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Xu T, Fan W, Chen C, Feng K, Sheng X, Wang H, Yang K, Chen B, Wang X, Wang Y. Transcriptome analysis of the diseased intervertebral disc tissue in patients with spinal tuberculosis. BMC Med Genomics 2024; 17:205. [PMID: 39135040 PMCID: PMC11318271 DOI: 10.1186/s12920-024-01981-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
OBJECTIVE To investigate the differential expression genes (DEGs) in spinal tuberculosis using transcriptomics, with the aim of identifying novel therapeutic targets and prognostic indicators for the clinical management of spinal tuberculosis. METHODS Patients who visited the Department of Orthopedics at the Second Hospital, Lanzhou University from January 2021 to May 2023 were enrolled. Based on the inclusion and exclusion criteria, there were 5 patients in the test group and 5 patients in the control group. Total RNA was extracted and paired-end sequencing was conducted on the sequencing platform. After processing the sequencing data with clean reads and annotating the reference genome, FPKM normalization and differential expression analysis were performed. The DEGs and long non-coding RNAs (LncRNAs) were analyzed for Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment. The cis-regulation of differentially expressed mRNAs (DE mRNAs) by LncRNAs was predicted and analyzed to establish a co-expression network. RESULTS This study identified 2366 DEGs, with 974 genes significantly upregulated and 1392 genes significantly downregulated. The upregulated genes are associated with cytokine-cytokine receptor interactions, tuberculosis, and TNF-α signaling pathways, primarily enriched in biological processes such as immunity and inflammation. The downregulated genes are related to muscle development, contraction, fungal defense response, and collagen metabolism processes. Analysis of LncRNAs from bone tuberculosis RNA-seq data detected a total of 3652 LncRNAs, with 356 significantly upregulated and 184 significantly downregulated. Further analysis identified 311 significantly different LncRNAs that could cis-regulate 777 target genes, enriched in pathways such as muscle contraction, inflammatory response, and immune response, closely related to bone tuberculosis. There are 51 genes enriched in the immune response pathway regulated by cis-acting LncRNAs. LncRNAs that regulate immune response-related genes, such as upregulated RP11-451G4.2, RP11-701P16.5, AC079767.4, AC017002.1, LINC01094, CTA-384D8.35, and AC092484.1, as well as downregulated RP11-2C24.7, may serve as potential prognostic and therapeutic targets. CONCLUSION The DE mRNAs and LncRNAs in spinal tuberculosis are both associated with immune regulatory pathways. These pathways promote or inhibit the tuberculosis infection and development at the mechanistic level and play an important role in the process of tuberculosis transferring to bone tissue.
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Affiliation(s)
- Tian'en Xu
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China
| | - Wenjuan Fan
- Departments of Cardiovascular Surgery, Gansu Provincial Maternity and Child care Hospital, Gansu Provincial Central Hospital, Lanzhou, Gansu, 730000, PR China
| | - Cong Chen
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China
| | - Kai Feng
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China
| | - Xiaoyun Sheng
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China
| | - Hong Wang
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China
| | - Kai Yang
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China
| | - Bao Chen
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China
| | - Xu Wang
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China
| | - Yapeng Wang
- Department of Orthopaedics, the Second Hospital & Clinical Medical School, Lanzhou University, 82 Cuiyingmen, Chengguan District, Lanzhou, Gansu, Lanzhou City, 730000, Gansu Province, PR China.
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2
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Ravesloot-Chávez MM, Van Dis E, Fox D, Anaya Sanchez A, Espich S, Nguyenla XH, Rawal SL, Samani H, Ballinger MA, Thomas H, Kotov D, Vance R, Nachman MW, Stanley SA. Tuberculosis susceptibility in genetically diverse mice reveals functional diversity of neutrophils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.29.547125. [PMID: 39211107 PMCID: PMC11361191 DOI: 10.1101/2023.06.29.547125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Tuberculosis (TB) is a heterogenous disease in humans with individuals exhibiting a wide range of susceptibility. This heterogeneity is not captured by standard laboratory mouse lines. We used a new collection of 19 wild-derived inbred mouse lines collected from diverse geographic sites to identify novel phenotypes during Mycobacterium tuberculosis ( Mtb ) infection. Wild derived mice have heterogenous immune responses to infection that result in differential ability to control disease at early timepoints. Correlation analysis with multiple parameters including sex, weight, and cellular immune responses in the lungs revealed that enhanced control of infection is associated with increased numbers of CD4 T cells, CD8 T cells and B cells. Surprisingly, we did not observe strong correlations between IFN-γ production and control of infection. Although in most lines high neutrophils were associated with susceptibility, we identified a mouse line that harbors high neutrophils numbers yet controls infection. Using single-cell RNA sequencing, we identified a novel neutrophil signature associated with failure to control infection.
