ETS DNA-binding Domain Research Articles

Ets-1: a new player in the pathogenesis of systemic lupus erythematosus?

v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) (Ets-1) is a member of the Ets family of transcription factors that share a unique Ets DNA binding domain. They control a wide variety of cellular processes including cell proliferation and differentiation. Recently, two genome-wide association studies in systemic lupus erythematosus (SLE) independently identified genetic variants in Ets-1 associated with SLE. Interestingly, previous studies have found that Ets-1-deficient mice develop lupus-like disease characterized by high titers of IgM and IgG autoantibodies, immune complex-mediated glomerulonephritis, and local activation of complement. In addition, Ets-1 is also involved in many cellular abnormalities that are known to participate in SLE pathogenesis, such as its role in negative regulation of Th17 cell and B cell differentiation. All these findings suggest that Ets-1 may play an important role in the pathogenesis of SLE. This article will focus on current understanding of the role of Ets-1 in the physiological and pathological functions associated with SLE. It is the intention of the article to provide insights which may assist in the development of Ets-1 based approaches for the treatment of SLE.

Gabp Transcription Factor Is Required for Myeloid Differentiation, In Part, through Its Control of Gfi-1 Expression

AbstractAbstract 740GABP is an ets transcription factor which regulates genes that are required for myeloid differentiation. The tetrameric GABP complex includes GABPα, which binds DNA via its ets domain, and GABPβ, which contains the transcription activation domain. In order to examine the role of Gabp in myeloid differentiation, we created mice in which exons that encode the ets DNA-binding domain are flanked by LoxP recombination sites (Gabpa fl/fl or floxed mice), and bred them to mice that bear Cre recombinase under the control of the pIC-inducible promoter, Mx1. Injection of these mice with pIC induces conditional deletion of Gabpa in hematopoietic tissues, and these mice are referred to as Gabpa knock-out mice (KO). Control mice that carry floxed Gabpa but lack Mx1-Cre were also treated with pIC. KO mice rapidly lost myeloid cells in peripheral blood, bone marrow, and spleen. Bone marrow cells from control and KO mice were sorted for CD11b and Gr1 to distinguish mature granulocytes from immature granulocytes and monocytes. KO mice had few mature myeloid cells, and the residual cells exhibited a dysplastic phenotypic appearance that did not resemble either normal maturing monocytes or granulocytes; instead they exhibited morphologic characteristics of both lineages. These KO myeloid cells simultaneously expressed differentiation-associated monocyte-restricted and granulocyte-restricted genes and markers of immaturity (Ly6C and c-kit). Thus, the patterns of gene and antigen expression by these dysplastic KO myeloid cells did not correspond to either normal monocytes or granulocytes. We recognized that these KO myeloid cells resemble those seen in mice with disruption of the transcriptional repressor, Gfi-1. We isolated granulocyte-monocyte progenitor (GMP) cells from control and KO bone mice, and found that expression of Gfi-1 was significantly reduced in KO GMPs, compared to controls. Chromatin immunoprecipitation demonstrated that Gabp bound the Gfi-1 promoter in vivo and transfection analysis showed that Gabp activated the Gfi-1 promoter. To test the hypothesis that Gabp controls myeloid differentiation through its regulation of Gfi-1, we grew bone marrow cells from both control and KO mice in liquid culture with SCF, Il-3 and Il-6, or GM-CSF. We transduced these cells with retrovirus bearing Gfi-1, and analyzed myeloid colony formation, and expression of CD11b and Gr1. Transduction of KO bone marrow cells with Gfi-1 partially restored myeloid colony formation in semi-solid media, and the percentage of Gr1+CD11b+ cells in liquid culture. We conclude that GABP plays a non-redundant role in myeloid development, and it controls differentiation of myeloid cells, at least in part, through its regulation of the transcriptional repressor, Gfi-1. Disclosures:No relevant conflicts of interest to declare.

Oncogenic Partnerships: EWS-FLI1 Protein Interactions Initiate Key Pathways of Ewing's Sarcoma

Targeted therapy for cancer, which is specifically directed toward the cancer without any potential for effects outside of controlling the tumor, is a gold standard for treatment. Ewing's sarcoma contains the potential target EWS-FLI1, as a result of a pathognomonic chromosomal translocation. The EWS-FLI1 fusion protein includes the EWS domain, a potent transcriptional activator alongside the highly conserved FLI1 ets DNA-binding domain. Because of the combination of these domains, the EWS-FLI1 fusion protein acts as an aberrant transcription factor whose expression results in cellular transformation. EWS-FLI1 functions by binding to normal cellular protein partners in transcription and splicing, similar to how a virus would corrupt normal cellular machinery for virion production. Therefore, understanding the protein-protein interactions of EWS-FLI1 and the pathways that are regulated by these partnerships will inform both oncogenesis and therapeutics. This review describes the known protein partners and transcriptional targets of EWS-FLI1, while proposing strategies for exploiting these partnerships with targeted therapy.

Amino acid residues in the β3 strand and subsequent loop of the conserved ETS domain that mediate basic leucine zipper (bZIP) recruitment and potentially distinguish functional attributes of Ets proteins

Ets family members share a conserved DNA-binding ETS domain, and serve a variety of roles in development, differentiation and oncogenesis. Besides DNA binding, the ETS domain also participates in protein-protein interactions with other structurally unrelated transcription factors. Although this mechanism appears to confer tissue- or development stage-specific functions on individual Ets proteins, the biological significance of many of these interactions remains to be evaluated, because their molecular basis has been elusive. We previously demonstrated a direct interaction between the ETS domain of the widely expressed GABPalpha (GA-binding protein alpha) and the granulocyte inducer C/EBPalpha (CCAAT/enhancer-binding protein alpha), and suggested its involvement in co-operative transcriptional activation of myeloid-specific genes, such as human FCAR encoding FcalphaR [Fc receptor for IgA (CD89)]. By deletion analysis, we identified helix alpha3 and the beta3/beta4 region as the C/EBPalpha-interacting region. Domain-swapping of individual sub-domains with those of other Ets proteins allowed us to highlight beta-strand 3 and the subsequent loop, which when exchanged by those of Elf-1 (E74-like factor 1) reduced the ability to recruit C/EBPalpha. Further analysis identified a four-amino acid swap mutation of this region (I387L/C388A/K393Q/F395L) that reduces both physical interaction and co-operative transcriptional activation with C/EBPalpha without affecting its transactivation capacity by itself. Moreover, re-ChIP (re-chromatin immunoprecipitation) analysis demonstrated that GABPalpha recruits C/EBPalpha to the FCAR promoter, depending on these residues. The identified amino acid residues could confer the specificity of the action on the Ets proteins in diverse biological processes through mediating the recruitment of its partner factor.

DNA Binding by the ETS Protein TEL (ETV6) Is Regulated by Autoinhibition and Self-association

The ETS protein TEL, a transcriptional repressor, contains a PNT domain that, as an isolated fragment in vitro, self-associates to form a head-to-tail polymer. How such polymerization might affect the DNA-binding properties of full-length TEL is unclear. Here we report that monomeric TEL binds to a consensus ETS site with unusually low affinity (K(d) = 2.8 x 10(-8) M). A deletion analysis demonstrated that the low affinity was caused by a C-terminal inhibitory domain (CID) that attenuates DNA binding by approximately 10-fold. An NMR spectroscopically derived structure of a TEL fragment, deposited in the Protein Data Bank, revealed that the CID consists of two alpha-helices, one of which appears to block the DNA binding surface of the TEL ETS domain. Based on this structure, we substituted two conserved glutamic acids (Glu-431 and Glu-434) with alanines and found that this activated DNA binding and enhanced trypsin sensitivity in the CID. We propose that TEL displays a conformational equilibrium between inhibited and activated states and that electrostatic interactions involving these negatively charged residues play a role in stabilizing the inhibited conformation. Using a TEL dimer as a model polymer, we show that self-association facilitates cooperative binding to DNA. Cooperativity was observed on DNA duplexes containing tandem consensus ETS sites at variable spacing and orientations, suggesting flexibility in the region of TEL linking its self-associating PNT domain and DNA-binding ETS domain. We speculate that TEL compensates for the low affinity, which is caused by autoinhibition, by binding to DNA as a cooperative polymer.

