Identification and Immune Assessment of T Cell Epitopes in Five Plasmodium falciparum Blood Stage Antigens to Facilitate Vaccine Candidate Selection and Optimization

The hurdles to effective blood stage malaria vaccine design include immune evasion tactics used by the parasite such as redundant invasion pathways and antigen variation among circulating parasite strains. While blood stage malaria vaccine development primarily focuses on eliciting optimal humoral responses capable of blocking erythrocyte invasion, clinically-tested Plasmodium falciparum (Pf) vaccines have not elicited sterile protection, in part due to the dramatically high levels of antibody needed. Recent development efforts with non-redundant, conserved blood stage antigens suggest both high antibody titer and rapid antibody binding kinetics are important efficacy factors. Based on the central role of helper CD4 T cells in development of strong, protective immune responses, we systematically analyzed the class II epitope content in five leading Pf blood stage antigens (RH5, CyRPA, RIPR, AMA1 and EBA175) using in silico, in vitro, and ex vivo methodologies. We employed in silico T cell epitope analysis to enable identification of 67 HLA-restricted class II epitope clusters predicted to bind a panel of nine HLA-DRB1 alleles. We assessed a subset of these for HLA-DRB1 allele binding in vitro, to verify the in silico predictions. All clusters assessed (40 clusters represented by 46 peptides) bound at least two HLA-DR alleles in vitro. The overall epitope prediction to in vitro HLA-DRB1 allele binding accuracy was 71%. Utilizing the set of RH5 class II epitope clusters (10 clusters represented by 12 peptides), we assessed stimulation of T cells collected from HLA-matched RH5 vaccinees using an IFN-γ T cell recall assay. All clusters demonstrated positive recall responses, with the highest responses – by percentage of responders and response magnitude – associated with clusters located in the N-terminal region of RH5. Finally, a statistically significant correlation between in silico epitope predictions and ex vivo IFN-γ recall response was found when accounting for HLA-DR matches between the epitope predictions and donor HLA phenotypes. This is the first comprehensive analysis of class II epitope content in RH5, CyRPA, RIPR, AMA1 and EBA175 accompanied by in vitro HLA binding validation for all five proteins and ex vivo T cell response confirmation for RH5.

Bridging Computational Vaccinology and Vaccine Development Through Systematic Identification, Characterization, and Downselection of Conserved and Variable Circumsporozoite Protein CD4 T Cell Epitopes From Diverse Plasmodium falciparum Strains

An effective malaria vaccine must prevent disease in a range of populations living in regions with vastly different transmission rates and protect against genetically-diverse Plasmodium falciparum (Pf) strains. The protective efficacy afforded by the currently licensed malaria vaccine, Mosquirix™, promotes strong humoral responses to Pf circumsporozoite protein (CSP) 3D7 but protection is limited in duration and by strain variation. Helper CD4 T cells are central to development of protective immune responses, playing roles in B cell activation and maturation processes, cytokine production, and stimulation of effector T cells. Therefore, we took advantage of recent in silico modeling advances to predict and analyze human leukocyte antigen (HLA)-restricted class II epitopes from PfCSP – across the entire PfCSP 3D7 sequence as well as in 539 PfCSP sequence variants – with the goal of improving PfCSP-based malaria vaccines. Specifically, we developed a systematic workflow to identify peptide sequences capable of binding HLA-DR in a context relevant to achieving broad human population coverage utilizing cognate T cell help and with limited T regulatory cell activation triggers. Through this workflow, we identified seven predicted class II epitope clusters in the N- and C-terminal regions of PfCSP 3D7 and an additional eight clusters through comparative analysis of 539 PfCSP sequence variants. A subset of these predicted class II epitope clusters was synthesized as peptides and assessed for HLA-DR binding in vitro. Further, we characterized the functional capacity of these peptides to prime and activate human peripheral blood mononuclear cells (PBMCs), by monitoring cytokine response profiles using MIMIC^® technology (Modular IMmune In vitro Construct). Utilizing this decision framework, we found sufficient differential cellular activation and cytokine profiles among HLA-DR-matched PBMC donors to downselect class II epitope clusters for inclusion in a vaccine targeting PfCSP. Importantly, the downselected clusters are not highly conserved across PfCSP variants but rather, they overlap a hypervariable region (TH2R) in the C-terminus of the protein. We recommend assessing these class II epitope clusters within the context of a PfCSP vaccine, employing a test system capable of measuring immunogenicity across a broad set of HLA-DR alleles.

