Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus)

Host-pathogen interactions are a major evolutionary force promoting local adaptation. Genes of the major histocompatibility complex (MHC) represent unique candidates to investigate evolutionary processes driving local adaptation to parasite communities. The present study aimed at identifying the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of European minnows (Phoxinus phoxinus). To this end, we isolated and genotyped exon 2 of two MHCIIB gene duplicates (DAB1 and DAB3) and 1665 amplified fragment length polymorphism (AFLP) markers in nine populations, and characterized local bacterial communities by 16S rDNA barcoding using 454 amplicon sequencing. Both MHCIIB loci exhibited signs of historical balancing selection. Whereas genetic differentiation exceeded that of neutral markers at both loci, the populations' genetic diversities were positively correlated with local pathogen diversities only at DAB3. Overall, our results suggest pathogen-mediated local adaptation in European minnows at both MHCIIB loci. While at DAB1 selection appears to favor different alleles among populations, this is only partially the case in DAB3, which appears to be locally adapted to pathogen communities in terms of genetic diversity. These results provide new insights into the importance of host-pathogen interactions in driving local adaptation in the European minnow, and highlight that the importance of adaptive processes driving MHCIIB gene evolution may differ among duplicates within species, presumably as a consequence of alternative selective regimes or different genomic context.

Modeling of the TCR-MHC-peptide complex.

The methodology for generating a homology model of the T1 TCR-PbCS-K(d) class I major histocompatibility complex (MHC) class I complex is presented. The resulting model provides a qualitative explanation of the effect of over 50 different mutations in the region of the complementarity determining region (CDR) loops of the T cell receptor (TCR), the peptide and the MHC's alpha(1)/alpha(2) helices. The peptide is modified by an azido benzoic acid photoreactive group, which is part of the epitope recognized by the TCR. The construction of the model makes use of closely related homologs (the A6 TCR-Tax-HLA A2 complex, the 2C TCR, the 14.3.d TCR Vbeta chain, the 1934.4 TCR Valpha chain, and the H-2 K(b)-ovalbumine peptide), ab initio sampling of CDR loops conformations and experimental data to select from the set of possibilities. The model shows a complex arrangement of the CDR3alpha, CDR1beta, CDR2beta and CDR3beta loops that leads to the highly specific recognition of the photoreactive group. The protocol can be applied systematically to a series of related sequences, permitting the analysis at the structural level of the large TCR repertoire specific for a given peptide-MHC complex.

Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism.

Abstract The plasmid pME6863, carrying the aiiA gene from the soil bacterium Bacillus sp. A24 that encodes a lactonase enzyme able to degrade N-acyl-homoserine lactones (AHLs), was introduced into the rhizosphere isolate Pseudomonas fluorescens P3. This strain is not an effective biological control agent against plant pathogens. The transformant P. fluorescens P3/pME6863 acquired the ability to degrade AHLs. In planta, P. fluorescens P3/pME6863 significantly reduced potato soft rot caused by Erwinia carotovora and crown gall of tomato caused by Agrobacterium tumefaciens to a similar level as Bacillus sp. A24. Little or no disease reduction was observed for the wild-type strain P3 carrying the vector plasmid without aiiA. Suppression of potato soft rot was observed even when the AHL-degrading P. fluorescens P3/pME6863 was applied to tubers 2 days after the pathogen, indicating that biocontrol was not only preventive but also curative. When antagonists were applied individually with the bacterial plant pathogens, biocontrol activity of the AHL degraders was greater than that observed with several Pseudomonas 2,4-diacetylphloroglucinol-producing strains and with Pseudomonas chlororaphis PCL1391, which relies on production of phenazine antibiotic for disease suppression. Phenazine production by this well characterized biological control strain P. chlororaphis PCL1391 is regulated by AHL-mediated quorum sensing. When P. chlororaphis PCL1391 was co-inoculated with P. fluorescens P3/pME6863 in a strain mixture, the AHL degrader interfered with the normally excellent ability of the antibiotic producer to suppress tomato vascular wilt caused by Fusarium oxysporum f. sp. lycopersici. Our results demonstrate AHL degradation as a novel biocontrol mechanism, but also demonstrate the potential for non-target interactions that can interfere with the biocontrol efficacy of other strains.

