Kenneth Kosik - US grants

The effects of injury on individually identified central neurons will be studies in the larval sea lamprey, a primitive vertebrate. The objective is to understand how injured neurons regenerate axons from the correct location on the cell surface following axonal amputation. It is known that these neurons regenerate axons from the correct site (i.e. the stump of the cut axon) when the axon is cut at a point distant from the soma, but regenerate axons at incorrect sites (the dendritic tips) following axotomy close to the soma. In this study, the distribution of subcellular structures that are thought to be important in controlling axonal regeneration (microtubules, microtubule organizing centers, neurofilaments, the Golgi apparatus etc.) will be determined both in intact neurons and at various times following either "close" or "distant" axotomy. Particular attention will focus on changes in these structures that occur early after axotomy and are correlated to changes in the sites of axonal regeneration. The role of microtubules in determining the localization of axonal regeneration will be directly tested by injecting microtubule stabilizing and destabilizing drugs into injured neurons.

Nerve cells, or neurons, extend complex branches that communicate with many other neurons by sending and capturing signals at functional contacts called synapses, specialized small sites where membranes of two nerve cells are very close together. When the presynaptic cell is active, chemical neurotransmitters are released to act on the post-synaptic cell membrane, to excite or inhibit activity in the postsynaptic cell. A single neuron can have thousands of synapses with hundreds or thousands of other neurons in the brain, and each synapse is potentially capable of changing its efficacy in transmitting signals. It is believed that a fundamental mechanism underlying neural functions such as memory formation is a strengthening of synapses through repeated activity. That strengthening requires synthesis of new proteins, which probably remodel the synapse. Recently a subcellular neuronal organelle called an RNA granule has been suggested to harbor messenger RNA (mRNA) molecules that provide templates for such remodeling proteins, with translocation and release of this mRNA locally at activated synapses in response to neural depolarization. This project uses molecular biological techniques on cultured neurons to define the functional roles of specific RNA granule proteins in a novel conceptual framework. First, the new RNAi (RNA-interference) technique allows selective inactivation or 'knock-down' of specific gene expression, and is used to investigate the role of a particular granule protein called Staufen, to see how it is involved in granule assembly. Second, micro-RNAs (miRNA) are a type of short RNA that can regulate gene expression post-transcriptionally, so miRNAs in the granule will be identified to see how they might modify the local protein synthesis.
This project has some technological risks, but potentially very high impact, because results will be important for understanding molecular mechanisms of modifying neural functions, and so of networks involved in memory and learning. The impact is likely to extend beyond neuroscience to cell biology and physiology in general. The project also continues active involvement of this highly regarded PI with training a postdoctoral researcher, with international collaborations, and with public outreach.

DESCRIPTION (provided by applicant): Alzheimer's disease, already a serious global disease afflicting large segments of the population, is about to burgeon into an even larger problem as the baby-boomer bubble approaches retirement age. The disease remains incurable;however validated therapeutic targets are known. RNA interference (RNAi) technology poses a potential therapeutic option which requires further investigation. Targeting the mRNA rather than the protein offers major advantages in the ease of designing a highly specific inhibitory agent and rapidly advancing approaches to RNAi delivery suggest that the method can be developed into a therapy. Our hypothesis is that RNAi will prove to be an effective and selective strategy to slow, and perhaps even reverse, the pathogenic processes in inherited and sporadic AD. This proposal follows the completion of an R21 award of the same title. The announcement for this award was an RFA from the Fogarty Institute for proposals related to Brain Disorders in the Developing World and a major goal of the program was to build research capacity at the foreign site. The successful completion of the R21 aims is described in the preliminary data. The collaborative effort poses two questions concerning the cause and possible treatment of neurofibrillary pathology in AD. One question is whether suppression of Cdk5, an increasingly accepted disease target, can modify neurofibrillary pathology in an animal model. Cdk5 is an enzyme that phosphorylates tau protein and in so doing is thought to contribute to the conversion of the protein into an insoluble aggregate known as the neurofibrillary tangle. Cdk5 will be targeted by RNAi delivered in a viral vector. The second question is whether BACE1 inhibition by RNAi delivery can retard or prevent the development of neurofibrillary pathology in an animal with both plaques and tangles. The studies proposed here are intended to continue building research capacity at the foreign site which is now in a position to launch these studies. In addition to the established collaboration between the Kosik laboratory and the foreign site, two consultants will contribute to capacity building. They are Bev Davidson who will advise on the establishment of a viral core and Frank LaFerla who will contribute the triple transgenic mice to the vivarium at the foreign site.

