Joseph G. Gleeson, MD - US grants

DESCRIPTION (provided by applicant): Almost nothing is known about how neurons migrate, or about the molecular mechanism regulating this migration. Understanding these mechanisms is critical for our understanding of childhood epilepsy and mental retardation, as defects in neuronal migration frequently underlie these disorders. Additionally, one of the major hurdles in neuronal transplantation or regeneration following damage is poor neuronal migration into target areas, which may be overcome through approaches derived from a better understanding of how neurons migrate. One common inherited cause of severe mental retardation and epilepsy in humans is classical lissencephaly, defined by a lack of cortical gyri and sulci formation and due to a failure of neurons to properly migrate. Mutations in either of two genes, doublecortin (DCX) or lissencephalyI (LIS1), leads to severe generalized defects in neuronal migration and produces nearly identical lissencephaly in humans. A mutation in the cdk5 gene in mouse also leads to a defect in neuronal migration that is strikingly similar to human lissencephaly. The central hypothesis of this application is that these common mutant phenotypes suggest that there may be interactions between the encoded proteins. The predicted DCX and LIS1 proteins are entirely novel, suggesting they may help define novel molecular mechanisms of neuronal migration, and both were previously shown to function as microtubuleassociated proteins that are localized around the nucleus. The cdk5 gene is a serinethreonine kinase that phosphorylates some cytoskeletal proteins. However, the role of DCX, LIS1 and cdk5 in neuronal migration is unknown. Additionally, despite the very similar mutant phenotypes, it is untested whether these proteins interact directly to mediate their effect or even act in a common pathway. Therefore the Specific Aims of this proposal are to determine whether: 1) There are genetic or physical interactions between DCX and LIS1. 2) DCX and LIS1 function to regulate nuclear movement during neuronal migration. 3) DCX is regulated by cdk5 during neuronal migration.

DESCRIPTION (provided by applicant): Recent studies have shown that many children with mental retardation and epilepsy have abnormalities of migration of neurons to the developing cerebral cortex, resulting in cortical dysplasia. Almost nothing is known about how neurons migrate, or about the molecular mechanism regulating this migration. Additionally, one of the major hurdles in neuronal transplantation or regeneration following damage is poor neuronal migration into target areas which may be overcome through approaches derived from a better understanding of how neurons migrate. One not uncommon inherited cause of severe mental retardation and epilepsy in humans is classical lissencephaly, defined by a lack of cortical gyri and sulci formation and apparently due to a failure of proper neuronal migration. Mutations in either of two genes, doublecortin (DCX) or lissencephaly-1 (LIS1) produces nearly identical lissencephaly in humans and are therefore required for proper neuronal migration. A mutation in the cdk5 gene in mouse also leads to a defect in neuronal migration that is strikingly similar to human lissencephaly. The central hypothesis of this application is that these common mutant phenotypes suggest that there may be interactions between the encoded proteins. The predicted DCX and LS1 proteins are entirely novel, suggesting they may help define novel molecular mechanisms of neuronal migration, and both were previously shown to function as microtubule-associated proteins that are localized around the nucleus. The cdk5 gene is a serine-threonine kinase that phosphorylates some cytoskeletal proteins. However, the underlying defect that is responsible for impaired migration when these genes are mutated is unknown. Additionally, despite the very similar mutant phenotypes, it is untested whether these proteins act in a common pathway or directly interact to mediate their effect. Therefore the aims of this proposal are: 1. Determine whether there are genetic or physical interactions between DCX and LIS1 2. Determine whether DCX and LIS1 function to regulate nuclear movement during neuronal migration. 3. Determine whether the function of DCX in neuronal migration is regulated by cdk5

DESCRIPTION (provided by applicant): This application requests funds to purchase and manage the Applied Precision Delta Vision deconvolution microscope system and the Zeiss Nonlinear Optics 510 Multiphoton microscope system that will constitute the Neuroscience Imaging Core at the. University of California, San Diego. Microscopic imaging is becoming an ever important aspect of neuroscience studies, and the requested systems will utilize the imaging strengths of deconvolution microscopy that excels in dissociated cell work, and multiphoton microscopy that excels in analysis in whole tissue. The proposed research involves neuronal stem-cell differentiation, migration, axon guidance, injury repair, comparative anatomy, degenerative disease and developmental biology, and together requires time lapse imaging, deep tissue light penetration, three dimensional reconstruction, analysis of multiple cells using two or more fluorophores to enable co localization, photoablation capabilities, environmental control, with minimization of photodamage. The requested systems were chosen because of their high image quality, excellent live-cell imaging capabilities and most importantly their ease of use, which will be critical for a multi-user Core. The Delta Vision system employs a standard epifluorescent microscope with highly optimized wide field illumination and x-y z-time series capabilities. The constrained iterative deconvolution is quantitative, conserves the maximum amount of data, and affords high sensitivity and resolution with minimum illumination, thus minimizing phototoxicity. The Zeiss system employs a Ti: Sapphire laser to provide tunable infrared illumination with absolute beam control over the entire field, and x-y-z time series capabilities that allows for imaging of neural tissue to depths of 300-500 pM. This Core will draw off of the expertise of the larger UCSD Medical School Imaging Core that combines conventional light, fluorescent and confocal microscopy, stereology, needle microinjection, tissue culture and image processing with an experienced staff of on-hand microscopists to provide training and technical expertise to users for each of the services offered. The flexibility, dynamic range, sensitivity, multiple cell sampling, rapid three-dimensional imaging properties and ease of use of the requested instruments is essential for the proposed, NINDS-funded work that has important implications for multiple nervous system diseases.

bioimaging /biomedical imaging; technology /technique development

Description Congenital ataxia presents in early childhood with non-progressive hypotonia, gross and fine motor delay and cognitive delays. These disorders are distinct from the progressive ataxias because of the presence of congenital cerebellar malformations and because they are typically inherited recessively. Joubert Syndrome and Related Disorders (JSRD) constitutes a major subset of these conditions, consisting of a cerebellar midline (vermis) malformation, a nearly pathognomonic Molar Tooth sign on brain Imaging (MTI) and co-existent oculomotor apraxia and episodic breathing dysrhythmias. The goal of this competing renewal is to characterize new JBTS chromosomal loci, identify the causative genes, and functionally validate mutations within the pathogenetic framework. In our published data, we have already: 1] Identified eight major clinical subtypes of JSRD, each with unique diagnostic criteria involving retinal, renal, hepatic, digit, and cerebral cortical manifestations, 2] Mapped the JBTS2 locus, 3] Identified the JBTS3 gene (AHI1), 4] Identified the JBTS4 gene (NPHP1), 5] Mapped and cloned the JBTS5 gene (CEP290), 6] Identified AHI1 mutations in approximately 20% of patients with the pure JS phenotype. 7] Identified CEP290 mutation in approximately 50% of JSRD patients with the oculo-renal form of disease. 8] Identified mutations in the JBTS6 gene in patients with liver involvement, 9] Identified and functionally validated the JBTS8 gene (ARL13B). In our unpublished work, we have 1] Mapped an additional seven (7) novel chromosomal loci, 2] Identified the CEP41 gene as mutated at one of these loci, 3] Ascertained an additional 27 genetically informative families for ongoing evaluation. Because the majority of patients still have unknown cause of disease, this renewal aims to advance knowledge through molecular characterization of new loci and genes, using newly evolving high-throughput techniques, integrated bioinformatics, and unique resource of consanguineous families recruited world-wide. We further aim to validate these mutations within a mechanistic framework, and a model that JSRD genes promote essential functions of neuronal cilia. Using a variety of positional cloning strategies, coupled with extensive clinical and pedigree information that we have assembled on over 120 genetically informative consanguineous families and over 200 sporadic patients, we are uniquely positioned to identify the genetic underpinnings of JSRD, correlate genotype with phenotype, and build models for the roles of these essential proteins in disease. Of particular interest will be whether there is a correlation between specific genes and the amazing breadth of JSRD phenotypes. Molecular characterization of the JSRDs will lead to a new genetic classification and a better understanding of these disorders. Characterization of the pathogenic mechanisms underlying the JSRDs will lead to improved diagnosis, and will shed light on the genetics of human cerebellar development as well as more complex neurocognitive disorders.

