Anti-angiogenics, inhibitors of pathological blood vessel growth, are an important class of targeted agent for the treatment of common cancers and ocular conditions. However, efficacy is compromised by the absence of biomarkers to guide patient selection or inform the management of resistance. We describe an assay for modified endothelial cell (EC) responses to the VEGF-A-neutralizing monoclonal antibody bevacizumab as part of a biomarker discovery program. ECs are transduced by lentivector expressing an experimental or non-silencing shRNA, each co-expressed with a different fluorescent protein. A 1:1 mixed cell population is then cultured with bevacizumab or control antibody under VEGF-A-dependent conditions. A normalized ratio of surviving cells, obtained by flow cytometry analysis, reflects EC resistance or sensitization to bevacizumab mediated by the experimental shRNA. With reagents prepared, the protocol takes 10 days and rigorously quantifies the impact of gene perturbation on the EC response to bevacizumab or other targeted anti-angiogenics.

Angiogenesis underlies development, physiology and pathogenesis of cancer, eye and cardiovascular diseases. Inhibiting aberrant angiogenesis using anti-angiogenic therapy (AAT) has been successful in the clinical treatment of cancer and eye diseases. However, resistance to AAT inevitably occurs and its molecular basis remains poorly understood. Here, we uncover molecular modifiers of the blood endothelial cell (EC) response to a widely used AAT bevacizumab by performing a pooled genetic screen using three-dimensional microcarrier-based cell culture and CRISPR–Cas9. Functional inhibition of the epigenetic reader BET family of proteins BRD2/3/4 shows unexpected mitigating effects on EC survival and/or proliferation upon VEGFA blockade. Moreover, transcriptomic and pathway analyses reveal an interaction between epigenetic regulation and anti-angiogenesis, which may affect chromosomal structure and activity in ECs via the cell cycle regulator CDC25B phosphatase. Collectively, our findings provide insight into epigenetic regulation of the EC response to VEGFA blockade and may facilitate development of quality biomarkers and strategies for overcoming resistance to AAT.

Social interaction and communication are evolutionary conserved behaviours that are developed in mammals to establish partner cognition. Deficit in sociability has been represented in human patients and animal models of neurodevelopmental disorders, which are connected with genetic variants of synaptic glutamate receptors and associated PDZ-binding proteins. However, it remains elusive how these key proteins are specialized in the cellular level for the initial social behaviour during postnatal developmental stage. Here we identify a hippocampal CA3 specifically expressed PDZ scaffold protein Lnx1 required for initial social behaviour. Through gene targeting we find that Lnx1 deficiency led to a hippocampal subregional disorder in neuronal activity and social memory impairments for partner discrimination observed in juvenile mice which also show cognitive defects in adult stage. We further demonstrate that Lnx1 deletion causes NMDA receptor (NMDAR) hypofunction and this is attributable to decreased GluN2B expression in PSD compartment and disruption of the Lnx1-NMDAR-EphB2 complex. Specific restoration of Lnx1 or EphB2 protein in the CA3 area of Lnx1-/- mice rescues the defective synaptic function and social memory. These findings thus reveal crucial roles of postsynaptic NMDAR multiprotein complex that regulates the formation of initial social memory during the adolescent period.

Neuronal connections are initiated by axon targeting to form synapses. However, how the maturation of axon terminals is modulated through interacting with postsynaptic elements remains elusive. In this study, we find that ligand of Numb protein X 1 (Lnx1), a postsynaptic PDZ protein expressed in hippocampal CA3 pyramidal neurons, is essential for mossy fiber (MF) axon targeting during the postnatal period. Lnx1 deletion causes defective synaptic arrangement that leads to aberrant presynaptic terminals. We further identify EphB receptors as novel Lnx1-binding proteins to form a multiprotein complex that is stabilized on the CA3 neuron membrane through preventing proteasome activity. EphB1 and EphB2 are independently required to transduce distinct signals controlling MF pruning and targeting for precise DG-CA3 synapse formation. Furthermore, constitutively active EphB2 kinase rescues structure of the wired MF terminals in Lnx1 mutant mice. Our data thus define a retrograde trans-synaptic regulation required for integration of post- and presynaptic structure that participates in building hippocampal neural circuits during the adolescence period.

