PXD004652

PXD004652 is an original dataset announced via ProteomeXchange.

Title	A Systems-Level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
Description	Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of non-coding ORFs during differentiation, we mapped new functions to well annotated long non-coding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology.
HostingRepository	PRIDE
AnnounceDate	2021-10-29
AnnouncementXML	Submission_2021-10-29_04:35:26.772.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Johannes Graumann
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-07-25 05:39:19	ID requested
1	2019-07-23 14:40:56	announced
2	2019-07-24 00:30:26	announced	Updated project metadata.
3	2019-07-26 00:30:17	announced	Updated project metadata.
4	2019-08-01 04:42:25	announced	Updated project metadata.
⏵ 5	2021-10-29 04:35:27	announced	2021-10-29: Updated project metadata.

Billing AM, Dib SS, Bhagwat AM, da Silva IT, Drummond RD, Hayat S, Al-Mismar R, Ben-Hamidane H, Goswami N, Engholm-Keller K, Larsen MR, Suhre K, Rafii A, Graumann J, A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells. Mol Cell Proteomics, 18(10):1950-1966(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Human embryonic stem cells, transcriptome, bone marrow, phosphoproteome, differentiation, human mesenchymal stem cells, quantitative proteomics, proteome, LC-MS/MS, RNA-seq

Johannes Graumann
contact affiliation	Weill Cornell Medicine - Qatar
contact email	jog2030@qatar-med.cornell.edu
lab head
Johannes Graumann
contact affiliation	Max Planck Institute for Heart and Lung Research
contact email	johannes.graumann@mpi-bn.mpg.de
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/2019/07/PXD004652

PRIDE project URI

• PRIDE
  1. PXD004652
     1. Label: PRIDE project
     2. Name: A Systems-Level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells