Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1125395 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29462213_1.fastq.gz | Fastqsanger.gz | |||
| SRR29462213_2.fastq.gz | Fastqsanger.gz | |||
| SRR29462214_1.fastq.gz | Fastqsanger.gz | |||
| SRR29462214_2.fastq.gz | Fastqsanger.gz | |||
| SRR29462215_1.fastq.gz | Fastqsanger.gz |
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Project description:Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds (Cdh5)
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Project description:Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds (EC sorted)
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Project description:Endothelial cells (ECs) display organ- and tissue-specific heterogeneity. In the eye, the retinal and choroidal vascular beds are distinct networks with different morphological and functional features with the former representing a tight barrier and the latter, a permeable fenestrated vasculature. Given that retinal health critically relies on the function of these vascular beds and that their dysfunction is implicated in a variety of retinal diseases, a molecular understanding of both physiological and pathophysiological characteristics of these distinct vasculatures is critical. Given their interspersed anatomic distribution among parenchymal cells, the study of EC gene expression, in vivo, has been hampered by the challenge of isolating pure populations of ocular ECs in sufficient quantities for large-scale transcriptomics. To address this challenge, we present a methodological and analytical workflow to facilitate inter-tissue comparisons of the in vivo EC translatome isolated from choroid, retina, and brain using the Cre-inducible NuTRAP flox construct and two widely-used endothelial cre mouse lines, constitutive Tie2-Cre and Tamoxifen-inducible Cdh5-CreERT2, which express EGFP and mCherry tags for cell-specific isolation of nuclei and ribosomes. Within each model, inter-tissue comparison of TRAP-RNAseq enrichment (TRAP translatome vs input transcriptome) showed tissue-specific gene enrichments with differential pathway representation. For each mouse model, inter-tissue comparison of the EC translatome (choroid vs brain, choroid vs retina, and brain vs retina) showed over 50% overlap of differentially expressed genes (DEGs) between the three paired comparisons, with differential pathway representation for each tissue. Pathway analysis of DEGs in the Cdh5-NT vs Tie2-NT comparison for retina, choroid, and brain predicted inhibition of processes related to myeloid cell function and activation, consistent with more specific targeting of ECs in the Cdh5-NT than in the Tie2-NT model. While TRAP enriches for EC transcripts in both models, it also captures myeloid transcripts in the Tie2-NT model. We confirmed these observations with a cell sorting approach. We suggest experimental/analytical considerations should be taken when selecting cre-lines to target ECs.
2024-12-31 | GSE270200 | GEO
Project description:Endothelial cells (ECs) display organ- and tissue-specific heterogeneity. In the eye, the retinal and choroidal vascular beds are distinct networks with different morphological and functional features with the former representing a tight barrier and the latter, a permeable fenestrated vasculature. Given that retinal health critically relies on the function of these vascular beds and that their dysfunction is implicated in a variety of retinal diseases, a molecular understanding of both physiological and pathophysiological characteristics of these distinct vasculatures is critical. Given their interspersed anatomic distribution among parenchymal cells, the study of EC gene expression, in vivo, has been hampered by the challenge of isolating pure populations of ocular ECs in sufficient quantities for large-scale transcriptomics. To address this challenge, we present a methodological and analytical workflow to facilitate inter-tissue comparisons of the in vivo EC translatome isolated from choroid, retina, and brain using the Cre-inducible NuTRAP flox construct and two widely-used endothelial cre mouse lines, constitutive Tie2-Cre and Tamoxifen-inducible Cdh5-CreERT2, which express EGFP and mCherry tags for cell-specific isolation of nuclei and ribosomes. Within each model, inter-tissue comparison of TRAP-RNAseq enrichment (TRAP translatome vs input transcriptome) showed tissue-specific gene enrichments with differential pathway representation. For each mouse model, inter-tissue comparison of the EC translatome (choroid vs brain, choroid vs retina, and brain vs retina) showed over 50% overlap of differentially expressed genes (DEGs) between the three paired comparisons, with differential pathway representation for each tissue. Pathway analysis of DEGs in the Cdh5-NT vs Tie2-NT comparison for retina, choroid, and brain predicted inhibition of processes related to myeloid cell function and activation, consistent with more specific targeting of ECs in the Cdh5-NT than in the Tie2-NT model. While TRAP enriches for EC transcripts in both models, it also captures myeloid transcripts in the Tie2-NT model. We confirmed these observations with a cell sorting approach. We suggest experimental/analytical considerations should be taken when selecting cre-lines to target ECs.
