Prediction of promiscuous peptides that bind HLA class I molecules

Promiscuous T-cell epitopes make ideal targets for vaccine development. We report here a computational system, multipred, for the prediction of peptide binding to the HLA-A2 supertype. It combines a novel representation of peptide/MHC interactions with a hidden Markov model as the prediction algorithm. multipred is both sensitive and specific, and demonstrates high accuracy of peptide-binding predictions for HLA-A*0201, *0204, and *0205 alleles, good accuracy for *0206 allele, and marginal accuracy for *0203 allele. multipred replaces earlier requirements for individual prediction models for each HLA allelic variant and simplifies computational aspects of peptide-binding prediction. Preliminary testing indicates that multipred can predict peptide binding to HLA-A2 supertype molecules with high accuracy, including those allelic variants for which no experimental binding data are currently available.

Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.

Generation and phenotypic characterization of new human ovarian cancer cell lines with the identification of antigens potentially recognizable by HLA-restricted cytotoxic T cells

This study describes a simple method for long-term establishment of human ovarian tumor lines and prediction of T-cell epitopes that could be potentially useful in the generation of tumor-specific cytotoxic T lymphocytes (CTLs), Nine ovarian tumor lines (INT.Ov) were generated from solid primary or metastatic tumors as well as from ascitic fluid, Notably all lines expressed HLA class I, intercellular adhesion molecule-1 (ICAM-1), polymorphic epithelial mucin (PEM) and cytokeratin (CK), but not HLA class II, B7.1 (CD80) or BAGE, While of the 9 lines tested 4 (INT.Ov1, 2, 5 and 6) expressed the folate receptor (FR-alpha) and 6 (INT.Ov1, 2, 5, 6, 7 and 9) expressed the epidermal growth factor receptor (EGFR); MAGE-1 and p185(HER-2/neu) were only found in 2 lines (INT.Ov1 and 2) and GAGE-1 expression in 1 line (INT.Ov2). The identification of class I MHC ligands and T-cell epitopes within protein antigens was achieved by applying several theoretical methods including: 1) similarity or homology searches to MHCPEP; 2) BIMAS and 3) artificial neural network-based predictions of proteins MACE, GAGE, EGFR, p185(HER-2/neu) and FR-alpha expressed in INT.Ov lines, Because of the high frequency of expression of some of these proteins in ovarian cancer and the ability to determine HLA binding peptides efficiently, it is expected that after appropriate screening, a large cohort of ovarian cancer patients may become candidates to receive peptide based vaccines. (C) 1997 Wiley-Liss, Inc.

Major histocompatibility complex (MHC) class II-positive dendritic cells in the rat iris - In situ development from MHC class II-negative precursors

Purpose. To examine the postnatal development of major histocompatibility complex (MHC) class II-positive dendritic cells (DC) in the iris of the normal rat eye. Methods. Single-and double-color immunomorphologic studies were performed on whole mounts prepared from rat iris taken at selected postnatal ages (2 to 3 days to 78 weeks). Immunopositive cells were enumerated, using a quantitative light microscope, and MHC class II expression on individual cells was assessed by microdensitometric analysis. Results. Major histocompatibility class II-positive DCs in the iris developed in an age-dependent manner and reached adult-equivalent density and structure at approximately 10 weeks of age, considerably later than previously described in other DC populations in the rat. In contrast, the anti-rat DC monoclonal antibody OX62 revealed a population of cells present at adult-equivalent levels as early as 3 weeks after birth. Dual-color immunostaining and microdensitometric analysis demonstrated that during postnatal growth, development of the network of MHC class II-positive DCs was a consequence of the progressive increase in expression of MHC class II antigen by OX62-positive cells. Conclusions. During postnatal growth, the DC population of the iris develops initially as an OX62-positive-MHC class II-negative population, which then develops increasing MHC class II expression in situ and finally resembles classic DC populations in other tissue sites. Maturation of the iris DC population is temporally delayed compared with time to maturation in other tissue sites in the rat.

Major histocompatibility complex (MHC) class II but not MHC class I molecules are required for efficient control of Strongyloides venezuelensis infection in mice

P>Strongyloides stercoralis is an intestinal nematode capable of chronic, persistent infection and hyperinfection of the host; this can lead to dissemination, mainly in immunosuppressive states, in which the infection can become severe and result in the death of the host. In this study, we investigated the immune response against Strongyloides venezuelensis infection in major histocompatibility complex (MHC) class I or class II deficient mice. We found that MHC II(-/-) animals were more susceptible to S. venezuelensis infection as a result of the presence of an elevated number of eggs in the faeces and a delay in the elimination of adult worms compared with wild-type (WT) and MHC I(-/-) mice. Histopathological analysis revealed that MHC II(-/-) mice had a mild inflammatory infiltration in the small intestine with a reduction in tissue eosinophilia. These mice also presented a significantly lower frequency of eosinophils and mononuclear cells in the blood, together with reduced T helper type 2 (Th2) cytokines in small intestine homogenates and sera compared with WT and MHC I(-/-) animals. Additionally, levels of parasite-specific immunoglobulin M (IgM), IgA, IgE, total IgG and IgG1 were also significantly reduced in the sera of MHC II(-/-) infected mice, while a non-significant increase in the level of IgG2a was found in comparison to WT or MHC I(-/-) infected mice. Together, these data demonstrate that expression of MHC class II but not class I molecules is required to induce a predominantly Th2 response and to achieve efficient control of S. venezuelensis infection in mice.

Fracture resistance of Class II glass-ionomer cement restorations

Purpose: To investigate in vitro the effect of retentive grooves, GIC type and insertion method on the fracture resistance of Class II glass-ionomer cement (GIC) restorations. Methods: Premolars were divided into 12 groups (n=10) according to three variables: retentive grooves [presence (PR) or absence AR)], GICs type [Ketac-Molar (KM), Fuji VIII (F8) and RelyX Luting (RX)], and insertion method [syringe injector (SI) or spoon excavator (SE)]. The specimens were subjected to fracture resistance test. Data were submitted to three-way ANOVA and multiple comparisons were performed using a Tukey test (P < 0.05). Results: Mean fracture resistance values (Kgf) +/- standard deviations (SD) were: KM (PR+SI) 65.66 +/- 2.5; KM (PR+SE) = 62.58 +/- 2.1; KM (AR+SI) = 57.11 +/- 1.9; KM (AR+SE) = 51.94 +/- 2.3; F8 (PR+SI) = 63.05 +/- 2.1; F8 (PR+SE) = 60.12 +/- 2.3; F8 (AR+SI) = 55.11 +/- 1.9; F8(AR+SE)=49.20 +/- 1.6; RX (PR+SI)=50.99 +/- 2.4; RX (PR+SE)=48.81 +/- 2.5; RX (AR+SI)=45.53 +/- 2.6; RX (AR+SE)=41.88 +/- 3.0. Statistically significant differences were observed among all the groups tested (P=0.001). There was significant difference when pooled means for GIC type were compared with retentive grooves (P=0.01) and when pooled means for retentive grooves were compared with insertion method (P=0.01).

Treatment stability in patients with Class II malocclusion treated with 2 maxillary premolar extractions or without extractions

Introduction: The purpose of this study was to compare the occlusal stability of Class II malocclusion treatment with and without extraction of 2 maxillary premolars. Methods: A sample of 59 records from patients with complete Class II malocclusion was used. This sample was divided into 2 groups with the following characteristics: group 1, comprising 29 patients treated without extractions, and group 2, comprising 30 patients treated with extraction of 2 maxillary premolars. Dental cast measurements were obtained before and after treatment and at a minimum of 2.4 years after treatment. The pretreatment, posttreatment, and postretention occlusal statuses were evaluated with the peer assesment rating index. The occlusal indexes at the postretention stage and the posttreatment changes and percentages of posttreatment changes were compared with t tests. Results: The nonextraction and the 2 maxillary premolar extraction treatment protocols of complete Class II malocclusions had no statistically significant differences in occlusal stability. Conclusions: Finishing Class II malocclusion treatment with the molars in a Class II relationship has similar occlusal stability as finishing with the molars in a Class I relationship. (Am J Orthod Dentofacial Orthop 2010;138:16-22)

Tooth-wear patterns in adolescents with normal occlusion and Class II Division 2 malocclusion

Introduction: In this study, we investigated tooth-wear patterns in adolescents with either normal occlusion or Class II Division 2 malocclusion. Methods: The sample consisted of dental casts from 165 subjects that were divided into 2 groups: 115 normal occlusion subjects (mean age, 14.3 years) and 50 complete Class II Division 2 subjects (mean age, 13.9 years). Dental wear was assessed by using a modified version of the tooth wear index. The 2 groups were compared with the Mann-Whitney test for the frequency and severity of wear on each surface of each group of teeth. The level of statistical significance was set at 5%. Results: The normal occlusion group statistically had greater tooth wear on the incisal surfaces of the maxillary lateral incisors and the incisal surfaces of the maxillary canines than did the Class II Division 2 malocclusion group. The malocclusion group showed statistically greater tooth wear on the labial surfaces of the mandibular lateral incisors, the occlusal surfaces of the maxillary premolars and first molars, the occlusal surfaces of the mandibular premolars, the palatal surfaces of the maxillary second premolars, and the buccal surfaces of the mandibular premolars and first molars than did the normal occlusion group. Conclusions: Subjects with normal occlusion and those with complete Class II Division 2 malocclusions have different tooth-wear patterns. Tooth wear on the malocclusion subjects should not be considered pathologic but, rather, the consequence of different interocclusal arrangements. (Am J Orthod Dentofacial Orthop 2010;137:730.e1-730.e5)

Tooth-wear patterns in subjects with Class II Division 1 malocclusion and normal occlusion

Introduction: The aim of this study was to investigate the prevalence of tooth wear in adolescents with Class II malocclusion, compared with those with normal occlusion. Methods: The sample consisted of dental casts obtained from 310 subjects, divided into 3 groups: group 1, 110 subjects with normal occlusion (mean age, 13.51 years); group 2, 100 complete Class II Division 1 patients (mean age, 13.44 years); and group 3, 100 half-cusp Class II Division 1 patients (mean age, 13.17 years). Dental wear was assessed by using a modified version of the tooth-wear index. The 3 groups were compared by means of the Kruskal-Wallis and Dunn tests, considering the frequency and the severity of wear on each surface of each group of teeth. The level of statistical significance was set at 5%. Results: The normal occlusion group had statistically greater tooth wear on the palatal surfaces of the maxillary central incisors and the incisal surfaces of the maxillary canines than the corresponding surfaces in both Class II malocclusion groups. The complete and half-cusp Class II Division 1 malocclusion groups had statistically greater tooth wear on the occlusal surfaces of the maxillary second premolar and first molar, the occlusal surfaces of the mandibular premolars, and the buccal surfaces of the mandibular posterior teeth compared with the normal occlusion group. The half-cusp Class II Division 1 malocclusion group had significantly greater tooth wear on the incisal surfaces of the mandibular incisors compared with the complete Class II Division 1 malocclusion group. Conclusions: Subjects with normal occlusion and complete or half-cusp Class II Division 1 malocclusions have different tooth-wear patterns. Tooth wear on the malocclusion subjects should not be considered pathologic but rather consequent to the different interocclusal tooth arrangement. (Am J Orthod Dentofacial Orthop 2010; 137: 14. e1-14.e7)

Effects of the pendulum appliance, cervical headgear, and 2 premolar extractions followed by fixed appliances in patients with Class II malocclusion

Introduction: In this retrospective study, we compared the cephalometric effects, the dental-arch changes, and the efficiency of Class II treatment with the pendulum appliance, cervical headgear, or extraction of 2 maxillary premolars, all associated with fixed appliance therapy. Methods: The sample of 82 patients with Class II malocclusion was divided into 3 groups: group 1 patients (n = 22; treatment time, 3.8 years) were treated with the pendulum appliance and fixed orthodontic appliances. Group 2 patients (n = 30; treatment time, 3.2 years) were treated with cervical headgear followed by fixed appliances; group 3 patients (n = 30; treatment time, 2.1 years) were treated with 2 maxillary premolar extractions and fixed appliances. The average starting ages of the groups ranged from 13.2 to 13.8 years. Data were obtained from serial cephalometric measurements and dental casts. The dental casts were analyzed with the treatment priority index. The treatment efficiency index was also used. Results: The 3 treatment protocols produced similar cephalometric effects, especially skeletally. Comparisons among the 2 distalizing appliances (pendulum and cervical headgear) and extraction of 2 maxillary premolars for Class II treatment showed changes primarily in the maxillary dentoalveolar component and dental relationships. The facial profile was similar after treatment, except for slightly more retrusion of the upper lip in the extraction patients. The treatment priority index demonstrated that occlusal outcomes also were similar among the groups. The treatment efficiency index had higher values for the extraction group. Conclusions: The effects of treatment with the pendulum appliance or cervical headgear and extraction of 2 maxillary premolars associated with fixed appliances were similar from both occlusal and cephalometric standpoints. Class II treatment with extraction of maxillary teeth was more efficient because of the shorter treatment time. Differences in maxillary incisor retraction should be noted, but these differences might have been due to greater maxillary dentoalveolar protrusion in the extraction group before treatment. (Am J Orthod Dentofacial Orthop 2009;136:833-42)

