Translational Predictive Biomarker Analysis of the Phase 1b Sorafenib and Bevacizumab Study Expansion Cohort

Predictive biomarkers are needed to triage patients to the best therapy. We prospectively planned examination of sequential blood, biopsy, and functional imaging with which to confirm the mechanism and to identify potential predictive biomarkers in a phase Ib clinical trial expansion of patients with solid tumors receiving sorafenib/bevacizumab. The maximally tolerated doses of sorafenib at 200 mg twice daily with bevacizumab at 5 mg/kg every other week were given to biopsiable patients. Patients were randomized to receive either sorafenib or bevacizumab monotherapy for the first 28-day cycle with the second drug added with cycle 2. Biopsies, dynamic contrast-enhanced MRI, and fluorodeoxyglucose-proton emission tomography were done pre-therapy and at 2 and 6 weeks (2 weeks into combination therapy). Tumor and serum proteomics, Ras/Raf mutational analysis, and functional imaging results were examined individually and across the dataset to identify potential changes predictive of response to therapy and those that confirm the biochemical drug mechanism(s). Therapy with sorafenib/bevacizumab resulted in clinical benefit in 45% of this mixed solid tumor group. ERK activation and microvessel density were decreased with monotherapy treatment with sorafenib or bevacizumab, respectively; whereas a decreased signal over the group of total AKT, phospho(p)-VEGF receptor2, p-endothelial nitric-oxide synthase, b-RAF, and cleaved poly(ADP-ribose) polymerase was associated with earlier progression of disease. Tumor metabolic activity decreased in those patients with clinical benefits lasting longer than 4 months, and activity increased with progression of disease. Cleavage of caspase 3 and poly(ADP-ribose) polymerase was increased, and Ki67 expression decreased in patients with prolonged clinical benefits, consistent with decreased proliferation and increased apoptosis. The conglomerate analysis, incorporating pharmacodynamic and tumor biochemistry, demonstrated sorafenib/bevacizumab-targeted vascular activity in the tumor. Results suggest potential biomarkers for which changes, as a group, during early therapeutic exposure may predict clinical benefit.Sorafenib and bevacizumab have demonstrated clinical utility as single agents or in combination with chemotherapy for solid tumors. Sorafenib, initially developed as a c-Raf kinase inhibitor, also has potent inhibitory activity against the vascular endothelial growth factor receptor-2 (VEGFR2).¹ Clinical activity has been shown for bevacizumab, the humanized neutralizing monoclonal antibody against VEGF, also alone and in chemotherapy combinations (1–5). The role of combining two agents with overlapping target biology had not yet been studied.We tested the clinical hypothesis that signal interruption at collaborative pathway points, both vertical and horizontal interactions, may yield equal or greater effect than the agents in isolation in a phase I trial combining bevacizumab and sorafenib ({"type":"clinical-trial","attrs":{"text":"NCT00095459","term_id":"NCT00095459"}}NCT00095459), and we now report the translational analyses (6). Sorafenib was selected for its ability to target both receptor and cytosolic kinases important in a variety of activated cells in the tumor microenvironment, including stromal, endothelial, and malignant cells. Because such kinase inhibitor treatment has been shown to up-regulate production of proangiogenic cytokines, we added bevacizumab to reduce VEGF ligand availability and augment inhibition of endothelial cells. We observed the clinical benefit, including partial response and prolonged disease stabilization, using attenuated doses of the individual agents as determined by safety assessments during the trial; partial response or disease stabilization of at least 4 months occurred in 59% of the daily sorafenib cohort and in 55% of those on the intermittent, 5 of 7 days, sorafenib schedule (6, 7). These benefits lasted up to 37+ months with over 25% of patients receiving 12 or more months of therapy. The trial prospectively planned comprehensive translational assessment using a randomized drug addition design (Fig. 1A) to evaluate individual drug target specificity and combination drug effects to identify potential predictive biomarkers to examine in the ongoing phase II study of sorafenib/bevacizumab in ovarian cancer.Open in a separate windowFig. 1.Treatment schema (A) and Consort diagram (B).Predictive biomarkers are increasingly important for the advancement of targeted therapies. Such knowledge should allow more effective triage of patients to interventions more likely to provide clinical benefit. Biomarkers that predict drug response may consist of direct measures of activity, such as modulation of biochemical signals in the tumor (8) or those that yield pharmacodynamic measures, such as functional imaging (9, 10). Changes in metabolic activity and/or blood flow using dynamic imaging may fall into both categories with decreased glucose uptake due to reduced glucose delivery and/or reduced glucose metabolism and altered vascular permeability in response to attenuation of the VEGF drive. Aggregate analysis of these varied translational measures may yield a more detailed view of the cancer and the drug combination, allowing broader dissection into potential predictive biomarkers. Linking modulation of activity with clinical benefit is a first step in validating prospective biomarkers.We designed a novel drug administration schema from which to examine the contribution of both sorafenib and bevacizumab on the modulation of tumor and the tumor microenvironment behavior. The biochemical and imaging data demonstrate changes consistent with alteration of tumor vascularity, demonstrate direct association of target effect with clinical outcome across solid tumor types, and confirm the benefit of complementary pathway targeting. Reduction in blood flow, up-regulation of cytokine production, and inhibition of a set of anti-apoptotic anti-proliferative signaling events together may define potentially predictive changes to examine in early drug administration in subsequent trials.     

