B cells as multi-functional players during Mycobacterium tuberculosis infection and disease

Single-cell transcriptome reveals highly complement activated microglia cells in association with pediatric tuberculous meningitis

Background

Tuberculous meningitis (TBM) is a devastating form of tuberculosis (TB) causing high mortality and disability. TBM arises due to immune dysregulation, but the underlying immune mechanisms are unclear.

Methods

We performed single-cell RNA sequencing on peripheral blood mononuclear cells (PBMCs) and cerebrospinal fluid (CSF) cells isolated from children (n=6) with TBM using 10 xGenomics platform. We used unsupervised clustering of cells and cluster visualization based on the gene expression profiles, and validated the protein and cytokines by ELISA analysis.

Results

We revealed for the first time 33 monocyte populations across the CSF cells and PBMCs of children with TBM. Within these populations, we saw that CD4_C04 cells with Th17 and Th1 phenotypes and Macro_C01 cells with a microglia phenotype, were enriched in the CSF. Lineage tracking analysis of monocyte populations revealed myeloid cell populations, as well as subsets of CD4 and CD8 T-cell populations with distinct effector functions. Importantly, we discovered that complement-activated microglial Macro_C01 cells are associated with a neuroinflammatory response that leads to persistent meningitis. Consistently, we saw an increase in complement protein (C1Q), inflammatory markers (CRP) and inflammatory factor (TNF-α and IL-6) in CSF cells but not blood. Finally, we inferred that Macro_C01 cells recruit CD4_C04 cells through CXCL16/CXCR6.

Discussion

We proposed that the microglial Macro_C01 subset activates complement and interacts with the CD4_C04 cell subset to amplify inflammatory signals, which could potentially contribute to augment inflammatory signals, resulting in hyperinflammation and an immune response elicited by Mtb-infected tissues.

Discovery of Novel Transketolase Epitopes and the Development of IgG-Based Tuberculosis Serodiagnostics

Despite advances in rapid molecular techniques for tuberculosis (TB) diagnostics, there is an unmet need for a point-of-care, nonsputum-based test. Previously, through a T7 phage antigen display platform and immunoscreening, we identified that the serum IgGs of active TB patients differentially bind to several antigen-clones and that this immunoreactivity discriminates TB from other respiratory diseases. One of these high-performance clones has some homology to the transketolase of Mycobacterium tuberculosis (M.tb TKT). In this study, we developed a direct enzyme-linked immunosorbent assay (ELISA) detecting IgG against the TKT antigen-clone (TKTμ). Through sequence alignment and in silico analysis, we designed two more peptides with potential antigenicity that correspond to M.tb-specific transketolase (M.tb TKT1 and M.tb TKT3) epitopes. After the development and standardization of a direct peptide ELISA for three peptides, we tested 292 subjects, including TB (n = 101), latent tuberculosis infection (LTBI) (n = 49), healthy controls (n = 66), and sarcoidosis (n = 76). We randomly assigned 60% of the subjects to a training set to create optimal models to distinguish positive TB samples, and the remaining 40% were used to validate the diagnostic power of the IgG-based assays that were developed in the training set. Antibodies against M.tb TKT3 yielded the highest sensitivity (0.845), and these were followed by TKTμ (0.817) and M.tb TKT1 (0.732). The specificities obtained by TKTμ, M.tb TKT3, and M.tb TKT1 on the test sets were 1, 0.95, and 0.875, respectively. The model using TKTμ obtained a perfect positive predictive value (PPV) of 1, and this was followed by M.tb TKT3 (0.968) and M.tb TKT1 (0.912). These results show that IgG antibodies against transketolase can discriminate active TB against LTBI, sarcoidosis, and controls. IMPORTANCE There is an unmet need for a point-of-care, nonsputum-based TB test. Through the immunoscreening of a novel T7 phage library, we identified classifiers that specifically bind to IgGs in active TB sera. We discovered that one of these clones is aligned with Mycobacterium tuberculosis transketolase (TKT). TKT is an essential enzyme for Mycobacterium tuberculosis growth. We designed three TKT epitopes (TKTμ, TKT1, and TKT3) to detect TKT-specific IgGs. After the development and standardization of three different ELISA-utilizing TKT peptides, we tested 292 subjects, including active TB, LTBI, healthy controls, and sarcoidosis. Rigorous statistical analyses using training and validation sets showed that ELISA-based detections of specific IgGs against TKT3 and TKTμ have the greatest sensitivity, specificity, and accuracy to distinguish active TB subjects from others, even LTBI. Our work provides a novel scientific platform from which to further develop a point-of-care test, thereby aiding in faster TB diagnoses.

