Comparison of Supervised Classification Methods for Protein Profiling in Cancer Diagnosis

A key challenge in clinical proteomics of cancer is the identification of biomarkers that could allow detection, diagnosis and prognosis of the diseases. Recent advances in mass spectrometry and proteomic instrumentations offer unique chance to rapidly identify these markers. These advances pose considerable challenges, similar to those created by microarray-based investigation, for the discovery of pattern of markers from high-dimensional data, specific to each pathologic state (e.g. normal vs cancer). We propose a three-step strategy to select important markers from high-dimensional mass spectrometry data using surface enhanced laser desorption/ionization (SELDI) technology. The first two steps are the selection of the most discriminating biomarkers with a construction of different classifiers. Finally, we compare and validate their performance and robustness using different supervised classification methods such as Support Vector Machine, Linear Discriminant Analysis, Quadratic Discriminant Analysis, Neural Networks, Classification Trees and Boosting Trees. We show that the proposed method is suitable for analysing high-throughput proteomics data and that the combination of logistic regression and Linear Discriminant Analysis outperform other methods tested

Serum Proteomic Profiling of Lung Cancer in High-Risk Groups and Determination of Clinical Outcomes

HypothesisLung cancer remains the leading cause of cancer-related mortality worldwide. Currently known serum markers do not efficiently diagnose lung cancer at early stage.MethodsIn the present study, we developed a serum proteomic fingerprinting approach coupled with a three-step classification method to address two important clinical questions: (i) to determine whether or not proteomic profiling differs between lung cancer and benign lung diseases in a population of smokers and (ii) to assess the prognostic impact of this profiling in lung cancer. Proteomic spectra were obtained from 170 pathologically confirmed lung cancer or smoking patients with benign chronic lung disease serum samples.ResultsAmong the 228 protein peaks differentially expressed in the whole population, 88 differed significantly between lung cancer patients and benign lung disease, with area under the curve diagnostic values ranging from 0.63 to 0.84. Multiprotein classifiers based on differentially expressed peaks allowed the classification of lung cancer and benign disease with an area under the curve ranging from 0.991 to 0.994. Using a cross-validation methodology, diagnostic accuracy was 93.1% (sensitivity 94.3%, specificity 85.9%), and more than 90% of the stage I/II lung cancers were correctly classified. Finally, in the prognosis part of the study, a 4628 Da protein was found to be significantly and independently associated with prognosis in advanced stage non-small cell lung cancer patients (p = 0.0005).ConclusionsThe potential markers that we identified through proteomic fingerprinting could accurately classify lung cancers in a high-risk population and predict survival in a non-small cell lung cancer population

KRAS Mutation Detection in Paired Frozen and Formalin-Fixed Paraffin-Embedded (FFPE) Colorectal Cancer Tissues

KRAS mutation has been unambiguously identified as a marker of resistance to cetuximab-based treatment in metastatic colorectal cancer (mCRC) patients. However, most studies of KRAS mutation analysis have been performed using homogenously archived CRC specimens, and studies that compare freshly frozen specimens and formalin-fixed paraffin-embedded (FFPE) specimens of CRC are lacking. The aim of the present study was to evaluate the impact of tissue preservation on the determination of KRAS mutational status. A series of 131 mCRC fresh-frozen tissues were first analyzed using both high-resolution melting (HRM) and direct sequencing. KRAS mutations were found in 47/131 (35.8%) using both approaches. Out of the 47 samples that were positive for KRAS mutations, 33 had available matched FFPE specimens. Using HRM, 2/33 (6%) demonstrated suboptimal template amplification, and 2/33 (6%) expressed an erroneous wild-type KRAS profile. Using direct sequencing, 6/33 (18.1%) displayed a wild-type KRAS status, and 3/33 (9.1%) showed discordant mutations. Finally, the detection of KRAS mutations was lower among the FFPE samples compared with the freshly frozen samples, demonstrating that tissue processing clearly impacts the accuracy of KRAS genotyping

HDL Proteome in Hemodialysis Patients: A Quantitative Nanoflow Liquid Chromatography-Tandem Mass Spectrometry Approach

Aside from a decrease in the high-density lipoprotein (HDL) cholesterol levels, qualitative abnormalities of HDL can contribute to an increase in cardiovascular (CV) risk in end-stage renal disease (ESRD) patients undergoing chronic hemodialysis (HD). Dysfunctional HDL leads to an alteration of reverse cholesterol transport and the antioxidant and anti-inflammatory properties of HDL. In this study, a quantitative proteomics approach, based on iTRAQ labeling and nanoflow liquid chromatography mass spectrometry analysis, was used to generate detailed data on HDL-associated proteins. The HDL composition was compared between seven chronic HD patients and a pool of seven healthy controls. To confirm the proteomics results, specific biochemical assays were then performed in triplicate in the 14 samples as well as 46 sex-matched independent chronic HD patients and healthy volunteers. Of the 122 proteins identified in the HDL fraction, 40 were differentially expressed between the healthy volunteers and the HD patients. These proteins are involved in many HDL functions, including lipid metabolism, the acute inflammatory response, complement activation, the regulation of lipoprotein oxidation, and metal cation homeostasis. Among the identified proteins, apolipoprotein C-II and apolipoprotein C-III were significantly increased in the HDL fraction of HD patients whereas serotransferrin was decreased. In this study, we identified new markers of potential relevance to the pathways linked to HDL dysfunction in HD. Proteomic analysis of the HDL fraction provides an efficient method to identify new and uncharacterized candidate biomarkers of CV risk in HD patients

