Publications by authors named "David M Lewinsohn"

107 Publications

Nutritional markers and proteome in patients undergoing treatment for pulmonary tuberculosis differ by geographic region.

PLoS One 2021 5;16(5):e0250586. Epub 2021 May 5.

Division of Pulmonary and Critical Care Medicine and UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, California, United States of America.

Introduction: Contemporary phase 2 TB disease treatment clinical trials have found that microbiologic treatment responses differ between African versus non-African regions, the reasons for which remain unclear. Understanding host and disease phenotypes that may vary by region is important for optimizing curative treatments.

Methods: We characterized clinical features and the serum proteome of phase 2 TB clinical trial participants undergoing treatment for smear positive, culture-confirmed TB, comparing host serum protein expression in clinical trial participants enrolled in African and Non-African regions. Serum samples were collected from 289 participants enrolled in the Centers for Disease Control and Prevention TBTC Study 29 (NCT00694629) at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment).

Results: After a peptide level proteome analysis utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS) and subsequent statistical analysis, a total of 183 core proteins demonstrated significant differences at both baseline and at week 8 timepoints between participants enrolled from African and non-African regions. The majority of the differentially expressed proteins were upregulated in participants from the African region, and included acute phase proteins, mediators of inflammation, as well as coagulation and complement pathways. Downregulated proteins in the African population were primarily linked to nutritional status and lipid metabolism pathways.

Conclusions: We have identified differentially expressed nutrition and lipid pathway proteins by geographic region in TB patients undergoing treatment for pulmonary tuberculosis, which appear to be associated with differential treatment responses. Future TB clinical trials should collect expanded measures of nutritional status and further evaluate the relationship between nutrition and microbiologic treatment response.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0250586PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099102PMC
May 2021

MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection.

Front Immunol 2021 9;12:631410. Epub 2021 Apr 9.

Africa Health Research Institute (AHRI), Durban, South Africa.

Mucosal associated invariant T (MAIT) cells are a class of innate-like T cells that utilize a semi-invariant αβ T cell receptor to recognize small molecule ligands produced by bacteria and fungi. Despite growing evidence that immune cells at mucosal surfaces are often phenotypically and functionally distinct from those in the peripheral circulation, knowledge about the characteristics of MAIT cells at the lung mucosal surface, the site of exposure to respiratory pathogens, is limited. HIV infection has been shown to have a profound effect on the number and function of MAIT cells in the peripheral blood, but its effect on lung mucosal MAIT cells is unknown. We examined the phenotypic, functional, and transcriptomic features of major histocompatibility complex (MHC) class I-related (MR1)-restricted MAIT cells from the peripheral blood and bronchoalveolar compartments of otherwise healthy individuals with latent () infection who were either HIV uninfected or HIV infected. Peripheral blood MAIT cells consistently co-expressed typical MAIT cell surface markers CD161 and CD26 in HIV-negative individuals, while paired bronchoalveolar MAIT cells displayed heterogenous expression of these markers. Bronchoalveolar MAIT cells produced lower levels of pro-inflammatory cytokine IFN-γ and expressed higher levels of co-inhibitory markers PD-1 and TIM-3 than peripheral MAIT cells. HIV infection resulted in decreased frequencies and pro-inflammatory function of peripheral blood MAIT cells, while in the bronchoalveolar compartment MAIT cell frequency was decreased but phenotype and function were not significantly altered. Single-cell transcriptomic analysis demonstrated greater heterogeneity among bronchoalveolar compared to peripheral blood MAIT cells and suggested a distinct subset in the bronchoalveolar compartment. The transcriptional features of this bronchoalveolar subset were associated with MAIT cell tissue repair functions. In summary, we found previously undescribed phenotypic and transcriptional heterogeneity of bronchoalveolar MAIT cells in HIV-negative people. In HIV infection, we found numeric depletion of MAIT cells in both anatomical compartments but preservation of the novel phenotypic and transcriptional features of bronchoalveolar MAIT cells.
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http://dx.doi.org/10.3389/fimmu.2021.631410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8062704PMC
September 2021

Functional and Activation Profiles of Mucosal-Associated Invariant T Cells in Patients With Tuberculosis and HIV in a High Endemic Setting.

Front Immunol 2021 22;12:648216. Epub 2021 Mar 22.

Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.

