scholarly journals Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Timothy I. Shaw ◽  
Li Dong ◽  
Liqing Tian ◽  
Chenxi Qian ◽  
Yu Liu ◽  
...  
Keyword(s):  
Network Analysis ◽  
Target Genes ◽  
Lymphoblastic Leukemia ◽  
Cancer Therapeutics ◽  
Physical Interaction ◽  
Loss Of Function ◽  
Protein Activity ◽  
E Proteins ◽  
Down Regulation ◽  
E Protein

AbstractUSP7, which encodes a deubiquitylating enzyme, is among the most frequently mutated genes in pediatric T-ALL, with somatic heterozygous loss-of-function mutations (haploinsufficiency) predominantly affecting the subgroup that has aberrant TAL1 oncogene activation. Network analysis of > 200 T-ALL transcriptomes linked USP7 haploinsufficiency with decreased activities of E-proteins. E-proteins are also negatively regulated by TAL1, leading to concerted down-regulation of E-protein target genes involved in T-cell development. In T-ALL cell lines, we showed the physical interaction of USP7 with E-proteins and TAL1 by mass spectrometry and ChIP-seq. Haploinsufficient but not complete CRISPR knock-out of USP7 showed accelerated cell growth and validated transcriptional down-regulation of E-protein targets. Our study unveiled the synergistic effect of USP7 haploinsufficiency with aberrant TAL1 activation on T-ALL, implicating USP7 as a haploinsufficient tumor suppressor in T-ALL. Our findings caution against a universal oncogene designation for USP7 while emphasizing the dosage-dependent consequences of USP7 inhibitors currently under development as potential cancer therapeutics.

scholarly journals Augmenting E Protein Activity Impairs cDC2 Differentiation at the Pre-cDC Stage

2020 ◽  
Vol 11 ◽  
Author(s):  
Sandra Bajana ◽  
Kevin Thomas ◽  
Constantin Georgescu ◽  
Ying Zhao ◽  
Jonathan D. Wren ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Protein Function ◽  
Loss Of Function ◽  
Protein Activity ◽  
E Proteins ◽  
Aberrant Expression ◽  
Precise Control ◽  
Helix Loop Helix ◽  
Id Proteins ◽  
E Protein

Dendritic cell (DC) specification and differentiation are controlled by a circuit of transcription factors, which regulate the expression of DC effector genes as well as the transcription factors themselves. E proteins are a widely expressed basic helix-loop-helix family of transcription factors whose activity is suppressed by their inhibitors, ID proteins. Loss-of-function studies have demonstrated the essential role of both E and ID proteins in different aspects of DC development. In this study, we employed a gain-of-function approach to illustrate the importance of the temporal control of E protein function in maintaining balanced differentiation of conventional DC (cDC) subsets, cDC1 and cDC2. We expressed an E protein mutant, ET2, which dimerizes with endogenous E proteins to overcome inhibition by ID proteins and activate the transcription of E protein targets. Induction of ET2 expression at the hematopoietic progenitor stage led to a dramatic reduction in cDC2 precursors (pre-cDC2s) with little impact on pre-cDC1s. Consequently, we observed decreased numbers of cDC2s in the spleen and lung, as well as in FLT3L-driven bone marrow-derived DC cultures. Furthermore, in mice bearing ET2, we detected increased expression of the IRF8 transcription factor in cDC2s, in which IRF8 is normally down-regulated and IRF4 up-regulated. This aberrant expression of IRF8 induced by ET2 may contribute to the impairment of cDC2 differentiation. In addition, analyses of the transcriptomes of splenic cDC1s and cDC2s revealed that ET2 expression led to a shift, at least in part, of the transcriptional profile characteristic of cDC2s to that of cDC1. Together, these results suggest that a precise control of E protein activity is crucial for balanced DC differentiation.

scholarly journals Dynamic changes in E-protein activity regulate T reg cell development

2014 ◽  
Vol 211 (13) ◽  
pp. 2651-2668 ◽  
Author(s):  
Ping Gao ◽  
Xiaojuan Han ◽  
Qi Zhang ◽  
Zhiqiong Yang ◽  
Ivan J. Fuss ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Signaling Pathways ◽  
Cell Lineage ◽  
Foxp3 Expression ◽  
Protein Activity ◽  
E Proteins ◽  
Tcr Signaling ◽  
Down Regulation ◽  
Protein Levels ◽  
E Protein

