Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia [RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA673717 | ENA |
REPOSITORIES: ENA
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Project description:The fetal-to-adult hemoglobin switch is regulated in a developmental stage-specific manner and reactivation of fetal hemoglobin (HbF) has therapeutic potential for β-hemoglobinopathies. Although BCL11A and ZBTB7A interact with their coregulators, reportedly mediating most γ-globin transcriptional silencing in erythroid in trans, and in cis, the molecular mechanism underlying the epigenetic dysregulation of the switch remains largely unclear. Here we showed that epigenetic inactivation of an ETS2 repressor factor (ERF) reactivates γ-globin expression during stress erythropoiesis, and ERF depletion elevates γ-globin in erythroid cells and in erythroid progenies from the edited HSPCs engrafted into immunodeficient mice. ERF represses γ-globin by directly binding to two motifs regulating HBG expression, independently of the major HbF repressors BCL11A and ZBTB7A. We further uncovered that an lncRNA, RP11-196G18.23 mediates ERF promoter hypermethylation resulting in reactivation of g-globin. Herein, the epigenetic alterations were identified as novel modulators ameliorating the severity of b-thalassemia, thus providing novel therapeutic targets for β-hemoglobinopathies.
2020-12-27 | GSE160602 | GEO
Project description:The fetal-to-adult hemoglobin switch is regulated in a developmental stage-specific manner and reactivation of fetal hemoglobin (HbF) has therapeutic potential for β-hemoglobinopathies. Although BCL11A and ZBTB7A interact with their coregulators, reportedly mediating most γ-globin transcriptional silencing in erythroid in trans, and in cis, the molecular mechanism underlying the epigenetic dysregulation of the switch remains largely unclear. Here we showed that epigenetic inactivation of an ETS2 repressor factor (ERF) reactivates γ-globin expression during stress erythropoiesis, and ERF depletion elevates γ-globin in erythroid cells and in erythroid progenies from the edited HSPCs engrafted into immunodeficient mice. ERF represses γ-globin by directly binding to two motifs regulating HBG expression, independently of the major HbF repressors BCL11A and ZBTB7A. We further uncovered that an lncRNA, RP11-196G18.23 mediates ERF promoter hypermethylation resulting in reactivation of g-globin. Herein, the epigenetic alterations were identified as novel modulators ameliorating the severity of b-thalassemia, thus providing novel therapeutic targets for β-hemoglobinopathies.
2020-12-27 | GSE160601 | GEO
Project description:Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia
| PRJNA673716 | ENA
Project description:Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia [ChIP-seq]
| PRJNA673718 | ENA
Project description: Not available
| S-EPMC8059375 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-12-27 | GSE160603 | GEO
Project description:The advent of human induced pluripotent stem (iPS) cells enables for the first time the derivation of unlimited numbers of patient-specific stem cells and holds great promise for regenerative medicine. However, realizing the full potential of iPS cells requires robust, precise and safe strategies for their genetic modification. Safe human iPS cell engineering is especially needed for therapeutic applications, as stem cell-based therapies that rely on randomly integrated transgenes pose oncogenic risks. Here we describe a strategy to genetically modify iPS cells from patients with beta-thalassemia in a potentially clinically relevant manner. Our approach is based on the identification and selection of âsafe harborâ sites for transgene expression in the human genome. We show that thalassemia patient iPS cell clones harboring a transgene can be isolated and screened according to chromosomal position. We next demonstrate that iPS cell clones that meet our âsafe harborâ criteria resist silencing and allow for therapeutic levels of beta-globin expression upon erythroid differentiation without perturbation of neighboring gene expression. Combined bioinformatics and functional analyses thus provide a robust and dependable approach for achieving desirable levels of transgene expression from selected chromosomal loci. This approach may be broadly applicable to introducing therapeutic or suicide genes into patient specific iPS cells for use in cell therapy. iPS cell clones were derived from beta-thalassemia patients. A single copy of beta-globin transgene cis-linked to locus control region (LCR) elements and an excisable Neo-eGFP transcription unit were inserted into these cell clones. beta-globin expression was induced by erythroid differentiation.
