Abstract P3-07-57: Development of a 6-gene qPCR RUO-validated assay as a predictive biomarker for response of vantictumab (OMP-18R5; anti-frizzled) in HER2- breast cancer patients

Background: We have developed a monoclonal antibody, vantictumab that blocks canonical WNT/β-catenin signaling through binding of five FZD receptors (1, 2, 5, 7, 8). This antibody inhibits the growth of several tumor types, including breast. Vantictumab reduces tumor-initiating cell frequency and exhibits synergistic activity with standard-of-care (SOC) agents (Gurney et al, 2012). To target breast cancer patients most likely to respond to vantictumab, we undertook a predictive biomarker study.

Methods: We have identified a 6-gene Wnt pathway-related signature, FBXW2, CCND2, RHOU, CTBP2, WIF1, and DKK1, based on microarray gene expression data from 8 breast cancer patient derived xenograft (PDX) models with established in vivo response to vantictumab plus SOC. This signature successfully predicted the response of 8 additional and independent PDX breast tumors. We further developed a qPCR Research Use Only (RUO) assay for the 6 genes to be used on FFPE human breast tumor samples. Multiple assays targeting different regions spanning each mRNA transcript were tested and selected based on PCR efficiency, specificity and sensitivity. We compared assay sensitivity under different cDNA synthesis and pre-amplification conditions: random vs. gene-specific priming, number of pre-amplification cycles, pre-amplification reaction volumes, and cDNA synthesis kits. A repeatability study was performed to test assay performance. The pre-amplification and PCR were repeated over three separate days and across two independent labs.

Results: Our results showed that cDNA synthesis by gene-specific priming followed by 18 cycles of pre-amplification performed the best and the assay is robust with minimal starting FFPE RNA input. The results of the repeatability study were consistent among the different days and the different labs (<5% CV). Using the 6-gene qPCR RUO assay, the signature score from the microarray data was further refined using 12 PDX HER2- breast tumors with known in vivo response to vantictumab with SOC. The prevalence of the 6-gene signature was established using ∼100 HER2- breast cancer samples.

Conclusions: A robust 6-gene RUO-validated assay was developed as a predictive biomarker for vantictumab in HER2- breast cancer. The assay is currently being evaluated in a Phase 1b study of vantictumab with paclitaxel in HER2- breast cancer.

Citation Format: Zhang C, O'Young G, Wikstrom K, Davison T, Yeung P, Cattaruzza F, Yen W-C, Hoey T, Lewicki J, Rachmann R, Kerr P, Hill L, Eason R, McErlean S, Liu Y, Kapoun AM. Development of a 6-gene qPCR RUO-validated assay as a predictive biomarker for response of vantictumab (OMP-18R5; anti-frizzled) in HER2- breast cancer patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-57.

Abstract P6-15-10: Targeting Delta-Like 4 Ligand (DLL4)/Notch Signaling by a Novel Anti-DLL4 Antibody Inhibits Tumor Growth through Altering Cancer Stem Cell and Epithelial-to-Mesenchymal Transition-Associated Genes in Triple Negative Breast Cancer

Triple negative breast cancer (TNBC, ER-, PR-Her2-) accounts for 10% of all types of breast cancer and is known to be particularly aggressive and refractory to current therapies. Chemotherapeutic agents, such as taxanes, are currently the only treatment option for this type of breast cancer. However, these treatments often result in local and systemic relapse. While several promising targeted agents have improved the relapse rate in the combination with chemotherapy in patients with pathologic complete response, those who do not achieve pathologic complete response still have a poor prognosis. We previously demonstrated that interfering with Deltalike 4 ligand (DLL4)/Notch signaling by an anti-DLL4 antibody decreased tumor growth and delayed tumor recurrence following paclitaxel treatment through reducing breast cancer stem cell fraction and tumorigenicity (Proc Am Asso Cancer Res. 51:4, 2010). CD44+/CD24low cells have been demonstrated to be highly tumorigenic in breast tumors and are associated with treatment resistance (PNAS U S A, 106: 13820-13825, 2009). To gain insights into the mechanism of action of anti-DLL4-mediated TNBC growth inhibition, we evaluated the effect of anti-DLL4 on breast cancer CD44+/CD24low the expression patterns of a list of genes involved in sternness, differentiation, and key stem cell signaling pathways in TNBC xenograft tumors following paclitaxel with and without antibody treatment in vivo. Our data showed that paclitaxel treatment resulted in significant changes of gene expression patterns in the CD44+/CD24low cells in the residual tumors. We further analyzed these genes and identified several genes related to Notch signaling, stem cell maintenance and epithelial-to-mesenchymal transition that were modulated differentially by treatment with paclitaxel and/or anti-DLL4. In a metastatic TNBC orthotopic tumor model, the anti-DLL4 treatment resulted in tumor growth inhibition at the primary site and distant organs. Taken together, our findings suggest that targeting DLL4 may improve the efficacy of current treatments, delay tumor recurrence, and reduce metastatic growth in TNBC.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-15-10.