Identification, Selection and Immune Assessment of Liver Stage CD8 T Cell Epitopes From Plasmodium falciparum

Immunization with radiation-attenuated sporozoites (RAS) has been shown to protect against malaria infection, primarily through CD8 T cell responses, but protection is limited based on parasite strain. Therefore, while CD8 T cells are an ideal effector population target for liver stage malaria vaccine development strategies, such strategies must incorporate conserved epitopes that cover a large range of class I human leukocyte antigen (HLA) supertypes to elicit cross-strain immunity across the target population. This approach requires identifying and characterizing a wide range of CD8 T cell epitopes for incorporation into a vaccine such that coverage across a large range of class I HLA alleles is attained. Accordingly, we devised an experimental framework to identify CD8 T cell epitopes from novel and minimally characterized antigens found at the pre-erythrocytic stage of parasite development. Through in silico analysis we selected conserved P. falciparum proteins, using P. vivax orthologues to establish stringent conservation parameters, predicted to have a high number of T cell epitopes across a set of six class I HLA alleles representative of major supertypes. Using the decision framework, five proteins were selected based on the density and number of predicted epitopes. Selected epitopes were synthesized as peptides and evaluated for binding to the class I HLA alleles in vitro to verify in silico binding predictions, and subsequently for stimulation of human T cells using the Modular IMmune In-vitro Construct (MIMIC®) technology to verify immunogenicity. By combining the in silico tools with the ex vivo high throughput MIMIC platform, we identified 15 novel CD8 T cell epitopes capable of stimulating an immune response in alleles across the class I HLA panel. We recommend these epitopes should be evaluated in appropriate in vivo humanized immune system models to determine their protective efficacy for potential inclusion in future vaccines.

Better Epitope Discovery, Precision Immune Engineering, and Accelerated Vaccine Design Using Immunoinformatics Tools

Computational vaccinology includes epitope mapping, antigen selection, and immunogen design using computational tools. Tools that facilitate the in silico prediction of immune response to biothreats, emerging infectious diseases, and cancers can accelerate the design of novel and next generation vaccines and their delivery to the clinic. Over the past 20 years, vaccinologists, bioinformatics experts, and advanced programmers based in Providence, Rhode Island, USA have advanced the development of an integrated toolkit for vaccine design called iVAX, that is secure and user-accessible by internet. This integrated set of immunoinformatic tools comprises algorithms for scoring and triaging candidate antigens, selecting immunogenic and conserved T cell epitopes, re-engineering or eliminating regulatory T cell epitopes, and re-designing antigens to induce immunogenicity and protection against disease for humans and livestock. Commercial and academic applications of iVAX have included identifying immunogenic T cell epitopes in the development of a T-cell based human multi-epitope Q fever vaccine, designing novel influenza vaccines, identifying cross-conserved T cell epitopes for a malaria vaccine, and analyzing immune responses in clinical vaccine studies. Animal vaccine applications to date have included viral infections of pigs such as swine influenza A, PCV2, and African Swine Fever. “Rapid-Fire” applications for biodefense have included a demonstration project for Lassa Fever and Q fever. As recent infectious disease outbreaks underscore the significance of vaccine-driven preparedness, the integrated set of tools available on the iVAX toolkit stand ready to help vaccine developers deliver genome-derived, epitope-driven vaccines.

In silico identification and modification of T cell epitopes in pertussis antigens associated with tolerance

The resurgence of whooping cough since the introduction of acellular (protein) vaccines has led to a renewed interest in the development of improved pertussis vaccines; Outer Membrane Vesicles (OMVs) carrying pertussis antigens have emerged as viable candidates. An in silico immunogenicity screen was carried out on 49 well-known Bordetella pertussis proteins in order to better understand their potential role toward the efficacy of pertussis OMVs for vaccine design; seven proteins were identified as being good candidates for including in optimized cellular and acellular pertussis vaccines. We then screened these antigens for putative tolerance-inducing sequences, as proteins with reduced tolerogenicity have improved vaccine potency in preclinical models. We used specialized homology tools (JanusMatrix) to identify peptides in the proteins that were cross-reactive with human sequences. Four of the 19 identified cross-reactive peptides were detolerized in silico using a separate tool, OptiMatrix, which disrupted the potential of these peptides to bind to human HLA and murine MHC. Four selected cross-reactive peptides and their detolerized variants were synthesized and their binding to a set of eight common HLA class II alleles was assessed in vitro. Reduced binding affinity to HLA class II was observed for the detolerized variants compared to the wild-type peptides, highlighting the potential of this approach for designing more efficacious pertussis vaccines.

Multi-antigen Vaccination With Simultaneous Engagement of the OX40 Receptor Delays Malignant Mesothelioma Growth and Increases Survival in Animal Models

Malignant Mesothelioma (MM) is a rare and highly aggressive cancer that develops from mesothelial cells lining the pleura and other internal cavities, and is often associated with asbestos exposure. To date, no effective treatments have been made available for this pathology. Herein, we propose a novel immunotherapeutic approach based on a unique vaccine targeting a series of antigens that we found expressed in different MM tumors, but largely undetectable in normal tissues. This vaccine, that we term p-Tvax, is comprised of a series of immunogenic peptides presented by both MHC-I and -II to generate robust immune responses. The peptides were designed using in silico algorithms that discriminate between highly immunogenic T cell epitopes and other harmful epitopes, such as suppressive regulatory T cell epitopes and autoimmune epitopes. Vaccination of mice with p-Tvax led to antigen-specific immune responses that involved both CD8⁺ and CD4⁺ T cells, which exhibited cytolytic activity against MM cells in vitro. In mice carrying MM tumors, p-Tvax increased tumor infiltration of CD4⁺ T cells. Moreover, combining p-Tvax with an OX40 agonist led to decreased tumor growth and increased survival. Mice treated with this combination immunotherapy displayed higher numbers of tumor-infiltrating CD8⁺ and CD4⁺ T cells and reduced T regulatory cells in tumors. Collectively, these data suggest that the combination of p-Tvax with an OX40 agonist could be an effective strategy for MM treatment.

Bridging the [Health Equity] Gap at a Free Clinic for Uninsured Residents of Rhode Island

Poor management of chronic diseases, such as hypertension and diabetes, particularly among the uninsured, places medical and financial burdens on the healthcare system. Clínica Esperanza/Hope Clinic initiated a chronic disease management program for uninsured residents of Rhode Island (RI) called Bridging the [Health Equity] Gap (BTG), which offers continuity of care, quarterly goal-setting appointments, and healthy lifestyle interventions. Outcomes for 549 participants from the initial evaluation period are presented here. Over the first 12 months of enrollment, mean hemoglobin A1c decreased from 10.2% to 8.3% (p<0.001), and mean blood glucose of individuals with diabetes decreased by 51 mg/dL (p<0.01). BTG participants used the local emergency department (ED) 60% less than Medicaid-insured RI residents and had 61% fewer "potentially preventable" ED visits. The positive impact of BTG on chronic disease outcomes and ED usage by uninsured patients suggests that programs like BTG may reduce overall healthcare costs in the state.

