PXD042875

PXD042875 is an original dataset announced via ProteomeXchange.

Title	Bottom-up proteomics of EZH2 mutants in isogenic cells
Description	The Enhancer of Zeste 2 Polycomb Repressive Complex 2 Subunit (EZH2) is an essential epigenetic modifier able to methylate lysine 27 on histone H3 (H3K27) to induce chromatin compaction, protein complex recruitment and ultimately transcriptional repression. Hematologic malignancies, including Diffuse Large B cell lymphoma (DLBCL) and Acute myeloid leukemia (AML) have shown a high EZH2-mutation frequency (>20%) associated with poor clinical outcomes. Particularly, two distinct oncogenic mutations, so-called gain-of-function (Y641F and A677G) and loss-of-function (H689A and F667I) are found in the catalytic domain of EZH2. In this study, a comprehensive multi-omics approach was employed to characterize downstream effects of H3K27me3 deposition driven by EZH2 mutations. Human embryonic kidney cells (HEK293T) were transfected to generate three stable EZH2 mutants: EZH2(Y641F), EZH2(A677G), and EZH2(H689A/F667I), which were validated via immunoblotting and DIA-MS-based histone profiling assay. Subsequently, constructs were analyzed under a comprehensive multi-omics approach including label-free whole-cell proteomics, acquired with a Bruker timsTOF Pro HPLC-MS/MS with Ion Mobility. Important protein interactors at nuclear level were dysregulated, such as SMYD3 (SET and MYND domain containing 3), NSD2 (nuclear receptor binding SET domain protein 2) and CHD7 (chromodomain helicase DNA binding protein 7), suggesting a cooperative network of chromatin remodelers for gene expression reprogramming.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:12:52.334.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julian Aldana
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetic acid derivatized residue
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-11 07:00:28	ID requested
1	2023-10-24 13:37:09	announced
2	2023-11-14 09:11:32	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:12:54	announced	2024-10-22: Updated project metadata.

10.3390/ijms241411378;

Aldana J, Gardner ML, Freitas MA, Integrative Multi-Omics Analysis of Oncogenic EZH2 Mutants: From Epigenetic Reprogramming to Molecular Signatures. Int J Mol Sci, 24(14):(2023) [pubmed]

submitter keyword: lymphoma, epigenetics, leukemia, mutations,EZH2

Michael A. Freitas
contact affiliation	Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
contact email	freitas.5@osu.edu
lab head
Julian Aldana
contact affiliation	The Ohio State University
contact email	aldanaaroca.1@osu.edu
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/2023/10/PXD042875

PRIDE project URI

• PRIDE
  1. PXD042875
     1. Label: PRIDE project
     2. Name: Bottom-up proteomics of EZH2 mutants in isogenic cells