Targeting Cancer Stem Cells and Vasculature by a Novel Anti-Delta-Like 4 Ligand (DLL4) Antibody for Treatment of Triple Negative Breast Cancer

Triple negative (ER-, PR- Her2-) breast cancer accounts for 10% of all types of breast cancer and is known to particularly aggressive and refractory to current therapies. Chemotherapeutic agents, such as taxanes, are currently the only treatment option for this type of breast cancer, however, these treatments often result in high rates of local and systemic relapse. It has been suggested that cancer stem cells drive tumor growth and progression and are preferentially resistant to many current therapies. Delta-like 4 ligand (DLL4) is an important component of the Notch signaling pathway which is known to mediate stem cell self-renewal and vascular development. We hypothesized that targeting cancer stem cells and the tumor vasculature by interfering with the DLL4/Notch pathway will improve treatment outcome. We developed anti-DLL4 antibodies that recognize either the human or murine protein and have potent binding and antagonist activities. We have used these antibodies to investigate the role of DLL4 in triple negative breast cancer and to probe the mechanism in tumor and stromal cells in xenograft models derived from primary breast tumors. These studies showed that anti-DLL4 was efficacious as a single agent and in combination with paclitaxel (Taxol) against triple negative breast tumors including a tumor that developed paclitaxel resistance. Gene expression analysis showed that anti-DLL4 affected vascular-related genes in the stroma and Notch target genes in the tumor and stroma. Furthermore, inclusion of anti-DLL4 delayed breast tumor recurrence following termination of paclitaxel treatment. A tumorigenicity study indicated that treatment with anti-DLL4 decreased cancer stem cell frequency as measured by in vivo limiting dilution assay, whereas paclitaxel alone was ineffective. The combination of anti-DLL4 and paclitaxel further decreased cancer stem cell frequency compared to single agents. Our findings provide a rationale for targeting cancer stem cells and tumor vasculature through inhibition of the DLL4/Notch signaling for breast cancer treatment.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5071.

Expression and purification of lacZ and trpE fusion proteins

Fusion proteins are commonly used as a source of antigen for producing antibodies and in many cases can be useful for biochemical analyses. This unit describes two widely used expression systems for producing large amounts of proteins in E. coli. One system expresses lacZ fusions using the pUR series of vectors and the other expresses trpE fusions using the pATH vectors. The gene of interest is first subcloned into either a pUR or pATH vector in the correct reading frame. The correct transformant is selected, grown, and then induced with either IPTG or IAA. Sonication of cells in the presence of protease inhibitors is used to prepare extracts containing both types of fusion proteins, as well as other types of proteins overexpressed in E. coli. The extracts are checked for the presence of fusion protein on an SDS-polyacrylamide gel.

Stat4 regulates multiple components of IFN-gamma-inducing signaling pathways

Stat4 is activated in response to IL-12. Most functions of IL-12, including the induction of IFN-gamma, are compromised in the absence of Stat4. Since the precise role of Stat4 in IFN-gamma induction has not been established, experiments were conducted to examine Stat4 activation of IFN-gamma and other genes required for cytokine-induced expression of IFN-gamma. We first examined IL-12 signaling components. Basal expression of IL-12Rss1 and IL-12Rss2 is decreased in Stat4-deficient cells compared with that in control cells. However, IL-12 was still capable of inducing equivalent phosphorylation of Jak2 and Tyk2 in wild-type and Stat4-deficient activated T cells. We have further determined that other cytokine signaling pathways that induce IFN-gamma production are defective in the absence of Stat4. IL-18 induces minimal IFN-gamma production from Stat4-deficient activated T cells compared with control cells. This is due to defective IL-18 signaling, which results from the lack of IL-12-induced, and Stat4-dependent, expression of the IL-18R. Following IL-12 pretreatment to induce IL-18R, wild-type, but not Stat4-deficient, activated T cells demonstrated IL-18-induced NF-kappaB DNA-binding activity. In addition, IL-12-pretreated Stat4-deficient activated T cells have minimal IFN-gamma production followed by stimulation with IL-18 alone or in combination with IL-12 compared with control cells. Thus, Stat4 activation by IL-12 is required for the function of multiple cytokine pathways that result in induction of IFN-gamma.

