PXD014781-1

PXD014781 is an original dataset announced via ProteomeXchange.

Title	Prion MRM assay development and clinical study
Description	Therapies currently in preclinical development for prion disease seek to lower prion protein (PrP) expression in the brain. Trials of such therapies are likely to rely on quantification of PrP in cerebrospinal fluid (CSF) as a pharmacodynamic biomarker and possibly as a trial endpoint. Studies using PrP ELISA kits have shown that CSF PrP is lowered in the symptomatic phase of disease, a potential confounder for reading out the effect of PrP-lowering drugs in symptomatic patients. Because misfolding or proteolytic cleavage could potentially render PrP undetectable by ELISA, we sought to establish an orthogonal method for CSF PrP quantification. We developed a multi-species targeted mass spectrometry method based on multiple reaction monitoring (MRM) of nine PrP tryptic peptides quantified by stable isotope dilution analysis. Analytical validation experiments showed intra-day and inter-day assay reproducibility coefficients of variation less than 15% (below the best practices threshold), 3 orders of dynamic linear range that encompass the entire expected range of PrP concentration in CSF, lower limits of detection near 10 ng/mL and a similar recovery response from both CSF and brain homogenate matrices. Critical for preclinical assay development, comparable assay performance was found for peptides unique to 4 species. In N=55 CSF samples from individuals referred to prion surveillance centers with rapidly progressive dementia, all six human PrP peptides, spanning the N- and C-terminal domains of PrP, were uniformly reduced in prion disease cases compared to individuals with non-prion diagnoses. Thus, lowered CSF PrP concentration in prion disease is a genuine result of the disease process and not merely an artifact of ELISA-based measurement. As a result, dose-finding studies for PrP lowering drugs may need to be conducted in pre-symptomatic at-risk individuals rather than in symptomatic patients. We provide a targeted mass spectrometry-based method suitable for preclinical and clinical quantification of CSF PrP as a tool for drug development.
HostingRepository	PanoramaPublic
AnnounceDate	2019-11-19
AnnouncementXML	Submission_2019-11-21_08:14:56.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Eric Kuhn
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Rattus norvegicus; NCBI TaxID: 10116; scientific name: Macaca fascicularis; NCBI TaxID: 9541; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Oxidation; Label:13C(6)15N(4); Label:13C(6)15N(2); Label:15N(1); Label:15N(2); Label:15N(3); Label:15N(4)
Instrument	TSQ Quantiva; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-26 14:17:41	ID requested
⏵ 1	2019-11-21 08:14:57	announced

Minikel EV, Kuhn E, Cocco AR, Vallabh SM, Hartigan CR, Reidenbach AG, Safar JG, Raymond GJ, McCarthy MD, O'Keefe R, Llorens F, Zerr I, Capellari S, Parchi P, Schreiber SL, Carr SA, Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry. Mol Cell Proteomics, 18(12):2388-2400(2019) [pubmed]

submitter keyword: targeted mass spectrometry, multiple reaction monitoring mass spectrometry, prion

cerebrospinal fluid, biomarker

Steve Carr
contact affiliation	Broad Institute of MIT and Harvard
contact email	scarr@broadinstitute.org
lab head
Eric Kuhn
contact affiliation	Broad Institute of MIT and Harvard
contact email	ekuhn@broadinstitute.org
dataset submitter

Panorama Public dataset URI