The use of cryopreserved lymphocytes in assessing inter-individual radiosensitivity with the micronucleus assay

PURPOSE

The feasibility of using cryopreserved lymphocytes to detect inter-individual differences in chromosomal radiosensitivity was investigated. Typically, such studies are conducted with fresh blood samples but, in a clinical setting, when availability of samples is unpredictable, this is not always convenient. The sensitivity of 23 normal healthy donors, 11 breast cancer patients who had shown severe acute skin reactions to radiotherapy and seven ataxia telangiectasia (A-T) heterozygotes was determined.

MATERIALS AND METHODS

Thawed lymphocytes were exposed to high (HDR) or low dose rate (LDR) gamma irradiation (3.5 Gy) in Go, stimulated with PHA, treated with cytochalasin-B 24 h later and then harvested at 90 h for the determination of micronucleus (MN) yields in binucleate cells.

RESULTS

Each normal donor was tested one to three times. Mean MN yields were 76.1 +/- 9.3/100 cells at HDR and 44.5 +/- 5.3 at LDR, giving an LDR sparing effect of 39.6 +/- 9.3%. A relatively high proportion of tests failed to yield sufficient binucleate cells for analysis. Inter-experimental variability was also high and it was not possible to demonstrate inter-individual differences in sensitivity in spite of the use of an internal control sample from a single normal donor in each experiment. There was a small but significant increase in radiation-induced MN in the breast cancer patients compared with the normals at LDR (but not at HDR), but a complete overlap with the normal range. There was no increase in sensitivity in the A-T heterozygotes at HDR. The LDR samples failed because the LDR protocol reduced proliferation rates, and radiation-induced mitotic inhibition in this group was higher than in normals.

CONCLUSIONS

In comparison with previous experience with fresh blood samples, the use of frozen lymphocytes is not as satisfactory because: (1) experimental failures are higher; (2) inter-experiment variability is higher: (3) dose-rate sparing is lower, suggesting poorer repair; and (4) the ability to discriminate between breast cancer cases and normals is probably lower.

Histamine release from human leucocytes by IgG4 subclass in the sera of allergic children

Our studies on histamine release from normal washed leucocytes sensitised with sera of children allergic to various inhaled and ingested allergens show that besides IgE, IgG4 present in these sera was capable of sensitising leucocytes of normal donors, and these leucocytes released histamine on challenge with anti-IgG4. By contrast, antisera of other subclasses of IgG released very small amounts of histamine from sensitised leucocytes. A discordant correlation between skin tests and RAST IgE was observed in some children. Significantly greater amounts of histamine were released from normal leucocytes sensitised with serum from these children when challenged with anti-IgG4 compared to anti-IgE. These studies indicate that IgG4 merits further study as a reaginic marker in atopic diseases of the children with possible prognostic significance.

Serum C-reactive protein in normal and infected neonates

Serum C-reactive protein determinations were performed on well and sick neonates, in order to gain information about normal values and its value in the diagnosis of neonatal septicaemia. The median value in 48 cord sera was 200 micrograms/l (range 15 to greater than 6,000 micrograms/L); there was no correlation between paired maternal and cord serum CRP levels (12 pairs). Thirty-six children were followed from birth for a mean of 20 days. There were 21 episodes of confirmed infection in 16 children, each associated with a sustained rise in C-reactive protein, often commencing before there was clinical evidence of infection. In four patients with raised levels, infection was suspected, but no firm evidence was obtained. In the remaining 16 children there were no values above 10 mg/l, and the 95th centile was about 6 mg/l, with no difference between values obtained in the first three days of life and those found subsequently. Hyaline membrane disease and jaundice were not associated with a rise. Raised serum C-reactive proteins is a good indicator of the presence of infection in the neonatal period.