Diabetes mellitus, a microRNA-related disease?

Diabetes mellitus is a complex disease resulting in altered glucose homeostasis. In both type 1 and type 2 diabetes mellitus, pancreatic β cells cannot secrete appropriate amounts of insulin to regulate blood glucose level. Moreover, in type 2 diabetes mellitus, altered insulin secretion is combined with a resistance of insulin-target tissues, mainly liver, adipose tissue, and skeletal muscle. Both environmental and genetic factors are known to contribute to the development of the disease. Growing evidence indicates that microRNAs (miRNAs), a class of small noncoding RNA molecules, are involved in the pathogenesis of diabetes. miRNAs function as translational repressors and are emerging as important regulators of key biological processes. Here, we review recent studies reporting changes in miRNA expression in tissues isolated from different diabetic animal models. We also describe the role of several miRNAs in pancreatic β cells and insulin-target tissues. Finally, we discuss the possible use of miRNAs as blood biomarkers to prevent diabetes development and as tools for gene-based therapy to treat both type 1 and type 2 diabetes mellitus.

Adherence as a predictor of the development of class-specific resistance mutations: the Swiss HIV Cohort Study.

BACKGROUND: Non-adherence is one of the strongest predictors of therapeutic failure in HIV-positive patients. Virologic failure with subsequent emergence of resistance reduces future treatment options and long-term clinical success. METHODS: Prospective observational cohort study including patients starting new class of antiretroviral therapy (ART) between 2003 and 2010. Participants were naïve to ART class and completed ≥1 adherence questionnaire prior to resistance testing. Outcomes were development of any IAS-USA, class-specific, or M184V mutations. Associations between adherence and resistance were estimated using logistic regression models stratified by ART class. RESULTS: Of 314 included individuals, 162 started NNRTI and 152 a PI/r regimen. Adherence was similar between groups with 85% reporting adherence ≥95%. Number of new mutations increased with increasing non-adherence. In NNRTI group, multivariable models indicated a significant linear association in odds of developing IAS-USA (odds ratio (OR) 1.66, 95% confidence interval (CI): 1.04-2.67) or class-specific (OR 1.65, 95% CI: 1.00-2.70) mutations. Levels of drug resistance were considerably lower in PI/r group and adherence was only significantly associated with M184V mutations (OR 8.38, 95% CI: 1.26-55.70). Adherence was significantly associated with HIV RNA in PI/r but not NNRTI regimens. CONCLUSION: Therapies containing PI/r appear more forgiving to incomplete adherence compared with NNRTI regimens, which allow higher levels of resistance, even with adherence above 95%. However, in failing PI/r regimens good adherence may prevent accumulation of further resistance mutations and therefore help to preserve future drug options. In contrast, adherence levels have little impact on NNRTI treatments once the first mutations have emerged.

Development and evaluation of antibody-MHC/peptide conjugates as a new form of cancer immunotherapy