MAIT cells are non-classically restricted T lymphocytes that recognize and rapidly respond to microbial metabolites or cytokines and have the capacity to kill bacteria-infected cells. Circulating MAIT cell numbers generally decrease in patients with active TB and HIV infection, but findings regarding functional changes differ. We conducted a cross-sectional study on the effect of HIV, TB, and HIV-associated TB (HIV-TB) on MAIT cell frequencies, activation and functional profile in a high TB endemic setting in South Africa. Blood was collected from (i) healthy controls (HC, = 26), 24 of whom had LTBI, (ii) individuals with active TB (aTB, = 36), (iii) individuals with HIV infection (HIV, = 50), 37 of whom had LTBI, and (iv) individuals with HIV-associated TB (HIV-TB, = 26). All TB participants were newly diagnosed and sampled before treatment, additional samples were also collected from 18 participants in the aTB group after 10 weeks of TB treatment. Peripheral blood mononuclear cells (PBMC) stimulated with BCG-expressing GFP (BCG-GFP) and heat-killed (HK) () were analyzed using flow cytometry. MAIT cells were defined as CD3 CD161 Vα7.2 T cells. Circulating MAIT cell frequencies were depleted in individuals with HIV infection ( = 0.009). MAIT cells showed reduced CD107a expression in aTB ( = 0.006), and reduced IFNγ expression in aTB ( < 0.001) and in HIV-TB ( < 0.001) in response to BCG-GFP stimulation. This functional impairment was coupled with a significant increase in activation (defined by HLA-DR expression) in resting MAIT cells from HIV ( < 0.001), aTB ( = 0.019), and HIV-TB ( = 0.005) patients, and higher HLA-DR expression in MAIT cells expressing IFNγ in aTB ( = 0.009) and HIV-TB ( = 0.002) after stimulation with BCG-GFP and HK-. After 10 weeks of TB treatment, there was reversion in the observed functional impairment in total MAIT cells, with increases in CD107a ( = 0.020) and IFNγ ( = 0.010) expression. Frequencies and functional profile of MAIT cells in response to mycobacterial stimulation are significantly decreased in HIV infected persons, active TB and HIV-associated TB, with a concomitant increase in MAIT cell activation. These alterations may reduce the capacity of MAIT cells to play a protective role in the immune response to these two pathogens.
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http://dx.doi.org/10.3389/fimmu.2021.648216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019701PMC
October 2021

T cell receptor diversity, specificity and promiscuity of functionally heterogeneous human MR1-restricted T cells.

Mol Immunol 2021 02 23;130:64-68. Epub 2020 Dec 23.

Department of Medicine, Oregon Health & Science University, Portland VA Medical Center, Portland, OR, United States. Electronic address:

The monomorphic MHC-class I-like molecule, MR1, presents small metabolites to T cells. MR1 is the restriction element for microbe-reactive mucosal-associated invariant T (MAIT) cells. MAIT cells have limited TCR usage, including a semi-invariant TCR alpha chain and express high levels of CD161 and CD26. In addition to microbial lumazine metabolites, recent studies have demonstrated that MR1 is able to capture a variety of diverse chemical entities including folate-derivatives, a number of drug-like and other synthetic small molecules, and as yet undefined compounds of self-origin. This capacity of MR1 to bind distinct ligands likely accounts for the recent identification of additional, non-canonical, subsets of MR1-restricted T (MR1T) cells. These subsets can be defined based on their ability to recognize diverse microbes as well as their reactivity to non-microbial cell-endogenous ligands, including tumor-associated antigens. Herein, we will discuss our current understanding of MR1T cell diversity in terms of TCR usage, ligand recognition and functional attributes.
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http://dx.doi.org/10.1016/j.molimm.2020.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7855563PMC
February 2021

Postnatal Expansion, Maturation, and Functionality of MR1T Cells in Humans.

Front Immunol 2020 16;11:556695. Epub 2020 Sep 16.

Division of Infectious Diseases, Department of Pediatrics, Oregon Health & Science University, Portland, OR, United States.

MR1-restricted T (MR1T) cells are defined by their recognition of metabolite antigens presented by the monomorphic MHC class 1-related molecule, MR1, the most highly conserved MHC class I related molecule in mammalian species. Mucosal-associated invariant T (MAIT) cells are the predominant subset of MR1T cells expressing an invariant TCR α-chain, TRAV1-2. These cells comprise a T cell subset that recognizes and mediates host immune responses to a broad array of microbial pathogens, including . Here, we sought to characterize development of circulating human MR1T cells as defined by MR1-5-OP-RU tetramer labeling and of the TRAV1-2 MAIT cells defined by expression of TRAV1-2 and high expression of CD26 and CD161 (TRAV1-2CD161CD26 cells). We analyzed postnatal expansion, maturation, and functionality of peripheral blood MR1-5-OP-RU tetramer MR1T cells in cohorts from three different geographic settings with different tuberculosis (TB) vaccination practices, levels of exposure to and infection with . Early after birth, frequencies of MR1-5-OP-RU tetramer MR1T cells increased rapidly by several fold. This coincided with the transition from a predominantly CD4 and TRAV1-2 population in neonates, to a predominantly TRAV1-2CD161CD26 CD8 population. We also observed that tetramer MR1T cells that expressed TNF upon mycobacterial stimulation were very low in neonates, but increased ~10-fold in the first year of life. These functional MR1T cells in all age groups were MR1-5-OP-RU tetramerTRAV1-2 and highly expressed CD161 and CD26, markers that appeared to signal phenotypic and functional maturation of this cell subset. This age-associated maturation was also marked by the loss of naïve T cell markers on tetramer TRAV1-2 MR1T cells more rapidly than tetramerTRAV1-2 MR1T cells and non-MR1T cells. These data suggest that neonates have infrequent populations of MR1T cells with diverse phenotypic attributes; and that exposure to the environment rapidly and preferentially expands the MR1-5-OP-RU tetramerTRAV1-2 population of MR1T cells, which becomes the predominant population of functional MR1T cells early during childhood.
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http://dx.doi.org/10.3389/fimmu.2020.556695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7524872PMC
May 2021

