Margaret E. Ross - US grants

The goal of this project is to examine, at the transcriptional level, expression and regulation of the catecholamine biosynthetic enzymes, tyrosine hydroxylase (TH), dopamine Beta hydroxylase (DBH) and phenylethanolamine N-methyltransferase (PNMT). The molecular biological methodology and cDNA probes are now available with which to address fundamental questions concerning the tissue specific expression of these genes, their transcriptional regulation by hormones and chemicals, their temporal development during ontogeny and mechanisms directing their subcellular localization. Preliminary to these studies, detailed analyses of the full length cDNAs and genomic clones of TH, DBH and PNMT will be performed using restriction mapping, S1 nuclease mapping and DNA sequencing techniques. With this information in hand, the tissue specific expression and regulation of these genes will be examined using transient expression and stable transformation of eukaryotic cell lines by techniques of DNA mediated gene transfer. Recombinant plasmids containing the entire gene or regions of the gene will be constructed for this transfer. Enzyme activities of the transfected gene products will be measured as an assay of gene exression. Site specific mutagenesis of these recombinant genes followed by expression assay will be used to define promotor regions, cis and trans acting enhancer-like elements and regulatory protein-DNA binding sites. These studies will provide important insights into the molecular mechanisms by which catecholamine genes are expressed and regulated. They will also provide the groundwork for studying the genetic factors associated with abnormal catecholamine metabolism that may contribute to neurological and psychiatric disorders.

DESCRIPTION (Verbatim from the Applicant's Abstract): Lissencephaly (smooth brain, LIS) syndromes are a group of presumed neuronal migration disorders producing brain malformations and epilepsy. The LISI gene in 17pl3.3 encodes the subunit of platelet activating factor acetylhydrolase (PAFAHlb) and its mutation results in Miller-Dieker syndrome (MDS) or isolated lissencephaly sequence (ILS). Mutations of the X-linked locus, XLIS, produce ILS in hemizygous males and less severe, subcortical band heterotopia (SBH or double cortex, DC), in heterozygous females. Investigators in this project and collaborators have identified a putative XLIS gene in Xq22.3, whose encoded protein is designated doublecortin (Dbcn). A novel protein, Dbcn contains a likely site for tyrosine phosphorylation by the cAbl kinase, a region of homology to a novel member of the CAM kinase family, and a Ser/Pro rich domain which is a potential site of protein-protein interactions. Experiments in the competing renewal will produce several mouse models to investigate the role of Dbcn in neuronal migration. The Co-principal investigator has already produced a mouse model of Lisl inactivation that will be compared with Xlis models. Aim 1 will inactivate Xlis by homologous recombination to test the hypothesis that loss of Dbcn function in mice will closely mimic the human malformations. Aim 2 will examine the development of Xlis null, Lisl and Xlis heterozygous cortices to test the hypothesis that loss of either Lisl or Dbcn will a) impair neuronal migration and b) affect tangential patterns of neuronal migration more than radial. Classical static histological and BrdU labeling techniques will be used to study the models created in Aim 1. In addition, the migration patterns of neurons in both the LISI heterozygotes and XLIS nulls will be compared in embryonic cortical slice cultures using time lapse confocal microscopy in which neurons are labeled by DiI or by GFP expressed under the direction of the Xlis promoter. In Aim 3, genetic crosses will test the hypothesis that Dbcn is part of an intracellular signaling cascade and is activated by the cAbl tyrosine kinase in response to adhesion, serving to link signals at the cell surface with neuronal migration. Possible interactions between Dbcn and BLisl or Dbcn and the mDabl migration protein will be examined in double mutants created by crossbreeding mutant mouse strains. Aim 4 will examine the hypothesis that point mutations in XLIS families produce milder phenotypes by virtue of partial loss of function or disregulation of Dbcn. A transgenic model will test whether over-expression of Dbcn activity can also disrupt migration. Mouse models of XLIS will help to reveal the pathogenesis of the X-linked form of LIS and SBHDC, will definitively determine whether XLIS is a neuronal migration gene, and will help to define genetic mechanisms leading to a major class of human developmental disorders and epilepsy.

DESCRIPTION (provided by applicant): The goal of this ongoing project is to characterize the gene mutated in the Crooked tail (Cd) mouse as a new locus associated with folic acid (FA) sensitive neural tube defects (NTD). Homozygous Cd are prone to rostral NTD and those completing neurulation display a subtle cortical dysplasia. In the first 3 years of funding, we have shown that the incidence of NTD is reduced in Cd by dietary folate in a manner closely resembling clinical observation, making it an important model for human NTD. Linkage analysis has fine-mapped the Cd locus to a 0.2 cM region of chromosome 6. Physical mapping and sequencing of the Cd critical region has identified 3 candidate genes. The project will identify the Cd gene, investigate the pathogenesis of its CNS malformations at the cellular and molecular levels and examine the relation between folate metabolism and these defects. First, the Cd gene will be sought through positional cloning and testing of identified candidates. Linkage analysis has beer completed and a genomic DNA contig covering the critical region has been established. In the renewal period we will identify Cd by: (a) cloning cDNAs corresponding to the genomic contig; (b) analysis of candidate genes from the region for large and small mutations in Cd mice. The identity of the gene producing Cd will be confirmed through demonstration that the phenotype can be rescued by introduction of BACs encompassing at entire candidate gene. Alternatively, the putative Cd mutation will be "knocked-in" to recapitulate the Cd phenotype. Second, The mechanisms leading to the Cd phenotype will be determined, whether due to altered cell proliferation, neuronal migration or programmed cell death. Morphogenesis of individual Cd embryos in culture will be examined by time-lapse confocal microscopy. In addition Cd brain histogenesis will be defined using markers of neural fate determination and CNS pattern formation. Third, Investigation of dietary folate will continue, to determine whether FA alters the proliferation of cells during neurulation, and whether FA can also ameliorate Cd cerebral cortical maldevelopment. Fourth, Functional studies of Cd will begin with structural analysis of the gene product. The status of FA-related metabolic pathways in Cd animals will be investigated for clues to potential mechanisms leading to FA-sensitive NTD. Function will be investigated by over-expression of Cd in mice, introduced by BAC vectors to permit transgene expression in appropriate temporal and anatomic sequence. Further functional studies will inactivate Cd in normal mice by a conditional homologous recombinant knockout. Study of the genetic, molecular and cellular events leading to abnormalities in Cd will contribute to mechanistic understanding of NTD and may lead to strategies for prenatal assessment of an individual family?s risk and tailored prevention of human brain maldevelopment.