Summary One of the major goals of cancer immunotherapy is the induction of a specific and effective antitumor cytotoxic T lymphocyte (CTL) response. However, the downregulation of Class I Major Histocompatibility Complexes (MHC) expression and the low level of tumor peptide presentation on tumor cell surface, ás well as the low immunogenicity of tumor specific antigens, limit the effectiveness of anti-tumor CTL responses. On the other hand, monoclonal antibodies, which bind with high affinity to tumor cell surface markers, are powerful tumor targeting tools. However, their capacity to .kill cancer cells is limited and mAb cancer treatments usually require the addition of different form of chemotherapy. The new cancer immunotherapy strategy described herein combines the advantage of the high tumor targeting capacity of monoclonal antibodies (mAb) with the powerful cytotoxicity of CD8 T lymphocytes directed against highly antigenic peptide-MHC complexes. Monoclonal antibody Fab fragments directed against a cell surface tumor associated antigen (TAA) are chemically coupled to soluble MHC class I complexes carrying a highly antigenic peptide. Antibody guided targeting and oligomerization of numerous antigenic class IMHC/peptide complexes on tumor cell surfaces can redirect the cytotoxicity of peptide-specific CD8 T cells towards target cancer cells. After the description of the production of murine anti-tumor xMHC/peptide conjugates in the first part of this thesis, the therapeutic potential of such conjugates were sequentially investigated in different syngeneic tumor mouse models. As a first proof of principle, transgenic OT-1 mice and later CEA transgenic C57BL/6 (B6) mice, adoptively transferred with OT-1 spleen cells and immunized with ovalbumin, were used as a model of high frequency of ova peptide specific T cells. In these mice, growth inhibition and regression of palpable colon carcinoma expressing CEA, were obtained by systemic injection of anti-CEA Fab/H-2Kb/ova peptide conjugates. Next, LCMV virus and influenza virus infection of B6 mice were used as viral models to redirect natural antiviral CTL responses to tumors via conjugates loaded with viral peptides. We showed that in mice infected with the LCMV virus, subcutaneous CEA-expressing tumor cells were inhibited by the H2Db/GP33 restricted anti-viral CTL response when preincubated before grafting with anti-CEA Fab-H-2Db/GP33 peptide conjugates. In mice infected with the influenza virus, lung metastases expressing the HER2 antigen were inhibited by the H-2Db/NP366 restricted CTLs response when preincubated before injection with anti-Her2 Fab-H-2Db/NP366 peptide conjugates. In the last chapter, the stability of the peptide in the anti-CEA Fab-H-2Db/GP33 conjugates was improved by the covalent photocross-link of the GP33 peptide in the H-2Db MHC groove. Thus, LCMV immune mice could reject CEA expressing tumors when treated with systemic injections of anti-CEA FabH-2Db/GP33 cross-linked conjugates. These results are encouraging for the potential application of this strategy in clinic. Such conjugates could be used alone in patients boosted by the relevant virus, or used in combination with existing T cell based ìmmunotherapy. Résumé Une des principales approches utilisées dans l'immunothérapie contre le cancer consiste en l'induction d'une réponse T cytotoxique (CTL) spécifiquement dirigée contre la tumeur. Cependant, le faible niveau d'expression des complexes majeurs d'histocompatibilité de classe I (CMH I) et de présentation des peptides tumoraux à la surface des cellules cancéreuses ainsi que la faible immunogenicité des antigens tumoraux, limitent l'efficacité de la réponse CTL. D'autre part,. l'injection d'anticorps monoclonaux (mAb), se liant avec une haute affinité aux marqueurs de surface des cellules tumorales, a fourni des résultats cliniques encourageant. Cependant l'efficacité de ces mAbs contre des tumeur solides reste limitée et necessite souvent l'addition de chimiotherapie. La nouvelle stratégie thérapeutique décrite dans ce travail associe le fort pouvoir de localisation des anticorps monoclonaux et le fort pouvoir cytotoxique des lymphocytes T CD8+. Des fragments Fab d'anticorps monoclonaux, dirigés contre des antigènes surexprimés à la surface de cellules tumorales, ont été chimiquement couplés à des CMH I solubles, portant un peptide fortement antigénique. Le ciblage et l'oligomérisation à la surface des cellules tumorales de nombreux CMH I présentant un peptide antigénique, va réorienter la cytotoxicité des cellules T CD8+ spécifiques du peptide présenté, vers les cellules tumorales cibles. Après une description de la production de conjugé anti-tumeur x CMH Upeptide dans la première partie de cette thèse, le potentiel thérapeutique de tels conjugés a été successivement étudiés in vivo dans différents modèles de tumeur syngénéiques. Tout d'abord, des souris OT-1 transgéniques, puis des souris C57BL/6 (B6) transférées avec des cellules de rate OT-1 puis immunisées avec l'ovalbumine, ont été employées comme modèle de haute fréquence de cellules T CD8+ spécifiques du peptide ova. Chez ces souris, l'inhibition de la croissance et la régression de nodules palpables de carcinomes exprimant l'antigène caccino embryonaire (ACE), ont été obtenues par l'injection systémique de conjugés anti-ACE Fab/H-2Kb/ova. Par la suite, l'infection de souris B6 par le virus LCMV et par le virus de la grippe, ont été utilisés comme modèles viraux pour redirigées des