PXD012574

PXD012574 is an original dataset announced via ProteomeXchange.

Title	Proteomic and Genomic Signatures of Repeat-instability in Cancer and Adjacent Normal Tissues
Description	Repetitive sequences are hotspots of evolution at multiple levels. However, due to technical difficulties involved in their assembly and analysis, the role of repeats in tumor evolution is poorly understood. We developed a rigorous motif-based methodology to quantify variations in the repeat content of proteomes and genomes, directly from proteomic and genomic raw sequence data, and applied it to analyze a wide range of tumors and normal tissues. We identify high similarity between the repeat-instability in tumors and their patient-matched normal tissues, but also tumor-specific signatures, both in protein expression and in the genome, that strongly correlate with cancer progression and robustly predict the tumorigenic state. In a patient, the hierarchy of genomic repeat instability signatures accurately reconstructs tumor evolution, with primary tumors differentiated from metastases. We find an inverse relationship between repeat-instability and point mutation load, within and across patients, and independently of other somatic aberrations. Thus, repeat-instability is a distinct, transient and compensatory adaptive mechanism in tumor evolution.
HostingRepository	PRIDE
AnnounceDate	2020-06-02
AnnouncementXML	Submission_2020-06-02_06:16:05.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tamar Geiger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-31 01:43:20	ID requested
⏵ 1	2020-06-02 06:16:06	announced

Persi E, Prandi D, Wolf YI, Pozniak Y, Barnabas GD, Levanon K, Barshack I, Barbieri C, Gasperini P, Beltran H, Faltas BM, Rubin MA, Geiger T, Koonin EV, Demichelis F, Horn D, Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues. Proc Natl Acad Sci U S A, 116(34):16987-16996(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Repeat-instability, tumor evolution, proteomic signatures,

Tamar geiger
contact affiliation	Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
contact email	geiger@tauex.tau.ac.il
lab head
Tamar Geiger
contact affiliation	Tel Aviv University
contact email	geiger@tauex.tau.ac.il
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/2020/06/PXD012574

PRIDE project URI

• PRIDE
  1. PXD012574
     1. Label: PRIDE project
     2. Name: Proteomic and Genomic Signatures of Repeat-instability in Cancer and Adjacent Normal Tissues