Identification of a STAT4 binding site in the interleukin-12 receptor required for signaling

The specificity of the various STAT SH2 domains for different tyrosine-containing peptides enables cytokines to activate different signaling pathways and to induce distinct patterns of gene expression. We show that STAT4 has a unique peptide specificity and binds to the peptide sequence pYLPSNID (where pY represents phosphotyrosine). This motif is found at tyrosine residue 800 in the beta2 subunit of the interleukin-12 receptor and is required for DNA binding and transcriptional activity of STAT4. Our data demonstrate that transfection of interleukin-12 receptor beta1 and beta2 subunits is sufficient for STAT4 activation but not for STAT1 or STAT3 activation.

The roles of nuclear factor of activated T cells and ying-yang 1 in activation-induced expression of the interferon-gamma promoter in T cells

Nuclear factor of activated T cells (NFAT) plays an important role in expression of many cytokine genes including interleukin-2 and interleukin-4. However, its role in interferon-gamma (IFN-gamma) expression is not well understood. In the current studies, two strong NFAT-binding sites in the IFN-gamma promoter were identified by DNase I footprint analysis at positions -280 to -270 and -163 to -155. NFATp bound independently to both sites and was required for the formation of a composite element with AP-1 spanning position -163 to -147. In Jurkat T cells and primary lymphocytes, activation-induced expression of IFN-gamma reporter constructs containing point mutations in either NFAT site or the AP-1 component of the composite site was decreased by approximately 40-65%. Despite elimination of both strong NFAT-binding sites, the IFN-gamma promoter remained completely sensitive to inhibition by cyclosporin. This suggests that other elements in the IFN-gamma promoter, such as the IFN-gamma proximal element, are sufficient for cyclosporin sensitivity of this gene. Ying-Yang 1 (YY1), a potential inhibitor of IFN-gamma expression, binds to sites located between the two NFAT sites. Mutation of the YY1 sites alone had little effect on IFN-gamma promoter activity. However, mutation of both the NFAT and YY1-binding sites abolished activation-induced expression in primary murine splenocytes but not in Jurkat T cells. This suggests that under some conditions, YY1 may play a positive role in activation-induced transcription of IFN-gamma.

STAT structure and function in signaling

The phenotypes of various STAT knockout mice reveal an unexpected specificity in the biological roles of these molecules. The mechanisms involved in generating selectivity and modulating STAT activity have been the focus of intense studies. This work has led to the discovery of novel families of proteins that regulate Jak-STAT signaling. Recently, the structures of a STAT dimer/DNA complex and of the amino-terminal domain have been solved, providing new insights into the function of these versatile proteins.

The transcription factor NFAT4 is involved in the generation and survival of T cells

Nuclear factor of activated T cells (NFAT) is a family of four related transcription factors implicated in cytokine and early response gene expression in activated lymphocytes. Here we report that NFAT4, in contrast to NFATp and NFATc, is preferentially expressed in DP thymocytes. Mice lacking NFAT4 have impaired development of CD4 and CD8 SP thymocytes and peripheral T cells as well as hyperactivation of peripheral T cells. The thymic defect is characterized by increased apoptosis of DP thymocytes. The increased apoptosis and hyperactivation may reflect heightened sensitivity to TcR-mediated signaling. Further, mice lacking NFAT4 have impaired production of Bcl-2 mRNA and protein. NFAT4 thus plays an important role in the successful generation and survival of T cells.

The transcription factor NF-ATc is essential for cardiac valve formation

Nuclear factor of activated T cells (NF-AT) is the name of a family of four related transcription factors that may be needed for cytokine gene expression in activated lymphocytes. Here we report that mice with a targeted disruption of the NF-ATc gene show an unexpected and dramatic defect in cardiac morphogenesis, with selective absence of the aortic and pulmonary valves, leading to death in utero from congestive heart failure at days 13.5-17.5 of gestation. In contrast, tricuspid and mitral valve morphogenesis is normal. NF-ATc is the first transcription factor known to be expressed only in the endothelial cells of the heart. As in T cells, nuclear translocation of NF-ATc in cardiac endothelial cells is controlled by the calcium-regulated phosphatase calcineurin: NF-ATc remains cytoplasmic in normal embryos cultured with cyclosporin A, an inhibitor of calcineurin. Abnormal development of the cardiac valves and septae is the most frequent form of birth defect, yet few molecular regulators of valve formation are known. Our results indicate that NF-ATc may play a critical role in signal-transduction processes required for normal cardiac valve formation.

