ATF4 Regulates MYB to Increase γ-Globin in Response to Loss of β-Globin

Boontanrart, Mandy; Schröder, Markus S.; G, Stehli; Banović, Marija; Wyman, Stacia K.; Lew, Rachel J.; Bordi, Matteo; Gowen, Benjamin G.; Dewitt, Mark; Corn, Jacob E.

doi:10.1016/j.celrep.2020.107993

Cited by 28 publications

(22 citation statements)

References 73 publications

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“…HUDEP2 cells are a commonly used tool for studying globin regulation [ 4 , 25 , 26 , 27 ]. We constructed a cellular model of HBB homozygous knockout in HUDEP2 cells, hereafter referred to as HBB-KO.…”

Section: Resultsmentioning

confidence: 99%

“…Fetal hemoglobin (HbF, α 2 γ 2 ) is comprised of two copies of γ-globin ( HBG1/2 ) and two copies of α-globin ( HBA ), while adult hemoglobin (HbA, α 2 β 2 ) is comprised of two copies of α-globin ( HBA ) and two copies of β-globin ( HBB ) [ 2 , 3 ]. The HBG1/2 gene is primarily expressed during development, but silenced soon after birth and replaced by HBB expression [ 2 , 4 ].…”

Section: Introductionmentioning

confidence: 99%

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Multi-Omics Analysis in β-Thalassemia Using an HBB Gene-Knockout Human Erythroid Progenitor Cell Model

Zhang

Lin

et al. 2022

IJMS

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β-thalassemia is a hematologic disease that may be associated with significant morbidity and mortality. Increased expression of HBG1/2 can ameliorate the severity of β-thalassemia. Compared to the unaffected population, some β-thalassemia patients display elevated HBG1/2 expression levels in their red blood cells. However, the magnitude of up-regulation does not reach the threshold of self-healing, and thus, the molecular mechanism underlying HBG1/2 expression in the context of HBB-deficiency requires further elucidation. Here, we performed a multi-omics study examining chromatin accessibility, transcriptome, proteome, and phosphorylation patterns in the HBB homozygous knockout of the HUDEP2 cell line (HBB-KO). We found that up-regulation of HBG1/2 in HBB-KO cells was not induced by the H3K4me3-mediated genetic compensation response. Deletion of HBB in human erythroid progenitor cells resulted in increased ROS levels and production of oxidative stress, which led to an increased rate of apoptosis. Furthermore, in response to oxidative stress, slower cell cycle progression and proliferation were observed. In addition, stress erythropoiesis was initiated leading to increased intracellular HBG1/2 expression. This molecular model was also validated in the single-cell transcriptome of hematopoietic stem cells from β-hemoglobinopathy patients. These findings further the understanding of HBG1/2 gene regulatory networks and provide novel clinical insights into β-thalassemia phenotypic diversity.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Multi-Omics Analysis in β-Thalassemia Using an HBB Gene-Knockout Human Erythroid Progenitor Cell Model

Zhang

Lin

et al. 2022

IJMS

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“…3A). 56,57 Two previous studies revealed that ATF4 serves as an important regulator of globin expression. 56,57 Depletion of ATF4 or disruption of the ATF4-binding motif in the +55kb enhancer in CD34+ HSPCs silences BCL11A expression in the erythroid lineage, resulting in increased production of fetal γ-globin protein in differentiated red blood cells.…”

Section: Xnls Enaspcas12a Efficiently Edits Genetic Regulatory Elemen...mentioning

confidence: 99%

Optimization of NLS Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells

Luk

Zeng

et al. 2022

Preprint

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Type V CRISPR Cas12a systems are an attractive alternative nuclease platform for specific genome editing applications. However, previous studies demonstrate that there is a gap in overall activity between Cas12a and Cas9 in primary cells. Here we describe optimization to the nuclear localization signal composition and architecture of Cas12a to facilitate highly efficient targeted mutagenesis in mammalian cell lines (HEK293T, Jurkat, and K562 cells) and primary cells (NK cells and CD34+ HSPCs), regardless of Cas12a ortholog. A 3xNLS Cas12a architecture resulted in the most robust editing platform. The improved editing activity of Cas12a in both NK cells and CD34+ HSPCs resulted in pronounced phenotypic changes associated with target gene editing. Lastly, we demonstrated that optimization of the NLS composition and architecture of Cas12a did not decrease the specificity of editing in HEK293T and CD34+ HSPCs. Our new Cas12a NLS variant provides an improved nuclease platform for therapeutic genome editing.

