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MBDxA 2013
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Plenary Presentations
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Poster Presentations
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Copy Number Alterations in DNA Repair/Repair-Related Genes Identify Disease-Specific Biomarkers with Potential Clinical Relevance to Hematologic Malignancies
Microarray copy number alterations (CNAs) were analyzed for 155 DNA repair-related genes in 425 cases representing diverse hematologic malignancies. Expected disease associations in RB1, TP53 and ATM were seen. Newly defined relationships included deletion of ERCC5 seen in B-ALL, with co-deletion of ERCC5 and LIG4 confined to NHL. CNAs specific to NHL (GTF2H4, POLQ, REV1L, FANCL, BRCA2, and NUDT1), AML [UBE2V2, APTX, APTX, MGMT and RPA2, with the latter found only in cases with translocations (PML/RARA or MLL)] myeloma (ALKBH3) and MDS (ALKBH5, TOP3A) were seen. Other CNAs occurred in multiple disorders (NEIL1, PMS2, ENDOV, CHEK2, and HELQ). The results reveal disease specificity for CNAs in DNA repair related genes. Further study is warranted to validate these alterations as disease specific diagnostic/prognostic biomarkers.
Detection of “oncometabolite” 2-hydroxyglutarate by Magnetic Resonance Analysis as a Biomarker of IDH1/2 Mutations in Glioma
Somatic mutations in isocitrate dehydrogenase (IDH)1 and 2 have been detected in a subset of gliomas, rendering these tumors with elevated levels of “oncometabolite”, D-2-Hydroxyglutarate (2HG). We demonstrate the detection of 2HG as a biomarker of this subset of gliomas ex vivo using a magnetic resonance (MR) approach. This study thus highlights the feasibility of using MR detection of 2HG for the diagnosis and classification of IDH1/2 mutation-positive brain tumors and opens up the possibility of performing analogous non-invasive MR-based imaging and spectroscopy studies directly in humans in the neuro-oncology clinic.
Mass Spectrometry Used To Define Plasma Protein-Based Classifiers That Discriminate Patients With Colon Polyps or Adenomas As Compared to Colonoscopy
Plasma samples were collected from patients undergoing colonoscopy and their plasma protein profiles were quantified via LCMS. 100 matched samples were used in this analysis. Approximately 150,000 molecular features were observed in at least 50% of the samples in at least one group. Ten rounds of 10-fold cross validation using Elastic Net feature selection, top 100 feature ranking, and SVM classifier assembly were performed to determine potential classifier performance. The average cross-validated AUC was 0.92 ± 0.12, indicating a high degree of predictive performance. These results demonstrate the feasibility of blood-based protein tests to help manage colonoscopy screen compliance.
ApoE typing from small amounts of blood samples
In clinical testing, ApoE levels in blood are determined by immunoassay. Combining ApoE immunoassay reagents with mass spectrometric analysis, we attempted to resequence ApoE protein from small amounts of sera for typing. Most ApoE mutant isoforms, such as ApoE2 and ApoE4, involve substitutions of lysine and arginine residues, and on trypsin digestion will result in fragments with a larger mass difference than a single amino acid substitution of other amino acids. ApoE types from sera, including heterozygous combinations (ApoE2/E3, E2/E4, E3/E4) corresponded exactly with the APOE genotyping results in each of the subjects. ApoE types from sera may be a novel clinical test that is performed using blood samples remaining from those collected for routine clinical tests and may enable retrospective studies using preserved body fluids.
Immuno-MALDI Assay for Plasma Renin Activity: Proof of Principle for a Translatable Proteomic Assay without Chromatography
The renin-angiotensin-aldosterone system (RAAS) plays an essential role in maintaining arterial blood pressure. Determination of plasma renin activity (PRA) is essential for screening and diagnosis of primary aldosteronism and other derangements of the RAAS pathway. Clinical laboratories have traditionally used radioimmunoassays (RIAs) for angiotensin-I in the determination of PRA. Recently however, there has been pressure to discontinue radioisotope-dependent assays in favour of stable isotope techniques. We have developed a MS approach for the determination of plasma renin activity utilizing immuno-MALDI (iMALDI) MS and have compared with both RIA and LC-MS/MS. The iMALDI method has the benefit of requiring no chromatography.
Differential solublization method to extract low-molecular-weight proteins/peptides for successful serum SRM analyses
Selected reaction monitoring mass spectrometry (SRM-MS) has been used to measure low abundance proteins/peptides in serum/plasma, owing to its high sensitivity and selectivity. However, the presence of highly abundant proteins in serum/plasma and the huge dynamic range of serum proteins/peptides make SRM analysis challenging. We previously developed differential solubilization (DS) method to extract low-molecular-weight proteins/peptides in serum with good reproducibility. Here we present data indicating that the DS method is useful as pretreatment for serum SRM analyses for biomarker validation.
Validation of Arsenic Speciation Method for Human Urine Using HPLC-ICP-MS
Arsenic is carcinogenic depending on its chemical nature and oxidation states. Quantitative determination of inorganic and organic Arsenic species in clinical samples could be used as potential biomarker for its toxic exposure. Arsenic can be ingested in form of one or more species. Arsenic species can be metabolized into several different inorganic and organic forms, including As-III and As-V, and the methylated species such as Monomethyl arsonic acid (MMA), and Dimethyl arsinic acid (DMA) or Arsenobetaine (AsB) and Arsenocholine (AsC) which most likely stay unaffected in the body. We have developed an analytical method for quantitative determination of six Arsenic species in clinical samples using isocratic LC coupled with ICP-MS. The results showed that each of the six Arsenic species was well separated and LOD of each of the species was approximately 1.0 ppb.
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