Lactobacillus mediated targeting of gastrointestinal pathogens

The mucosal membranes of the gastrointestinal, genitourinary and respiratory tract are the main targets for infection in the human body and are repeatedly challenged by pathogens. Passive immunization using delivery of antibodies at the mucosal membrane may thus provide a new first line of defense against these pathogens. The objective of this work was to genetically modify Lactobacillus, a natural inhabitant of the gastrointestinal tract, for in situ delivery of passive immunity against gastrointestinal infections. With the aim of identifying colonizing strains of Lactobacillus that could be used vehicle for delivery of passive immunity in the gastrointestinal tract, a collection of ninet three Lactobacillus strains, derived from human fecal samples, was screened for marke for survival and persistence in the gastrointestinal tract (paper I). Five strains show promising results and will be taken forward for testing of survivability in human gut a confirm their safety in human volunteers. A novel expression system for production and delivery of therapeutic molecules in Lactobacillus was constructed based on the framework of the apf gene from L. crispatus. This expression system was tested for delivery of antibody fragments both in a secreted form and cell wall anchored on the surface of the Lactobacillus. The expression cassettes were stably integrated on the chromosome using the integrase gene from the bacteriophage A2 to create “food grade” strains of Lactobacillus, devoid of antibiotic markers, for delivery of antibody fragments (paper II). The feasibility of delivering passive immunity against bacterial toxins in the gastrointestinal tract was tested with L. paracasei BL23 engineered to express a single chain antibody binding the anthrax protective antigen. The engineered Lactobacillus was able to provide protection in mice orally challenged with the anthrax edema toxin, validating the concept of in situ toxin neutralization in the gastrointestinal tract (paper III). Members of the family of Camilidae, to which llamas belong, express a subset of their IgG antibodies as heavy chain only antibodies. Their antigen binding domain is encoded in the single variable domain (VHH) that can be produced as a single polypeptide. The VHH has higher acid and proteolytic stability compared to conventional IgG making them ideally suitable for therapeutic use in the gastrointestinal tract. Llamas were immunized with the toxins A and B, the two causative elements of C. difficile associated diarrhea. A range of VHH neutralizing the dominant virulence factor, toxin B, were isolated and cloned for expression in L. paracasei. When expressed either in a secreted or cell wall anchored form, the Lactobacillus produced VHH were able to provide protection against the cytotoxic effects of toxin B. Prophylactic treatment with a combination of two strains of engineered L. paracasei expressing two toxin B neutralizing VHH could delay and provide partial protection against the effect of a toxin B producing strain of C. difficile in an in vivo hamster model (paper IV). In summary this work has shown the potential of using Lactobacillus for the delivery of passive immunity against gastrointestinal infections. Lactobacillus strains colonizing the gastrointestinal tract for delivery of antibody fragments could represent a potential new approach to management of the C. difficile associated diarrhea that could be used both prophylactically or for the prevention of recurrent infections

A hidden Markov model approach for determining expression from genomic tiling micro arrays

BACKGROUND: Genomic tiling micro arrays have great potential for identifying previously undiscovered coding as well as non-coding transcription. To-date, however, analyses of these data have been performed in an ad hoc fashion. RESULTS: We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM) is used to model the distributions of tiling array probe scores in expressed and non-expressed regions. The HMM is trained on sets of probes mapped to regions of annotated expression and non-expression. Subsequently, prediction of transcribed fragments is made on tiled genomic sequence. The prediction is accompanied by an expression probability curve for visual inspection of the supporting evidence. We test ExpressHMM on data from the Cheng et al. (2005) tiling array experiments on ten Human chromosomes [1]. Results can be downloaded and viewed from our web site [2]. CONCLUSION: The value of adaptive modelling of fluorescence scores prior to categorisation into expressed and non-expressed probes is demonstrated. Our results indicate that our adaptive approach is superior to the previous analysis in terms of nucleotide sensitivity and transfrag specificity

In situ gastrointestinal protection against anthrax edema toxin by single-chain antibody fragment producing lactobacilli

<p/> <p>Background</p> <p>Anthrax is caused by the bacterium <it>Bacillus anthracis </it>and is regarded as one of the most prominent bioterrorism threats. Anthrax toxicity is induced by the tripartite toxin complex, composed of the receptor-binding anthrax protective antigen and the two enzymatic subunits, lethal factor and edema factor. Recombinant lactobacilli have previously been used to deliver antibody fragments directed against surface epitopes of a variety of pathogens, including <it>Streptococcus mutans, Porphyromonas gingivalis</it>, and rotavirus. Here, we addressed whether or not anthrax toxins could be targeted and neutralised in the gastrointestinal tract by lactobacilli producing recombinant antibody fragments as a model system for toxin neutralisation in the gastrointestinal lumen.</p> <p>Results</p> <p>The neutralising anti-PA scFv, 1H, was expressed in <it>L. paracasei </it>as a secreted protein, a cell wall-anchored protein or both secreted and wall-anchored protein. Cell wall display on lactobacilli and PA binding of the anchored constructs was confirmed by flow cytometry analysis. Binding of secreted or attached scFv produced by lactobacilli to PA were verified by ELISA. Both construct were able to protect macrophages in an <it>in vitro </it>cytotoxicity assay. Finally, lactobacilli producing the cell wall attached scFv were able to neutralise the activity of anthrax edema toxin in the GI tract of mice, <it>in vivo</it>.</p> <p>Conclusion</p> <p>We have developed lactobacilli expressing a neutralising scFv fragment against the PA antigen of the anthrax toxin, which can provide protection against anthrax toxins both <it>in vitro </it>and <it>in vivo</it>. Utilising engineered lactobacilli therapeutically for neutralising toxins in the gastrointestinal tract can potential be expanded to provide protection against a range of additional gastrointestinal pathogens. The ability of lactobacilli to colonise the gastrointestinal tract may allow the system to be used both prophylactically and therapeutically.</p