Sequential study of C reactive protein in neonatal septicaemia using a latex agglutination test

The usefulness of serial study of C reactive protein in the early detection of neonatal septicaemia was evaluated in a neonatal unit using a commercially available latex agglutination slide test as a rapid screening method and electroimmunoassay as a reference method for C reactive protein determination. A positive latex test was obtained in 11 infants with verified septicaemia (positive blood culture), two infants with clinically evident infection but without bacteriological confirmation, one infant with recurrent chest infection due to Pseudomonas aeruginosa, and one infant who showed signs of birth asphyxia with meconium aspiration, but was not infected. Positive latex test results correlated with raised concentrations of C reactive protein, measured by immunoassay. In some instances, however, concentrations of C reactive protein in excess of 12 mg/100 ml gave weaker agglutination results in the slide test, which could be interpreted as negative results. In a sequential study of the infected infants, 6.3% of the values recorded on a slide test were false negatives. In contrast, false positive values were observed on a slide test in 1.9% of 27 non-infected infants. The higher percentage of false negative values may be due to the presence of excess antigen in the sera of some infected children. It is suggested that the latex test should be carried out on suitable dilutions of serum. Although the slide test may reliably indicate infection at an early stage in neonates, the C reactive protein response is non-specific, as seen in a non-infected infant who showed signs of birth asphyxia with meconium aspiration. Provided the non-specific nature of the C reactive protein response is recognised, the latex test may be a useful serum measurement for early diagnosis of neonatal septicaemia of the newborn. The test has the advantage of being performed easily, quickly, and cheaply.

Impaired opsonophagocytosis of serotypes Ib and II of group B streptococci as compared with serotypes Ia and III: role of the alternative pathway of complement in opsonisation of serotype III of group B streptococci

Using the technique of phagocytic chemiluminescence, we have shown that serotypes Ib and II of group B streptococci are resistant to opsonophagocytosis. The resistant strains became susceptible to opsonophagocytosis by trypsin treatment, but neuraminidase had no effect. Several studies have failed to define a significant role for the alternative pathway of complement in opsonisation of group B streptococci. By simple chelation and heat inactivation studies, we have shown that the alternative pathway of complement is activated by serotype III of group B streptococci.

Serial study of C reactive protein in neonatal septicaemia

Serial C reactive protein concentrations were assayed by electroimmunoassay in 41 infants. Values in most of the non-infected infants were below 0.3 mg/dl, the lower limit of detection of C reactive protein by electroimmunoassay. Eleven of 12 infants with proved sepsis (positive blood cultures) had significantly raised concentrations and one infant with recurrent pseudomonas chest infection had a raised C reactive protein concentration. High C reactive protein concentrations were also found in infants with suspected infection. Successful treatment was followed by a decrease in the C reactive protein concentration. Total white blood cell count was not as appropriate as C reactive protein determination in the early identification of bacterial infection in the newborn.

In vitro effect of Panax ginseng on phytohaemagglutinin-induced lymphocyte transformation

The effect of hydrocortisone or Panax ginseng, and/or a combination of hydrocortisone and Panax ginseng on phytohaemagglutinin (PHA-P)-induced transformation of peripheral blood lymphocytes were studied in 4 normal healthy adult volunteers. Increasing concentrations of Panax ginseng 0.16-1.60 micrograms X ml-1 caused a dose-related inhibition of PHA-P transformation of lymphocytes. A combination of 500 micrograms X ml-1 hydrocortisone and 0.80 micrograms X ml-1 Panax ginseng produced a greater suppression of PHA-P stimulation than either drug used alone. This suggests that Panax ginseng has a steroid-like effect in vitro, and may have a potentiating effect with hydrocortisone on T-cell-mediated immunity.

Flat small intestinal mucosa and autoantibodies against the gut epithelium

A male infant, aged 1 year 3 months, was admitted to the hospital with protracted diarrhoea, vomiting, and weight loss. The diarrhoea and vomiting coincided with an outbreak of acute diarrhoea and vomiting affecting other family members. Biopsy showed a flat small intestinal mucosa which did not respond to a diet free of gluten, cow's milk, and eggs, or during 8 weeks of intravenous alimentation. Steroids were given, and courses of nalcrom and later cimetidine, but these did not produce any significant improvement. A rare IgG autoantibody specific for gut epithelium was found, which, when present, was associated with a cytological abnormality of crypt enteroblasts. The autoantibody disappeared after treatment with cyclophosphamide, and the cytological abnormality subsequently diminished. However, the mucosa remained severely abnormal and has been so for 23 months. It is possible that an autoimmune reaction against the patient's small intestinal mucosa has led to persistence of the enteropathy.