Abstract 3897: EWS-FLI1 is regulated by acetylation

Abstract Introduction: EWS-FLI1 (EF) is the oncogenic transcription factor that is pathognomonic for the Ewing's Sarcoma Family of Tumors (ESFT). Lysine acetylation is an important mechanism in transcription factor regulation including protein stability, protein-protein interaction, DNA-binding, and transcription activation. We hypothesized that EF is acetylated and that acetylation modulates its function. Methods: We used in vitro acetylation assays, mass spectrometry, mutagenesis, EMSA, reporter luciferase assays, western blot and cellular cytotoxicity studies to test this hypothesis. Results: We found that ESFT cells express all three major eukaryotic histone acetyl transferases (HAT): PCAF, CBP and p300. The EF amino acid sequence possesses a number of lysine residues that might constitute potential acetylation sites almost all reside in the C-terminal FLI1 domain (CTD), which contains the DNA binding ets-domain. We show that the CTD is acetylated by CBP, PCAF and P300 and identified four lysines as major sites for acetylation (K240, K252, K380 and K397). Full length EF directly binds to both PCAF and P300, and can be acetylated in vitro. Expression of several HAT(s) stimulates transcription of a typical EF target promoter (NR0B1), placed upstream of a luciferase reporter. Furthermore, histone deacetylase inhibitor (HDACi) treated Cos7 cells that artificially express EF, show increased activity of the NR0B1 reporter compared to non-treated cells. We provide evidence that this increased reporter activity relies upon the ability of acetylation to increase EF DNA binding activity and thus, transcription activation. HDACi (SAHA and TSA) demonstrated potent inhibition of ESFT cell lines with each of the different fusion types including TC71 (type 1, IC50 SAHA/TSA 1068/24 nM), SKES-1 (type 2, IC50 SAHA/TSA 1068/24 nM), and A4573 (type 3, IC50 SAHA/TSA 739/16 nM). Discussion: In conclusion, we show for the first time that EF is acetylated at functionally important residues, and provide evidence that acetylation may play a positive role in the oncogenic activity of EF fusion proteins. At a molecular level, at least one key function of acetylation might consist of the enhancement of EF DNA binding- and transcriptional activity. On the other side, our data pose an apparent contradiction, because ESFT expressing cells undergo cell death when treated with HDAC inhibitors. We believe that one likely explanation for this phenomenon is that the anti-tumor effects of HDACi are rather pleiotropic, and may converge on pro-apoptotic molecules not necessarily related to EF function. Since the expression of EF is crucial for the survival of ESFT cells and maintenance of the tumor the therapy must not support the oncogene's function. Current studies are investigating whether the hyper-sensitivity of ESFT cells to HDACi treatment is sustained by broader effects of protein acetylation, and to determine the specific contribution of EF acetylation in regulation of proliferation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3897.

GABPalpha is required for normal T cell development (36.67)

Abstract GA binding protein (GABP) consists of GABPalpha and GABPbeta subunits. GABPalpha is a member of Ets family transcription factors and binds DNA via its conserved Ets domain, whereas GABPbeta does not bind DNA but possesses transactivation activity. In T cells, GABP has been demonstrated to regulate the gene expression of interleukin-7 receptor alpha chain (IL-7Ralpha) and postulated to be critical in T cell development. To directly investigate its function in early thymocyte development, we used GABPalpha conditional knockout mice where the exons encoding the Ets DNA-binding domain are flanked with LoxP sites. Ablation of GABPalpha with the Lck-Cre transgene greatly diminished thymic cellularity, blocked thymocyte development at the double negative (DN)-3 stage, and resulted in reduced expression of T cell receptor (TCR) beta chain in DN4 thymocytes. By chromatin immunoprecipitation, we demonstrated in DN thymocytes that GABPalpha is associated with transcription initiation sites of genes encoding key molecules in TCR rearrangements. Among these GABP-associated genes, knockdown of GABPalpha expression by RNA interference diminished expression of DNA ligase IV, Artemis, and Ku80 components in DNA-dependent protein kinase complex. Interestingly, forced expression of pre-arranged TCR but not IL-7Ralpha can alleviate the DN3 block in GABPalpha-targeted mice. Our observations collectively GABP is critically required for TCR rearrangements and hence normal T cell development.