Delayed lymphoid repopulation with defects in IL-4-driven responses produced by inactivation of NF-ATc

The NF-AT family of transcription factors activates early immune response genes such as cytokines. In the adult, NF-ATc is expressed exclusively in the lymphoid system and is induced upon lymphocyte activation. NF-ATc null mutant mice die in utero of cardiac failure, precluding analysis of the role of NF-ATc in lymphocyte activation. By using RAG-2-deficient blastocyst complementation, we now demonstrate that young, highly chimeric mice lacking NF-ATc have impaired repopulation of both thymus and peripheral lymphoid organs. Furthermore, NF-ATc deficiency impaired T lymphocyte activation and secretion of IL-4. B lymphocytes displayed reduced proliferation and a selective loss of IL-4-driven immunoglobulin isotypes both in vivo and in vitro. Our data demonstrate that NF-ATc is essential for the optimal generation and function of mature T and B lineage cells, with an especially profound effect on IL-4-driven responses.

Cooperative DNA binding and sequence-selective recognition conferred by the STAT amino-terminal domain

STAT proteins (signal transducers and activators of transcription) activate distinct target genes despite having similar DNA binding preferences. The transcriptional specificity of STAT proteins was investigated on natural STAT binding sites near the interferon-gamma gene. These sites are arranged in multiple copies and required cooperative interactions for STAT binding. The conserved amino-terminal domain of STAT proteins was required for cooperative DNA binding, although this domain was not essential for dimerization or binding to a single site. Cooperative binding interactions enabled the STAT proteins to recognize variations of the consensus site. These sites can be specific for the different STAT proteins and may function to direct selective transcriptional activation.

Impaired IL-12 responses and enhanced development of Th2 cells in Stat4-deficient mice

Interactions between cytokine and receptor lead to the activation of multiple signalling molecules, including the family of signal transducer and activator of transcription (STAT) proteins. STAT4 is one member of this family, and is activated only in response to the cytokine interleukin (IL)-12 (refs 5, 6). By gene targeting, we have generated mice deficient in STAT4 to determine whether the function of this transcription factor is redundant with other signalling molecules activated by IL-12. IL-12-induced increases in the production of interferon (IFN)-gamma cellular proliferation and natural killer (NK) cell cytotoxicity are abrogated in lymphocytes from STAT4-deficient mice. The development of Th1 cells in response to either IL-12 of Listeria monocytogenes is also impaired in the absence of Stat4. Furthermore, Stat4-deficient lymphocytes demonstrate a propensity towards the development of Th2 cells. These results demonstrate that Stat4 is essential for mediating responses to IL-12 in lymphocytes, and regulating the differentiation of both Th1 and Th2 cells.

Differentiation of T-helper lymphocytes: selective regulation by members of the STAT family of transcription factors

Interleukin-4 (IL-4) and interleukin-12 (IL-12) control the differentiation of T-helper cells. Here we summarize studies which investigate the mechanism by which these cytokines selectively reprogramme gene expression in T-lymphocytes. Cytokine stimulation leads to the phosphorylation of specific tyrosine residues within the intracellular domain of the corresponding cytokine receptor. These phosphotyrosines serve as docking sites for latent, cytoplasmic transcription factors known as signal transducers and activators of transcription (Stat) proteins. Receptor/Stat interaction is mediated by the src homology 2 (SH2) domain of the corresponding Stat protein. Although Stat binding to the intracellular domain of the cytokine receptor strongly depends on the phosphotyrosine residue, the recruitment of a specific Stat protein is dictated by amino acid residues C-terminal to the phosphotyrosine. Specific docking sites within individual cytokine receptors have been identified for almost all Stat proteins. The direct coupling between cytokine receptor and transcription factor helps to explain how different cytokines elicit distinct patterns of gene expression.

Hyperproliferation and dysregulation of IL-4 expression in NF-ATp-deficient mice

NF-ATp is a member of a family of genes that encodes the cytoplasmic component of the nuclear factor of activated T cells (NF-AT). In this study, we show that mice with a null mutation in the NF-ATp gene have splenomegaly with hyperproliferation of both B and T cells. They also display early defects in the transcription of multiple genes encoding cytokines and cell surface receptors, including CD40L and FasL. A striking defect in early IL-4 production was observed after ligation of the TCR complex by treatment with anti-CD3 in vivo. The transcription of other cytokines including IL-13, GM-CSF, and TNF alpha was also affected, though to a lesser degree. Interestingly, the cytokines IL-2 and IFN gamma were minimally affected. Despite this early defect in IL-4 transcription, Th2 development was actually enhanced at later timepoints as evidenced by increased IL-4 production and IgE levels in situations that favor the formation of Th2 cells both in vitro and in vivo. These data suggest that NF-ATp may be involved in cell growth, and that it is important for the balanced transcription of the IL-4 gene during the course of an immune response.

