Development and evaluation of a multiplexed mass spectrometry based assay for measuring candidate peptide biomarkers in Alzheimer's Disease Neuroimaging Initiative (ADNI) CSF

Abstract

Purpose We describe the outcome of the Biomarkers Consortium CSF Proteomics Project, a public-private partnership of government, academia, non-profit, and industry. The goal of this study was to evaluate a multiplexed mass spectrometry-based approach for the qualification of candidate Alzheimer’s Disease (AD) biomarkers using CSF samples from the AD Neuroimaging Initiative (ADNI). Experimental Design Reproducibility of sample processing, analytic variability, and ability to detect a variety of analytes of interest were thoroughly investigated. Multiple approaches to statistical analyses assessed whether panel analytes were associated with baseline pathology (MCI, AD) vs. Healthy Controls (CN) or associated with progression for MCI patients, and included: (i) univariate association analyses, (ii) univariate prediction models, (iii) exploratory multivariate analyses, and (iv) supervised multivariate analysis. Results A robust targeted mass spectrometry-based approach for the qualification of candidate AD biomarkers was developed. The results identified several peptides with potential diagnostic or predictive utility, with the most significant differences observed for the following peptides for differentiating (including peptides from Hemoglobin A (HBA), Hemoglobin B (HBB), and Superoxide dismutase (SODE)) or predicting (including peptides from Neuronal pentraxin-2 (NPTX2), Neurosecretory protein VGF (VGF), and Secretogranin-2 (SCG2)) progression vs. non-progression from mild cognitive impairment to AD. Conclusions and Clinical Relevance These data provide potential insights into the biology of CSF in AD and MCI progression and provide a novel tool for AD researchers and clinicians working to improve diagnostic accuracy, evaluation of treatment efficacy, and early diagnosis.

Neurodegeneration and Alzheimer's disease (AD). What Can Proteomics Tell Us About the Alzheimer's Brain?

“…More specifically, no changes were identified in the level of apoE, independent of the genotypes of the patients (46). This point has been controversial in the literature.…”

“…Because apoE4 is the major risk factor for developing AD, it was expected that there would be a correlation between apoE genotypes and apoE levels in the CSF, as previously reported (37,47). At least two different studies that used either common peptides to detect all apoE variants or peptides that were specific for each apoE variant found no differences (46,48), strongly suggesting that apoE levels in the CSF do not differentiate AD or MCI patients from HC or patients who progress from those who do not progress to AD in the MCI population (46). More studies will be required to settle this controversy.…”

“…Of these four proteins, only TTR differentiated AD versus HC and MCI versus HC. However, when an FDR (Benjamini-Hochberg false discovery rate) correction was applied, no significant differences were found in the levels of TTR or indeed in any of the proteins analyzed in this panel (46).…”

“…These focus the resources of the mass spectrometer on a defined subset of analytes (peptides) (36,41,42,45). To facilitate this process, the biomarker consortium CSF proteomics project team (Alzheimer's Association, www.alz.org) developed a targeted proteomic, multiplexed, mass spectrometry-based approach for the qualification of candidate biomarkers in the well-characterized AD neuroimaging initiative (ADNI) cohort (46). They have defined a panel of peptides that were extrapolated from previously published biomarkers studies to discriminate between AD patients and healthy controls (HC) and MCI patients and HC.…”

An Industry update: what's New in the Field of Therapeutic delivery?

“…The collaboration will build on earlier work in which 142 potential biomarkers were monitored in both patients and healthy controls [20]. The new study, as with the previous one, will exploit Caprion's targeted multiple reaction monitoring mass spectrometry-based platform to quantify large numbers of proteins in less than 0.1 ml of cerebral spinal fluid.…”