stages corresponding to early- and mid-gestational ages. Results Using the Illumina Infinium 450K array, we assessed the DNA methylation pattern of known CpG regions and promoters across the genome in trisomic neural iPSC derivatives, and we identified a total of 500 stably and differentially methylated CpGs that were annotated to CpG islands of 151 genes. The genes were enriched within the DNA binding category, uncovering 37 factors of importance for transcriptional regulation and chromatin structure. In particular, we observed regional epigenetic changes of the transcription factor genes ZNF69, ZNF700 and ZNF763 as well as the HOXA3, HOXB3 and HOXD3 genes. A similar clustering of differential methylation was found in the CpG islands of the HIST1 genes suggesting effects on chromatin remodeling. Conclusions The study shows that early established differential methylation in neural iPSC derivatives with T21 are associated with a set of genes relevant for DS brain development, providing a novel framework for further studies on epigenetic changes and transcriptional dysregulation during T21 neurogenesis.
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Affiliation(s)
- Loora Laan
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Maria Sobol
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Jan Hoeber
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | | | - Malin Kele
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ambrin Fatima
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Muhammad Zakaria
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jens Schuster
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden.
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12
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Haertle L, Müller T, Lardenoije R, Maierhofer A, Dittrich M, Riemens RJM, Stora S, Roche M, Leber M, Riedel-Heller S, Wagner M, Scherer M, Ravel A, Mircher C, Cieuta-Walti C, Durand S, van de Hove DLA, Hoffmann P, Ramirez A, Haaf T, El Hajj N, Mégarbané A. Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer's disease-related dysregulation. Clin Epigenetics 2019; 11:195. [PMID: 31843015 PMCID: PMC6916110 DOI: 10.1186/s13148-019-0787-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/25/2019] [Indexed: 11/28/2022] Open
Abstract
Abstract Background Trisomy 21 (T21) is associated with intellectual disability that ranges from mild to profound with an average intellectual quotient of around 50. Furthermore, T21 patients have a high risk of developing Alzheimer’s disease (AD) early in life, characterized by the presence of senile plaques of amyloid protein and neurofibrillary tangles, leading to neuronal loss and cognitive decline. We postulate that epigenetic factors contribute to the observed variability in intellectual disability, as well as at the level of neurodegeneration seen in T21 individuals. Materials and Methods A genome-wide DNA methylation study was performed using Illumina Infinium® MethylationEPIC BeadChips on whole blood DNA of 3 male T21 patients with low IQ, 8 T21 patients with high IQ (4 males and 4 females), and 21 age- and sex-matched control samples (12 males and 9 females) in order to determine whether DNA methylation alterations could help explain variation in cognitive impairment between individuals with T21. In view of the increased risk of developing AD in T21 individuals, we additionally investigated the T21-associated sites in published blood DNA methylation data from the AgeCoDe cohort (German study on Ageing, Cognition, and Dementia). AgeCoDe represents a prospective longitudinal study including non-demented individuals at baseline of which a part develops AD dementia at follow-up. Results Two thousand seven hundred sixteen differentially methylated sites and regions discriminating T21 and healthy individuals were identified. In the T21 high and low IQ comparison, a single CpG located in the promoter of PELI1 was differentially methylated after multiple testing adjustment. For the same contrast, 69 differentially methylated regions were identified. Performing a targeted association analysis for the significant T21-associated CpG sites in the AgeCoDe cohort, we found that 9 showed significant methylation differences related to AD dementia, including one in the ADAM10 gene. This gene has previously been shown to play a role in the prevention of amyloid plaque formation in the brain. Conclusion The differentially methylated regions may help understand the interaction between methylation alterations and cognitive function. In addition, ADAM10 might be a valuable blood-based biomarker for at least the early detection of AD.