[unreadable] DESCRIPTION (provided by applicant): [unreadable] The tau protein in the Alzheimer neurofibrillary tangle has been recognized for many years as a substrate for ubiquitination. More recently impaired proteasomal degradation has emerged as a theme related to many neurodegenerative diseases. In all the diseases with ubiquitinated inclusions, the relationship of the impaired degradation to the clinical disease remains uncertain. The evidence on this issue spans from the idea that the inclusions harm cells for a variety of reasons from triggering apoptosis to sequestering proteins of the ubiquitin pathway to the opposite idea that the inclusions are protective against some more toxic protofibrillar form of a self-assembled protein. Our goal for this proposal is to identity the specific modifications of tau that trigger ubiquitination and the specific proteins in the pathway that lead to tau ubiquitination. The delineation of this pathway represents an initial step toward understanding the role of tau ubiquitination in the pathogenesis of Alzheimer's disease and the tauopathies. We have amassed considerable preliminary data in support of the aims. Briefly, these findings are (a) tau phosphorylation represents a recognition signal for the tau E3 ligase; (2) the tau E2 ubiquitin conjugating enzyme is UbcH5B; (3) the tau complex which undergoes ubiquitination includes several chaperone proteins and their presence suggests a pathway that involves the E3 ligase CHIP (carboxyl terminus of Hsc70-interacting protein); (4) having detected several chaperone proteins by mass spectroscopy CHIP was identified immunocytochemically in the fraction with tau ubiquitin ligase activity. Often the pathway to the proteasome requires a collaboration between the ubiquitin-proteasome and chaperone systems. Because chaperone proteins have been identified in screens that rescue cells containing inclusions, understanding this pathway may be critical to devising therapeutic opportunities. [unreadable] [unreadable]

DESCRIPTION (provided by applicant): This proposal originates from data obtained under grant R21 NS45327 entitled Compound Identification in Assays for Tau Pathology. With those funds we established a high throughput screen and discovered novel compounds that inhibit Cdk5. The in vitro screen detects compounds that inhibit the phosphorylation of recombinant full-length tau by purified Cdk5 performed in the presence of high amounts of ATP. This strategy was designed to obtain 'hits' that do not bind to the ATP pocket of the kinase, and therefore differ from the known Cdk5 inhibitors. From an initial screen of 58,000 drug-like compounds, we have three lead compounds with single digit or sub-micromolar ICso's and with distinct mechanisms of action. One compound is competitive with ATP and has a high affinity for the Cdk5 ATP-binding pocket. The second compound also competes with ATP, is non-competitive with tau, and uniquely among this class of inhibitors, displaces adjacent amino acid residues to make room for the nitrophenyl group. Most importantly for our strategy was the third compound, which did not compete with ATP, but did compete with tau, and therefore may prove to be more specific than compounds which bind the conserved ATP pocket. Indeed, this compound has an approximately three-fold lower IC50 for Cdk5 than for GSK3P and an approximately six-fold lower IC5o for Cdk5 than for Cdc2. We propose to increase the number of lead compounds to twenty by screening additional libraries for in vitro IC50<100 nM, and with EC50<1 mM and LD50>100 mM in cell based and in vivo assays. To enhance the likelihood of finding compounds that do not compete with ATP we have modified our screening strategy and our preliminary data supports the idea that such compounds can be detected. Based on ranking of several factors including chemical tractability, toxicology, pharmacokinetics, and some ADME, five compounds will be selected for chemical modification. The optimized compounds from each of the five series will'be assessed for efficacy in animal models of neurofibrillary pathology developed within our collaborative group. From these data we will select one or two compounds for complete safety pharmacology. By the end of Year 5 we will apply for an Investigation of New Drug (IND) to the Food and Drug Administration (FDA) for a human phase I clinical trial to treat frontotemporal dementia. Because compound validation requires a broad expertise that is unlikely to be present in a single lab we have assembled individuals who collectively have the expertise to complete the aims.