DESCRIPTION (provided by applicant): This application seeks support for the first Translational Cerebellar and Midbrain-Hindbrain Developmental Malformation Meeting, to be held in Washington, DC on Oct. 15-16, 2005. Disorders involving the development of the human cerebellum and midbrain-hindbrain have suffered from a lack of uniformity in clinical, radiographic and molecular classification, and a lack of adequate animal models to probe molecular and developmental underpinnings or to develop potential therapeutic interventions. In the last several years, however, there have been major advances in the understanding of these conditions, with the proposal of new clinical entities, new systems for patient classification and the cloning of the first several genes for these human conditions. However, the lack of uniformity in diagnosis, the rarity of genetically informative families for study, and the dearth of appropriate animal models has significantly hampered progress in this area. This is an optimal time to bring together the key participants in these advances, to help overcome these hurdles. The meeting proposes to bring together clinical and basic science researchers studying cerebellar and midbrain-hindbrain malformations, to align the field in the direction of understanding of key mechanisms. It will serve as a forum to build consensus regarding the diagnosis of these important clinical entities, to standardize diagnostic and imaging protocols for proper phenotyping, to build collaborations among clinician researchers that will advance gene identification, and to develop appropriate animal model counterparts of these conditions. We propose to host a two-day meeting with emphasis on four major areas: clinical advances, radiographic advances, molecular advances, animal model advances. The meeting will address the major subgroups of these conditions, including Dandy-Walker malformation, Joubert syndrome, pontocerebellar hypoplasia, isolated cerebellar hypoplasia and combined cerebellar and cortical hypoplasia. This application at the invitation from three NIH branches, and with matching financial support from patient support groups and a private donor, highlighting the importance of this meeting to the public. The information content will be made available on the Internet. Thus this Meeting will serve as a resource for both the scientific and lay community throughout the world.

[unreadable] DESCRIPTION (provided by applicant): [unreadable] [unreadable] The ability to test hypotheses in a variety of neuroscience fields has exploded through the ability to monitor and manipulate key cellular events from acutely dissociated neurons, neuronal tissue explants and intact nervous system tissue in living animals. Our previous application provided for three advanced imaging systems that have been instrumental in addressing hypotheses in support of NINDS funded aims. However, these systems have several inadequacies, most importantly their inability to capture rapid neuronal events, to manipulate neuronal events, and to image events in living animals. In this application, we propose to broaden the scope of our original aims to allow for 1. Rapid image acquisition through spinning disc confocal microscopy. 2. Manipulation and isolation of individual cells and events through laser microsurgery. 3. In vivo neuronal imaging through fiber optic laser scanning confocal microscopy. 4. High resolution visualization and manipulation of in vivo events through ultrasound imaging. 5. Increased capabilities of the current systems through laser upgrade and software analysis tools. The research that this equipment will support involves neuronal stem cell differentiation, migration, axon guidance, injury repair, comparative neuroanatomy, degenerative disease, and developmental biology. The requested systems were chosen because of their high image quality, unsurpassed abilities to visualize events in the nervous system not previously possible, and their ease of use, which is critical for a multi-user Core. The Core draws off of the expertise of the larger UCSD Medical School Imaging Core that combines other imaging tools and an experienced staff of on-hand microscopists to provide training for each of the services provided. The flexibility, dynamic range, sensitivity, and image processing capabilities that will be provided by this expanded scope is essential for the next phase of the NINDS funded work that has important implications for multiple nervous systems diseases. [unreadable] [unreadable]

DESCRIPTION (provided by applicant): On a global basis, recessively inherited childhood neurological diseases take an enormous human toll, especially in relatively poor populations with high consanguinity rates. The candidate, an Associate Professor in Neurosciences with tenure, proposes a multifaceted mentoring and career development plan in patient-oriented research towards expanding research capacity in the field of recessive pediatric brain diseases and contributing to improvements in genetic diagnoses and predictions of outcome. This plan will build on the candidate's established strengths in family ascertainment, genetic mapping, disease gene identification and animal models, and apply it towards recessively inherited conditions in the Middle East, which displays among the highest known rates of consanguinity. This will provide opportunities for junior physician scientists both in the US and abroad to obtain formal training in patient-oriented neurogenetic research. The K24 Award will allow for protected time so that 80% of his professional effort can be devoted towards research and mentoring. This program will include: One-on-one mentoring of patient-oriented researchers across the spectrum of training, including medical students, pediatric residents and pediatric neurology fellows, through several innovative institutional programs including the UGSD K12-funded Clinical Research Training program, and will include training in international health and global neurogenetic disease. It will also include professional development for the candidate to allow for new knowledge and skills to be incorporated into the current research platform, with formal, mentored training in complex genetics and epidemiology and systems biology to allow him to translate clinical findings into advances in knowledge and clinical outcomes. Dr. Gleeson's ongoing patient-oriented research on the genetic basis of pediatric brain diseases will serve as research vehicles. His genetic research focuses on the genetic basis of 1) Joubert syndrome, a recessive condition with absence of the cerebellar vermis; 2) Recessive agenesis of the corpus callosum; 3) Recessive epilepsy syndromes; 4) Recessively inherited neuropsychiatric conditions including autism spectrum disorder. The K24 Award will augment his successful patient-oriented research programs and provide the intellectual environment needed to increase the number of physician-scientists capable of carrying out cutting edge global oriented patient-oriented neurogenetic research.

DESCRIPTION (provided by applicant): Congenital ataxia presents in early childhood with non-progressive hypotonia, cognitive, gross and fine motor delays. These disorders are distinct from the progressive ataxias because of the presence of congenital cerebellar malformations and recessive modes of inheritance. Joubert Syndrome and Related Disorders (JSRD) constitutes a subset of these conditions, consisting of a cerebella midline (vermis) malformation, and a nearly pathognomonic Molar Tooth sign on brain Imaging (MTI). There is significant phenotypic heterogeneity in JSRD: some patients display the classical form (limited to brain), and others display additionally congenital retinal blindness, progressive kidney failure, cerebral cortical abnormalities or a striking brain wiring phenotype in which each cerebral cortical hemisphere projects output to the ipsilateral side of the body, but receives sensory information from the contralateral side. The cellular and developmental bases of these conditions are not understood. Mutations in two genes, NPHP1 and AHI1, are associated with JSRD. In an exciting new development, we identified the third JSRD gene, CEP290 (submitted). Compelling evidence suggests these proteins function at the cilia/centrosome. Here we propose to apply molecular techniques to study roles of these three genes by performing mutational analyses, genotype-phenotype correlations, test the encoded proteins for a possible role in cilia-based intraflagellar transport, and test animal models for defects in neuronal proliferation and axon guidance. Together this data will provide a framework to understand the role of these genes in the spectrum of conditions seen in JSRD. 1. We will perform comprehensive mutation analysis and genotype-phenotype correlations in a cohort of 180 JSRD probands to test the hypothesis that NPHP1 or CEP290 mutations are associated with JSRD plus kidney failure, whereas AHI1 mutations are associated with JSRD plus cortical abnormalities. 2. We will test the possibility that these genes function at the cilia/centrosome to mediate transduction of Wnt or Sonic Hedgehog signals, using loss- and gain-of-function analyses. 3. We will analyze the brain phenotype of mice with targeted deletions of each gene to test whether these pathways regulate cerebella granule neuron proliferation and axon guidance.

