Molecular Signature in HCV-Positive Lymphomas

Hepatitis C virus (HCV) is a positive, single-stranded RNA virus, which has been associated to different subtypes of B-cell non-Hodgkin lymphoma (B-NHL). Cumulative evidence suggests an HCV-related antigen driven process in the B-NHL development. The underlying molecular signature associated to HCV-related B-NHL has to date remained obscure. In this review, we discuss the recent developments in this field with a special mention to different sets of genes whose expression is associated with BCR coupled to Blys signaling which in turn was found to be linked to B-cell maturation stages and NF-κb transcription factor. Even if recent progress on HCV-B-NHL signature has been made, the precise relationship between HCV and lymphoma development and phenotype signature remain to be clarified

Levels of Soluble E-Cadherin in Breast, Gastric, and Colorectal Cancers

Soluble E-cadherin is a 80 kDa protein fragment coming from the proteolytic cleavage of the extracellular domain of the full length epithelial cadherin, a molecule involved in cell adhesion/polarity and tissue morphogenesis. In comparison with normal epithelia, cancer cells show a decreased cadherin-mediated intercellular adhesion, and sE-cad levels normally increase in body fluids (blood and urine). This review focuses on soluble E-cadherin in sera of patients affected by three solid cancers (breast, gastric, and colorectal cancers) and how its levels correlate or not with some cancer parameters (e.g., dimension, progression, and localisation). We will describe the main proteomics approaches adopted to measure sE-cad both in vivo and in vitro and the most important findings about its behaviour in cancer dynamics. The Soluble E-Cadherin The E-cadherins (E-cad), or "classical" cadherins of type I, belong to the large family of cadherins, transmembrane or membrane-associated glycoproteins, mediating cell-cell adhesion and playing a pivotal role in epithelial cell behaviour and tissue morphogenesis/remodelling (reviewed in Other mechanisms potentially influencing E-cad normal functions such as its binding to other proteins include the levels of its phosphorylation together with specific proteolytic events At present, serum levels of sE-cad are known to increase in patients affected by cancer (e.g., breast, gastric, and colorectal cancers; Table 1) in respect to healthy patients, so that there is a growing interest in sE-cad as "candidate sentinel molecule" in cancer research (reviewed by Generally, since the first observations in 1990, the global decrease in E-cad in dissociating/metastasising cancer cells was accompanied by an increase in sE-cad fragments in patient sera, so that the first emerging idea was to consider the soluble sE-cad as originating from the rapid turnover of tumor cells and to relate the sE-cad concentration to the tumor size. Here, we report proteomics applied to the characterization of sE-cad amount in three solid cancers (breast, gastric, and colorectal cancers) and describe the most common techniques adopted since sE-cad discovery. Since sE-cad presence is not only limited to these three pathologies, we also briefly summarized the findings of other works in a recapitulative table Proteomics Approaches Applied to Cadherin Characterization Western Blotting (WB). In most reports, in patients, the sE-cad amount is also evaluated with WB after protein separation by one-dimensional acrylamide gel electrophoresis (1-DE), and it can be compared with the full length E-cad expression, which in turn is analysed by immunostaining in situ. WB analyses reveal the presence of multiple bands, among which are the full length E-cad at 120 kDa and the sEcad at 80 kDa. Reverse Phase Protein Array (RPPA). Another targeted approach was used by Perez-Rivas et al. Soluble E-Cadherin in Breast Cancer In BC patients, first studies started in 2005 when Hofmann and colleagues measured sE-cad levels in sera of 133 patients before and after neoadjuvant chemotherapy with an enzymebased immunoassay technique, and they positively correlated them with the pre-and posttherapeutic tumor size as well as the disease-free interval [34] evaluated by 1-DE and WB (anti-HECD-1) the release of sE-cad in the media of MCF-7/AZ BC cells grown in presence or absence of the nerve growth factor (NGF), a small secreted protein that is important for the development and survival of certain target neurons, and their results supported a relation between sE-cad levels and the BC cell acquisition of an invasive phenotype. In order to identify markers for BC patient response to surgery, the following analyses were addressed to characterize the differential serum proteomes "before versus after surgery" by RPP

