Z. Josh Huang - US grants

Early postnatal experience can profoundly influence the structure and function of the mammalian neocortex. The cellular and molecular mechanisms underlying the critical period plasticity in visual cortex will provide insight into the development of other sensory and cognitive functions, learning and memory, rehabilitation, and regeneration. It has been suggested that the development of GABAergic inhibitory mechanisms may initiate and drive the critical period for ocular dominance (OD) plasticity in visual cortex. GABAergic interneurons are morphologically and physiologically diverse and control cortical excitability at precise spatial and temporal domains. We hypothesize that the functional maturation of distinct classes of GABAergic circuits allows enhanced GABAergic synaptic transmission during the critical period and contributes to OD plasticity. We will use cell type-specific promoters and bacterial artificial chromosome transgenics in mice to label specific classes of GABAergic interneurons in living tissue. We will then characterize the functional maturation of such GFP labeled interneurons in cortical slices using electrophysiology and two-photon imaging. Furthermore, we will alter the expression of the GABA synthetic enzyme GAD65 in two classes of GABAergic circuits: the parvalbumin- containing basket interneurons and the somatostatin- containing bitufted interneurons. We will then examine the consequences of such cell type-specific manipulation of GABAergic transmission on the critical period of OD plasticity using single unit recording in visual cortex. Maturation of cortical GABAergic circuitry is in turn strongly influenced by visual experience. We hypothesize that the brain-derived neurotrophic factor (BDNF) is a key molecular signal that promotes the normal maturation of GABAergic interneurons and retards their development during visual deprivation. We will examine whether BDNF overexpression in visual cortex in transgenic mice can rescue the effects of dark rearing on the maturation of GABAergic circuits and on visual function using immunohistochemistry and electrophysiology. A genetic approach to the function and development of specific classes of GABAergic circuits will contribute to our understanding of the microarchitecture and information processing in normal neocortex and its deregulated states such as epilepsy.

DESCRIPTION (provided by applicant): GABAergic transmission regulates neuronal excitability, integration, plasticity, and has been implicated in the generation and entrainment of oscillatory population activity patterns in mammalian brain during perception, learning, and cognition. A salient feature of GABAergic innervation is the targeting of specific classes of GABAergic synapses to restricted subcellular compartments of principal neurons (dendrite, soma, and axon initial segment-AIS). Such spatial organization of inhibitory synapses contributes to the temporal precision of GABAergic regulation, yet the underlying mechanism is almost entirely unknown. We hypothesize that subcellular localization and function of L1 family immunoglobulin cell adhesion molecules in principal neurons and glia cells constitutes a set of common molecular code, which directs the subcellular organization of distinct classes of GABAergic synapses along principal neurons through both permissive and repulsive signaling. Combining GABAergic cell type specific promoters, bacterial artificial chromosome transgenic mice, and high resolution imaging, we have developed both in vivo and in vitro methods to visualize and genetically manipulate specific classes of interneurons and to test our hypothesis. In particular, we will examine the role of neurofascin and CHL1 in targeting GABAergic synapses to soma-AIS and dendrites of principal neurons both in cerebellum and neocortex. Aberrant GABAergic function is correlated with states of mental illness. "Subtle" defects in cortical GABAergic connectivity, including subcellular synapse targeting, have been implicated in devastating neurological and psychiatric disorders such as epilepsy and schizophrenia. Mutations in L1 and CHL1 genes have also been linked to mental retardation, aphasia, and Tourette syndrome. The establishment of a causal link between L1CAMs and construction of GABAergic circuits should provide a new perspective for understanding the molecular pathology of these mental illnesses and for treatment strategies.