Novel NFAT sites that mediate activation of the interleukin-2 promoter in response to T-cell receptor stimulation

The transcription factors NFAT and AP-1 have been shown to be essential for inducible interleukin-2 (IL-2) expression in activated T cells. NFAT has been previously reported to bind to two sites in the IL-2 promoter: in association with AP-1 at the distal antigen response element at -280 and at -135. On the basis of DNase I footprinting with recombinant NFAT and AP-1 proteins, gel shift assays, and transfection experiments, we have identified three additional NFAT sites in the IL-2 promoter. Strikingly, all five NFAT sites are essential for the full induction of promoter activity in response to T-cell receptor stimulation. Four of the five NFAT sites are part of composite elements able to bind AP-1 in association with NFAT. These sites display a diverse range of cooperativity and interdependency on NFAT and AP-1 proteins for binding. One of the NFAT sites directly overlaps the CD28-responsive element. We present evidence that CD28 inducibility is conferred by the AP-1 component in NFAT-AP-1 composite elements. These findings provide further insight into the mechanisms involved in the regulation of the IL-2 promoter.

Isolation of two new members of the NF-AT gene family and functional characterization of the NF-AT proteins

The activation of cytokine genes in response to antigenic stimulation of T cells is mediated by NF-AT proteins. Previous studies have identified two NF-AT proteins, NF-ATp and NF-ATc, that are homologous within a 290 aa domain distantly related to the Rel domain. We have isolated two additional members of this gene family, NF-AT3 and NF-AT4, which encode proteins 65% identical to the other NF-AT proteins within the Rel domain. The four NF-AT genes are transcribed in different sets of tissues that included many sites of expression outside the immune system. The Rel homology domain is sufficient for DNA recognition and cooperative binding interactions with AP-1. Although other members of the Rel family bind DNA as dimers, NF-AT proteins are monomers in solution or bound to DNA. Transfection assays indicate that each of the four NF-AT proteins can activate the IL-2 promoter in T cells.

Coordinate and cooperative roles for NF-AT and AP-1 in the regulation of the murine IL-4 gene

The transcription factor NF-AT plays an essential role in the inducible transcription of several cytokine genes during T cell activation. The distal NF-AT site of the murine IL-2 promoter binds both NF-AT and AP-1 proteins, and thus represents a composite regulatory site that integrates Ca(2+)- and PKC-dependent signaling pathways in T cell activation. However, the individual contributions of the NF-AT and AP-1 components to promoter activity via this composite site have not been resolved, owing to the absence of a clearly defined AP-1 binding site, which, when mutated abolishes AP-1 binding. We describe here an apparently analogous NF-AT/AP-1 composite site in the murine IL-4 promoter, which can be mutated to selectively block the recruitment of each component. We show that the cooperative and coordinate involvement of both NF-AT and AP-1 is necessary for full activity of the NF-AT/AP-1 composite site, and, ultimately, the entire IL-4 promoter.

Drosophila TAFII40 interacts with both a VP16 activation domain and the basal transcription factor TFIIB

Enhancement of RNA polymerase II transcription by the viral transactivator VP16 requires the TFIID complex, which consists of the TATA-binding protein (TBP) and TBP-associated factors (TAFs). Here we report the molecular cloning, expression, and biochemical characterization of Drosophila TAFII40 (dTAFII40), a subunit of TFIID. In vitro protein-protein interaction assays revealed direct binding between dTAFII40 and a 39 amino acid VP16 activation domain. In addition, affinity chromatography indicated a direct binding of the basal factor TFIIB to immobilized dTAFII40. Since VP16 also binds TFIIB, our results suggest a ternary interaction among an activator, a coactivator, and a basal transcription factor. Antibodies directed against dTAFII40 inhibited activation by GAL4-VP16 without affecting basal transcription. These results, taken together with previous studies of Sp1 and dTAFII110, establish that different activators interact with distinct TAFs in the TFIID complex and that TAFs can contact both activators and basal factors.

A new factor related to TATA-binding protein has highly restricted expression patterns in Drosophila

The TATA-binding protein TBP is necessary for the transcription of eukaryotic genes. Multi-protein complexes formed by TBP and different TBP-associated factors are involved in the initiation of transcription by polymerases I and II, and probably III as well. During the formation of an active initiation complex, TBP makes specific contacts with other proteins, for example TFIIB and RNA polymerase II (refs 2-4). Here we describe the cloning and characterization of a Drosophila gene product with considerable sequence similarity to TBP and a highly restricted expression pattern in the embryo. This TBP-related factor is a DNA-binding protein but is not likely to be a basal transcription factor. Our results suggest that TBP-related factor is a sequence-specific transcription factor that shares the DNA-binding properties of TBP.

