PXD002669

PXD002669 is an original dataset announced via ProteomeXchange.

Title	Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples
Description	Histone post-translational modifications (hPTMs) generate a complex combinatorial code that has been implicated with various pathologies, including cancer. Dissecting such a code in physiological and diseased states may be exploited for epigenetic biomarker discovery, but hPTM analysis in clinical samples has been hindered by technical limitations. Here, we developed a method (PAThology tissue Histones by Mass Spectrometry - PAT-H-MS) that allows to perform a comprehensive, unbiased and quantitative MS-analysis of hPTM patterns on formalin-fixed paraffin-embedded (FFPE) samples. In pairwise comparisons, histone extracted from FFPE tissues showed patterns similar to fresh frozen samples for 24 differentially modified peptides from histone H3. In addition, when coupled with a histone-focused version of the super-SILAC approach, this method allows the accurate quantification of modification changes among breast cancer patient samples. We applied this strategy to the analysis of breast cancer subtypes, revealing significant changes between Luminal A and Triple Negative samples in peptides containing K27me3 and K9me3, which were validated by immunohistochemistry and western blot analysis. These results pave the way for retrospective epigenetic studies that combine the power of MS-based hPTM analysis with the extensive clinical information associated with FFPE archives.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_03:59:02.463.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roberta Noberini
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; 3x(2)H labeled N6-acetyl-L-lysine; isotope labeled residue; acetylated residue; formylated residue; dimethylated residue; N6,N6,N6-trimethyl-L-lysine
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-05 02:47:42	ID requested
1	2015-10-14 04:50:54	announced
2	2015-10-20 03:39:09	announced	Updated publication reference for PubMed record(s): 26463340.
⏵ 3	2024-10-22 03:59:04	announced	2024-10-22: Updated project metadata.

Noberini R, Uggetti A, Pruneri G, Minucci S, Bonaldi T, Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples. Mol Cell Proteomics, 15(3):866-77(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: biomarker

epigenetics

FFPE

super-SILAC

cancer

Tiziana Bonaldi
contact affiliation	Dept. Exp. Oncology Istituto Europeo di Oncologia Via Giuseppe Ripamonti, 435, 20141 Milano
contact email	tiziana.bonaldi@ieo.eu
lab head
Roberta Noberini
contact affiliation	Istituto Europeo di Oncologia
contact email	roberta.noberini@ieo.it
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/2015/10/PXD002669

PRIDE project URI

• PRIDE
  1. PXD002669
     1. Label: PRIDE project
     2. Name: Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples