2005 — 2007 |
Zhao, Guoyan |
F32Activity Code Description: To provide postdoctoral research training to individuals to broaden their scientific background and extend their potential for research in specified health-related areas. |
Regulatory Modules: Identification and Verification
DESCRIPTION (provided by applicant): Dissecting the transcriptional regulatory networks is essential for understanding development and the molecular basis of many diseases. Great progress has been made and the emerging view is that the presence of individual regulatory elements is rarely sufficient to explain spatial-temporal specific gene expression and regulatory elements usually are organized into functional units - modules. Modules control gene expression in a particular context independent of its position and orientation. Experimental identification of modules is often a laborious and expensive process. Computational approaches can be fast and inexpensive, however, the development of computational methods to identify modules is still in its infancy. The goal of the proposed research is to use C. elegans as a model system, to develop and validate computational strategies to identify regulatory modules in the genomic sequences. First, the regulatory region of a set of genes that are preferentially expressed in the muscle tissue of C. elegans, together with that of the orthologous genes in related species will be used to identify muscle-specific regulatory motifs. Several different computational approaches and various existing computational tools will be employed. Next, statistic analysis will be used to exploit the enrichment of certain combinations of motifs in muscle specific genes in comparison with the genome at large and to analyze the interactions among motifs. This will provide insight into the rules that govern the organization of cis-regulatory elements to form biologically active modules. The information will be used to develop computational tools to identify modules that control muscle - specific transcription. To validate computational predictions in vivo, GFP reporter gene constructs will be used to determine whether a gene is expressed in muscle tissue and to test putative regulatory modules. The results of the validation experiments will be used to refine and improve our algorithms. Although I will focus my efforts on muscle specific gene expression, I believe the approaches and tools I develop will be of general use for many other context-specific module identification. The computational tools I develop will be made freely available to the scientific community.
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2021 |
Xu, Jinbin Zhao, Guoyan |
R03Activity Code Description: To provide research support specifically limited in time and amount for studies in categorical program areas. Small grants provide flexibility for initiating studies which are generally for preliminary short-term projects and are non-renewable. |
Define Molecular Events Driving Selective Neuronal Death in Multiple Neurodegenerative Diseases by Snrna-Seq
Project Summary Despite decades of research, currently the mechanisms of neurodegeneration in Alzheimer?s disease (AD) and Parkinson Disease (PD) remain controversial and there are no therapies can prevent, slow, or halt disease progression. Neurodegenerative diseases have two fundamental general characteristics. 1) The pathology associated with the disease only affects particular neurons (?selective neuronal vulnerability?); 2) The pathology worsens with time and impacts more regions in a stereotypical and predictable fashion. The discovery of key pathways that regulate this differential susceptibility of neurons to degeneration holds great potential for the discovery of novel drug targets and the development of promising neuroprotective treatment strategies. However, the mechanisms underlying selective neuronal and regional vulnerability have been difficult to dissect because of our limited ability to distinguish different neuronal subpopulations. Loss of dopaminergic neurons in the SN is a hallmark of PD which underlies the parkinsonian motor symptoms such as rigidity and tremor. Neuronal loss also occurs in the SN of AD [8, 9], however, often without co-occurring parkinsonian motor symptoms. Dopaminergic neurons within the SN are highly heterogeneous [10] and the loss of the dopaminergic neurons in PD is heterogeneous across different axes [11-14]. It is unclear whether the same population of neurons were lost in AD and PD and whether the mechanisms of neuronal loss are shared between the two diseases. Neuroinflammation - activation of the neuroimmune cells (e.g. microglia) into proinflammatory states - are shared pathological contributors in AD and PD. However, the molecular identity of different microglia subpopulations and the role of neuroinflammation in the selective neuronal death remain unclear. Therefore, we propose to use single nucleus RNA-seq (snRNA-seq), an unbiased approach to identify and characterize distinct cell populations in tissues, to dissect the mechanisms underlying selective neuronal death. Specifically, our specific aims are: Aim 1: Characterize and validate cellular heterogeneity, cellular and transcriptomic changes of neuron and microglia from the SN brain tissues of AD, PD patients and age-matched controls. Aim 2: Dissect the mechanisms of cell composition and transcriptome dysregulation in AD and PD. Our study will provide 1) molecular markers and tools for targeted neuronal and microglia subpopulation isolation and manipulation; 2) better understanding of the dynamic change of different neuronal and microglia subpopulation, their transcriptomic changes and the putative regulatory mechanisms in AD and PD; 3) high- confidence new candidate genes and pathways as targets to develop effective immunotherapies or neuroprotective strategies.
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2021 |
Xu, Jinbin Zhao, Guoyan |
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. |
Dissect the Mechanisms of Selective Regional Vulnerability in Lewy Body Dementias Via Comparative Snrna-Seq Analysis
Project Summary Lewy body diseases (LBDs) are highly heterogeneous neurodegenerative disorders including Parkinson's disease (PD), Parkinson's disease dementia (PDD), and dementia with Lewy bodies (DLB). LBDs are characterized by the abnormal aggregation of the protein ?-synuclein in neuronal cell bodies (Lewy Body) and neurites which are currently considered to be the common cause of the diseases. Lewy Body deposition starts in the caudal brainstem of PD but in the neocortex of DLB cases. The regional differences of initial ?-synuclein deposition correlate with neuronal loss in the corresponding regions - dopamine neurons in the substantia nigra (SN) and neurons of unknown identity in the neocortex, and the unique clinical manifestations with a predominant motor symptom in PD whereas early dementia in DLB. Why some particular neurons and brain regions are affected at the disease onset, whereas the neighboring cells and regions not? This is a fundamental question in the field of neurodegenerative diseases that this proposal will address via novel genomics technologies and bioinformatics tools. In an initial pilot study, using single nucleus RNA-sequencing (snRNA-seq) analyses, we identified a novel disease-associated astrocyte (DAA) subpopulation and demonstrated that DAA contributed to increased inflammation, amyloid pathology, and neurodegenerative disease pathogenesis whereas parenchymal astrocytes had compromised functionality in both AD and PD brains. Additionally, we identified three microglia subpopulations that were similar to but with marker gene expression profiles distinct from the conventional resting (M0), M1, and M2 activated microglia. We observed deficient microglia functionality shared across all microglia subpopulations and uniquely up-regulated inflammatory pathways in PD suggesting common and PD-specific mechanisms of neurodegeneration. These data provide us with an exclusive opportunity to analyze the relationships between these glia subpopulations and selective regional and neuronal vulnerability in different diseases. In Aim 1, we will identify vulnerable neuronal types in the frontal cortex (FC) and SN of patients with PD, PDD, and DLB. In Aim 2, we will test the hypothesis that astrocyte/microglia dysfunction underlies the mechanism of the selective regional vulnerability of LBD. In Aim 3, we will test the hypothesis that dysregulated interactions between neurons and astrocytes/microglia underlie the mechanism of the selective neuronal vulnerability of LBD. Our study will provide deep insights into the molecular mechanisms of selective neuronal and regional vulnerability in LBDs. Besides, our study will provide molecular biomarkers and tools for neuron cell-type-specific protection and targeted astrocyte/microglia subpopulation isolation and manipulation. Furthermore, our study will provide molecular biomarkers for distinguishing PD, PDD, and DLB, which is very important but a considerable challenge today.
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