Critical Requirement of GABPα for Normal T Cell Development

GA binding protein (GABP) consists of GABPalpha and GABPbeta subunits. GABPalpha is a member of Ets family transcription factors and binds DNA via its conserved Ets domain, whereas GABPbeta does not bind DNA but possesses transactivation activity. In T cells, GABP has been demonstrated to regulate the gene expression of interleukin-7 receptor alpha chain (IL-7Ralpha) and postulated to be critical in T cell development. To directly investigate its function in early thymocyte development, we used GABPalpha conditional knock-out mice where the exons encoding the Ets DNA-binding domain are flanked with LoxP sites. Ablation of GABPalpha with the Lck-Cre transgene greatly diminished thymic cellularity, blocked thymocyte development at the double negative 3 (DN3) stage, and resulted in reduced expression of T cell receptor (TCR) beta chain in DN4 thymocytes. By chromatin immunoprecipitation, we demonstrated in DN thymocytes that GABPalpha is associated with transcription initiation sites of genes encoding key molecules in TCR rearrangements. Among these GABP-associated genes, knockdown of GABPalpha expression by RNA interference diminished expression of DNA ligase IV, Artemis, and Ku80 components in DNA-dependent protein kinase complex. Interestingly, forced expression of prearranged TCR but not IL-7Ralpha can alleviate the DN3 block in GABPalpha-targeted mice. Our observations collectively indicate that in addition to regulating IL-7Ralpha expression, GABP is critically required for TCR rearrangements and hence normal T cell development.

Differential Regulation of Dopaminergic Gene Expression byEr81

A recent study proposed that differentiation of dopaminergic neurons requires a conserved "dopamine motif" (DA-motif) that functions as a binding site for ETS DNA binding domain transcription factors. In the mammalian olfactory bulb (OB), the expression of a set of five genes [including tyrosine hydroxylase (Th)] that are necessary for differentiation of dopaminergic neurons was suggested to be regulated by the ETS-domain transcription factor ER81 via the DA-motif. To investigate this putative regulatory role of ER81, expression levels of these five genes were compared in both olfactory bulbs of adult wild-type mice subjected to unilateral naris closure and the olfactory bulbs of neonatal Er81 wild-type and mutant mice. These studies found that ER81 was necessary only for Th expression and not the other cassette genes. Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays (EMSA) experiments showed that ER81 bound directly to a consensus binding site/DA-motif in the rodent Th proximal promoter. However, the ER81 binding site/DA-motif in the Th proximal promoter is poorly conserved in other mammals. Both ChIP assays with canine OB tissue and EMSA experiments with the human Th proximal promoter did not detect ER81 binding to the Th DA-motif from these species. These results suggest that regulation of Th expression by the direct binding of ER81 to the Th promoter is a species-specific mechanism. These findings indicate that ER81 is not necessary for expression of the OB dopaminergic gene cassette and that the DA-motif is not involved in differentiation of the mammalian OB dopaminergic phenotype.

Crystal Structure of Mouse Elf3 C-terminal DNA-binding Domain in Complex with Type II TGF-β Receptor Promoter DNA

The Ets family of transcription factors is composed of more than 30 members. One of its members, Elf3, is expressed in virtually all epithelial cells as well as in many tumors, including breast tumors. Several studies observed that the promoter of the type II TGF-β receptor gene (TβR-II) is strongly stimulated by Elf3 via two adjacent Elf3 binding sites, the A-site and the B-site. Here, we report the 2.2 Å resolution crystal structure of a mouse Elf3 C-terminal fragment, containing the DNA-binding Ets domain, in complex with the B-site of mouse type II TGF-β receptor promoter DNA (mTβR-II DNA). Elf3 contacts the core GGAA motif of the B-site from a major groove similar to that of known Ets proteins. However, unlike other Ets proteins, Elf3 also contacts sequences of the A-site from the minor groove of the DNA. DNA binding experiments and cell-based transcription studies indicate that minor groove interaction by Arg349 located in the Ets domain is important for Elf3 function. Equally interesting, previous studies have shown that the C-terminal region of Elf3, which flanks the Ets domain, is required for Elf3 binding to DNA. In this study, we determined that Elf3 amino acid residues within this flanking region, including Trp361, are important for the structural integrity of the protein as well as for the Efl3 DNA binding and transactivation activity.

