Metabolite changes in blood predict the onset of tuberculosis

Immunogenetics and cellular immunology of bacterial infectious disease

Combined Use of Mycobacterium tuberculosis-Specific CD4 and CD8 T-Cell Responses Is a Powerful Diagnostic Tool of Active Tuberculosis.

Immune-based assays are promising tools to help to formulate diagnosis of active tuberculosis. A multiparameter flow cytometry assay assessing T-cell responses specific to Mycobacterium tuberculosis and the combination of both CD4 and CD8 T-cell responses accurately discriminated between active tuberculosis and latent infection

Comparison of CyTOF assays across sites: Results of a six-center pilot study.

For more than five years, high-dimensional mass cytometry has been employed to study immunology. However, these studies have typically been performed in one laboratory on one or few instruments. We present the results of a six-center study using healthy control human peripheral blood mononuclear cells (PBMCs) and commercially available reagents to test the intra-site and inter-site variation of mass cytometers and operators. We used prestained controls generated by the primary center as a reference to compare against samples stained at each individual center. Data were analyzed at the primary center, including investigating the effects of two normalization methods. All six sites performed similarly, with CVs for both Frequency of Parent and median signal intensity (MSI) values<30%. Increased background was seen when using the premixed antibody cocktail aliquots at each site, suggesting that cocktails are best made fresh. Both normalization methods tested performed adequately for normalizing MSI values between centers. Clustering algorithms revealed slight differences between the prestained and the sites-stained samples, due mostly to the increased background of a few antibodies. Therefore, we believe that multicenter mass cytometry assays are feasible

Four-gene Pan-African Blood Signature Predicts Progression to Tuberculosis.

Contacts of tuberculosis (TB) patients constitute an important target population for preventative measures as they are at high risk of infection with Mycobacterium tuberculosis and progression to disease. We investigated biosignatures with predictive ability for incident tuberculosis. In a case-control study nested within the Grand Challenges 6-74 longitudinal HIV-negative African cohort of exposed household contacts, we employed RNA sequencing, polymerase chain reaction (PCR) and the Pair Ratio algorithm in a training/test set approach. Overall, 79 progressors, who developed tuberculosis between 3 and 24 months following exposure, and 328 matched non-progressors, who remained healthy during 24 months of follow-up, were investigated. A four-transcript signature (RISK4), derived from samples in a South African and Gambian training set, predicted progression up to two years before onset of disease in blinded test set samples from South Africa, The Gambia and Ethiopia with little population-associated variability and also validated on an external cohort of South African adolescents with latent Mycobacterium tuberculosis infection. By contrast, published diagnostic or prognostic tuberculosis signatures predicted on samples from some but not all 3 countries, indicating site-specific variability. Post-hoc meta-analysis identified a single gene pair, C1QC/TRAV27, that would consistently predict TB progression in household contacts from multiple African sites but not in infected adolescents without known recent exposure events. Collectively, we developed a simple whole blood-based PCR test to predict tuberculosis in household contacts from diverse African populations, with potential for implementation in national TB contact investigation programs

Key recent advances in TB vaccine development and understanding of protective immune responses against Mycobacterium tuberculosis

Tuberculosis is the leading infectious disease killer globally due to a single pathogen. Despite wide deployment of standard drug regimens, modern diagnostics and a vaccine (bacille Calmette Guerin, BCG), the global tuberculosis epidemic is inadequately controlled. Novel, effective vaccine(s) are a crucial element of the World Health Organization End TB Strategy. TB vaccine research and development has recently been catalysed by several factors, including a revised strategy focused first on preventing pulmonary TB in adolescents and adults who are the main source of transmission, and encouraging evaluations of novel efficacy endpoints. Renewed enthusiasm for TB vaccine research has also been stimulated by recent preclinical and clinical advancements. These include new insights into underlying protective immune responses, including potential roles for 'trained' innate immunity and Th1/Th17 CD4+ (and CD8+) T cells. The field has been further reinvigorated by two positive proof of concept efficacy trials: one evaluating a potential new use of BCG in preventing high risk populations from sustained Mycobacterium tuberculosis infection and the second evaluating a novel, adjuvanted, recombinant protein vaccine candidate (M72/AS01(E)) for prevention of disease in adults already infected. Fourteen additional candidates are currently in various phases of clinical evaluation and multiple approaches to next generation vaccines are in discovery and preclinical development. The two positive efficacy trials and recent studies in nonhuman primates have enabled the first opportunities to discover candidate vaccine-induced correlates of protection, an effort being undertaken by a broad research consortium

