In silico prediction discontinuous B cell epitope peptide vaccine against leishmaniasis

Introduction: The kinetoplastid protozoan parasites of the genus Leishmania cause diseases for which treatment is difficult and there is still no vaccine for use in humans. Leishmanolysin is the major enzymatic protein component of the promastigote surface. Because of its role as a ligand involved in the interaction of the parasite with defensive systems of the host, including components of the complement system and the macrophage surface is an attractive candidate for designing peptide vaccines.  Methods and Results: In the current study, PEPOP was used to predict peptides from Leishmanolysin in the form of discontinuous B-cell epitopes. PEPOP identified segments comprised of accessible and sequence continuous amino acids. These segments were clustered according to their spatial distances using method of extensions: Optimized Nearest Neighbor (ONN), Optimized Flanking Nearest Neighbor (OFN), Optimized Patched segments Path (OPP), Traveling Salesman Problem (TSP), and Shortest Path (SHP). Each peptide sequence has been generally comprised of several segments. From 3D structure of Leishmanolysin, PEPOP identified 100 segments gathered in three clusters according to their spatial distances. In this study, we wanted to predict peptides from a specific region of the protein, the residue 264-345 on the active site of Leishmanolysin. It corresponds to the segments S34 to S48. The predicted peptides, which did not relate to this region (264-345) were removed and at last 29 peptides were selected. Conclusions: These results using bioinformatics analyses could be conducted in vaccine design against Leishmania infections

Identification of B and T cell epitope peptide vaccines from IGF-1 Receptor in breast cancer

Introduction: The insulin-like growth factor-1 receptor (IGF-1R) plays a key role in proliferation, growth, differentiation, and development of several human malignancies including breast and pancreatic adenocarcinoma. IGF-1R targeted immunotherapeutic approaches are particularly attractive, as they may potentially elicit even stronger antitumor responses than traditional targeted approaches. Cancer peptide vaccines can produce immunologic responses against cancer cells by triggering helper T cell (Th) or cytotoxic T cells (CTL) in association with Major Histocompatibility Complex (MHC) class I or II molecules on the cell surface of antigen presenting cells.  Methods and Results: In our previous study, we set a technique based on molecular docking in order to find the best MHC class I and II binder peptides using GOLD. In the present work, molecular docking analyses on a library consisting of 30 peptides mimicking discontinuous epitopes from IGF-1R extracellular domain identified peptides 249 and 86, as the best MHC binder peptides to both MHC class I and II molecules. The receptors most often targeted by peptide 249 are HLA-DR4, HLA-DR3 and HLA-DR2 and those most often targeted by peptide 86 are HLA-DR4, HLA-DP2 , and HLA-DR3. Conclusions: These findings, based on bioinformatics analyses, can be conducted in further experimental analyses in cancer therapy and vaccine design

PEPOP: Computational design of immunogenic peptides

© 2008 Moreau et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

J Biol Chem

The GTPase-activating protein (GAP) p190RhoGAP (p190A) is encoded by ARHGAP35 which is found mutated in cancers. p190A is a negative regulator of the GTPase RhoA in cells and must be targeted to RhoA-dependent actin-based structures to fulfill its roles. We previously identified a functional region of p190A called the PLS (protrusion localization sequence) required for localization of p190A to lamellipodia but also for regulating the GAP activity of p190A. Additional effects of the PLS region on p190A localization and activity need further characterization. Here, we demonstrated that the PLS is required to target p190A to invadosomes. Cellular expression of a p190A construct devoid of the PLS (p190AΔPLS) favored RhoA inactivation in a stronger manner than WT p190A, suggesting that the PLS is an autoinhibitory domain of p190A GAP activity. To decipher this mechanism, we searched for PLS-interacting proteins using a two-hybrid screen. We found that the PLS can interact with p190A itself. Coimmunoprecipitation experiments demonstrated that the PLS interacts with a region in close proximity to the GAP domain. Furthermore, we demonstrated that this interaction is abolished if the PLS harbors cancer-associated mutations: the S866F point mutation and the Δ865-870 deletion. Our results are in favor of defining PLS as an inhibitory domain responsible for masking the p190A functional GAP domain. Thus, p190A could exist in cells under two forms: an inactive closed conformation with a masked GAP domain and an open conformation allowing p190A GAP function. Altogether, our data unveil a new mechanism of p190A regulation

