PXD020958

PXD020958 is an original dataset announced via ProteomeXchange.

Title	Identification of transcriptional drifts in endothelial cells associated with environmental changes
Description	Environmental cues, such as shear stress and heterotypic cell interactions play a critical role in endothelial cell function, yet their unique contributions to the endothelial cell transcriptome remain unclear. Using cell preparations from human umbilical cords (ex vivo), we performed individual sample analysis to assess transcriptional drifts associated with environmental changes but independent of sex or background. Global gene expression profiling by RNA-seq, ATACseq, and MS/MS directed proteomics distinguished freshly isolated endothelial cells from genetically matched culture (in vitro) samples. Over 43% of the transcriptome was significantly changed by the in vitro environment. Amongst several signatures, we observed that TGF-beta and BMP target genes were reduced. In contrast, cytoskeleton-based processes and proliferation-related genes were increased. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes including targets of BMP and Notch signaling known to be sensitive to flow. In contrast, co-culture of endothelial cells with smooth muscle cells normalized networks related to cell growth and differentiation, clathrin-vesicle related genes, and recovered targets downstream TGF-beta, recovering approximately 9% of the original in vivo signature. Our findings highlight specific genes, pathways and functional features of endothelial cells that require contextual information and exposure to physical forces. This transcriptional modulation is important to consider in all paradigms that are focused on understanding the ability of endothelial cells to maintain homeostasis and respond to disease processes.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:03:02.969.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020958
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yasaman Jami-Alahmadi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-17 03:37:27	ID requested
1	2023-07-20 11:05:22	announced
⏵ 2	2023-11-14 09:03:09	announced	2023-11-14: Updated project metadata.

10.6019/PXD020958;

Afshar Y, Ma F, Quach A, Jeong A, Sunshine HL, Freitas V, Jami-Alahmadi Y, Helaers R, Li X, Pellegrini M, Wohlschlegel JA, Romanoski CE, Vikkula M, Iruela-Arispe ML, Transcriptional drifts associated with environmental changes in endothelial cells. Elife, 12():(2023) [pubmed]

submitter keyword: RNA-seq,proteomics,endothelial cell,ATACseq,human umbilical cords

Luisa Iruela-Arispe
contact affiliation	Feinberg School of Medicine Northwestern University 303 ESuperior Street – SQ 8-522 Chicago, IL 60611
contact email	arispe@northwestern.edu
lab head
Yasaman Jami-Alahmadi
contact affiliation	UCLA
contact email	yjami@ucla.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD020958
     1. Label: PRIDE project
     2. Name: Identification of transcriptional drifts in endothelial cells associated with environmental changes