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3
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Meade RK, Smith CM. Immunological roads diverged: mapping tuberculosis outcomes in mice. Trends Microbiol 2024:S0966-842X(24)00170-7. [PMID: 39034171 DOI: 10.1016/j.tim.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
The journey from phenotypic observation to causal genetic mechanism is a long and challenging road. For pathogens like Mycobacterium tuberculosis (Mtb), which causes tuberculosis (TB), host-pathogen coevolution has spanned millennia, costing millions of human lives. Mammalian models can systematically recapitulate host genetic variation, producing a spectrum of disease outcomes. Leveraging genome sequences and deep phenotyping data from infected mouse genetic reference populations (GRPs), quantitative trait locus (QTL) mapping approaches have successfully identified host genomic regions associated with TB phenotypes. Here, we review the ongoing optimization of QTL mapping study design alongside advances in mouse GRPs. These next-generation resources and approaches have enabled identification of novel host-pathogen interactions governing one of the most prevalent infectious diseases in the world today.
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Affiliation(s)
- Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA.
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4
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Dolezalova K, Hadlova P, Ibrahimova M, Golias J, Baca L, Kopecka E, Sukholytka M, Koziar Vasakova M. Flow cytometry-based method using diversity of cytokine production differentiates between Mycobacterium tuberculosis infection and disease. Tuberculosis (Edinb) 2024; 147:102518. [PMID: 38739968 DOI: 10.1016/j.tube.2024.102518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
Authors present a pilot study of the development of innovative flow cytometry-based assay with a potential for use in tuberculosis diagnostics. Currently available tests do not provide robust discrimination between latent tuberculosis infection (TBI) and tuberculosis disease (TB). The desired application is to distinguish between the two conditions by evaluating the production of a combination of three cytokines: IL-2 (interleukin-2), IFNɣ (interferon gamma) and TNFɑ (tumor necrosis factor alpha) in CD4+ and CD8+ T cells. The study was conducted on 68 participants, divided into two arms according to age (paediatric and adults). Each arm was further split into three categories (non-infection (NI), TBI, TB) based on the immune reaction to Mycobacterium tuberculosis (M.tb) after a close contact with pulmonary TB. Each blood sample was stimulated with specific M.tb antigens present in QuantiFERON tubes (TB1 and TB2). We inferred TBI or TB based on the predominant cytokine response of the CD4+ and/or CD8+ T cells. Significant differences were detected between the NI, TBI and the TB groups in TB1 in the CD4+TNFɑ+parameter in children. Along with IL-2, TNFɑ seems to be the most promising diagnostic marker in both CD4+and CD8+ T cells. However, more detailed analyses on larger cohorts are needed to confirm the observed tendencies.
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Affiliation(s)
- Karolina Dolezalova
- Department of Paediatrics of the First Faculty of Medicine, Charles University, Thomayer University Hospital, Prague, Czech Republic.
| | - Petra Hadlova
- Childhood Leukaemia Investigation Prague (CLIP), 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marketa Ibrahimova
- Laboratory of Immunology, Thomayer University Hospital, Prague, Czech Republic
| | - Jaroslav Golias
- Laboratory of Immunology, Thomayer University Hospital, Prague, Czech Republic
| | - Lubos Baca
- Department of Paediatrics of the First Faculty of Medicine, Charles University, Thomayer University Hospital, Prague, Czech Republic
| | - Emilia Kopecka
- Department of Respiratory Medicine of the First Faculty of Medicine Charles University, Thomayer University Hospital, Prague, Czech Republic
| | - Mariia Sukholytka
- Department of Respiratory Medicine of the First Faculty of Medicine Charles University, Thomayer University Hospital, Prague, Czech Republic
| | - Martina Koziar Vasakova
- Department of Respiratory Medicine of the First Faculty of Medicine Charles University, Thomayer University Hospital, Prague, Czech Republic
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5
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Choi S, Lee JM, Kim KES, Park JH, Kim LH, Park J, Jeon Y, Jhun BW, Kim SY, Hong JJ, Shin SJ. Protein-energy restriction-induced lipid metabolism disruption causes stable-to-progressive disease shift in Mycobacterium avium-infected female mice. EBioMedicine 2024; 105:105198. [PMID: 38889480 PMCID: PMC11237864 DOI: 10.1016/j.ebiom.2024.105198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Disease susceptibility and progression of Mycobacterium avium complex pulmonary disease (MAC-PD) is associated with multiple factors, including low body mass index (BMI). However, the specific impact of low BMI on MAC-PD progression remains poorly understood. This study aims to examine the progression of MAC-PD in the context of low BMI, utilising a disease-resistant mouse model. METHODS We employed a MAC infection-resistant female A/J mouse model to compare the progression of MAC-PD under two dietary conditions: one group was fed a standard protein diet, representing protein-energy unrestricted conditions, and the other was fed a low protein diet (LPD), representing protein-energy restriction. FINDINGS Our results reveal that protein-energy restriction significantly exacerbates MAC-PD progression by disrupting lipid metabolism. Mice fed an LPD showed elevated fatty acid levels and related gene expressions in lung tissues, similar to findings of increased fatty acids in the serum of patients who exhibited the MAC-PD progression. These mice also exhibited increased CD36 expression and lipid accumulation in macrophages upon MAC infection. In vitro experiments emphasised the crucial role of CD36-mediated palmitic acid uptake in bacterial proliferation. Importantly, in vivo studies demonstrated that administering anti-CD36 antibody to LPD-fed A/J mice reduced macrophage lipid accumulation and impeded bacterial growth, resulting in remarkable slowing disease progression. INTERPRETATION Our findings indicate that the metabolic status of host immune cells critically influences MAC-PD progression. This study highlights the potential of adequate nutrient intake in preventing MAC-PD progression, suggesting that targeting CD36-mediated pathways might be a host-directed therapeutic strategy to managing MAC infection. FUNDING This research was funded by the National Research Foundation of Korea, the Korea Research Institute of Bioscience and Biotechnology, and the Korea National Institute of Health.