Molecular cloning and functional analysis of Drosophila TAF110 reveal properties expected of coactivators

The general transcription factor TFIID is a multiprotein complex containing the TATA-binding protein and several associated factors (TAFs), some of which may function as coactivators that are essential for activated, but not basal, transcription. Here we describe the isolation and characterization of the first gene encoding a TAF protein. The deduced amino acid sequence of TAF110 revealed the presence of several glutamine- and serine/threonine-rich regions reminiscent of the protein-protein interaction domains of the regulatory transcription factor Sp1 that are involved in transcription activation and multimerization. In both Drosophila cells and yeast, TAF110 specifically interacts with the glutamine-rich activation domains of Sp1. Moreover, purified Sp1 selectively binds recombinant TAF110 in vitro. These findings taken together suggest that TAF110 may function as a coactivator by serving as a site of protein-protein contact between activators like Sp1 and the TFIID complex.

Isolation of coactivators associated with the TATA-binding protein that mediate transcriptional activation

A key step in the regulation of transcription involves interactions between promoter-selective factors and various components of the transcriptional apparatus. Here we report the requirements for transcriptional activation directed by NTF-1, a developmentally regulated transcription factor in Drosophila. Reconstituted transcription with fractionated Drosophila basal factors reveals that activation by NTF-1 requires factors present in the endogenous TFIID fraction that are distinct from the purified TATA-binding protein (TBP). Glycerol gradient sedimentation and immunoprecipitation analyses indicate that TFIID is a multiprotein complex containing TBP and at least six tightly bound TBP-associated factors (TAFs). Preparations of TBP lacking TAFs after fractionation with denaturants no longer support activation by NTF-1 but retain basal level activity. Addition of immunopurified and renatured TAFs to free TBP restores the ability of NTF-1 to activate transcription without influencing basal transcription. These results suggest that one or more of the TAF polypeptides confer coactivator function.

Transcriptional regulation of a pair-rule stripe in Drosophila

The periodic, seven-stripe pattern of the primary pair-rule gene even-skipped (eve) is initiated by crude, overlapping gradients of maternal and gap gene proteins in the early Drosophila embryo. Previous genetic studies suggest that one of the stripes, stripe 2, is initiated by the maternal morphogen bicoid (bcd) and the gap protein hunchback (hb), while the borders of the stripe are formed by selective repression, involving the gap protein giant (gt) in anterior regions and the Krüppel (Kr) protein in posterior regions. Here, we present several lines of evidence that are consistent with this model for stripe 2 expression, including in vitro DNA-binding experiments and transient cotransfection assays in cultured cells. These experiments suggest that repression involves a competition or short-range quenching mechanism, whereby the binding of gt and Kr interferes with the binding or activity of bcd and hb activators at overlapping or neighboring sites within the eve stripe 2 promoter element. Such short-range repression could reflect a general property of promoters composed of multiple, but autonomous regulatory elements.

Autoregulation of a segmentation gene in Drosophila: combinatorial interaction of the even-skipped homeo box protein with a distal enhancer element

Autoregulation has been implicated in the expression of many patterning genes in Drosophila, but the molecular details of this process are largely unknown. In the case of the segmentation gene even-skipped (eve), autoregulation is important for the specification of sharp stripes of gene expression at the onset of gastrulation. Here, we use a combination of DNA binding and P-transformation assays to characterize the cis- and trans-acting factors responsible for autoregulation. We show that eve autoregulation is mediated, at least in part, by a 100-bp minimal autoregulatory sequence (MAS) located approximately 5 kb upstream from the eve transcription start site. Multimerization of a 200-bp DNA fragment that encompasses the MAS drives optimal autoregulatory activity, comparable to that obtained with the native distal enhancer element located between -5.9 and -5.2 kb. The MAS contains two eve protein-binding sites, as well as binding sites for two nuclear factors present in early embryos. Directed mutagenesis of these binding sites suggests that both the eve protein and nuclear factors are essential for autoregulation. These results provide evidence that the eve protein acts combinatorially with other transcription factors to enhance its own expression.

Isolation and characterization of the Drosophila gene encoding the TATA box binding protein, TFIID

To investigate the biochemical mechanisms involved in interactions between regulatory factors and the general transcription complex, we have cloned, expressed, and characterized the Drosophila gene encoding the TATA binding protein, dTFIID. Comparison of the protein sequences of the Drosophila and yeast TATA binding proteins reveals a bipartite organization consisting of a highly conserved, basic carboxy-terminal domain and a nonconserved amino-terminal region rich in Gln, Gly, Ser, and Met residues. Purified dTFIID protein binds specifically to the TATA sequence and activates basal-level transcription, and the conserved carboxy-terminal half of the molecule is sufficient for both activities. Partially purified TFIID from Drosophila cells mediates activation by the transcription factor Sp1. In contrast, purified dTFIID expressed from the cloned gene is unable to support Sp1-dependent activation, suggesting that other factors may be required to mediate interactions between upstream activators like Sp1 and the TATA binding protein.

