Molecular characterization of the contribution of autophagy to antigen presentation using quantitative proteomics

L’autophagie est une voie hautement conservée de dégradation lysosomale des constituants cellulaires qui est essentiel à l’homéostasie cellulaire et contribue à l’apprêtement et à la présentation des antigènes. Les rôles relativement récents de l'autophagie dans l'immunité innée et acquise sous-tendent de nouveaux paradigmes immunologiques pouvant faciliter le développement de nouvelles thérapies où la dérégulation de l’autophagie est associée à des maladies auto-immunes. Cependant, l'étude in vivo de la réponse autophagique est difficile en raison du nombre limité de méthodes d'analyse pouvant fournir une définition dynamique des protéines clés impliquées dans cette voie. En conséquence, nous avons développé un programme de recherche en protéomique intégrée afin d’identifier et de quantifier les proteines associées à l'autophagie et de déterminer les mécanismes moléculaires régissant les fonctions de l’autophagosome dans la présentation antigénique en utilisant une approche de biologie des systèmes. Pour étudier comment l'autophagie et la présentation antigénique sont activement régulés dans les macrophages, nous avons d'abord procédé à une étude protéomique à grande échelle sous différentes conditions connues pour stimuler l'autophagie, tels l’activation par les cytokines et l’infection virale. La cytokine tumor necrosis factor-alpha (TNF-alpha) est l'une des principales cytokines pro-inflammatoires qui intervient dans les réactions locales et systémiques afin de développer une réponse immune adaptative. La protéomique quantitative d'extraits membranaires de macrophages contrôles et stimulés avec le TNF-alpha a révélé que l'activation des macrophages a entrainé la dégradation de protéines mitochondriales et des changements d’abondance de plusieurs protéines impliquées dans le trafic vésiculaire et la réponse immunitaire. Nous avons constaté que la dégradation des protéines mitochondriales était sous le contrôle de la voie ATG5, et était spécifique au TNF-alpha. En outre, l’utilisation d’un nouveau système de présentation antigènique, nous a permi de constater que l'induction de la mitophagie par le TNF-alpha a entrainée l’apprêtement et la présentation d’antigènes mitochondriaux par des molécules du CMH de classe I, contribuant ainsi la variation du répertoire immunopeptidomique à la surface cellulaire. Ces résultats mettent en évidence un rôle insoupçonné du TNF-alpha dans la mitophagie et permet une meilleure compréhension des mécanismes responsables de la présentation d’auto-antigènes par les molécules du CMH de classe I. Une interaction complexe existe également entre infection virale et l'autophagie. Récemment, notre laboratoire a fourni une première preuve suggérant que la macroautophagie peut contribuer à la présentation de protéines virales par les molécules du CMH de classe I lors de l’infection virale par l'herpès simplex virus de type 1 (HSV-1). Le virus HSV1 fait parti des virus humains les plus complexes et les plus répandues. Bien que la composition des particules virales a été étudiée précédemment, on connaît moins bien l'expression de l'ensemble du protéome viral lors de l’infection des cellules hôtes. Afin de caractériser les changements dynamiques de l’expression des protéines virales lors de l’infection, nous avons analysé par LC-MS/MS le protéome du HSV1 dans les macrophages infectés. Ces analyses nous ont permis d’identifier un total de 67 protéines virales structurales et non structurales (82% du protéome HSV1) en utilisant le spectromètre de masse LTQ-Orbitrap. Nous avons également