Identification of new MHC class I-restricted human tumor antigens for immunotherapy

Summary Cancer is a leading cause of morbidity and mortality in Western countries (as an example, colorectal cancer accounts for about 300'000 new cases and 200'000 deaths each year in Europe and in the USA). Despite that many patients with cancer have complete macroscopic clearance of their disease after resection, radiotherapy and/or chemotherapy, many of these patients develop fatal recurrence. Vaccination with immunogenic peptide tumor antigens has shown encouraging progresses in the last decade; immunotherapy might therefore constitute a fourth therapeutic option in the future. We dissect here and critically evaluate the numerous steps of reverse immunology, a forecast procedure to identify antigenic peptides from the sequence of a gene of interest. Bioinformatic algorithms were applied to mine sequence databases for tumor-specific transcripts. A quality assessment of publicly available sequence databanks allowed defining strengths and weaknesses of bioinformatics-based prediction of colon cancer-specific alternative splicing: new splice variants could be identified, however cancer-restricted expression could not be significantly predicted. Other sources of target transcripts were quantitatively investigated by polymerase chain reactions, as cancer-testis genes or reported overexpressed transcripts. Based on the relative expression of a defined set of housekeeping genes in colon cancer tissues, we characterized a precise procedure for accurate normalization and determined a threshold for the definition of significant overexpression of genes in cancers versus normal tissues. Further steps of reverse immunology were applied on a splice variant of the Melan¬A gene. Since it is known that the C-termini of antigenic peptides are directly produced by the proteasome, longer precursor and overlapping peptides encoded by the target sequence were synthesized chemically and digested in vitro with purified proteasome. The resulting fragments were identified by mass spectroscopy to detect cleavage sites. Using this information and based on the available anchor motifs for defined HLA class I molecules, putative antigenic peptides could be predicted. Their relative affinity for HLA molecules was confirmed experimentally with functional competitive binding assays and they were used to search patients' peripheral blood lymphocytes for the presence of specific cytolytic T lymphocytes (CTL). CTL clones specific for a splice variant of Melan-A could be isolated; although they recognized peptide-pulsed cells, they failed to lyse melanoma cells in functional assays of antigen recognition. In the conclusion, we discuss advantages and bottlenecks of reverse immunology and compare the technical aspects of this approach with the more classical procedure of direct immunology, a technique introduced by Boon and colleagues more than 10 years ago to successfully clone tumor antigens.

Identification of pharmaceutical tablets by Raman spectroscopy and chemometrics

Raman spectroscopy has become an attractive tool for the analysis of pharmaceutical solid dosage forms. In the present study it is used to ensure the identity of tablets. The two main applications of this method are release of final products in quality control and detection of counterfeits. Twenty-five product families of tablets have been included in the spectral library and a non-linear classification method, the Support Vector Machines (SVMs), has been employed. Two calibrations have been developed in cascade: the first one identifies the product family while the second one specifies the formulation. A product family comprises different formulations that have the same active pharmaceutical ingredient (API) but in a different amount. Once the tablets have been classified by the SVM model, API peaks detection and correlation are applied in order to have a specific method for the identification and allow in the future to discriminate counterfeits from genuine products. This calibration strategy enables the identification of 25 product families without error and in the absence of prior information about the sample. Raman spectroscopy coupled with chemometrics is therefore a fast and accurate tool for the identification of pharmaceutical tablets.

Identification of the SPLUNC1 ENaC-inhibitory domain yields novel strategies to treat sodium hyperabsorption in cystic fibrosis airway epithelial cultures.

The epithelial sodium channel (ENaC) is responsible for Na(+) and fluid absorption across colon, kidney, and airway epithelia. Short palate lung and nasal epithelial clone 1 (SPLUNC1) is a secreted, innate defense protein and an autocrine inhibitor of ENaC that is highly expressed in airway epithelia. While SPLUNC1 has a bactericidal permeability-increasing protein (BPI)-type structure, its NH2-terminal region lacks structure. Here we found that an 18 amino acid peptide, S18, which corresponded to residues G22-A39 of the SPLUNC1 NH2 terminus inhibited ENaC activity to a similar degree as full-length SPLUNC1 (∼2.5 fold), while SPLUNC1 protein lacking this region was without effect. S18 did not inhibit the structurally related acid-sensing ion channels, indicating specificity for ENaC. However, S18 preferentially bound to the βENaC subunit in a glycosylation-dependent manner. ENaC hyperactivity is contributory to cystic fibrosis (CF) lung disease. Unlike control, CF human bronchial epithelial cultures (HBECs) where airway surface liquid (ASL) height was abnormally low (4.2 ± 0.6 μm), addition of S18 prevented ENaC-led ASL hyperabsorption and maintained CF ASL height at 7.9 ± 0.6 μm, even in the presence of neutrophil elastase, which is comparable to heights seen in normal HBECs. Our data also indicate that the ENaC inhibitory domain of SPLUNC1 may be cleaved away from the main molecule by neutrophil elastase, suggesting that it may still be active during inflammation or neutrophilia. Furthermore, the robust inhibition of ENaC by the S18 peptide suggests that this peptide may be suitable for treating CF lung disease.

Identification of a novel splice-site mutation in the CYP1A2 gene.

AIMS: To identify the molecular basis for a low CYP1A2 metabolic status, as determined by a caffeine phenotyping test, in a 71-year-old, nonsmoking, Caucasian woman who presented with very high clozapine concentrations despite being administered a standard dose of the drug. METHODS: The nucleotide sequence of the 7 exons, exon-intron boundaries and 5'-flanking region of the CYP1A2 gene was analysed by direct sequencing. RESULTS: Only one heterozygous point mutation was identified in the donor splice site of intron 6 (3534G > A) of CYP1A2. This mutation could cause abnormal RNA splicing and therefore lead to a truncated nonfunctional enzyme. No other carrier of this mutation was identified in a population of 100 unrelated healthy Caucasians. CONCLUSIONS: This is the first report of a splice-site mutation affecting the CYP1A2 gene. This polymorphism is a likely explanation for the low CYP1A2 activity associated with high clozapine concentrations in this patient.

Identification of structural variation in mouse genomes.

Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation.

Phosphorylation of the Na,K-ATPase alpha-subunit by protein kinase A and C in vitro and in intact cells. Identification of a novel motif for PKC-mediated phosphorylation.

Na,K-ATPase is a potential target for regulatory phosphorylation by protein kinase A and C (PKA and PKC). To identify the phosphorylation sites, we have mutated the alpha 1-subunit of Bufo marinus in a highly conservative PKA and in 20 different PKC consensus sequences. The mutants were expressed in Xenopus oocytes and their phosphorylation capacity tested in homogenates upon stimulation of PKA or PKC. While serine 943 (Ser-943) was identified as a unique target site for PKA, none of the PKC consensus serine or threonine residues are implicated in PKC phosphorylation. Controlled trypsinolysis of phosphorylated alpha-subunits of various purified enzyme preparations and of alpha/beta complexes from oocyte homogenates revealed that PKC phosphorylation was exclusively associated with the N terminus. A fusion protein containing the first 32 amino acids of the Bufo alpha-subunit was phosphorylated in vitro and serine and threonine residues (Thr-15 and Ser-16) in this region were identified by site-directed mutagenesis as the PKC phosphorylation sites. Finally, the Bufo alpha-subunit was phosphorylated by protein kinases in transfected COS-7 cells. In intact cells, PKA stimulation induced phosphorylation exclusively on Ser-943 and PKC stimulation mainly on Thr-15 and Ser-16, which are contained in a novel PKC phosphorylation motif.

Nucleotide sequence of the 5' noncoding region and part of the gag gene of mouse mammary tumor virus; identification of the 5' splicing site for subgenomic mRNAs.