E-proteins are TCR-sensitive transcription factors essential for intrathymic T cell transitions. Here, we show that deletion of E-proteins leads to both enhanced peripheral TGF-β–induced regulatory T (iT reg) cell and thymic naturally arising T reg cell (nT reg cell) differentiation. In contrast, deletion of Id proteins results in reduced nT reg cell differentiation. Mechanistic analysis indicated that decreased E-protein activity leads to de-repression of signaling pathways that are essential to Foxp3 expression. Decreased E-protein binding to an IL-2Rα enhancer locus facilitated TCR-induced IL-2Rα expression. Similarly, decreased E-protein activity facilitated TCR-induced NF-κB activation and generation of c-Rel. Consistent with this, microarray analysis indicated that cells with E-protein depletion that are not yet expressing Foxp3 exhibit activation of the IL-2 and NF-κB signaling pathways as well as enhanced expression of many of the genes associated with Foxp3 induction. Finally, studies using Nur77-GFP mice to monitor TCR signaling showed that TCR signaling strength sufficient to induce Foxp3 differentiation is accompanied by down-regulation of E-protein levels. Collectively, these data suggest that TCR stimulation acts in part through down-regulation of E-protein activity to induce T reg cell lineage development.

scholarly journals E proteins orchestrate dynamic transcriptional cascades to suppress ILC2 differentiation

2020 ◽  
Author(s):  
Vincent Peng ◽  
Constantin Georgescu ◽  
Anna Bakowska ◽  
Liangyue Qian ◽  
Jonathan D Wren ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Innate Lymphoid Cells ◽  
Transcriptional Network ◽  
Lymphoid Cells ◽  
Loss Of Function ◽  
Sequencing Data ◽  
E Proteins ◽  
Down Regulation ◽  
E Protein

AbstractThe basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of group2 innate lymphoid cells from bone marrow and thymic progenitors. Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively. Cross-examination of RNA sequencing and ATAC sequencing data obtained at different time points reveals a set of genes which are likely direct targets of E proteins. Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2. The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.SummaryDifferentiation of group 2 innate lymphoid cells is forcefully repressed by E protein transcription factors. This report elucidates how E proteins repress a transcriptional network important for ILC2 differentiation by up-regulating the expression of transcriptional repressors.

scholarly journals E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells

2020 ◽  
Vol 295 (44) ◽  
pp. 14866-14877
Author(s):  
Vincent Peng ◽  
Constantin Georgescu ◽  
Anna Bakowska ◽  
Aneta Pankow ◽  
Liangyue Qian ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Microbial Pathogens ◽  
Loss Of Function ◽  
Sequencing Data ◽  
E Proteins ◽  
Down Regulation ◽  
Group 2

Group 2 innate lymphoid cells (ILC2s) represent a subset of newly discovered immune cells that are involved in immune reactions against microbial pathogens, host allergic reactions, as well as tissue repair. The basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of ILC2s from bone marrow and thymic progenitors while promoting the development of B and T lymphocytes. How E proteins exert the suppression is not well understood. Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively. Cross-examination of RNA-seq and ATAC sequencing data obtained at different time points reveals a set of genes that are likely direct targets of E proteins. Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2. The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.

scholarly journals Early B Cell Factor Promotes B Lymphopoiesis with Reduced Interleukin 7 Responsiveness in the Absence of E2A

2004 ◽  
Vol 199 (12) ◽  
pp. 1689-1700 ◽  
Author(s):  
Christopher S. Seet ◽  
Rachel L. Brumbaugh ◽  
Barbara L. Kee
Keyword(s):  
Transcription Factors ◽  
B Cell ◽  
B Lymphopoiesis ◽  
Protein Activity ◽  
E Proteins ◽  
Helix Loop Helix ◽  
Interleukin 7 ◽  
E Protein ◽  
B Lineage ◽  
Early B Cell Factor

The basic helix-loop-helix transcription factors encoded by the E2A gene function at the apex of a transcriptional hierarchy involving E2A, early B cell factor (EBF), and Pax5, which is essential for B lymphopoiesis. In committed B lineage progenitors, E2A proteins have also been shown to regulate many lineage-associated genes. Herein, we demonstrate that the block in B lymphopoiesis imposed by the absence of E2A can be overcome by expression of EBF, but not Pax5, indicating that EBF is the essential target of E2A required for development of B lineage progenitors. Our data demonstrate that EBF, in synergy with low levels of alternative E2A-related proteins (E proteins), is sufficient to promote expression of most B lineage genes. Remarkably, however, we find that E2A proteins are required for interleukin 7–dependent proliferation due, in part, to a role for E2A in optimal expression of N-myc. Therefore, high levels of E protein activity are essential for the activation of EBF and N-myc, whereas lower levels of E protein activity, in synergy with other B lineage transcription factors, are sufficient for expression of most B lineage genes.

scholarly journals Mtg16-dependent repression of E protein activity is required for early lymphopoiesis