neural plate /tube

[unreadable] Description (provided by applicant): This PPG examines genetic regulation of brain formation and function from the perspective of cortical[unreadable] interneuron development. Increasing evidence suggests that selective developmental interneuron deficits[unreadable] are intimately linked with,failure of neural progenitor proliferation and specification. Lost function of the cell[unreadable] cycle gene cyclin D2 results in reduced brain volumes and selective loss of interneurons, e.g. cerebellar[unreadable] stellate and granule neurons, while sparing basket and Golgi interneurons as well as projection (Purkinje)[unreadable] neurons (Ross, Projl). Studies of neurogenic divisions in the cerebral cortical VZ suggest that GABAergic[unreadable] interneurons influence proliferation and differentiation of cortical neural cells (Kriegstein, ProjS). Evidence in[unreadable] rodent models suggests that most cortical interneurons originate from the medial ganglionic eminence[unreadable] (MGE) (Anderson, Proj2); thus investigations of interneuron development must involve MGE. The goal of[unreadable] the Program is to tease out the relative contributions of inteneuronal populations to brain formation,[unreadable] structure and function, examining the role of proliferation and interneuron specification to brain[unreadable] development.[unreadable] Project 1 will examine the consequences of reduced cell proliferation in brains of mice lacking cyclin D2,[unreadable] associated with small telencephalon and selective interneuron deficits. Conditional knockouts of cyclin D2[unreadable] that further restrict the neural cell populations affected will be used to examine the dynamic role of specific[unreadable] neural subpopulations in brain formation.[unreadable] Project 2 will pursue the roles of Shh signaling to 1) specify cortical interneurons that originate in the[unreadable] MGE, and 2) (collaborating with Project 3) to regulate proliferation within the cortex. Several Cre-loxP[unreadable] conditional nulls will be examined with distinct patterns inactivating Shh or its receptor in the embryonic[unreadable] forebrain. These mice and in vitro studies will be used to explore the multiple roles of Shh on cortical[unreadable] neurogenesis.[unreadable] Project 3 will examine the dynamic behavior of neurogenic divisions in the VZ and SVZ of the MGE[unreadable] compared to cortex to determine how intrinsic and epigenetic factors modulate neurogenesis, and how[unreadable] regional alterations in the pattern of division might contribute to developmental interneuron deficits.[unreadable] Project 4 will examine the neurophysiology and behavioral consequences of the selective alterations of[unreadable] interneuronal subpopulations in animal models produced by Projects 1 and 2.[unreadable] The Projects are supported by administrative, statistical, histological and quantitative neuroanatomical[unreadable] services provided in Cores A and B.[unreadable] These genetic mouse models with highly selective interneuron deficits enable the Program to examine the[unreadable] contributions of neuron subsets to brain structure, complex behaviors and cognitive function. The proposed[unreadable] studies are relevant to epilepsy, schizophrenia, affective disorders and cognitive disorders including autism.[unreadable]

model; sectioning

Previous studies indicate a role for G1 active cyclin D2 (cD2) in the patterning and function of mammalian brain. Unexpected of a cell cycle protein, loss of cD2 leads to small brains and to selective loss of interneurons in the cerebellum. This project will examine cD2's role in the regulation of progenitor cell divisions and genesis of telencephalic interneurons. Pilot data indicate that, like the striking deficits in cerebellar granule and stellate neurons in this model, cD2-/- neocortex and hippocampus contain significantly fewer parvalbumin (Pv) containing interneurons while seeming to spare calretinin (CLR) and somatostatin (SSN) subtypes. These mice display rare spontaneous seizures and studies with Project 4 indicate cD2 nulls have a lower seizure threshold to drugs affecting GABAergic systems. Four hypotheses will be pursued in four Specific Aims: 1. cD2 regulates the number and differentiation of selected neural precursors in cerebral cortex. Experiments will determine: a. cD2 expression mapped during histogenesis of the telencephalon. b. which progenitor pools are most affected in cD2 null brain. c. which neuronal types are dependent upon cD2 expression during histogenesis. 2. Reduced cell division can affect subpopulations of cortical interneurons disproportionately. The interneuron subtypes lost in cD2-/- will be identified and compared with projection neuron populations. 3. cD2 promotes symmetric progenitor divisions, favoring the secondary proliferative population, to keep precursors in cycle that would otherwise exit. Studies will use: a. time-lapse imaging of progenitors in slice cultures from WT, cD2-/- and cD1-/- mice (in collaboration with Project 3). b. acute over- and under-expression of cD2 protein in vivo and in vitro. 4. Conditional loss of cD2 can be used to probe cortical vs. subcortical contributions of cD2 to brain structure and behavior. A floxP cD2 mouse will be produced and used to inactivate cD2 in MGE or neocortex/hippocampus. a. structural consequences will be examined in Project 1. b. behavioral studies will be pursued in Project 4.

The administrative and biostatistical core will function as a resource for the entire Program. The administrative core is responsible for the financial management of the Program, coordination of training, production and maintenance of all PPG correspondence, communication and operational support. Core A will support the regular meetings of the PPG investigators, coordinating schedules, meeting space and videoconferencing with distant sites (UCSF and University of Chicago). The Core provides for internal and external advisers, who give critical feedback but do not have a governance role in the Program. Core A will support communications with and coordinate an annual meeting of an internal advisory committee with Program investigators. Core A will arrange individual visits of 3 external advisers per year to provide consultation to the Program and present in the Developmental Biology and Neuroscience Seminar Series at Cornell or UCSF. The core will coordinate the distribution of reports to the external advisers and critiques to the Executive Committee of Project Pis as well as arrange an annual end-of-year discussion among external advisers and Pis via phone conference. The Biostatistics subcore is housed within Core A and maintains a centralized Access" database that is shared across all projects. This database is designed to standardize data classification and archiving so that investigators from all Projects and Cores can access developmental, anatomical, neurophysiological and behavioral data on all genetic models. The administrative Core also coordinates statistical support for all projects through consultants from the Department of Public Health of the Medical College of Cornell (see section on the Biostatistical subcore). Because their primary faculty appointments are at Cornell, Core A will administer Dr. Polan's and Dr. Suh's salaries that are related to their research efforts on Project 4 (Moore PI, Columbia University). Thus, Core A serves every project and core in the Program.

