Identification of probable early-onset biomarkers for tuberculosis disease progression

Metabolites enhance innate resistance to human Mycobacterium tuberculosis infection

To determine the mechanisms that mediate resistance to Mycobacterium tuberculosis (M. tuberculosis) infection in household contacts (HHCs) of patients with tuberculosis (TB), we followed 452 latent TB infection-negative (LTBI-) HHCs for 2 years. Those who remained LTBI- throughout the study were identified as nonconverters. At baseline, nonconverters had a higher percentage of CD14+ and CD3-CD56+CD27+CCR7+ memory-like natural killer (NK) cells. Using a whole-transcriptome and metabolomic approach, we identified deoxycorticosterone acetate as a metabolite with elevated concentrations in the plasma of nonconverters, and further studies showed that this metabolite enhanced glycolytic ATP flux in macrophages and restricted M. tuberculosis growth by enhancing antimicrobial peptide production through the expression of the surface receptor sialic acid binding Ig-like lectin-14. Another metabolite, 4-hydroxypyridine, from the plasma of nonconverters significantly enhanced the expansion of memory-like NK cells. Our findings demonstrate that increased levels of specific metabolites can regulate innate resistance against M. tuberculosis infection in HHCs of patients with TB who never develop LTBI or active TB.

Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals

Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host–pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host–pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.

A systematic review on Correlates of Risk of TB disease in children and adults

BACKGROUND

Tuberculosis (TB) remains one of the leading causes of death in the world. Targeted treatment to prevent progression from TB exposure and infection to disease is a key element of WHO End-TB strategy. A systematic review to identify and develop correlates of risk (COR) of TB disease is timely.

METHOD

EMBASE, MEDLINE, PUBMED were searched using relevant keywords and MeSH terms published between 2000 and 2020 on COR of TB disease in children and adults. Preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA) framework was used for structuring and reporting of outcomes. Risk of bias was assessed using Quality Assessment of Diagnostic Accuracy Studies tool-2 (QUADAS-2).

RESULTS

4105 studies were identified. Following eligibility screening, 27 studies were quality assessed. Risk of bias was high in all studies. Broad variations in COR type, study population, methodology and result reporting were observed. Tuberculin skin test (TST) and interferon gamma release essays (IGRA) are poor COR. Transcriptomic signatures although promising require validation studies to assess wider applicability. Performance consistency of other CORs-cell marker, cytokines and metabolites are much needed.

CONCLUSION

This review identifies the need for a standardized approach to identify a universally applicable COR signature to achieve the WHO END-TB targets.

Framing the Detection of Incipient Tuberculosis Infection: a qualitative study of political prioritization

Objective

Incipient Tuberculosis (ITB) refers to Mycobacterium tuberculosis infection that is likely to progress to active disease in the absence of treatment, but without clinical signs, symptoms, radiographic or microbiological evidence of disease. Biomarker‐based tests to diagnose incipient TB hold promise for better prediction and, through TB preventive therapy, prevention of disease. This study explored current and future framing and prioritisation of ITB.

Methods

Twenty‐two interviews across eight countries were conducted. A modified Shiffman & Smith Framework, containing four categories—Ideas, Issue Characteristics, Actor Power, and Political Contexts—was used to analyse the current landscape and potential for prioritisation of diagnosis and treatment of ITB.

Results

Latent TB policy implementation has been slow due to technical, logistical and financial challenges, and because it has been framed in a manner non‐conducive to gaining political priority. Framing ITB testing as ‘early detection’ rather than ‘prediction’, and its management as ‘treatment’ rather than ‘preventive therapy’, may help raise its importance in policies, and its acceptance among actors.

Conclusion

Consensus surrounding the framing of ITB will be crucial for the successful adoption of ITB diagnostics and treatment. When designing ITB tools and policies, it will be important to address challenges that pertain to latent TB policies.

A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes

Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (Mtb), is one of the world's deadliest infectious diseases and remains a significant global health burden. TB disease and pathology can present clinically across a spectrum of outcomes, ranging from total sterilization of infection to active disease. Much remains unknown about the biology that drives an individual towards various clinical outcomes as it is challenging to experimentally address specific mechanisms driving clinical outcomes. Furthermore, it is unknown whether numbers of immune cells in the blood accurately reflect ongoing events during infection within human lungs. Herein, we utilize a systems biology approach by developing a whole-host model of the immune response to Mtb across multiple physiologic and time scales. This model, called HostSim, tracks events at the cellular, granuloma, organ, and host scale and represents the first whole-host, multi-scale model of the immune response following Mtb infection. We show that this model can capture various aspects of human and non-human primate TB disease and predict that biomarkers in the blood may only faithfully represent events in the lung at early time points after infection. We posit that HostSim, as a first step toward personalized digital twins in TB research, offers a powerful computational tool that can be used in concert with experimental approaches to understand and predict events about various aspects of TB disease and therapeutics.