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Project description:Endothelial cells (ECs) display organ- and tissue-specific heterogeneity. In the eye, the retinal and choroidal vascular beds are distinct networks with different morphological and functional features with the former representing a tight barrier and the latter, a permeable fenestrated vasculature. Given that retinal health critically relies on the function of these vascular beds and that their dysfunction is implicated in a variety of retinal diseases, a molecular understanding of both physiological and pathophysiological characteristics of these distinct vasculatures is critical. Given their interspersed anatomic distribution among parenchymal cells, the study of EC gene expression, in vivo, has been hampered by the challenge of isolating pure populations of ocular ECs in sufficient quantities for large-scale transcriptomics. To address this challenge, we present a methodological and analytical workflow to facilitate inter-tissue comparisons of the in vivo EC translatome isolated from choroid, retina, and brain using the Cre-inducible NuTRAP flox construct and two widely-used endothelial cre mouse lines, constitutive Tie2-Cre and Tamoxifen-inducible Cdh5-CreERT2, which express EGFP and mCherry tags for cell-specific isolation of nuclei and ribosomes. Within each model, inter-tissue comparison of TRAP-RNAseq enrichment (TRAP translatome vs input transcriptome) showed tissue-specific gene enrichments with differential pathway representation. For each mouse model, inter-tissue comparison of the EC translatome (choroid vs brain, choroid vs retina, and brain vs retina) showed over 50% overlap of differentially expressed genes (DEGs) between the three paired comparisons, with differential pathway representation for each tissue. Pathway analysis of DEGs in the Cdh5-NT vs Tie2-NT comparison for retina, choroid, and brain predicted inhibition of processes related to myeloid cell function and activation, consistent with more specific targeting of ECs in the Cdh5-NT than in the Tie2-NT model. While TRAP enriches for EC transcripts in both models, it also captures myeloid transcripts in the Tie2-NT model. We confirmed these observations with a cell sorting approach. We suggest experimental/analytical considerations should be taken when selecting cre-lines to target ECs.
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Project description:We developed a new technique named as Differential Systemic Decellularization in vivo (DISDIVO) for the molecular profiling of vascular beds throughout the body. This method can by applied to murine models. Thus, the data provided here correspond to mice vascular beds obtained in vivo by DISDIVO.
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Project description:Blood vessel endothelial cells (EC) display heterogeneity across vascular beds, which is at the bases of organ specificity and anticipated to drive site-specific vascular pathology. It is assessed in vivo using transcriptomics, and in vitro using functional assays, but how proteomes compare across human in vitro cultured ECs remains incompletely characterized. We generated an in-depth human EC proteomic landscape (>8000 proteins) across 6 vascular beds and 2 in vitro models both in steady-state and upon IFNγ-induced inflammation. EC proteomes displayed a high similarity and organ specific proteins were limited. Variation between ECs and donors was mainly based in biological processes underlying proliferation and differentiation. BOECs and HUVECs represented the extremes of proteomic phenotypes. IFNγ responses were highly conserved across cellular sources. Harnessing dynamics in protein abundances we delineated interactor networks of VWF and VE-Cadherin. This EC landscape provides an extensive proteomic addition in studying EC biology and heterogeneity from an in vitro perspective.
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