Genomic evidence for adaptation to tuberculosis in the Andes before European contact

Most studies focusing on human high-altitude adaptation in the Andean highlands have thus far been focused on Peruvian populations. We present high-coverage whole genomes from Indigenous people living in the Ecuadorian highlands and perform multi-method scans to detect positive natural selection. We identified regions of the genome that show signals of strong selection to both cardiovascular and hypoxia pathways, which are distinct from those uncovered in Peruvian populations. However, the strongest signals of selection were related to regions of the genome that are involved in immune function related to tuberculosis. Given our estimated timing of this selection event, the Indigenous people of Ecuador may have adapted to Mycobacterium tuberculosis thousands of years before the arrival of Europeans. Furthermore, we detect a population collapse that coincides with the arrival of Europeans, which is more severe than other regions of the Andes, suggesting differing effects of contact across high-altitude populations.

Single-cell transcriptomic landscape identifies the expansion of peripheral blood monocytes as an indicator of HIV-1-TB co-infection

Certain circulating cell subsets are involved in immune dysregulation in human immunodeficiency virus type 1 (HIV-1) and tuberculosis (TB) co-infection; however, the characteristics and role of these subclusters are unknown. Peripheral blood mononuclear cells (PBMCs) of patients with HIV-1 infection alone (HIV-pre) and those with HIV-1-TB co-infection without anti-TB treatment (HIV-pre & TB-pre) and with anti-TB treatment for 2 weeks (HIV-pre & TB-pos) were subjected to single-cell RNA sequencing (scRNA-seq) to characterize the transcriptome of different immune cell subclusters. We obtained > 60,000 cells and identified 32 cell subclusters based on gene expression. The proportion of immune-cell subclusters was altered in HIV-1-TB co-infected individuals compared with that in HIV-pre-group, indicating immune dysregulation corresponding to different disease states. The proportion of an inflammatory CD14+CD16+ monocyte subset was higher in the HIV-pre & TB-pre group than in the HIV-pre group; this was validated in an additional cohort (n = 80) via a blood cell differential test, which also demonstrated a good discriminative performance (area under the curve, 0.8046). These findings depicted the atlas of immune PBMC subclusters in HIV-1-TB co-infection and demonstrate that monocyte subsets in peripheral blood might serve as a discriminating biomarker for diagnosis of HIV-1-TB co-infection.

Designing of a Chimeric Vaccine Using EIS (Rv2416c) Protein Against Mycobacterium tuberculosis H37Rv: an Immunoinformatics Approach

Mycobacterium tuberculosis (Mtb) is a respiratory pathogen that causes tuberculosis (TB). There are a large number of proteins that are involved in the pathogenesis of TB. Stimulating the immune response against TB is very important to clear the pathogens from host. In the present study, an immunoinformatics conduit is used for designing an epitope based chimeric vaccine against TB. Enhanced intracellular survival (EIS) protein from Mtb is used for designing the chimeric vaccine. One B cell epitope, 8 cytotoxic T lymphocyte (CTL), and 6 helper T lymphocyte (HTL) epitopes were predicted based on the MHC allele binding, immunogenicity, antigenicity, allergenicity, toxicity and IFN epitopes. The selected epitopes were used for chimeric vaccine designing. Furthermore, 3D structure elucidation, structural refinement and validation of the designed chimeric vaccine were carried out. The 3D structure was used for protein-protein docking studies with Toll-like receptor 4 (TLR-4), followed by molecular dynamic simulation (MDS) and the interaction between the chimeric vaccine and TLR-4 complex was verified.

Single-cell transcriptomics of blood reveals a natural killer cell subset depletion in tuberculosis

Background

Tuberculosis (TB) continues to be a critical global health problem, which killed millions of lives each year. Certain circulating cell subsets are thought to differentially modulate the host immune response towards Mycobacterium tuberculosis (Mtb) infection, but the nature and function of these subsets is unclear.

Methods

Peripheral blood mononuclear cells (PBMC) were isolated from healthy controls (HC), latent tuberculosis infection (LTBI) and active tuberculosis (TB) and then subjected to single-cell RNA sequencing (scRNA-seq) using 10 × Genomics platform. Unsupervised clustering of the cells based on the gene expression profiles using the Seurat package and passed to tSNE for clustering visualization. Flow cytometry was used to validate the subsets identified by scRNA-Seq.