Sequence-specific DNA-binding activities of the gap proteins encoded by hunchback and Krüppel in Drosophila

The segmentation of the Drosophila body plan depends on a hierarchy of interactions among approximately 20-25 regulatory genes that are active in the early embryo (refs 1-4; for a review see ref. 5). The gap genes have a key role in this process and are responsible for the periodic expression of certain pair-rule genes and the localized expression of several homoeotic genes. The two best characterized gap genes, hunchback (hb) and Krüppel (Kr), contain homologies with the zinc-finger DNA-binding motif, although their mode of action in the early embryo is unknown. Here we report that both of the proteins encoded by these genes possess sequence-specific DNA-binding activities, which indicates that they might regulate gene expression at the level of transcription. The binding sites of the hb gene product are related by a 10-base pair (bp) consensus sequence, G/A C/C ATAAAAAA, whereas the binding sites of the Kr gene product share a distinct 10-bp motif, AACGGGTTAA. It is possible that the hb and Kr proteins cooperatively regulate gene expression, because they are expressed in broad, overlapping gradients in the early embryo. We also provide evidence that the on/off periodicity of the pair-rule gene even-skipped (eve) involves the interaction of the hb and Kr proteins with defined eve promoter elements.

Autoregulatory and gap gene response elements of the even-skipped promoter of Drosophila

The pair-rule gene even-skipped (eve) plays a key role in the regulatory hierarchy governing segmentation in Drosophila. Here we describe the use of P-transformation and eve promoter fusions to identify cis elements that regulate the periodic seven-stripe eve pattern. A distal region of the eve promoter, located between -5.9 and -5.2 kb, controls autoregulation. Sequences from this region will induce striped expression of a heterologous hsp70 basal promoter in the presence, but not absence, of endogenous eve+ products. Autoregulatory activity was localized to a 200-bp region of the distal eve promoter. We also provide evidence that individual eve expression stripes are regulated by separate cis sequences. eve promoter sequences located between -4.7 and -3 kb upstream of the transcription start site are important for the initiation of stripe 3, whereas sequences between -1.7 and -0.4 kb are needed for stripes 2 and 7. It is possible that these latter regions are directly regulated by the products of gap genes.

DNA-binding activities of the Drosophila melanogaster even-skipped protein are mediated by its homeo domain and influenced by protein context

The homeo box gene even-skipped (eve) encodes a 376-amino-acid protein that binds with high affinity to sequences located near the 5' termini of the eve and en genes. The 5' en sites are A + T rich and contain copies of the 10-base-pair (bp) consensus sequence T-C-A-A-T-T-A-A-A-T. In contrast, the 5' eve sites are G + C rich and contain the 9-bp sequence T-C-A-G-C-A-C-C-G. Among the five different homeo box proteins that have been tested for binding, eve is unique in that it shows virtually equal preference for the A + T-rich 5' en binding sites and the G + C-rich 5' eve sites. Most of the other proteins bind with a relatively higher affinity to the en sites than to the eve sites. In an effort to identify the regions of the eve protein that are responsible for its efficient binding to both classes of recognition sequences, we analyzed the DNA-binding properties of various mutant eve proteins. These studies suggest that the homeo domain of the eve protein is responsible for both binding activities. However, mutations in distant regions of the protein influenced the binding behavior of the eve homeo domain and caused a reduction in binding to the G + C class of recognition sites. We propose that the protein context of the homeo domain can influence its DNA-binding properties.

Divergent homeo box proteins recognize similar DNA sequences in Drosophila

A member of a small group of genes in Drosophila that define the segmentation pattern of the early embryo even-skipped (eve), which plays a key role in a network of interactions among segmentation genes. It appears to control morphogenesis by regulating the expression of the segmentation gene engrailed (en), and by autoregulating its own expression (M. Frasch and M.L., in preparation). Here we show that these regulatory interactions could occur at the level of transcription as a full-length eve protein binds with high affinity to specific sequences located near the 5' ends of the eve and en genes. The en binding sites contain at least one copy of a 10-base pair consensus sequence: T-C-A-A-T-T-A-A-A-T. In contrast, the 5' eve binding sites are relatively G-C rich and do not share obvious similarities with the 10-base pair consensus sequence associated with en. Other homeo box proteins can recognize both classes of eve binding sites, lending support to the proposal that regulatory interactions among homeo box genes involve a competition of different homeo box proteins for similar cis regulatory sequences.

