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Transcriptome analysis by RNA sequencing of human trisomy 21 and normal control blood cells

ABSTRACT: Transcriptome analysis by RNA sequencing of human trisomy 21 and normal control blood cells

PROVIDER: PRJNA635385 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11856162_1.fastq.gz	Fastqsanger.gz
	SRR11856162_2.fastq.gz	Fastqsanger.gz
	SRR11856163_1.fastq.gz	Fastqsanger.gz
	SRR11856163_2.fastq.gz	Fastqsanger.gz
	SRR11856164_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis by RNA sequencing of human trisomy 21 and normal control blood cells

Project description:The aim of this study is to analyse trisomy 21 (T21) transcriptome. We generated RNA sequencing (RNA-Seq) paired-end data from ribosomal RNA-depleted total RNA isolated from blood cell samples of four T21 and four normal control individuals.

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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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