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Affiliation(s)
- Sangwon Choi
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Ju Mi Lee
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Keu Eun San Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Ji-Hae Park
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Lee-Han Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jiyun Park
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Yaerin Jeon
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, South Korea
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, South Korea; KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea.
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6
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Cohen SB, Plumlee CR, Engels L, Mai D, Murray TA, Jahn AN, Alexander B, Delahaye JL, Cross LM, Maciag K, Schrader S, Durga K, Gold ES, Aderem A, Gerner MY, Gern BH, Diercks AH, Urdahl KB. Host and pathogen genetic diversity shape vaccine-mediated protection to Mycobacterium tuberculosis. Front Immunol 2024; 15:1427846. [PMID: 39007152 PMCID: PMC11239334 DOI: 10.3389/fimmu.2024.1427846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
To investigate how host and pathogen diversity govern immunity against Mycobacterium tuberculosis (Mtb), we performed a large-scale screen of vaccine-mediated protection against aerosol Mtb infection using three inbred mouse strains [C57BL/6 (B6), C3HeB/FeJ (C3H), Balb/c x 129/SvJ (C129F1)] and three Mtb strains (H37Rv, CDC1551, SA161) representing two lineages and distinct virulence properties. We compared three protective modalities, all of which involve inoculation with live mycobacteria: Bacillus Calmette-Guérin (BCG), the only approved TB vaccine, delivered either subcutaneously or intravenously, and concomitant Mtb infection (CoMtb), a model of pre-existing immunity in which a low-level Mtb infection is established in the cervical lymph node following intradermal inoculation. We examined lung bacterial burdens at early (Day 28) and late (Day 98) time points after aerosol Mtb challenge and histopathology at Day 98. We observed substantial heterogeneity in the reduction of bacterial load afforded by these modalities at Day 28 across the combinations and noted a strong positive correlation between bacterial burden in unvaccinated mice and the degree of protection afforded by vaccination. Although we observed variation in the degree of reduction in bacterial burdens across the nine mouse/bacterium strain combinations, virtually all protective modalities performed similarly for a given strain-strain combination. We also noted dramatic variation in histopathology changes driven by both host and bacterial genetic backgrounds. Vaccination improved pathology scores for all infections except CDC1551. However, the most dramatic impact of vaccination on lesion development occurred for the C3H-SA161 combination, where vaccination entirely abrogated the development of the large necrotic lesions that arise in unvaccinated mice. In conclusion, we find that substantial TB heterogeneity can be recapitulated by introducing variability in both host and bacterial genetics, resulting in changes in vaccine-mediated protection as measured both by bacterial burden as well as histopathology. These differences can be harnessed in future studies to identify immune correlates of vaccine efficacy.