Ryk is a member of the receptor tyrosine kinase (RTK) family of proteins that control and regulate cellular processes. It is distinguished by binding Wnt ligands and having no detectable intrinsic protein tyrosine kinase activity suggesting Ryk is a pseudokinase. Here, we show an essential role for Ryk in directing morphogenetic events required for normal cardiac development through the examination of Ryk-deficient mice. We employed vascular corrosion casting, vascular perfusion with contrast dye, and immunohistochemistry to characterize cardiovascular and pharyngeal defects in Ryk(-/-) embryos. Ryk(-/-) mice exhibit a variety of malformations of the heart and outflow tract that resemble human congenital heart defects. This included stenosis and interruption of the aortic arch, ventriculoarterial malalignment, ventricular septal defects and abnormal pharyngeal arch artery remodelling. This study therefore defines a key intersection between a subset of growth factor receptors involved in planar cell polarity signalling, the Wnt family and mammalian cardiovascular development.

GABAergic interneurons have many important functions in cortical circuitry, a reflection of their cell diversity. The developmental origins of this diversity are poorly understood. Here, we identify rostral-caudal regionality in Wnt exposure within the interneuron progenitor zone delineating the specification of the two main interneuron subclasses. Caudally situated medial ganglionic eminence (MGE) progenitors receive high levels of Wnt signaling and give rise to somatostatin (SST)-expressing cortical interneurons. By contrast, parvalbumin (PV)-expressing basket cells originate mostly from the rostral MGE, where Wnt signaling is attenuated. Interestingly, rather than canonical signaling through β-catenin, signaling via the non-canonical Wnt receptor Ryk regulates interneuron cell-fate specification in vivo and in vitro. Indeed, gain of function of Ryk intracellular domain signaling regulates SST and PV fate in a dose-dependent manner, suggesting that Ryk signaling acts in a graded fashion. These data reveal an important role for non-canonical Wnt-Ryk signaling in establishing the correct ratios of cortical interneuron subtypes.

Abstract The receptor tyrosine kinases (RTKs) are a well-characterized family of growth factor receptors that have central roles in human disease and are frequently therapeutically targeted. The RYK, ROR, PTK7 and MuSK subfamilies make up an understudied subset of WNT-binding RTKs. Numerous developmental, stem cell and pathological roles of WNTs, in particular WNT5A, involve signalling via these WNT receptors. The WNT-binding RTKs have highly context-dependent signalling outputs and stimulate the β-catenin-dependent, planar cell polarity and/or WNT/Ca2+ pathways. RYK, ROR and PTK7 members have a pseudokinase domain in their intracellular regions. Alternative signalling mechanisms, including proteolytic cleavage and protein scaffolding functions, have been identified for these receptors. This review explores the structure, signalling, physiological and pathological roles of RYK, with particular attention paid to cancer and the possibility of therapeutically targeting RYK. The other WNT-binding RTKs are compared with RYK throughout to highlight the similarities and differences within this subset of WNT receptors.

