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Transcriptomic profile of Fanconi anemia (FA) epidermal stem and progenitor cells (ESPCs)

ABSTRACT: Transcriptomic profile of Fanconi anemia (FA) epidermal stem and progenitor cells (ESPCs)

PROVIDER: PRJNA481882 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7540700_1.fastq.gz	Fastqsanger.gz
	SRR7540700_2.fastq.gz	Fastqsanger.gz
	SRR7540701_1.fastq.gz	Fastqsanger.gz
	SRR7540701_2.fastq.gz	Fastqsanger.gz
	SRR7540702_1.fastq.gz	Fastqsanger.gz

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Transcriptomic profile of Fanconi anemia (FA) epidermal stem and progenitor cells (ESPCs)

Project description:Squamous cell carcinoma (SCC) is a common cancer with global public health burden that arises from ESPCs in the skin or mucosa. To understand how genetic risk factors lay the foundation for SCC and develop effective prevention strategies, it is critical to understand the biology of ESPCs. Extreme predisposition to SCC is a hallmark of FA, an inherited disorder caused by germline loss-of-function mutations in any of 22 genes associated with the FA DNA repair pathway. Although DNA damage is the presumed cause, this does not explain the unique involvement of skin and mucosa as opposed to other solid tissues. To identify new epidermal vulnerabilities beyond DNA damage, we generated the first personalized model of FA epidermis. FA patient-derived induced pluripotent stem cells (PSCs) with a conditional FA pathway (+/-Doxycycline, DOX) were differentiated into ESPCs and 3D epidermis. The goal of this study is to uncover FA-dependent biological processes, performing transcriptome analyses of ESPCs in presence or absence of DOX in monolayer cultures.

2018-09-12 | GSE117362 | GEO

Transcription profiling of human bone marrow cells from normal volunteers and from children and adults with Fanconi anemia

Project description:Fanconi anemia (FA) is a rare inherited disease complicated by aplastic anemia. There is evidence that hematopoietic stem cells have lost self replicative capacity and undergo apoptosis when exposed to inhibitory cytokines including interferon gamma and tumor necrosis factor-alpha. We used gene expression microarrays to identify transcriptomal differences between bone marrow cells from normal volunteers and from children and adults with Fanconi anemia Experiment Overall Design: Fanconi anemia patients were identified using mitomycin C and/or diepoxybutane chromosomal breakage analysis. Eleven normal volunteers and 21 FA patients were studied. All FA patients with cytogenetic evidence of clonal evolution were excluded. All FA patients with acute leukemia were excluded. RNA was prepared from freshly obtained low density mononuclear cell fractions.

2009-09-18 | E-GEOD-16334 | biostudies-arrayexpress

Expression data from normal and Fanconi anemia low density bone marrow cells

2009-09-15 | GSE16334 | GEO

Whole-exome sequencing of Fanconi anemia

Project description:We performed whole-exome sequencing of two Fanconi anemia patients without mutation of known FA genes, and identified a novel FA gene FANCT.

| EGAS00001001103 | EGA

Global gene expression analysis for neuron stem cells (NSC) derived from iPSCs with Fanconi Anemia

2014-06-14 | GSE40865 | GEO

Global gene expression analysis for neuron stem cells (NSC) derived from iPSCs with Fanconi Anemia

Project description:Fanconi Anemia (FA) is a recessive disorder associated with genomic instability We generated iPSC from FA patient fibroblasts and further corrected the mutated FANCA gene with a homologous recombination-based approach. The NSCs were differentiated from control-iPSCs, FA-iPSCs, and corrected FA-NSCs, and their gene expressions were determined by microarray analysis.

2014-06-14 | E-GEOD-40865 | biostudies-arrayexpress

Gene expression based identification of potential genes involved in Fanconi anemia

Project description:Fanconi anemia is a rare inherited hematological disorder which commonly presents with bone marrow failure, developmental abnormalities and susceptibility to cancer with high rates of prevalence in ethnic populations. The objective of this study was to identify potential genes that aid in the progression of the disease or produce its principal symptoms and to hypothesize enabling roles for certain genes that are not part of the central molecular machinery causing the disease. A total of 2 Fanconi anemia samples were collected from patients who displayed characteristic FA features. All of them gave positive results for the DNA breakage test after mitomycin C treatment. Samples were referred by Dr. Sheila Mohan of REFAIN (Registry for Fanconi anemia in India). Whole genome microarray analysis of peripheral blood from 2 patient samples and one normal individual. Sequential analysis of microarray data was carried out using gene ontology and pathway analysis to identify candidate genes.

2010-06-24 | E-GEOD-17233 | biostudies-arrayexpress

Crosslinking/mass spectrometry analysis of Fanconi anemia (FA) pathway FANCD2-FANCI complexes

Project description:DNA interstrand crosslinks (ICLs) are repaired by the Fanconi anemia (FA) pathway. The FA pathway is activated by phosphorylation of FANCI in FANCD2-FANCI complex. To investigate how phosphorylation regulates FA pathway activation and function, recombinant FANCD2-FANCI complexes prepared using either the wild-type FANCI or the phosphomimetic FANCI, were comparied using crosslinking/mass spectrometry.

2022-11-18 | PXD031632 | JPOST Repository

Pluripotent cell models of Fanconi anemia identify the early pathological defect in human hemoangiogenic progenitors

Project description:Fanconi anemia (FA) is a disorder of genomic instability characterized by progressive bone marrow failure (BMF), developmental abnormalities and an increased susceptibility to cancer. Although various consequences in hematopoietic stem/progenitor cells have been attributed to FA-BMF, the quest to identify the initial pathological event is still ongoing. To address this issue, we established induced pluripotent stem cells (iPSCs) from fibroblasts of six FA patients with FANCA mutations. An improved reprogramming method yielded iPSC-like colonies from all patients, and iPSC clones were propagated from two patients. Quantitative evaluation of the differentiation ability demonstrated that the differentiation propensity toward the hematopoietic and endothelial lineages is already defective in early hemoangiogenic progenitors. The expression levels of critical transcription factors were significantly downregulated in these progenitors. These data indicate that the hematopoietic consequences in FA patients originate from the early hematopoietic stage, and highlight the potential usefulness of iPSC technology for elucidating the pathogenesis of FA-BMF. The investigation of the RNA-seq analysis of iPSC-derived HAPCs.

2015-02-03 | E-GEOD-65507 | biostudies-arrayexpress

A surge of DNA damage links transcriptional reprogramming and hematopoietic deficit in Fanconi anemia

Project description:Impaired DNA crosslink repair leads to Fanconi anemia (FA), characterized by a unique manifestation of bone marrow failure and pancytopenia among diseases caused by DNA damage response defects. As a germline disorder, why the hematopoietic hierarchy is specifically affected is not fully understood. We find that reprogramming transcription during hematopoietic differentiation results in an overload of genotoxic stress, which causes aborted differentiation and depletion of FA mutant progenitor cells. The onset of DNA damage most likely arises from formaldehyde, an obligate by-product of oxidative protein demethylation during transcription regulation. Our results demonstrate that rapid and extensive transcription reprogramming associated with hematopoietic differentiation poses a major threat to genome stability and cell viability in the absence of the FA pathway. The connection between differentiation and DNA damage accumulation reveals a novel mechanism of genome scarring and is critical to exploring therapies to counteract the aplastic anemia for the treatment of FA patients.

2021-01-21 | GSE161891 | GEO

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