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Affiliation(s)
- Sara B Cohen
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Courtney R Plumlee
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Lindsay Engels
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Dat Mai
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Tara A Murray
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Ana N Jahn
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Bridget Alexander
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Jared L Delahaye
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Lauren M Cross
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Karolina Maciag
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
- Department of Medicine, Division of Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Sam Schrader
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Kaitlin Durga
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Elizabeth S Gold
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Alan Aderem
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Michael Y Gerner
- Department of Immunology, University of Washington, Seattle, WA, United States
| | - Benjamin H Gern
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Alan H Diercks
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Kevin B Urdahl
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
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7
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Cardoso MS, Gonçalves R, Oliveira L, Silvério D, Téllez É, Paul T, Sarrias MR, Carmo AM, Saraiva M. CD5L is upregulated upon infection with Mycobacterium tuberculosis with no effect on disease progression. Immunology 2024. [PMID: 38922694 DOI: 10.1111/imm.13825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Tuberculosis (TB) alone caused over a billion deaths in the last 200 years, making it one of the deadliest diseases to humankind. Understanding the immune mechanisms underlying protection or pathology in TB is key to uncover the much needed innovative approaches to tackle TB. The scavenger receptor cysteine-rich molecule CD5 antigen-like (CD5L) has been associated with TB, but whether and how CD5L shapes the immune response during the course of disease remains poorly understood. Here, we show an upregulation of CD5L in circulation and at the site of infection in C57BL/6 Mycobacterium tuberculosis-infected mice. To investigate the role of CD5L in TB, we studied the progression of M. tuberculosis aerosol infection in a recently described genetically engineered mouse model lacking CD5L. Despite the increase of CD5L during infection of wild-type mice, absence of CD5L did not impact bacterial burden, histopathology or survival of infected mice. Absence of CD5L associated with a modest increase in the numbers of CD4+ T cells and the expression of IFN-γ in the lungs of infected mice, with no major effect in overall immune cell dynamics. Collectively, this study confirms CD5L as a potential diagnostic biomarker to TB, showing no discernible impact on the outcome of the infection.
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Affiliation(s)
- Marcos S Cardoso
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ESS, Politécnico do Porto, Porto, Portugal
| | - Rute Gonçalves
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ESS, Politécnico do Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Liliana Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Diogo Silvério
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Érica Téllez
- Innate Immunity Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Tony Paul
- Innate Immunity Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Maria Rosa Sarrias
- Innate Immunity Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Alexandre M Carmo
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Margarida Saraiva
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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8
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Painter H, Larsen SE, Williams BD, Abdelaal HFM, Baldwin SL, Fletcher HA, Fiore-Gartland A, Coler RN. Backtranslation of human RNA biosignatures of tuberculosis disease risk into the preclinical pipeline is condition dependent. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600067. [PMID: 38948876 PMCID: PMC11212953 DOI: 10.1101/2024.06.21.600067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
It is not clear whether human progression to active tuberculosis disease (TB) risk signatures are viable endpoint criteria for evaluations of treatments in clinical or preclinical development. TB is the deadliest infectious disease globally and more efficacious vaccines are needed to reduce this mortality. However, the immune correlates of protection for either preventing infection with Mycobacterium tuberculosis or preventing TB disease have yet to be completely defined, making the advancement of candidate vaccines through the pipeline slow, costly, and fraught with risk. Human-derived correlate of risk (COR) gene signatures, which identify an individual's risk to progressing to active TB disease, provide an opportunity for evaluating new therapies for TB with clear and defined endpoints. Though prospective clinical trials with longitudinal sampling are prohibitively expensive, characterization of COR gene signatures is practical with preclinical models. Using a 3Rs (Replacement, Reduction and Refinement) approach we reanalyzed heterogeneous publicly available transcriptional datasets to determine whether a specific set of COR signatures are viable endpoints in the preclinical pipeline. We selected RISK6, Sweeney3 and BATF2 human-derived blood-based RNA biosignatures because they require relatively few genes to assign a score and have been carefully evaluated across several clinical cohorts. Excitingly, these data provide proof-of-concept that human COR signatures seem to have high fidelity across several tissue types in the preclinical TB model pipeline and show best performance when the model most closely reflected human infection or disease conditions. Human-derived COR signatures offer an opportunity for high-throughput preclinical endpoint criteria of vaccine and drug therapy evaluations. One Sentence Summary Human-derived biosignatures of tuberculosis disease progression were evaluated for their predictive fidelity across preclinical species and derived tissues using available public data sets.
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9
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Cui X, Wang YT. Function of autophagy genes in innate immune defense against mucosal pathogens. Curr Opin Microbiol 2024; 79:102456. [PMID: 38554450 DOI: 10.1016/j.mib.2024.102456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 04/01/2024]
Abstract
Mucosal immunity is posed to constantly interact with commensal microbes and invading pathogens. As a fundamental cell biological pathway affecting immune response, autophagy regulates the interaction between mucosal immunity and microbes through multiple mechanisms, including direct elimination of microbes, control of inflammation, antigen presentation and lymphocyte homeostasis, and secretion of immune mediators. Some of these physiologically important functions do not involve canonical degradative autophagy but rely on certain autophagy genes and their 'autophagy gene-specific functions.' Here, we review the relationship between autophagy and important mucosal pathogens, including influenza virus, Mycobacterium tuberculosis, Salmonella enterica, Citrobacter rodentium, norovirus, and herpes simplex virus, with a particular focus on distinguishing the canonical versus gene-specific mechanisms of autophagy genes.