Alternative splicing of MR1 regulates antigen presentation to MAIT cells.

Sci Rep 2020 09 22;10(1):15429. Epub 2020 Sep 22.

VA Portland Health System, Portland, OR, USA.

Mucosal Associated Invariant T (MAIT) cells can sense intracellular infection by a broad array of pathogens. These cells are activated upon encountering microbial antigen(s) displayed by MR1 on the surface of an infected cell. Human MR1 undergoes alternative splicing. The full-length isoform, MR1A, can activate MAIT cells, while the function of the isoforms, MR1B and MR1C, are incompletely understood. In this report, we sought to characterize the expression and function of these splice variants. Using a transcriptomic analysis in conjunction with qPCR, we find that that MR1A and MR1B transcripts are widely expressed. However only MR1A can present mycobacterial antigen to MAIT cells. Coexpression of MR1B with MR1A decreases MAIT cell activation following bacterial infection. Additionally, expression of MR1B prior to MR1A lowers total MR1A abundance, suggesting competition between MR1A and MR1B for either ligands or chaperones required for folding and/or trafficking. Finally, we evaluated CD4/CD8 double positive thymocytes expressing surface MR1. Here, we find that relative expression of MR1A/MR1B transcript is associated with the prevalence of MR1 + CD4/CD8 cells in the thymus. Our results suggest alternative splicing of MR1 represents a means of regulating MAIT activation in response to microbial ligand(s).
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http://dx.doi.org/10.1038/s41598-020-72394-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508857PMC
September 2020

Atypical TRAV1-2 T cell receptor recognition of the antigen-presenting molecule MR1.

J Biol Chem 2020 10 14;295(42):14445-14457. Epub 2020 Aug 14.

Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia

MR1 presents vitamin B-related metabolites to mucosal associated invariant T (MAIT) cells, which are characterized, in part, by the TRAV1-2 αβ T cell receptor (TCR). In addition, a more diverse TRAV1-2 MR1-restricted T cell repertoire exists that can possess altered specificity for MR1 antigens. However, the molecular basis of how such TRAV1-2 TCRs interact with MR1-antigen complexes remains unclear. Here, we describe how a TRAV12-2 TCR (termed D462-E4) recognizes an MR1-antigen complex. We report the crystal structures of the unliganded D462-E4 TCR and its complex with MR1 presenting the riboflavin-based antigen 5-OP-RU. Here, the TRBV29-1 β-chain of the D462-E4 TCR binds over the F'-pocket of MR1, whereby the complementarity-determining region (CDR) 3β loop surrounded and projected into the F'-pocket. Nevertheless, the CDR3β loop anchored proximal to the MR1 A'-pocket and mediated direct contact with the 5-OP-RU antigen. The D462-E4 TCR footprint on MR1 contrasted that of the TRAV1-2 and TRAV36 TCRs' docking topologies on MR1. Accordingly, diverse MR1-restricted T cell repertoire reveals differential docking modalities on MR1, thus providing greater scope for differing antigen specificities.
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http://dx.doi.org/10.1074/jbc.RA120.015292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7573270PMC
October 2020

Mucosal-Associated Invariant T Cells Develop an Innate-Like Transcriptomic Program in Anti-mycobacterial Responses.

Front Immunol 2020 9;11:1136. Epub 2020 Jun 9.

Division of Environmental Genetics and Molecular Toxicology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, United States.