Strategic maxillary second-molar extraction in Class II malocclusion

Maxillary second-molar extraction in Class II malocclusion is a controversial issue in orthodontics. This treatment protocol is rigorous and not routine. In this case report, we present the orthodontic treatment of a patient with a Class II malocclusion, maxillary crowding, and no mandibular first molars, treated with extraction of the maxillary second molars. The mechanotherapy and indications of maxillary second- molar extraction are discussed. (Am J Orthod Dentofacial Orthop 2009;136:878-86)

Long-term stability of Class II malocclusion treated with 2-and 4-premolar extraction protocols

Introduction: The objective of this study was to cephalometrically compare the stability of complete Class II malocclusion treatment with 2 or 4 premolar extractions after a mean period of 9.35 years. Methods: A sample of 57 records from patients with complete Class II malocclusion was selected and divided into 2 groups. Group 1 consisted of 30 patients with an initial mean age of 12.87 years treated with extraction of 2 maxillary premolars. Group 2 consisted of 27 patients with an initial mean age of 13.72 years treated with extraction of 4 premolars. T tests were used to compare the groups` initial cephalometric characteristics and posttreatment changes. Pearson correlation coefficients were calculated to determine the correlation between treatment and posttreatment dental-relationship changes. Results: During the posttreatment period, both groups had similar behavior, except that group 1 had a statistically greater maxillary forward displacement and a greater increase in the apical-base relationship than group 2. On the other hand, group 2 had a statistically greater molar-relationship relapse toward Class II. There were significant positive correlations between the amounts of treatment and posttreatment dentoalveolar-relationship changes. Conclusions: Treatment of complete Class II malocclusions with 2 maxillary premolar extractions or 4 premolar extractions had similar long-term posttreatment stability. (Am J Orthod Dentofacial Orthop 2009;136:154.e1-154.e10)

Comparative efficiency of Class II malocclusion treatment with the pendulum appliance or two maxillary premolar extractions and edgewire appliances

The objective of this study was to compare, on study models and initial cephalograms, the efficiency of Class II malocclusion treatment with the pendulum appliance, and with two maxillary premolar extraction protocol. The sample consisted of 48 treated Class II malocclusion patients: group 1 comprised 22 patients (7 males, 15 females) treated with the pendulum appliance, with an initial mean age of 14.44 years and group 2, 26 patients (14 males, 12 females) treated with two maxillary premolar extractions at an initial mean age of 13.66 years. To compare the efficiency of each treatment protocol, the occlusal outcomes were evaluated on dental casts using the Peer Assessment Rating (PAR) Index and the treatment time (TT) of each group was calculated on clinical charts. The degree of treatment efficiency was calculated as the ratio between the percentage of occlusal improvement, evaluated through the PAR index, and TT. Statistical analysis was undertaken by means of t-tests. The findings demonstrated that the two maxillary premolar extraction protocol provided the occlusal outcomes in a shorter time (group 1: 45.7 months, group 2: 23.01 months) and, therefore, demonstrated greater treatment efficiency than the pendulum appliance.

Treatment of a Class II subdivision malocclusion with multiple congenitally missing teeth

This case report describes the treatment of a patient with a Class II Division 1 subdivision right malocclusion with 8 congenitally missing teeth, incompetent lips, and incisor protrusion. The treatment plan included extractions and space closure with retraction of the anterior teeth; symmetric mechanics were used in the mandibular arch and asymmetric mechanics in the maxillary arch. Because of the mechanics used, some midline deviations were expected. Knowledge of diagnosis and treatment planning of asymmetric malocclusions and dental esthetics are essential for success when correcting asymmetic problems, but, even so, small clinical compromises should be expected. (Am J Orthod Dentofacial Orthop 2009; 135: 663-70)