Reuniting philosophy and science to advance cancer research

Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer

Analyse bioinformatique des sites d'intéractions protéine-protéine et prédictions épitopiques

Pour mieux comprendre les interactions protéine-protéine, deux outils bioinformatiques dédiés à la prédiction d'épitopes ont été conçus. Le premier, MIMOP, localise l'épitope par analyse de la séquence de mimotopes sélectionnés par l'anticorps (Ac) reconnaissant l'antigène (Ag). MIMOP propose deux approches : l'une recherche des similarités de séquences entre Ag et mimotopes, l'autre recherche sur l'Ag des résidus clés identifiés dans les séquences des mimotopes. Le deuxième outil, PEPOP, prédit des séquences peptidiques à partir de la structure 3D de l'Ag. Ces peptides permettent soit de localiser l'épitope (peptides antigéniques) soit d'obtenir des Acs ciblant une zone spécifique de l'Ag (peptides immunogéniques). Les différentes méthodes de conception des peptides sont basées sur l'identification de segments à la surface de l'Ag et leurs distances spatiales. La performance des deux outils a été validée par comparaison des prédictions avec des données expérimentales.MONTPELLIER-BU Pharmacie (341722105) / SudocPARIS-BIUP (751062107) / SudocSudocFranceF

Etude de la formation des podosomes dans les cellules endothéliales (signalisation par le PKCs et les GTPases de la famille Rho)

Les podosomes sont des structures adhérentes, riches en actine polymérisée, et sont naturellement retrouvés dans les cellules d'origine hématopoïétique comme les ostéoclastes, les cellules dendritiques ou les macrophages. Ces structures ont été découvertes pour la première fois dans les cellules endothéliales au sein du laboratoire en réponse à l'activation d'une protéine régulatrice de la polymérisation du cytosquelette d'actine, la GTPase Cdc42. Au cours de mon projet de thèse, nous avons exploré les voies de signalisation mises en jeu dans la formation des podosomes. L'activation des PKCs par les esters de phorbol dans les cellules endothéliales primaires HUVECs induit un profond réarrangement du cytosquelette d'actine, et la formation de ces structures ponctuelles. La GTPase Cdc42 est essentielle à la formation des podosomes, et son activité est sous le contrôle des PKCs dans les cellules endothéliales. Les podosomes sont des structures qui adhérent à la matrice extracellulaire à l'aide des intégrines, et sont dotés d'une capacité de dégradation de la matrice extracellulaire par le recrutement de métalloprotéases. Cette activité protéolytique associée aux podosomes et l'implication des PKCs dans l'angiogénèse nous amène à formuler l'hypothèse, que ces structures sont impliquées dans le remodelage vasculaire.BORDEAUX1-BU Sciences-Talence (335222101) / SudocSudocFranceF

p190RhoGAPs, the <i>ARHGAP35</i>- and <i>ARHGAP5</i>-Encoded Proteins, in Health and Disease

Small guanosine triphosphatases (GTPases) gathered in the Rat sarcoma (Ras) superfamily represent a large family of proteins involved in several key cellular mechanisms. Within the Ras superfamily, the Ras homolog (Rho) family is specialized in the regulation of actin cytoskeleton-based mechanisms. These proteins switch between an active and an inactive state, resulting in subsequent inhibiting or activating downstream signals, leading finally to regulation of actin-based processes. The On/Off status of Rho GTPases implicates two subsets of regulators: GEFs (guanine nucleotide exchange factors), which favor the active GTP (guanosine triphosphate) status of the GTPase and GAPs (GTPase activating proteins), which inhibit the GTPase by enhancing the GTP hydrolysis. In humans, the 20 identified Rho GTPases are regulated by over 70 GAP proteins suggesting a complex, but well-defined, spatio-temporal implication of these GAPs. Among the quite large number of RhoGAPs, we focus on p190RhoGAP, which is known as the main negative regulator of RhoA, but not exclusively. Two isoforms, p190A and p190B, are encoded by ARHGAP35 and ARHGAP5 genes, respectively. We describe here the function of each of these isoforms in physiological processes and sum up findings on their role in pathological conditions such as neurological disorders and cancers