Polymorphisms of the BCL2 gene associated with susceptibility to tuberculosis

Although tuberculosis (TB) is a serious public health concern, we still don’t understand why only 10% of people infected will develop the disease. Apoptosis plays a role in the interaction of Mycobacterium tuberculosis (Mtb) with the human host and it may be modified by subtle alterations in the B-cell lymphoma 2 (BCL2) gene, an anti-apoptotic regulatory element. Therefore, we investigated whether there is an association between BCL2 polymorphisms and susceptibility to TB by analyzing 130 TB cases, 108 subjects with latent TB infection (LTBI), and 163 healthy controls (HC). Logistic regression was used to calculate odds ratios (ORs) and 95% confidential intervals (95% CIs) for possible associations between single nucleotide polymorphisms (SNPs) in BCL2 and the risk of tuberculosis. We found that the G allele of rs80030866 (OR=0.62, 95%CI:0.42-0.91, P=0.015), and also the G allele of rs9955190 (OR=0.58, 95%CI:0.38-0.88, P=0.011) were less frequent in the TB group compared with the LTBI group. In addition, individuals with rs2551402 CC genotype were more likely to have LTBI than those with AA genotype (OR=2.166, 95%CI:1.046-4.484, P=0.037). Our study suggests that BCL2 gene polymorphisms may be correlated with susceptibility to both TB and LTBI.

Increased vegetable and fruit intake is associated with reduced failure rate of tuberculosis treatment: a hospital-based cohort study in China

Increased intake of vegetables and fruits has been associated with reduced risk of tuberculosis infection. Vegetables and fruits exert immunoregulatory effects; however, it is not clear whether vegetables and fruits have an adjuvant treatment effect on tuberculosis. Between 2009 and 2013, a hospital-based cohort study was conducted in Linyi, Shandong Province, China. Treatment outcome was ascertained by sputum smear and chest computerised tomography, and dietary intake was assessed by a semi-quantitative FFQ. The dietary questionnaire was conducted at the end of month 2 of treatment initiation. Participants recalled their dietary intake of the previous 2 months. A total of 2309 patients were enrolled in this study. After 6 months of treatment, 2099 patients were successfully treated and 210 were uncured. In multivariate models, higher intake of total vegetables and fruits (OR 0·70; 95 % CI 0·49, 0·99), total vegetables (OR 0·68; 95 % CI 0·48, 0·97), dark-coloured vegetables (OR 0·61; 95 % CI 0·43, 0·86) and light-coloured vegetables (OR 0·67; 95 % CI 0·48, 0·95) were associated with reduced failure rate of tuberculosis treatment. No association was found between total fruit intake and reduced failure rate of tuberculosis treatment (OR 0·98; 95 % CI 0·70, 1·37). High intake of total vegetables and fruits, especially vegetables, is associated with lower risk of failure of tuberculosis treatment in pulmonary tuberculosis patients. The results provide important information for dietary guidelines during tuberculosis treatment.

New Concepts in Tuberculosis Host Defense

Tuberculosis (TB) host defense depends on cellular immunity, including macrophages and adaptively acquired CD4⁺ and CD8⁺ T cells. More recently, roles for new immune components, including neutrophils, innate T cells, and B cells, have been defined, and the understanding of the function of macrophages and adaptively acquired T cells has been advanced. Moreover, the understanding of TB immunology elucidates TB infection and disease as a spectrum. Finally, determinates of TB host defense, such as age and comorbidities, affect clinical expression of TB disease. Herein, the authors comprehensively review TB immunology with an emphasis on new advances.

Moroccan lymphocyte subsets reference ranges: age, gender, ethnicity, and socio-economic factors dependent differences

Lymphocyte subsets reference ranges are helpful for a precise diagnosis and therapy of various diseases. We attempted in the current study to establish Moroccan lymphocyte reference range and reveal age, gender, ethnicity, income, and instructional levels dependent differences. Lymphocyte subsets percentage and absolute count were determined by 4-color flow cytometry in a population study of 145 adults Moroccan healthy volunteers. Analysis showed significant age-dependent changes. Age was associated with a decrease of naïve CD4+ and CD8+ T cells and an increase of memory CD4+ or CD8+ T cells. Activated CD4+ CD38+ and CD8+ CD38+ T cells, Treg as well as NK cell showed age-dependent alterations. In contrast, B cells remained unchanged. A higher percentage of CD3+ and CD4+ T cells was observed in females while CD8+, B and NK cells count were higher in men. Ethnicity, instructional levels, and personal income seem to not influence lymphocyte subsets reference values. This study provides reference ranges for lymphocyte subsets of healthy Moroccan adults. These results can be used for other North African (Maghrebian) countries considering their geographic, ethnic, economic, and cultural similarities.

M. Ottenhoff T, M. Cliff J, C. Haks M. Gene expression profiles classifying clinical stages of tuberculosis and monitoring treatment responses in Ethiopian HIV-negative and HIV-positive cohorts

Background

Validation of previously identified candidate biomarkers and identification of additional candidate gene expression profiles to facilitate diagnosis of tuberculosis (TB) disease and monitoring treatment responses in the Ethiopian context is vital for improving TB control in the future.

Methods

Expression levels of 105 immune-related genes were determined in the blood of 80 HIV-negative study participants composed of 40 active TB cases, 20 latent TB infected individuals with positive tuberculin skin test (TST+), and 20 healthy controls with no Mycobacterium tuberculosis (Mtb) infection (TST-), using focused gene expression profiling by dual-color Reverse-Transcription Multiplex Ligation-dependent Probe Amplification assay. Gene expression levels were also measured six months after anti-TB treatment (ATT) and follow-up in 38 TB patients.

Results

The expression of 15 host genes in TB patients could accurately discriminate between TB cases versus both TST+ and TST- controls at baseline and thus holds promise as biomarker signature to classify active TB disease versus latent TB infection in an Ethiopian setting. Interestingly, the expression levels of most genes that markedly discriminated between TB cases versus TST+ or TST- controls did not normalize following completion of ATT therapy at 6 months (except for PTPRCv1, FCGR1A, GZMB, CASP8 and GNLY) but had only fully normalized at the 18 months follow-up time point. Of note, network analysis comparing TB-associated host genes identified in the current HIV-negative TB cohort to TB-associated genes identified in our previously published Ethiopian HIV-positive TB cohort, revealed an over-representation of pattern recognition receptors including TLR2 and TLR4 in the HIV-positive cohort which was not seen in the HIV-negative cohort. Moreover, using ROC cutoff ≥ 0.80, FCGR1A was the only marker with classifying potential between TB infection and TB disease regardless of HIV status.

Conclusions

Our data indicate that complex gene expression signatures are required to measure blood transcriptomic responses during and after successful ATT to fully diagnose TB disease and characterise drug-induced relapse-free cure, combining genes which resolve completely during the 6-months treatment phase of therapy with genes that only fully return to normal levels during the post-treatment resolution phase.

Host Gene Expression Kinetics During Treatment of Tuberculosis in HIV-Coinfected Individuals Is Independent of Highly Active Antiretroviral Therapy

Background

Limitations in diagnostic tools to discriminate between active tuberculosis and latent Mycobacterium tuberculosis infection and for monitoring antituberculosis treatment responses are major challenges in tuberculosis control, especially in human immunodeficiency virus (HIV)-coinfected individuals.

Methods

Expression levels of 105 immune-related genes were determined in 131 HIV-infected patients with active tuberculosis (n = 48), patients with latent M. tuberculosis infection (LTBI; n = 37), and controls with no M. tuberculosis infection (n = 46) in Addis Ababa, Ethiopia, using focused gene expression profiling with a dual-color reverse-transcription multiplex ligation-dependent probe amplification assay.

Results

Within the cohort of HIV-positive subjects, the expression profiles of 7 genes at baseline (FCGR1A, RAB24, TLR1, TLR4, MMP9, NLRC4, and IL1B) could accurately discriminate between active tuberculosis and both latent and no M. tuberculosis infection, largely independently of (in)eligibility for highly active antiretroviral therapy (HAART). Six months after antituberculosis treatment, biomarker profiles of patients with tuberculosis became indistinguishable from those of patients with LTBI and controls. Importantly, host gene expression kinetics during antituberculosis treatment in HIV-coinfected individuals was found to be independent of HAART use.

Conclusions

Blood transcriptomic profiles can potentially be used as biomarkers to discriminate the different clinical stages of tuberculosis in HIV-coinfected individuals and to monitor tuberculosis treatment responses in both HAART recipients and untreated individuals.

Precision medicine in resistant Tuberculosis: Treat the correct patient, at the correct time, with the correct drug

Human genomic mapping has advanced molecular medicine health care and created a transformative paradigm shift towards Precision Medicine. In 2015, President Obama launched the PM initiative, encapsulated as "unique individualized data-driven treatments". Since then, this field is rapidly advancing both curative treatment and disease prevention by accounting for both individual and environmental variability. While a substantial evidence for accelerating adoption of Precision Medicine in other spheres of medicine exists, application of Precision Medicine in infectious diseases is far more complex. One of the most warranted applications of precision healthcare is in the management and treatment of Drug-resistant Tuberculosis. Application of Precision Medicine to Drug-resistant Tuberculosis could potentially change the landscape of treatment and prevention of a disease affecting vulnerable patients in impoverished communities. Poorly diagnosed and treated Drug-resistant Tuberculosis not only leads to increased mortality and morbidity but also increased transmission of DR-TB strains, fuelling ongoing high incidence rates and further infection. A Precision medicine model using individual clinical case histories used in conjunction with Mycobacterium Tuberculosis infection genomic data will better guide health care practitioners in more appropriate drug selection, and an individualized management approach. This viewpoint deliberates the intricacies of adopting a PM approach in the management of DR-TB. If applied correctly, we postulate that the research, application, and deployment of PM in DR-TB management may address the fundamental rule of PM in infectious disease: to treat the correct patient, at the correct time, with the correct drug.

Incipient and Subclinical Tuberculosis: a Clinical Review of Early Stages and Progression of Infection

Tuberculosis (TB) is the leading infectious cause of mortality worldwide, due in part to a limited understanding of its clinical pathogenic spectrum of infection and disease. Historically, scientific research, diagnostic testing, and drug treatment have focused on addressing one of two disease states: latent TB infection or active TB disease. Recent research has clearly demonstrated that human TB infection, from latent infection to active disease, exists within a continuous spectrum of metabolic bacterial activity and antagonistic immunological responses. This revised understanding leads us to propose two additional clinical states: incipient and subclinical TB. The recognition of incipient and subclinical TB, which helps divide latent and active TB along the clinical disease spectrum, provides opportunities for the development of diagnostic and therapeutic interventions to prevent progression to active TB disease and transmission of TB bacilli. In this report, we review the current understanding of the pathogenesis, immunology, clinical epidemiology, diagnosis, treatment, and prevention of both incipient and subclinical TB, two emerging clinical states of an ancient bacterium.