Abstract Angiogenesis inhibition is a useful strategy for treating cancer. However, the efficacy of anti-angiogenic therapy (AAT) in clinical oncology has been limited largely by highly variable patient response and the inevitable occurrence of resistance. The modest patient benefits have underscored a pressing need for qualified biomarkers and better knowledge of resistance mechanisms. Blood endothelial cells (ECs) are one of the main targets of AAT in the tumor microenvironment. Hence, understanding the EC response to AAT will provide insight into tumor response. To identify molecular modifiers of the EC response to AAT (in this study, bevacizumab, a humanized neutralizing anti-VEGF-A monoclonal antibody), we developed a high-throughput genetic screening platform. This involved a three-dimensional microcarrier-based culture system, CRISPR-Cas9-driven gene loss-of-function (LOF) and VEGF-A-dependent serum-free culture conditions for response modifiers. A pooled kinome-wide CRISPR-Cas9-based screen of 763 genes (with four single guide RNAs/sgRNAs targeting each gene) identified 18 candidate genes that upon LOF (represented by sgRNAs) were significantly enriched or depleted in the bevacizumab versus control treatment arm (P ≤ 0.005, FDR ≤ 0.3). Further candidate evaluation using siRNAs validated six genes whose knockdown conferred EC resistance or sensitization to bevacizumab (P < 0.05). Of these, knockdown of BRD2 or BRD3, which encode the epigenetic reader bromodomain-containing protein 2 or 3 (BRD2 or BRD3), respectively, conferred EC resistance to bevacizumab. The bromodomain and extraterminal domain (BET) inhibitors JQ1 and I-BET762, which selectively target the BET family of proteins (BRD2, BRD3, BRD4 and BRDT), reproduced the results of BRD2 or BRD3 LOF, with a more prominent phenotype (P < 0.05). Drug dose-response assessment indicated an anti-angiogenic effect of BET inhibitors regardless of the presence of bevacizumab. This inhibitory effect was unexpectedly attenuated when cells were co-treated with bevacizumab under VEGF-A-dependent conditions. Experiments to investigate the mechanistic basis for this phenotype of resistance are ongoing and include differential gene expression analysis using RNA-Seq and in vivo evaluation. Applying a non-biased approach to identify molecular modifiers of the EC response to AAT, we demonstrate in this study that BET inhibition is unexpectedly associated with resistance to bevacizumab, despite BET inhibition alone having an anti-angiogenic effect. These observations prompt further evaluation of epigenetic regulation in tumor angiogenesis, particularly in the context of interaction between BET inhibition and VEGF blockade. Clinically, these findings may facilitate development of potential predictive and/or response biomarkers and strategies to overcome resistance to AAT and/or BET inhibitors. Citation Format: Michael Y. He, Michael M. Halford, Marc G. Achen, Steven A. Stacker. A kinome-wide CRISPR screen reveals BET inhibition-associated endothelial cell resistance to anti-angiogenic therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1.

Counting nuclei released from intact cells is a convenient and reliable approach to assess cell density during microcarrier-based culture of adherent cells. However, commonly used methods for counting nuclei, such as crystal violet staining and quantification with a hemocytometer/automated imaging system or a Coulter counter, are imprecise, laborious and, limited in throughput. Here, we describe the use of high-affinity pro-fluorescent nucleic acid stains and volumetric flow cytometry for automated counting of nuclei released from cells attached to microcarriers with improved precision and high sample throughput. This simple procedure facilitates rapid and precise assessment of cell attachment, survival, and proliferation on microcarriers, and can provide information about the cell cycle, all without the need for cell detachment. Consequently, various microcarrier-based applications, from small-scale multi-factor experiments to large-scale functional genetic screens and clinical/industrial cultures, could be enhanced by this approach.

The analysis of receptor tyrosine kinases and their interacting ligands involved in vascular biology is often challenging due to the constitutive expression of families of related receptors, a broad range of related ligands and the difficulty of dealing with primary cultures of specialized endothelial cells. Here we describe a bioassay for the detection of ligands to the vascular endothelial growth factor receptor-2 (VEGFR-2), a key transducer of signals that promote angiogenesis and lymphangiogenesis. A cDNA encoding a fusion of the extracellular (ligand-binding) region of VEGFR-2 with the transmembrane and cytoplasmic regions of the erythropoietin receptor (EpoR) is expressed in the factor-dependent cell line Ba/F3. This cell line grows in the presence of interleukin-3 (IL-3) and withdrawal of this factor results in death of the cells within 24 hr. Expression of the VEGFR-2/EpoR receptor fusion provides an alternative mechanism to promote survival and potentially proliferation of stably transfected Ba/F3 cells in the presence of a ligand capable of binding and cross-linking the extracellular portion of the fusion protein (i.e., one that can cross-link the VEGFR-2 extracellular region). The assay can be performed in two ways: a semi-quantitative approach in which small volumes of ligand and cells permit a rapid result in 24 hr, and a quantitative approach involving surrogate markers of a viable cell number. The assay is relatively easy to perform, is highly responsive to known VEGFR-2 ligands and can accommodate extracellular inhibitors of VEGFR-2 signaling such as monoclonal antibodies to the receptor or ligands, and soluble ligand traps.