Conventional T cells exhibit a delayed response to the initial priming of peptide antigens presented by major histocompatibility complex (MHC) proteins. Unlike conventional T cells, mucosal-associated invariant T (MAIT) cells quickly respond to non-peptidic metabolite antigens presented by MHC-related protein 1 (MR1). To elucidate the MR1-dependent activation program of MAIT cells in response to mycobacterial infections, we determined the surface markers, transcriptomic profiles, and effector responses of activated human MAIT cells. Results revealed that mycobacterial-incubated antigen-presenting cells stimulated abundant human CD8 MAIT cells to upregulate the co-expression of CD69 and CD26, as a combinatorial activation marker. Further transcriptomic analyses demonstrated that CD69CD26 CD8MAIT cells highly expressed numerous genes for mediating anti-mycobacterial immune responses, including pro-inflammatory cytokines, cytolytic molecules, NK cell receptors, and transcription factors, in contrast to inactivated counterparts CD69CD26 CD8MAIT cells. Gene co-expression, enrichment, and pathway analyses yielded high statistical significance to strongly support that activated CD8 MAIT cells shared gene expression and numerous pathways with NK and CD8 T cells in activation, cytokine production, cytokine signaling, and effector functions. Flow cytometry detected that activated CD8MAIT cells produced TNFα, IFNγ, and granulysin to inhibit mycobacterial growth and fight mycobacterial infection. Together, results strongly support that the combinatorial activation marker CD69CD26 labels the activated CD8MAIT cells that develop an innate-like activation program in anti-mycobacterial immune responses. We speculate that the rapid production of anti-mycobacterial effector molecules facilitates MAIT cells to fight early mycobacterial infection in humans.
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http://dx.doi.org/10.3389/fimmu.2020.01136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295940PMC
April 2021

The MAIT TCRβ chain contributes to discrimination of microbial ligand.

Immunol Cell Biol 2020 10 12;98(9):770-781. Epub 2020 Jul 12.

Department of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA.

Mucosal-associated invariant T (MAIT) cells are key players in the immune response against microbial infection. The MAIT T-cell receptor (TCR) recognizes a diverse array of microbial ligands, and recent reports have highlighted the variability in the MAIT TCR that could further contribute to discrimination of ligand. The MAIT TCR complementarity determining region (CDR)3β sequence displays a high level of diversity across individuals, and clonotype usage appears to be dependent on antigenic exposure. To address the relationship between the MAIT TCR and microbial ligand, we utilized a previously defined panel of MAIT cell clones that demonstrated variability in responses against different microbial infections. Sequencing of these clones revealed four pairs, each with shared (identical) CDR3α and different CDR3β sequences. These pairs demonstrated varied responses against microbially infected dendritic cells as well as against 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil, a ligand abundant in Salmonella enterica serovar Typhimurium, suggesting that the CDR3β contributes to differences in ligand discrimination. Taken together, these results highlight a key role for the MAIT CDR3β region in distinguishing between MR1-bound antigens and ligands.
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http://dx.doi.org/10.1111/imcb.12370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7541710PMC
October 2020

Quantitative and Qualitative Perturbations of CD8 MAITs in Healthy -Infected Individuals.

Immunohorizons 2020 06 4;4(6):292-307. Epub 2020 Jun 4.

Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037.

CD8 T cells are considered important contributors to the immune response against , yet limited information is currently known regarding their specific immune signature and phenotype. In this study, we applied a cell population transcriptomics strategy to define immune signatures of human latent tuberculosis infection (LTBI) in memory CD8 T cells. We found a 41-gene signature that discriminates between memory CD8 T cells from healthy LTBI subjects and uninfected controls. The gene signature was dominated by genes associated with mucosal-associated invariant T cells (MAITs) and reflected the lower frequency of MAITs observed in individuals with LTBI. There was no evidence for a conventional CD8 T cell-specific signature between the two cohorts. We, therefore, investigated MAITs in more detail based on Vα7.2 and CD161 expression and staining with an MHC-related protein 1 (MR1) tetramer. This revealed two distinct populations of CD8Vα7.2CD161 MAITs: MR1 tetramer and MR1 tetramer, which both had distinct gene expression compared with memory CD8 T cells. Transcriptomic analysis of LTBI versus noninfected individuals did not reveal significant differences for MR1 tetramer MAITs. However, gene expression of MR1 tetramer MAITs showed large interindividual diversity and a tuberculosis-specific signature. This was further strengthened by a more diverse TCR-α and -β repertoire of MR1 tetramer cells as compared with MR1 tetramer Thus, circulating memory CD8 T cells in subjects with latent tuberculosis have a reduced number of conventional MR1 tetramer MAITs as well as a difference in phenotype in the rare population of MR1 tetramer MAITs compared with uninfected controls.
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http://dx.doi.org/10.4049/immunohorizons.2000031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7543048PMC
June 2020

Ligand-dependent downregulation of MR1 cell surface expression.

Proc Natl Acad Sci U S A 2020 05 27;117(19):10465-10475. Epub 2020 Apr 27.

MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.

