Ira L. Goldknopf

Proteomic Analysis of S-Nitrosylated Proteins in Mesangial Cells

NO participates in numerous biological events in a variety of cell types including activated glomerular mesangial cells. Many of these events appear to be independent of the known effects of NO on soluble guanylyl cyclase. NO derived from all major isoforms of NO synthase can S-nitrosylate cysteine residues in target proteins, potentially altering their functional activities. Recent evidence suggests that S-nitrosylation is specific, is regulated, and may play an important regulatory role akin to phosphorylation. In the present study, the “biotin-switch” method of isolating S-nitrosylated proteins was coupled with two-dimensional PAGE protein separation followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and peptide mass fingerprinting to identify target proteins for S-nitrosylation in murine mesangial cells treated with NO donors or appropriate controls. This approach resolved 790 protein spots. We analyzed the most abundant spots and identified 34 known proteins. Of these, 31 are unique S-nitrosylated proteins not previously identified, including signaling proteins, receptors and membrane proteins, cytoskeletal or cell matrix proteins, and cytoplasmic proteins. Prominent among these were peroxisome proliferator activated receptor γ, uroguanylin, GTP-binding protein α, protein 14-3-3, NADPH-cytochrome P450 oxidoreductase, transcription factor IIA, melusin, mitosin, phospholipase A2-activating protein, and protein-tyrosine phosphatase. The in vivo induction of S-nitrosylation was assayed by treating mesangial cells with interleukin-1β followed by the biotin-switch and Western blot of selected targets. These results broaden our knowledge of potential signal transduction pathways and other cell functions mediated by NO S-nitrosylation.

2D gel blood serum biomarkers reveal differential clinical proteomics of the neurodegenerative diseases

This review addresses the challenges of neuroproteomics and recent progress in biomarkers and tests for neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease and amyotrophic lateral sclerosis. The review will discuss how the application of quantitative 2D gel electrophoresis, combined with appropriate single-variable and multivariate biostatistics, allows for selection of disease-specific serum biomarkers. It will also address how the use of large cohorts of specifically targeted patient blood serum samples and complimentary age-matched controls, in parallel with the use of selected panels of these biomarkers, are being applied to the development of blood tests to specifically address unmet pressing needs in the differential diagnosis of these diseases, and to provide potential avenues for mechanism-based drug targeting and treatment monitoring. While exploring recent findings in this area, the review discusses differences in critical pathways of immune/inflammation and amyloid formation between Parkinson’s disease and amyotrophic lateral sclerosis, as well as discernable synergistic relationships between these pathways that are revealed by this approach. The potential for pathway measurement in blood tests for differential diagnosis, disease burden and therapeutic monitoring is also outlined.

Alterations in Barrett's‐related adenocarcinomas: A proteomic approach

In this study, we applied high‐resolution, two‐dimensional, gel electrophoresis and matrix‐assisted laser desorption/ionization, time‐of‐flight and tandem mass spectrometry analysis (MALDI TOF MS) to identify novel proteins that are involved in Barretts tumorigenesis. We analyzed 12 primary tissue samples that included 8 Barretts‐related adenocarcinomas (BA) and 4 normal mucosae samples. Twenty‐three spots were consistently altered (≥2‐fold) in at least half of the tumors when compared with all normal samples and thus subjected to further analysis. The MALDI TOF MS analysis demonstrated biologically interesting upregulated proteins such as ErbB3, Dr5 and Cyclin D1 as well as several members of the zinc finger proteins (Znf146, Znf212 and Znf363). Examples of downregulated proteins included Lgi1 and Klf6. We selected four proteins (ErbB3, Dr5, Znf146 and Lgi1) that are novel for BAs for validation using quantitative real‐time reverse‐transcription PCR on 39 BA tissue samples when compared with normal samples. We demonstrated mRNA upregulation of ERBB3 (51.3%), DR5 (41%) and ZNF146 (30.7%) and downregulation of LGI1 (100%) in BA. We have further validated the protein overexpression of ErbB3, Dr5 and Znf146, using immunohistochemical (IHC) analysis on a tissue microarray that contained 75 BAs and normal gastric and esophageal mucosae samples. BA tissue samples demonstrated overexpression of ErbB3 (42%), Dr5 (90%) and Znf146 (30%) when compared with normal tissues. In conclusion, we have identified and validated several novel proteins that are involved in Barretts carcinogenesis.

Abnormal serum concentrations of proteins in Parkinson's disease

Blood serum was used to identify protein biomarkers for diagnosis of Parkinsons disease (PD) using analytically validated quantitative 2D-gel electrophoresis, and single variable and multivariate statistics. Using banked samples from a first medical center, we identified 57 specific protein spot biomarkers with disease-specific abnormal levels in serum of patients with PD, Alzheimers disease, amyotrophic lateral sclerosis and similar neurodegenerative conditions (337 samples), when compared to age-matched normal controls (132 samples). To further assess their clinical usefulness in Parkinsons disease, we obtained prospective newly drawn blood serum samples from a second (56 PD, 30 controls) and third (6 PD, 48 controls) medical center. The protein concentrations of the 57 biomarkers were assessed by 2D-gel electrophoresis. Stepwise linear discriminant analysis selected a combination of 21 of the 57 as optimal to distinguish PD patients from controls. When applied to the samples from the second site, the 21 proteins had sensitivity of 93.3% (52 of 56 PD correctly classified), specificity of 92.9% (28 of 30 controls correctly classified); 15 of 15 patients with mild, 28 of 30 with moderate to severe symptoms, and all of the 6 PD patients from the third site were correctly classified. Eleven of the 21 proteins showed statistically significant abnormal concentrations in patients with mild symptoms, and 14 in patients with moderate-severe symptoms. The protein identities reflect the heterogeneity of Parkinsons disease, and thus may provide the capability of monitoring the blood for a diverse range of PD pathophysiological mechanisms: cellular degeneration, oxidative stress, inflammation, and transport.

Differential diagnosis of neurodegenerative diseases using serum: A new paradigm

Background: With research in preventative medicine and early treatment gaining fast momentum, the importance of detection, in particular early detection of Alzheimer’s disease (AD) is now prevalent. On top of the growing list of known biomarkers of AD is Amyloid-b (Ab) which has long being known as central to the pathology of AD. Although the detection of its two major isoforms in cerebrospinal fluid (CSF) has been well established, a high degree of invasiveness involved in sample collection of CSF prevents its usefulness for detection in the wider community. Recent studies have turned to blood products as an attractive alternative but had resulted in conflicting results. One of the contributing factors to conflicting results may be the low amount of participant in these studies. We present here the biomarker studies from the first phase of The Australian Imaging, Biomarker and Lifestyle (AIBL) Flagship Study of Ageing. Methods: Blood plasma samples of over 1000 participants across two cities in Australia were collected and analysed for the levels of the two isoforms Ab-40 and Ab-42 using the INNO-BIA Ab detection kits. Neuropsychological assessment data of the participants were correlated against the levels of Ab40 and Ab42. Results: Mild cognitively impaired patients (MCI) showed significantly higher levels of Ab-42 that subsequently caused the increase of Ab-42/Ab-40 ratio when compared with healthy volunteers (HV) and memory complaining volunteers (MC). Conclusions: Even with the statistical power of over 1000 participant samples collected, it was still uncleared as to whether blood plasma Ab levels can determine differences between AD patients and HV. We showed evidence that the levels of other plasma biomarkers may also help when taken into account with plasma Ab levels. However, with the second phase of AIBL study on the way which will incorporate data collected at 18 months from the phase I studies, a clearer relationship between Ab and AD will be promising.