CRISP; Cell/Tissue, Immunohistochemistry; Cellular Matrix; Computer Retrieval of Information on Scientific Projects Database; Cytoskeletal System; Cytoskeleton; Data; Disruption; Electron Microscope; Event; Funding; Grant; IHC; Immunohistochemistry; Immunohistochemistry Staining Method; Institution; Investigators; Knockout Mice; Mammals, Mice; Mice; Mice, Knock-out; Mice, Knockout; Micro-tubule; Microtubules; Murine; Mus; NIH; National Institutes of Health; National Institutes of Health (U.S.); Neurites; Null Mouse; Research; Research Personnel; Research Resources; Researchers; Resources; Role; Source; Two Hybrid; United States National Institutes of Health; Yeast One Hybrid System; Yeast One/Two-Hybrid System; Yeasts; intracellular skeleton; neurabin II; social role; spinophilin; yeast two hybrid system

Project 1. Real-time analysis of the effect of gene manipulation on neuronal migration and cell morphology Joseph G. Gleeson, Principal Investigator A. Background and Significance We showed that the doublecortin (OCX) gene is mutated in humans with X-lined lissencephaly and subcortical band heterotopia [1, 2], that it functions as a microtubule associated protein [3], and that patient mutations disrupt this function [4]. We also showed that disruption of the murine homologue of OCX results in aberrant brain development due to a defect in migration of neurons from the ventricular area into various brain regions. Some of these effects are specific to OCX [5] and some occur in a redundant fashion with the homologous gene doublecortin-like kinase 1 (DCLK1) [6]. We also showed that the gene Ableson-helper integration-1 (AHI1) and centrosomalassociated protein 290 (CEP290) are mutated in humans with Joubert syndrome (JS), characterized by absence of the cerebellar vermis [7, 8]. Patients with JS display congenital ataxia, mental retardation, oculomotor apraxia, and frequent retinal blindness and renal failure. Because of the shared phenotypes with these disorders of retinal ciliated photoreceptors, and renal ciliated epithelial cells, and because of localization of this family of genes to the cilia, we and others have proposed that JS gene products may function in regulation of cilia structure or function [9]. We have utilized each of the imaging systems that are available in the UCSD Neurosciences Microscopy Imaging Core to advance our research goals. The DeltaVision and DG5 Spinning Disc Systems have been used in acutely dissociated neurons to monitor fluorescently-tagged cytoskeletal markers during migration [10-12]. The ability to obtain images with an environmentallycontrol chamber, with minimal phototoxicity, and sampling from up to 20 cells simultaneously with the automated x-y-z stages had a huge impact on our ability to rapidly evaluate our hypotheses. The FV300 and FV1000 Multiphoton systems have been used predominantly to image living brain slices in which a small subset of neurons have been labeled to mark, to overexpress or to silence a gene of interest. The ability to image cells at depths of up to 300 uM has been critical in elucidating how neurons migrate in their natural environment rather than at the exposed surface of the section (Fig. 1). We have begun to use the MMI Cell-Cut system to sever microtubules (MTs), to acutely injure nerve or growing neurites or to ablate subcellular structures in neurons such as the centrosome. Although we are still gaining experience with this system, we expect it to be perfectly suited to address the next generation of questions in neuroscience cell biology.

DESCRIPTION (provided by applicant): The University of California, San Diego Neuroscience Microscopy Imaging Core has grown to be a centerpiece for neuroscience research within the community, and has resulted in remarkable yields in productivity, expanded scientific scope and the ability to test hypotheses in in vivo settings. This success can be measured in over 40 publications in the neuroscience field that have critically relied on the Core to provide expertise in just the short time that it has been in existence. The Core currently has five imaging systems that provide confocal, deconvolution, spinning disk, two-photon and laser dissection microscopy and an onsite microscopist to make maximum use of the tools. The Core provides neuroscientists flexible platforms to determine the ideal imaging modality for specific applications, and provides training opportunities in a broad array of modern imaging tools. In this application, we seek to expand the scope to include several new NINDS-funded Major Users, and acquire two new imaging systems that will greatly benefit our dynamic community and address the major deficiencies of the facility: 1. Confocal imaging with the ability to perform photoinduced conversion in real- time. 2. High-throughput imaging through multi-well live cell microscopy. The requested systems were chosen because of their high image quality, unsurpassed abilities to visualize events in neural systems that were not previously possible, and their ease of use, which is critical for a facility with over 100 regular users. The research that this equipment will support includes studies of neuronal stem cell differentiation, migration, axon guidance, injury repair, stroke, hypoxia, degenerative disease and disordered development that has important implications for understanding and treatment of nervous system disease. The Core draws off of the expertise of the larger UCSD Medical School Imaging Core that combines other complementary tools. The flexibility, dynamic range, sensitivity and image processing capabilities with the proposed tools are essential for the next phase of the NINDS-funded work. Public Health Relevance: This application proposes to advance microscopy imaging capabilities at the University of California, San Diego School of Medicine in a host of areas within cellular neuroscience. The work to be supported by this application will provide imaging tools for over 17 different NINDS R-awards from 12 Major User and other investigators working in areas that the NINDS has already determined to be important.

instmctions): The Imaging and Cell Sorting Core (Core C) is a new Core facility that was added to the Program Project in response to new technological opportunifies and the changing needs of Program investigators. The overall goal of the Core is to facilitate and enhance the research efforts in the individual Units by offering the following imaging and fiow cytometry services to Program members: 1. Advanced microscopic imaging a. Light and confocal microscopy b. Laser capture and microdissection c. Assistance in experimental design and data analysis of imaging studies 2. Multi-parameter flow cytometry and cell sorting a. Cell subset analysis b. Fluorescence-activated cell sorting The Core facilities are located within easy walking distance of the Research Units in the School of Medicine on the UCSD Main Campus in La Jolla. The necessary equipment and support staff is available in the Core facilities, so the Core is fully functional at this time and requires no additional investment in new equipment. RELEVANCE (See instructions): Analysis of cell numbers and location in whole tissues, and the ability to isolate and characterize specific cell types, are critical for the success of molecular physiologic research in immunology. The necessary tools and expertise is only available through shared resource arrangements.

DESCRIPTION (provided by applicant): The University of California, San Diego Microscopy Imaging Core has grown to be a centerpiece for cellular imaging research within the community, with over 150 labs and 400 regular users. Its existence has resulted in remarkable yields in productivity, expanded scientific scope and ability to test hypotheses using cutting edge technology and in vivo approaches. The success can be measured in over 100 publications in all areas of biological and health-related fields that rely on the Core to provide expertise. The Core currently has nine imaging systems that provide confocal, deconvolution, spinning disk, two photon, laser dissection low power, and high content microscopy imaging and onsite microscopists to make maximal use of the tools. These tools provide UCSD researchers flexible platforms to determine the ideal imaging modality for specific applications, and to provide training opportunities in a broad array of modern imaging tools. In this application, we seek to expand the scope of the Core by providing Super-high resolution microscopy to the Users. Recent breakthroughs in photonics research have led to the development of several methods that break the theoretical diffraction-limited resolution of fluorescent microscopy. These systems all utilize novel methods to essentially "shrink" the effective ring of excitation within a sample to greatly enhance the signal:noise ratio, providing resolution of objects in the 50-200 nm range, which is 2-10X higher than previous generation systems. We have performed demonstrations of these systems, and determined that the Applied Precision OMX Super-Resolution system, the only one designed and manufactured in the USA, is the best match for our Core. The OMX system utilizes "structure illumination" to enhance resolution, works with all currently available fluores, increases resolution in all three dimensions (x-y-z) and is perfectly suited for a multi-user facility. We have obtained institutional support and competitive pricing that will us to purchase and manage this system with the help of this NCRR-based funding mechanism. This system will bring the reality of super-resolution imaging, which will allows flexibility, dynamic range, sensitivity and imaging processing capabilities into an already highly-integrated campus-wide Core which supports the imaging needs a multitude of NIH-funded projects.

