Lee Lomas

Classification of cancer types by measuring variants of host response proteins using SELDI serum assays

Protein expression profiling has been increasingly used to discover and characterize biomarkers that can be used for diagnostic, prognostic or therapeutic purposes. Most proteomic studies published to date have identified relatively abundant host response proteins as candidate biomarkers, which are often dismissed because of an apparent lack of specificity. We demonstrate that 2 host response proteins previously identified as candidate markers for early stage ovarian cancer, transthyretin and inter‐alpha trypsin inhibitor heavy chain 4 (ITIH4), are posttranslationally modified. These modifications include proteolytic truncation, cysteinylation and glutathionylation. Assays using Surface Enhanced Laser Desorption/Ionization Time of Flight Mass Spectrometry (SELDI‐TOF‐MS) may provide a means to confer specificity to these proteins because of their ability to detect and quantitate multiple posttranslationally modified forms of these proteins in a single assay. Quantitative measurements of these modifications using chromatographic and antibody‐based ProteinChip® array assays reveal that these posttranslational modifications occur to different extents in different cancers and that multivariate analysis permits the derivation of algorithms to improve the classification of these cancers. We have termed this process host response protein amplification cascade (HRPAC), since the process of synthesis, posttranslational modification and metabolism of host response proteins amplifies the signal of potentially low‐abundant biologically active disease markers such as enzymes.

Selection of Thioaptamers for Diagnostics and Therapeutics

Abstract:  Thioaptamers offer advantages over normal phosphate ester backbone aptamers due to their enhanced affinity, specificity, and higher stability, largely due to the properties of the sulfur backbone modifications. Over the past several years, in vitro thioaptamer selection and bead‐based thioaptamer selection techniques have been developed in our laboratory. Furthermore, several thioaptamers targeting specific proteins such as transcription factor NF‐κB and AP‐1 proteins have been identified. Selected thioaptamers have been shown diagnostic promise in proteome screens. Moreover, some promising thioaptamers have been shown in preliminary animal therapeutic dosing to increase survival in animal models of infection with West Nile virus.

A novel proteomic biomarker panel as a diagnostic tool for patients with ovarian cancer.

BACKGROUND Previous reports have shown that the proteomic markers apolipoprotein A1, hepcidin, transferrin, inter-alpha trypsin IV internal fragment, transthyretin, connective-tissue activating protein 3 and beta-2 microglobulin may discriminate between a benign pelvic mass and ovarian cancer (OC). The aim was to determine if these serum proteomic biomarkers alone as well as in combination with age and serum CA125, could be helpful in triage of women with a pelvic mass. METHODS We included prospectively 144 patients diagnosed with (OC), 40 with a borderline tumor and 469 with a benign tumor. Surface-enhanced laser desorption/ionization time of flight-mass spectrometry was used for analyses. The Danish Index (DK-Index) based on the proteomic data, age and CA125 was developed using logistic regression models. RESULTS Multivariate logistic regression analysis demonstrated that the selected proteomic markers, CA125 and age were independent predictors of OC and the combination of these is proposed as the DK-index. A sensitivity (SN) of 99% had a specificity (SP) of 57% for DK-index and 49% for CA125. At a SN of 95%, the SP increased to 81% for DK-index compared to 68% for CA125 alone. For stage I+II the SP was 58% for DK-index and 49% for CA125. For stage III+IV the corresponding values were 94% and 86% respectively. CONCLUSIONS The DK-index warrants further evaluation in independent cohorts.

Proteomic biomarkers for overall and progression‐free survival in ovarian cancer patients

Purpose: To determine if the level of apolipoprotein A1, hepcidin, transferrin, inter‐α trypsin IV internal fragment, transthyretin (TT), connective‐tissue activating protein 3 (CTAP3), serum amyloid A1, β‐2 microglobulin (B2M) might have impact on overall and progression‐free survival for ovarian cancer (OC) patients.

Proteomic analysis of Pichindé virus infection identifies differential expression of prothymosin-alpha.

The arenaviruses include a number of important pathogens including Lassa virus and Junin virus. Presently, the only treatment is supportive care and the antiviral Ribavirin. In the event of an epidemic, patient triage may be required to more effectively manage resources; the development of prognostic biomarker signatures, correlating with disease severity, would allow rational triage. Using a pair of arenaviruses, which cause mild or severe disease, we analyzed extracts from infected cells using SELDI mass spectrometry to characterize potential biomarker profiles. EDGE analysis was used to analyze longitudinal expression differences. Extracts from infected guinea pigs revealed protein peaks which could discriminate between mild or severe infection, and between times post-infection. Tandem mass-spectrometry identified several peaks, including the transcriptional regulator prothymosin-α. Further investigation revealed differences in secretion of this peptide. These data show proof of concept that proteomic profiling of host markers could be used as prognostic markers of infectious disease.