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Affiliation(s)
- Xiaoyan Cui
- Center for Infectious Disease Research, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ya-Ting Wang
- Center for Infectious Disease Research, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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10
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Truong T, Martin K, Salemi M, Ray A, Phinney BS, Penn BH. The balance between antiviral and antibacterial responses during M. tuberculosis infection is regulated by the ubiquitin ligase CBL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594178. [PMID: 38798543 PMCID: PMC11118416 DOI: 10.1101/2024.05.15.594178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
As a first line of host defense, macrophages must be able to effectively sense and respond to diverse types of pathogens, and while a particular type of immune response may be beneficial in some circumstances, it can be detrimental in others. Upon infecting a macrophage, M. tuberculosis (Mtb) induces proinflammatory cytokines that activate antibacterial responses. Surprisingly, Mtb also triggers antiviral responses that actually hinder the ability of macrophages to control Mtb infection. The ubiquitin ligase CBL suppresses these antiviral responses and shifts macrophages toward a more antibacterial state during Mtb infection, however, the mechanisms by which CBL regulates immune signaling are unknown. We found that CBL controls responses to multiple stimuli and broadly suppresses the expression of antiviral effector genes. We then used mass-spectrometry to investigate potential CBL substrates and identified over 46,000 ubiquitylated peptides in Mtb-infected macrophages, as well as roughly 400 peptides with CBL-dependent ubiquitylation. We then performed genetic interaction analysis of CBL and its putative substrates, and identified the Fas associated factor 2 (FAF2) adapter protein as a key signaling molecule protein downstream of CBL. Together, these analyses identify thousands of new ubiquitin-mediated signaling events during the innate immune response and reveal an important new regulatory hub in this response.
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Affiliation(s)
- Tina Truong
- Department of Internal Medicine, University of California, Davis, Davis, California, United States of America
- Graduate Group in Immunology, University of California, Davis, Davis, California, United States of America
| | - Kelsey Martin
- Department of Internal Medicine, University of California, Davis, Davis, California, United States of America
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, Davis, California, United States of America
| | - Abigail Ray
- Department of Internal Medicine, University of California, Davis, Davis, California, United States of America
- Microbiology Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, Davis, California, United States of America
| | - Bennett H. Penn
- Department of Internal Medicine, University of California, Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, United States of America
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11
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Krause R, Ogongo P, Tezera L, Ahmed M, Mbano I, Chambers M, Ngoepe A, Magnoumba M, Muema D, Karim F, Khan K, Lumamba K, Nargan K, Madansein R, Steyn A, Shalek AK, Elkington P, Leslie A. B cell heterogeneity in human tuberculosis highlights compartment-specific phenotype and functional roles. Commun Biol 2024; 7:584. [PMID: 38755239 PMCID: PMC11099031 DOI: 10.1038/s42003-024-06282-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
B cells are important in tuberculosis (TB) immunity, but their role in the human lung is understudied. Here, we characterize B cells from lung tissue and matched blood of patients with TB and found they are decreased in the blood and increased in the lungs, consistent with recruitment to infected tissue, where they are located in granuloma associated lymphoid tissue. Flow cytometry and transcriptomics identify multiple B cell populations in the lung, including those associated with tissue resident memory, germinal centers, antibody secretion, proinflammatory atypical B cells, and regulatory B cells, some of which are expanded in TB disease. Additionally, TB lungs contain high levels of Mtb-reactive antibodies, specifically IgM, which promotes Mtb phagocytosis. Overall, these data reveal the presence of functionally diverse B cell subsets in the lungs of patients with TB and suggest several potential localized roles that may represent a target for interventions to promote immunity or mitigate immunopathology.
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Affiliation(s)
- Robert Krause
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Paul Ogongo
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Liku Tezera
- National Institute for Health Research Southampton Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mohammed Ahmed
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ian Mbano
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mark Chambers
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Magalli Magnoumba
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel Muema
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Rajhmun Madansein
- Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Adrie Steyn
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for AIDS Research and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alex K Shalek
- Institute for Medical Engineering & Science, Department of Chemistry, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul Elkington
- National Institute for Health Research Southampton Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Al Leslie
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Division of Infection and Immunity, University College London, London, UK.