A chronic hyperactivated angiogenic state in cancer plays an important role in tumour growth and metastasis and has been identified as one of the hallmarks of cancer. Inhibition of this process has been associated with tumour suppression in many pre-clinical contexts using different animal tumour models. Anti-angiogenic therapeutics were subsequently developed and used to treat several prevalent types of human cancer. However, recent clinical experience has revealed limitations of this approach in treating cancer as patient response varies over a wide range. Given that there are complex underlying molecular and cellular changes provoked by anti-angiogenic treatment within the tumour microenvironment (TME), it is not surprising that modest effectiveness and resistance have been observed in the clinical setting. This article discusses these issues in the context of VEGF-A-targeted anti-angiogenic treatment of cancer and provides insight into the importance of tumour endothelium for understanding the tumour response to anti-angiogenic therapy. Special consideration is also given to possible approaches for investigating how endothelium contributes to the tumour response to anti-angiogenic agents and for exploring the therapeutic and biomarker potential of targeting tumour endothelium.

The Wnt receptor Ryk is an evolutionary-conserved protein important during neuronal differentiation through several mechanisms, including γ-secretase cleavage and nuclear translocation of its intracellular domain (Ryk-ICD). Although the Wnt pathway may be neuroprotective, the role of Ryk in neurodegenerative disease remains unknown. We found that Ryk is up-regulated in neurons expressing mutant huntingtin (HTT) in several models of Huntington's disease (HD). Further investigation in Caenorhabditis elegans and mouse striatal cell models of HD provided a model in which the early-stage increase of Ryk promotes neuronal dysfunction by repressing the neuroprotective activity of the longevity-promoting factor FOXO through a noncanonical mechanism that implicates the Ryk-ICD fragment and its binding to the FOXO co-factor β-catenin. The Ryk-ICD fragment suppressed neuroprotection by lin-18/Ryk loss-of-function in expanded-polyQ nematodes, repressed FOXO transcriptional activity, and abolished β-catenin protection of mutant htt striatal cells against cell death vulnerability. Additionally, Ryk-ICD was increased in the nucleus of mutant htt cells, and reducing γ-secretase PS1 levels compensated for the cytotoxicity of full-length Ryk in these cells. These findings reveal that the Ryk-ICD pathway may impair FOXO protective activity in mutant polyglutamine neurons, suggesting that neurons are unable to efficiently maintain function and resist disease from the earliest phases of the pathogenic process in HD.

The secreted adhesive glycoprotein vitronectin (VTN) is a multifunctional component of plasma and the extracellular matrix. A high-yielding, inexpensive, low endotoxin source of bioactive recombinant human vitronectin (rhVTN) is highly desirable for in vitro use in diverse cell culture systems ranging from basic research settings to clinical-grade production of human cells. We describe modifications to a previously reported heparin-based affinity chromatography procedure that improve yield and achieve efficient removal of endotoxin from washed and urea-solubilized human VTN inclusion bodies following standard autoinduction of expression in Escherichia coli. This simple procedure makes accessible the low-cost expression and purification of large quantities of bioactive rhVTN using basic equipment and facilitates its use in a spectrum of endotoxin-sensitive applications.

RYK is an unusual member of the receptor tyrosine kinase (RTK) family that is classified as a putative pseudokinase. RYK regulates fundamental biological processes including cell differentiation, migration and target selection, axon outgrowth and pathfinding by transducing signals across the plasma membrane in response to the high affinity binding of Wnt family ligands to its extracellular Wnt inhibitory factor (WIF) domain. Here we report the generation and initial characterization of a fully human inhibitory monoclonal antibody to the human RYK WIF domain. From a naïve human single chain fragment variable (scFv) phage display library, we identified anti-RYK WIF domain-specific scFvs then screened for those that could compete with Wnt3a for binding. Production of a fully human IgG1κ from an inhibitory scFv yielded a monoclonal antibody that inhibits Wnt5a-responsive RYK function in a neurite outgrowth assay. This antibody will have immediate applications for modulating RYK function in a range of settings including development and adult homeostasis, with significant potential for therapeutic use in human pathologies.

SUMMARY Clinical oncology experience with recently marketed antiangiogenic agents, which inhibit proteins important for tumor angiogenesis, has exposed significant limitations to their efficacy. Bevacizumab, a humanized neutralizing anti-VEGF-A monoclonal antibody, used in combination with cytotoxic chemotherapy for the treatment of metastatic colorectal cancer, represents the best-studied clinical example of targeted antiangiogenic therapy. In this context, bevacizumab provides modestly improved progression-free and overall survival in unselected patient populations via poorly understood mechanisms. Here we review concepts central to the identification and development of biomarkers in order to refine clinical use of bevacizumab in treating colorectal cancer and outline a phenotype-driven strategy for the discovery of high-value candidate biomarkers based on large-scale screening by molecular perturbation.