Purification and properties of the Drosophila zen protein

The zen protein is encoded by the zerknullt gene required for normal early development in Drosophila. Like many regulatory proteins of this type, zen contains a 60 amino acid homeobox sequence. We have purified the zen protein and studied its solution behavior and its interaction with DNA. The zen protein exists as a monomer in solution with a molecular weight of about 40,000. It binds specifically to a site about 900 bases upstream from the zen gene. Within this binding site DNase protection experiments indicate that binding is confined to two regions approximately 11 and 14 bases in length that are separated by about 30 base pairs. The protein concentration dependence of the binding curve suggests that protein binding is non cooperative.

Molecular characterization of the zerknüllt region of the Antennapedia gene complex in Drosophila

zerknüllt (zen) is unique among the 18 known homeo box genes in Drosophila since it is required for the differentiation of the dorsal-ventral pattern, and does not appear to be involved in the process of segmentation. Here we show that the zen region of the Antennapedia complex (ANT-C) consists of two closely linked homeo box genes, designated z1 and z2. The z1 and z2 transcription units show essentially identical patterns of expression during early development, which are consistent with the timing and sites of zen+ gene activity. The putative proteins encoded by z1 and z2 are highly divergent and are related only by virtue of homeo box homology. We have used P-element-mediated germ line transformation to show that z1 alone can provide zen+ gene function, suggesting that the z2 gene might be dispensable. The occurrence of closely linked homeo box genes that display similar patterns of expression is not unique to the zen locus. Such gene duplications might provide important clues to the evolution of the homeo box gene family in Drosophila and other organisms.

Characterization and localization of the even-skipped protein of Drosophila

On the basis of homeo box cross-homology we have isolated the pair-rule gene even-skipped (eve) of Drosophila. The eve transcription unit appears to be less than 1.5 kb in length, and encodes a single mRNA of approximately 1.4 kb. The nucleotide sequence of genomic and cDNA clones indicates that the eve protein is composed of 376 amino acid residues, and that its homeo domain shares only approximately 50% amino acid identity with the homeo domains of previously characterized genes. Using antibodies raised against a beta-galactosidase fusion protein we show that the eve protein is distributed in a series of seven transverse stripes at the cellular blastoderm stage, and is localized primarily within the nuclear regions of those embryonic cells that express the gene. After gastrulation, seven weakly stained stripes of eve expression appear, resulting in a transient pattern that consists of a total of 14 evenly spaced stripes. Both the original and new stripes gradually disappear during germ band elongation. A second expression pattern emerges during neurogenesis, whereby eve protein is detected in discrete subsets of neurons in each of the ventral ganglia.

Transcripts encoded by a homoeo box gene are restricted to dorsal tissues of Drosophila embryos

In Drosophila elaboration of positional identity along the anterior-posterior and dorsal-ventral embryonic body axes involves early zygotic gene functions that are expressed in response to maternal cues present in the unfertilized egg. Zygotic loci that are required for the specification of positional identity along the anterior-posterior body axis have been described in detail. Less is known about the zygotic loci responsible for differentiation of the dorsal-ventral pattern; however, several genes that might be involved have been identified. Zerknüllt (zen) is an example of a zygotic gene required for correct differentiation of dorsally derived embryonic tissues. On the basis of homoeo box cross homology, we have now isolated a gene, called S60, that derives from the zen region of the Antennapedia complex (ANT-C). Transcripts encoded by S60 transiently accumulate in the dorsal-most tissues of developing embryos. This pattern of expression suggests that S60 corresponds to zen. Since S60 contains a homoeo box, it is possible that differentiation of the anterior-posterior and dorsal-ventral embryonic patterns involves similar molecular mechanisms.

Cross-regulatory interactions among pair-rule genes in Drosophila

The pair-rule genes of Drosophila are required for the subdivision of the developing embryo into a repeating series of homologous body segments. One of the pair-rule genes, even-skipped (eve), appears to be particularly important for the overall segmentation pattern since eve- embryos lack all segmental subdivisions in the middle body region. On the basis of homeo box cross-homology we have isolated a gene, S72, which probably corresponds to eve. In embryo tissue sections S72 transcripts show a periodic distribution pattern. The eve- phenotype appears to involve altered patterns of fushi tarazu and engrailed expression. These and other findings suggest that pair-rule gene expression might involve hierarchical cross-regulatory interactions.

Homeo box gene expression in anterior and posterior regions of the Drosophila embryo

The homeo box is a 180-base-pair coding sequence that has been implicated in the control of Drosophila development. A common feature of the nine previously reported homeo box genes is their involvement in the establishment of the segmentation pattern of the embryo. In this report we describe the isolation and properties of two additional homeo box genes, F90-2 and S67. Transcripts encoded by the two genes are detected in embryonic tissues that derive from regions near the anterior and posterior poles of the embryo, which are outside the limits of expression of known homeotic genes. These results suggest that at least some homeo box genes specify positional identity along the anterior-posterior body axis that is independent of the process of segmentation.