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12
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Tsareva A, Shelyakin PV, Shagina IA, Myshkin MY, Merzlyak EM, Kriukova VV, Apt AS, Linge IA, Chudakov DM, Britanova OV. Aberrant adaptive immune response underlies genetic susceptibility to tuberculosis. Front Immunol 2024; 15:1380971. [PMID: 38799462 PMCID: PMC11116662 DOI: 10.3389/fimmu.2024.1380971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) remains a major threat worldwide, although only a fraction of infected individuals develops tuberculosis (TB). TB susceptibility is shaped by multiple genetic factors, and we performed comparative immunological analysis of two mouse strains to uncover relevant mechanisms underlying susceptibility and resistance. C57BL/6 mice are relatively TB-resistant, whereas I/St mice are prone to develop severe TB, partly due to the MHC-II allelic variant that shapes suboptimal CD4+ T cell receptor repertoire. We investigated the repertoires of lung-infiltrating helper T cells and B cells at the progressed stage in both strains. We found that lung CD4+ T cell repertoires of infected C57BL/6 but not I/St mice contained convergent TCR clusters with functionally confirmed Mtb specificity. Transcriptomic analysis revealed a more prominent Th1 signature in C57BL/6, and expression of pro-inflammatory IL-16 in I/St lung-infiltrating helper T cells. The two strains also showed distinct Th2 signatures. Furthermore, the humoral response of I/St mice was delayed, less focused, and dominated by IgG/IgM isotypes, whereas C57BL/6 mice generated more Mtb antigen-focused IgA response. We conclude that the inability of I/St mice to produce a timely and efficient anti-Mtb adaptive immune responses arises from a suboptimal helper T cell landscape that also impacts the humoral response, leading to diffuse inflammation and severe disease.
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Affiliation(s)
- Anastasiia Tsareva
- Precision Oncology Division, Boston Gene Laboratory, Waltham, MA, United States
| | - Pavel V. Shelyakin
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
| | - Irina A. Shagina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Mikhail Yu. Myshkin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ekaterina M. Merzlyak
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Valeriia V. Kriukova
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexander S. Apt
- Laboratory for Immunogenetics, Central Tuberculosis Research Institute, Moscow, Russia
| | - Irina A. Linge
- Laboratory for Immunogenetics, Central Tuberculosis Research Institute, Moscow, Russia
| | - Dmitriy M. Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Olga V. Britanova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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13
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Gern BH, Klas JM, Foster KA, Cohen SB, Plumlee CR, Duffy FJ, Neal ML, Halima M, Gustin AT, Diercks AH, Aderem A, Gale M, Aitchison JD, Gerner MY, Urdahl KB. CD4-mediated immunity shapes neutrophil-driven tuberculous pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589315. [PMID: 38659794 PMCID: PMC11042216 DOI: 10.1101/2024.04.12.589315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Pulmonary Mycobacterium tuberculosis (Mtb) infection results in highly heterogeneous lesions ranging from granulomas with central necrosis to those primarily comprised of alveolitis. While alveolitis has been associated with prior immunity in human post-mortem studies, the drivers of these distinct pathologic outcomes are poorly understood. Here, we show that these divergent lesion structures can be modeled in C3HeB/FeJ mice and are regulated by prior immunity. Using quantitative imaging, scRNAseq, and flow cytometry, we demonstrate that Mtb infection in the absence of prior immunity elicits dysregulated neutrophil recruitment and necrotic granulomas. In contrast, prior immunity induces rapid recruitment and activation of T cells, local macrophage activation, and diminished late neutrophil responses. Depletion studies at distinct infection stages demonstrated that neutrophils are required for early necrosis initiation and necrosis propagation at chronic stages, whereas early CD4 T cell responses prevent neutrophil feedforward circuits and necrosis. Together, these studies reveal fundamental determinants of tuberculosis lesion structure and pathogenesis, which have important implications for new strategies to prevent or treat tuberculosis.
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Affiliation(s)
- Benjamin H Gern
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- University of Washington, Dept. of Pediatrics, Seattle, Washington, United States of America
| | - Josepha M Klas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Kimberly A Foster
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- University of Washington, Dept. of Immunology, Seattle, Washington, United States of America
| | - Sara B Cohen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Courtney R Plumlee
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Fergal J Duffy
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Maxwell L Neal
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Mehnaz Halima
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Andrew T Gustin
- University of Washington, Dept. of Immunology, Seattle, Washington, United States of America
| | - Alan H Diercks
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Michael Gale
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- University of Washington, Dept. of Immunology, Seattle, Washington, United States of America
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Michael Y Gerner
- University of Washington, Dept. of Immunology, Seattle, Washington, United States of America
| | - Kevin B Urdahl
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- University of Washington, Dept. of Pediatrics, Seattle, Washington, United States of America
- University of Washington, Dept. of Immunology, Seattle, Washington, United States of America
- Lead Contact
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14
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Feng S, McNehlan ME, Kinsella RL, Sur Chowdhury C, Chavez SM, Naik SK, McKee SR, Van Winkle JA, Dubey N, Samuels A, Swain A, Cui X, Hendrix SV, Woodson R, Kreamalmeyer D, Smirnov A, Artyomov MN, Virgin HW, Wang YT, Stallings CL. Autophagy promotes efficient T cell responses to restrict high-dose Mycobacterium tuberculosis infection in mice. Nat Microbiol 2024; 9:684-697. [PMID: 38413834 DOI: 10.1038/s41564-024-01608-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Although autophagy sequesters Mycobacterium tuberculosis (Mtb) in in vitro cultured macrophages, loss of autophagy in macrophages in vivo does not result in susceptibility to a standard low-dose Mtb infection until late during infection, leaving open questions regarding the protective role of autophagy during Mtb infection. Here we report that loss of autophagy in lung macrophages and dendritic cells results in acute susceptibility of mice to high-dose Mtb infection, a model mimicking active tuberculosis. Rather than observing a role for autophagy in controlling Mtb replication in macrophages, we find that autophagy suppresses macrophage responses to Mtb that otherwise result in accumulation of myeloid-derived suppressor cells and subsequent defects in T cell responses. Our finding that the pathogen-plus-susceptibility gene interaction is dependent on dose has important implications both for understanding how Mtb infections in humans lead to a spectrum of outcomes and for the potential use of autophagy modulators in clinical medicine.