An OBSL1-Cul7Fbxw8 ubiquitin ligase signaling mechanism regulates Golgi morphology and dendrite patterning

The elaboration of dendrites in neurons requires secretory trafficking through the Golgi apparatus, but the mechanisms that govern Golgi function in neuronal morphogenesis in the brain have remained largely unexplored. Here, we report that the E3 ubiquitin ligase Cul7(Fbxw8) localizes to the Golgi complex in mammalian brain neurons. Inhibition of Cul7(Fbxw8) by independent approaches including Fbxw8 knockdown reveals that Cul7(Fbxw8) is selectively required for the growth and elaboration of dendrites but not axons in primary neurons and in the developing rat cerebellum in vivo. Inhibition of Cul7(Fbxw8) also dramatically impairs the morphology of the Golgi complex, leading to deficient secretory trafficking in neurons. Using an immunoprecipitation/mass spectrometry screening approach, we also uncover the cytoskeletal adaptor protein OBSL1 as a critical regulator of Cul7(Fbxw8) in Golgi morphogenesis and dendrite elaboration. OBSL1 forms a physical complex with the scaffold protein Cul7 and thereby localizes Cul7 at the Golgi apparatus. Accordingly, OBSL1 is required for the morphogenesis of the Golgi apparatus and the elaboration of dendrites. Finally, we identify the Golgi protein Grasp65 as a novel and physiologically relevant substrate of Cul7(Fbxw8) in the control of Golgi and dendrite morphogenesis in neurons. Collectively, these findings define a novel OBSL1-regulated Cul7(Fbxw8) ubiquitin signaling mechanism that orchestrates the morphogenesis of the Golgi apparatus and patterning of dendrites, with fundamental implications for our understanding of brain development.     

The effect of dolichol on the structure and phase behaviour of phospholipid model membranes

The effect of dolichol C₉₅ on the structure and thermotropic phase behaviour of dipalmitoylphosphatidylcholine, dipalmitoylphosphatidylethanolamine and stearoyloleoylphosphatidylethanolamine has been examined by synchrotron X-ray diffraction and differential scanning calorimetry. The presence of dolichol C₉₅ had no detectible effects on the temperature of either the gel to ripple or the ripple to liquid-crystal phase transition of dipalmitoylphosphatidylcholine. A proportionate increase of a few degrees in the temperature of the gel to lamellar liquid-crystal phase transition is observed in dispersions of dipalmitoylphosphatidylethanolamine and significantly there is a decrease in the temperature of the lamellar to non-lamellar phase transition of stearoyloleoylphosphatidylethanolamine. There was no significant change in the bilayer repeat spacing of all three mixed dispersions in gel phase in the presence of up to 20 mol% dolichol C₉₅. Electron density calculations showed that there was no change of bilayer thickness of dipalmitoylphosphatidylcholine with incorporation of up to 7.5 mol% dolichol C₉₅. These data suggest that effect of dolichol on the phospholipid model membranes depend on both the head group and the hydrocarbon chains of the phospholipid molecules. The presence of dolichol in phosphatidylcholine bilayers conforms to a model in which the polyisoprene compound is phase separated into a central domain sandwiched between the two monolayers in gel phase. In bilayers of phosphatidylethanolamines dolichol tends to stabilize the bilayers in gel phase at low temperatures and destabilize the bilayers in lamellar disordered structure at high temperatures. Non-lamellar structures coexist with lamellar disordered phase over a wide temperature range suggesting that dolichol is enriched in domains of non-lamellar structure and depleted from lamellar phase. These findings are useful to understand the function of dolichol in cell membranes.     

A conserved PTEN/FOXO pathway regulates neuronal morphology during C. elegans development

The phosphatidylinositol 3-kinase (PI3K) signaling pathway is a conserved signal transduction cascade that is fundamental for the correct development of the nervous system. The major negative regulator of PI3K signaling is the lipid phosphatase DAF-18/PTEN, which can modulate PI3K pathway activity during neurodevelopment. Here, we identify a novel role for DAF-18 in promoting neurite outgrowth during development in Caenorhabditis elegans. We find that DAF-18 modulates the PI3K signaling pathway to activate DAF-16/FOXO and promote developmental neurite outgrowth. This activity of DAF-16 in promoting outgrowth is isoform-specific, being effected by the daf-16b isoform but not the daf-16a or daf-16d/f isoform. We also demonstrate that the capacity of DAF-16/FOXO in regulating neuron morphology is conserved in mammalian neurons. These data provide a novel mechanism by which the conserved PI3K signaling pathway regulates neuronal cell morphology during development through FOXO.     

Regulation of Neuronal Morphogenesis and Positioning by Ubiquitin-Specific Proteases in the Cerebellum

Ubiquitin signaling mechanisms play fundamental roles in the cell-intrinsic control of neuronal morphogenesis and connectivity in the brain. However, whereas specific ubiquitin ligases have been implicated in key steps of neural circuit assembly, the roles of ubiquitin-specific proteases (USPs) in the establishment of neuronal connectivity have remained unexplored. Here, we report a comprehensive analysis of USP family members in granule neuron morphogenesis and positioning in the rodent cerebellum. We identify a set of 32 USPs that are expressed in granule neurons. We also characterize the subcellular localization of the 32 USPs in granule neurons using a library of expression plasmids encoding GFP-USPs. In RNAi screens of the 32 neuronally expressed USPs, we uncover novel functions for USP1, USP4, and USP20 in the morphogenesis of granule neuron dendrites and axons and we identify a requirement for USP30 and USP33 in granule neuron migration in the rodent cerebellar cortex in vivo. These studies reveal that specific USPs with distinct spatial localizations harbor key functions in the control of neuronal morphogenesis and positioning in the mammalian cerebellum, with important implications for our understanding of the cell-intrinsic mechanisms that govern neural circuit assembly in the brain.