PXD019893

PXD019893 is an original dataset announced via ProteomeXchange.

Title	Proteomics of the transition to naïve human pluripotency
Description	Epigenetic reprogramming is a cancer hallmark but how it unfolds during early neoplastic events and its role in carcinogenesis and cancer progression is not fully understood. Here we show that resetting from primed to naïve human pluripotency results in acquisition of a DNA methylation landscape mirroring the cancer DNA methylome, with gradual hypermethylation of bivalent developmental genes. We hypothesised that unknown proteins and transcription factors play a role in the DNA hypermethylation process and analysed therefore the proteomics of the very early stages of the resetting process which involves overexpression of Nanog and Klf2. The samples analysed were Primed hESCs (Conventional stem cells), 72hours after induction and 1 week after induction, in triplicate. For our purposes we identified candidate transcription factors and subsequently knocked them down to test their involvement in the DNA hypermethylation (as described in the manuscript related to this data, Patani et al. Nature Communications). More broadly, we believe, this dataset is a useful resource for the wider community interested in pluripotency, resetting, reprogramming, cell identity transitions etc. Our results indicate that transition to naïve pluripotency and oncogenic transformation share common epigenetic trajectories, which implicates reprogramming and the pluripotency network as a central hub in cancer formation.
HostingRepository	PRIDE
AnnounceDate	2020-07-13
AnnouncementXML	Submission_2020-08-27_09:07:11.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019893
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Vinothini Rajeeve
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-19 03:05:21	ID requested
1	2020-07-12 23:54:27	announced
2	2020-08-27 07:42:54	announced	2020-08-27: Updated publication reference for PubMed record(s): 32699299.
3	2020-08-27 08:24:24	announced	2020-08-27: Updated publication reference for PubMed record(s): 32699299. 2020-08-27: Updated publication reference for PubMed record(s): 32699299.
⏵ 4	2020-08-27 09:07:12	announced	2020-08-27: Updated publication reference for PubMed record(s): 32699299. 2020-08-27: Updated publication reference for PubMed record(s): 32699299. 2020-08-27: Updated publication reference for PubMed record(s): 32699299.

Patani H, Rushton MD, Higham J, Teijeiro SA, Oxley D, Cutillas P, Sproul D, Ficz G, ve human pluripotency mirrors pan-cancer DNA hypermethylation. Nat Commun, 11(1):3671(2020) [pubmed]

submitter keyword: hESC, naive embryonic stem cells, resetting, epigenetics, DNA methylation, Transcription factors, reprogramming

Dr Pedro R Cutillas
contact affiliation	Reader | Centre for Genomics and Computational Biology Barts Cancer Institute Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ Tel: +44 (0)20 7882 8266
contact email	p.cutillas@qmul.ac.uk
lab head
Vinothini Rajeeve
contact affiliation	Centre for Haemato Oncology
contact email	v.rajeeve@qmul.ac.uk
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/2020/07/PXD019893

PRIDE project URI

• PRIDE
  1. PXD019893
     1. Label: PRIDE project
     2. Name: Proteomics of the transition to naïve human pluripotency