identifié 90 nouveaux sites de phosphorylation et de dix nouveaux sites d’ubiquitylation sur différentes protéines virales. Suite à l’ubiquitylation, les protéines virales peuvent se localiser au noyau ou participer à des événements de fusion avec la membrane nucléaire, suggérant ainsi que cette modification pourrait influer le trafic vésiculaire des protéines virales. Le traitement avec des inhibiteurs de la réplication de l'ADN induit des changements sur l'abondance et la modification des protéines virales, mettant en évidence l'interdépendance des protéines virales au cours du cycle de vie du virus. Compte tenu de l'importance de la dynamique d'expression, de l’ubiquitylation et la phosphorylation sur la fonction des proteines virales, ces résultats ouvriront la voie vers de nouvelles études sur la biologie des virus de l'herpès. Fait intéressant, l'infection HSV1 dans les macrophages déclenche une nouvelle forme d'autophagie qui diffère remarquablement de la macroautophagie. Ce processus, appelé autophagie associée à l’enveloppe nucléaire (nuclear envelope derived autophagy, NEDA), conduit à la formation de vésicules membranaires contenant 4 couches lipidiques provenant de l'enveloppe nucléaire où on retrouve une grande proportion de certaines protéines virales, telle la glycoprotéine B. Les mécanismes régissant NEDA et leur importance lors de l’infection virale sont encore méconnus. En utilisant un essai de présentation antigénique, nous avons pu montrer que la voie NEDA est indépendante d’ATG5 et participe à l’apprêtement et la présentation d’antigènes viraux par le CMH de classe I. Pour comprendre l'implication de NEDA dans la présentation des antigènes, il est essentiel de caractériser le protéome des autophagosomes isolés à partir de macrophages infectés par HSV1. Aussi, nous avons développé une nouvelle approche de fractionnement basé sur l’isolation de lysosomes chargés de billes de latex, nous permettant ainsi d’obtenir des extraits cellulaires enrichis en autophagosomes. Le transfert des antigènes HSV1 dans les autophagosomes a été determine par protéomique quantitative. Les protéines provenant de l’enveloppe nucléaire ont été préférentiellement transférées dans les autophagosome lors de l'infection des macrophages par le HSV1. Les analyses protéomiques d’autophagosomes impliquant NEDA ou la macroautophagie ont permis de decouvrir des mécanismes jouant un rôle clé dans l’immunodominance de la glycoprotéine B lors de l'infection HSV1. Ces analyses ont également révélées que diverses voies autophagiques peuvent être induites pour favoriser la capture sélective de protéines virales, façonnant de façon dynamique la nature de la réponse immunitaire lors d'une infection. En conclusion, l'application des méthodes de protéomique quantitative a joué un rôle clé dans l'identification et la quantification des protéines ayant des rôles importants dans la régulation de l'autophagie chez les macrophages, et nous a permis d'identifier les changements qui se produisent lors de la formation des autophagosomes lors de maladies inflammatoires ou d’infection virale. En outre, notre approche de biologie des systèmes, qui combine la protéomique quantitative basée sur la spectrométrie de masse avec des essais fonctionnels tels la présentation antigénique, nous a permis d’acquérir de nouvelles connaissances sur les mécanismes moléculaires régissant les fonctions de l'autophagie lors de la présentation antigénique. Une meilleure compréhension de ces mécanismes permettra de réduire les effets nuisibles de l'immunodominance suite à l'infection virale ou lors du développement du cancer en mettant en place une réponse immunitaire appropriée.