DESCRIPTION (provided by applicant): The central goal of this Program Project application is to address the central mechanism of human structural brain defects (SBD), utilizing the unique strengths of the Principal Investigators and the new breakthroughs in genetics and modeling. This Program Project Grant Application is designed to advance biomedical knowledge and make a high impact on our understanding of the basis of SBDs across the evolutionary scale, with the purpose of advancing our ability to diagnose and treat disease. In our preliminary data, we have established: 1] A broad database consisting of over 1500 human families with structural brain defects, highly enriched for first cousin consanguinity with multiple affected members. 2] Extensive development of mouse lines with neural-specific expression of Cre-recombinase. 3] A broad array of tools to study gene requirements in zebrafish development. 4] A proven track record of utilization of these unique reagents to study mechanisms of disease. As a result of our preliminary data, we have formulated this Program Project Grant Application with a two-fold thrust: 1] By taking advantage of the technical revolution in DNA sequencing and genetic engineering, we will uncover new causes of disease in humans. 2] By comparing phenotypes across these unique systems, each with its own strength/weakness we will enhance our understanding of the basic mechanisms of SBD. Since all Principal Investigators in this Program Project Grant Application have evidence for considering cell polarity as central to the developmental mechanisms of SBD, each Project has a focus on investigating cell polarity within the spectrum of the proposed Aims. Two Cores will be essential to the Program Project Grant Application since they will carry out essential functions of the Program Project Grant Application and benefit each Project: 1] Next-generation Sequencing Core to uncover new genetic causes of SBDs in each species. 2] Bioinformatics Core will provide essential functions to provide experimental design and analytical services with one-on-one training and data management and custom computational solutions. Specific Aims of the Program Project Grant Application are: 1] To uncover a host of new developmental causes of SBD from this unique human DNA resource, as well as from mutagenized mice and zebrafish. 2] To explore cell-type specificities of disease and pathogenic mechanisms of SBDs using mice and zebrafish models. 3] To utilize newly uncovered mice and zebrafish genes involved in SBDs for analysis in this human population. We believe that this Program Project Grant Application will have a major impact on our understanding of the cellular and molecular mechanisms that underlie a variety of SBDs, fully taking advantage of new breakthroughs in genomics technologies, which will set the stage for improved diagnosis and treatment.

Bioinformatics is the application of statistics and computer science to the field of molecular biology. It has emerging as a field unto itself, as the datasets that are generated by modern biomedical researchers easily exceeds what can be directiy analyzed. Core C will work with the data generated from massive parallel sequencing from human, mouse and zebrafish, to extract variants that are potential to cause disease. The PIs of Cores A, B and C have worked together extensively in the past, and have an established track record of productivity in the area of next generation sequencing (NGS) data analysis. Dr. Bafna has worked broadly in bioinformatics and genomics in the development computational methodologies employing novel algorithms and statistical techniques for NGS datasets. We envision that the WES data generated from Core B will be delivered to Core C for extraction ofthe potentially deleterious sequence variants (PDSVs), which will be delivered back to each of the Projects for segregation analysis and further validation. This will be accomplished by developing the four key pipelines of Core C: 1] WES data tracking and storage pipeline, 2] WES data analysis pipeline, 3] Mutation identification pipeline, 4] Comparative genomics pipeline. The analysis of WES datasets is presented in this application as a series of filters that is applied to the primary sequence to extract all relevant variants, and then apply a heuristic ranking strategy to detect the PDSVs mostly likely associated with the phenotype. The output of this FILTER and PRIORITIZE programs are then reported as both SNPs and INDELs in a ranked fashion, for later validation and segregation testing. Further analysis will help uncover the contribution of these genes to common disease as well as genome- wide gene-gene interactions using other software we have developed. We are also well-positioned to take full advantage of the 3rd generation DNA sequencers, and are excited that UCSD will serve as one of the national HHMI PacBio Sequencing Centers. These tools, together with the outstanding and unique human and animal resources, will make for a powerful combination to investigate new causes of structural brain disorders.

The amazing advances brought forward by the completion of the Human Genome Project, new sequencing technologies and new methodologies to extract specific fragments of genomic DNA (gDNA), have now made it possible to sequence the "exome" in an individual patient in a relatively short time-frame (whole exome sequencing, WES). The Core PI and Co-PI of are thoroughly expert in the design and implementation of next-generation sequencing (NGS) experiments, and will establish and operate the NGS Core B to generate WES data across each ofthe proposed Projects, involving human, mouse and zebrafish. It has long been appreciated that the vast majority of alleles with strong effect are located in the exome, which constitutes just 1% of most vertebrate genomes. The methodologies to capture and sequence the exome in humans was the first to emerge and is transforming the way scientists approach genetic disease. Methodologies to capture and sequence the mouse and zebrafish exomes will be available shortly. In this Core, we will bring these technologies to bear on structural brain diseases (SBDs) across the evolutionary spectrum. We have been successful at generating WES data that produces 95% target bases at >10X coverage. For dominant disease, the ability to systematically identify heterozygous variants is limited by this coverage, but for recessive disease, this hurdle is easily overcome. Because recessive disease due to homozygous mutations in humans, mouse and zebrafish is the focus of this application, we will be extraordinarily well-powered to identify causative mutations in these species using this approach. An important aspect of Core B is the close ties that will develop not just to the Scientific Projects but also with Core C (Bioinformatics Core) and Core A (Administrative Core). Core C will develop and utilize new software that is specifically devised for identifying homozygous potentially deleterious sequence variants (PDSVs) in the data from Core B. Core A will support the technological infrastructure of both Core B and Core C. Projects I, II and III will be well-positioned to uncover new mechanisms of SBDs, and translate these into new discoveries about underlying mechanisms.

(Instructions): Human structural birth defects are present in 4-5% of live births in the US, contributing to half of all pediatric hospitalizations. Importantly, the rates are double in most of the Middle East, Central Asia and North Africa where consanguinity rates approaching 60% are the norm. Of these. Structural Brain Disorders (SBDs) are probably the single biggest component to the long-term medical complications, greatly increased morbidity and mortality. Our data demonstrate tremendous locus and genetic heterogeneity among patients with SBDs from these geographic regions, presenting both a challenge as well as an opportunity. The challenge is to derive strategies to molecularly classify patients with these diseases. The opportunity is that these populations offer the chance to identify a much fuller picture of the genes contributing to SBDs in humans. Comprehensive discovery of mutations contributing to SBDs holds great promise for advancing understanding of determinants of brain development and function, and its consequences including epilepsy, developmental delay, and motor deficits. The search for SBD genes has been hampered by the lack of well-characterized pedigrees to perform gene discovery. The ability to generate whole exome sequence (WES) from such patients only increases the need for multiplex consanguineous pedigrees for these strategies, because the validation of potentially deleterious sequence variants (PDSV) requires segregation analysis. Dr. Gleeson has collected probably the world¿s largest cohort of such pedigrees with SBDs over the past 10 years, which will continue in Y1-5. From these, we will perform WES on 30 probands per year in Core A, and sequence analysis in Core B. Segregation analysis in the initial family and subsequent screening in patient cohorts, both from the Gleeson lab, as well as local clinics and the massive California Birth Defects Monitoring Service will help will validate the gene's involvement in the disease. Finally, genes identified from Project 11 and III will be screened in the cohort using similar high-throughput re-sequencing strategies. In Project II and III, animal models will be created and utilized to identify underlying cellular pathophysiology, with a focus on altered cell polarity.