Findings

Cluster analysis based on differential gene expression revealed both known and novel markers for all main PBMC cell types and delineated 29 cell subsets. By comparing the scRNA-seq datasets from HC, LTBI and TB, we found that infection changes the frequency of immune-cell subsets in TB. Specifically, we observed gradual depletion of a natural killer (NK) cell subset (CD3-CD7+GZMB+) from HC, to LTBI and TB. We further verified that the depletion of CD3-CD7+GZMB+ subset in TB and found an increase in this subset frequency after anti-TB treatment. Finally, we confirmed that changes in this subset frequency can distinguish patients with TB from LTBI and HC.

Interpretation

We propose that the frequency of CD3-CD7+GZMB+ in peripheral blood could be used as a novel biomarker for distinguishing TB from LTBI and HC.

Fund

The study was supported by Natural Science Foundation of China (81770013, 81525016, 81772145, 81871255 and 91942315), National Science and Technology Major Project (2017ZX10201301), Science and Technology Project of Shenzhen (JCYJ20170412101048337) and Guangdong Provincial Key Laboratory of Regional Immunity and Diseases (2019B030301009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Thinking Outside the Box: Innate- and B Cell-Memory Responses as Novel Protective Mechanisms Against Tuberculosis

Tuberculosis (TB) is currently the deadliest infectious disease worldwide. Failure to create a highly effective vaccine has limited the control of the TB epidemic. Historically, the vaccine field has relied on the paradigm that IFN-γ-mediated CD4+ T cell memory responses are the principal correlate of protection in TB. Nonetheless, the demonstration that other cellular subsets offer protective memory responses against Mycobacterium tuberculosis (Mtb) is emerging. Among these are memory-like features of macrophages, myeloid cell precursors, natural killer (NK) cells, and innate lymphoid cells (ILCs). Additionally, the dynamics of B cell memory responses have been recently characterized at different stages of the clinical spectrum of Mtb infection, suggesting a role for B cells in human TB. A better understanding of the immune mechanisms underlying such responses is crucial to better comprehend protective immunity in TB. Furthermore, targeting immune compartments other than CD4+ T cells in TB vaccine strategies may benefit a significant proportion of patients co-infected with Mtb and the human immunodeficiency virus (HIV). Here, we summarize the memory responses of innate immune cells and B cells against Mtb and propose them as novel correlates of protection that could be harnessed in future vaccine development programs.

MTB driven B cells producing IL-35 and secreting high level of IL-10 in the patients with active pulmonary tuberculosis

Regulatory B cells (Bregs) have critical roles as a negative regulator of immunity, mainly due to the fact that it secrets high a level of interleukin 10 (IL-10). Recently, a new subset of Bregs was identified as a key source of IL-35, which is an immunosuppressive cytokine and conventionally thought to be secreted by regulatory T cells (Tregs). Our previous study showed that the level of IL-35 in serum was elevated in the patients with active tuberculosis (ATB). However, none of the studies reported that IL-35 is secreted by B cells in ATB patients. In the current study, we found that the mRNA expressions of the both subunits (p35 and Ebi3) of IL-35 by circulating B cells were increased in ATB patients. By using immunohistochemistry and immunofluorescence staining, we found a subset of B cells infiltrated into the tuberculous granuloma of ATB patients also expressed IL-35. Moreover, Mycobacterium tuberculosis (MTB) lysate stimulation assay also demonstrated higher levels of IL-35 were exerted by MTB lysate within purified B cells from healthy control group (HC). Flow cytometry analysis further showed that the IL-35-producing B cells from ATB patients produced a higher level of IL-10. Taken together, IL-35-producing B cells may play a regulatory role during MTB infection by producing IL-10.

A polymeric immunoglobulin-antigen fusion protein strategy for enhancing vaccine immunogenicity

In this study, a strategy based on polymeric immunoglobulin G scaffolds (PIGS) was used to produce a vaccine candidate for Mycobacterium tuberculosis. A genetic fusion construct comprising genes encoding the mycobacterial Ag85B antigen, an immunoglobulin γ-chain fragment and the tailpiece from immunoglobulin μ chain was engineered. Expression was attempted in Chinese Hamster Ovary (CHO) cells and in Nicotiana benthamiana. The recombinant protein assembled into polymeric structures (TB-PIGS) in N. benthamiana, similar in size to polymeric IgM. These complexes were subsequently shown to bind to the complement protein C1q and FcγRs with increased affinity. Modification of the N-glycans linked to TB-PIGS by removal of xylose and fucose residues that are normally found in plant glycosylated proteins also resulted in increased affinity for low-affinity FcγRs. Immunization studies in mice indicated that TB-PIGS are highly immunogenic with and without adjuvant. However, they did not improve protective efficacy in mice against challenge with M. tuberculosis compared to conventional vaccination with BCG, suggesting that additional or alternative antigens may be needed to protect against this disease. Nevertheless, these results establish a novel platform for producing polymeric antigen-IgG γ-chain molecules with inherent functional characteristics that are desirable in vaccines.