Essential Role of CR6-interacting Factor 1 (Crif1) in E74-like Factor 3 (ELF3)-mediated Intestinal Development

Although terminal differentiation of intestinal epithelium is essential for the efficient digestion and absorption of nutrients, little is known about the molecular mechanisms underlying this process. Recent studies have shown that Elf3 (E74-like factor 3), a member of the ETS transcription factor family, has an essential role in the terminal differentiation of absorptive enterocytes and mucus-secreting goblet cells. Here, we demonstrated that Crif1 (CR6-interacting factor 1) functions as transcriptional coactivator of Elf3 in intestinal epithelium differentiation. The intestinal epithelium-specific Crif1-deficient mice died soon after birth and displayed severe alterations of tissue architecture in the small intestine, including poor microvillus formation and abnormal differentiation of absorptive enterocytes. Strikingly, these phenotypes are largely similar to that of Elf3-deficient mice, suggesting that Elf3 signaling in the intestinal epithelium depends on the Crif1 expression. We dissected this relationship further and found that Crif1 indeed interacted with Elf3 through its ETS DNA binding domain and enhanced the transcriptional activity of Elf3 by regulating the DNA binding activity. Knockdown of Crif1 by RNA interference conversely attenuated the transcriptional activity of Elf3. Consistently, the expression level of Tgf-betaRII (transforming growth factor beta type II receptor), a critical target gene of Elf3, was dramatically reduced in the Crif1-deficient mice. Our results reveal that Crif1 is a novel and essential transcriptional coactivator of Elf3 for the terminal differentiation of absorptive enterocytes.

Conserved structural features of ETS domain-DNA complexes

ETS proteins comprise a family of widespread transcription factors regulating expression of many animal genes. Structurally ETS proteins are characterized by conserved DNA-binding ETS domain, recognizing DNA sequences with trinucleotide GGA. Comparative analysis of structural features of ETS domain-DNA complexes was carried out and conserved contacts, important in terms of interaction stability and specificity were identified. The analysis revealed 9 conserved hydrogen bonds with DNA backbone phosphates and 2 conserved bidentate hydrogen bonds with DNA major groove atoms, one conserved hydrophobic cluster on protein-DNA interface, important for binding site recognition, and 12 conserved water molecules, possibly mediating ETS domain-DNA interaction. The results are represented in specialized data bank of protein-DNA complexes NPIDB.

Fgf-Dependent Etv4/5 Activity Is Required for Posterior Restriction of Sonic hedgehog and Promoting Outgrowth of the Vertebrate Limb

Crosstalk between the fibroblast growth factor (FGF) and Sonic Hedgehog (Shh) pathways is critical for proper patterning and growth of the developing limb bud. Here, we show that FGF-dependent activation of the ETS transcription factors Etv4 and Etv5 contributes to proximal-distal limb outgrowth. Surprisingly, blockage of Etv activity in early distal mesenchyme also resulted in ectopic, anterior expansion of Shh, leading to a polydactylous phenotype. These data indicate an unexpected function for an FGF/Etv pathway in anterior-posterior patterning. FGF activity in the limb is not only responsible for maintaining posterior-specific Shh expression, but it also acts via Etvs to prevent inappropriate anterior expansion of Shh. This study identifies another level of genetic interaction between the orthogonal axes during limb development.

