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Deep single-cell RNAseq of Gpnmb+Clec7a+ microglia from postnatal day 7 cerebellum

ABSTRACT: Deep single-cell RNAseq of Gpnmb+Clec7a+ microglia from postnatal day 7 cerebellum

PROVIDER: PRJNA507268 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8249570_1.fastq.gz	Fastqsanger.gz
	SRR8249570_2.fastq.gz	Fastqsanger.gz
	SRR8249580_1.fastq.gz	Fastqsanger.gz
	SRR8249580_2.fastq.gz	Fastqsanger.gz
	SRR8249590_1.fastq.gz	Fastqsanger.gz

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Deep single-cell RNAseq of Gpnmb+Clec7a+ microglia from postnatal day 7 cerebellum

Project description:We generated single-cell RNAseq profiles of 143 microglia, sorted in the gate CD45lowCD11+Gpnmb+Clec7a+, from postnatal day 7 cerebellum to validate the newly identified “proliferative region-associated microglia (PAM)” (Gpnmb and Clec7a are PAM surface markers). Single cells were FACS index sorted followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). These cells showed characteristic PAM gene expression and clustered together with other PAM cells sequenced in the same study.

2018-12-31 | GSE123024 | GEO

Deep single-cell RNAseq of postnatal day 7 microglia from wild type and Trem2 knockout brains

Project description:We generated single-cell RNAseq profiles of 369 microglia (183 from wild type and 186 from Trem2 knock-out), sorted in the gate CD45lowCD11+ or CD45lowCD11+Gpnmb+Clec7a+ (PAM enrichment), to compare gene expression of wild type vs. Trem2 knock-out microglia on the postnatal day 7. Single cells were FACS index sorted from the whole brain followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). A total of 334 cells passed quality control for data analysis. Microglia in the Trem2 knock-out contained a similar PAM population with characteristic gene expression, suggesting that the presence of early postnatal PAM do not depend on TREM2.

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Human VCP mutant ALS/FTD microglia display immune and lysosomal phenotypes independently of GPNMB

Project description:Background: Microglia play crucial roles in mediating neuronal homeostasis but have been implicated in contributing to amyotrophic lateral sclerosis (ALS). However, the role of microglia in ALS remains incompletely understood. Methods: Here, we generated highly enriched cultures of VCP mutant microglia derived from human induced pluripotent stem cells (hiPSCs) to investigate their cell autonomous and non-cell autonomous roles in ALS pathogenesis. We used RNA-sequencing, proteomics and functional assays to study hiPSC derived VCP mutant microglia and their effects on hiPSC derived motor neurons and astrocytes. Results: Transcriptomic, proteomic and functional analyses revealed immune and lysosomal dysfunction in VCP mutant microglia. Stimulating healthy microglia with inflammatory inducer lipopolysaccharide (LPS) showed partial overlap with VCP mutant microglia in their reactive transformation. LPS-stimulated VCP mutant microglia displayed differential activation of inflammatory pathways compared with LPS-stimulated healthy microglia. Conserved gene expression changes were identified between VCP mutant microglia, SOD1 mutant mice microglia, and postmortem ALS spinal cord microglial signatures, including increased expression of the transmembrane glycoprotein GPNMB. While knockdown of GPNMB affected inflammatory and phagocytosis processes in microglia, this was not sufficient to ameliorate cell autonomous phenotypes in VCP mutant microglia. Secreted factors from VCP mutant microglia were sufficient to activate the JAK-STAT pathway in hiPSC derived motor neurons and astrocytes. Conclusions: VCP mutant microglia undergo cell autonomous reactive transformation involving immune and lysosomal dysfunction that partially recapitulate key phenotypes of microglia from ALS models and post mortem tissue and are independent of GPNMB. VCP mutant microglia elicit non cell autonomous responses in motor neurons and astrocytes involving the JAK-STAT pathway.

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Project description:Recently we demonstrated that amoeboid microglia in white matter regions are essential for proper oligodendrocyte homeostasis and myelinogenesis in the first postnatal week of mice. Amoeboid microglia in the corpus callosum change their activation profile already within few days after postnatal day (P)7 and microglia of the cerebellum show similar features to callosal microglia. Here we expanded our previous transcriptional analysis and performed bulk RNA sequencing of microglia during development in a detailed way in P7, P10 and P42 microglia from corpus callosum, cortex and cerebellum. The goal of this study was to identify a specific gene profile for both, white matter and grey matter microglia during development.

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Single-Cell Transcriptomes Reveal Molecular Specializations of Neuronal Cell Types in the Developing Cerebellum

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RNA Sequencing of postnatal mouse Math1-Cre Sufu flox/- cerebellum

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Microarray gene expression profiling of a fibrosarcoma GPNMB-induced cell line MCA-1-GPNMB at basal condition and in the form of spheroids

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Transcription profiling by array of mouse Ts1Cje (mouse model of Down syndrome) and euploids murine cerebellum during postnatal development

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