PROJECT SUMMARY      Tau is a microtubule-­stabilizing protein that is abundant in neurons. It is a highly soluble, intrinsically disordered  protein (IDP) with little tendency for aggregation under native conditions. However, under several experimental  conditions and in a variety of neurodegenerative disorders including Alzheimer?s disease, Tau can spread from  cell  to  cell  and  aggregates  as  intra-­cellular  ?-­sheet  fibrilar  deposits.  Our  laboratories  have  critical  new  data  concerning the temporal, structural and cell biological details of Tau misfolding and fluid-­phase assembly?the  basis  of  this  proposal.  Our  research  team  consists  of  a  cell  biologist,  a  physical  chemist,  and  a  theoretical  biophysicist. Working together closely in an iterative manner we intend to determine the pathway from normal  Tau to disease-­related Tau fibrils. The tools for this analysis include (a) cellular systems capable of addressing  in vivo Tau interactions, and indirectly its conformational state based on a variety of molecular probes;? (b) site-­ directed spin labeling, electron paramagnetic resonance (EPR) line shape analysis and pulsed dipolar EPR to  determine  conformational  signatures  of  Tau;?  and  (c)  fully  atomistic  modeling  of  IDP  conformations,  their  populations and energetics, and coarse-­grained simulation of higher-­order assemblies of Tau. The conceptual  flow of the proposal begins with a remarkable observation from the Han lab: When exposed to sub-­stoichiometric  amounts of heparin, segments of Tau dramatically extend by a nanometer to solvent-­expose the hydrophobic  PHF6(*)  segment  capable  of  stacking  into  neat  ?-­sheets.  This  observation  correlates  with  the  appearance  of  fibrils, and thus we refer to this initiating step as ?on pathway? seeding. In vivo, Tau is known to populate a vast  conformational landscape controlled by alternative splicing, mutations and post-­translational modifications. We  propose  that  the  IDP  Tau  populates  an  ensemble  of  different  conformations  with  different  aggregation  propensities,  fibril  morphologies  and  interaction  partners,  depending  on  the  exact  Tau  variant.  However,  the  defining  and  specific  conformational  signatures  within  this  ensemble  are  unknown.  Determining  the  conformational signatures of aggregation-­prone Tau variants is our core objective, while a missing puzzle piece  in connecting Tau conformation to cellular interactions is the existence and nature of aggregation intermediates.  In this vein, the Han lab discovered that RNA induces liquid-­liquid phase separation of Tau in vitro into protein  droplets held together by weak electrostatic forces. At the in vivo cellular level, the Kosik lab discovered Tau-­ tRNA complexes, thereby adding Tau to the growing list of RNA-­binding proteins involved in neurodegeneration,  and capable of establishing liquid-­liquid phase separation in the cytoplasm. The Tau-­tRNA complexes may be a  physiologic  or  pathological  entity?we  will  obtain  clues  by  determining  their  loci  in  neuronal  cells.  Finally,  we  intend to learn whether the conformation of Tau, as modulated by disease mutations or co-­factors, influences  the stability and in vivo locality of the Tau-­tRNA complexes. Our goal is to discover a detailed route from soluble  Tau to fibrils, from the nanometer to the cellular level, and discover the pathological entities of Tau aggregation.   

The complex interaction between Alzheimer drivers and aging Project Summary/Abstract (30 lines of text) The greatest risk for Alzheimer?s disease is age. This extremely tight correlation with age has no explanation. However, most of what know about Alzheimer?s comes from early onset cases. We will utilize the 100 cases of early onset AD stored in the Colombian brain bank all with the same PSEN1[E280A] mutation to determine the full range of pathology observed due to a monogenic defect and compare these data to sporadic older onset disease. Some of the Colombian individuals in the bank have had amyloid and tau PET studies. In sporadic disease among the elderly, brain changes related to aging are frequent and in the absence of their clear delineation, treatments targeted solely at dominant genetic forms of the disease may be ineffective. Factors which might distinguish and promote AD in the elderly include inflammation, compromised brain vasculature, excessive microgliosis, cellular aging such as break down of the nuclear membrane and consequently escape of TDP-43 from the nucleus and possible contributions of synuclein. We will explore interactions of these factors with aging through descriptive neuropathology and experimental neuropathology methods. Comparisons will utilize sporadic AD post-mortem from several brain banks. These studies include state of the art single cell RNAseq and advanced assessment of inflammation markers. Cellular models will be explored using human induced pluripotent stem cell-derived neurons that harbor the PSEN1[E280A] mutation and are intended to discover downstream pathways affected by the mutation. Co-cultures with microglia to capture autonomous and non-autonomous effects of the mutation will be determined. To accomplish the aims we have assembled a multi-institutional international team with a long history of collaboration. Dr. Lopera, who first recognized the families and manages the Alzheimer Prevention Trial, heads the team in Colombia, an NIH supported project. To support the neuropathology effort we have enlisted the expertise of Dr. Eric Huang. Kosik has a nearly 30 year collaboration with Lopera, is familiar with the conduct of research in Colombia and recently traveled to visit the Colombian brain bank with Eric Huang. Kosik is closely connected institutionally with UCSF through his role as co-director of the Tau Consortium along with Bruce Miller. Kosik has published with Ellisman and serves on the review board for the National Center for Microscopy and Imaging Research center at UCSD. Thus the project consists of a strong, experienced and highly integrated team capable of conducting a complex project and dealing with any of the obstacles that will inevitably arise.