Quantitative Plasma Proteomics to Identify Candidate Biomarkers of Relapse in Pediatric/Adolescent Hodgkin Lymphoma

Classical pediatric Hodgkin Lymphoma (HL) is a rare malignancy. Therapeutic regimens for its management may be optimized by establishing treatment response early on. The aim of this study was to identify plasma protein biomarkers enabling the prediction of relapse in pediatric/adolescent HL patients treated under the pediatric EuroNet-PHL-C2 trial. We used untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics at the time of diagnosis—before any therapy—as semiquantitative method to profile plasma proteins specifically associated with relapse in 42 children with nodular sclerosing HL. In both the exploratory and the validation cohorts, six proteins (apolipoprotein E, C4b-binding protein α chain, clusterin, fibrinogen γ chain, prothrombin, and vitronectin) were more abundant in the plasma of patients whose HL relapsed (|fold change| ≥ 1.2, p < 0.05, Student’s t-test). Predicting protein function with the Gene Ontology classification model, the proteins were included in four biological processes (p < 0.01). Using immunoblotting and Luminex assays, we validated two of these candidate biomarkers—C4b-binding protein α chain and clusterin—linked to innate immune response function (GO:0045087). This study identified C4b-binding protein α chain and clusterin as candidate early plasma biomarkers of HL relapse, and important for the purpose of shedding light on the molecular scenario associated with immune response in patients treated under the EuroNet-PHL-C2 trial

Identification of protein clusters predictive of tumor response in rectal cancer patients receiving neoadjuvant chemo-radiotherapy

Preoperative neoadjuvant chemoradiotherapy (nCRT) is the gold standard in locally advanced rectal cancer, only 10-30% of patients achieving benefits. Currently, there is a need of a reliable selection of markers for the identification of poor or non-responders prior to therapy. In this work, we compared protein profiles before therapy of patients differing in their responses to nCRT to find novel predictive markers of response to therapy. Patients were grouped into 3 groups according to their tumor regression grading (TRG) after surgery: 'TRG 1-2', good responders, 'TRG 3' and 'TRG 4', poor responders. Paired surgical specimens of rectal cancer and healthy (histologically confirmed) rectal tissues from 15 patients were analysed before nCRT by two dimensional difference in gel electrophoresis followed by mass spectrometry. Thirty spots were found as differentially expressed (p < 0.05). Among them, 3 spots (spots 471, 683 and 684) showed an increased amount of protein in poor responders compared with good responders, and they were more tumor associated compared with healthy tissues. Proteins of these spots were identified as fibrinogen beta chain fragment D, actin isoforms, B9 and B5 serpins, cathepsin D isoforms and peroxiredoxin-4. In an independent validation set of 20 rectal carcinomas we validated the increased fibrinogen beta chain abundance before nCRT in poor responders by immunoblotting. In conclusion, we propose a risk-stratification tool in predicting the response to nCRT treatment in rectal cancer based on the quantity of these proteins

Cadmium effects on populations of root nuclei in two pea genotypes inoculated or not with the arbuscular mycorrhizal fungus Glomus mosseae

International audiencePlants possess a broad range of strategies to cope with cadmium (Cd) stress, including the arbuscular mycorrhizal (AM) symbiosis. In cell responses towards Cd, the contribution of changes in ploidy levels is still unclear. We used flow cytometry to investigate if nuclear ploidy changes are involved in response mechanisms toward Cd and to analyze the effect of the symbiotic status on populations of nuclei. The impact of Cd was investigated in roots of two pea (Pisum sativum L.) genotypes differing in their Cdsensitivity (Cd-sensitive VIR4788 and Cd-tolerant VIR7128). In pea seedlings grown under hydropony, 25 and 250 μM Cd concentrations lead to an increase in 4 C together with a decrease in 2 C nuclei. The same genotypes, grown in soil/sand substrate, were inoculated or not with the AM fungus Glomus mosseae BEG12 and treated or not with Cd at transplanting (Cd1) or 2 weeks after (Cd2). The Cd2 increased the proportion of 6 and 8 C nuclei in the mycorrhizal VIR4788 and in the non-mycorrhizal VIR7128 genotypes. Thus, changes in ploidy levels reflect pea responses towards Cd, which are modulated by the symbiotic interaction. The Cd-induced increase in ploidy may account for changes in DNA transcription and/or translation

