PXD016678

PXD016678 is an original dataset announced via ProteomeXchange.

Title	Endothelial metabolic transcriptome plasticity in pathological angiogenesis
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:02:10.124.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Delphi Van Haver
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-10 05:10:28	ID requested
1	2020-04-14 02:59:34	announced
⏵ 2	2024-10-22 05:02:17	announced	2024-10-22: Updated project metadata.

10.1016/j.cmet.2020.03.009;

Rohlenova K, Goveia J, Garc, í, a-Caballero M, Subramanian A, Kalucka J, Treps L, Falkenberg KD, de Rooij LPMH, Zheng Y, Lin L, Sokol L, Teuwen LA, Geldhof V, Taverna F, Pircher A, Conradi LC, Khan S, Stegen S, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Vinckier S, Van Bergen T, Ectors N, De Haes P, Wang J, Bolund L, Schoonjans L, Karakach TK, Yang H, Carmeliet G, Liu Y, Thienpont B, Dewerchin M, Eelen G, Li X, Luo Y, Carmeliet P, Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis. Cell Metab, 31(4):862-877.e14(2020) [pubmed]

curator keyword: Biomedical

submitter keyword: Endothelial cells

Angiogenesis

choroidal neovascularization

tumor angiogenesis

scRNA-seq

transcriptional regulation

Peter Carmeliet
contact affiliation	Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium
contact email	peter.carmeliet@kuleuven.vib.be
lab head
Delphi Van Haver
contact affiliation	VIB Proteomics Core
contact email	delphi.vanhaver@vib-ugent.be
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016678

PRIDE project URI

• PRIDE
  1. PXD016678
     1. Label: PRIDE project
     2. Name: Endothelial metabolic transcriptome plasticity in pathological angiogenesis