réponses anti-virales naturelles vers les tumeurs, en utilisant des conjugés chargés avec des peptides viraux. Nous avons montré que .chez les souris infectées par le LCMV, la croissance de carcinome sous-cutané est empêchée par la réponse anti-virale, spécifique du complexe H2Db/GP33, lorsque les cellules tumorales greffées sont pré-incubées avec des conjugés anti-CEA Fab-H-2Db/GP33. Dans le cas de souris infectées par le virus de la grippe, la métastatisation de mélanomes pulmonaires exprimant l'antigène HER-2 est inhibée par la réponse anti-virale spécifique du complexe H-2Db/NP366, après pré-incubation des cellules tumorales avec des conjugés anti-Her2 FabxH-2Db/NP366. Dans le dernier chapitre, la liaison covalente du peptide GP33 dans le complexe H-2Db a amélioré la stabilité des conjugés correspondants et a permis le traitement systémique de souris greffées avec des tumeurs exprimant l'ACE et infectées par le LCMV. L'ensemble de ces résultats sont encourageant pour l'application de cette strategie en clinique. De tels conjugués pourraient être employés seuls ou en combinaison avec des protocols d'immunisation peptidique anti-tumoral. Résumé pour un large public Dans les pays industrialisés, le cancer se situe au deuxième rang des causes de mortalité après les maladies cardiovasculaires. Les principaux traitement de nombreux cancers sont la chirurgie, en association avec la radiothérapie et la chimiothérapie. L'immunothérapie est l'une des nouvelles approches mises en oeuvre pour la lutte contre le cancer. Elle peut être humorale, et s'appuyer alors sur la perfusion d'anticorps monoclonaux dirigés contre des antigènes tumoraux, par exemple les anticorps dirigés contre les protéines oncogéniques Her-2/neu dans le cancer du sein. Ces anticorps ont le grand avantage de spécifiquement se localiser à la tumeur et d'induire la lyse ou d'inhiber la proliferation des cellules tumorales exprimant l'antigène. Certains sont utilisés en clinique pour le traitement de lymphomes, de carcinomes de l'ovaire et du sein ou encore de carcinomes metastatiques du côlon. Cependant l'efficacité de ces anticorps contre des tumeurs solides reste limitée et les traitements exigent souvent d'être combiner avec de la chimiothérapie. L'immunothérapie spécifique peut également être cellulaire et reposer sur une démarche de type vaccinal, consistant à générer des lymphocytes T cytotoxiques (cytotoxic T lymphocytes :CTL) capables de détruire spécifiquement les cellules malignes. Pour obtenir une réponse lymphocytaire T cytotoxique antitumorale, la cellule T doit reconnaître un antigène associé à la tumeur, présenté sous forme de peptide dans un complexe majeur d'histocompatibilité de classe I. Or les cellules tumorales ne presentent pas efficacement les peptides antigèniques, car elles se caractérisent par une diminution ou une absence d'expression des antigènes d'histocompatibilité de classe I, des molécules d'adhésion et des cytokines costimulatrices, et par une faible expression des antigènes associés aux tumeurs. C'est en partie pourquoi, malgré l'induction de fortes réponses CTL specifiquement dirigés contre des antigens tumoraux, les régressions tumorales obtenus grace à ces vaccinations sont relativement rares. Alors que chez les personnes atteintes du cancer on observe l'instauration d'une tolérance immunitaire vis-à-vis de la tumeur, à l'inverse, notre systeme immunitaire reste parfaitement capable de combattre des infection virales classiques, tels que la grippe, qui font aussi appel à une réponse T cytotoxique. Notre groupe de recherche a donc eu l'idee de développer une nouvelle approche thérapeutique où une réponse immunitaire anti-virale très efficace serait redirigée vers les tumeurs par des anticorps monoclonaux. Concrètement, nous avons chimiquement couplés des fragments d'anticorps monoclonaux dirigés contre des antigènes surexprimés à la surface de cellules tumorales, à des CMH I portant un peptide viral antigénique. Les cellules tumorales, ciblées par le fragment anticorps et couvertes d' antigènes viraux présentés par des molécules de CMH I, peuvent ainsi tromper les lymphocytes cytotoxiques anti-viraux qui vont détruire les cellules tumorales comme si elles étaient infectées par le virus. Suite à des résultats prometteurs obtenus in vitro avec différents conjugués anticorps-CMH humain de type HLA.A2/peptide Flu, le but du projet était de tester in vivo des conjugués anticorps-CMH I murins sur des modèles expérimentaux de souris. Tout d'abord, des souris transgéniques pour un recepteur T specifique du peptide ova, puis des transferts adoptifs de ces cellules T specifiques dans des souris immunocompétentes, ont été choisi comme modèle de haute fréquence des cellules T spécifiques, et ont permi de valider le principe de la strategie in vivo. Puis, deux modèles viraux ont été elaboré avec le virus LCMV et le virus Influenza, pour réorienter des réponses antivirales naturelles vers les tumeurs grâce à des conjugés chargés avec des peptides viraux. Nous avons montré la grande capacité de nos conjugués à rediriger des réponses cytotoxiques vers les tumeurs et inhiber la croissance de tumeurs syngénéiques sous cutanés et pulmonaires. Ces résultats d'inhibition tumorales obtenus dans des souris immunocompétentes, grâce à l'injection de conjugués anticorps xCMH/peptide et réorientant deux réponses antivirales différentes vers deux modèles tumoraux syngeneiques, sont encourageant pour l'application de cette nouvelle stratégie en clinique.