The antigen-presenting molecule MR1 presents riboflavin-based metabolites to Mucosal-Associated Invariant T (MAIT) cells. While MR1 egress to the cell surface is ligand-dependent, the ability of small-molecule ligands to impact on MR1 cellular trafficking remains unknown. Arising from an in silico screen of the MR1 ligand-binding pocket, we identify one ligand, 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoic acid, DB28, as well as an analog, methyl 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoate, NV18.1, that down-regulate MR1 from the cell surface and retain MR1 molecules in the endoplasmic reticulum (ER) in an immature form. DB28 and NV18.1 compete with the known MR1 ligands, 5-OP-RU and acetyl-6-FP, for MR1 binding and inhibit MR1-dependent MAIT cell activation. Crystal structures of the MAIT T cell receptor (TCR) complexed with MR1-DB28 and MR1-NV18.1, show that these two ligands reside within the A'-pocket of MR1. Neither ligand forms a Schiff base with MR1 molecules; both are nevertheless sequestered by a network of hydrophobic and polar contacts. Accordingly, we define a class of compounds that inhibits MR1 cellular trafficking.
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http://dx.doi.org/10.1073/pnas.2003136117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229755PMC
May 2020

Peripheral Blood Mucosal-Associated Invariant T Cells in Tuberculosis Patients and Healthy Mycobacterium tuberculosis-Exposed Controls.

J Infect Dis 2020 08;222(6):995-1007

Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

Background: In human blood, mucosal-associated invariant T (MAIT) cells are abundant T cells that recognize antigens presented on non-polymorphic major histocompatibility complex-related 1 (MR1) molecules. The MAIT cells are activated by mycobacteria, and prior human studies indicate that blood frequencies of MAIT cells, defined by cell surface markers, decline during tuberculosis (TB) disease, consistent with redistribution to the lungs.

Methods: We tested whether frequencies of blood MAIT cells were altered in patients with TB disease relative to healthy Mycobacterium tuberculosis-exposed controls from Peru and South Africa. We quantified their frequencies using MR1 tetramers loaded with 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil.

Results: Unlike findings from prior studies, frequencies of blood MAIT cells were similar among patients with TB disease and latent and uninfected controls. In both cohorts, frequencies of MAIT cells defined by MR1-tetramer staining and coexpression of CD161 and the T-cell receptor alpha variable gene TRAV1-2 were strongly correlated. Disease severity captured by body mass index or TB disease transcriptional signatures did not correlate with MAIT cell frequencies in patients with TB.

Conclusions: Major histocompatibility complex (MHC)-related 1-restrictied MAIT cells are detected at similar levels with tetramers or surface markers. Unlike MHC-restricted T cells, blood frequencies of MAIT cells are poor correlates of TB disease but may play a role in pathophysiology.
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http://dx.doi.org/10.1093/infdis/jiaa173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7430171PMC
August 2020

The status of tuberculosis vaccine development.

Lancet Infect Dis 2020 03 31;20(3):e28-e37. Epub 2020 Jan 31.

European and Developing Countries Clinical Trials Partnership, Hague, Netherlands; Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark. Electronic address:

Tuberculosis represents the leading global cause of death from an infectious agent. Controlling the tuberculosis epidemic thus represents an urgent global public health priority. Epidemiological modelling suggests that, although drug treatments for tuberculosis continue to improve, WHO timelines to control the spread of the disease require a new vaccine capable of preventing tuberculosis, particularly in adolescents and adults. The spread of strains resistant to multiple drugs adds additional urgency to the vaccine development effort yet attempts to develop new vaccines with wider applicability and better, longer-lasting efficacy than BCG-the only tuberculosis vaccine licensed for use globally-have proven challenging. Results from clinical efficacy trials, particularly a completed, phase 2b trial for preventing tuberculosis disease in people infected with Mycobacterium tuberculosis using the adjuvanted protein subunit vaccine M72/AS01E give hope. We review the current status of tuberculosis vaccine candidates and outline the diversified vaccine development that are underway.
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http://dx.doi.org/10.1016/S1473-3099(19)30625-5DOI Listing
March 2020

Clonal enrichments of Vδ2- γδ T cells in Mycobacterium tuberculosis-infected human lungs.

J Clin Invest 2020 01;130(1):68-70

Department of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, Oregon, USA.

Unconventional T cell subsets, including donor-unrestricted T cells (DURTs) and γδ T cells, are promising new players in the treatment and prevention of infectious diseases. In this issue of the JCI, Ogongo et al. used T cell receptor (TCR) sequencing to characterize unconventional T cell subsets in surgical lung resections and blood from Mycobacterium tuberculosis-infected (Mtb-infected) individuals with and without HIV coinfection. The study revealed highly localized expansions of γδ T cell clonotypes not previously associated with the immune response to Mtb and demonstrates the power of high-throughput analysis of the TCR repertoire directly from infected tissue. The findings contribute to our understanding of tuberculosis control and have implications for the development of both therapeutic and vaccination strategies.
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http://dx.doi.org/10.1172/JCI133119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934183PMC
January 2020

Tuberculosis.

