An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions

Reverse immunogenetic approaches attempt to optimize the selection of candidate epitopes, and thus minimize the experimental effort needed to identify new epitopes. When predicting cytotoxic T cell epitopes, the main focus has been on the highly specific MHC class I binding event. Methods have also been developed for predicting the antigen-processing steps preceding MHC class I binding, including proteasomal cleavage and transporter associated with antigen processing (TAP) transport efficiency. Here, we use a dataset obtained from the SYFPEITHI database to show that a method integrating predictions of MHC class I binding affinity, TAP transport efficiency, and C-terminal proteasomal cleavage outperforms any of the individual methods. Using an independent evaluation dataset of HIV epitopes from the Los Alamos database, the validity of the integrated method is confirmed. The performance of the integrated method is found to be significantly higher than that of the two publicly available prediction methods BIMAS and SYFPEITHI. To identify 85% of the epitopes in the HIV dataset, 9% and 10% of all possible nonamers in the HIV proteins must be tested when using the BIMAS and SYFPEITHI methods, respectively, for the selection of candidate epitopes. This number is reduced to 7% when using the integrated method. In practical terms, this means that the experimental effort needed to identify an epitope in a hypothetical protein with 85% probability is reduced by 20-30% when using the integrated method.The method is available at http://www.cbs.dtu.dk/services/NetCTL. Supplementary material is available at http://www.cbs.dtu.dk/suppl/immunology/CTL.php.     

Carcinoembryonic antigen like antigen in granular cell myoblastomas

Summary A series of granular cell myoblastomas (GCM) and other benign and malignant tumours of soft tissue were examined for cytoplasmic content of carcinoembryonic antigen (CEA) by the two-layer conjugated immunoperoxidase technique. Using a commercial rabbit anti-CEA serum only granular cell myoblastomas showed positive cytoplasmic reaction. Pretreatment with periodic acid made this reaction less intense, but when the commercial rabbit anti-CEA serum was absorbed with tissue powder from normal human spleen the positive reaction was totally abolished. It is concluded that the positivity of GCM for CEA using commercial rabbit anti-CEA serum is due to the content of non-specific cross-reacting antigen (NCA) and maybe other cross-reacting glycoproteins in this tumour, and not to CEA as claimed in a previous study.     

Apical and basolateral expression of Aquaporin-1 in transfected MDCK and LLC-PK cells and functional evaluation of their transcellular osmotic water permeabilities

 Aquaporin-1 is present in the apical and basolateral membranes in proximal tubules and descending limbs of Henlé’s loop. In order to be able to study the routing of Aquaporin-1 and the regulation of Aquaporin-1-mediated transcellular water flow, we stably transfected LLC-PK₁ and MDCK-HRS cell lines with an Aquaporin-1 expression construct. LLC-PK₁ clone 7 and MDCK clone K integrated two and one copies, respectively, which was reflected in the amount of Aquaporin-1 mRNA expressed in both clones. The Aquaporin-1 protein levels, however, were similar. In both clones, immuno-electronmicroscopy showed extensive labelling of Aquaporin-1 on the basolateral plasma membrane, endosomal vesicles and the apical plasma membrane, including the microvilli. To measure transcellular water permeation, a simple method was applied using phenol-red as a cell-impermeant marker of concentration. In contrast to the native cell lines, both clones revealed a high transcellular osmotic water permeability, which could not be influenced by forskolin add/3-isobutyl-1-methylxanthine (IBMX) or the phorbol ester 12-O-tetradecanoyl 13-acetate (TPA). After glutaraldehyde fixation, it was inhibitable by HgCl₂. These results indicate that targeting of Aquaporin-1 to the apical and basolateral plasma membrane is independent of cell type and show for the first time that water flow through a cultured epithelium can be blocked by mercurial compounds. Received: 9 October 1996 / Received after revision: 3 January 1997 / Accepted: 8 January 1997     

Circulating immune complexes in ulcerative colitis.--II. Correlation with serum protein concentrations and complement conversion products

Several serum proteins were quantified in twenty-two patients with active ulcerative colitis, and the findings were related to disease activity and occurrence of circulating immune complexes (IC). Conversion of C3 was significantly more frequent in the IC-positive group (eight patients) as compared to the IC-negative group (fourteen patients). Factor B was demonstrable in fifteen out of the twenty-two patients and seven out of the eight IC-positive patients had detectable levels of factor B. There was no difference between the IC-positive and the IC-negative group as regards serum concentrations of the complement factors C3, C4 and factor B, or serum orosomucoid, albumin, IgM and IgG. In contrast, the serum IgA levels tended to be reduced in the IC-positive group. C3 and factor B were significantly elevated in four patients with severe disease activity. In addition, C3, factor B and C4 concentrations showed a positive correlation to the serum orosomucoid levels. The serum concentrations of orosomucoid and albumin were inversely correlated to each other.     