Natalizumab treatment alters the expression of T-cell trafficking marker LFA-1 α-chain (CD11a) in MS patients.

OBJECTIVE: To determine the long-term effect of natalizumab (NTZ) treatment on the expression of integrins and chemokine receptors involved in the migration of T cells towards the central nervous system (CNS). METHODS: We drew the blood of 23 patients just before starting NTZ therapy and every 12 months thereafter, for up to 48 months of treatment. We assessed the ex-vivo expression of phenotype markers (CCR7 and CD45RA), CNS-addressing integrins (CD11a, CD49d and CD29) and chemokine receptors (CXCR3 and CCR6) in CD4+ or CD8+ T-cell subsets by flow cytometry. RESULTS: As compared to the pre-NTZ values, there was a marked increase in central memory (CCR7+/CD45RA-) CD4+ T cells and in effector memory (CCR7-/CD45RA-) CD8+ T cells at 12 and 24 months. In addition to an expected downregulation of both VLA-4 subunits (CD49d/CD29), we also found decreased T-cell expression of CXCR3 at 12 months, and of CD11a (LFA-1 αL subunit) at 12 months, but mostly at 24 months of NTZ treatment. CONCLUSION: Our data show a nadir of CD11a expression at 2 years of NTZ treatment, at the peak of incidence of progressive multifocal leukoencephalopathy (PML), indirectly suggesting that a lack of these molecules may play a role in the onset of PML in NTZ-treated patients.

Molecular modeling study of the binding and signaling properties of the TCRpMHC complex