Structural Brain Defects (SBDs) constitutes an immense health problem. Approximately 4-6% ofthe human population is affected by developmental disorders that affect the structure ofthe nervous system. A large number of SBD cases are or genetic origin. Despite major advances in human genetics and genome research, the majority of genes that are linked SBDs still need to be identified. There is also a pressing need for animal models to study gene function in the developing brain, to define the molecular pathogenesis of SBDs, and to develop therapeutic approaches for their treatment. Significantly, the brain of human and mice share many anatomical and molecular features, suggesting that the genetic program controlling CNS development is in large parts conserved between the two species. The mouse is also a leading research tool for genetic studies. We therefore hypothesize that we will generate by forward and reverse genetics in mice valuable animal models for studying the genetic program that controls brain development and for defining the molecular pathogenesis of inherited forms of SBDs in humans. This hypothesis is supported by our preliminary data, which show that we can generate mouse models for SBDs by forward and reverse genetics. Based on these findings, we therefore proposes two specific aims. In Aim 1, we will capitalize on our expertise in forward genetics in mice using ENU as a mutagen, to generate mouse lines afflicted with inherited forms of SBDs, to positionally clone the affected genes, and to study gene function. The other participants of the program project grants will test the extent to which the genes that we identify are associated with SBDs in humans and zebrafish. In Aim 2, we will use reverse genetics approaches to generate mouse lines carrying mutations associated with SBDs in humans or zebrafish that have been identified by the other participants of this program project proposal. We anticipate that we will identify a wide range of mutations that cause SBDs and generate important mouse models to study disease mechanisms. RELEVANCE (See instructions): Structural brain defects (SBDs) are frequently of genetic origin and one ofthe most common forms of structural birth defects in humans. This proposal seeks to identify genes that are linked to SBDs and to develop mouse models for studying disease mechanisms. The animal models hold great promise as tools for the development of therapeutic approaches towards the treatment of SBDs.

Vertebrate organogenesis is a complex process that is mediated by a coordinated set of cellular and molecular events. Analyzing these dynamic processes can be particularly difficult in mammalian animal models due to the development of mammalian embryos in utero. However, because of the optical clarity and external fertilization of zebrafish embryos/larvae, this vertebrate animal model system can be used to image in vivo the dynamic cellular processes of how specialized cells organize to become vertebrate organs. Exploiting these particularly useful imaging properties, the zebrafish community including our own lab has developed neural specific transgenic tools to further illuminate the dynamic cellular mechanisms that transform the neuroepithelium/neural tube into mature brain structures. Utilizing these tools, we have initiated a fonward genetic screen with the Gleeson lab to identify novel SBD mutants which may provide further insight into the conserved mechanisms during brain morphogenesis. As a result, we have recovered SBD mutants with early brain defects that harbor mutations in genes that are in the cell polarity pathway further supporting the significance of cell polarization during brain morphogenesis. Because ofthe importance of polarity genes in establishing the cellular organization required for cell shape and movement, we hypothesize that cell polarity regulates the cell morphology and migration of neural cell lineages during CNS/brain development in order to direct overall brain morphogenesis and function. The Specific Aims of Project III are: 1] Aim 1: To uncover novel cell polarity pathways that may modulate CNS/brain morphogenesis and function; 2] Aim 2: To investigate SBD mutations discovered from human genetic studies and mouse forward genetic screens as described in Project I and II, respectively; 3] Aim 3: To investigate how cell polarity genes direct neural cell lineage morphology and migration. Overall, our interdisciplinary approach including the utilization of a genetically tractable yet optically transparent animal system, innovative live imaging tools and techniques, and synergies with human and mouse genetic studies will provide in vivo mechanistic insight into how cell polarity may directiy guide neurodevelopment. RELEVANCE (See instructions): The proposed studies are focused to investigate the direct impact of cell polarity on the development of neural specific lineages into a fully mature and functional brain. The combination of zebrafish genetic studies and live animal imaging will reveal novel mechanisms that direct this process and subsequently lead to new diagnostic and therapeutic approaches towards the clinical management of SBDs.

This Administrative Core (Core A) will have two major functions. First, it will provide administrative support and intellectual enrichment for the investigators in this program. Due to the fact that the Program includes 5 senior investigators from two institutions (UCSD and the Scripps Research Institute) belonging to several Departments: Pediatrics, Medicine, Neuroscience (School of Medicine at UCSD), Computer Science (UCSD) and the Scripps Research Institute. Additionally, three different species will be used forthis work (Human, Mouse, Zebrafish) and work accomplished at four different campuses (UCSD School of Medicine, UCSD Cancer Center, UCSD Computer Sciences, Scripps Research Institute). Because of this and the multi-disciplinary nature ofthe Program, a central administrative core is essential. The Core will work closely with the Administration of the two major institutions, as well as administrators, business managers, and scientists in each Department involved. The Administrative Core will assist individual investigators in budgeting as well as coordinate travel, purchasing, meetings and seminars. The second function of the Administrative Core will be to provide and encourage intellectual collaboration between members ofthe Program Project, faculty within the University (who are not members of this Program Project), and outside consultants. The Core will achieve these objectives in two ways: A) We will have a monthly two-hour seminar for all investigators in this Program. Research progress will be presented by one of the Program's investigators during each seminar. This will average about 10-12 seminars per year and about 2-3 per Project/year. We will also have the Directors of Cores B and C present new data generation and analytical techniques, especially in the rapidly moving field of genomics and bioinformatics. B) The Program Project plans to have outside experts visit each year as consultants, at least one of the Project groups. The role of the consultant will be to work directly with his/her host, to advise regarding their progress, to suggest possible new directions for both the individual Projects and potentially the overall Program. In addition, we propose also to have mid-term whole day symposium during which we invite consultants whose work is on some aspects of the research of each Project. During these workshops, each of the PIs will presents their progress over the preceding 2 years and the outside experts are asked to critically evaluate the progress of each project.

The Microscopy Shared Resource comprises valuable, modern tools that are made available as routine services to Cancer Center Members. The services provided have been crucial for individual laboratory projects, and intra- and inter-programmatic research. With increasing frequency, Center investigators are addressing the molecular and cellular functions and intracellular localization of gene products implicated in the genesis or growth modulation of cancer cells. As new cloning technologies have become available, investigators in Cancer Biology, Cancer Genetics and our clinical investigation programs have been identifying candidate genes that may be responsible for various components of the malignant phenotype at a rapid pace. Accordingly, the Center has taken steps to provide cost-effective support for these cellular and tissue-based studies. However, solving the functions of these genes is often rate limiting. As clues to the functions of candidate genes are often gained by studying the location of the gene products in cells, services provided by the Microscopy Shared Resource assist investigators in their quest for answers. Exciting new collaborations with the VisLab of the San Diego Supercomputer Center (SDSC) continue, which have radically altered the way we quantitate and visually analyze 3-dimensional data.

DESCRIPTION (provided by applicant): Molecular characterization of hemimegalencephaly Abstract Somatic mutations, in which a fraction of the cells in the body have a deleterious mutation, is well recognized in cancer but only recently appreciated in neurological disease. In the setting of a somatic mutation in a population of progenitor cells, all daughter cells inherit te mutation and are able to express the resultant phenotype as a function of the differentiation program. We recently identified the first de novo somatic mutations in the developing brain in the condition hemimegalencephaly, (HME) a catastrophic focal epilepsy condition associated with a malformation of cerebral cortical development (MCD). HME is one of the most severe MCD syndromes, characterized by massive hamartomatous overgrowth of either of the two cerebral hemispheres. Cerebral hemispherectomy is a frequent treatment for the refractory epilepsy, allowing sampling of diseased tissue. By comparing DNA from diseased brain with DNA from blood/saliva, we identified de novo somatic mutations in PIK3CA, AKT3 or MTOR, part of the mTOR pathway. Mutations were present in 8-40% of sequenced alleles in various brain regions sampled during surgery, and some in codons known to activate the protein. However, the pilot study was based on a limited sample size. The goal of this application is to expand upon our initial findings, and elucidate the genetic, developmental, signaling and cell biological mechanisms of HME, particularly in the context of mammalian cortex development. We will combine next-generation sequencing of diseased brain from HME patients with advanced bioinformatics, complete clinical correlated neuroanatomy, and mouse modeling to help advance our understanding of the mechanism of this important disease. We will: 1] Test for de novo somatic mutations in a larger retrospectively and prospectively collected cohort of HME patients. 2] Correlate genetic disease burden with clinical, imaging, and histopathological findings (phenotype). 3] Test how these de novo mutations alter progenitor cell functions in the developing cerebral cortex. The goal of the experiments is to determine how mutations in these genes lead to disrupted cortical development, why these lesions are epileptogenic, and whether repurposing approved medications might benefit patients, with relevance to other focal dysplasias and focal epilepsies.