Clin Chest Med 2019 12;40(4):xi

Division of Mycobacterial and Respiratory Infections, National Jewish Health, Room J204, 1400 Jackson Street, Denver, CO 80206, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccm.2019.08.004DOI Listing
December 2019

New Concepts in Tuberculosis Host Defense.

Clin Chest Med 2019 12;40(4):703-719

Oregon Health and Science University, 707 Southwest Gaines Road, Portland, OR 97239, USA. Electronic address:

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.
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http://dx.doi.org/10.1016/j.ccm.2019.07.002DOI Listing
December 2019

MR1-Independent Activation of Human Mucosal-Associated Invariant T Cells by Mycobacteria.

J Immunol 2019 12 14;203(11):2917-2927. Epub 2019 Oct 14.

South African Tuberculosis Vaccine Initiative, University of Cape Town, Cape Town 7925, South Africa.

Tuberculosis (TB) is the leading cause of mortality from a single infectious agent, Relevant immune targets of the partially efficacious TB vaccine bacille Calmette-Guérin (BCG) remain poorly defined. Mucosal-associated invariant T (MAIT) cells are MHC-related protein 1 (MR1)-restricted T cells, which are reactive against , and underexplored as potential TB vaccine targets. We sought to determine whether BCG vaccination activated mycobacteria-specific MAIT cell responses in humans. We analyzed whole blood samples from infected South African adults who were revaccinated with BCG after a six-month course of isoniazid preventative therapy. In vitro BCG stimulation potently induced IFN-γ expression by phenotypic (CD8CD26CD161) MAIT cells, which constituted the majority (75%) of BCG-reactive IFN-γ-producing CD8 T cells. BCG revaccination transiently expanded peripheral blood frequencies of BCG-reactive IFN-γ MAIT cells, which returned to baseline frequencies a year following vaccination. In another cohort of healthy adults who received BCG at birth, 53% of mycobacteria-reactive-activated CD8 T cells expressed CDR3α TCRs, previously reported as MAIT TCRs, expressing the canonical TRAV1-2-TRAJ33 MAIT TCRα rearrangement. CD26 and CD161 coexpression correlated with TRAV1-2CD161 phenotype more accurately in CD8 than CD4CD8 MAIT cells. Interestingly, BCG-induced IFN-γ expression by MAIT cells in vitro was mediated by the innate cytokines IL-12 and IL-18 more than MR1-induced TCR signaling, suggesting TCR-independent activation. Collectively, the data suggest that activation of blood MAIT cells by innate inflammatory cytokines is a major mechanism of responsiveness to vaccination with whole cell vaccines against TB or in vitro stimulation with mycobacteria ( NCT01119521).
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http://dx.doi.org/10.4049/jimmunol.1900674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859375PMC
December 2019

TRAV1-2 CD8 T-cells including oligoconal expansions of MAIT cells are enriched in the airways in human tuberculosis.

Commun Biol 2019 5;2:203. Epub 2019 Jun 5.

5Department of Pulmonary & Critical Care Medicine, Oregon Health & Science University, Portland, OR USA.

Mucosal-associated invariant T (MAIT) cells typically express a TRAV1-2 semi-invariant TCRα that enables recognition of bacterial, mycobacterial, and fungal riboflavin metabolites presented by MR1. MAIT cells are associated with immune control of bacterial and mycobacterial infections in murine models. Here, we report that a population of pro-inflammatory TRAV1-2 CD8 T cells are present in the airways and lungs of healthy individuals and are enriched in bronchoalveolar fluid of patients with active pulmonary tuberculosis (TB). High-throughput T cell receptor analysis reveals oligoclonal expansions of canonical and donor-unique TRAV1-2 MAIT-consistent TCRα sequences within this population. Some of these cells demonstrate MR1-restricted mycobacterial reactivity and phenotypes suggestive of MAIT cell identity. These findings demonstrate enrichment of TRAV1-2 CD8 T cells with MAIT or MAIT-like features in the airways during active TB and suggest a role for these cells in the human pulmonary immune response to .
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http://dx.doi.org/10.1038/s42003-019-0442-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6549148PMC
May 2020

Tuberculosis Screening, Testing, and Treatment of U.S. Health Care Personnel: Recommendations from the National Tuberculosis Controllers Association and CDC, 2019.

MMWR Morb Mortal Wkly Rep 2019 May 17;68(19):439-443. Epub 2019 May 17.

