Dataset Information

Endothelial metabolic transcriptome plasticity in pathological angiogenesis

ABSTRACT: Endothelial cell (EC) metabolism is an emerging target for anti-angiogenic therapy in tumor and choroidal neovascularization (CNV), but little is known about individual EC metabolic transcriptomes. Here, by scRNA-sequencing 28,337 murine choroidal ECs (CECs) and sprouting CNV-ECs, we constructed a taxonomy to characterize their heterogeneity. Comparison with murine lung tumor ECs (TECs) revealed congruent marker gene expression by distinct EC phenotypes across tissues and diseases, suggesting similar angiogenic mechanisms. Trajectory inference of CNV-ECs revealed that differentiation of venous to angiogenic ECs was accompanied by metabolic transcriptome plasticity. EC phenotypes displayed metabolic transcriptome heterogeneity. Hypothesizing that conserved genes are more important, we used an integrated analysis, based on congruent transcriptome analysis, CEC-tailored genome scale metabolic modeling, and gene expression meta-analysis in multiple cross-species datasets, followed by functional validation, to identify the top-ranking metabolic targets SQLE and ALDH18A1, involved in EC proliferation and collagen production, respectively, as novel angiogenic targets. The effect of SQLE and ALDH18A1 silencing in ECs was investigated by transcriptomics and proteomics analysis.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Endothelial Cell

SUBMITTER: Delphi Van Haver

LAB HEAD: Peter Carmeliet

PROVIDER: PXD016678 | Pride | 2020-04-14

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	H083562_uPAC_10_PRC-4970_CarmelietLab_PLKO-1.raw	Raw
	H083564_uPAC_10_PRC-4970_CarmelietLab_SQLE-1.raw	Raw
	H083566_uPAC_10_PRC-4970_CarmelietLab_ALD18A1-1.raw	Raw
	H083568_uPAC_10_PRC-4970_CarmelietLab_PLKO-2.raw	Raw
	H083570_uPAC_10_PRC-4970_CarmelietLab_SQLE-2.raw	Raw

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Publications

Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis.

Rohlenova Katerina K Goveia Jermaine J García-Caballero Melissa M Subramanian Abhishek A Kalucka Joanna J Treps Lucas L Falkenberg Kim D KD de Rooij Laura P M H LPMH Zheng Yingfeng Y Lin Lin L Sokol Liliana L Teuwen Laure-Anne LA Geldhof Vincent V Taverna Federico F Pircher Andreas A Conradi Lena-Christin LC Khan Shawez S Stegen Steve S Panovska Dena D De Smet Frederik F Staal Frank J T FJT Mclaughlin Rene J RJ Vinckier Stefan S Van Bergen Tine T Ectors Nadine N De Haes Patrik P Wang Jian J Bolund Lars L Schoonjans Luc L Karakach Tobias K TK Yang Huanming H Carmeliet Geert G Liu Yizhi Y Thienpont Bernard B Dewerchin Mieke M Eelen Guy G Li Xuri X Luo Yonglun Y Carmeliet Peter P

Cell metabolism 20200401 4

Endothelial cell (EC) metabolism is an emerging target for anti-angiogenic therapy in tumor angiogenesis and choroidal neovascularization (CNV), but little is known about individual EC metabolic transcriptomes. By single-cell RNA sequencing 28,337 murine choroidal ECs (CECs) and sprouting CNV-ECs, we constructed a taxonomy to characterize their heterogeneity. Comparison with murine lung tumor ECs (TECs) revealed congruent marker gene expression by distinct EC phenotypes across tissues and diseas ...[more]

PMID: 32268117

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Project description:Background: As a widespread post-transcriptional RNA modification, N5-methylcytosine (m5C) is implicated in a variety of cellular responses and processes that regulate RNA metabolism. Despite this, a clear understanding of m5C modification’s role and mechanism in angiogenesis is still lacking. Methods: Single-cell RNA sequencing data was analyzed to determine expression of m5C methylase NSUN2. m5C levels were determined by mRNA isolation and anti-m5C dot blot in both hypoxia-induced endothelial cells (ECs) and laser-induced choroidal neovascularization (CNV). In addition, endothelial cell and endothelium‐specific NSUN2‐knockout mouse model were used to investigate the effect of NSUN2 silence on angiogenic phenotype. Genome-wide multiomics analyses were performed to identify the functional target of NSUN2, including proteomic analysis, transcriptome screening and m5C-methylated RNA immunoprecipitation sequencing (m5C-meRIP-seq). CUT&Tag sequencing was performed to test the histone lactylation signal in the promoter region of NSUN2. Finally, AAV-mediated short hairpin RNAi knockdown of NSUN2 gene expression (AAV-shNSUN2) was constructed to investigate the effect of inhibiting CNV. Results: First, we discovered that m5C methylase NSUN2 expression level and mRNA m5C level were significantly higher in CNV-ECs than in normal ECs. NSUN2 knockdown in ECs inhibited proliferative, migration, and tube formation activities of ECs. Moreover, compared with EC NSUN2flox/flox mice, EC-specific NSUN2-deficient (EC NSUN2-/-) mice displayed less retinal vascular leakage after laser induction. Through multiomics analyses, we subsequently identified A-kinase anchoring protein 2 (AKAP2), a scaffolding protein which isolate Protein kinase A (PKA) to specific subcellular locations through binding to its regulatory subunit, as a downstream candidate target of NSUN2 in ECs. Overexpression of exogenous AKAP2 markedly reversed the inhibitory phenotypes in NSUN2-deficient ECs. Interestingly, laser induced NSUN2 up-regulation was driven by lactate-mediated lactylation on histone H3K18. In CNV models, AAV-mediated repression of NSUN2 modulated highly retinal vascular leakage and choroidal thickness. Conclusion: Overall, our findings indicate that NSUN2 is a novel therapeutic target for choroidal neovascularization.