PXD053175

PXD053175 is an original dataset announced via ProteomeXchange.

Title	In vivo RNA Affinity Purification of wildtype and nonstop mutant VHL tumor suppressor mRNA
Description	Nonstop extension or stop-loss mutations in the von Hippel Lindau (VHL) tumor suppressor gene are recurrently found in kidney cancer patients as observed from the NonStopDB database. We observed that presence of this nonstop extension mutation caused loss of the protein via the ubiquitin-proteasome pathway. Stabilization of the nonstop extended VHL with proteasome inhibitor Bortezomib revealed that the mutant protein was preferentially translated from an upstream alternative start site compared to the wild-type. The objective of this study was to identify proteins bound to the VHL mRNA that could be responsible for the differential start site selection. For this, we employed the in vivo RNA-affinity purification method to pull down wild-type and nonstop mutant VHL mRNAs along with their bound proteins after cross-linking using UV irradiation and pull-down with raPOOLs, which are a pool of biotinylated DNA oligonucleotides reverse complementary to the VHL mRNA. The RNA-protein complexes were then pulled down by streptavidin beads, the bound proteins were isolated and subjected to mass-spectrometry based identification.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_19:43:37.761.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sven Diederichs
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-17 08:48:43	ID requested
⏵ 1	2025-05-06 19:43:38	announced

Pal J, Riester M, Ganner A, Ghosh A, Dhamija S, Mookherjee D, Voss C, Frew IJ, Kotsis F, Neumann-Haefelin E, Spang A, Diederichs S, and affect multiple stages of protein translation. Sci Adv, 11(7):eadr6375(2025) [pubmed]

10.1126/sciadv.adr6375;

submitter keyword: RNA affinity purification, nonstop extension mutation, von Hippel Lindau, VHL,Nonstop mutation, protein isoform, start codon, translation initiation, stop-loss, RAP

Sven Diederichs
contact affiliation	Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany German Cancer Consortium (DKTK), partner site Freiburg, a partnership between DKFZ and University Medical Center Freiburg, Germany
contact email	s.diederichs@dkfz.de
lab head
Sven Diederichs
contact affiliation	Division of Cancer Research, Dept. of Thoracic Surgery, University Medical Center Freiburg
contact email	s.diederichs@dkfz.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053175
     1. Label: PRIDE project
     2. Name: In vivo RNA Affinity Purification of wildtype and nonstop mutant VHL tumor suppressor mRNA