The Affinity of Ets-1 for DNA is Modulated by Phosphorylation Through Transient Interactions of an Unstructured Region

Binding of the transcription factor Ets-1 to DNA is allosterically regulated by a serine-rich region (SRR) that modulates the dynamic character of the adjacent structured DNA-binding ETS domain and its flanking autoinhibitory elements. Multi-site phosphorylation of the flexible SRR in response to Ca2+ signaling mediates variable regulation of Ets-1 DNA-binding affinity. In this study, we further investigated the mechanism of this regulation. First, thermal and urea denaturation experiments demonstrated that phosphorylation of the predominantly unstructured SRR imparts enhanced thermodynamic stability on the well-folded ETS domain and its inhibitory module. We next identified a minimal fragment (residues 279–440) that exhibits both enhanced autoinhibition of Ets-1 DNA-binding and allosteric reinforcement by phosphorylation. To test for intramolecular interactions between the SRR and the rest of the fragment that were not detectable by 1H-1H NOE measurements, paramagnetic relaxation enhancements were performed using Cu2+ bound to the N-terminal ATCUN motif. Increased relaxation detected for specific amide and methyl groups revealed a preferential interaction surface for the flexible SRR extending from the inhibitory module to the DNA-binding interface. Phosphorylation enhanced the localization of the SRR to this surface. We therefore hypothesize that the positioning of the SRR at the DNA-binding interface and its role in shifting Ets-1 to an inhibited conformation are linked. In particular, transient interactions dampen the conformational flexibility of the ETS domain and inhibitory module required for high-affinity binding, as well as possibly occlude the DNA interaction site. Surprisingly, the phosphorylation-dependent effects were relatively insensitive to changes in ionic strength, suggesting that electrostatic forces are not the dominant mechanism for mediating these interactions. The results of this study highlight the role of flexibility and transient binding in the variable regulation of Ets-1 activity.

The Transactivation Function of the Pea3 Subfamily Ets Transcription Factors Is Regulated by Sumoylation

Pea3, an Ets transcriptional factor, comprises multiple regulatory domains that affect its DNA binding and transcriptional activation. The aim of this work is to uncover the mechanism of action of negative regulatory regions flanking the transactivation domain. Mutagenesis of amino acid residues in the C-terminal negative regulatory region for transactivation revealed critical residues, including a lysine residue, K96, required for its function. Corresponding mutations in the closely related Pea3 subfamily members, Erm and Er81, also dramatically increased the transactivation capacity of their activation domains. Interestingly, all three proteins are sumoylated at this conserved lysine residue. Pea3 contains four other lysines, K222, K256, K318, and K437, embedded in a perfect SUMO consensus motif. The contribution of these lysine residues to the regulation of Pea3 activity and their sumoylation pattern was explored using a GAL4-PEA3 chimera devoid of the ETS DNA-binding domain and by analyzing the native protein. All four candidate SUMO sites included in the GAL4-PEA3 chimera were modified by sumoylation, and their simultaneous mutation dramatically increased the transactivation potential of Pea3. Similar analysis of full-length Pea3 confirmed K96, K222, and K256 as major SUMO modification sites. Collectively, these observations suggest that the activity of Pea3 and its paralogs, Erm and Er81, is negatively regulated by sumoylation.

TLS-ERG Leukemia Fusion Protein Deregulates Cyclin-Dependent Kinase 1 and Blocks Terminal Differentiation of Myeloid Progenitor Cells

TLS-ERG fusion protein is derived from the t(16;21) translocation found in human myeloid leukemia. Here, we show that retroviral transduction of TLS-ERG confers a growth advantage to L-G myeloid progenitor cells and blocks terminal differentiation. We found that the level of cyclin-dependent kinase 1 (Cdk1) protein was significantly decreased in controls but unchanged in TLS-ERG-expressing cells after granulocyte colony-stimulating factor treatment or interleukin-3 withdrawal. Injection of TLS-ERG-expressing L-G cells induced rapid development of a leukemia-like disease in syngeneic mice. Through site-directed mutagenesis, we showed that transformation and deregulation of Cdk1 by TLS-ERG require an intact ets DNA-binding domain within the fusion protein. Interestingly, treatment of TLS-ERG-expressing L-G cells with 5-aza-2'-deoxycytidine (Decitabine) or trichostatin A resulted in down-regulation of Cdk1 and induction of terminal differentiation. To investigate whether Cdk1 deregulation is indeed responsible for transformation by TLS-ERG, we constructed lentiviral vectors for delivery of Cdk1 mutants and small interfering RNA (siRNA). Both dominant-negative inhibition and siRNA knockdown of Cdk1 were able to restore the ability of TLS-ERG-expressing L-G cells to undergo terminal differentiation. In addition, siRNA knockdown of Cdk1 in YNH-1 cells derived from a t(16;21) acute myelogenous leukemia patient also resulted in terminal differentiation. As restoration of terminal myeloid differentiation to TLS-ERG cells is dependent on cell cycle arrest, our findings suggest an important role for Cdk1 in cellular transformation and may be useful in the search for new treatments of TLS-ERG-associated myeloid leukemia.