The amazing advances brought forward by the completion of the Human Genome Project, new sequencing technologies and new methodologies to extract specific fragments of genomic DNA (gDNA), have now made it possible to sequence the exome in an individual patient in a relatively short time-frame (whole exome sequencing, WES). The Core PI and Co-PI of are thoroughly expert in the design and implementation of next-generation sequencing (NGS) experiments, and will establish and operate the NGS Core B to generate WES data across each ofthe proposed Projects, involving human, mouse and zebrafish. It has long been appreciated that the vast majority of alleles with strong effect are located in the exome, which constitutes just 1% of most vertebrate genomes. The methodologies to capture and sequence the exome in humans was the first to emerge and is transforming the way scientists approach genetic disease. Methodologies to capture and sequence the mouse and zebrafish exomes will be available shortly. In this Core, we will bring these technologies to bear on structural brain diseases (SBDs) across the evolutionary spectrum. We have been successful at generating WES data that produces 95% target bases at >10X coverage. For dominant disease, the ability to systematically identify heterozygous variants is limited by this coverage, but for recessive disease, this hurdle is easily overcome. Because recessive disease due to homozygous mutations in humans, mouse and zebrafish is the focus of this application, we will be extraordinarily well-powered to identify causative mutations in these species using this approach. An important aspect of Core B is the close ties that will develop not just to the Scientific Projects but also with Core C (Bioinformatics Core) and Core A (Administrative Core). Core C will develop and utilize new software that is specifically devised for identifying homozygous potentially deleterious sequence variants (PDSVs) in the data from Core B. Core A will support the technological infrastructure of both Core B and Core C. Projects I, II and III will be well-positioned to uncover new mechanisms of SBDs, and translate these into new discoveries about underlying mechanisms.

Structural Brain Defects (SBDs) constitutes an immense health problem. Approximately 4-6% ofthe human population is affected by developmental disorders that affect the structure ofthe nervous system. A large number of SBD cases are or genetic origin. Despite major advances in human genetics and genome research, the majority of genes that are linked SBDs still need to be identified. There is also a pressing need for animal models to study gene function in the developing brain, to define the molecular pathogenesis of SBDs, and to develop therapeutic approaches for their treatment. Significantly, the brain of human and mice share many anatomical and molecular features, suggesting that the genetic program controlling CNS development is in large parts conserved between the two species. The mouse is also a leading research tool for genetic studies. We therefore hypothesize that we will generate by forward and reverse genetics in mice valuable animal models for studying the genetic program that controls brain development and for defining the molecular pathogenesis of inherited forms of SBDs in humans. This hypothesis is supported by our preliminary data, which show that we can generate mouse models for SBDs by forward and reverse genetics. Based on these findings, we therefore proposes two specific aims. In Aim 1, we will capitalize on our expertise in forward genetics in mice using ENU as a mutagen, to generate mouse lines afflicted with inherited forms of SBDs, to positionally clone the affected genes, and to study gene function. The other participants of the program project grants will test the extent to which the genes that we identify are associated with SBDs in humans and zebrafish. In Aim 2, we will use reverse genetics approaches to generate mouse lines carrying mutations associated with SBDs in humans or zebrafish that have been identified by the other participants of this program project proposal. We anticipate that we will identify a wide range of mutations that cause SBDs and generate important mouse models to study disease mechanisms. RELEVANCE (See instructions): Structural brain defects (SBDs) are frequently of genetic origin and one ofthe most common forms of structural birth defects in humans. This proposal seeks to identify genes that are linked to SBDs and to develop mouse models for studying disease mechanisms. The animal models hold great promise as tools for the development of therapeutic approaches towards the treatment of SBDs.

? DESCRIPTION (provided by applicant): The recent discovery that de novo zygotic mutations in the form of CNVs and point mutations make major contributions to neuropsychiatric diseases such as schizophrenia and autism begs the question as to the degree to which de novo post-zygotic mosaic mutations also contribute to disease. In this model, a mutation that occurs post-zygotically can seed some percentage of cells in the brain, and is sufficient to lead to neuronal dysfunction and disease. The approach of sequencing only non-neural tissues such as blood may underpower the detection of mosaicism, because mutations may be restricted to neural tissue. This proposal brings together a highly productive and collaborative team, in which each member contributes a special resource to make this effort truly unique. Gleeson and Mathern recently identified among the first de novo somatic mutations in the developing brain in the condition known as `hemimegalencephaly' (HME), a catastrophic neuropsychiatric condition associated with focal cortical disorganization (FCD). By comparing DNA from diseased brain vs. blood, we identified de novo somatic mutations in PIK3CA, AKT3 and MTOR, part of the mTOR pathway, in as few as 8% of brain cells, resulting in perturbations in an entire cerebral hemisphere. Courchesne and Roy recently identified focal patches of abnormal laminar cytoarchitecture in frontal and temporal cortex in the majority of available brain samples of children studied with autism (ASD), and we suggest focal patches akin to FCD may have similar mutations and contribute to disease. The goal of this application is to extend the discovery of mosaicism in patients with epilepsy and autism in which neurohistopathological evidence points to FCD, by sequencing dysplasias compared with adjacent normal tissue and/or blood at the DNA and RNA level at the single-cell level. We aim to uncover key sets of genes, in which specific de novo mutations, in specific locations, at specific mosaicism levels, is sufficient to produce clinically defined disease. We will combine next-generation sequencing of FCD brain from patients with neuropsychiatric disease with advanced bioinformatics, single-cell sequencing, complete clinical correlated neuroanatomy and mouse modeling. We will: 1] Test for de novo somatic mutations in a retrospective and prospective cohort of FCD presenting with autism or epilepsy. 2] Correlate genetic disease burden with clinical, imaging, histopathological and single-cell sequencing findings. 3] Test mechanisms by which uncovered de novo mutations alter progenitor cell functions in mammalian cerebral cortex.

Project Summary/Abstract Pontocerebellar hypoplasia (PCH) is a heterogeneous group of rare recessive pediatric neurodevelopmental/neurodegenerative disorders, characterized clinically by severe age-dependent neurological impairment, and notable radiographic volume loss of the pons and cerebellum. Currently there are 10 partially overlapping subtypes and 13 genes known mutated in PCH, but most cases remain without genetic diagnosis, suggesting new causes remain to be identified. Several of the genes are implicated in protein synthesis including key steps of tRNA maturation, mRNA splicing, protein translation and apoptosis, but fundamental questions remain: 1] How many genetic subtypes remain to be discovered? 2] Why do these mutations predispose to neuropathology? 3] Can we effect new treatments for these disorders? Through an international recruitment effort, we have ascertained a cohort of 190 families with recessive PCH and have begun sequencing to identify new causes and mechanisms. Our preliminary data suggests new treatments may emerge from these studies. In our preliminary data we have: 1] Recruited a cohort of 190 PCH probands, including 124 still without cause identified. 2] Identified mutations in AMPD2 associated with a syndromic form of PCH, leading to GTP depletion and subsequent collapse of protein synthesis. 3] Identified a common founder mutation in CLP1 leading to defective assembly of the tRNA splicing machinery. 4] Identified mutations in TOE1 as the long-sought snRNA 3'-exonuclease, leading to defective mRNA splicing. 5] Identified mutations in several other genes encoding tRNA processing factors. 6] Identified mutations in PPIL1 predicted to lead to defective mRNA splicing. 7] Uncovered a total of 13 new genetic causes of PCH, more than doubling the number of known causes. These novel PCH candidate genes are mutated in patients with unique presenting features, highlighting new genotype-phenotype correlations, emphasizing the protein synthetic defect model and pointing to new mechanisms of disease. The goal of this application is to identify the remaining `discoverable' genes that when mutated lead to PCH, functionally validate mutations within a pathogenic framework, and test the hypothesis that mutations in PCH genes lead to collapse of protein synthesis and vulnerability to apoptosis.