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Affiliation(s)
- Larissa Haertle
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Division of Hematology and Oncology, Department of Internal Medicine II, University Hospital, Wuerzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilian University, Wuerzburg, Germany
| | - Roy Lardenoije
- Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Department of Bioinformatics, Julius Maximilian University, Wuerzburg, Germany
| | - Renzo J M Riemens
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands
| | - Samantha Stora
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Mathilde Roche
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Markus Leber
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937, Cologne, Germany.,Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, 04103, Leipzig, Germany
| | - Michael Wagner
- Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Centre Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Aimé Ravel
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Clotilde Mircher
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | | | - Sophie Durand
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Daniel L A van de Hove
- Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands.,Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 53127, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, 53127, Bonn, Germany.,Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, CH-4058, Basel, Switzerland
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937, Cologne, Germany.,Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - André Mégarbané
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France.
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13
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Dobosz A, Grabowska A, Bik-Multanowski M. Hypermethylation of NRG1 gene correlates with the presence of heart defects in Down's syndrome. J Genet 2019; 98:110. [PMID: 31819021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Congenital heart defects can decrease the quality of life and life expectancy in affected individuals, and constitute a major burden for the health care systems. Endocardial cushion defects are among the most prevalent heart malformations in the general population, and are extremely frequent (approximately a 100-fold higher prevalence) in children with Down syndrome. Several genes have been proposed to be involved in the pathogenesis of these malformations, but no common pathogenic DNA variants have been identified so far. Here, we focussed on constitutive, epigenetic alterations of function of selected genes, potentially important for endocardial cushion development. We used two types of microarrays, dedicated for assessment of gene promoter methylation and whole genome expression. First, we compared the gene promoter methylation profiles between two groups of Down syndrome patients, with and without heart defects of endocardial cushion-type. Then, to determine the functional role of the detected methylation alterations, we assessed the expression of the genes of interest. We detected significant hypermethylation of the NRG1 gene promoter region in children with heart defects. NRG1 is a key factor in maturation of endocardial cushions. Supplementary gene expression assessment revealed significantly decreased activity of the ERBB3, SHC3 and SHC4 genes in children with heart defects. The above three genes are closely related to the NRG1 gene and are crucial elements of the NRG/ErbB pathway. The results of this pilot study show that hypermethylation of the NRG1 gene promoter can reflect the functional genome alteration contributing to development of congenital heart defects of endocardial cushion-type.
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Affiliation(s)
- Artur Dobosz
- Department of Medical Genetics, Faculty of Medicine, Jagiellonian University Medical College, ul. Wielicka 265, 30-663 Krakow, Poland.
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14
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15
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Yu YE, Xing Z, Do C, Pao A, Lee EJ, Krinsky-McHale S, Silverman W, Schupf N, Tycko B. Genetic and epigenetic pathways in Down syndrome: Insights to the brain and immune system from humans and mouse models. PROGRESS IN BRAIN RESEARCH 2019; 251:1-28. [PMID: 32057305 PMCID: PMC7286740 DOI: 10.1016/bs.pbr.2019.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The presence of an extra copy of human chromosome 21 (Hsa21) leads to a constellation of phenotypic manifestations in Down syndrome (DS), including prominent effects on the brain and immune system. Intensive efforts to unravel the molecular mechanisms underlying these phenotypes may help developing effective therapies, both in DS and in the general population. Here we review recent progress in genetic and epigenetic analysis of trisomy 21 (Ts21). New mouse models of DS based on syntenic conservation of segments of the mouse and human chromosomes are starting to clarify the contributions of chromosomal subregions and orthologous genes to specific phenotypes in DS. The expression of genes on Hsa21 is regulated by epigenetic mechanisms, and with recent findings of highly recurrent gene-specific changes in DNA methylation patterns in brain and immune system cells with Ts21, the epigenomics of DS has become an active research area. Here we highlight the value of combining human studies with mouse models for defining DS critical genes and understanding the trans-acting effects of a simple chromosomal aneuploidy on genome-wide epigenetic patterning. These genetic and epigenetic studies are starting to uncover fundamental biological mechanisms, leading to insights that may soon become therapeutically relevant.
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Affiliation(s)
- Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States; Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, United States.
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Catherine Do
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Eun Joon Lee
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Sharon Krinsky-McHale
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, United States
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pediatrics, University of California at Irvine, Irvine, CA, United States
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Benjamin Tycko
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States.