Plasma Cytokine Predictors of Tuberculosis Recurrence in Antiretroviral-Treated Human Immunodeficiency Virus-infected Individuals from Durban, South Africa

Background

Immune correlates of tuberculosis (TB) risk in populations infected with human immunodeficiency virus (HIV) remain understudied, despite HIV being associated with a high burden of TB disease. Here we describe plasma cytokine correlates of TB recurrence in a well-characterized cohort of HIV-infected individuals on antiretroviral therapy (ART) with a history of prior TB cure.

Methods

Study participants were drawn from a prospective cohort study initiated at the conclusion of a randomized clinical trial in which individuals presented with untreated HIV infection and active pulmonary TB. At baseline, ART was initiated, and TB successfully cured. Participants were screened for TB recurrence quarterly for up to 4 years. TB recurrent cases (n = 63) were matched to controls (n = 123) on sex, study arm assignment in the original trial, and month of enrollment with a subset of cases sampled longitudinally at several time-points.

Results

Three cytokines were associated with increased rates of TB recurrence in univariate models: interleukin 6 (IL6) (odds ratio [OR] 2.66, 95% confidence interval [CI] 1.34-5.28, P = .005), IP10 (OR 4.62, 95% CI 1.69-12.65, P = .003), monokine induced by IFN-γ (MIG) (OR 3.11, 95% CI 1.10-8.82, P = .034). Conversely, interferon β (IFNβ) was associated with decreased TB risk (OR 0.34, 95% CI 0.13-0.87, P = .025). Following multivariate analyses adjusting for covariates IL6, interleukin 1β (IL1β), and interleukin 1Rα (IL1Rα) were associated with increased risk and IFNβ with decreased TB risk. Longitudinal analysis showed that levels of many TB-associated markers, including IL6, IP10, sCD14, and interferon γ (IFNγ) are reduced following TB treatment.

Conclusion

These data show that TB recurrence, in HIV-infected individuals on ART is predicted by biomarkers of systemic inflammation, many of which are implicated in more rapid HIV disease progression.

Clinical Trials Registration

NCT 01539005.

Molecular Signatures of Immunity and Immunogenicity in Infection and Vaccination

Vaccinology aims to understand what factors drive vaccine-induced immunity and protection. For many vaccines, however, the mechanisms underlying immunity and protection remain incompletely characterized at best, and except for neutralizing antibodies induced by viral vaccines, few correlates of protection exist. Recent omics and systems biology big data platforms have yielded valuable insights in these areas, particularly for viral vaccines, but in the case of more complex vaccines against bacterial infectious diseases, understanding is fragmented and limited. To fill this gap, the EC supported ADITEC project (http://www.aditecproject.eu/; http://stm.sciencemag.org/content/4/128/128cm4.full) featured a work package on “Molecular signatures of immunity and immunogenicity,” aimed to identify key molecular mechanisms of innate and adaptive immunity during effector and memory stages of immune responses following vaccination. Specifically, technologies were developed to assess the human immune response to vaccination and infection at the level of the transcriptomic and proteomic response, T-cell and B-cell memory formation, cellular trafficking, and key molecular pathways of innate immunity, with emphasis on underlying mechanisms of protective immunity. This work intersected with other efforts in the ADITEC project. This review summarizes the main achievements of the work package.

Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome

Identifying biomarkers for tuberculosis (TB) is an ongoing challenge in developing immunological correlates of infection outcome and protection. Biomarker discovery is also necessary for aiding design and testing of new treatments and vaccines. To effectively predict biomarkers for infection progression in any disease, including TB, large amounts of experimental data are required to reach statistical power and make accurate predictions. We took a two-pronged approach using both experimental and computational modeling to address this problem. We first collected 200 blood samples over a 2- year period from 28 non-human primates (NHP) infected with a low dose of Mycobacterium tuberculosis. We identified T cells and the cytokines that they were producing (single and multiple) from each sample along with monkey status and infection progression data. Machine learning techniques were used to interrogate the experimental NHP datasets without identifying any potential TB biomarker. In parallel, we used our extensive novel NHP datasets to build and calibrate a multi-organ computational model that combines what is occurring at the site of infection (e.g., lung) at a single granuloma scale with blood level readouts that can be tracked in monkeys and humans. We then generated a large in silico repository of in silico granulomas coupled to lymph node and blood dynamics and developed an in silico tool to scale granuloma level results to a full host scale to identify what best predicts Mycobacterium tuberculosis (Mtb) infection outcomes. The analysis of in silico blood measures identifies Mtb-specific frequencies of effector T cell phenotypes at various time points post infection as promising indicators of infection outcome. We emphasize that pairing wetlab and computational approaches holds great promise to accelerate TB biomarker discovery.

Tuberculosis (TB) is a disease that is caused by infection after inhaling the bacterium Mycobacterium tuberculosis. Not everyone infected with TB bacteria becomes sick. As a result, two TB-related conditions have been categorized: latent TB infection (not sick but still harboring the bacteria) and active TB disease. If not treated properly, active TB disease can be fatal. Almost 1.3 million die of TB worldwide each year, with ~8,6 million new infections in 2013. No effective vaccine is available to protect against TB and treatment of infection with multiple antibiotics is lengthy (6–9 months), with non-compliance being a major factor for the emergence of drug-resistant strains. A key step in developing effective vaccines and possibly shorter treatment regimens is the ability to identify biomarkers that correlate prognosis and progression to infection (similar to how cholesterol levels are a measure of heart health). In this study we show how pairing computer modeling, statistics and mathematics with datasets derived from non-human primate studies can accelerate biomarker discovery, and offer a new approach to identifying correlates of protection that will be useful in clinical practice, particularly in developing countries where TB is most prevalent.

