Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cell specific gene silencing of lipid-siRNA conjugates in the mouse central nervous system (CNS)

ABSTRACT: We developed a lipid-siRNA conjugate, termed EG18, that potentiates prolonged gene silencing throughout the CNS after injection into CSF. To help inform viable therapeutic targets, we used scRNAseq to determine cell-specific gene silencing. Here, we used an siRNA sequencing targeting Ppib and inject 15 nmol of either Ppib-EG18 or a non-targeting control (NTC)-EG18 into the lateral ventricles of adult mice. After 1 month, brains were dissociated into single cells and bead-sorted into Cd11b+ and Cd11b- populations. The Cd11b+ dataset contains microglia and macrophages, while the Cd11b- sample comprised a sampling of other isolated perivascular and parenchymal populations. scRNAseq revealed gene silencing activity across diverse cell populations in the parenchyma and at brain borders, which may provide new avenues for disease-modifying therapies.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Andrew Kjar

PROVIDER: E-MTAB-13964 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Microglia are innate immune cells of the brain that perform phagocytic and inflammatory functions in disease conditions. Transcriptomic studies of acutely-isolated microglia have provided novel insights into their molecular and functional diversity in homeostatic and neurodegenerative disease states. State-of-the-art mass spectrometric methods can comprehensively characterize proteomic alterations in microglia in neurodegenerative disorders, potentially providing novel functionally-relevant molecular insights that are not provided by transcriptomics. However, proteomic profiling of adult primary microglia in neurodegenerative disease conditions has not been performed. We performed quantitative proteomic analyses of purified CD11b+ acutely-isolated microglia adult mice in normal, acute neuroinflammatory (LPS-treatment) and chronic neurodegenerative states (5xFAD model of Alzheimer’s disease [AD]) using tandem mass tag mass spectrometry. Differential expression analyses were performed to characterize specific microglial proteomic changes in 5xFAD mice and identify overlap with LPS-induced pro-inflammatory changes. Our results were also contrasted with existing proteomic data from wild-type mouse microglia and from existing microglial transcriptomic data from wild-type and 5xFAD mice. Neuropathological validation studies of select proteins were performed in human AD and 5xFAD brains. Of 4,133 proteins identified, 187 microglial proteins were differentially expressed in the 5xFAD mouse model of AD pathology, including proteins with previously known (Apoe, Clu and Htra1) as well as previously unreported relevance to AD biology (Cotl1 and Hexb). Proteins upregulated in 5xFAD microglia shared significant overlap with pro-inflammatory changes observed in LPS-treated mice. Several proteins increased in human AD brain were also upregulated by 5xFAD microglia (Aβ peptide, Apoe, Htra1, Cotl1 and Clu). Cotl1 was identified as a novel microglia-specific marker with increased expression and strong association with AD neuropathology. Apoe protein was also detected within plaque-associated microglia in which Apoe and Aβ were highly co-localized suggesting a role for Apoe in phagocytic clearance of Aβ. We report the first comprehensive comparative proteomic study of adult mouse microglia derived from acute neuroinflammatory and AD models, representing a valuable resource to the neuroscience research community. We highlight shared and unique microglial proteomic changes in acute neuroinflammatory, aging and AD mouse models in addition to identifying novel roles for microglial proteins in human neurodegeneration.

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Cell specific gene silencing of lipid-siRNA conjugates in the mouse central nervous system (CNS)

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