Characterizing PvARP, a novel Plasmodium vivax antigen

Background Plasmodium vivax continues to be the most widely distributed malarial parasite species in tropical and sub-tropical areas, causing high morbidity indices around the world. Better understanding of the proteins used by the parasite during the invasion of red blood cells is required to obtain an effective vaccine against this disease. This study describes characterizing the P. vivax asparagine-rich protein (PvARP) and examines its antigenicity in natural infection. Methods The target gene in the study was selected according to a previous in silico analysis using profile hidden Markov models which identified P. vivax proteins that play a possible role in invasion. Transcription of the arp gene in the P. vivax VCG-1 strain was here evaluated by RT-PCR. Specific human antibodies against PvARP were used to confirm protein expression by Western blot as well as its subcellular localization by immunofluorescence. Recognition of recombinant PvARP by sera from P. vivax-infected individuals was evaluated by ELISA. Results VCG-1 strain PvARP is a 281-residue-long molecule, which is encoded by a single exon and has an N-terminal secretion signal, as well as a tandem repeat region. This protein is expressed in mature schizonts and is located on the surface of merozoites, having an apparent accumulation towards their apical pole. Sera from P. vivax-infected patients recognized the recombinant, thereby suggesting that this protein is targeted by the immune response during infection.

PvRON2, a new Plasmodium vivax rhoptry neck antigen

Background: Rhoptries are specialized organelles from parasites belonging to the phylum Apicomplexa; they secrete their protein content during invasion of host target cells and are sorted into discrete subcompartments within rhoptry neck or bulb. This distribution is associated with these proteins’ role in tight junction (TJ) and parasitophorous vacuole (PV) formation, respectively. Methods: Plasmodium falciparum RON2 amino acid sequence was used as bait for screening the codifying gene for the homologous protein in the Plasmodium vivax genome. Gene synteny, as well as identity and similarity values, were determined for ron2 and its flanking genes among P. falciparum, P. vivax and other malarial parasite genomes available at PlasmoDB and Sanger Institute databases. Pvron2 gene transcription was determined by RT-PCR of cDNA obtained from the P. vivax VCG-1 strain. Protein expression and localization were assessed by Western blot and immunofluorescence using polyclonal anti-PvRON2 antibodies. Co-localization was confirmed using antibodies directed towards specific microneme and rhoptry neck proteins. Results and discussion: The first P. vivax rhoptry neck protein (named here PvRON2) has been identified in this study. PvRON2 is a 2,204 residue-long protein encoded by a single 6,615 bp exon containing a hydrophobic signal sequence towards the amino-terminus, a transmembrane domain towards the carboxy-terminus and two coiled coil a-helical motifs; these are characteristic features of several previously described vaccine candidates against malaria. This protein also contains two tandem repeats within the interspecies variable sequence possibly involved in evading a host’s immune system. PvRON2 is expressed in late schizonts and localized in rhoptry necks similar to what has been reported for PfRON2, which suggests its participation during target cell invasion. Conclusions: The identification and partial characterization of the first P. vivax rhoptry neck protein are described in the present study. This protein is homologous to PfRON2 which has previously been shown to be associated with PfAMA-1, suggesting a similar role for PvRON2.

Glycan alterations of serum proteins as tumour markers. Prostate-specific antigen in prostate cancer and acute-phase proteins in pancreatic cancer

Els pacients amb càncer presenten una taxa de supervivència superior si es diagnostiquen a estadis inicials, per la qual cosa és indispensable disposar de marcadors tumorals adequats. Glicoformes de proteïnes específiques es podrian utilizar com marcadors tumorals. S’han investigat les subformes i glicosilació de l’Antígen Prostàtic Específic (PSA) per millorar la seva capacitat de diagnosis de pacients amb càncer de pròstata vs aquells amb hiperplàsia benigna prostàtica. També s’han avaluat glicoproteïnes sèriques amb alteracions glucídiques en pacients de càncer de pàncrees, comparat amb pacients amb pancreatitis crònica i controls. S’ha observat una disminució de la fucosilació core i sialilació del PSA en càncer de pròstata i un augment de la fucosilació core i Sialyl-Lewis X en algunes Proteïnes de fase Aguda en càncer de pàncrees. Aquest canvis s’haurien d’avaluar en un cohort de pacients més gran per determinar el seu paper en el cribratge, diagnòstic o monitorització dels cancers estudiats.

Intra-individual variation of serum prostate specific antigen levels in men with benign prostate biopsies

To determine the intra-individual (physiological) variation of prostate-specific antigen (PSA) measurements in men after a benign prostatic biopsy. Sixty-four men were prospectively assessed, all of whom had a benign prostatic biopsy within the preceding 13 months. The degree of intra-individual variability was established by calculating the coefficient of variation on four PSA levels obtained from each patient weekly over a month. Six patients were subsequently diagnosed with prostate cancer and their data are presented separately. In the remaining 58 patients the median (range) individual mean PSA value was 6.3 (0.5-34.1) ng/mL. The median (range) coefficient of variation within the group was 9.5 (2.4-76.1)%. There was a clear linear relationship between mean PSA level and the standard deviation. In 48 of the 63 patients analysed, the coefficient of variation for serum PSA values in the group as a whole was greater than the variation claimed for the assay technique. The significance of the linear relationship between PSA and the standard deviation is discussed, with particular reference to those men who had a benign prostate biopsy.

Analysis of the antigen combining site: Correlations between length and sequence composition of the hypervariable loops and the nature of the antigen

It has long been suggested that the overall shape of the antigen combining site (ACS) of antibodies is correlated with the nature of the antigen. For example, deep pockets are characteristic of antibodies that bind haptens, grooves indicate peptide binders, while antibodies that bind to proteins have relatively flat combining sites. In. 1996, MacCallum, Martin and Thornton used a fractal shape descriptor and showed a strong correlation of the shape of the binding region with the general nature of the antigen. However, the shape of the ACS is determined primarily by the lengths of the six complementarity-determining regions (CDRs). Here, we make a direct correlation between the lengths of the CDRs and the nature of the antigen. In addition, we show significant differences in the residue composition of the CDRs of antibodies that bind to different antigen classes. As well as helping us to understand the process of antigen recognition, autoimmune disease and cross-reactivity these results are of direct application in the design of antibody phage libraries and modification of affinity. (C) 2003 Elsevier Science Ltd. All rights reserved.

Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: Preserved folding energy drives fiber formation

Most gram-negative pathogens express fibrous adhesive virulence organelles that mediate targeting to the sites of infection. The F1 capsular antigen from the plague pathogen Yersinia pestis consists of linear fibers of a single subunit (Caf1) and serves as a prototype for nonpilus organelles assembled via the chaperone/usher pathway. Genetic data together with high-resolution X-ray structures corresponding to snapshots of the assembly process reveal the structural basis of fiber formation. Comparison of chaperone bound Caf1 subunit with the subunit in the fiber reveals a novel type of conformational change involving the entire hydrophobic core of the protein. The observed conformational change suggests that the chaperone traps a high-energy folding intermediate of Caf1. A model is proposed in which release of the subunit allows folding to be completed, driving fiber formation.

Non-promoting diterpene esters can induce Epstein-Barr Virus early antigen expression in the Raji cell line

A range of diterpene ester ligands with selective biological activity (e.g., irritant but not tumour promoting) were tested for their ability to induce Epstein-Barr virus (EBV) early antigen expression in the lymphoblastoid Raji cell line. All substituted compounds were found to be capable of inducing some antigen expression at nM−μM levels, including desacetyl-α-sapinine, a compound largely devoid of biological activity. The non-promoting, fluorescent compound, sapintoxin A, was virtually equipotent with promoting compounds. It was concluded that, although the assay has relevance to the specific condition of chronic diterpene ester exposure occurring in conjunction with high EBV infection rates, there was relatively poor correlation with mouse skin tumour promoting potential.

Carnauba wax nanoparticles enhance strong systemic and mucosal cellular and humoral immune responses to HIV-gp140 antigen

Induction of humoral responses to HIV at mucosal compartments without inflammation is important for vaccine design. We developed charged wax nanoparticles that efficiently adsorb protein antigens and are internalized by DC in the absence of inflammation. HIV-gp140-adsorbed nanoparticles induced stronger in vitro T-cell proliferation responses than antigen alone. Such responses were greatly enhanced when antigen was co-adsorbed with TLR ligands. Immunogenicity studies in mice showed that intradermal vaccination with HIV-gp140 antigen-adsorbed nanoparticles induced high levels of specific IgG. Importantly, intranasal immunization with HIV-gp140-adsorbed nanoparticles greatly enhanced serum and vaginal IgG and IgA responses. Our results show that HIV-gp140-carrying wax nanoparticles can induce strong cellular/humoral immune responses without inflammation and may be of potential use as effective mucosal adjuvants for HIV vaccine candidates.

Conserved hydrophobic clusters on the surface of the Caf1A usher C-terminal domain are important for F1 antigen assembly

The outer membrane usher protein Caf1A of the plague pathogen Yersinia pestis is responsible for the assembly of a major surface antigen, the F1 capsule. The F1 capsule is mainly formed by thin linear polymers of Caf1 (capsular antigen fraction 1) protein subunits. The Caf1A usher promotes polymerization of subunits and secretion of growing polymers to the cell surface. The usher monomer (811 aa, 90.5 kDa) consists of a large transmembrane β-barrel that forms a secretion channel and three soluble domains. The periplasmic N-terminal domain binds chaperone-subunit complexes supplying new subunits for the growing fiber. The middle domain, which is structurally similar to Caf1 and other fimbrial subunits, serves as a plug that regulates the permeability of the usher. Here we describe the identification, characterization, and crystal structure of the Caf1A usher C-terminal domain (Caf1A(C)). Caf1A(C) is shown to be a periplasmic domain with a seven-stranded β-barrel fold. Analysis of C-terminal truncation mutants of Caf1A demonstrated that the presence of Caf1A(C) is crucial for the function of the usher in vivo, but that it is not required for the initial binding of chaperone-subunit complexes to the usher. Two clusters of conserved hydrophobic residues on the surface of Caf1A(C) were found to be essential for the efficient assembly of surface polymers. These clusters are conserved between the FGL family and the FGS family of chaperone-usher systems.