Approaching a diagnostic point-of-care test for pediatric tuberculosis through evaluation of immune biomarkers across the clinical disease spectrum

The World Health Organization (WHO) calls for an accurate, rapid, and simple point-of-care (POC) test for the diagnosis of pediatric tuberculosis (TB) in order to make progress "Towards Zero Deaths". Whereas the sensitivity of a POC test based on detection of Mycobacterium tuberculosis (MTB) is likely to have poor sensitivity (70-80% of children have culture-negative disease), host biomarkers reflecting the on-going pathological processes across the spectrum of MTB infection and disease may hold greater promise for this purpose. We analyzed transcriptional immune biomarkers direct ex-vivo and translational biomarkers in MTB-antigen stimulated whole blood in 88 Indian children with intra-thoracic TB aged 6 months to 15 years, and 39 asymptomatic siblings. We identified 12 biomarkers consistently associated with either clinical groups "upstream" towards culture-positive TB on the TB disease spectrum (CD14, FCGR1A, FPR1, MMP9, RAB24, SEC14L1, and TIMP2) or "downstream" towards a decreased likelihood of TB disease (BLR1, CD3E, CD8A, IL7R, and TGFBR2), suggesting a correlation with MTB-related pathology and high relevance to a future POC test for pediatric TB. A biomarker signature consisting of BPI, CD3E, CD14, FPR1, IL4, TGFBR2, TIMP2 and TNFRSF1B separated children with TB from asymptomatic siblings (AUC of 88%).

Differential expression of CD57 in antigen-reactive CD4+ T cells between active and latent tuberculosis infection

The development of diagnostic tests that predict the progression of latent tuberculosis infection to active disease is pivotal for the eradication of tuberculosis. As an initial step to achieve this goal, our study's aim was to identify biomarkers that differentiate active from latent tuberculosis infection. We compared active and latent tuberculosis infection groups in terms of the precursor frequency, functional subset differentiation, and senescence/exhaustion surface marker expression of antigen-specific CD4(+) T cells, which were defined as dividing cells upon their encountering with Mycobacterium (M.) tuberculosis antigens. Among several parameters shown to have statistically significant differences between the two groups, the frequency of CD57-expressing cells could differentiate effectively between active disease and latent infection. Our results suggest that the expression of CD57 in M. tuberculosis-reactive CD4(+) T cells could be a promising candidate biomarker with which to identify individuals with latent tuberculosis infection prone to progression to active disease.

Focused human gene expression profiling using dual-color reverse transcriptase multiplex ligation-dependent probe amplification

To investigate the human immune response to newly developed or existing vaccines, or during infection/disease on a population scale, we have recently developed a dual-color Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification (dcRT-MLPA) assay, which can rapidly profile mRNA expression of multiple host genes. dcRT-MLPA has a dynamic range and sensitivity comparable to real-time QPCR and RNA-Sequencing. Since this assay is high-throughput, it is an exceptionally suitable technique for monitoring host biomarkers in semi-large scale human cohorts, such as cross sectional studies with multiple groups, or longitudinal studies with multiple time points. Multicomponent host biomarker signatures with excellent predictive values can easily be identified using lasso regression analysis, while exploring additional data adjustment methods like RUV-2 may further optimize the identification of informative host biomarker signatures. dcRT-MLPA also allows comparisons of gene expression patterns across different human populations to explore the impact of geographical diversity on for example vaccine induced responses. The use of dcRT-MLPA is not limited to peripheral blood but can be adapted to analyze host biomarkers derived from any tissue or body fluids, further demonstrating the versatility of the dcRT-MLPA platform. Several examples will be given and discussed.

Dysregulation of Apoptosis Is a Risk Factor for Tuberculosis Disease Progression

BACKGROUND

A major barrier to effective tuberculosis control is our limited understanding of risk factors for tuberculosis disease progression. This study examined the role of apoptosis in immunity to tuberculosis.

METHODS

Cell subsets from tuberculosis cases and tuberculin skin test-positive (TST(+)) and TST-negative (TST(-)) household contacts (HHCs) were analyzed for expression of annexin-V and propidium iodide by flow cytometry. RNA microarrays were used to determine differences in apoptotic gene expression levels and multiplex ligation-dependent probe amplification was used to analyze gene expression in HHCs who progressed to active tuberculosis.

RESULTS

T cells from TST(+)HHC exhibited higher levels of apoptosis than tuberculosis cases; however, tuberculosis cases had a higher proportion of late apoptotic cells within the CD3(+)PD-1(+) subset. Tuberculosis cases had reduced levels of antiapoptotic genes compared to HHCs with a significant reduction in BCL2 associated with disease progression at least 1 year prior to progression.

CONCLUSIONS

While T cells are clearly able to mount a robust immune response to Mycobacterium tuberculosis, there are increased levels of apoptosis seen in effector T cells from tuberculosis patients. Dysregulation of several apoptotic genes suggest that apoptosis is a major functional pathway that could be targeted for future host-directed therapeutics.