2010-10-26 | E-GEOD-24901 | biostudies-arrayexpress
Project description:Disrupting the adult-globin promoter alleviates promoter competition and reactivates foetal-globin gene expression
| PRJNA798972 | ENA
Project description:Background: The thalassemias are highly diverse at both the molecular and clinical levels. Many of the HBB mutations that result in β-thalassemia are missense mutations in the coding region of the β-globin gene, but a few cause alternative splicing, and interfere with normal processing of the β-globin transcripts. Transcriptome profiling in individuals affected with β-thalassemia, especially in individuals who carry novel mutations in the HBB, may improve our understanding of the heterogeneity and molecular mechanisms of the disease. Methods: Members of a family with a daughter affected with thalassemia intermedia, although her mother was not clinically affected, were examined for physical characteristics, hematological parameters and β-globin gene sequences. We also characterized genome-wide gene expression in the family using RT-qPCR and high-throughput RNA-sequencing mRNA expression profiling of blood. Results: Clinical findings, hematological indices, DNA and RNA sequence analysis of individuals with β-thalassemia, including the description of a novel mutation in the β-globin gene, which introduces a cryptic donor splice site. More than 300 genes are differentially expressed in β-thalassemic blood with many of the DEGs involved in pathways relevant to the clinical management of β-thalassemia. β-thalassemia shows important similarities and differences with sickle cell disease at the transcriptome level. Conclusions: We described the down-regulation of the β-globin gene in β-thalassemia by RNA-sequencing analysis using a sample from an affected individual and her mother, who have a novel mutation in the HBB that creates a cryptic donor splice site. The daughter has a typical β-thalassemia allele as well, and an unexpectedly severe phenotype. The DEGs are enriched in pathways that are directly or indirectly related to β-thalassemia such as hemopoiesis, heme biosynthesis, response to oxidative stress, inflammatory responses, immune responses, control of circadian rhythm, apoptosis, and other cellular activities. We compare our findings with published results of RNA-Sequencing analysis of sickle cell disease (SCD) and erythroblasts from a KLF1-null neonate with hydrops fetalis, and recognize similarities and differences in their transcriptional expression patterns.
2019-03-09 | GSE96060 | GEO
Project description:The benign condition Hereditary Persistence of Foetal Haemoglobin (HPFH) is known to ameliorate symptoms when co-inherited with beta-haemoglobinopathies, such as sickle cell disease and beta-thalassaemia. The condition is sometimes associated with point mutations in the foetal globin promoters that disrupt the binding of the repressors BCL11A or ZBTB7A/LRF, which have been extensively studied. HPFH is also associated with a range of deletions within the beta-globin locus that all reside downstream of the foetal HBG2 gene. These deletional forms of HPFH are poorly understood and are the focus of this study. Numerous different mechanisms have been proposed to explain how downstream deletions can boost the expression of the foetal globin genes, including the deletion of silencer elements, of genes encoding non-coding RNA, and bringing downstream enhancer elements into proximity with the foetal globin gene promoters. Here we systematically analyse the deletions associated with both HPFH and a related condition known as beta-thalassaemia and propose a unifying mechanism. In all cases where foetal globin is up-regulated, the proximal adult beta-globin (HBB) promoter is deleted. We use CRISPR gene editing to delete or disrupt elements within the promoter and find that virtually all mutations that reduce promoter activity, result in elevated foetal globin expression. These results fit with previous models where the foetal and adult globin genes compete for the distal Locus Control Region and suggest that targeting the promoter might be explored to elevate foetal globin and reduce sickle globin expression as a treatment for beta-haemoglobinopathies.
2022-01-20 | GSE194064 | GEO