Failure of neural tube closure is a complex genetic disorder, rarely if ever seen as a simple Mendelian trait. In the clinical population, NTDs are probably most often caused by partial inactivation and/or gain of function mutations of multiple genes, acting in conjunction with the gestational environment. Recognizing such changes as disease associated mutations rather than simple polymorphisms is a challenge for assessment of risk in individual families. Another challenge is determining the most appropriate means to reduce NTD occurrence for a particular couple. Recent studies from these three collaborating laboratories lead us to hypothesize that a systematic examination of gene network interactions in mouse models will elucidate patterns that are applicable to risk assessment and prevention of NTDs in humans. In a mouse line with a folic acid (FA) responsive NTD, we identified a point mutation in Lrp6, a co-receptor for Wnt canonical signaling, which implicates several important developmental genetic pathways likely to be encountered clinically. Using this Crooked tail (Cd) mouse, we identified a possible gene expression and metabolism "signature" in liver tissue and blood, predicting a genetic make-up that will respond to FA supplementation by preventing NTD. In addition, we used ENU mutagenesis screens to identify NTD associated mouse mutations that provide candidates for human testing and which can be tested for response to FA and other potential NTD preventive agents. We propose to pursue a multi-institution effort to characterize genetic susceptibility profiles in mice and identify genetic backgrounds that respond to prevention measures such as dietary supplementation. Experiments will use FA and inositol supplementation to test whether these agents prevent NTD in Lrp6 null and NTD-prone mice with defined ENU-generated mutations. Gene transcript arrays will examine expression in the neural tube during closure in these mutants using cluster analysis to compare patterns in the mutant vs. wildtype siblings. In addition, the genetic and metabolic signature identified in Cd non-neural tissues will be compared against signatures in other ENU-generated and naturally occurring NTD mouse mutants to determine the predictive power of this pattern. This project will build a framework for rational approaches to new treatments based on molecular pathways. To this end, the relationship between the biochemical pathway that is disrupted and the responsiveness or resistance to FA supplementation will be examined in several mouse lines. This will begin to reveal mechanisms by which FA, and inositol, acts to suppress NTD.

The administrative core functions as a resource for the entire Program. Core A is responsible for the financial management of the Program, tracking accounts and expenditures. These are reconciled monthly with accounting statements prepared by central accounting at the College. Core A also provides Program operational support for the preparation of annual progress reports, coordination of training, production and maintenance of all PPG documentation including tracking of research compliance requirements of Program investigator institutions to ensure approvals are kept current. Core A will support the regular meetings of the PPG investigators, coordinating schedules and arranging meeting space. The Core provides for internal and external advisers, who give critical feedback but do not have a governance role in the Program. Core A will support communications with and coordinate an annual meeting of the internal advisory committee with Program investigators. Core A will arrange individual visits of 2 to 3 external advisers per year to provide consultation to the Program. The core will coordinate the distribution of reports to the external advisers and critiques to the Executive Committee of Project PIs. Thus, Core A serves every project and core in the Program.

GENE VARIANTS &THEIR INTERACTIONS DEFINING HUMAN NTD RISK Neural tube defects (NTDs), primarily spina bifida and anencephaly, arise from a complex interplay of multiple gene interactions and environmental exposures. After 30 years of clinical and basic research, the field remains unable to accurately predict the risk for an individual couple of having a child affected by NTD, how folic acid (FA) works to prevent NTDs, whether or what dose of FA is likely provide effective prevention for them or whether there is another nutrient/supplement or intervention that would provide greater benefit The recent confluence of information from genetic mouse models, capabilities of molecular biological and biochemical detection in embryonic systems and advances in genomics and computational genetics now provides sufficient power to successfully address this complex genetic disorder. Project 1 will test the following hypotheses: 1. that combinations of rare variant single nucleotide polymorphisms (SNPs) will display associations useful for the definition of individual NTD risk in humans, and 2. that recognition of interactions between these genetic patterns with environmental conditions, including FA intake and factors common to inflammation or oxidative/nitrosative stress, can further increase their predictive value. This project will use deep resequencing of NTD patient DNA, targeted to human counterparts of some 1,000 genes implicated in NTD pathogenesis by clinical and animal model studies, to identify rare variant alleles that are overrepresented in NTD patients. These will be used to design custom SNP assays for screening larger patient numbers for analyses of single gene and pair-wise associations with NTD. Computational modeling will assess the potential impact of NTD associated SNPs on key developmental and metabolic pathways. The functional significance of SNP associations in humans will be functionally tested first for impact on Wnt/PCP, FA metabolism and oxidative/nitrosative stress using in vitro and mouse systems assays that will also be used to validate and inform computational modeling. Because the overt NTD phenotypes are readily recognized in humans and experimental animals, NTDs may well be the first complex genetic disorder for which gene-gene and gene-environment interactions can be understood in depth. Progress made for this disorder can provide useful analytical tools for identifying molecular network interactions relevant to later-onset complex genetic disorders, like schizophrenia and autism. RELEVANCE (See instructions): Enhanced capabilities for assessment of individual risk for developing NTDs would permit prevention regimens to be tailored to individuals rather than applied 'shot-gun'to populations. In broadest scope, data generated in Project 1 will have implications for every reproductive-age woman worldwide. In addition, folate metabolism can exert a lasting impact on gene expression by influencing DNA methylation, making it imperative that we understand the ramifications of FA supplementation. A fuller grasp of the relationships between the FA pathway and risk genes will have important relevance for a broad range of other diseases in which folate status may have a role.