Inflammation and tuberculosis: host-directed therapies

Tuberculosis (TB) is an airborne infectious disease that kills almost two million individuals every year. Multidrug-resistant (MDR) TB is caused by strains of Mycobacterium tuberculosis (M. tb) resistant to isoniazid and rifampin, the backbone of first-line antitubercular treatment. MDR TB affects an estimated 500,000 new patients annually. Genetic analysis of drug-resistant MDR-TB showed that airborne transmission of undetected and untreated strains played a major role in disease outbreaks. The need for new TB vaccines and faster diagnostics, as well as the development of new drugs, has recently been highlighted. The major problem in terms of current TB research and clinical demands is the increasing number of cases of extensively drug-resistant and 'treatment-refractory' TB. An emerging scenario of adjunct host-directed therapies is intended to target pulmonary TB where inflammatory processes can be deleterious and lead to immune exhaustion. 'Target-organ-saving' strategies may be warranted to prevent damage to infected tissues and achieve focused, clinically relevant and long-lasting anti-M. tb cellular immune responses. Candidates for such interventions may be biological agents or already approved drugs that can be 're-purposed' to interfere with biologically relevant cellular checkpoints. Here, we review current concepts of inflammation in TB disease and discuss candidate pathways for host-directed therapies to achieve better clinical outcomes.

Iron homeostasis and progression to pulmonary tuberculosis disease among household contacts

Early identification of individuals at risk for progressing to active tuberculosis (TB) disease may limit new transmission and improve clinical outcomes. Evidence indicates altered iron homeostasis may identify those at greater risk of disease progression in HIV co-infection. We aimed to investigate iron homeostasis biomarkers as risk factors for progression to TB. Archived plasma samples were analyzed from household contacts of pulmonary TB index cases in The Gambia. Contacts were classified as asymptomatic non-progressors (n = 17) or TB-progressors (n = 10), which included two HIV-infected participants. Iron homeostasis (hemoglobin, ferritin, hepcidin, soluble transferrin receptor, transferrin) was assessed in all contacts at study recruitment. Plasma was collected a median of 910 days prior to TB diagnosis. Low transferrin around the time of known exposure to infectious TB was a disease progression risk factor among all TB-progressors (Poisson incidence rate ratio: 0.55; 95% CI: 0.35-0.89). Iron homeostasis also differed between early and delayed TB-progressors, with higher ferritin and hepcidin concentrations observed among early TB-progressors (mean ferritin 50.2 vs. 26.2 ng/ml; P = 0.027; mean hepcidin 37.7 vs. 5.6 ng/ml; P = 0.036). Iron homeostasis is associated with progression to TB among household contacts. Further studies are needed to elucidate mechanisms and determine the clinical utility of monitoring iron homeostasis biomarkers.

Clinical immunology and multiplex biomarkers of human tuberculosis

The discovery of tuberculosis (TB) biomarkers is an important goal in current TB research, because the availability of such markers would have significant impact on TB prevention and treatment. Correlates of protection would greatly facilitate vaccine development and evaluation, whereas correlates of TB disease risk would facilitate early diagnosis and help installing early or preventive treatment. Currently, no such markers are available. This review describes several strategies that are currently being pursued to identify TB biomarkers and places these in a clinical context. The approaches discussed include both targeted and untargeted hypothesis-free strategies. Among the first are the measurements of specific biomarkers in antigen-stimulated peripheral blood, in serum or plasma, and detailed immune cell phenotyping. Among the latter are proteomic, genomic, and transcriptomic (mRNA, miRNA) approaches. Recent and promising developments are described.

Control lymphocyte subsets: can one country's values serve for another's?

Lymphocyte subsets can be affected by host and environmental factors, yet direct comparisons of their patterns across continents are lacking. This work compares proportions and counts of lymphocyte subsets between healthy children from Thailand, Malawi and the USA. We analyzed subsets of 1,399 healthy children aged between 0 and 15 years: 281 Thai, 397 Malawian and 721American children. Existing data for five subsets were available for all three cohorts (Total T, CD4+ T, CD8+ T, natural killer (NK) and B cells), with data for another six subsets from the Thai and American cohorts (naïve, memory and activated CD4+ and CD8+ T cells). Cellular patterns between cohorts differed mainly in children under two years. Compared to American children, Thai children had higher median numbers of total T cells, CD8+ T cells and NK cells while Malawian children under 18 months, on average, had more CD8+ T cells and B cells. Both Thai and Malawian children had lower median CD4+ T cell percentages and CD4/CD8 ratios than American children. Thai children had more memory and activated CD8+ T cells than American children. Approximately one-fifth of Thai and Malawian HIV-uninfected healthy children aged 0-3 years met WHO-defined CD4+ count criteria for immune-deficiency in HIV-infected children. Healthy children from Thailand, Malawi and the USA have differences in lymphocyte subsets that are likely to be due to differences in ethnicity, exposure to infectious diseases and environmental factors. These results indicate the need for country-specific reference ranges for diagnosis and management of immunologic disorders.