The activation of the specific immune response against tumor cells is based on the recognition by the CD8+ Cytotoxic Τ Lymphocytes (CTL), of antigenic peptides (p) presented at the surface of the cell by the class I major histocompatibility complex (MHC). The ability of the so-called T-Cell Receptors (TCR) to discriminate between self and non-self peptides constitutes the most important specific control mechanism against infected cells. The TCR/pMHC interaction has been the subject of much attention in cancer therapy since the design of the adoptive transfer approach, in which Τ lymphocytes presenting an interesting response against tumor cells are extracted from the patient, expanded in vitro, and reinfused after immunodepletion, possibly leading to cancer regression. In the last decade, major progress has been achieved by the introduction of engineered lypmhocytes. In the meantime, the understanding of the molecular aspects of the TCRpMHC interaction has become essential to guide in vitro and in vivo studies. In 1996, the determination of the first structure of a TCRpMHC complex by X-ray crystallography revealed the molecular basis of the interaction. Since then, molecular modeling techniques have taken advantage of crystal structures to study the conformational space of the complex, and understand the specificity of the recognition of the pMHC by the TCR. In the meantime, experimental techniques used to determine the sequences of TCR that bind to a pMHC complex have been used intensively, leading to the collection of large repertoires of TCR sequences that are specific for a given pMHC. There is a growing need for computational approaches capable of predicting the molecular interactions that occur upon TCR/pMHC binding without relying on the time consuming resolution of a crystal structure. This work presents new approaches to analyze the molecular principles that govern the recognition of the pMHC by the TCR and the subsequent activation of the T-cell. We first introduce TCRep 3D, a new method to model and study the structural properties of TCR repertoires, based on homology and ab initio modeling. We discuss the methodology in details, and demonstrate that it outperforms state of the art modeling methods in predicting relevant TCR conformations. Two successful applications of TCRep 3D that supported experimental studies on TCR repertoires are presented. Second, we present a rigid body study of TCRpMHC complexes that gives a fair insight on the TCR approach towards pMHC. We show that the binding mode of the TCR is correctly described by long-distance interactions. Finally, the last section is dedicated to a detailed analysis of an experimental hydrogen exchange study, which suggests that some regions of the constant domain of the TCR are subject to conformational changes upon binding to the pMHC. We propose a hypothesis of the structural signaling of TCR molecules leading to the activation of the T-cell. It is based on the analysis of correlated motions in the TCRpMHC structure. - L'activation de la réponse immunitaire spécifique dirigée contre les cellules tumorales est basée sur la reconnaissance par les Lymphocytes Τ Cytotoxiques (CTL), d'un peptide antigénique (p) présenté à la suface de la cellule par le complexe majeur d'histocompatibilité de classe I (MHC). La capacité des récepteurs des lymphocytes (TCR) à distinguer les peptides endogènes des peptides étrangers constitue le mécanisme de contrôle le plus important dirigé contre les cellules infectées. L'interaction entre le TCR et le pMHC est le sujet de beaucoup d'attention dans la thérapie du cancer, depuis la conception de la méthode de transfer adoptif: les lymphocytes capables d'une réponse importante contre les cellules tumorales sont extraits du patient, amplifiés in vitro, et réintroduits après immunosuppression. Il peut en résulter une régression du cancer. Ces dix dernières années, d'importants progrès ont été réalisés grâce à l'introduction de lymphocytes modifiés par génie génétique. En parallèle, la compréhension du TCRpMHC au niveau moléculaire est donc devenue essentielle pour soutenir les études in vitro et in vivo. En 1996, l'obtention de la première structure du complexe TCRpMHC à l'aide de la cristallographie par rayons X a révélé les bases moléculaires de l'interaction. Depuis lors, les techniques de modélisation moléculaire ont exploité les structures expérimentales pour comprendre la spécificité de la reconnaissance du pMHC par le TCR. Dans le même temps, de nouvelles techniques expérimentales permettant de déterminer la séquence de TCR spécifiques envers un pMHC donné, ont été largement exploitées. Ainsi, d'importants répertoires de TCR sont devenus disponibles, et il est plus que jamais nécessaire de développer des approches informatiques capables de prédire les interactions moléculaires qui ont lieu lors de la liaison du TCR au pMHC, et ce sans dépendre systématiquement de la résolution d'une structure cristalline. Ce mémoire présente une nouvelle approche pour analyser les principes moléculaires régissant la reconnaissance du pMHC par le TCR, et l'activation du lymphocyte qui en résulte. Dans un premier temps, nous présentons TCRep 3D, une nouvelle méthode basée sur les modélisations par homologie et ab initio, pour l'étude de propriétés structurales des répertoires de TCR. Le procédé est discuté en détails et comparé à des approches standard. Nous démontrons ainsi que TCRep 3D est le plus performant pour prédire des conformations pertinentes du TCR. Deux applications à des études expérimentales des répertoires TCR sont ensuite présentées. Dans la seconde partie de ce travail nous présentons une étude de complexes TCRpMHC qui donne un aperçu intéressant du mécanisme d'approche du pMHC par le TCR. Finalement, la dernière section se concentre sur l'analyse détaillée d'une étude expérimentale basée sur les échanges deuterium/hydrogène, dont les résultats révèlent que certaines régions clés du domaine constant du TCR sont sujettes à un changement conformationnel lors de la liaison au pMHC. Nous proposons une hypothèse pour la signalisation structurelle des TCR, menant à l'activation du lymphocyte. Celle-ci est basée sur l'analyse des mouvements corrélés observés dans la structure du TCRpMHC.