DESCRIPTION (provided by applicant): This Program examines the interaction of proliferation and interneuron fate determination in the developing medial ganglionic eminence (MGE), and probes functional consequences of altering interneuron subpopulations. Two broad classes of neurons}}}glutamatergic excitatory and GABAergic inhibitory}}} comprise virtually every neural circuit in cerebral cortex. Their morphology, biochemical constituents, electrophysiological properties and synaptic connections can distinguish a remarkable variety of interneuron subtypes. Despite the importance of these GABAergic cells to brain function, surprisingly little is known about how their production is regulated on a cellular or molecular level. Project 1 (Ross PI) studies the roles of cell cycle constituents in the patterning and function of mammalian brain. They found that two Gl-phase active cyclins, cDI and cD2, are expressed in different progenitor subsets in the MGE where genetic ablation of cD2 produces a loss of cortical PV+ but not SST+ interneurons. Experiments probe the hypothesis that cDI functions primarily to promote asymmetric divisions of radial glial cells (RGCs), some of which generate SST+ interneurons. In contrast, cD2 may promote the symmetric divisions of intermediate progenitor cells (IPCs) that will primarily generate PV+ interneurons Project 2 (Anderson PI) investigates the interacting roles of Notch, Wnt and Shh signaling systems to regulate the number and subtypes of neurons generated from the MGE. They have found that modulation of Notch signaling enhances cD2 expression in dorsal MGE (dMGE) and hypothesize that this will increase PV+ output at the expense of SST+ interneurons. Pilot data implicate interactions between Shh and Wnt signaling regulate Notch activity to impact interneuron production and these relationships will be explored Project 3 (Shi PI) uses in utero intraventricular injection of retroviral fluorescent proteins with state-of- the-art time-lapse videomicroscopy and immunohistochemistry to examine cell intrinsic and extrinsic mechanisms regulating divisions in the MGE. These istudies are heavily integrated with cell cycle and signaling investigations in Projects 1 and 2. Core B (Moore Dir.) will determine the functional significance of selective interneuron deficits that involve different interneuron subtypes and anatomical regions in mouse models generated within the Program. Consequences of interneuron subset loss on behavior, brain structure and physiology are sought. It is widely appreciated that key signaling pathways like Notch, Shh, and Wnt and cell cycle regulators like D-cyclins extensively interact to regulate neuronal generation and fate. However the complexity of the interactions, diversity of ventral forebrain-derived neuronal fates and challenges for gene manipulation in this region pose major impediments to comprehensive study in the MGE. This Program tackles this complexity through the combined efforts of 4 Pis using cutting edge approaches to the elucidation of how developmental signals regulate fate and output of these critically important neurons. PUBLIC HEALTH RELEVANCE: Interneuron deficits have been implicated in the pathobiology of major neurological and psychiatric illnesses, including epilepsy, anxiety disorders, autism and schizophrenia. While a great deal has been learned over the last 20 years about proliferation of excitatory, glutamatergic precursors in cortex, a number of challenges have slowed the pace of discovery for studies of the ventral niches that generate interneurons. This Program strives to address this knowledge gap and our work over the past 4 years positions us well to succeed. PROJECT 1 Principal Investigator: M. Elizabeth Ross Title: Cell Cycle Regulation in Interneuron Genesis &Cortical Construction Description (provided by applicant): Inhibitory cortical interneurons, most originating in the medial ganglionic eminence (MGE), are part of virtually every cortical circuit. Normal cortical function critically depends on generating these GABAergic cells in numbers and subtypes in proper proportion to excitatory projection neurons. This requires exquisite coordination of progenitor subtype proliferation with differentiation. Project 1 studies the roles of cell cycle constituents in the patterning and function of mammalian brain and showed that two G1-phase active cyclins, cD1 and cD2, are expressed in distinct progenitor subsets in the MGE. Ablation of cD2 results in loss of cortical PV+ but not SST+ interneurons. We hypothesize that cD1 functions to promote asymmetric divisions of radial glial cells, some of which generate SST+ interneurons. In contrast, cD2 may promote the symmetric divisions of intermediate progenitor cells that will primarily generate PV+ interneurons Aim 1. The distinct roles of cD2 vs. cD1 in MGE divisions will be examined using acute overexpression and knockdown of these cyclins in utero, together with analyses of cell position, morphology, and colabeling with markers of proliferative and post-mitotic subpopulations. Via collaboration with Project 3, timelapse imaging in WT, c D I - / - and cD2-/- MGE will examine how loss of cD2 or cD1 affects symmetric vs. asymmetric divisions. We will take advantage of a fluorescence tagging method to compare cell cycle phase duration in cD2-/- vs. cD1-/- MGE. The hypothesis that cD2 expression favors symmetric while cD1 promotes asymmetric divisions will be tested. Aim 2. The transcriptome of cD2+ MGE progenitors will be investigated using two different approaches to capture RNA from cD2+ MGE cells in transgenic mice;Translating Ribosome Affinity Purification (TRAP) or fluorescence activated cell sorting (FACS) followed by microarray. Data will define the molecular context in which cD2 is operating in the MGE. Interpretation of these arrays will be greatly facilitated by insights from Project 2 studies that have identified a connection between Notch signaling and regulation of cD2 expression in the dorsal MGE, while Wnt and Shh signaling have effects on proliferation, likely upstream of Notch. Thus, potentially meaningful expression patterns will be more readily recognizable. Aim 3. Inducible cD2-CreER[T2] will be used to map the fate outcomes of cD2+ progenitors while conditional inactivation in Nkx2.1-Cre:cD2fl/fl and Dlx1/2-Cre:cD2fl/fl models will probe contributions of cD2 to interneuron specification. We hypothesize that PV+ interneurons arise primarily from cD2+ progenitors in the SVZ while SST+ interneurons derive primarily from neurogenic divisions in the VZ. Project 2 expertise will be essential as we establish fate maps of MGE-derived cD2+ progenitors. Outcomes of cD2 loss selectively within the MGE on interneuron distribution and function will be tested in the Neurobehavioral Analysis Core, to probe cognitive changes due to loss of these interneuron subsets. Public Health Relevance: The mechanisms linking cell division to neural specification, particularly in subcortical brain, are appreciated at only a rudimentary level. That VZ and SVZ cells use different cell cycle components and that disturbing this balance can alter the interneuron composition in the cerebral cortex adds to the rich complexity of ways neurogenesis is regulated in the developing brain. This Program brings together 4 laboratories with the advanced capabilities that place us in an unprecedented position to understand the mechanisms regulating genesis of these neuron subtypes that are targets of many neuropsychiatric diseases.

DESCRIPTION (provided by applicant): Neural tube defects (NTDs), primarily spina bifida and anencephaly, arise from a complex interplay of multiple gene interactions and environmental exposures. After 30 years of clinical and basic research, the field remains unable to accurately predict the risk for an individual couple of having a child affected by NTD, how folic acid (FA) works to prevent NTDs, whether or what dose of FA is likely provide effective prevention for them or whether there is another nutrient/supplement or intervention that would provide greater benefit The recent confluence of information from genetic mouse models, capabilities of molecular biological and biochemical detection in embryonic systems and advances in genomics and computational genetics now provides sufficient power to successfully address this complex genetic disorder. Project 1 will test the following hypotheses: 1. that combinations of rare variant single nucleotide polymorphisms (SNPs) will display associations useful for the definition of individual NTD risk in humans, and 2. that recognition of interactions between these genetic patterns with environmental conditions, including FA intake and factors common to inflammation or oxidative/nitrosative stress, can further increase their predictive value. This project will use deep resequencing of NTD patient DNA, targeted to human counterparts of some 1,000 genes implicated in NTD pathogenesis by clinical and animal model studies, to identify rare variant alleles that are overrepresented in NTD patients. These will be used to design custom SNP assays for screening larger patient numbers for analyses of single gene and pair-wise associations with NTD. Computational modeling will assess the potential impact of NTD associated SNPs on key developmental and metabolic pathways. The functional significance of SNP associations in humans will be functionally tested first for impact on Wnt/PCP, FA metabolism and oxidative/nitrosative stress using in vitro and mouse systems assays that will also be used to validate and inform computational modeling. Because the overt NTD phenotypes are readily recognized in humans and experimental animals, NTDs may well be the first complex genetic disorder for which gene-gene and gene-environment interactions can be understood in depth. Progress made for this disorder can provide useful analytical tools for identifying molecular network interactions relevant to later-onset complex genetic disorders, like schizophrenia and autism.