The Wnt signaling pathways control many critical developmental and adult physiological processes. In vertebrates, one fundamentally important function of Wnts is to provide directional information by regulating the evolutionarily conserved planar cell polarity (PCP) pathway during embryonic morphogenesis. However, despite the critical roles of Wnts and PCP in vertebrate development and disease, little is known about the molecular mechanisms underlying Wnt regulation of PCP. Here, we have found that the receptor-like tyrosine kinase (Ryk), a Wnt5a-binding protein required in axon guidance, regulates PCP signaling. We show that Ryk interacts with Vangl2 genetically and biochemically, and such interaction is potentiated by Wnt5a. Loss of Ryk in a Vangl2(+/-) background results in classic PCP defects, including open neural tube, misalignment of sensory hair cells in the inner ear, and shortened long bones in the limbs. Complete loss of both Ryk and Vangl2 results in more severe phenotypes that resemble the Wnt5a(-/-) mutant in many aspects such as shortened anterior-posterior body axis, limb, and frontonasal process. Our data identify the Wnt5a-binding protein Ryk as a general regulator of the mammalian Wnt/PCP signaling pathway. We show that Ryk transduces Wnt5a signaling by forming a complex with Vangl2 and that Ryk regulates PCP by at least in part promoting Vangl2 stability. As human mutations in WNT5A and VANGL2 are found to cause Robinow syndrome and neural tube defects, respectively, our results further suggest that human mutations in RYK may also be involved in these diseases.

Wnts are essential for a wide range of developmental processes, including cell growth, division, and differentiation. Some of these processes signal via the planar cell polarity (PCP) pathway, which is a β-catenin-independent Wnt signaling pathway. Previous studies have shown that Ryk, a member of the receptor tyrosine kinase family, can bind to Wnts. Ryk is required for normal axon guidance and neuronal differentiation during development. Here, we demonstrate that mammalian Ryk interacts with the Wnt/PCP pathway. In vitro analysis showed that the Wnt inhibitory factor domain of Ryk was necessary for Wnt binding. Detailed analysis of two vertebrate model organisms showed Ryk phenotypes consistent with PCP signaling. In zebrafish, gene knockdown using morpholinos revealed a genetic interaction between Ryk and Wnt11 during the PCP pathway-regulated process of embryo convergent extension. Ryk-deficient mouse embryos displayed disrupted polarity of stereociliary hair cells in the cochlea, a characteristic of disturbed PCP signaling. This PCP defect was also observed in mouse embryos that were double heterozygotes for Ryk and Looptail (containing a mutation in the core Wnt/PCP pathway gene Vangl2) but not in either of the single heterozygotes, suggesting a genetic interaction between Ryk and Vangl2. Co-immunoprecipitation studies demonstrated that RYK and VANGL2 proteins form a complex, whereas RYK also activated RhoA, a downstream effector of PCP signaling. Overall, our data suggest an important role for Ryk in Wnt/planar cell polarity signaling during vertebrate development via the Vangl2 signaling pathway, as demonstrated in the mouse cochlea.

Signaling proteins driving the proliferation of stem and progenitor cells are often encoded by proto-oncogenes. EphB receptors represent a rare exception; they promote cell proliferation in the intestinal epithelium and function as tumor suppressors by controlling cell migration and inhibiting invasive growth. We show that cell migration and proliferation are controlled independently by the receptor EphB2. EphB2 regulated cell positioning is kinase-independent and mediated via phosphatidylinositol 3-kinase, whereas EphB2 tyrosine kinase activity regulates cell proliferation through an Abl-cyclin D1 pathway. Cyclin D1 regulation becomes uncoupled from EphB signaling during the progression from adenoma to colon carcinoma in humans, allowing continued proliferation with invasive growth. The dissociation of EphB2 signaling pathways enables the selective inhibition of the mitogenic effect without affecting the tumor suppressor function and identifies a pharmacological strategy to suppress adenoma growth.