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Modelling erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I) for diagnosis and molecular dissection.

ABSTRACT: Modelling erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I) for diagnosis and molecular dissection.

PROVIDER: PRJNA515475 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8447920_1.fastq.gz	Fastqsanger.gz
	SRR8447920_2.fastq.gz	Fastqsanger.gz
	SRR8447930_1.fastq.gz	Fastqsanger.gz
	SRR8447930_2.fastq.gz	Fastqsanger.gz
	SRR8447940_1.fastq.gz	Fastqsanger.gz

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Modelling erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I) for diagnosis and molecular dissection.

Project description:Congenital Dyserythropoietic Anaemia type 1 (CDA-I) is an inherited anaemia arising primarily from mutations in C15orf41 and CDAN1, however the molecular mechanisms that cause the disease remain to be fully elucidated. We use an in vitro culture system to study multiple stages of erythropoiesis from CD34+ progenitors of patients with CDA-I. Applying a number of techniques, including ATAC-seq, we show that differentiation of CDA-I patient erythroblasts closely matches that of healthy donors during the early and intermediate stages of erythroid differentiation and maturation. However, a defect in terminal erythropoiesis can be observed in the CDA-I patient derived erythroblasts, resulting in a reduction in the number of enucleated erythroid cells.

2020-11-02 | GSE125175 | GEO

Gene expression profile of erythroblastic cells induced from congenital dyserythropoietic anemia (CDA) patient-derived induced pluripotent stem cells

Project description:Analysis of erythroblastic cells differentiated from induced pluripotent stem cells (iPSCs) generated from peripheral blood T lymphocytes of CDA type IV patient. Type IV congenital dyserythropoietic anemia (CDA) is due to a monoallelic mutation at the second zinc finger of KLF1 (c.973G>A). Results provide insight into molecular mechanisms underlying CDA pathogenesis.

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Novel human cellular model of CDA IV enables comprehensive analysis revealing molecular basis of disease phenotype.

Project description:Red blood cell disorders can result in severe anemia. One such disease, congenital dyserythropoietic anemia IV (CDA IV) is caused by heterozygous mutation E325K in the transcription factor KLF1. However, studying the molecular basis of CDA IV is severely impeded by paucity of suitable and adequate quantities of material from anaemic patients and rarity of the disease. We therefore took a novel approach, creating a human cellular disease model system for CDA IV, which accurately recapitulates the disease phenotype. Next, using comparative proteomics we reveal extensive distortion of the proteome and a wide range of disordered biological processes in CDA IV erythroid cells. These include down-regulated pathways governing cell cycle, chromatin separation, DNA repair, cytokinesis, membrane trafficking and global transcription, and upregulated networks governing mitochondria biogenesis. The diversity of such pathways elucidates the spectrum of phenotypic abnormalities that occur with CDA IV and impairment to erythroid cell development and survival, collectively explaining the CDA IV disease phenotype. The data also reveal far more extensive involvement of KLF1 in previously assigned biological processes, along with novel roles in the regulation of intracellular processes not previously attributed to this transcription factor. Overall, the data demonstrate the power of such a model cellular system to unravel the molecular basis of disease and how studying effects of a rare mutation can reveal fundamental biology.

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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (ChIP-seq)

Project description:Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. Despite the abundance of GWAS associations, functional identification and characterization of causative variants and effector genes remains a challenging prospect. Human erythropoiesis provides a highly tractable model system for the development of tools for GWAS analysis. We have developed a three-phase protocol for differentiation of peripheral CD34+ Haematopoietic Stem Cells (HSC) into mature enucleating erythrocytes. This protocol has been characterized for it’s the changes observed morphologically, immunologically (by FACS) and epigenetically (by ATAC-seq, ChIP-seq, and RNA-seq). We have used this protocol to study the effects of common GWAS variants affecting red blood cell traits, and more severe mutations causing Type-1 Congenital Dyserythropoietic Anemia (CDA-I).

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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (RNA-seq)

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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (ATAC-seq)

2021-05-28 | GSE125922 | GEO

Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (NG Capture-C)

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CDA-HFD induced NASH liver fibrosis

Project description:To understand the fibrotic response in the CDA-HFD induced NASH fibrosis model, we performed RNA-seq on liver samples collected from mice fed with normal chow (week 0) or CDA-HFD chow (weeks 8 and 16).

2022-08-19 | GSE207856 | GEO

RNA sequencing reveals global gene expression changes in response to codanin-1 knockdown in erythroid-committed cells

Project description:Congenital dyserythropoietic anemia type I (CDA-I) is an autosomal recessive disorder marked by ineffective erythropoiesis, abnormal morphology of bone marrow erythroblasts, and iron overload. Most cases of CDA-I are caused by mutations in the CDAN1 gene, which encodes for a ubiquitous protein of unknown function, codanin-1. To study the function of codanin-1 in CDA-I erythroid pathophysiology several erythroid models were developed. Here we show that codanin-1 expression is required for erythroid progenitor development and normal erythroid cell differentiation. Erythroid cells lacking codanin-1 demonstrated morphologic changes similar to that observed in CDA-I. Global gene expression changes after codanin-1 knockdown revealed alterations in a set of key erythroid genes. In particular, the AHSP gene, which showed decreased mRNA expression after codanin-1 knockdown in CD34+ cells, also demonstrated increased codanin-1 occupancy at its gene regulatory region by chromatin immunoprecipitation coupled to high-throughput sequencing. Using cell models recapitulating many features of CDA-I, we have confirmed the importance of codanin-1 during erythroid differentiation and provide mechanistic insight into how loss of codanin-1 expression results in CDA-I.

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Genome-wide identification of codanin-1 binding sites in human K562 erythroleukemia cells with chromatin immunoprecipitation coupled with next-generation sequencing

2022-05-19 | GSE131510 | GEO