In vivo targeting of an anti-tumor antibody coupled to antigenic MHC class I complexes induces specific growth inhibition and regression of established syngeneic tumor grafts.

The concept of antibody-mediated targeting of antigenic MHC/peptide complexes on tumor cells in order to sensitize them to T-lymphocyte cytotoxicity represents an attractive new immunotherapy strategy. In vitro experiments have shown that an antibody chemically conjugated or fused to monomeric MHC/peptide can be oligomerized on the surface of tumor cells, rendering them susceptible to efficient lysis by MHC-peptide restricted specific T-cell clones. However, this strategy has not yet been tested entirely in vivo in immunocompetent animals. To this aim, we took advantage of OT-1 mice which have a transgenic T-cell receptor specific for the ovalbumin (ova) immunodominant peptide (257-264) expressed in the context of the MHC class I H-2K(b). We prepared and characterized conjugates between the Fab' fragment from a high-affinity monoclonal antibody to carcinoembryonic antigen (CEA) and the H-2K(b) /ova peptide complex. First, we showed in OT-1 mice that the grafting and growth of a syngeneic colon carcinoma line transfected with CEA could be specifically inhibited by systemic injections of the conjugate. Next, using CEA transgenic C57BL/6 mice adoptively transferred with OT-1 spleen cells and immunized with ovalbumin, we demonstrated that systemic injections of the anti-CEA-H-2K(b) /ova conjugate could induce specific growth inhibition and regression of well-established, palpable subcutaneous grafts from the syngeneic CEA-transfected colon carcinoma line. These results, obtained in a well-characterized syngeneic carcinoma model, demonstrate that the antibody-MHC/peptide strategy can function in vivo. Further preclinical experimental studies, using an anti-viral T-cell response, will be performed before this new form of immunotherapy can be considered for clinical use.

Activated group 3 innate lymphoid cells promote T-cell-mediated immune responses.

Group 3 innate lymphoid cells (ILC3s) have emerged as important cellular players in tissue repair and innate immunity. Whether these cells meaningfully regulate adaptive immune responses upon activation has yet to be explored. Here we show that upon IL-1β stimulation, peripheral ILC3s become activated, secrete cytokines, up-regulate surface MHC class II molecules, and express costimulatory molecules. ILC3s can take up latex beads, process protein antigen, and consequently prime CD4(+) T-cell responses in vitro. The cognate interaction of ILC3s and CD4(+) T cells leads to T-cell proliferation both in vitro and in vivo, whereas its disruption impairs specific T-cell and T-dependent B-cell responses in vivo. In addition, the ILC3-CD4(+) T-cell interaction is bidirectional and leads to the activation of ILC3s. Taken together, our data reveal a novel activation-dependent function of peripheral ILC3s in eliciting cognate CD4(+) T-cell immune responses.

SwissParam: a fast force field generation tool for small organic molecules.

The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand-protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol(-1), and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer-aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch.

Characterization and detection of naturally occurring antibodies against IL-1 alpha and IL-1 beta in normal human plasma.