Identification of soluble protein fragments by gene fragmentation and genetic selection.

We describe a new method, which identifies protein fragments for soluble expression in Escherichia coli from a randomly fragmented gene library. Inhibition of E. coli dihydrofolate reductase (DHFR) by trimethoprim (TMP) prevents growth, but this can be relieved by murine DHFR (mDHFR). Bacterial strains expressing mDHFR fusions with the soluble proteins green fluroscent protein (GFP) or EphB2 (SAM domain) displayed markedly increased growth rates with TMP compared to strains expressing insoluble EphB2 (TK domain) or ketosteroid isomerase (KSI). Therefore, mDHFR is affected by the solubility of fusion partners and can act as a reporter of soluble protein expression. Random fragment libraries of the transcription factor Fli1 were generated by deoxyuridine incorporation and endonuclease V cleavage. The fragments were cloned upstream of mDHFR and TMP resistant clones expressing soluble protein were identified. These were found to cluster around the DNA binding ETS domain. A selected Fli1 fragment was expressed independently of mDHFR and was judged to be correctly folded by various biophysical methods including NMR. Soluble fragments of the cell-surface receptor Pecam1 were also identified. This genetic selection method was shown to generate expression clones useful for both structural studies and antibody generation and does not require a priori knowledge of domain architecture.

Inhibition of IL-1β transcription by peptides derived from the hCMV IE2 transactivator

The immediate early (IE) proteins of human cytomegalovirus (hCMV) have diverse roles in directing viral and host cell transcription. Among these is the ability of IE2 to induce transcription of the IL1B gene that codes for IL-1β in monocytes. This function is partially explained by interaction between IE2 and the host cell transcription factor Spi-1/PU.1 (Spi-1). We now show that maximal IE2 function also depends on productive interactions localizing to two C/EBP sites on the IL1B promoter suggesting either bi- or tri-molecular interactions between IE2, Spi-1 and C/EBPβ at two different locations on the promoter. The IE2 interaction region on Spi-1 was previously mapped to the DNA-binding ETS domain and overlaps the region of Spi-1 that interacts with the transcription factor C/EBPβ, a factor known to be critical for the induction of IL1B in response to Toll/IL-1 receptor (TIR) family signal transduction. The Spi-1 interacting region of IE2 maps to amino acids 315–328, a sequence that also interacts with the bZIP domain of C/EBPβ. An expression vector coding for amino acids 291–364 of IE2 can suppress LPS induction of a co-transfected IL1B enhancer–promoter fragment in a monocyte cell line. This inhibition is likely the result of competition between Spi-1 and C/EBPβ, thus blunting gene induction.

ERG Deletions Define a Novel Subtype of B-Progenitor Acute Lymphoblastic Leukemia.