We have determined the sequence of the first 1371 nucleotides at the 5' end of the genome of mouse mammary tumor virus using molecularly cloned proviral DNA of the GR virus strain. The most likely initiation codon used for the gag gene of mouse mammary tumor virus is the first one, located 312 nucleotides from the 5' end of the viral RNA. The 5' splicing site for the subgenomic mRNA's is located approximately 288 nucleotides downstream from the 5' end of the viral RNA. From the DNA sequence the amino acid sequence of the N-terminal half of the gag precursor protein, including p10 and p21, was deduced (353 amino acids).

Identification of key amino acids of the mouse mammary tumor virus superantigen involved in the specific interaction with T-cell receptor V(beta) domains.

Mouse mammary tumor virus (MMTV) is a retrovirus encoding a superantigen that is recognized in association with major histocompatibility complex class II by the variable region of the beta chain (V(beta)) of the T-cell receptor. The C-terminal 30 to 40 amino acids of the superantigen of different MMTVs display high sequence variability that correlates with the recognition of particular T-cell receptor V(beta) chains. Interestingly, MMTV(SIM) and mtv-8 superantigens are highly homologous but have nonoverlapping T-cell receptor V(beta) specificities. To determine the importance of these few differences for specific V(beta) interaction, we studied superantigen responses in mice to chimeric and mutant MMTV(SIM) and mtv-8 superantigens expressed by recombinant vaccinia viruses. We show that only a few changes (two to six residues) within the C terminus are necessary to modify superantigen recognition by specific V(beta)s. Thus, the introduction of the MMTV(SIM) residues 314-315 into the mtv-8 superantigen greatly decreased its V(beta)12 reactivity without gain of MMTV(SIM)-specific function. The introduction of MMTV(SIM)-specific residues 289 to 295, however, induced a recognition pattern that was a mixture of MMTV(SIM)- and mtv-8-specific V(beta) reactivities: both weak MMTV(SIM)-specific V(beta)4 and full mtv-8-specific V(beta)11 recognition were observed while V(beta)12 interaction was lost. The combination of the two MMTV(SIM)-specific regions in the mtv-8 superantigen established normal MMTV(SIM)-specific V(beta)4 reactivity and completely abolished mtv-8-specific V(beta)5, -11, and -12 interactions. These new functional superantigens with mixed V(beta) recognition patterns allowed us to precisely delineate sites relevant for molecular interactions between the SIM or mtv-8 superantigen and the T-cell receptor V(beta) domain within the 30 C-terminal residues of the viral superantigen.

Control of pancreatic β-cell mass and function by gluco-incretin hormones : identification of novel regulatory mechanisms for the treatment of diabetes