During the development and testing of a radioreceptor assay (RRA) for human IL-1, we have detected and identified the presence of auto-antibodies to IL-1 in normal human plasma (NHP). The RRA is based on the competition between human 125I-labeled rIL-1 alpha and standard or unknown quantities of IL-1 alpha or IL-1 beta for binding to a limited amounts of IL-1 receptor (IL-1R) isolated from the EL4 mouse thymoma cell line. NHP from 20 out of 100 unselected blood donors were found to completely inhibit the binding of 125I-labeled IL-1 alpha to its receptor, suggesting the presence in these NHP samples of either abnormal amounts of IL-1 or of a factor binding to the 125I-labeled IL-1 alpha. Special care was taken to ascertain that the inhibitory factors were antibodies and not soluble IL-1 receptor antagonist. When plasma samples with inhibiting activity were incubated with labeled IL-1 alpha and chromatographed on a Sephadex G200 column, they were found to contain 125I-labeled complexes with an apparent molecular weight of 150-200kD. The IL-1 binding factor could be eliminated from plasma by incubation with protein A-Sepharose, suggesting that it consisted in IgG antibodies directed against IL-1. Furthermore, the antibody nature of the inhibiting factor was confirmed by its binding to purified rIL-1 coupled to Sepharose. Screening of 200 NHP samples by incubation with 100 pg of 125I-labeled IL-1 followed by precipitation with 12% of polyethylene glycol (PEG) confirmed that about 25% of NHP contain detectable IgG antibodies to IL-1 alpha, while only 2% of NHP contain antibodies to IL-1 beta. No correlation between the presence of these anti-IL-1 antibodies and any particular major histocompatibility complex or any pathological conditions was detected. We suggest that all serum samples assayed for IL-1 alpha or IL-1 beta content should be pretested with the PEG precipitation assay described here.

Assessment of vaccine-induced CD4 T cell responses to the 119-143 immunodominant region of the tumor-specific antigen NY-ESO-1 using DRB1*0101 tetramers.

Abstract: Purpose: NY-ESO-1 (ESO), a tumor-specific antigen of the cancer/testis group, is presently viewed as an important model antigen for the development of generic anticancer vaccines. The ESO119-143 region is immunodominant following immunization with a recombinant ESO vaccine. In this study, we generated DRB1*0101/ESO119-143 tetramers and used them to assess CD4 T-cell responses in vaccinated patients expressing DRB1*0101 (DR1). Experimental Design: We generated tetramers of DRB1*0101 incorporating peptide ESO119-143 using a previously described strategy. We assessed ESO119-143-specific CD4 T cells in peptide-stimulated post-vaccine cultures using the tetramers. We isolated DR1/ESO119-143 tetramer(+) cells by cell sorting and characterized them functionally. We assessed vaccine-induced CD4(+) DR1/ESO119-143 tetramer(+) T cells ex vivo and characterized them phenotypically. Results: Staining of cultures from vaccinated patients with DR1/ESO119-143 tetramers identified vaccine-induced CD4 T cells. Tetramer(+) cells isolated by cell sorting were of T(H)1 type and efficiently recognized full-length ESO. We identified ESO123-137 as the minimal optimal epitope recognized by DR1-restricted ESO-specific CD4 T cells. By assessing DR1/ESO119-143 tetramer(+) cells using T cell receptor (TCR) beta chain variable region (V beta)-specific antibodies, we identified several frequently used V beta. Finally, direct ex vivo staining of patients' CD4 T cells with tetramers allowed the direct quantification and phenotyping of vaccine-induced ESO-specific CD4 T cells. Conclusions: The development of DR1/ESO119-143 tetramers, allowing the direct visualization, isolation, and characterization of ESO-specific CD4 T cells, will be instrumental for the evaluation of spontaneous and vaccine-induced immune responses to this important tumor antigen in DR1-expressing patients

Precursors of functional MHC class I- or class II-restricted CD8alphaalpha(+) T cells are positively selected in the thymus by agonist self-peptides.

The origin and specificity of alphabeta TCR(+) T cells that express CD8alphaalpha have been controversial issues. Here we provide direct evidence that precursors of functional CD8alphaalpha T cells are positively selected in the thymus in the presence of agonist self-peptides. Like conventional positive selection, this agonist selection process requires functional TCR alpha-CPM, whereas it is independent of CD8beta expression. Furthermore, CD8alphaalpha expression on mature, agonist-selected T cells does not imply selection by MHC class I, and CD8alphaalpha(+) T cells can be either class I or class II restricted. Our data define a distinct agonist-dependent, positive selection process in the thymus, and they suggest a function for CD8alphaalpha distinct from the conventional TCR coreceptor function of CD8alphabeta or CD4.