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Affiliation(s)
- Siwei Feng
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Michael E McNehlan
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L Kinsella
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Chanchal Sur Chowdhury
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Sthefany M Chavez
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Sumanta K Naik
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel R McKee
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacob A Van Winkle
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Neha Dubey
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Samuels
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyan Cui
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Skyler V Hendrix
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Reilly Woodson
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Darren Kreamalmeyer
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Asya Smirnov
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ya-Ting Wang
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
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15
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Amaral EP, Namasivayam S, Queiroz ATL, Fukutani E, Hilligan KL, Aberman K, Fisher L, Bomfim CCB, Kauffman K, Buchanan J, Santuo L, Gazzinelli-Guimaraes PH, Costa DL, Teixeira MA, Barreto-Duarte B, Rocha CG, Santana MF, Cordeiro-Santos M, Barber DL, Wilkinson RJ, Kramnik I, Igarashi K, Scriba T, Mayer-Barber KD, Andrade BB, Sher A. BACH1 promotes tissue necrosis and Mycobacterium tuberculosis susceptibility. Nat Microbiol 2024; 9:120-135. [PMID: 38066332 PMCID: PMC10769877 DOI: 10.1038/s41564-023-01523-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 10/11/2023] [Indexed: 01/07/2024]
Abstract
Oxidative stress triggers ferroptosis, a form of cellular necrosis characterized by iron-dependent lipid peroxidation, and has been implicated in Mycobacterium tuberculosis (Mtb) pathogenesis. We investigated whether Bach1, a transcription factor that represses multiple antioxidant genes, regulates host resistance to Mtb. We found that BACH1 expression is associated clinically with active pulmonary tuberculosis. Bach1 deletion in Mtb-infected mice increased glutathione levels and Gpx4 expression that inhibit lipid peroxidation. Bach1-/- macrophages exhibited increased resistance to Mtb-induced cell death, while Mtb-infected Bach1-deficient mice displayed reduced bacterial loads, pulmonary necrosis and lipid peroxidation concurrent with increased survival. Single-cell RNA-seq analysis of lungs from Mtb-infected Bach1-/- mice revealed an enrichment of genes associated with ferroptosis suppression. Bach1 depletion in Mtb-infected B6.Sst1S mice that display human-like necrotic lung pathology also markedly reduced necrosis and increased host resistance. These findings identify Bach1 as a key regulator of cellular and tissue necrosis and host resistance in Mtb infection.
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Affiliation(s)
- Eduardo P Amaral
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA.
| | | | - Artur T L Queiroz
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
| | - Eduardo Fukutani
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
| | - Kerry L Hilligan
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Kate Aberman
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Logan Fisher
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Caio Cesar B Bomfim
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Keith Kauffman
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Jay Buchanan
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Leslie Santuo
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Pedro Henrique Gazzinelli-Guimaraes
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Diego L Costa
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
- Departmento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Mariane Araujo Teixeira
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | - Beatriz Barreto-Duarte
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Curso de Medicina, Universidade Salvador (UNIFACS), Laureate Universities, Salvador, Bahia, Brazil
| | - Clarissa Gurgel Rocha
- Department of Pathology, School of Medicine of the Federal University of Bahia, Salvador, Bahia, Brazil
- Center for Biotechnology and Cell Therapy, D'Or Institute for Research and Education (IDOR), Sao Rafael Hospital, Salvador, Bahia, Brazil
| | - Monique Freire Santana
- Departmento de Ensino e Pesquisa, Fundação Centro de Controle de Oncologia do Estado do Amazonas-FCECON, Manaus, Amazonas, Brazil
- Fundação Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
| | - Marcelo Cordeiro-Santos
- Fundação Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
- Faculdade de Medicina, Universidade Nilton Lins, Manaus, Amazonas, Brazil
| | - Daniel L Barber
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Igor Kramnik
- Boston University School of Medicine, Boston, MA, USA
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Thomas Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Bruno B Andrade
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
- Curso de Medicina, Universidade Salvador (UNIFACS), Laureate Universities, Salvador, Bahia, Brazil
- Department of Pathology, School of Medicine of the Federal University of Bahia, Salvador, Bahia, Brazil
- Curso de Medicina, Escola Bahiana de Medicina e Saúde Pública, Salvador, Bahia, Brazil
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Curso de Medicina, Universidade Faculdade de Tecnologia e Ciências (UniFTC), Salvador, Bahia, Brazil
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA.