Summary : Control of pancreatic ß-cell mass and function by gluco-incretin hormones: Identification of novel regulatory mechanisms for the treatment of diabetes The ß-cells of islets of Langerhans secrete insulin to reduce hyperglycemia. The number of pancreatic islet ß-cells and their capacity to secrete insulin is modulated in normal physiological conditions to respond to the metabolic demand of the organism. A failure of the endocrine pancreas to maintain an adequate insulin secretory capacity due to a reduced ß-cell number and function underlies the pathogenesis of both type 1 and type 2 diabetes. The molecular mechanisms controlling the glucose competence of mature ß-cells, i.e., the magnitude of their insulin secretion response to glucose, ß-cell replication, their differentiation from precursor cells and protection against apoptosis are poorly understood. To investigate these mechanisms, we studied the effects on ß-cells of the gluco-incretin hormones, glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) which are secreted by intestinal endocrine cells after food intake. Besides acutely potentiating glucose-stimulated insulin secretion, these hormones induce ß-cell differentiation from precursor cells, stimulate mature ß-cell replication, and protect them against apoptosis. Therefore, understanding the molecular basis for gluco-incretin action may lead to the uncovering of novel ß-cell regulatory events with potential application for the treatment or prevention of diabetes. Islets from mice with inactivation of both GIP and GLP-1 receptor genes (dK0) present a defect in glucose-induced insulin secretion and are more sensitive than control islets to cytokine-induced apoptosis. To search for regulatory genes, that may control both glucose competence and protection against apoptosis, we performed comparative transcriptomic analysis of islets from control and dK0 mice. We found a strong down-regulation of the IGF1 Rexpression in dK0 islets. We demonstrated in both a mouse insulin-secreting cell line and primary islets, that GLP-1 stimulated IGF-1R expression and signaling. Importantly, GLP-1induced IGF-1R-dependent Akt phosphorylation required active secretion, indicating the presence of an autocrine activation mechanism. We further showed that activation of IGF-1R signaling was dependent on the secretion of IGF-2 and IGF-2 expression was regulated by nutrients. Finally, we demonstrated that the IGF-Z/IGF-1R autocrine loop was required for GLP-1 i) to protect ß-cells against cytokine-induced apoptosis, ii) to enhance their glucose competence and iii) to increase ß-cell proliferation. Résumé : Contrôle de la masse des cellules ß pancréatiques et de leur fonction par les hormones glucoincrétines: Identification de nouveaux mécanismes régulateurs pour le traitement du diabète Les cellules ß des îlots de Langerhans sécrètent l'insuline pour diminuer l'hyperglycémie. Le nombre de cellules ß et leur capacité à sécréter l'insuline sont modulés dans les conditions physiologiques normales pour répondre à la demande métabolique de l'organisme. Un échec du pancréas endocrine à maintenir sa capacité sécrétoire d'insuline dû à une diminution du nombre et de la fonction des cellules ß conduit au diabète de type 1 et de type 2. Les mécanismes moléculaires contrôlant la compétence au glucose des cellules ß matures, tels que, l'augmentation de la sécrétion d'insuline en réponse au glucose, la réplication des cellules ß, leur différentiation à partir de cellules précurseurs et la protection contre l'apoptose sont encore peu connus. Afin d'examiner ces mécanismes, nous avons étudié les effets sur les cellules ß des hormones gluco-incrétines, glucose-dépendent insulinotropic polypeptide (G1P) et glucagon-like peptide-1 (GLP-1) qui sont sécrétées par les cellules endocrines de l'intestin après la prise alimentaire. En plus de potentialiser la sécrétion d'insuline induite par le glucose, ces hormones induisent la différentiation de cellules ß à partir de cellules précurseurs, stimulent leur prolifération et les protègent contre l'apoptose. Par conséquent, comprendre les mécanismes d'action des gluco-incrétines permettrait de découvrir de nouveaux processus régulant les cellules ß avec d'éventuelles applications dans le traitement ou la prévention du diabète. Les îlots de souris ayant une double inactivation des gènes pour les récepteurs du GIP et du GLP-1 (dK0) présentent un défaut de sécrétion d'insuline stimulée par le glucose et une sensibilité accrue à l'apoptose induite par les cytokines. Afin de déterminer les gènes régulés, qui pourraient contrôler à la fois la compétence au glucose et la protection contre l'apoptose, nous avons effectué une analyse comparative transcriptomique sur des îlots