Suppressor cells in asthmatic children

Peripheral blood mononuclear cells (PBMC) from thirteen asthmatic children, and from normal control subjects, were pre-incubated with and without concanavalin A (con A), washed, and cultured with fresh allogenic PBMC from healthy donors. The con A pre-treated cells from fifteen of seventeen normal controls clearly suppressed the blast transformation response to con A by normal allogeneic PBMC. However, con A-generated suppressor activity was found in only seven of the asthmatic patients studied, most of whom could be classified as "short-term' asthmatics. It is thus possible that either dysfunction or a reduction of the (con A)-inducible, T-suppressor cell subpopulation in peripheral blood is frequent among "long-term' asthmatic patients. This may suggest that a different pathogenesis may be operating in early-onset, long-continued asthma, when compared with those investigated early in the course of asthma which has begun later in childhood.

Traveller's diarrhoea with a vengeance in children of UK immigrants visiting their parental homeland

Six healthy children, born in the UK, travelled to their parental homeland and developed a severe form of traveller's diarrhoea. This was characterised by rapid loss of weight and chronic diarrhoea. On return to this country, investigation in 5 of them showed an abnormal, small intestinal mucosa. There was a high incidence of pathogens and potential pathogens found in stools and duodenal juice. Immunodeficiency was found in 2 of them. Small intestinal mucosal damage related to gut infection in previously well children appears to be of cardinal importance in the interaction between chronic diarrhoea and malnutrition. This observation may point the way to future research into the primary role of gut infection in the initiation of the cycle of malnutrition and chronic diarrhoea in developing communities.

Acute phase proteins in chronic inflammatory bowel disease in childhood

The serum levels of five acute phase proteins (APP) were measured in 18 children with Crohn's Disease (CD) or ulcerative colitis (UC) and in two control groups. The levels of C-reactive protein, alpha 1-acid glycoprotein, alpha 1-antitrypsin, C9, and Factor B were significantly raised in patients with CD and UC with good separation from controls, but they were not entirely reliable used as screening tests unless used in combination. The levels of APP were monitored for periods varying from 18 to 28 months in each patient and found to reflect the disease activity in both CD and UC. On seven occasions the APP levels did not match the clinically assessed disease activity, but when the serum levels were related to outcome of the disease, C-reactive protein was found to be elevated--whether or not there were symptoms of the disease--in all patients who later had a relapse, while normal values were found in those who had a long remission. These results suggest that the estimation of Creative protein is of prognostic value and that its measurement is particularly useful in children with mild symptoms in whom disease activity and prognosis are difficult to assess.

The placental transfer of IgG subclasses in human pregnancy

Total IgG concentrations and the concentrations of the four subclasses of IgG were estimated in thirty-four pairs of maternal and foetal sera from pregnancies of various gestations ranging from 28 to 42 weeks using the method of radial immunodiffusion. It was found that: (1) all subclasses of IgG cross the human placenta freely, (2) foetal levels of IgG and each subclass of IgG exceed maternal levels in full-term pregnancies and (3) there was a close linear relationship between gestational age and the placental transfer of IgG and each of its subclasses.

Human chorionic somato-mammotrophin in serum and urine in various stages of pregnancy: its correlation with enzymes and oestrogens

Human chorionic somato-mammotrophin (HCS) and the activities of heat-stable alkaline phosphatase (HSAP) and cysteine aminopeptidase (CAP) in the serum of normal pregnant women were studied. The hormone and enzymes were detectable at the early stage of pregnancy and all showed an increase with the progress of gestation. A highly significant correlation was found between HCS and activities of HSAP and CAP during all stages of gestation.

Human chorionic somato-mammotrophin and oestrogens were measured in the urine of pregnant women. The correlation coefficient between these factors was smaller than that found between serum enzymes and HCS but was still significant.