High-resolution serum proteomic profiling of Alzheimer disease samples reveals disease-specific, carrier-protein-bound mass signatures.

BACKGROUND: Researchers typically search for disease markers using a "targeted" approach in which a hypothesis about the disease mechanism is tested and experimental results either confirm or disprove the involvement of a particular gene or protein in the disease. Recently, there has been interest in developing disease diagnostics based on unbiased quantification of differences in global patterns of protein and peptide masses, typically in blood from individuals with and without disease. We combined a suite of methods and technologies, including novel sample preparation based on carrier-protein capture and biomarker enrichment, high-resolution mass spectrometry, a unique cohort of well-characterized persons with and without Alzheimer disease (AD), and powerful bioinformatic analysis, that add statistical and procedural robustness to biomarker discovery from blood. METHODS: Carrier-protein-bound peptides were isolated from serum samples by affinity chromatography, and peptide mass spectra were acquired by a matrix-assisted laser desorption/ionization (MALDI) orthogonal time-of-flight (O-TOF) mass spectrometer capable of collecting data over a broad mass range (100 to >300,000 Da) in a single acquisition. Discriminatory analysis of mass spectra was used to process and analyze the raw mass spectral data. RESULTS: Coupled with the biomarker enrichment protocol, the high-resolution MALDI O-TOF mass spectra provided informative, reproducible peptide signatures. The raw mass spectra were analyzed and used to build discriminant disease models that were challenged with blinded samples for classification. CONCLUSIONS: Carrier-protein enrichment of disease biomarkers coupled with high-resolution mass spectrometry and discriminant pattern analysis is a powerful technology for diagnostics and population screening. The mass fingerprint model successfully classified blinded AD patient and control samples with high sensitivity and specificity.

A distinctive molecular signature of multiple sclerosis derived from MALDI-TOF/MS and serum proteomic pattern analysis: detection of three biomarkers.

Although multiple sclerosis (MS) is an immune-mediated disorder, serological testing to aid in its diagnosis has not been developed. To test the hypothesis that the pathological changes in MS can be detected by analyzing a molecular signature of serum proteomic patterns, we tested sera from 25 newly diagnosed relapsing-remitting MS patients and 25 healthy controls with matrix-assisted laser desorption/ ionization time of flight (MALDI-TOF) mass spectrometry, following albumin depletion and desalting. Analysis of MALDI-TOF/mass spectrometry data, using proteomic spectral pattern recognition software, revealed a distinct proteomic pattern in the MS group determined by 3 biomarkers at 8687, 8773, and 8818 mass-to-charge ratios. Although our data are representative of analysis on a small number of samples and are preliminary, we conclude that MALDI-TOF/mass spectrometry, in combination with serum proteomic pattern analysis, could be useful in the diagnosis of MS, and a larger, masked trial to identify proteomic spectral patterns characteristic of relapsing-remitting, primary progressive and secondary progressive variants of MS is justified.

Epigenetic modification of plants with systemic RNA viruses.

Knowledge of gene function is critical to the development of new plant traits for improved agricultural and industrial applications. Viral expression vectors offer a rapid and proven method to provide epigenetic expression of foreign sequences throughout infected plants. Expression of these sequences from viral vectors can lead to gain- or loss-of-function phenotypes, allowing gene function to be determined by phenotypic or biochemical effects in the infected plant. Tobacco mosaic virus and barley stripe mosaic virus expression vectors have been developed to express foreign gene sequences in dicotyledonous and monocotyledonous hosts, respectively. Large-scale application of both viral vector systems for gene function discovery in Nicotiana and barley hosts resulted in high infection rates and produced distinctive visual phenotypes in approximately 5% of transfected plants. Novel genes expressing potential herbicide target proteins in addition to genes promoting stem elongation, leaf development and apical dominance were identified in the large-scale screening. This report illustrates the adaptability of viral vectors for gene function discovery in higher plants.