Studies into the role of the SEF14 fimbrial antigen in the pathogenesis of Salmonella enteritidis

To investigate the role of the SEF14 fimbrial antigen in pathogenesis, a single defined sefA (SEF14(-)) inactivated mutant of Salmonella enteritidis strain LA5 was constructed and tested in a number of biological assay systems. There was no significant difference between the wild-type strain and the isogenic SEF14(-) mutant in their abilities to adhere to and invade HEp-2 epithelial cells or their survival in mouse peritoneal macrophages, whereas the SEF14(-) mutant was ingested more rapidly by isolated human PMN. Both the strains colonized the intestine, invaded and spread systemically in 1 day-old chicks, laying hens and BALB/c mice equally well. A significantly greater number of chicks excreted the wildtype SEF14(+) strain during the first week following infection as compared to those infected with the SEF14(-) mutant. However, similar numbers of chicks excreted the two strains between 2 and 7 weeks after infection. These results indicate that possession of SEF14 fimbriae alone do not appear to play a significant role in the pathogenesis of S. enteritidis although its contribution to virulence may be dependent on the host species infected. (C) 1996 Academic Press Limited

Distribution, gene sequence and expression in vivo of the plasmid encoded fimbrial antigen of Salmonella serotype Enteritidis

The pefA gene which encoded the serotype associated plasmid (SAP) mediated fimbrial major subunit antigen of Salmonella enterica serotype Typhimurium shared genetic identity with 128 of 706 salmonella isolates as demonstrated by dot (colony) hybridization. Seventy-seven of 113 isolates of Typhimurium and individual isolates of serotypes Bovis-morbificans, Cholerae-suis and Enteritidis phage type 9b hybridized pefA strongly, whereas 48 isolates of Enteritidis hybridized pefA weakly and one Enteritidis isolate of phage type 14b failed to hybridize. Individual isolates of 294 serotypes and 247 individual isolates of serotype Dublin did not hybridize pefA. Southern hybridization of plasmids extracted from Enteritidis demonstrated that the pefA gene probe hybridized strongly an atypical SAP of 80 kb in size harboured by one Enteritidis isolate of phage-type 9b, whereas the typical SAP of 58 kb in size harboured by 48 Enteritidis isolates hybridized weakly. One Enteritidis isolate of phage type 14b which failed to hybridize pefA in dot (colony) hybridization experiments was demonstrated to be plasmid free. A cosmid library of Enteritidis phage type 4 expressed in Escherichia coli K12 was screened by hybridization for the presence of pef sequences. Recombinant clones which were deduced to harbour the entire pef operon elaborated a PEF-like fimbrial structure at the cell surface. The PEF-like fimbrial antigen was purified from one cosmid clone and used in western blot experiments with sera from chickens infected with Enteritidis phage-type 4. Seroconversion to the fimbrial antigen was observed which indicated that the Enteritidis PEF-like fimbrial structure was expressed at some stage during infection. Nucleotide sequence analysis demonstrated that the pefA alleles of Typhimurium and Enteritidis phage-type 4 shared 76% DNA nucleotide and 82% deduced amino acid sequence identity.

The SEF14 fimbrial antigen of Salmonella enterica serovar Enteritidis is encoded within a pathogenicity islet

The DNA sequence of the chromosomal gene cluster encoding the SEF14 fimbriae of Salmonella enterica serovar Enteritidis was determined. Five contiguous open reading frames, sefABCDE, were identified. The sefE gene shared significant homology with araC-like positive regulators. Serovar-associated virulence plasmid (SAP) genes orf7,8,9 and pefI were identified immediately adjacent to the sef operon. The pefI gene encoded a putative regulator of the Plasmid-encoded fimbrial antigen (PEF) expression. The entire sef-pef region, Ranked by two IS-like elements, was inserted adjacent to leuX that encoded a transfer RNA molecule. The organisation of this region was suggestive of a classic pathogenicity islet. Southern hybridisation confirmed two copies of the SAP derived orf7,8,9 and pefI region in S. Enteritidis, one in the chromosome and one on the SAP. Of other group D Salmonella, only S. Blegdam and S. Moscow harboured both chromosomal and plasmid copies of pefI-orf9 region although polymorphism was evident. Crown Copyright (C) 2001 Published by Elsevier Science B.V. All rights reserved.