Description (Provided by Applicant): GABAergic neurons regulate nearly all aspects of neural communication and computation in diverse brain regions and circuits. In addition, GABA signaling profoundly influences the development, maturation, and plasticity of the nervous system. GABAergic dysfunctions have been implicated in diseases as diverse as epilepsy, Huntington's disease, autism and schizophrenia. For decades, the heterogeneity and complexity of the GABAergic network has hampered progress in understanding their development and function. Genetically engineered mice provide an ideal system to study the GABAergic neurons, but tools for these studies are thus far limited. What is particularly needed are lines of mice in which genetic manipulations can be performed in specific classes of GABAergic neurons in restricted brain regions during a defined developmental window. We propose to achieve this goal using the Cre-loxP based binary genetic system. In the first two components of this grant (Project A&B), we will generate up to 20 driver lines expressing Cre or inducible form of Cre recombinase in different classes GABAergic neurons and their progenitors. In addition, we will construct a new generation of Cre-activated reporter mice at the Rosa26 locus to achieve high level GFP expression by incorporating the Gal4-UAS amplification cassettes. All driver and reporter lines will be generated in the C57BL/6 strain. In the third component (Project C), we will characterize and validate these driver and reporter lines and establish a web-based platform for disseminating the mice, related reagents, and data obtained from the mice to other investigators. These GABAergic Cre drivers and related reporter lines will significantly accelerate progress in understanding nearly all aspects of the normal development and function of the GABAergic system, and the etiology of a variety of debilitating brain diseases.

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (08) Genomics and specific Challenge Topic, 08- MH-103: Understanding the genomic risk architecture of mental disorders. Rett syndrome (RTT), caused by mutations in the X-linked gene encoding methyl-CpG-binding protein 2 (MeCP2), is arguably the best characterized of the autism spectrum neurodevelopmental disorders. RTT is hypothesized to result from inappropriate neuronal maturation, altered synaptic connectivity and plasticity, possibly through abnormal experience-dependent synapse development and maintenance. However, the biological function of MeCP2 and the pathogenic mechanisms of MeCP2 mutations remain unclear. Current evidence indicates that modulation of transcription is a major component of MeCP2 function. The genetic architecture of MeCP2-mediated gene regulation in the brain is complex, involving both cell autonomous and circuitry mechanisms, direct transcriptional targets and subsequent compensatory changes, and is dependent on developmental stage and postnatal experience. Therefore, characterizing altered gene expression profiles in relevant neuron types, brain regions, and developmental stages is essential for understanding the pathogenic mechanism of RTT. However, a major challenge in the analysis of gene expression in mammalian brain is the extraordinary cellular heterogeneity. We have developed a cell type-based Nucleic acid ImmunoPrecipitation technique (cNIP) to purify mRNA and miRNA from distinct cell types in the mouse brain. We have implemented cNIP by Cre/loxP-regulated expression of epitope-tagged polyA- binding protein (PABP, for mRNA) or argonaute2 (AGO2, for miRNA) in specific cell types. Here we propose to apply this technique to study mRNA and miRNA profiles in major classes of glutamatergic and GABAergic neurons in the motor and cognitive areas of the mouse neocortex at 3 stages of postnatal development. We will then examine the alterations in gene expression profiles in these neurons in germline MeCP2 mutant mice. We will further combine cell type-specific manipulation of MeCP2 and cell based gene expression analysis to distinguish the cell autonomous and non-autonomous action of MeCP2. Our cell based genomic approach will establish a new experimental paradigm to study the genetic architecture of MeCP2 mutations which can be applied to neurodevelopmental disorders in general. Simultaneous analysis of mRNA and miRNA profiles will generate a comprehensive molecular portrait of the relevant cell types and their developmental trajectories. Because of the increasingly well-defined role of these neuron populations in neural synchrony and network oscillations, the rich molecular information can be readily "plugged in" to the functional units of neural circuits, linking genetic mutations and altered gene networks to neural networks, brain dynamics, and cognitive dysfunction. PUBLIC HEALTH RELEVANCE: We will develop novel genetic and genomic technology and use mouse models to study the pathogenic mechanism of RTT syndrome, one of the best characterized of the autism spectrum neurodevelopmental disorders.