The ability to test hypotheses in a variety of neuroscience fields has expanded exponentially due to new and emerging technologies that detect and probe molecular, cellular and physiological events in terminally collected samples or living model organisms with ever increasing power and capabilities. Supported by an NINDS P30 grant since 2003, the University of California San Diego Neuroscience Microscopy Imaging Core has grown into a world-class core and a centerpiece for local neuroscience research. Importantly, the Core serves an otherwise unmet neuroscience research need in microscopy imaging of many laboratories. Its existence has resulted in remarkable yields in productivity, expanded scientific scope and ability to test hypotheses using cutting edge technologies. In this application, we seek to acquire a Zeiss Lightsheet Z.1 microscope for fast, gentle, multiview imaging deep into thick samples such as cleared brain and spinal cord tissue blocks or living organisms. The requested system was chosen because of the high quality of data that it generates, unsurpassed abilities to document events in the nervous system not previously feasible and its ease of use, which is critical for a multi-user core. In addition, we ask for funds to help maintain, operate and support a number of existing cutting edge imaging tools at the Core. On top of 35 NINDS-funded Major User labs with 44 qualifying projects, a wider base of neuroscience investigators benefit from access to our Core. UCSD is a leading institution in neuroscience research, with our neuroscience graduate program consistently ranked among the top in the nation. The strong support of local neuroscience researchers along with that of institutional leadership, the synergies and the economies of scale that the Core has created and the continued P30 grant support will ensure the future success of our Core. In return, our Core supports the mission of the NINDS by serving a wide range of outstanding research programs that aim to gain fundamental knowledge of the nervous system and to reduce the burden of neurological diseases.

  Abstract    Zika  virus  (ZIKV)  represents  a  new  threat  to  global  health,  with  particular  relevance  to  the  developing  brain  and  risk  of  congenital  microcephaly.  The  basis  by  which  ZIKV  leads  to  neuronal  death  in  the  brain  of  the  fetus  is  unknown,  but  presumably  relates  to  effects  of  ZIKV  proteins  on  cellular  health.  ZIKV  is  an  RNA  Flavivirus  encoding  10  proteins  including  the  NS2B/NS3 heterodimer  that  forms an active  serine protease  involved  in  cleavage  of  the  ZIKV  polypeptide  into individual proteins.    Here  we  propose  to  study  the  molecular  basis  of  ZIKV-­induced  microcephaly.  We  hypothesize  that  the  ZIKV  protease  can  function  to  cleave  cytosolic host  cellular  proteins  in  neural  precursor  cells,  leading  to  a  range  of  cellular  defects, contributing to toxicity. This application brings together three experienced research groups with a track record of  collaboration on ZIKV. Our published work has focused on tropism of ZIKV for neural precursor cells, interaction of ZIKV  with  the  immune  system,  small  molecule  inhibitors  of  ZIKV,  and  effect  of  ZIKV  on  neuronal  survival.  We  have  also  published  on  neural  stem  cell  biology,  recessive  human  genetic  microcephaly  mutations,  and  flavivirus  molecular  pathology.  Our preliminary data  demonstrates  that ZIKV  NS2B/NS3 misexpression  can  mediate  cell death,  in  a manner  similar  to  ZIKV-­induced  cell  death.  Cell  death  can  be  abrogated  with  a  protease-­inactive  mutation  or  by  inhibition  of  protease  activity  through  ZIKV  protease  inhibitors  (ZPIs).  Proteomic  analysis  identified  a  series  of  proteins  bound  to  the  ZIKV  protease,  which  we  term  the  ZIKV  Protease-­Ome  (ZPO),  at  least  one of  which  is  a direct  cleavage  target  of  ZIKV  NS2B/NS3,  and  leads  to  blocked  cytokinesis  and  cell  death  when  inactivated,  in  a  manner  similar  to  ZIKV-­induced  cell  death.    The  goal  of  this  application  is  to  discover  the  molecular,  cellular  and  genetic  basis  by  which  ZIKV  proteins  mediate  neuronal  cell  death,  particularly  in  the  context  of  mammalian  cerebral  cortical  development.  We  combine  mass  spectrometry  analysis,  protein  interaction  networks,  advanced  bioinformatics,  neuronal  culture  models,  analysis  of  cell  cycle  dynamics,  and  in  vivo  modeling.  Importantly,  we  will  focus  on  differences  between  toxicity  observed  with  ZIKV  proteins  and  other  sequence-­similar  flaviviruses  that  do  not  mediate  neuronal  death,  and  will  study  the  mechanisms  of  the particular neuronal vulnerability to cell death following ZIKV exposure. We will: 1] Test ZPO constituents to determine  which  are  direct  protease  targets  of  ZIKV  NS2B/NS3.  2]  Test  ZPO  to  determine  mechanisms  by  which  ZIKV  NS2B/NS3-­mediated  cleavage  leads  to  neuronal  death.  3]  Test  the  short  and  long  term  effects  of  ZIKV  protease  expression  on  the  developing  brain,  and  the  degree  of  rescue  by  inhibition  of  the  ZIKV  protease.  The  goal  of  these  experiments  is  to  determine  how  specific  components  of  the  ZIKV  genome  lead  to  disrupted  cortical  development,  to  determine  mechanisms  by  which  ZIKV  impairs  cell  survival,  and  whether  medications  might  benefit  women  exposed  to  ZIKV during fetal brain development.      

Abstract ? Project I: Human genetics of meningomyelocele and risk mitigation by folic acid This project focuses on the characterization of genomic variation in human patients with Meningomyelocele (MM), the most common CNS birth defect, with heritability estimated at 70-75% 1,2, and a cumulative incidence of 3.72/10,000 live US births. MM is a debilitating structural birth defect, the most common form of NTD compatible with life, and with substantial associated morbidity and mortality. National folic acid (FA) supplementation has reduced incidence >3-fold, but there is little understanding of the mechanism of this Gene-Environment interaction (GXE). Here we propose to study the molecular basis of human MM through a world-wide recruitment of trios with narrowly defined inclusion/exclusion criteria, stratified by prenatal FA exposure. We hypothesize that de novo mutations (DNMs) make a critical contribution to the risk of MM, and that FA increases the mutational burden required for phenotypic expressivity. MM shares features with other severe childhood diseases that show strong DNM contributions such as congenital structural disorders and autism. Our preliminary data point to a strong DNM contribution to MM, but like autism, these DNM increase risk but likely act with other factors to determine risk. We propose to ascertain a total of 2000 carefully phenotyped MM trios, recruited worldwide, stratified based upon national dietary FA supplementation status at the time of conception (+FA:fortified vs -FA:nonfortified). Trios will undergo whole genome sequencing (WGS), then analyzed for de novo and inherited mutations as risk factors, compared with control trios. Results from Project I will be incorporated into workflow of Project II and III to model mutations, and results from Project II and III will be used to refine WGS analysis in Project I. Project I will rely on Core B to identify candidate FA-responsive genes from changes in epigenetic signatures, and on Core C for bioinformatic analysis. Project I has already: 1] Founded the Spina Bifida Sequencing Consortium and enrolled a cohort of >1500 MM trios using social media, and historic cohorts, stratified as +FA or -FA. 2] Extracted and QC?d DNA from >700 of these trios. 3] Competed successfully for NICHDs Gabriella Miller-Kids First program access for 1000 WGS samples. 4] Performed sequencing on 600 trios, as well as optimized algorithms to achieve uniform mutation calling. 5] Identified 12 MM candidate genes, including 3 recurrently mutated genes, and one recurrent copy number variant (CNV). 6] Found that +FA trios but not -FA trios demonstrate a striking accumulation of damaging DNMs compared with controls. We will test the model that de novo and inherited mutations interact with FA to determine risk. The application proposes to complete recruitment, identify de novo and inherited gene mutations in MM, correlate with maternal FA exposure, and uncover mechanisms of disease within a clinical context.

