DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors
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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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Altered methylation of the ZNF69 gene has been suggested to play a role in neurogenesis and brain development in Down syndrome.
“Altered methylation of the Zinc Finger Protein 69 (ZNF69) gene has been suggested to play a role in neurogenesis and brain development in Down syndrome (Laan et al., 2020).”
From Epigenome-wide DNA methylation in unipolar depression: predictive biomarker of antidepressant treatment response? (2024) · cites this paper as Laan et al., 2020
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MicroRNAs and epigenetic signatures in Down syndrome
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- Authors
- Laan, L., Klar, J., Sobol, M., Hoeber, J., Shahsavani, M., Kele, M., Fatima, A., Zakaria, M., Annerén, G., Falk, A., Schuster, J., & Dahl, N.
- Affiliations
- Uppsala University (SE)
- Karolinska Institutet (SE)
- Corresponding author
- Dahl, Niklas
- ORCID
- Venue
- Clinical Epigenetics
- Published
- 2020-01-08
- Volume
- 12
- Issue
- 1
- Pages
- 9-9
- ISSN
- 1868-7075 (ISSN-L)
- 1868-7083
- PMC
- PMC6950999
- OpenAlex
- W3000476446
- Cited by
- 33
- References
- 68
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 8 · 2023: 6 · 2022: 3 · 2021: 7 · 2020: 2
- FWCI
- 3.37
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Clinical Epigenetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
- Funders
- Swedish Research Council (2015-02424)
- Hjärnfonden (FO2018-0100 and FO2019-0210)
- Sävstaholm Society (ST 2018-031)
- Knut och Alice Wallenbergs Stiftelse, Bioinformatic support
- AstraZeneca
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Down syndrome and intellectual disability research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Keywords
- Down syndrome, DNA methylation, epigenetic dysregulation, HOXA3, HOXB3, HOXD3, CpG islands, chromatin remodeling, neurogenesis, brain development
- MeSH terms
- Adult, Brain, Down Syndrome, Female, Fetus, Gene Expression Regulation, Humans, Male, Pregnancy, Promoter Regions, Genetic, Transcription Factors, Trisomy, CpG Islands, DNA Methylation, Chromatin Assembly and Disassembly, Neurogenesis, Induced Pluripotent Stem Cells, Epigenomics, High-Throughput Nucleotide Sequencing, Neurodevelopmental Disorders
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