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The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis

ABSTRACT: The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis

PROVIDER: PRJNA673834 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12964656_1.fastq.gz	Fastqsanger.gz
	SRR12964656_2.fastq.gz	Fastqsanger.gz
	SRR12964657_1.fastq.gz	Fastqsanger.gz
	SRR12964657_2.fastq.gz	Fastqsanger.gz
	SRR12964658_1.fastq.gz	Fastqsanger.gz

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PolyA RNA-seq from whole blood of subjects with Trisomy 21 ± clonal hematopoiesis

Project description:Analysis of steady-state mRNA levels in trisomy 21 subjects ± clonal hematopoiesis. This dataset is part of the Human Trisome Project run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

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Expression data from trisomy 21 and euploid induced pluripotent stem cell hematopoietic progenitors

Project description:We modeled human Trisomy 21 primitive hematopoiesis using induced pluripotent stem cells (iPSCs). Primitive multipotent progenitor populations generated from Trisomy 21 iPSCs showed normal proliferative capacity and megakaryocyte production, enhanced erythropoiesis and reduced myeloid development compared to euploid iPSCs.

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Trisomy 21 and TS13

Project description:Gene expression was measured in trisomy 21 and trisomy 13 human fetal samples. For TS21, regions assayed were cerebrum, cerebellum, heart, and cerebrum-derived astrocyte cell lines. Keywords = trisomy 21 Keywords = Down syndrome Keywords = aneuploidy Keywords = brain Keywords = heart Keywords = trisomy 13 Keywords: other

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The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis

Project description:Background: Down syndrome (DS) is associated with a wide range of phenotypes. To address the hypothesis that the genome-wide perturbation of gene regulation in DS is modulated by epigenetic changes, we performed an epigenome-wide association study (EWAS) on neonatal bloodspots comparing 196 newborns with DS and 439 newborns without DS. Results: We identified 652 epigenome-wide significant CpGs (P<7.67x10-8) and 1,052 differentially methylated regions (DMRs) across the genome. Differential methylation at promoters/enhancers correlated with gene expression changes in DS versus non-DS fetal liver hematopoietic stem/progenitor cells (HSPC) (P<0.0001). Two of the top 3 DS-associated CpGs overlapped RUNX1, and were highly significantly hypermethylated in DS newborns (P<1.0x10-21). The top two DMRs overlapped promoters of RUNX1 and FLI1, both important regulators of megakaryopoiesis. FLI1 expression was markedly reduced in DS fetal liver HSCs (P<0.0001) and myeloid progenitors (P<0.0001). By contrast, RUNX1 expression was increased in DS fetal liver myeloid progenitors (P<0.0001), consistent with selective hypermethylation of the RUNX1 P2 promoter, which dominates in embryonic development, but sparing the P1 promoter that drives definitive hematopoiesis. Targeted sequencing of GATA1 revealed somatic, preleukemic mutations in 16.3% DS newborns, consistent with the high frequency of these mutations in DS newborns. Removal of DS newborns with GATA1 mutations had minimal impact on the EWAS results. Conclusions: DS 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 DS. Blood-detectable DS-related epigenetic changes may underlie an array of DS outcomes, including neurologic and immune-related morbidities.

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Trisomy 21 and RNA-seq of family

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Trisomy 21 and GRO-seq of family

Project description:GRO-seq of lymphoblastoid cells from a family of individuals (one of which has Trisomy 21) was used to determine the molecular origin of dosage compensation in Trisomy 21.

2023-04-29 | GSE230994 | GEO

Transcriptional Consequences of Trisomy 21 on Neural Induction

Project description:Down syndrome, caused by trisomy 21, is a complex developmental disorder associated with intellectual disability and reduced growth of multiple organs. Structural pathologies are present at birth, reflecting embryonic origins. A fundamental unanswered question is how an extra copy of human chromosome 21 contributes to organ-specific pathologies that characterize individuals with Down syndrome. Relevant to the hallmark intellectual disability in Down syndrome, how does trisomy 21 affect neural development? We tested the hypothesis that trisomy 21 exerts effects on human neural development as early as neural induction. Bulk RNA sequencing was performed on isogenic trisomy 21 and euploid human induced pluripotent stem cells (iPSCs) at successive stages of neural induction: embryoid bodies at Day 6, early neuroectoderm at Day 10, and differentiated neuroectoderm at Day 17. Gene expression analysis revealed over 1,300 differentially expressed genes in trisomy 21 cells along the differentiation pathway compared to euploid controls. Less than 5% of the gene expression changes included upregulated chromosome 21 encoded genes at every timepoint. Genes involved in specific growth factor signaling pathways (Wnt and Notch), metabolism (including interferon response and oxidative stress), and extracellular matrix were altered in trisomy 21 cells. Further analysis revealed heterochronic expression of genes. This comprehensive analysis reveals that trisomy 21 impacts discrete developmental pathways at the earliest stages of neural development. Further, the results suggest that metabolic dysfunction arises early in embryogenesis in trisomy 21 and may thus affect development and function more broadly.

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Gene expression variation increase in trisomy 21 tissues

Project description:Congenital development disorders with variable severity occur in trisomy 21. However, how these phenotypic abnormalities develop with variations remains elusive. We hypothesize that the difference in euploidy gene expression variation among trisomy 21 tissues are perturbed by the presence of an extra copy of chromosome 21 and this may contribute to the phenotypic variations in Down syndrome. Keywords: Disease state analysis

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PolyA RNA-seq from whole blood of subjects with Trisomy 21 ± clonal hematopoiesis

Project description:PolyA RNA-seq from whole blood of subjects with Trisomy 21 ± clonal hematopoiesis

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