de souris contrôles et dKO. Nous avons constaté une forte diminution de l'expression d'IGF-1R dans les îlots dKO. Nous avons démontré, à la fois dans une lignée cellulaire murine sécrétant l'insuline et dans îlots primaires, que le GLP-1 stimulait l'expression d'IGF-1R et sa voie de signalisation. Par ailleurs, la phosphorylation d'Akt dépendante d'IGF1-R induite parle GLP-1 nécessite une sécrétion active, indiquant la présence d'un mécanisme d'activation autocrine. Nous avons ensuite montré que l'activation de la voie de signalisation d'IGF-1R était dépendante de la sécrétion d'IGF-2, dont l'expression est régulée par les nutriments. Finalement, nous avons démontré que la boucle autocrine IGF-2/IGF-1R est nécessaire pour le GLP-1 i) pour protéger les cellules ß contre l'apoptose induite par les cytokines, ii) pour améliorer la compétence au glucose et iii) pour augmenter la prolifération des cellules ß. Résumé tout public : Contrôle de la masse des cellules ß pancréatiques et de leur fonction par les hormones gluco-incrétines: Identification de nouveaux mécanismes régulateurs pour le traitement du diabète Chez les mammifères, la concentration de glucose sanguine (glycémie) est régulée et maintenue à une valeur relativement constante d'environ 5 mM. Cette régulation est principalement contrôlée par 2 hormones produites par les îlots pancréatiques de Langerhans: l'insuline sécrétée par les cellules ß et le glucagon sécrété par les cellules a. A la suite d'un repas, l'augmentation de la glycémie entraîne la sécrétion d'insuline ce qui permet le stockage du glucose dans le foie, les muscles et le tissu adipeux afin de diminuer le taux de glucose circulant. Lors d'un jeûne, la diminution de la glycémie permet la sécrétion de glucagon favorisant alors la production de glucose par le foie, normalisant ainsi la glycémie. Le nombre de cellules ß et leur capacité sécrétoire s'adaptent aux variations de la demande métabolique pour assurer une normoglycémie. Une destruction complète ou partielle des cellules ß conduit respectivement au diabète de type 1 et de type 2. Bien que l'augmentation de la glycémie soit le facteur stimulant de la sécrétion d'insuline, des hormones gluco-incrétines, principalement le GLP-1 (glucagon-like peptide-1) et le GIP (glucose-dependent insulinotropic polypeptide) sont libérées par l'intestin en réponse aux nutriments (glucose, acides gras) et agissent au niveau des cellules ß, potentialisant la sécrétion d'insuline induite par le glucose, stimulant leur prolifération, induisant la différentiation de cellules précurseurs en cellules ß matures et les protègent contre la mort cellulaire (apoptose). Afin d'étudier plus en détail ces mécanismes, nous avons généré des souris déficientes pour les récepteurs du GIP et du GLP-l. Les îlots pancréatiques de ces souris présentent un défaut de sécrétion d'insuline stimulée par le glucose et une sensibilité accrue à l'apoptose par rapport aux îlots de souris contrôles. Nous avons donc cherché les gènes régulés pas ces hormones contrôlant la sécrétion d'insuline et la protection contre l'apoptose. Nous avons constaté une forte diminution de l'expression du récepteur à l'IGF-1 (IGF-1R) dans les îlots de souris déficientes pour les récepteurs des gluco-incrétines. Nous avons démontré dans un model de cellules ß en culture et d'îlots que le GLP-1 augmentait l'expression d'IGF-1R et la sécrétion de son ligand (IGF-2) permettant l'activation de la voie de signalisation. Finalement, nous avons montré que l'activation de la boucle IGF-2/IGF-1R induite par le GLP-1 était nécessaire pour la protection contre l'apoptose, l'augmentation de la sécrétion et la prolifération des cellules ß.

Molecular markers allow sibling species identification in red wood ants (Formica rufa group)

Red wood ants (Formica rufa group) constitute a group of species that are considered to be among the most promising bioindicators in forest ecosystems. However, because of their morphological similarity and intraspecific variability, morphological species identification can be difficult. Considerable expertise is necessary to discriminate between the sibling species F. lugubris and F. paralugubris, two species that often live in sympatry in the same Alpine forests. New taxonomic tools providing rapid and reliable species identification are needed. We present a simple and reliable molecular technique based on mtDNA (COI gene) and a restriction enzyme for discriminating between F. lugubris and F. paralugubris. We confirm the validity of this method with a Bayesian analysis based on microsatellites. This new molecular tool represents a clear breakthrough for discriminating between F. lugubris and F. paralugubris and is likely to be helpful in large-scale biomonitoring.