Early clearance of Mycobacterium tuberculosis: a new frontier in prevention

Early clearance (EC) is the successful eradication of inhaled Mycobacterium tuberculosis before an adaptive immune response develops. Evidence for EC comes from case contact studies that consistently show that a proportion of heavily exposed individuals do not develop M. tuberculosis infection. Further support for the existence of this phenotype comes from genetic loci associated with tuberculin reactivity. In this review we discuss aspects of the innate response that may underpin EC and hypotheses that can be tested through field laboratory link studies in M. tuberculosis case contacts. Specifically, we consider mechanisms whereby alveolar macrophages recognize and kill intracellular M. tuberculosis, and how other cell types, such as neutrophils, natural killer T cells, mucosa-associated invariant T cells and cd T cells may assist. How EC may be impaired by HIV infection or vitamin D deficiency is also explored. As EC is a form of protective immunity, further study may advance the development of vaccines and immunotherapies to prevent M. tuberculosis infection.

Unmet needs in respiratory diseases : "You can't know where you are going until you know where you have been"--Anonymous

The care of patients with respiratory diseases has improved vastly in the past 50 years. In spite of that, there are still massive challenges that have not been resolved. Although the incidence of tuberculosis has decreased in the developed world, it is still a significant public health problem in the rest of the world. There are still over 2 million deaths annually from tuberculosis, with most of these occurring in the developing world. Even with the development of new pharmaceuticals to treat tuberculosis, there is no indication that the disease will be eradicated. Respiratory syncytial virus, severe acute respiratory syndrome, and pertussis are other respiratory infectious diseases with special problems of their own, from vaccine development to vaccine coverage. Asthma, one of the most common chronic diseases in children, still accounts for significant mortality and morbidity, as well as high health care costs worldwide. Even in developed countries such as the USA, there are over 4,000 deaths per year. Severe asthma presents a special problem, but the question is whether there can be one treatment pathway for all patients with severe asthma. Severe asthma is a heterogeneous disease with many phenotypes and endotypes. The gene for cystic fibrosis was discovered over 24 years ago. The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. What are the prospects for gene therapy in the twenty-first century? Autoimmune diseases of the lung pose a different set of challenges, including the development of biomarkers to diagnose and monitor the disease and biological modulators to treat the disease.

A review of preclinical animal models utilised for TB vaccine evaluation in the context of recent human efficacy data

There is an urgent need for an improved TB vaccine. Vaccine development is hindered by the lack of immune correlates and uncertain predictive value of preclinical animal models. As data become available from human efficacy trials, there is an opportunity to evaluate the predictive value of the criteria used to select candidate vaccines. Here we review the efficacy in animal models of the MVA85A candidate vaccine in light of recent human efficacy data and propose refinements to the preclinical models with the aim of increasing their predictive value for human efficacy.

T-cell immunophenotyping distinguishes active from latent tuberculosis

BACKGROUND

Changes in the phenotype and function of Mycobacterium tuberculosis (M. tuberculosis)-specific CD4+ and CD8+ T-cell subsets in response to stage of infection may allow discrimination between active tuberculosis and latent tuberculosis infection.

METHODS

A prospective comparison of M. tuberculosis-specific cellular immunity in subjects with active tuberculosis and latent tuberculosis infection, with and without human immunodeficiency virus (HIV) coinfection. Polychromatic flow cytometry was used to measure CD4+ and CD8+ T-cell subset phenotype and secretion of interferon γ (IFN-γ), interleukin 2 (IL-2), and tumor necrosis factor α (TNF-α).

RESULTS

Frequencies of CD4+ and CD8+ cells secreting IFN-γ-only, TNF-α-only and dual IFN-γ/TNF-α were greater in active tuberculosis vs latent tuberculosis infection. All M. tuberculosis-specific CD4+ subsets, with the exception of IL-2-only cells, switched from central to effector memory phenotype in active tuberculosis vs latent tuberculosis infection, accompanied by a reduction in IL-7 receptor α (CD127) expression. The frequency of PPDspecific CD4+ TNF-α-only-secreting T cells with an effector phenotype accurately distinguished active tuberculosis from latent tuberculosis infection with an area under the curve of 0.99, substantially more discriminatory than measurement of function alone.

CONCLUSIONS

Combined measurement of T-cell phenotype and function defines a highly discriminatory biomarker of tuberculosis disease activity. Unlocking the diagnostic and monitoring potential of this combined approach now requires validation in large-scale prospective studies.

Biomarkers of tuberculosis: a research roadmap

Tuberculosis (TB) continues to represent a major public health problem worldwide. Prompt and accurate diagnosis and effective treatment are fundamental to reducing morbidity and mortality and curtailing spread of infection. Furthermore, tackling the large reservoir of latent infection is the cornerstone to TB control in many high income low TB incidence countries. However, our existing toolkit for prevention, diagnosis and treatment remains outdated and inadequate. Here, we discuss the key targets for biomarker research and discovery in TB and recent developments in the field. We focus on host biomarkers, in particular: correlates of vaccine efficacy and sterilizing immunity; biomarkers of latent TB infection, including diagnosis, risk of progression to active TB and response to treatment; and markers of active TB, including diagnosis, response to treatment and risk of relapse. Recent scientific and technological advances have contributed to significant recent progression in biomarker discovery. Although there are clear remaining paucities, continued efforts within scientific, translational and clinical studies are likely to yield a number of clinically useful biomarkers of TB in the foreseeable future.