Adaptation of wild-type measles virus to CD46 receptor usage

Summary.  Vaccine strains of measles virus (MV) use CD46 as receptor and downregulate CD46 from the surface of infected cells. MVs isolated and passaged on B-lymphoid cells (wild-type MVs) seem to use another receptor and do not downregulate CD46. In the present study, we found that isolation of MV on human or marmoset B-lymphoid cells did not alter the MV haemagglutinin (H) protein relative to that in the patient. The wild-type isolates were adapted to the human epithelial HEp-2 cell line or the monkey fibroblast Vero cell line. All HEp-2 cell adapted viruses and 1 out of 4 Vero cell adapted viruses acquired the capacity to use CD46 as receptor, as measured by their ability to infect murine cells expressing human CD46. Adaptation to CD46 receptor usage was coupled to substitution of amino acid 481 of the MV H protein from asparagine to tyrosine but not to CD46 downregulation. The present study demonstrates that CD46 receptor usage can be induced by adaptation of wild-type MV to cells that do not express a wild-type receptor and suggests that a similar mechanism acted on the progenitor viruses of the present MV vaccine strains during their isolation and attenuation. Received June 5, 2000 Accepted October 5, 2000     

High-dose inhaled steroids in the management of asthma A comparison of the effects of budesonide and beclomethasone dipropionate on pulmonary function, symptoms, bronchial responsiveness and the adrenal function

Svendsen UG, Frølund L, Heinig JH, Madsen F, Nielsen NH, Weeke B. High-dose inhaled steroids in the management of asthma. A comparison of the effects of budesonide and beclomethasone dipropionate on pulmonary function, symptoms, bronchial responsiveness and the adrenal function.
The efficacy of budesonide (800 μg b.d.) and beclomethasone dipropionate (750 μg b.d.) in controlling the symptoms of asthma, pulmonary function, bronchial responsiveness to histamine, and adrenal function, was assessed in a double-blind, double-dummy cross-over study of 36 adult chronic asthmatic patients. The patients, the majority of whom were assessed to be affected to a severe degree, were insufficiently controlled in their current regimen of inhaled steroids and/or inhaled and oral bronchodilators. A 2 weeks baseline period preceded 6 weeks of treatment with each of the study drugs. Both treatment groups showed improvements from baseline in clinical assessment of lung function carried out after the first 6 weeks of treatment. No significant differences were seen throughout the entire 12 weeks study, when comparing the effects of the treatments on FEV₁ FVC, PEF or the histamine PC₂₀. Asthma severity, symptom score and inhaled bronchodilator use showed the same results after both treatments. It is concluded that inhalations of budesonide and beclomethasone dipropionate in high doses are equally potent in the treatment of severe asthma. There is no significant influence on the adrenal function and no significant side effects during a period equal to that of the present study.     

Ethylenediaminetetraacetic acid (disodium salt)-labile bovine immunoglobulin M Fc binding to Brucella abortus: a cause of nonspecific agglutination.

It was demonstrated by a radioimmunoassay procedure that Brucella abortus agglutinins from noninfected cattle sera, absorbed to B. abortus antigen and eluted with ethylenediaminetetraacetic acid (EDTA), was immunoglobulin M that bound to that bacterium by its Fc portion. The EDTA-eluted immunoglobulin M agglutinated intact B. abortus cells but not erythrocytes treated with B. abortus lipopolysaccharide. The specificity of the EDTA-eluted immunoglobulin was for B. abortus, although a small titer to Yersinia enterocolitica serotype O:9 was observed. In contrast, immunoglobulin M purified from the serum of a cow injected 7 days previously with heat-killed B. abortus bound to the antigen by its Fab portion, was not labile to EDTA treatment, cross-reacted extensively with Y. enterocolitica serotype O:9, and agglutinated various other bacterial antigens and normal erythrocytes.     

Anaerobic and aerobic skin bacteria before and after skin-disinfection with chlorhexidine: an experimental study in volunteers.

The amount, composition, and localization of anaerobic and aerobic bacteria in the normal skin before and after disinfection were the subject of a volunteer study. The superficial bacterial flora were sampled by velvet pad imprints, and the deep flora were determined from whole skin biopsies. Only one anaerobic species, Propionebacterium acnes, was encountered even though other and more strict anaerobic bacteria could have been grown with the anaerobic technique employed. Staphylococcus albus dominated among the aerobic superficial bacteria, while diphtheroids, Micrococcus spp., and lactobacilli occurred sporadically. The deep aerobic bacteria were present in a significantly greater amount than the anaerobic. A two-step cleansing/disinfection procedure was evaluated in vivo in volunteers as well as in surgical patients, and aqueous cetrimide/chlorhexidine (Savlon) followed by chlorhexidine in alcohol (Hibitane) almost eradicated both the superficial and deep anaerobic and aerobic skin flora.