2020 ◽  
Author(s):  
Pankaj Acharya ◽  
Shilpa Sampathi ◽  
David K. Flaherty ◽  
Brittany K. Matlock ◽  
Christopher S. Williams ◽  
...  
Keyword(s):  
Stem Cell ◽  
Germ Line ◽  
Adult Stem Cell ◽  
The Cancer Genome Atlas ◽  
Single Nucleotide Variants ◽  
Protein Activity ◽  
E Proteins ◽  
Cell Functions ◽  
E Protein ◽  
Cancer Genome Atlas

AbstractThe ETO/MTG family of transcriptional co-repressors play a key role in adult stem cell functions in various tissues. These factors are commonly found in complex with E proteins such as E2A, HEB, and Lyl1 as well as PRDM14 and BTB/POZ domain factors. Structural studies identified a region in the first domain of MTGs that is conserved in the Drosophila homologue Nervy (Nervy Homology Domain-1, or NHR1) that is essential for ETO/MTG8 to inhibit E protein-dependent transcription. The Cancer Genome Atlas (TCGA) identified cancer associated single nucleotide variants (SNVs) near the MTG16:E protein contact site. We tested these SNVs using sensitive yeast two-hybrid association assays, which suggested that only P209T significantly affected E protein binding. We then used CRISPR-Cas9 and homology directed DNA repair to insert P209T and a known inactivating mutation, F210A, into NHR1 of Mtg16 in the germ line of mice. These mice developed normally, but in competitive bone marrow transplantation assays, the F210A-containing stem cells failed to contribute to lymphopoiesis, while P209T mutant cells were reduced in mature T cell populations. High content fluorescent activated analytical flow cytometry assays identified a defect in the multi-potent progenitor to common lymphoid progenitor transition during lymphopoiesis. These data indicate that the cancer associated changes are likely benign polymorphisms, and the MTG:E protein association is required for lymphopoiesis, but less important for myelopoiesis and stem cell functions.

Involvement of Ets Factor Spi-B, E Protein E2-2, and Id2 in Waldenström's Macroglobulinemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2946-2946
Author(s):  
Yangsheng Zhou ◽  
Xia Liu ◽  
Lian Xu ◽  
Zachary Hunter ◽  
Jenny Sun ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
B Cells ◽  
B Cell ◽  
Plasma Cells ◽  
Conflicts Of Interest ◽  
B Cell Differentiation ◽  
Protein Activity ◽  
E Proteins ◽  
E Protein ◽  
Nuclear Extracts

Abstract Abstract 2946 Poster Board II-922 Waldenström's macroglobulinemia (WM) is an incurable B cell disorder with a lymphoplasmacytic infiltrate in the bone marrow (BM) and IgM monoclonal gammopathy. WM tumor cells show variable differentiation, ranging from mature B-cells to plasma cells, which likely results from failure to fully undergo differentiation. In this study, we analyzed the expression of several genes involved in B cell differentiation by real time RT-PCR, such as Ets factors, the basic helix-loop-helix (bHLH) E proteins, as well as the inhibitors of DNA binding (Id) proteins which antagonize E protein activity. Comparison of BM CD19+ B cells obtained from 13 WM patients with 6 age-matched healthy donors showed that expression of the Ets factor Spi-B was increased four-fold, while Id2 was decreased three-fold. However, transcript levels of E proteins were similar between the two groups. Transduction of Spi-B in BCWM.1 WM cells resulted in two-fold higher levels of Id2 and five-fold lower levels of E2-2 compared with control. Id2 transduced BCWM.1 cells expressed two-fold lower levels of E2-2 and Spi-B. Taken together, these results implicate that increased expression of Spi-B alone cannot suppress Id2 transcription in the absence of E2-2 activity. Interestingly, overexpressing Spi-B while concomitantly knocking down Id2 increased the expression of the XBP-1 splicing isoform 2.5-fold without changing levels of Blimp-1 and IRF4. Moreover, inhibition of Spi-B expression by RNA interference or forced expression of Id2 in transduced BCWM.1 cells induced a significant decrease of anti-apoptotic Bcl-2. Importantly, we also showed that Spi-B co-immunoprecipated with Blimp-1 in nuclear extracts. Collectively, these data suggest that the regulatory network of the Spi-B, E2-2, and Id2 plays an essential role in B cell differentiation as well as the pathogenesis of WM, and suggests that Spi-B overexpression may block WM cell differentiation by sequestration of Blimp-1 while promoting tumor cell survival though up-regulation of Bcl-2. Disclosures: No relevant conflicts of interest to declare.

scholarly journals HDAC3 functions as a positive regulator in Notch signal transduction

2020 ◽  
Vol 48 (7) ◽  
pp. 3496-3512 ◽  
Author(s):  
Francesca Ferrante ◽  
Benedetto Daniele Giaimo ◽  
Marek Bartkuhn ◽  
Tobias Zimmermann ◽  
Viola Close ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Acute Lymphoblastic Leukemia ◽  
Chronic Lymphocytic Leukemia ◽  
Target Genes ◽  
Lymphoblastic Leukemia ◽  
Lymphocytic Leukemia ◽  
Loss Of Function ◽  
Local Reduction ◽  
Cell Acute Lymphoblastic Leukemia ◽  
Dependent Mechanism

