Effect of LRP1 deletion in vascular mural cells and APOE gentotype on gene expression in mouse brains
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ABSTRACT:
PROVIDER: PRJNA933636 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23403975_1.fastq.gz | Fastqsanger.gz | |||
| SRR23403975_2.fastq.gz | Fastqsanger.gz | |||
| SRR23403976_1.fastq.gz | Fastqsanger.gz | |||
| SRR23403976_2.fastq.gz | Fastqsanger.gz | |||
| SRR23403977_1.fastq.gz | Fastqsanger.gz |
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Project description:In the study we show that a specific peripheral glial population, derived from boundary cap (BC) cells, constitutes a major source of mural cells for the developing vasculature. Using Cre-based reporter cell tracing and single cell transcriptomics, we show that BC cell derivatives migrate along the nerves and differentiate into pericytes and vascular smooth muscle cells in the skin. The switch from glial to mural molecular identity is initiated while the cells are still associated with nerves To further characterize this transition glial to vascular identity, we performed single cell transcriptomic analyses (scRNA-seq) on FACS-purified traced cells from dissociated E12.5 skin. Tomato-positive cells were isolated by FACS from embryonic skin at E12.5. Around 10,000 cells were loaded into one channel of the Chromium system using the V3 single cell reagent kit (10X Genomics) We analyzed 2527 single cell transcriptomes with a mean number of expressed genes per cell of 4,696. This study highlights the plasticity of BC derivatives and uncovers a novel, nerve-derived origin for skin mural cells.
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Project description:Many important cell types in adult vertebrates have a mesenchymal origin, including fibroblasts and vascular mural cells (pericytes and smooth muscle cells). Although their biological importance is undisputed, the level of mesenchymal cell heterogeneity within and between organs, while appreciated, has not been analysed in detail. Here, we compare single-cell transcriptional profiles of fibroblasts and vascular mural cells across four murine muscular organs: heart, skeletal muscle, intestine and bladder. We reveal gene expression signatures that demarcate fibroblasts from mural cells across these four as well as other organs and provide molecular signatures for cell subtype identification. Striking inter- and intra-organ heterogeneity and specialization were observed amongst the fibroblasts, primarily reflecting differences in the expression of extracellular matrix components. In comparison, mural cells appeared more homogenous. Fibroblast subtypes localize to discrete anatomical positions in all four organs, offering novel predictions about physiological function(s) and regulatory signalling circuits. Our data shed new light on the diversity and relationships between hitherto poorly defined classes of cells and provide a foundation for improved understanding of their roles in physiological and pathological processes.
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Project description:Many important cell types in adult vertebrates have a mesenchymal origin, including fibroblasts and vascular mural cells (pericytes and smooth muscle cells). Although their biological importance is undisputed, the level of mesenchymal cell heterogeneity within and between organs, while appreciated, has not been analysed in detail. Here, we compare single-cell transcriptional profiles of fibroblasts and vascular mural cells across four murine muscular organs: heart, skeletal muscle, intestine and bladder. We reveal gene expression signatures that demarcate fibroblasts from mural cells across these four as well as other organs and provide molecular signatures for cell subtype identification. Striking inter- and intra-organ heterogeneity and specialization were observed amongst the fibroblasts, primarily reflecting differences in the expression of extracellular matrix components. In comparison, mural cells appeared more homogenous. Fibroblast subtypes localize to discrete anatomical positions in all four organs, offering novel predictions about physiological function(s) and regulatory signalling circuits. Our data shed new light on the diversity and relationships between hitherto poorly defined classes of cells and provide a foundation for improved understanding of their roles in physiological and pathological processes.
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Project description:Purpose: Pericytes, the mural cells of blood microvessels, have come into focus as regulators of microvascular development and function, but due to paucity of defining markers, the identification and functional characterization of PC remain problematic, and reported data are often controversial. Here, we used a new approach for the isolation of mural cell from mouse brain in combination with RNA-sequencing (RNA-seq) and previously published vascular transcriptome data to assemble a state-of-the-art catalogue of brain mural cell-enriched gene transcripts. Methods: We isolated double positive cells from the brain of Pdgfrb-eGFP/NG2-DsRed transgenic mice using FACS. Cells were lysed, RNA extracted and sequenced with next-generation sequencing (NGS). For comparison, we also determined the transcriptome of brain microvascular fragments (containing both endothelial cells and mural cells) isolated by mechanical tissue disintegration, collagenase digestion and immune-panning using anti-CD31 antibodies coupled to magnetic beads. The reads were aligned to the Ensembl mouse gene assembly (NCBIM37) using Tophat2 software (version 2.0.4). The duplicated reads were removed using the picard tool (version 1.92). To identify the genes significantly enriched in the pericyte samples as compared with microvascular samples, statistical tests were performed using the Cufflinks tool (version 2.2.1) Results: The result showed that mRNA transcripts representing 856 different genes were enriched more than two-fold in FACS isolated Pdgfrb-eGFP/NG2-DsRed double positive cells compared with whole microvascular fragments (False Discovery Rate < 0.05) The RNA from three FACS sorted brain mural cell samples and three whole brain microvascular samples isolated from three animals were processed and sequenced on the Illumina HiSeq 2500 platform in the sequencing facility in Uppsala University.
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