The 2005 CDC guidelines for preventing Mycobacterium tuberculosis transmission in health care settings include recommendations for baseline tuberculosis (TB) screening of all U.S. health care personnel and annual testing for health care personnel working in medium-risk settings or settings with potential for ongoing transmission (1). Using evidence from a systematic review conducted by a National Tuberculosis Controllers Association (NTCA)-CDC work group, and following methods adapted from the Guide to Community Preventive Services (2,3), the 2005 CDC recommendations for testing U.S. health care personnel have been updated and now include 1) TB screening with an individual risk assessment and symptom evaluation at baseline (preplacement); 2) TB testing with an interferon-gamma release assay (IGRA) or a tuberculin skin test (TST) for persons without documented prior TB disease or latent TB infection (LTBI); 3) no routine serial TB testing at any interval after baseline in the absence of a known exposure or ongoing transmission; 4) encouragement of treatment for all health care personnel with untreated LTBI, unless treatment is contraindicated; 5) annual symptom screening for health care personnel with untreated LTBI; and 6) annual TB education of all health care personnel.
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http://dx.doi.org/10.15585/mmwr.mm6819a3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522077PMC
May 2019

Harnessing donor unrestricted T-cells for new vaccines against tuberculosis.

Vaccine 2019 05 27;37(23):3022-3030. Epub 2019 Apr 27.

Department of Medicine, Division of Infectious Diseases, University of Washington, Seattle, USA; Tuberculosis Research & Training Center, University of Washington, Seattle, USA. Electronic address:

Mycobacterium bovis bacille Calmette-Guérin (BCG) prevents extrapulmonary tuberculosis (TB) and death among infants but fails to consistently and sufficiently prevent pulmonary TB in adults. Thus, TB remains the leading infectious cause of death worldwide, and new vaccine approaches are urgently needed. T-cells are important for protective immunity to Mycobacterium tuberculosis (Mtb), but the optimal T-cell antigens to be included in new vaccines are not established. T-cells are often thought of as responding mainly to peptide antigens presented by polymorphic major histocompatibility complex (MHC) I and II molecules. Over the past two decades, the number of non-peptidic Mtb derived antigens for αβ and γδ T-cells has expanded rapidly, creating broader perspectives about the types of molecules that could be targeted by T-cell-based vaccines against TB. Many of these non-peptide responsive T-cell subsets in humans are activated in a manner that is unrestricted by classical MHC-dependent antigen-presenting systems, but instead require essentially nonpolymorphic presentation systems. These systems are Cluster of differentiation 1 (CD1), MHC related protein 1 (MR1), butyrophilin 3A1, as well as the nonclassical MHC class Ib family member HLA-E. Thus, the resulting T-cell responses can be shared among a genetically diverse population, creating the concept of donor-unrestricted T-cells (DURTs). Here, we review evidence that DURTs are an abundant component of the human immune system and recognize many antigens expressed by Mtb, including antigens that are expressed in BCG and other candidate whole cell vaccines. Further, DURTs exhibit functional diversity and demonstrate the ability to control microbial infection in small animal models. Finally, we outline specific knowledge gaps and research priorities that must be addressed to realize the full potential of DURTs as part of new TB vaccines approaches.
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http://dx.doi.org/10.1016/j.vaccine.2019.04.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525272PMC
May 2019

MR1 recycling and blockade of endosomal trafficking reveal distinguishable antigen presentation pathways between Mycobacterium tuberculosis infection and exogenously delivered antigens.

Sci Rep 2019 03 18;9(1):4797. Epub 2019 Mar 18.

VA Portland Health Care System, Research and Development, 3710 SW US Veterans Hospital Road, Portland, 97239, Oregon, USA.

The MHC-Ib molecule MR1 presents microbial metabolites to MR1-restricted T cells (MR1Ts). Given the ubiquitous expression of MR1 and the high prevalence of human MR1Ts, it is important to understand the mechanisms of MR1-dependent antigen presentation. Here, we show that MR1-dependent antigen presentation can be distinguished between intracellular Mycobacterium tuberculosis (Mtb) infection and exogenously added antigens. Although both Mtb infection and exogenously added antigens are presented by preformed MR1, only exogenously added antigens are capable of reusing MR1 that had been bound to the folic acid metabolite 6-formylpterin (6-FP). In addition, we identify an endosomal trafficking protein, Syntaxin 4, which is specifically involved in the presentation of exogenously delivered antigens but not Mtb-dependent antigen presentation. These data reveal there are multiple ways that MR1 can sample antigens and that MR1-mediated sampling of intracellular Mtb infection is distinguishable from the sampling of exogenously added antigens.
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http://dx.doi.org/10.1038/s41598-019-41402-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423294PMC
March 2019

Casting a wider net: Immunosurveillance by nonclassical MHC molecules.

PLoS Pathog 2019 02 21;15(2):e1007567. Epub 2019 Feb 21.

Laboratory of Viral Diseases, NIAID, Bethesda, Maryland, United States of America.