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“…(chr11:5273147), by whole genome sequencing (WGS) analysis. [10][11][12] In addition, significantly changed mRNA levels of the four transcription factors for Hb F expression were identified in the patient compared to his sister, by RNA-sequencing, including increased expression levels of TAL1, ATF2, and ATF4, which act as positive regulators of Hb F levels, [13][14][15] and decreased LYAR, which is essential for silencing the γ-globin gene. 16 Likewise, qPCR assay further validated the altered expression of these four genes in the patient (Figure S1(C), methods in Appendix S1).…”

mentioning

confidence: 98%

“…2 Prominently, several single-nucleotide polymorphisms (SNPs) associated with high Hb F levels were identified in the index, including rs7719521 (chr5:151049404), rs4910742 (chr11:5306509), rs1391619 (chr11:5455929), rs2855123 (chr11:5277078), and rs2855126 (chr11:5273147), by whole genome sequencing (WGS) analysis. [10][11][12] In addition, significantly changed mRNA levels of the four transcription factors for Hb F expression were identified in the patient compared to his sister, by RNA-sequencing, including increased expression levels of TAL1, ATF2, and ATF4, which act as positive regulators of Hb F levels, [13][14][15] and decreased LYAR, which is essential for silencing…”

mentioning

confidence: 99%

A rare complex rearrangement in the β‐globin gene cluster causing a novel homozygous ^Gγ(^Aγδβ)⁰‐thalassemia

et al. 2021

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0.75 years. There is also evidence that NOTCH1 mutations found in transformed patients are commonly present at CLL diagnosis either in clonal or subclonal levels well before transformation occurs and thus a baseline driving mutation, and it is possible these regulatory pathway mutations could follow the same paradigm. 7 Additionally, this is a retrospective study from a single institution with no sample size justification and needs validation from other cohorts. Despite these limitations, we believe that our study provides important and useful novel information about three mutations in CLL to both the practicing clinician and academic researcher.In summary, we identified three mutations in genes associated with the regulation of NOTCH1 signaling or target gene transcription that associate with aggressive CLL behavior similar to that seen with NOTCH1 mutated CLL. Our study shows that these mutations predict for a shorter TTFT in a univariate analysis and associate with similar baseline factors to NOTCH1 mutated CLL, such as trisomy 12, CD38 positivity, and IGHV unmutated status. The strong association with trisomy 12 among the NOTCH1 rpm patients is particularly interesting as NOTCH1 mutations are also associated with trisomy 12 in CLL. 8 Our study suggests the prevalence of NOTCH1 activation in trisomy 12 CLL may be underappreciated and deserves further investigation.We believe that the presence of any these three mutations in CLL should prompt consideration of clinicians to manage patients in a similar way as they might a NOTCH1 mutated patient with CLL. Future research is needed to determine whether mutations in MED12, FBXW7, or SPEN may also associate with increased transformation risk or poor response to frontline chemoimmunotherapy or targeted agents currently used in CLL.

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ATF4 Regulates MYB to Increase γ-Globin in Response to Loss of β-Globin

Abstract: Highlights d Loss of b-globin leads to upregulation of g-globin via altered ATF4 signaling d Reduced ATF4 decreases the levels of MYB and BCL11A d ATF4 induces MYB through binding at the HBS1L-MYB intergenic enhancer

Cited by 28 publications

References 73 publications

Multi-Omics Analysis in β-Thalassemia Using an HBB Gene-Knockout Human Erythroid Progenitor Cell Model

Multi-Omics Analysis in β-Thalassemia Using an HBB Gene-Knockout Human Erythroid Progenitor Cell Model

Optimization of NLS Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells

A rare complex rearrangement in the β‐globin gene cluster causing a novel homozygous ^Gγ(^Aγδβ)⁰‐thalassemia

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ATF4 Regulates MYB to Increase γ-Globin in Response to Loss of β-Globin

Abstract: Highlights d Loss of b-globin leads to upregulation of g-globin via altered ATF4 signaling d Reduced ATF4 decreases the levels of MYB and BCL11A d ATF4 induces MYB through binding at the HBS1L-MYB intergenic enhancer

Cited by 28 publications

References 73 publications

Multi-Omics Analysis in β-Thalassemia Using an HBB Gene-Knockout Human Erythroid Progenitor Cell Model

Multi-Omics Analysis in β-Thalassemia Using an HBB Gene-Knockout Human Erythroid Progenitor Cell Model

Optimization of NLS Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells

A rare complex rearrangement in the β‐globin gene cluster causing a novel homozygous Gγ(Aγδβ)0‐thalassemia

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A rare complex rearrangement in the β‐globin gene cluster causing a novel homozygous ^Gγ(^Aγδβ)⁰‐thalassemia