Simultaneous monitoring of multiple kinase activities by SELDI-TOF mass spectrometry.

Cellular response to the external environment is often controlled by one or more protein kinases. We report a methodology for simultaneously monitoring multiple kinase activities across multiple signal-transduction pathways using ProteinChip Array technology. Based on the addition of specific peptide reporters, kinase activity is detected by the presence of a mass shift of 80 Da (or multiple thereof) corresponding to the addition of one or more phosphate groups. These phosphorylated peptide substrates are then enriched using an immobilized metal affinity capture (IMAC)-Ga array and detected directly by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). SELDI-TOF MS is sensitive, tagless (nonradioactive, nonfluorescent), can be easily multiplexed for the analysis of several different kinases in a single reaction mixture (limited only by the specificity of the kinase for its substrate peptides), and is directly scalable through the use of robotic sample processing. By multiplexing kinase assays, one can dramatically increase the amount of information obtained from rare or volume-limited samples. More important, results reflect closely the complex interrelationships between kinases and show high correlation with in vivo assays.

A proteomics panel for predicting optimal primary cytoreduction in stage III/IV ovarian cancer.

The objective of this prospective study was to evaluate CA-125 and a 7-marker panel as predictors of incomplete primary cytoreduction in patients with stage III/IV ovarian cancer (OC). From September 2004 to January 2008, serum from 201 patients referred to surgery for a pelvic tumor was analyzed for CA-125. In addition, serum was analyzed for 7 biomarkers using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. These biomarkers were combined into a single-valued ovarian-cancer-risk index (OvaRI). CA-125 and OvaRI were evaluated as predictors of cytoreduction in 75 stage III/IV patients using receiver operating characteristic curves. Complete primary cytoreduction (no macroscopic residual disease) was achieved in 31% (23/75) of the patients. The area under the receiver operating characteristic curve was 0.66 for CA-125 and 0.75 for OvaRI. The sensitivity and specificity of CA-125 for predicting incomplete cytoreduction were 71% (37/52) and 57% (13/23), respectively (P = 0.04). The sensitivity and specificity of OvaRI for predicting incomplete cytoreduction were 73% (38/52) and 70% (16/23), respectively (P = 0.001). In conclusion, CA-125 and an index of 7 biomarkers were found to be predictors of cytoreduction. However, future studies of biomarkers are anticipated to promote early diagnosis and provide prognostic information to guide treatment of OC patients. In addition, new biomarkers might also play a role in predicting outcome from primary surgery in OC patients.

Optimized Conditions for a Quantitative SELDI TOF MS Protein Assay

The development of peptide/protein analyte assays for the purpose of diagnostic tests is driven by multiple factors, including sample availability, required throughput, and quantitative reproducibility. Laser Desorption/ionization mass spectrometry methods (LDI-MS) are particularly well suited for both peptide and protein characterization, and combining chromatographic surfaces directly onto the MS probe in the form of surface enhanced laser desorption/ionization (SELDI)-biochips has improved the reproducibility of analyte detection and provided effective relative quantitation. Here, we provide methods for developing reproducible SELDI-based assays by providing a complex artificial protein matrix background within the sample to be analyzed that allows for a common and reproducible ionization background as well as internal normalization standards. Using this approach, quantitative assays can be developed with CVs typically less than 10% across assays and days. Although the method has been extensively and successfully implemented in association with a protein matrix from E. coli, any other source for the complex protein matrix can be considered as long as it adheres to a set of conditions including the following: (1) the protein matrix must not provide interferences with the analyte to be detected, (2) the protein matrix must be sufficiently complex such that a majority of ion current generated from the desorption of the sample comes from the complex protein matrix, and (3) specific and well-resolved protein matrix peaks must be present within the mass range of the analyte of interest for appropriate normalization.

Surface-Enhanced Laser Desorption/Ionization (SELDI) Technology

Surface enhanced laser desorption/ionization (SELDI) protein array technology represents a collection of analytical tools and protocols that address the challenges of protein separation, protein purification, and protein detection by mass spectrometry (MS). Commercially, SELDI has been embodied within Ciphergen Biosystems Inc. ProteinChip®Array products (Fremont, CA, USA). First introduced as a commercial product in 1997, this collection of tools has played a significant role, although at times controversial, in the shaping of the proteomics field and in particular the role of “biomarkers” and their relevance to translational medicine. Most recently, SELDI technology has demonstrated the ability to translate the fundamental discovery of protein biomarkers into predictive assays for the purpose of diagnosing the presence of metabolic disease and cancer. This chapter serves as an introduction to the fundamentals of SELDI biochip array technology and providing a recent review of new technologies and achievements in basic proteomic and clinical proteomic research. Keywords: protein biochips; proteomics; translational medicine; SELDI; mass spectrometry