DESCRIPTION (provided by applicant): Modifications of DNA and chromatin impact the accessibility of the genetic code to the biological machinery of the cell. Relating epigenomic changes to neurodevelopmental disorders has been challenging. One obstacle is the need to study the relevant tissues at an appropriate stage of the disease process, while another is the difficulty of understanding the relationship of nucleotide and chromatin modifications to complex genetic disorders in which multiple loci interactions underlie expression of the disease. We propose to take advantage of a disorder, neural tube defects (NTDs), in which the existing mouse models closely parallel the human disease and in which several lines of evidence indicate a strong influence in both mouse and man of epigenetic modifications regulating disease expression. We will combine proof of principle studies in the mouse with investigations of human NTD cohorts to examine the relationship between DNA/chromatin methylation and the expressivity of NTDs in genetically susceptible individuals. The study of epigenetic events contributing to NTDs has multiple distinct advantages over epigenomic investigation of other human diseases, as more than 200 genes are implicated in NTDs by human or animal studies. These provide critical clues to molecular pathways important for normal neurulation. Supporting the existing clinical data, we discovered several NTD-prone mouse mutant lines in which NTD occurrence is sensitive to folic acid supplementation. Folate metabolism is the source of al S-adenosyl methoinine (SAM), which is the primary methyl donor for methylating nucleic acids, proteins and lipids. Providing methyl donors is thought to be a major route through which folate supplementation exerts its beneficial effects on neurulation. We will use cutting edge and emerging technologies applied to mouse and human patient material to interrogate genome wide methylation and chromatin remodeling interactions, correlated with individual genotype, to examine epigenetic effects on the transcriptome and on phenotypic outcome. This proposal tests the hypothesis that epigenetic modifications in DNA and chromatin in the setting of prenatal supplementation that modulates DNA and chromatin methylation will impact a recognizable pattern of gene expression to either favor or impair neurulation in a manner that can be predicted based on individual genotype. Moreover, we hypothesize that certain patterns will be evident not only in the developing neural tube but also in the peripheral blood and so will be useful in evaluating risk and optimal NTD prevention in a clinical setting. We predict that some DNA and chromatin methylation signatures acquired in utero wil persist postnatally, regardless of whether supplementation continues after birth. Finally, we expect that DNA methylation patterns found in mouse will be present as well-at least at the level of pathways if not individual genes-in human patients affected by an NTD.

RISK GENES AND ENVIRONMENT INTERACTIONS IN NTDS ADMINISTRATIVE CORE Core A will provide an anchor for the Program, assisting in grant administration and budget management as well as preparation of annual reports. It will organize annual meetings of the Internal and External Advisory committees with Program investigators. Annual Internal Advisory Board meetings will take place in Manhattan, while yearly External Advisory Board meetings will take place alternately in NY or TX. The Core will continue to schedule the monthly meetings of the project participants, which take place via videoconferencing. It will organize and administratively support the periodic meetings in NY and TX of Program investigators. Core A will coordinate training opportunities for Program investigators (students, postdocs, faculty). It will support collaborative experiments across Projects by facilitating the shipment of materials between NY and TX. It will serve as the administrative link between the Cornell University Life Sciences Core (CLC) facility and the laboratories at WCMC in New York, and in Texas, at TMHRI and the University of Texas at Austin, Dell Pediatric Research Institute.

Inhibitory cortical interneurons, most originating in the medial ganglionic eminence (MGE), are part of virtually every cortical circuit. Normal cortical function critically depends on generating these GABAergic cells in numbers and subtypes in proper proportion to excitatory projection neurons. This requires exquisite coordination of progenitor subtype proliferation with differentiation. Project 1 studies the roles of cell cycle constituents in the patterning and function of mammalian brain and showed that two G1-phase active cyclins, cD1 and cD2, are expressed in distinct progenitor subsets in the MGE. Ablation of cD2 results in loss of cortical PV+ but not SST+ interneurons. We hypothesize that cD1 functions to promote asymmetric divisions of radial glial cells, some of which generate SST+ interneurons. In contrast, cD2 may promote the symmetric divisions of intermediate progenitor cells that will primarily generate PV+ interneurons Aim 1. The distinct roles of cD2 vs. cD1 in MGE divisions will be examined using acute overexpression and knockdown of these cyclins in utero, together with analyses of cell position, morphology, and colabeling with markers of proliferative and post-mitotic subpopulations. Via collaboration with Project 3, timelapse imaging in WT, c D I - / - and cD2-/- MGE will examine how loss of cD2 or cD1 affects symmetric vs. asymmetric divisions. We will take advantage of a fluorescence tagging method to compare cell cycle phase duration in cD2-/- vs. cD1-/- MGE. The hypothesis that cD2 expression favors symmetric while cD1 promotes asymmetric divisions will be tested. Aim 2. The transcriptome of cD2+ MGE progenitors will be investigated using two different approaches to capture RNA from cD2+ MGE cells in transgenic mice;Translating Ribosome Affinity Purification (TRAP) or fluorescence activated cell sorting (FACS) followed by microarray. Data will define the molecular context in which cD2 is operating in the MGE. Interpretation of these arrays will be greatly facilitated by insights from Project 2 studies that have identified a connection between Notch signaling and regulation of cD2 expression in the dorsal MGE, while Wnt and Shh signaling have effects on proliferation, likely upstream of Notch. Thus, potentially meaningful expression patterns will be more readily recognizable. Aim 3. Inducible cD2-CreER[T2] will be used to map the fate outcomes of cD2+ progenitors while conditional inactivation in Nkx2.1-Cre:cD2fl/fl and Dlx1/2-Cre:cD2fl/fl models will probe contributions of cD2 to interneuron specification. We hypothesize that PV+ interneurons arise primarily from cD2+ progenitors in the SVZ while SST+ interneurons derive primarily from neurogenic divisions in the VZ. Project 2 expertise will be essential as we establish fate maps of MGE-derived cD2+ progenitors. Outcomes of cD2 loss selectively within the MGE on interneuron distribution and function will be tested in the Neurobehavioral Analysis Core, to probe cognitive changes due to loss of these interneuron subsets.