The seed nuclear proteome

OPEN ACCESS Cette revue date de 2010 mini review article Repetto, Ombretta : ex UMR LEG 0102, n'a jamais intégré l'UMR Agro Present adress : CRO, IRCCS, Centro di Riferimento Oncologico, Istituto di Ricovero e Cura a Carattere Scientifico - Proteomics Core Facility, Experimental and Clinical Pharmacology, Aviano PN, Italie. BAP GEAPSI CT2International audienceUnderstanding the regulatory networks coordinating seed development will help to manipulate seed traits, such as protein content and seed weight, in order to increase yield and seed nutritional value of important food crops, such as legumes. Because of the cardinal role of the nucleus in gene expression, sub-proteome analyses of nuclei from developing seeds were conducted, taking advantage of the sequences available for model species. In this review, we discuss the strategies used to separate and identify the nuclear proteins at a stage when the seed is preparing for reserve accumulation. We present how these data provide an insight into the complexity and distinctive features of the seed nuclear proteome. We discuss the presence of chromatin-modifying enzymes and proteins that have roles in RNA-directed DNA methylation and which may be involved in modifying genome architecture in preparation for seed filling. Specific features of the seed nuclei at the transition between the stage of cell divisions and that of cell expansion and reserve deposition are described here which may help to manipulate seed quality traits, such as seed weight

Nuclear proteomics to identify key molecules implicated in reserve accumulation in Medicago truncatula and Pisum sativum seeds

En théorie p 265 du proceeding "Legumes for the benefits of agriculture nutrition and the environment : their genomics, their products, and their improvement", mais erreur : jamais paruNational audienc

Protein signature characterizing Helicobacter pylori strains of patients with autoimmune atrophic gastritis, duodenal ulcer and gastric cancer

Abstract Background Helicobacter pylori (H. pylori) represents a key factor in the etiology of autoimmune atrophic gastritis (AAG), duodenal ulcer (DU) and gastric cancer (GC). The aim of this study was to characterize the differential protein expression of H. pylori isolated from gastric biopsies of patients affected by either AAG, DU or GC. Methods The H. pylori strains were isolated from endoscopic biopsies from the stomach of patients with gastric disease. Protein profiles of H. pylori were compared by two-dimensional difference in gel electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) for the identification of significantly different spots (Student t-test, p 1.5). These spots corresponded to 35 unique proteins. The identity of 7 protein spots was validated after one-dimensional electrophoresis and MS/MS analyses of excised gel portions. In H. pylori isolated from DU-patients a significant increase in proteins with antioxidant activity emerged (AroQ, AspA, FldA, Icd, OorA and ScoB), together with a higher content of proteins counteracting the high acid environment (KatA and NapA). In H. pylori isolated from AAG-patients proteins neutralizing hydrogen concentrations through organic substance metabolic processes decreased (GroL, TrxB and Tuf). In addition, a reduction of bacterial motility (FlhA) was found to be associated with AAG-H. pylori isolates. In GC-H. pylori strains it was found an increase in nucleic acid-binding proteins (e.g. DnaG, Tuf, RpoA, RplU) which may be involved in a higher demand of DNA- and protein-related processes. Conclusion Our data suggest the presence of specific protein signatures discriminating among H. pylori isolated from either AAG, DU or GC. Changes in protein expression profiles evaluated by DIGE succeeded in deciphering part of the molecular scenarios associated with the different H. pylori-related gastric diseases