DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

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.

Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles

“…( 5 ), 7) neural induced pluripotent stem cell (iPSC) derivative CpGs assayed by 450 K from Laan et al . ( 17 ), 8) fetal frontal cortex CpGs assayed by 450 K from El Hajj et al. ( 6 ), and 9) adult frontal cortex DMRs assayed by WGBS from Laufer et al .…”

StableDNMT3LOverexpression in SH-SY5Y Neurons Recreates a Facet of the Genome-Wide Down Syndrome DNA Methylation Signature

“…To determine the similarities between the DNMT3L-specific DMRs and the DNA methylation changes previously observed in DS, a pan-tissue comparison with differentially methylated DS sites across diverse tissues was performed (30,(39)(40)(41)(42)(43)(44)(45)(46)(47). These results revealed significant overlap with DS differentially methylated sites, predominantly within the hypermethylated DNMT3L DMRs (Figure 6C).…”

Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature

“…To test the hypothesis that the DNMT3L DMRs represent a facet of the differentially methylated genes observed in DS, cross-tissue and pan-tissue comparisons with differentially methylated DS sites across diverse tissues were performed [26][27][28][29][30][31][32][33][34][35]. These results revealed a significant (q < 0.05) enrichment of the DNMT3L DMRs within DS differentially methylated sites identified from multiple tissues (Fig.…”

“…7d). Differential methylation of the HOX clusters has been observed in a number of tissues, which includes adult brain, fetal brain, neonatal blood, whole-blood, T-lymphocytes, placenta, buccal epithelial cells, and neural induced pluripotent stem cell (iPSC) derivatives [26,27,[30][31][32][33][34][35]. DNMT3L DMRs mapping to HOXB7, HOXC4, HOXC5, HOXD10, and HOXD12 were present in the growth comparison, while those mapping to HOXD-AS2, HOTAIR ("HOX transcript antisense RNA" for the HOXC cluster), HOXC5, HOXC6, HOXC12, and HOXC13, and HOXD12 were present in the phase 1 comparison, and those mapping to HOTTIP ("HOXA distal transcript antisense RNA"), HOXC-AS2, HOXC-AS3, HOXC12, and HOTTAIR were present in the phase 3 comparison.…”