DESCRIPTION (provided by applicant): GABA-mediated inhibition is crucial for the function and plasticity of neural circuits in neocortex, but the cellular diversity of the GABAergic system has been resistant to conventional anatomical, physiological, and genomic approaches. For example, maturation of inhibitory circuitry in primary visual cortex (V1) promotes the development of ocular dominance (OD) plasticity and its critical period, but the cellular and molecular mechanisms underlying the developmental and experience-dependent maturation of GABA interneurons remain poorly understood. Analysis of gene expression profiles should provide fundamental insights into this issue, but the heterogeneity of GABA interneurons has precluded such studies. Here we propose a genetic strategy to implement a novel method for cell type-based analysis of gene expression in GABAergic system and in complex brain tissues in general. Using Cre/loxP-regulated gene expression strategy, we will generate knockin mice expressing an epitope (FLAG)-tagged polyA binding protein (PABP) in different classes of interneurons. Actively translated mRNAs from interneurons in V1 will be harvested by co-immunoprecipitation against the FLAG peptide and subjected to microarray analysis. Three major classes of interneurons will be analyzed during the critical period of OD plasticity. Since the critical period can be either accelerated or delayed by BDNF (brain-derived neurotrophic factor) overexpression or dark-rearing (DR), respectively, the same cell types will be analyzed in BDNF transgenic and dark-reared mice. We aim to identify genes in specific cell types whose expression 1) correlate with the progression of critical period, 2) are regulated by BDNF and DR in a manner that corresponds to alterations in critical period. These studies will provide a comprehensive picture of transcriptomes in defined GABAergic cell types during the critical period, unravel the molecular mechanisms which direct experience-dependent maturation of inhibitory interneurons, and guide future experiments to examine specific cellular processes. Because cell types are functional units of neural circuits, this approach will 1) substantially increase the sensitivity for detecting alterations of gene expression in complex brain tissues, 2) allow meaningful interpretation of gene expression data in the context of neural circuit development and function, 3) greatly enhance the power of gene expression analysis in system neuroscience and in mouse model of brain disorders. PUBLIC HEALTH RELEVANCE: Here we proposed to establish a cell type-based genetic strategy to study gene expression profiles in mouse brain. This method will greatly enhance the sensitivity and explanatory power of genomic studies of mouse model of brain disorders, such as Rett Syndrome, schizophrenia, and autism.

DESCRIPTION (provided by applicant): In mammalian cerebral cortex, GABAergic inhibitory interneurons regulate the functional organization of neural circuitry. Inhibitory interneurons consist of diverse classes with distinct morphology, connectivity patterns, and physiological properties. The stereotypy and specificity in cortical interneurons suggest stringent genetic programs in their construction and assembly. Understanding the development of GABA interneurons is necessary to gaining a coherent knowledge on the assembly cortical circuits. Although much progress has made in understanding the early development of cortical interneurons, from their generation in the ventral telencephalon to their long distance migration into the cortex, it is still unclear how distinct classes of interneuron are specified and delivered to appropriate cortical areas and layers. Furthermore, little is known about how interneurons are integrated into cortical circuitry. A key obstacle is the lack of method and strategy that allow the developmental history of any well-defined class of interneurons to be tracked from their origin to their integration into cortical circuits. We have undertaken a systematic genetic approach to target major classes of cortical interneurons. In particular, we have genetically captured chandelier cells (CHCs), the most distinctive class of cortical interneurons that exclusively innervate pyramidal cells at axon initial segments, the site of action potential generation. CHCs are thus likely the most powerful cortical neurons that exert decisive control over pyramidal cell firing, thereby dynamically configure neural ensembles. However, current knowledge on CHCs is poor, and their origin and development are almost entirely unknown. Because of their exceptional stereotypy and specificity, genetic capture of CHCs establishes a powerful experimental paradigm for studying their entire developmental history. We will examine three developmental milestones of CHCs: origin, settlement into specific cortical lamina, and massive pruning during circuit integration. Using genetic engineering, fate mapping, in vivo imaging, and electrophysiology, we will achieve a high resolution description of these key events, and begin to explore the underlying molecular mechanisms. We aim to establish a cell type-based experimental paradigm that will longitudinally integrate key developmental steps in the larger context of making and integrating CHCs into cortical circuits. Deficiencies in CHCs have been implicated in several brain disorders such as epilepsy and schizophrenia. Genetic analysis of CHCs not only will provide a key entry point to understanding the assembly of neocortical circuitry but also will shed light into the pathogenic mechanisms of neuropsychiatric disorders and suggest new strategies for therapy.