Abstract Brain somatic mosaicism (BSM) refers to the accumulation of mutations within any of the billions of cells in the human brain, which can occur from embryogenesis through adulthood. The extent, impact and mechanisms of BSM on brain disease remain poorly understood. Prior work from the Brain Somatic Mosaicism Network (BSMN), on which the PI served, made critical breakthroughs in reliability of mosaicism detection, but also raised new questions, including the degree to which BSM exists in the healthy brain, and the mechanisms by which BSM mutations explain disease. Focal cortical dysplasia (FCD) is associated with substantial neuropsychiatric disability, and is the most common cause of intractable epilepsy in childhood. Neuropsychiatric features are seen in 15-59% of patients 5-7, and neuropathologically shows disrupted neurogenesis, migration, differentiation, and altered neural excitability. We and others previously identified mosaic mutations in the mTOR pathway in a minority of FCD cases, but most cases remain unsolved, and fundamental mechanisms are lacking. We hypothesize that: 1] FCD mutations are similar to neutral somatic mutations in their patterns and distributions, dictated by developmental processes, but differ in their functional effect. 2] BSM patterns, allelic fractions (AFs) and allele sharing between cells can reconstruct cellular lineages and migratory histories. 3] Study of FCD resected tissue can uncover novel causes of disease that would not be tolerated if present in every cell. 4] BSM modeling in mouse can unravel disrupted signaling networks of complex mosaic mutations. Our preliminary data shows: 1] From a post-mortem control cadaver, we validated 259 somatic variants using 300X genome sequencing, and started to use these variants as ?barcodes? to reconstruct lineage histories. 2] Deep sequencing from 314 FCD patient brain resections identified 12 new candidate genes, highlighting signaling and synaptic dysfunction, and a novel ?two-hit? disease mechanisms. 3] We established in utero mouse electroporation models to assess putative FCD variants as gain or loss of function, and to assess effects of ?single-hit? and ?two-hit? mutations. We propose three aims: 1] From control cadavers, we will reconstruct cell lineage across anatomical domains using BSM as barcodes. 2] With this lineage information, we will study the origins of BSM mutations in FCD, by recruiting new patients, performing both targeted and unbiased sequencing, and identifying novel causes. 3] We will functionally validate putative deleterious alleles in animal models for both ?single-hit? and ?two-hit? causes. The goal is to achieve a mechanistic understanding of the extent of BSM in control individuals, to reconstruct neural lineages and to identify novel mechanisms in developmental brain disease.

Project Summary ? Overall: Developmental Mechanisms of Human Meningomyelocele The central goal of this Program Project application is to understand mechanisms of Meningomyelocele (MM), the most severe neural tube defect (NTD) compatible with survival, a condition in which folic acid (FA) fortification has had a major impact on disease risk. This PPG is designed to advance biomedical knowledge and make a high impact on our understanding of the molecular genetics of MM across the evolutionary scale, with the purpose of advancing our ability to determine disease risk, and establish mechanisms by which FA alters risk. MM is the most common birth defect of the central nervous system, affecting 3.7 per 10,000 live births, and is one of the high impact conditions prioritized by the NIH for research. In our preliminary data we have: 1] Constructed a cohort of over 1500 human trios with MM, stratified by whether the child was conceived in a FA-supplemented geography. 2] Established Xenopus laevis as a high-throughput model to assess human mutant alleles, gene-gene interactions, and FA exposure. 3] Established a number of murine NTD models with measured effect of FA on penetrance and expressivity. 4] Demonstrated a proven track record of applying these tools to study mechanisms of disease. As a result of the extensive preliminary data presented below, we have formulated this PPG with a two-fold thrust: 1] By taking advantage of the technical revolution in next generation sequencing and CRISPR genetic engineering, we will uncover and functionally assess new MM risk factors. 2] By comparing phenotypes across the evolutionary timescale, we will enhance our understanding of the basic mechanisms of NTDs and the impact of FA. The central theme running throughout the application is Gene-Environment Interaction (GXE), because of the important role FA has on MM risk in human, mouse and frog, and because the theme applies to all three Projects and Cores. Three Cores will carry out essential functions and benefit each Project. 1] Administrative Core to facilitate communication and provide opportunities for scientific collaboration. 2] Epigenomics Sequencing Core to provide essential functions in assessing FA-dependent DNA methylation and other impacts on chromatin and transcription. 3] Bioinformatics Core to provide essential functions in data processing and harmonization, mutation identification, and custom computational solutions. Specific Aims of the PPG are: 1] To uncover a host of new developmental causes of MM from this unique human cohort, as well as from mouse and frog models. 2] To explore mechanisms by which FA reduces disease incidence in human, mouse and frog. 3] To utilize mechanisms uncovered in mouse and frog NTD models to inform gene prioritization in human MM. We believe that this PPG will have a major impact on our understanding of the cellular and molecular mechanisms underlying NTDs, taking advantage of new breakthrough technology, and will set the stage for improved diagnosis and ultimately prevention of disease.

PROJECT SUMMARY ? Core A: Administrative Core This Administrative Core (Core A) will have two major functions. First, it will provide administrative support and intellectual enrichment for the investigators in this Program. Due to the fact that the Program includes five senior investigators from three institutions (UCSD, Salk, U Colorado), each in a different department, Core A will be essential to integrate the disparate administrative hierarchies. Additionally three different vertebrate species will be used for this work (human, mouse, frog), with the need to move animals between institutions. Because of this, and because of the multi-disciplinary nature of the Program, a central Administrative Core is essential. The Core will work closely with the administration of the three partner institutions, as well as administrators, business managers, and scientists in each department involved. The Administrative Core will: 1] Provide and encourage intellectual collaboration between members of the Program Project, Internal and External Advisory Panels, university faculty who are not members of the Project, and outside consultants. 2] Assist individual PIs in budgeting as well as coordinating travel, purchasing, meetings, and seminars. The Core will achieve these objectives in several ways: 1] We will support a Slack instant messaging/video portal for routine programmatic issues. 2] We will have monthly two-hour seminars for all Program members in this program via video conference. 3] We will have semiannual review by the Internal Advisory Group, and biennial Retreats by the External Advisory Group, with presentation by each PI. We will also have the Directors of Core B and C present new data, analytical techniques, and technological innovations, especially in the rapidly moving fields of genomics, epigenomics, and bioinformatics. Seminars will average 10-12 per year, with each Project or Core presenting 2-3 times per year. Internal and External Advisors are selected to advise each project specifically and will work directly with his/her PI regarding their progress, to suggest possible new directions for both the individual Projects, and potentially the overall Program. In addition, we propose to have two whole day symposia during Year 2 and Year 4, overlapping with the External Advisory Group meetings, in which will invite scientists whose work is on the same aspect of the research of each project. During these symposia, each of the PI?s will present their progress over the preceding two years in the outside experts will be asked to critically evaluate progress of each Project.