Expression of TNF-alpha-dependent apoptosis-related genes in the peripheral blood of Malagasy subjects with tuberculosis

The majority of Mycobacterium tuberculosis (Mtb) infections remain asymptomatic with only up to 10% progressing to clinical tuberculosis. However, the constituents of the effective “protective immunity” against tuberculosis responsible for containing most infections remain unknown. Evaluating gene transcriptional profiles in tuberculosis clinical cohorts is one approach to understanding the spectrum of tuberculosis progression. It is clear that apoptosis plays a role in the control of tuberculosis but the utility of apoptosis-related genes as surrogate markers of protection against tuberculosis has not been well investigated. To characterize potential surrogate markers that could discriminate different phases of the clinical tuberculosis spectrum, we investigated gene expression of several TNF-alpha dependent apoptotic genes (TNFR1, TNFR2, FLICE, FLIPs) by real-time RT-PCR of peripheral blood cells from cohorts of individuals with active tuberculosis or potential exposure to tuberculosis.

Newly diagnosed tuberculosis patients (n = 23), their close household contacts (n = 80), and community controls (n = 46) were tested at intervals over a period of up to two years. Latent infection or previous Mtb contact was assessed by ELISPOT and TST and complete blood counts were performed during the follow up.

Results showed significant upregulation of FLIPs expression by infected individuals regardless of clinical status at entry to the study. A higher percentage of lymphocytes was found in the infected household contacts that remained healthy. In contrast, in individuals with active TB, a significant upregulation of TNFR2 expression, a significantly higher percentage of monocytes and a significantly decreased lymphocyte count were seen, compared to subjects that remained healthy. Moreover, the household contacts who subsequently developed signs of TB also had a significantly high number of monocytes.

These data suggest tuberculosis may be associated with decreased T-cell survival (perhaps due to apoptosis) while inhibition of apoptosis in monocytes could lead to a relative increase in these cells: a situation predicted to favour Mtb.

Prospects for tuberculosis elimination

The target for TB elimination is to reduce annual incidence to less than one case per million population by 2050. Meeting that target requires a 1,000-fold reduction in incidence in little more than 35 years. This can be achieved only by combining the effective treatment of active TB-early case detection and high cure rates to interrupt transmission-with methods to prevent new infections and to neutralize existing latent infections. Vigorous implementation of the WHO Stop TB Strategy is needed to achieve the former, facilitated by the effective supply of, and demand for, health services. The latter calls for new technology, including biomarkers of TB risk, diagnostics, drugs, and vaccines. An important milestone en route to elimination will be reached when there is less than 1 TB death per 100,000 population, marking entry into the elimination phase. This landmark can be reached by many countries within 1-2 decades.

Long-lived memory B-cell responses following BCG vaccination

The role of T-cells in immunity against Mycobacterium tuberculosis (M. tuberculosis) infection has been extensively studied, however, that of B-cells still remains comparatively unexplored. In this study, we determined the presence and frequencies of mycobacteria-specific memory B-cells (MBCs) in peripheral blood from clinically healthy, Bacillus Calmette Guerin (BCG) vaccinated (n = 79) and unvaccinated (n = 14) donors. Purified protein derivative (PPD)-specific MBCs were present in most donors (both vaccinated and unvaccinated) but their frequencies were significantly higher in vaccinated than in unvaccinated donors. MBCs specific for other mycobacterial antigens [antigen-85A (Ag85A), antigen-85B (Ag85B), 6 kDalton early secretory antigenic target (ESAT-6) and the 10 kDalton-culture filtrate protein (CFP-10)] were less prevalent than those recognising PPD. Furthermore, PPD-specific MBCs were detected in BCG vaccinated donors without ESAT-6 and CFP-10 specific responses. Together, these results indicate that BCG vaccination induces long-lived MBC responses. Similar patterns of response were seen when we examined mycobacteria-specific antibody and T-cell responses in these donors. Our data show for the first time that BCG vaccination elicits long-lived mycobacteria-specific MBC responses in healthy individuals, suggesting a more substantial role of B-cells in the response to BCG and other mycobacterial infections than previously thought.

Analysis of LAM and 38 kDa Antibody Levels for Diagnosis of TB in a Case-Control Study in West Africa

CD4+ T cells are required for protection against tuberculosis (TB) disease progression, but interest in the role of antibodies in early protection, as biomarkers for disease status, and use in diagnostic tests has recently increased. In this study we analyzed plasma antibody levels in TB cases before and after treatment in both HIV-positive and -negative individuals and compared them with tuberculin skin test (TST+) (latently infected) household contacts (HHC). We also analyzed HHC that subsequently progressed to active disease within 2 years in order to see if antibodies play a role in protection against disease progression. We used a commercially available kit to 38 kDa antigen and lipoarabinomannan (LAM) and found that immunoglobulin (Ig) G levels were 4-fold higher in subjects with disease compared to latently infected controls (P<0.001) and were 2-fold higher than pretreatment levels following successful TB treatment (P<0.001 compared to both pretreated cases and latently infected controls). HIV infection resulted in low antibody levels regardless of disease status or treatment outcome. Furthermore, levels in disease progressors (incident cases) were similar to nonprogressors and were not elevated until just prior to disease progression confirming previous reports that IgG antibodies, at least in the periphery, do not confer protection against TB disease progression.