2013 — 2017 |
Madisen, Linda Tasic, Bosiljka |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Temporal, Cell Type- and Locus-Specific Epigenetic Control in Transgenic Mice
DESCRIPTION (provided by applicant): Mammalian organs are built of a variety of intermingled cell types, the full extent and diversity of which are unknown. Specification and maintenance of cell identity, from a single cell embryo to any terminally differentiated cell such as an adult neuron, rely heavily on epigenetic mechanisms that act upon the genome to enable or prevent expression of specific sets of genes. In doing so, epigenetic regulation of gene expression enables a single genome to encode a diverse array of cell types in a multicellular organism. Epigenetic modifications ensure that a cell proceeds through a limited set of gene expression possibilities, and once differentiated, that a cell maintains its phenotype throughout its lifetime. As a consequence, disruption of epigenetic modification can result in a variety of diseases, including neurodevelopmental and psychiatric diseases, and cancer. We propose to develop a set of mouse transgenic tools that have the potential to transform the way epigenetic modifications can be studied and understood in this mammalian model system. The new tools will provide regulated expression of epigenetic modifiers in a variety of cell types and their progenitors, while permanently marking these cells or their progeny for examination at any later time point. Moreover, we will develop technology, in which a single locus in the mouse genome can be subjected to epigenetic perturbations in specific cells and at specific times in the animal's life. We will employ these tools to gain understanding of cell-type identity in the cortex as well as the mechanisms responsible for generating and maintaining this identity. Epigenetic regulators have been implicated in a number of brain diseases, and the tools we are developing will facilitate modeling or testing specific hypotheses that relate to perturbations of epigenetic phenomena. The insights gained may also provide guidance for the generation of specific cell types in vitro, and directions for 'repurposing' certain cell types in vivo. Although the focus of ur studies will be on the mouse brain, the versatile and modular design of our tools will enable their use in studying development, function or disease in any other tissue or cell type. We will ensure easy access to all tools we generate to maximize their impact on understanding various aspects of mammalian biology.
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2019 |
Tasic, Bosiljka |
RF1Activity Code Description: To support a discrete, specific, circumscribed project to be performed by the named investigator(s) in an area representing specific interest and competencies based on the mission of the agency, using standard peer review criteria. This is the multi-year funded equivalent of the R01 but can be used also for multi-year funding of other research project grants such as R03, R21 as appropriate. |
Cell Class- or Type-Specific Viruses For Brain-Wide Labeling and Neural Circuit Examination
ABSTRACT Experimental access to specific cell classes or types in the brain is essential for elucidating their roles in neural circuit function. Single cell transcriptomics has enabled unprecedented definition of cell types at the molecular level and has uncovered numerous marker genes, which can be used to generate genetic tools for access to specific cell populations. However, high-precision genetic tools for experimental access to specific cell-types still rely on genome modification and subsequent crossing of animals harboring different transgenes to generate experimental animals. Specificity can also be achieved by stereotaxic injection of viruses, but this approach still usually requires a combination with transgenes, and produces only local infection which can result in significant expression variability between animals and can cause reactive gliosis. Animal crosses are laborious and inefficient, especially if more than two transgenes are needed to achieve specific cell-type labeling. We propose to develop a suite of enhancer viruses that can provide access to specific brain cell types or classes to the whole brain when delivered by retroorbital injections. The viruses will be endowed with specificity by containing enhancers defined experimentally from the combination of single-cell RNA-seq and single cell ATAC-seq data (Assay for Transposase-Accessible Chromatin with next generation sequencing). The viruses will be screened for specificity by several methods including whole-brain imaging, single-cell RNA-seq and multiplex FISH. Intersectional genetic approaches to further refine specificity and enable functional interrogation of specific cell types will also be established. DNA constructs, virus packaging techniques, recommended titers, and whole- brain expression data will be made publicly available.