Abstract Aberrant Notch signaling plays a pivotal role in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL). Amplitude and duration of the Notch response is controlled by ubiquitin-dependent proteasomal degradation of the Notch1 intracellular domain (NICD1), a hallmark of the leukemogenic process. Here, we show that HDAC3 controls NICD1 acetylation levels directly affecting NICD1 protein stability. Either genetic loss-of-function of HDAC3 or nanomolar concentrations of HDAC inhibitor apicidin lead to downregulation of Notch target genes accompanied by a local reduction of histone acetylation. Importantly, an HDAC3-insensitive NICD1 mutant is more stable but biologically less active. Collectively, these data show a new HDAC3- and acetylation-dependent mechanism that may be exploited to treat Notch1-dependent leukemias.

scholarly journals Multivalent Binding of the ETO Corepressor to E Proteins Facilitates Dual Repression Controls Targeting Chromatin and the Basal Transcription Machinery

2009 ◽  
Vol 29 (10) ◽  
pp. 2644-2657 ◽  
Author(s):  
Chun Guo ◽  
Qiande Hu ◽  
Chunxia Yan ◽  
Jinsong Zhang
Keyword(s):  
Fusion Protein ◽  
Protein Fusion ◽  
Protein Activity ◽  
E Proteins ◽  
Basal Transcription ◽  
Activation Domains ◽  
Basal Transcription Machinery ◽  
Transcription Machinery ◽  
Helix Loop Helix ◽  
E Protein

ABSTRACT E proteins are a family of helix-loop-helix transcription factors that play important roles in cell differentiation and homeostasis. They contain at least two activation domains, AD1 and AD2. ETO family proteins and the leukemogenic AML1-ETO fusion protein are corepressors of E proteins. It is thought that ETO represses E-protein activity by interacting with AD1, which competes away p300/CBP histone acetyltransferases. Here we report that E proteins contain another conserved ETO-interacting region, termed DES, and that differential associations with AD1 and DES allow ETO to repress transcription through both chromatin-dependent and chromatin-independent mechanisms. At the chromatin level, AD1 and AD2 cooperatively recruit p300. ETO interacts with AD1 to abolish p300 recruitment and to allow HDAC-dependent silencing. At the post-chromatin-remodeling level, binding to DES enables ETO to directly inhibit activation of the basal transcription machinery. This novel repression mechanism is conserved in ETO family proteins and in the AML1-ETO fusion protein. In addition, the repression capacity exerted by each mechanism is differentially modulated by cross talk among various ETO domains and the AML1 domain of AML1-ETO. In particular, the oligomerization domain of ETO plays a major role in targeting ETO to the DES region and independently potentiates the TAFH domain-mediated AD1 interaction. The ability to exert repression at different levels not only may allow these corepressors to impose robust inhibition of signal-independent transcription but may also allow a rapid response to signals. In addition, our newly defined domain interactions and their interplays have important implications in effectively targeting both E-protein fusion proteins and AML1-ETO found in cancers.

scholarly journals Mutation of the receptor tyrosine phosphatase PTPRC (CD45) in T-cell acute lymphoblastic leukemia

Blood ◽  
2012 ◽  
Vol 119 (19) ◽  
pp. 4476-4479 ◽  
Author(s):  
Michaël Porcu ◽  
Maria Kleppe ◽  
Valentina Gianfelici ◽  
Ellen Geerdens ◽  
Kim De Keersmaecker ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
T Cell ◽  
Lymphoblastic Leukemia ◽  
Tyrosine Phosphatase ◽  
Cell Receptor ◽  
Loss Of Function ◽  
Down Regulation ◽  
Activating Mutations ◽  
Cell Acute Lymphoblastic Leukemia ◽  
Cytokine Stimulation

Abstract The protein tyrosine phosphatase CD45, encoded by the PTPRC gene, is well known as a regulator of B- and T-cell receptor signaling. In addition, CD45 negatively regulates JAK family kinases downstream of cytokine receptors. Here, we report the presence of CD45 inactivating mutations in T-cell acute lymphoblastic leukemia. Loss-of-function mutations of CD45 were detected in combination with activating mutations in IL-7R, JAK1, or LCK, and down-regulation of CD45 expression caused increased signaling downstream of these oncoproteins. Furthermore, we demonstrate that down-regulation of CD45 expression sensitizes T cells to cytokine stimulation, as observed by increased JAK/STAT signaling, whereas overexpression of CD45 decreases cytokine-induced signaling. Taken together, our data identify a tumor suppressor role for CD45 in T-cell acute lymphoblastic leukemia.

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