DESCRIPTION (provided by applicant): Genetic targeting of cortical pyramidal neuron subtypes in the mouse Abstract A key obstacle to studying the development, organization, and function of neural circuits in the cerebral cortex is the stunning diversity of neuron types and a lack of comprehensive knowledge about their basic biology. The problem of neuronal diversity and identity in the cortex is fundamental, transcending developmental and systems neuroscience, and lies at the heart of defining the biology of cognition and psychiatric disorders. Glutamatergic pyramidal neurons (PyNs) constitute ~80% of cortical neurons, are endowed with large capacity for information coding, storage, plasticity, and carry the output of cortical computation. PyNs consist of diverse subtypes based on their specific laminar locations, axonal projection patterns, and gene expression profiles. Subsets of PyNs form multiple and hierarchical subnetworks of information processing, with distinct output channels to cortical and subcortical targets that subserve sensory, motor, cognitive and emotional functions. Importantly, PyN subtypes are differentially affected in various neuropsychiatric and neurodegenerative disorders. However, the severe lack of specific and effective genetic tools for studying PyNs has hampered progress in understanding cortical circuits. We propose to build a comprehensive genetic tool set for major PyN subtypes in the mouse through a joint project led by Dr. Josh Huang at Cold Spring Harbor Laboratory and Dr. Paola Arlotta at Harvard University with key collaboration from Dr. Hongkui Zeng at the Allen Institute for Brain Science. We have discovered a set of specific and combinatorial markers that distinguish major PyNs subtypes. We will use intersection, subtraction, and inducible strategies to target PyN subtypes. Aim 1 will generate ~25 knockin Cre and Flp driver lines that target major subclasses and lineages of pyramidal neurons. Aim 2 will generate multiple intersectional and subtractive reporters that are broadly useful for labeling distinct neuronal subtypes. Aim 3 will characterize the specificity of drivers, and organize and display data and resource in public databases. We will combine anatomical tracing with mRNA in situ and immunocytochemistry to determine the specificity of genetic targeting. We will use high- throughput and high- resolution pipeline at the Allen Institut to characterize PyN subtype labeling and axon projections. We will deposit all tools and reagents in major repositories (JAX) that are publically accessible (Allen Brain Atlas website). Genetic targeting will provide entry points to cortical circuits by integrating the full range of modern technologies and facilitate a systematic and comprehensive analysis of PyNs, from cell fate specification to circuit integration, connectivity, and function in cortical processing and behavior. These genetic tools will further provide sensitive probes to pathogenic mechanisms in models of brain disorders including autism, schizophrenia, bipolar and ALS, epilepsy, Alzheimer's, dementia, and may yield cell and molecular targets for therapeutic intervention. Although this grant is not hypothesis-driven as a traditional R01, it is certainly hypothesis-enabling for many future R01s to elucidate the fundamental role of the cerebral cortex in the larger framework of CNS architecture and function. 1

DESCRIPTION (provided by applicant): Mutations in the Methyl-CpG binding protein 2 gene (MeCP2) cause Rett syndrome, an autism spectrum disorder. RTT is hypothesized to result from deficient neuronal maturation and plasticity, possibly through abnormal experience-dependent synapse development and maintenance. MeCP2 has been implicated in chromatin and transcription regulation through binding to methyl-cytosines, which includes 5-methylcytosine (5mC) as well as 5-hydroxymethylcytosine (5hmC). While 5mC is generally viewed as a silencing mark, 5hmC might represent methylation dynamics and play complex roles in gene regulation. However, the genomic distributions of 5mC and 5hmC in brain cells are poorly characterized, and it is unclear how MeCP2 might interpret 5mC and 5hmC patterns, thereby influencing transcription. It remains controversial whether MeCP2 is primarily a transcriptional repressor that modulates gene-specific targets or act globally in chromatin regulation. Identifying the transcriptional impact is a critical step toward understanding the mechanism of MeCP2 function. Characterizing altered transcription in relevant brain regions, neuron types, developmental and physiological context in mouse models is necessary for unraveling the pathogenic mechanism of RTT. A key challenge in studying the role of MeCP2 in gene regulation in the brain is cellular heterogeneity. For example, it has been difficult to achieve high-resolution mapping of methylome in defined neuron types. Further, nerve cells modify their epigenomes and transcriptomes during development and in response to neuronal input. Thus an additional challenge is to examine functionally relevant cells in an appropriate developmental and plasticity context. We have developed methods and experimental systems for cell-based genomic analysis and for studying MeCP2 in a well established paradigm of cortical plasticity. Our General Hypothesis is that by tracking genome wide 5mC and 5hmC distributions and dynamics, MeCP2 regulates chromatin structures and gene transcription in a cell type- and cell state-dependent manner during experience-dependent neuronal maturation. We will apply cell-based analysis of DNA methylome (including 5mC and 5hmC) and transcriptome to examine the relationship among these profiles in cortical glutamatergic and GABAergic neurons during postnatal maturation. We will then examine the impact of MeCP2 mutations on methylomes and transcriptome in these neurons. We will further examine whether MeCP2 functions as an activity-regulated brake of experience-driven maturation of parvalbumin-positive GABA interneurons, which time the onset and progression of the critical period plasticity in primary visual cortex. Combining cell specificity, base resolution analysis of methylomes and their impact on transcriptomes in a well-defined context of neural development, these studies will provide insight into the regulatory relationships among cytosine methylation, MeCP2 function and gene expression, a fundamental issue in epigenetic regulation of the brain. We aim to reveal the developmental trajectory and genetic architecture of MeCP2 mutation and suggest strategies for intervention for RTT.