GENE VARIANTS & THEIR INTERACTIONS DEFINING HUMAN NTD RISK Neural tube defects (NTDs), primarily spina bifida and anencephaly, arise from a complex interplay of multiple gene interactions and environmental exposures. After 30 years of clinical and basic research, the field remains unable to accurately predict the risk for an individual couple of having a child affected by NTD, how folic acid (FA) works to prevent NTDs, whether or what dose of FA is likely provide effective prevention for them or whether there is another nutrient/supplement or intervention that would provide greater benefit The recent confluence of information from genetic mouse models, capabilities of molecular biological and biochemical detection in embryonic systems and advances in genomics and computational genetics now provides sufficient power to successfully address this complex genetic disorder. Project 1 will test the following hypotheses: 1. that combinations of rare variant single nucleotide polymorphisms (SNPs) will display associations useful for the definition of individual NTD risk in humans, and 2. that recognition of interactions between these genetic patterns with environmental conditions, including FA intake and factors common to inflammation or oxidative/nitrosative stress, can further increase their predictive value. This project will use deep resequencing of NTD patient DNA, targeted to human counterparts of some 1,000 genes implicated in NTD pathogenesis by clinical and animal model studies, to identify rare variant alleles that are overrepresented in NTD patients. These will be used to design custom SNP assays for screening larger patient numbers for analyses of single gene and pair-wise associations with NTD. Computational modeling will assess the potential impact of NTD associated SNPs on key developmental and metabolic pathways. The functional significance of SNP associations in humans will be functionally tested first for impact on Wnt/PCP, FA metabolism and oxidative/nitrosative stress using in vitro and mouse systems assays that will also be used to validate and inform computational modeling. Because the overt NTD phenotypes are readily recognized in humans and experimental animals, NTDs may well be the first complex genetic disorder for which gene-gene and gene-environment interactions can be understood in depth. Progress made for this disorder can provide useful analytical tools for identifying molecular network interactions relevant to later-onset complex genetic disorders, like schizophrenia and autism. RELEVANCE (See instructions): Enhanced capabilities for assessment of individual risk for developing NTDs would permit prevention regimens to be tailored to individuals rather than applied 'shot-gun' to populations. In broadest scope, data generated in Project 1 will have implications for every reproductive-age woman worldwide. In addition, folate metabolism can exert a lasting impact on gene expression by influencing DNA methylation, making it imperative that we understand the ramifications of FA supplementation. A fuller grasp of the relationships between the FA pathway and risk genes will have important relevance for a broad range of other diseases in which folate status may have a role.

DESCRIPTION (provided by applicant): This Program examines the interaction of proliferation and interneuron fate determination in the developing medial ganglionic eminence (MGE), and probes functional consequences of altering interneuron subpopulations. Two broad classes of neurons}}}glutamatergic excitatory and GABAergic inhibitory}}} comprise virtually every neural circuit in cerebral cortex. Their morphology, biochemical constituents, electrophysiological properties and synaptic connections can distinguish a remarkable variety of interneuron subtypes. Despite the importance of these GABAergic cells to brain function, surprisingly little is known about how their production is regulated on a cellular or molecular level. Project 1 (Ross PI) studies the roles of cell cycle constituents in the patterning and function of mammalian brain. They found that two Gl-phase active cyclins, cDI and cD2, are expressed in different progenitor subsets in the MGE where genetic ablation of cD2 produces a loss of cortical PV+ but not SST+ interneurons. Experiments probe the hypothesis that cDI functions primarily to promote asymmetric divisions of radial glial cells (RGCs), some of which generate SST+ interneurons. In contrast, cD2 may promote the symmetric divisions of intermediate progenitor cells (IPCs) that will primarily generate PV+ interneurons Project 2 (Anderson PI) investigates the interacting roles of Notch, Wnt and Shh signaling systems to regulate the number and subtypes of neurons generated from the MGE. They have found that modulation of Notch signaling enhances cD2 expression in dorsal MGE (dMGE) and hypothesize that this will increase PV+ output at the expense of SST+ interneurons. Pilot data implicate interactions between Shh and Wnt signaling regulate Notch activity to impact interneuron production and these relationships will be explored Project 3 (Shi PI) uses in utero intraventricular injection of retroviral fluorescent proteins with state-of- the-art time-lapse videomicroscopy and immunohistochemistry to examine cell intrinsic and extrinsic mechanisms regulating divisions in the MGE. These istudies are heavily integrated with cell cycle and signaling investigations in Projects 1 and 2. Core B (Moore Dir.) will determine the functional significance of selective interneuron deficits that involve different interneuron subtypes and anatomical regions in mouse models generated within the Program. Consequences of interneuron subset loss on behavior, brain structure and physiology are sought. It is widely appreciated that key signaling pathways like Notch, Shh, and Wnt and cell cycle regulators like D-cyclins extensively interact to regulate neuronal generation and fate. However the complexity of the interactions, diversity of ventral forebrain-derived neuronal fates and challenges for gene manipulation in this region pose major impediments to comprehensive study in the MGE. This Program tackles this complexity through the combined efforts of 4 Pis using cutting edge approaches to the elucidation of how developmental signals regulate fate and output of these critically important neurons.

Inhibitory cortical interneurons, most originating in the medial ganglionic eminence (MGE), are part of virtually every cortical circuit. Normal cortical function critically depends on generating these GABAergic cells in numbers and subtypes in proper proportion to excitatory projection neurons. This requires exquisite coordination of progenitor subtype proliferation with differentiation. Project 1 studies the roles of cell cycle constituents in the patterning and function of mammalian brain and showed that two G1-phase active cyclins, cD1 and cD2, are expressed in distinct progenitor subsets in the MGE. Ablation of cD2 results in loss of cortical PV+ but not SST+ interneurons. We hypothesize that cD1 functions to promote asymmetric divisions of radial glial cells, some of which generate SST+ interneurons. In contrast, cD2 may promote the symmetric divisions of intermediate progenitor cells that will primarily generate PV+ interneurons Aim 1. The distinct roles of cD2 vs. cD1 in MGE divisions will be examined using acute overexpression and knockdown of these cyclins in utero, together with analyses of cell position, morphology, and colabeling with markers of proliferative and post-mitotic subpopulations. Via collaboration with Project 3, timelapse imaging in WT, c D I - / - and cD2-/- MGE will examine how loss of cD2 or cD1 affects symmetric vs. asymmetric divisions. We will take advantage of a fluorescence tagging method to compare cell cycle phase duration in cD2-/- vs. cD1-/- MGE. The hypothesis that cD2 expression favors symmetric while cD1 promotes asymmetric divisions will be tested. Aim 2. The transcriptome of cD2+ MGE progenitors will be investigated using two different approaches to capture RNA from cD2+ MGE cells in transgenic mice; Translating Ribosome Affinity Purification (TRAP) or fluorescence activated cell sorting (FACS) followed by microarray. Data will define the molecular context in which cD2 is operating in the MGE. Interpretation of these arrays will be greatly facilitated by insights from Project 2 studies that have identified a connection between Notch signaling and regulation of cD2 expression in the dorsal MGE, while Wnt and Shh signaling have effects on proliferation, likely upstream of Notch. Thus, potentially meaningful expression patterns will be more readily recognizable. Aim 3. Inducible cD2-CreER[T2] will be used to map the fate outcomes of cD2+ progenitors while conditional inactivation in Nkx2.1-Cre:cD2fl/fl and Dlx1/2-Cre:cD2fl/fl models will probe contributions of cD2 to interneuron specification. We hypothesize that PV+ interneurons arise primarily from cD2+ progenitors in the SVZ while SST+ interneurons derive primarily from neurogenic divisions in the VZ. Project 2 expertise will be essential as we establish fate maps of MGE-derived cD2+ progenitors. Outcomes of cD2 loss selectively within the MGE on interneuron distribution and function will be tested in the Neurobehavioral Analysis Core, to probe cognitive changes due to loss of these interneuron subsets.