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2020 |
Bernard, Amy Close, Jennie Leigh (co-PI) [⬀] Hawrylycz, Michael Keene, Christopher Dirk (co-PI) [⬀] Lein, Ed Nicovich, Philip Russell (co-PI) [⬀] Tasic, Bosiljka |
U19Activity Code Description: To support a research program of multiple projects directed toward a specific major objective, basic theme or program goal, requiring a broadly based, multidisciplinary and often long-term approach. A cooperative agreement research program generally involves the organized efforts of large groups, members of which are conducting research projects designed to elucidate the various aspects of a specific objective. Substantial Federal programmatic staff involvement is intended to assist investigators during performance of the research activities, as defined in the terms and conditions of award. The investigators have primary authorities and responsibilities to define research objectives and approaches, and to plan, conduct, analyze, and publish results, interpretations and conclusions of their studies. Each research project is usually under the leadership of an established investigator in an area representing his/her special interest and competencies. Each project supported through this mechanism should contribute to or be directly related to the common theme of the total research effort. The award can provide support for certain basic shared resources, including clinical components, which facilitate the total research effort. These scientifically meritorious projects should demonstrate an essential element of unity and interdependence. |
A Platform For Cell Type-Level Transcriptomic, Epigenomic and Spatial Interrogation of Alzheimer's Disease
ABSTRACT (OVERALL) Our understanding of the neuropathology in Alzheimer?s disease is crude and largely centered on characteristic deposition of a few pathological proteins. Catalyzed by the BRAIN Initiative, a new generation of molecular tools to characterize the transcriptome, epigenome and spatial organization of single cells in complex brain tissues is rapidly revolutionizing our understanding of the diversity of cell types and their selective genetic profiles. These tools are applicable to postmortem human brain tissues and promise to expand our understanding of the core cellular and molecular correlates and mechanisms underlying Alzheimer?s disease. The goal of the proposed Center is to bring together experts in Alzheimer?s disease research and large-scale molecular/anatomical brain mapping to modernize Alzheimer?s disease tissue banking methods, and to combine traditional and quantitative neuropathology with emerging single nucleus transcriptomics, single nucleus epigenomics and spatial transcriptomics technologies. Applied to clinically typical Alzheimer?s cases of varying severity in an iterative and adaptive design, these techniques are expected to identify increasingly refined molecular pathways associated with specific neuronal and non-neuronal cell types and yield valuable insights into cell-type selective vulnerability or resistance to pathology. This increased resolution of AD pathology in terms of cell types and molecular pathways should provide mechanistic insights and hypotheses on disease initiation and progression, which we aim to use to catalyze the AD research community through the creation of an open access data resource linked with other large-scale brain mapping efforts. This Center framework is designed to be extensible to additional data modalities and technological advances as well as broader cohorts representing Alzheimer?s disease subtypes and Alzheimer?s disease related disorders in the future.
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2021 |
Tasic, Bosiljka Zeng, Hongkui [⬀] |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Molecular and Anatomical Characterization of Cell Types in the Aging Mouse Brain
Project Summary One of the most fundamental questions in brain aging research is whether age-related alterations affect all brain regions equally, or whether some regions, and cell types within those regions, are more vulnerable to the effects of aging than others. Aging is associated with cognitive decline, and is reported to cause alterations in a variety of important cellular processes and in a variety of cell types (e.g., microglia, astrocytes, neurons). Broad classes of cells in affected brain regions are known to be selectively vulnerable to age-related neurodegenerative diseases, but the specific molecular mechanisms underlying this vulnerability are unclear. An essential prerequisite to understanding this selective vulnerability is to understand the detailed changes at cell type and circuit levels during the aging process. Cataloging brain cell types and their connectivity in normal aging brain is foundational to uncovering the mechanisms and therapeutic opportunities for age-related brain disorders. State-of-the-art single-cell technologies, in particular single-cell transcriptomics with its high dimensional molecular information, but also spatial transcriptomics, single-cell epigenomics and single-cell morphology, are providing transformative information about brain cell types at an unprecedented scale and resolution. We propose to utilize our well-established omics pipelines to characterize and classify cell types in 18 months old male and female C57BL/6J mice and compare the results with the extensive brain-wide datasets in young adult (~P56) mice already being generated in the current BRAIN Initiative Cell Census Network (BICCN). We will use single-nucleus transcriptomics and epigenomics to obtain a high-level survey of neuronal and non-neuronal cell classes/types across the entire mouse brain, and then an in-depth single-cell and spatial transcriptomic study in brain areas showing age-related changes and/or vulnerable to neurodegenerative diseases. We will utilize our imaging?based registration process to map all data into the Common Coordinate Framework (CCF), which allows accurate cross-age quantitative comparisons that will be crucial for uncovering age-related changes. By conducting concurrent single-cell gene expression and chromatin accessibility measurements in the same brain regions, and a detailed spatial transcriptomic map of the proportion and distribution of different cell types and specific molecular pathways, we will chart an integrated path towards gaining mechanistic insight underlying the cognitive decline in aging and age-related disease pathology.
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