Nouveaux aspects de la biologie de la protéine prion

La protéine prion joue un rôle majeur dans le déclenchement et la transmission des encéphalopathies spongiformes subaiguës transmissibles. Au cours de la maladie, cette protéine adopte une conformation différente lui conférant des propriétés biochimiques nouvelles. En dépit d’avancées significatives, il existe encore de nombreuses incertitudes concernant la fonction normale de la protéine prion et les mécanismes impliqués dans la neurodégénérescence liée à la maladie. Cet article détaille les récents développements de la biologie de la protéine prion tels que la description de nouvelles formes topologiques de la molécule, sa localisation dans des compartiments cellulaires multiples et ses interactions potentielles avec des partenaires. Toutes ces données semblent essentielles pour la compréhension des fonctions physiologiques et pathologiques de la protéine

Nouveaux aspects de la biologie de la protéine prion

La protéine prion joue un rôle majeur dans le déclenchement et la transmission des encéphalopathies spongiformes subaiguës transmissibles. Au cours de la maladie, cette protéine adopte une conformation différente lui conférant des propriétés biochimiques nouvelles. En dépit d’avancées significatives, il existe encore de nombreuses incertitudes concernant la fonction normale de la protéine prion et les mécanismes impliqués dans la neurodégénérescence liée à la maladie. Cet article détaille les récents développements de la biologie de la protéine prion tels que la description de nouvelles formes topologiques de la molécule, sa localisation dans des compartiments cellulaires multiples et ses interactions potentielles avec des partenaires. Toutes ces données semblent essentielles pour la compréhension des fonctions physiologiques et pathologiques de la protéine.Transmissible spongiform encephalopathies form a group of fatal neurodegenerative disorders represented principally by Creutzfeldt-Jakob disease in humans, and by scrapie and bovine spongiform encephalopathy in animals. Also called prion diseases, these disorders are infectious, sporadic, or genetic in origin. Although the nature of the responsible agent of these diseases is uncertain, it is clear that a protein called PrPSc plays a central role in their pathology. PrPSc is a conformational variant of a normal protein called PrPC. PrPC is a glycoprotein expressed by most tissues and is attached on the cell membrane through a glycosyl-phosphatidylinositol anchor, which is consistent with roles in cell adhesion, ligand uptake, or transmembrane signaling. NMR studies revealed that the protein has a globular domain and a long amino-terminal tail that contains repeated octapeptide domains, which bind metal ions with high affinities. PrPC is localized on the cell membrane in detergent resistant microdomains and may be part of functional complexes with other molecules such as N-CAM, Laminin or kinases. This is particularly relevant in view of the possible role of the molecule in signal transduction, resistance to oxidative stress and neuronal survival. The description both in vitro and in vivo, of a transmembrane form of PrP that can accumulate in the endoplasmic reticulum has attracted a lot of attention. The role of such isoforms in neurodegeneration, as well as the presence of PrP into the cytoplasm and in the nucleus where it may interact with nucleic acids are still debated. In conclusion, it appeared that the understanding of the PrP biology is essential to the understanding of the physiological function of this protein as well as for its pathological conversion since its trafficking governs the generation of PrPSc

Étude de la réaction immunitaire humorale aux cancers par des approches protéomiques

International audienceDiscovery of new serum biomarkers exhibiting an increased sensitivity and specificity for cancer are of major importance for diagnosis improvement. There is considerable evidence for an immune response to cancer in humans, as demonstrated in part by the identification of autoantibodies against a number of tumour-associated antigens in sera from patients with different cancer types. Thus, identification of tumour-associated antigens and their associated antibodies is a promising strategy to find relevant biomarkers. Proteomic approaches such as SEREX and SERPA have allowed identification of great numbers of antigens and their cognate autoantibodies during these past few years. They show many advantages, and allowed identification of relevant autoantigens in different types of cancer. However, they are also time consuming, and lack sensibility and specificity. To circumvent these drawbacks, new proteomic techniques, based on protein or antibody arrays, allow high throughput analysis of multiple targets in a single experiment. Specific combinations of markers should thus be identified, theoretically being more efficient to detect a tumor compared to a single marker. In conclusion, these approaches promise great advances in the field of biomarkers for cancer. They also further need to be validated for clinical application on large populations

Use of autoantibodies to detect the onset of breast cancer

International audienceThe widespread use of screening mammography has resulted in increased detection of early-stage breast disease, particularly for in situ carcinoma and early-stage breast cancer. However, the majority of women with abnormalities noted on screening mammograms are not diagnosed with cancer because of several factors, including radiologist assessment, patient age, breast density, malpractice concerns, and quality control procedures. Although magnetic resonance imaging is a highly sensitive detection tool that has become standard for women at very high risk of developing breast cancer, it lacks sufficient specificity and costeffectiveness for use as a general screening tool. Therefore, there is an important need to improve screening and diagnosis of early-invasive and noninvasive tumors, that is, in situ carcinoma. The great potential for molecular tools to improve breast cancer outcomes based on early diagnosis has driven the search for diagnostic biomarkers. Identification of tumor-specific markers capable of eliciting an immune response in the early stages of tumor development seems to provide an effective approach for early diagnosis. The aim of this review is to describe several autoantibodies identified during breast cancer diagnosis. We will focus on these molecules highlighted in the past two years and discuss the potential future use of autoantibodies as biomarkers of early-stage breast cancer