ABSTRACT PROJECT 1: Gene Variants and their Interactions Defining Human NTD Risk Neural tube defects (NTDs), primarily spina bifida and anencephaly, arise from a complex interplay of multiple gene interactions and environmental exposures. After 30 years of clinical and basic research, the field remains unable to accurately predict the risk for an individual couple of having a child affected by NTD, how folic acid (FA) works to prevent NTDs, whether or what dose of FA is likely provide effective prevention for them, or whether there is another nutrient/supplement or intervention that would provide greater benefit. The recent confluence of advances in genomics and computational genetics, enhanced by information from genetic mouse models, capabilities of molecular biological and biochemical detection in embryonic systems, now provide outstanding opportunity to address this complex genetic disorder. In the initial funding period, Project 1 has accumulated 200 whole genome sequences (WGS) from cases and 200 controls and has identified rare nonsense, frameshift and non-coding variants associated with spina bifida. This has thus far generated over 100 candidate gene and transcription factor binding sites associated in both expected and novel molecular interaction pathways in humans that are enriched for rare sequence variants in NTD cases compared to non-malformed controls and public databases. Among the most striking findings are that pathways modulating or affected by oxidative stress are heavily represented among the rare variants in our NTD cohort. In the renewal, we will employ a powerful high throughput method using molecular inversion probes (MIPs) to resequence a replication cohort of over 2,000 NTD cases and validate the most highly significant genes and non-coding, regulatory regions of the genome associated with NTD risk. Cutting edge CRISPR-Cas9 dependent genome editing in hESCs and mice will probe the functional impact of identified variants on neuroepithelial cell polarity, proliferation, differentiation, survival and the generation of reactive oxidative/nitrosative species (RONS). With Projects 2 and 3 we will explore the impact of these variants on oxidative stress in in vitro hESC models bearing patient variants, and the ability of compounds that manipulate RONS in these mutant cells to exacerbate or reverse aberrant cell morphology, differentiation and, in genome edited mouse models, promote successful neural tube closure (NTC). Building upon the results obtained in our original funding period, Project 1, in collaboration with Projects 2 and 3, rigorously applies next generation DNA sequencing, genome editing, animal modeling, protein chemistry, and transcriptomic approaches to illuminate the causes of human NTDs, with a goal to ultimately reduce their prevalence.

RISK GENES AND ENVIRONMENT INTERACTIONS IN NTDS ADMINISTRATIVE CORE: ABSTRACT Core A provides an anchor for the Program, assisting in grant administration and budget management as well as preparation of annual reports. It organizes annual meetings of the Internal and External Advisory faculty with Program investigators. Internal Advisory Board meetings will take place in Manhattan, while yearly External Advisory Board meetings will take place alternately in NY or TX. The Core will continue to schedule the monthly meetings of the project participants, which take place via videoconferencing and at times with in person participation of TX and OR members. It will organize and administratively support the periodic meetings in NY of Program investigators with those from TX and OR sites. Core A will coordinate training opportunities for Program investigators (students, postdocs, faculty). It will support collaborative experiments across Projects by facilitating the shipment of materials between NY, TX and OR. It will serve as the administrative link between the WCMC Genome Resources Core Facility (GRCF), the NY Genome Center and the laboratories at WCMC in New York, the University of Texas at Austin, Dell Pediatric Research Institute, and Oregon Health & Science University, Department of Genetics. These activities will continue to ensure the cohesiveness of this highly integrated Program.

Summary Our project brings together the large NewYork-Presbyterian (NYP) health system with its affiliated Medical Centers ? Weill Cornell Medicine (WCM) and the Columbia University Medical Center (CUMC), as well as the CUMC partner, Harlem Hospital (HH), a community-based public health facility, to achieve the aims of the national Precision Medicine Initiative (PMI). We will leverage our pre-existing Hospital Network Infrastructure to enroll at least 150,000 patients over 5 years from our ethnically diverse New York City population into a cohort named the NYC Precision Medicine Initiative cohort (NYC-PMI). We will collect and pre-process appropriate biospecimens from all participants including blood sample, saliva sample, and a urine sample. We will extract all electronic health record data for our participants, and provide standardized physical exam, survey data and all other phenotypic data as required for the national cohort to ensure harmonization with PMI data standards. Our HPO will also perform real-time epidemiological modeling of the characteristics of the participants enrolled and adjust enrollment to meet the goals of the National Cohort. Finally, we will actively engage community members, leaders, and organizations throughout New York City to ensure that the aims of the National PMI are appreciated by the broader community and that participants understand the initiative, its benefits and the importance of remaining engaged through their lifespan. We will bring into the national study a demographically diverse cohort that will feature a broad range of rare and common clinical disorders for which we provide expert care at our HPO. Thus, we will not only enroll the requisite number of participants and contribute diversity to the national cohort, but we will provide the clinical and research expertise necessary to make effective use of genomic data. We have long-standing experience with community engagement in research, and have long-standing experience collaboratively in cooperative NIH grant activities to ensure that the overall scientific aims of the PMI are achieved.

RISK GENES AND ENVIRONMENT INTERACTIONS IN NTDS Neural tube defects (NTDs) arise from a complex interplay of multiple genes and environmental exposures. In human populations, folic acid (FA) supplementation can prevent up to 70% of NTD occurrences- -including anencephaly and spina bifida?by as yet unknown mechanism(s). Nevertheless, FA fails to benefit at least a third of families and recent data suggest that in some specific genetic contexts, FA may be deleterious to the developing embryo. Clearly, families would be far better served if their individual risks could be accurately assessed, including identification of which aspect of the FA metabolic pathway--or which supplement involving another pathway entirely--would provide the most benefit to them, so that NTD prevention strategies could be optimized according to individual genetic risk factors. This program aims to improve NTD risk assessment and prevention by integrating advanced human genomics with biological paradigms in humans and mice for identifying key gene-environment interactions. Project 1 (Ross PI with Finnell & Gross) has accumulated 200 whole genome sequences (WGS) from cases and 200 controls and has identified rare nonsense, frameshift and non-coding variants associated with spina bifida. In the renewal, we will employ a powerful high throughput method using molecular inversion probes (MIPs) to resequence a replication cohort of over 2,000 NTD cases. Cutting edge CRISPR-Cas9 dependent genome editing in hESCs and mice will probe the functional impact of identified variants on neuroepithelial cell polarity, proliferation, and the generation of reactive oxidative/nitrosative species (RONS). Project 2 (Gross PI with Ross & Finnell) will test the hypothesis that a major role for folate protection against NTD is to suppress the generation of RONS. They will employ a novel untargeted stable isotope method to trace folate-mediated 1-C trafficking in NTD-susceptible mouse models. In addition, they will employ a novel redoxome platform to quantify oxidatively-modified small molecules in NTD prone mice. With Projects 1&3, they will examine the impact of identified NTD associated human variants on cellular redox status and 1- C trafficking and the extent to which supplementation with small molecules can modulate these actions. Project 3 (Finnell PI with Gross & Ross) will examine the interaction of genetic variants and RONS to disrupt signaling pathways and cause cell damage during NT closure. They will test the ability of a human NTD-associated variant in NO synthase, NOS3, to increase ROS peroxynitrite in cells due to the phosphorylation of NOS3 on Ser633. It will test whether mitochondria are a major source of RONS during neurulation. Together, Projects 1, 2, & 3 will help define interactions of maternal/embryonic genetics, nutritional status and 1-C metabolism with NTD risk, using extensive human genomics, proteomics/metabolomics, and CRISPR-Cas9-dependent genome editing in hESCs, patient stem cells (iPSCs) and mice.