Epidemiologic Evidence of and Potential Mechanisms by Which Second-Hand Smoke Causes Predisposition to Latent and Active Tuberculosis

Many studies have linked cigarette smoke (CS) exposure and tuberculosis (TB) infection and disease although much fewer have studied second-hand smoke (SHS) exposure. Our goal is to review the epidemiologic link between SHS and TB as well as to summarize the effects SHS and direct CS on various immune cells relevant for TB. PubMed searches were performed using the key words "tuberculosis" with "cigarette," "tobacco," or "second-hand smoke." The bibliography of relevant papers were examined for additional relevant publications. Relatively few studies associate SHS exposure with TB infection and active disease. Both SHS and direct CS can alter various components of host immunity resulting in increased vulnerability to TB. While the epidemiologic link of these 2 health maladies is robust, more definitive, mechanistic studies are required to prove that SHS and direct CS actually cause increased susceptibility to TB.

Human Immunology of Tuberculosis

Immunology is a central theme when it comes to tuberculosis (TB). The outcome of human infection with Mycobacterium tuberculosis is dependent on the ability of the immune response to clear or contain the infection. In cases where this fails, the bacterium replicates, disseminates within the host, and elicits a pathologic inflammatory response, and disease ensues. Clinical presentation of TB disease is remarkably heterogeneous, and the disease phenotype is largely dependent on host immune status. Onward transmission of M. tuberculosis to new susceptible hosts is thought to depend on an excessive inflammatory response causing a breakdown of the lung matrix and formation of lung cavities. But this varies in cases of underlying immunological dysfunction: for example, HIV-1 infection is associated with less cavitation, while diabetes mellitus comorbidity is associated with increased cavitation and risk of transmission. In compliance with the central theme of immunology in tuberculosis, we rely on detection of an adaptive immune response, in the form of interferon-gamma release assays or tuberculin skin tests, to diagnose infection with M. tuberculosis. Here we review the immunology of TB in the human host, focusing on cellular and humoral adaptive immunity as well as key features of innate immune responses and the underlying immunological dysfunction which associates with human TB risk factors. Our review is restricted to human immunology, and we highlight distinctions from the immunological dogma originating from animal models of TB, which pervade the field.

T7 Phage Display Library a Promising Strategy to Detect Tuberculosis Specific Biomarkers

One-third of the world's population is infected with tuberculosis, only 10% will develop active disease and the remaining 90% is considered to have latent TB (LTB). While active TB is contagious and can be lethal, the LTB can evolve to active TB. The diagnosis of TB can be challenging, especially in the early stages, due to the variability in presentation and nonspecific signs and symptoms. Currently, we have limited tools available to diagnose active TB, predict treatment efficacy and cure of active tuberculosis, the reactivation of latent tuberculosis infection, and the induction of protective immune responses through vaccination. Therefore, the identification of robust and accurate tuberculosis-specific biomarkers is crucial for the successful eradication of TB. In this commentary, we summarized the available methods for diagnosis and differentiation of active TB from LTB and their limitations. Additionally, we present a novel peptide microarray platform as promising strategy to identify TB biomarkers.

B cell responses in older adults with latent tuberculosis: Considerations for vaccine development

Reactivation of latent tuberculosis (LTBI) is more common among the aging population and may contribute to increased transmission in long-term health care facilities. Difficulties in detecting LTBI due to potential blunting of the tuberculin skin test (TST), and the lowered ability of the elderly to tolerate the course of antibiotics, underscore the need for an effective vaccine. Immuno-senescence reduces the capacity of vaccines to induce sufficient levels of protective immunity against many pathogens, further increasing the susceptibility of the elderly to infectious diseases. We sought to evaluate the response of B cells to Mycobacterium tuberculosis (Mtb) in residents of long-term care facilities to determine the feasibility of using a vaccine to control infection and transmission from reactivated LTBI. Our results demonstrate that although B cell responses were higher in subjects with LTBI, Mtb antigens could stimulate B cell activation and differentiation in vitro in TST negative subjects. B cells from elderly subjects expressed high basal levels of Toll-like receptor (TLR)2 and TLR4 and responded strongly to Mtb ligands with some activation pathways dependent on TLR2. B cells derived from blood, tonsil and spleen from younger subjects responded similarly and to the same magnitude. These results suggest that B cell responses are robust in the elderly and modifications to a TB vaccine, such as TLR2 ligand-based adjuvants, may help increase immune responses to a protective level.