In a previous gene expression profiling study of acute lymphoblastic leukemia (ALL), we identified a novel subtype of B-progenitor ALL (4.9% of 284 cases) with a unique gene expression profile, aberrant expression of CD2 and the absence of recurring cytogenetic abnormalities (Cancer Cell 2002; 1:133). Efforts to identify rearrangement or mutation of many of the top-ranked genes in the novel expression signature failed to identify a causative lesion. To further investigate the genetic basis of this subtype, we performed integrated genomic analysis of 277 ALL cases. Affymetrix 250k Sty and Nsp SNP microarrays were used in all cases, and Affymetrix U133A gene expression profiles were obtained on 183 of the cases. Unsupervised clustering of gene expression data identified 16 cases of the novel subtype, including all of the 14 previously defined cases. Remarkably, focal mono-allelic deletions of the ETS family member ERG (v-ets erythroblastosis virus E26 oncogene homolog) were detected by genome-wide copy number analysis in 11/16 (69%) of the novel cases, but not in any other ALL subtype. Extensive analysis failed to reveal evidence of translocations involving the altered ERG allele, indicating that these are intragenic deletions limited to ERG. The ERG deletions involved a subset of exons (ERG isoform 1 exons 3–7 or 3–9) resulting in the expression of internally deleted ERG transcripts with altered reading frames predicted to produce a prematurely truncated N-terminal protein fragment. However, using an alternative translational start site 5′ to exon 10, the transcripts also encode a ∼28kDa C-terminal ERG fragment that contains the entire C-terminal ETS DNA-binding and transactivation domains, but lacks all N-terminal domains. Importantly, western blot analysis of primary leukemic blasts revealed expression of only the 28kDa C-terminal ERG protein, along with full length ERG expressed from the retained wild type allele. Remarkably, the C-terminal ERG protein was also detected in 4 of 5 novel ALL cases that lacked detectable ERG deletions, but not in any other ALL subtype. In luciferase reporter assays, this aberrant ERG protein acts as a competitive inhibitor of wild type ERG. Analysis of a second cohort of 35 B-progenitor ALL cases lacking recurring cytogenetic abnormalities identified two cases with ERG deletions and a third expressing the aberrant ERG protein, all of which had the novel gene expression profile. Sequencing of ERG in 252 ALL cases identified only one case with an ERG mutation that resulted in a frameshift in the ETS domain. This case did not share the novel signature nor express the aberrant C-terminal ERG protein. Finally, in an analysis of 37 acute leukemia cell lines, the B-progenitor ALL line NALM-6 was found to harbor a focal, internally truncating ERG deletion, expressed the aberrant ERG protein, and shared the novel gene expression profile, thus identifying it as a model of this novel ALL subtype. These data establish focal ERG deletions as the genetic lesion underlying a novel subtype of ALL, and have expanded the genetic mechanisms that lead to the dysregulation of ERG from chromosomal translocations that result in enhanced transcriptional activity, to deletions that generate dominant negative forms of the transcription factor.

Neuregulin‐1 induces acetylcholine receptor transcription in the absence of GABPα phosphorylation

Localization of acetylcholine receptors (AChRs) to the postsynaptic region of muscle is mediated in part by transcriptional mechanisms, because the genes encoding AChR subunits are transcribed selectively in synaptic myofiber nuclei. Neuregulin-1 (NRG-1) is a synaptic signal and induces transcription of AChRs in muscle cells. Signaling by NRG-1 is thought to involve the transcription factor GA-binding protein (GABP), a heterodimer of GABPalpha, which is a member of the Ets family, and GABPbeta. Phosphorylation of certain other Ets proteins outside the Ets DNA-binding domain serves to stimulate transcriptional activation in response to extracellular signals. According to previous studies, NRG-1 stimulates phosphorylation of GABPalpha at threonine 280 in the N-terminal region adjacent to the Ets domain, suggesting that GABPalpha phosphorylation might contribute to NRG-1 responsiveness. To determine the functional importance of the N-terminal region of GABPalpha and whether its function is regulated by phosphorylation, we generated muscle cell lines in which the endogenous GABPalpha gene was deleted and replaced by variants of GABPalpha mutated in the N-terminal region. We found that NRG-1 can induce transcription in cells with mutated T280 phosphorylation site, indicating that T280 phosphorylation does not contribute to NRG-1 responsiveness. We also found that NRG-1-induced transcription occurs in cells missing the entire N-terminal region of GABPalpha. Because NRG-1 signaling is not expected to alter the function of the C-terminal region, which remains in these cells, these results suggest that GABPbeta, or other interacting components, rather than GABPalpha directly, is targeted by NRG-1 signaling.