PROGENITOR REGULATION UNDERLYING CORTICAL INTERNEURON SPECIFICATION Inhibitory GABAergic interneurons modulate complex cortical circuit operation. Most cortical interneurons originate from medial ganglionic eminence (MGE) progenitors that express the transcription factors, NKX2.1 in the ventral MGE and NKX6.2 in the dorsal MGE. While excitatory principal neuron production has been extensively studied, understanding of interneuron genesis, particularly the behavior and regulation of MGE progenitors, remains very limited. The proposed project addresses this outstanding knowledge gap. Although mature cortical interneurons are highly diverse, primary decisions to adopt a glial or somatostatin (SOM+) or parvalbumin (PV+) expressing neuronal fate are made as progenitors in the MGE. Based on strong preliminary data from the Shi and Ross laboratories, we hypothesize that a tight spatial and temporal regulation of the behavior and gene expression properties of MGE progenitors is essential for proper production of interneurons destined for the cortex. The project encompasses two major goals: Aim 1 probes the functional interactions between progenitor cell polarity determinant, partition defective 3 (PARD3), and G1-phase active cell cycle proteins, cyclins D1 (cD1) vs. D2 (cD2), in regulating MGE cell division, testing 2 hypotheses: 1a. MGE progenitor division modes and dynamics are spatially and temporally regulated to generate proper PV+ and SOM+ interneuron numbers. Retroviral and MADM technologies with computational modeling will be used to determine spatial (dorsal vs. ventral) and temporal dynamics of MGE radial glial progenitor (RGP) and intermediate progenitor cell (IPC) division modes and interneuron output. 1b. Differential interactions between PARD3 and cD1 vs. cD2 coordinate MGE progenitor division mode and dynamics to regulate proper PV+ vs. SOM+ fates. Studies pursue differential interactions between PARD3 and cD2 vs. cD1 in governing division mode, dynamics, and cortical interneuron output of MGE RGPs and IPCs. Aim 2 explores the core molecular program regulating the spatial and temporal behavior of MGE RGPs and IPCs using 10X Genomics-based single cell RNA sequencing of wildtype, cD2?/?, cD1?/?, Pard3 cKO and Pard3cKO;cD2?/? double mutants. Hypothesis: MGE output depends on gene expression defining cD1 and cD2 dependent progenitor pools, their division mode and dynamics. Expression networks will be validated by histological and molecular manipulation, including CRISPR/Cas9 genome editing of candidates for key drivers of MGE progenitor specification and whose expression is altered in cD1 or cD2 and Pard3 mutant MGE. The project will address a substantial knowledge gap regarding cortical interneuron genesis and provides a fundamental framework for the spatial and temporal regulation of MGE progenitors, elucidating their division mode and dynamics, their interneuron output, and the underlying core program coordinating MGE progenitor division regulation and interneuron specification.

DNA TO PROTEINS: GENE REGULATION, PROTEIN EXPRESSION AND FUNCTION IN EPILEPSY Loss of function (LOF) mutations in hundreds of genes are associated with human epilepsy. However, the high frequency of sequence variation among individuals presents a challenge to ascribe missense variants as causing epilepsy. This highly multidisciplinary research team develops a modular platform approach to accelerate determination of the functional, pharmacological, neuronal network and whole animal consequences of genetic variants of uncertain significance (VUS) encountered in patients with a range of epilepsy types. The ultimate goal is to devise strategies for establishing genetic diagnostic criteria and identifying potential targets for intervention. To this end, Project 1 will join Project 2 investigators in the interrogation of multiple VUS in 1 to 2 frequently encountered, non-ion channel encoding epilepsy genes per year (up to 10 genes in 5 years). Project 1 employs moderate-throughput assessment of 12-15 VUSs per gene, examined in 3 Milestones: Milestone 1 will assess in silico and in vitro model systems for VUS functional analyses to: 1a. with the gene and variant curation core (GVCC), generate and assess In silico tools to improve modeling of VUS pathogenicity; 1b. use 2-dimentional (2-D) cultures of HEK293T cells in biochemical tests of each studied VUS to examine mutant protein stability, known protein interactions and aggregation; 1c. test the impact of a VUS on subcellular localization, protein trafficking and/or post translational processing. Milestone 2 will establish assays of cell autonomous effects in vitro. The human epilepsy tool core (HETC) will inactivate selected genes and generate human pluripotent stem cells (hPSC) that express dox- induced Neurogenin 2 (iNeurons) or ASCL1 & DLX2 (iGNs) for direct induction of neurons. Knockout neurons will be made to overexpress WT or VUS containing protein and their ability to rescue LOF phenotypes in knockout cells will be examined in 2-D cultures through assessing progenitor proliferation, cell survival, potential for differentiation and gene expression using cell morphology, motility, and RNAseq. Milestone 3. Functional impact of VUS on synapse formation and network properties. These iNeurons (e.g. expressing WT or VUS-containing STXBP1) will be examined for synapse formation, turnover (plasticity), transport, and firing properties using multi-electrode arrays (MEA). These 2-D cultures will screen cells differentiated toward either glutamatergic excitatory or GABAergic inhibitory phenotypes, picking the most promising lines in Project 1 that Project 2 will use in cell systems of mixed cell types in 2-D and 3-D. As a whole, this U54 delivers: 1) multiple optimized, cross-validated hPSC platforms to interrogate epilepsy genes; 2) in vitro and in vivo determination of human VUS pathogenicity for up to 10 non-ion channel epilepsy genes; 3) optimized models for each epilepsy gene; and 4) platforms for future precision therapeutic testing.!