Immunological biomarkers of tuberculosis

Currently there are no sufficiently validated biomarkers to aid the evaluation of new tuberculosis vaccine candidates, the improvement of tuberculosis diagnostics or the development of more effective and shorter treatment regimens. To date, the detection of Mycobacterium tuberculosis or its products has not been able to adequately address these needs. Understanding the interplay between the host immune system and M. tuberculosis may provide a platform for the identification of suitable biomarkers, through both unbiased and targeted hypothesis-driven approaches. Here, we review immunological markers, their relation to M. tuberculosis infection stages and their potential use in the fight against tuberculosis. © 2011 Macmillan Publishers Limited. All rights reserved.Revie

Characterization and phylogenetic analysis of South African HIV-1 subtype C accessory genes

To acquire new knowledge about the genetic diversity and potential impact on vaccine strategies of HIV-1 subtype C in South Africa, we have characterized the vif, vpr, and vpu genes of 15 isolates. Phylogenetic analysis of the genomic fragment encompassing these genes revealed subtype C subclusters, suggesting close relatedness with subtype C strains from other geographic locations and excluded isolation of South African strains. The putative T155 phosphorylation site in the C terminal of Vif was absent in all subtype C sequences. Variation in the predicted amino acid sequences of the three genes further showed strong correlation with other subtype C sequences.Articl

Functional analysis of novel SLC11A1 (NRAMP1) promoter variants in susceptibility to HIV-1

The divalent cation transporter is the natural resistance associated macrophage protein 1 (formerly NRAMP1 and now named SLC11A1) for solute carrier 11A1 (OMIM accession number 600266). The gene that codes for this transporter has been studied intensively for its role in conferring susceptibility to infectious diseases such as tuberculosis, leprosy, meningococcal meningitis, visceral leishmaniasis, and HIV infection, as well as to autoimmune diseases such as rheumatoid arthritis, diabetes, sarcoidosis, inflammatory bowel disease, and, more recently, Kawasaki disease. Most studies have investigated a functional GT repeat sequence in the promoter region of this gene and have identified two commonly occurring repeat alleles and four rare repeat alleles. The common alleles are T(GT)5-AC(GT)5AC(GT)10 (allele 2) and T(GT)5AC(GT)5AC(GT)9 (allele 3; GenBank accession number AF229163, 5768 to 5808). Allele 2, which decreases gene expression, has been associated with susceptibility to infectious diseases; the more common allele 3 enhances gene expression to protect against infectious diseases while enhancing susceptibility to autoimmune diseases. Although HIV is classified as an infectious disease, it affects the autoimmune system, which may explain why allele 3 is associated with susceptibility to HIV-1. This study aimed to screen the promoter region of SLC11A1 for novel sequence variations in people from sub- Saharan Africa infected with HIV-1 compared with uninfected people and to determine the effect of novel variants on normal promoter function

Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town, South Africa

Understanding the origin, distribution, and evolving dominance of HIV-1 subtype C strains is an important component in the design and evaluation of a globally effective AIDS vaccine. To better understand subtype C viruses, we constructed complete molecular clones of primary, CCR-5-using isolates from South Africa and analyzed the molecular phylogenies of these clones using best fitting evolutionary substitution models. Analyses were performed on three full-length sequences, and on the individual genes. All clones were nonrecombinant, and although two of three had open reading frames and intact splice sites, they were not infectious. At the genomic level, the models demonstrated the increasing variability of subtype C in South Africa. At the subgenomic level, they revealed marked differences in the evolutionary patterns of individual genes, a finding that suggests that the genes are under different selective pressures and constraints. These data underscore the dynamic nature of the subtype C epidemic and emphasize the need for continuous monitoring of local strains.Articl

Characterization of the South African HIV type 1 subtype C complete 5′ long terminal repeat, nef, and regulatory genes

Human immunodeficiency virus type 1 (HIV-1) subtype C has become the major etiological agent in the global and especially African epidemic. To gain better understanding of the genetic diversity and rapid transmission of HIV-1 subtype C, we have characterized the complete 5′ long terminal repeat (LTR) region along with the regulatory genestat andrev as well as the accessory genenef of 14 South African HIV-1 subtype C isolates. Phylogenetic analysis revealed a subtype C 5′ LTR cluster, as well as subclustering of ournef sequences with various subtype C strains separate from the India and China subclusters. At least 3 NF-κB sites were present in the 5′ LTR of most isolates and 13 isolates had the subtype C-specific Rev truncation. Some length variation in exon 2 and the absence of a critical cysteine were found in Tat. Residue variation in the myris-toylation signal and motifs involved in CD4 and MHC-I downregulation was recorded in our nef gene sequences.Articl