Most studies of T lymphocytes focus on recognition of classical major histocompatibility complex (MHC) class I or II molecules presenting oligopeptides, yet there are numerous variations and exceptions of biological significance based on recognition of a wide variety of nonclassical MHC molecules. These include αβ and γδ T cells that recognize different class Ib molecules (CD1, MR-1, HLA-E, G, F, et al.) that are nearly monomorphic within a given species. Collectively, these T cells can be considered "unconventional," in part because they recognize lipids, metabolites, and modified peptides. Unlike classical MHC-specific cells, unconventional T cells generally exhibit limited T-cell antigen receptor (TCR) repertoires and often produce innate immune cell-like rapid effector responses. Exploiting this system in new generation vaccines for human immunodeficiency virus (HIV), tuberculosis (TB), other infectious agents, and cancer was the focus of a recent workshop, "Immune Surveillance by Non-classical MHC Molecules: Improving Diversity for Antigens," sponsored by the National Institute of Allergy and Infectious Diseases. Here, we summarize salient points presented regarding the basic immunobiology of unconventional T cells, recent advances in methodologies to measure unconventional T-cell activity in diseases, and approaches to harness their considerable clinical potential.
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http://dx.doi.org/10.1371/journal.ppat.1007567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383864PMC
February 2019

MR1-dependent antigen presentation.

Semin Cell Dev Biol 2018 12;84:58-64

Pulmonary & Critical Care Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Portland VA Medical Center, 3710 SW US Veterans Hospital Road, Portland, OR 97239, USA; Molecular Microbiology and Immunology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road. Portland, OR 97239, USA. Electronic address:

MR1 is a non-classical class I molecule that is highly conserved among mammals. Though discovered in 1995, only recently have MR1 ligands and antigens for MR1-restricted T cells been described. Unlike the traditional class I molecules HLA-A, -B, and -C, little MR1 is on the cell surface. Rather, MR1 resides in discrete intracellular vesicles and the endoplasmic reticulum, and can present non-peptidic small molecules such as those found in the riboflavin biosynthesis pathway. Since mammals do not synthesize riboflavin, MR1 can serve as a sensor of the microbial metabolome and could be key to the early detection of intracellular infection. This review will summarize the current understanding of MR1-dependent antigen presentation.
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http://dx.doi.org/10.1016/j.semcdb.2017.11.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061520PMC
December 2018

Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis.

Tuberculosis (Edinb) 2018 09 18;112:52-61. Epub 2018 Jul 18.

Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA.

Rationale: The monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment.

Objective: We utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy.

Methods: Serum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points.

Results: A total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort. In response to TB treatment, 244 proteins were significantly altered. Pathway/network comparisons helped visualize the interconnected proteins, identifying up regulated (lipid transport, coagulation cascade, endopeptidase activity) and down regulated (acute phase) processes and pathways in addition to other cross regulated networks (inflammation, cell adhesion, extracellular matrix). Detection of possible lung injury serum proteins such as HPSE, significantly downregulated upon treatment. Analyses of microbiologic data over time identified a core set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2) which change in response to treatment and also strongly correlate with culture status. A similar set of proteins at baseline were found to be predictive of week 6 and 8 culture status.

Conclusion: A comprehensive host serum protein dataset reflective of TB treatment effect is defined. A repeating set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2, among others) were found to change significantly in response to treatment, to strongly correlate with culture status, and at baseline to be predictive of future culture conversion. If validated in cohorts with long term follow-up to capture failure and relapse of TB, these protein markers could be developed for monitoring of treatment in clinical trials and in patient care.
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http://dx.doi.org/10.1016/j.tube.2018.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181582PMC
September 2018

Diagnostic Challenge of Tuberculosis Heterogeneity.

Semin Respir Crit Care Med 2018 Jun 2;39(3):286-296. Epub 2018 Aug 2.

Department of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, Oregon.

For the ICU physician, the failure to consider, diagnose, and treat tuberculosis (TB) results in increased morbidity and mortality, and poses risks to both patients and health care providers. At present, the diagnosis of TB depends on the detection of either mycobacteria or mycobacterial products from clinical specimens. Given the risks posed to both the patient and health care providers by undiagnosed and/or untreated TB, the ability to diagnose TB rapidly in the ICU cannot be understated. In this regard, nucleic acid amplification tests provide relatively quick information about the presence of (Mtb) DNA. If available, a blood-based test that would accurately identify persons with TB would be of use in the ICU. Currently available tests such as the T-Spot.TB or QuantiFERON-TB Gold In-Tube can discern infection with Mtb, but are not recommended for the ICU as they cannot rule out TB. In this review, we will discuss the increasing literature that would suggest that a blood-based diagnostic that reflects the host response to TB could be used to diagnose TB in the ICU.
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http://dx.doi.org/10.1055/s-0038-1660471DOI Listing
June 2018

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

Clin Microbiol Rev 2018 10 18;31(4). Epub 2018 Jul 18.

Department of Global Health, University of Washington, Seattle, Washington, USA.

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.
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http://dx.doi.org/10.1128/CMR.00021-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6148193PMC
October 2018
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