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16
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Baburamani AA, Patkee PA, Arichi T, Rutherford MA. New approaches to studying early brain development in Down syndrome. Dev Med Child Neurol 2019; 61:867-879. [PMID: 31102269 PMCID: PMC6618001 DOI: 10.1111/dmcn.14260] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/28/2019] [Indexed: 12/19/2022]
Abstract
Down syndrome is the most common genetic developmental disorder in humans and is caused by partial or complete triplication of human chromosome 21 (trisomy 21). It is a complex condition which results in multiple lifelong health problems, including varying degrees of intellectual disability and delays in speech, memory, and learning. As both length and quality of life are improving for individuals with Down syndrome, attention is now being directed to understanding and potentially treating the associated cognitive difficulties and their underlying biological substrates. These have included imaging and postmortem studies which have identified decreased regional brain volumes and histological anomalies that accompany early onset dementia. In addition, advances in genome-wide analysis and Down syndrome mouse models are providing valuable insight into potential targets for intervention that could improve neurogenesis and long-term cognition. As little is known about early brain development in human Down syndrome, we review recent advances in magnetic resonance imaging that allow non-invasive visualization of brain macro- and microstructure, even in utero. It is hoped that together these advances may enable Down syndrome to become one of the first genetic disorders to be targeted by antenatal treatments designed to 'normalize' brain development. WHAT THIS PAPER ADDS: Magnetic resonance imaging can provide non-invasive characterization of early brain development in Down syndrome. Down syndrome mouse models enable study of underlying pathology and potential intervention strategies. Potential therapies could modify brain structure and improve early cognitive levels. Down syndrome may be the first genetic disorder to have targeted therapies which alter antenatal brain development.
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Affiliation(s)
- Ana A Baburamani
- Centre for the Developing BrainDepartment of Perinatal Imaging and HealthSchool of Biomedical Engineering & Imaging SciencesKing's College LondonKing's Health PartnersSt Thomas’ HospitalLondonUK
| | - Prachi A Patkee
- Centre for the Developing BrainDepartment of Perinatal Imaging and HealthSchool of Biomedical Engineering & Imaging SciencesKing's College LondonKing's Health PartnersSt Thomas’ HospitalLondonUK
| | - Tomoki Arichi
- Centre for the Developing BrainDepartment of Perinatal Imaging and HealthSchool of Biomedical Engineering & Imaging SciencesKing's College LondonKing's Health PartnersSt Thomas’ HospitalLondonUK,Department of BioengineeringImperial College LondonLondonUK,Children's NeurosciencesEvelina London Children's HospitalLondonUK
| | - Mary A Rutherford
- Centre for the Developing BrainDepartment of Perinatal Imaging and HealthSchool of Biomedical Engineering & Imaging SciencesKing's College LondonKing's Health PartnersSt Thomas’ HospitalLondonUK
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17
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Sadikovic B, Aref-Eshghi E, Levy MA, Rodenhiser D. DNA methylation signatures in mendelian developmental disorders as a diagnostic bridge between genotype and phenotype. Epigenomics 2019; 11:563-575. [PMID: 30875234 DOI: 10.2217/epi-2018-0192] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epigenetic and genetic mechanisms regulate the establishment and maintenance of gene expression in its proper context. Recent genome-wide mapping approaches have identified DNA methylation (DNAm) signatures in patients clinically diagnosed with syndromes manifesting as developmental disabilities with intellectual impairments. Here, we review recent studies in which these DNA methylation signatures have enabled highly sensitive and specific screening of such individuals and have clarified ambiguous cases where subjects present with genetic sequence variants of unknown clinical significance (VUS). We propose that these episignatures be considered as echoes and/or legacies of the initiating mutational events within proteins of the so-called epigenetic machinery. As well, we discuss approaches to directly confirm the functional consequences and the implications of these episignatures to patient management and treatment.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - David Rodenhiser
- Departments of Pediatrics, Biochemistry & Oncology, Western University, London, ON, N6A 3K7, Canada.,Children's Health Research Institute & Lawson Health Research Institute, London, ON, N6C 2V5, Canada.,London Regional Cancer Program, Lawson Health Research Institute, London, ON, N6A 5W9, Canada
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