DESCRIPTION (provided by applicant): Mutations in the Methyl-CpG binding protein 2 gene (MeCP2) cause Rett syndrome, an autism spectrum disorder. RTT is hypothesized to result from deficient neuronal maturation and plasticity, possibly through abnormal experience-dependent synapse development and maintenance. MeCP2 has been implicated in chromatin and transcription regulation through binding to methyl-cytosines, which includes 5-methylcytosine (5mC) as well as 5-hydroxymethylcytosine (5hmC). While 5mC is generally viewed as a silencing mark, 5hmC might represent methylation dynamics and play complex roles in gene regulation. However, the genomic distributions of 5mC and 5hmC in brain cells are poorly characterized, and it is unclear how MeCP2 might interpret 5mC and 5hmC patterns, thereby influencing transcription. It remains controversial whether MeCP2 is primarily a transcriptional repressor that modulates gene-specific targets or act globally in chromatin regulation. Identifying the transcriptional impact is a critical step toward understanding the mechanism of MeCP2 function. Characterizing altered transcription in relevant brain regions, neuron types, developmental and physiological context in mouse models is necessary for unraveling the pathogenic mechanism of RTT. A key challenge in studying the role of MeCP2 in gene regulation in the brain is cellular heterogeneity. For example, it has been difficult to achieve high-resolution mapping of methylome in defined neuron types. Further, nerve cells modify their epigenomes and transcriptomes during development and in response to neuronal input. Thus an additional challenge is to examine functionally relevant cells in an appropriate developmental and plasticity context. We have developed methods and experimental systems for cell-based genomic analysis and for studying MeCP2 in a well established paradigm of cortical plasticity. Our General Hypothesis is that by tracking genome wide 5mC and 5hmC distributions and dynamics, MeCP2 regulates chromatin structures and gene transcription in a cell type- and cell state-dependent manner during experience-dependent neuronal maturation. We will apply cell-based analysis of DNA methylome (including 5mC and 5hmC) and transcriptome to examine the relationship among these profiles in cortical glutamatergic and GABAergic neurons during postnatal maturation. We will then examine the impact of MeCP2 mutations on methylomes and transcriptome in these neurons. We will further examine whether MeCP2 functions as an activity-regulated brake of experience-driven maturation of parvalbumin-positive GABA interneurons, which time the onset and progression of the critical period plasticity in primary visual cortex. Combining cell specificity, base resolution analysis of methylomes and their impact on transcriptomes in a well-defined context of neural development, these studies will provide insight into the regulatory relationships among cytosine methylation, MeCP2 function and gene expression, a fundamental issue in epigenetic regulation of the brain. We aim to reveal the developmental trajectory and genetic architecture of MeCP2 mutation and suggest strategies for intervention for RTT.

? DESCRIPTION (provided by applicant): Multiple NIH supported neuroscientists at Cold Spring Harbor Laboratory form a highly integrated community studying rodent neural circuit development and function and models of neuropsychiatric disorders. We integrate multiple approaches and techniques from mouse genetic engineering to state of the art neuroimaging, electrophysiology, and behavior analysis. A key component of neural circuit study is to visualize, reconstruct, and quantify neuronal morphology and connectivity at cellular and subcellular resolution and in large brain volume. Semi-automated fluorescence microscopy combined with Neurolucida serial reconstruction, quantification, and display has proven to be an effective system. Our current work station was acquired over 12 years ago, with very limited functionality and capacity. We are requesting funds to purchase a Neurolucida BrainMaker Imaging System from MBF Bioscience for cell resolution whole brain imaging and reconstruction. This will allow us to continue to carry out cutting edge neural circuit research and support multiple NIH funded researchers.