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16
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Mishra R, Hannebelle M, Patil VP, Dubois A, Garcia-Mouton C, Kirsch GM, Jan M, Sharma K, Guex N, Sordet-Dessimoz J, Perez-Gil J, Prakash M, Knott GW, Dhar N, McKinney JD, Thacker VV. Mechanopathology of biofilm-like Mycobacterium tuberculosis cords. Cell 2023; 186:5135-5150.e28. [PMID: 37865090 PMCID: PMC10642369 DOI: 10.1016/j.cell.2023.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/23/2023]
Abstract
Mycobacterium tuberculosis (Mtb) cultured axenically without detergent forms biofilm-like cords, a clinical identifier of virulence. In lung-on-chip (LoC) and mouse models, cords in alveolar cells contribute to suppression of innate immune signaling via nuclear compression. Thereafter, extracellular cords cause contact-dependent phagocyte death but grow intercellularly between epithelial cells. The absence of these mechanopathological mechanisms explains the greater proportion of alveolar lesions with increased immune infiltration and dissemination defects in cording-deficient Mtb infections. Compression of Mtb lipid monolayers induces a phase transition that enables mechanical energy storage. Agent-based simulations demonstrate that the increased energy storage capacity is sufficient for the formation of cords that maintain structural integrity despite mechanical perturbation. Bacteria in cords remain translationally active despite antibiotic exposure and regrow rapidly upon cessation of treatment. This study provides a conceptual framework for the biophysics and function in tuberculosis infection and therapy of cord architectures independent of mechanisms ascribed to single bacteria.
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Affiliation(s)
- Richa Mishra
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Melanie Hannebelle
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Vishal P Patil
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Anaëlle Dubois
- BioElectron Microscopy Facility, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Gabriela M Kirsch
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Maxime Jan
- Bioinformatics Competence Centre, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Centre, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Kunal Sharma
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Centre, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Centre, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jessica Sordet-Dessimoz
- Histology Core Facility, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jesus Perez-Gil
- Department of Biochemistry, University Complutense Madrid, 28040 Madrid, Spain
| | - Manu Prakash
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Graham W Knott
- BioElectron Microscopy Facility, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Neeraj Dhar
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - John D McKinney
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Vivek V Thacker
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
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17
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Yamamoto K, Tsujimura Y, Ato M. Catheter-associated Mycobacterium intracellulare biofilm infection in C3HeB/FeJ mice. Sci Rep 2023; 13:17148. [PMID: 37816786 PMCID: PMC10564925 DOI: 10.1038/s41598-023-44403-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/07/2023] [Indexed: 10/12/2023] Open
Abstract
Non-tuberculosis mycobacterial (NTM) diseases are steadily increasing in prevalence and mortality worldwide. Mycobacterium avium and M. intracellulare, the two major pathogens of NTM diseases, are resistant to antibiotics, and chlorine, necessitating their capacity to survive in natural environments (e.g. soil and rivers) and disinfected municipal water. They can also form biofilms on artificial surfaces to provide a protective barrier and habitat for bacilli, which can cause refractory systemic disseminated NTM disease. Therefore, preventing biofilm formation by these pathogens is crucial; however, not many in vivo experimental systems and studies on NTM biofilm infection are available. This study develops a mouse model of catheter-associated systemic disseminated disease caused by M. intracellulare that reproduces the pathophysiology of catheter-associated infections observed in patients undergoing peritoneal dialysis. In addition, the bioluminescence system enabled noninvasive visualization of the amount and distribution of bacilli in vivo and conveniently examine the efficacy of antimicrobials. Furthermore, the cellulose-based biofilms, which were extensively formed in the tissue surrounding the catheter insertion site, reduced drug therapy effectiveness. Overall, this study provides insights into the cause of the drug resistance of NTM and may guide the development of new therapies for NTM diseases.
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Affiliation(s)
- Kentaro Yamamoto
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Aoba-cho, Higashimurayama, Tokyo, Japan.
| | - Yusuke Tsujimura
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Aoba-cho, Higashimurayama, Tokyo, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Aoba-cho, Higashimurayama, Tokyo, Japan
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18
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Mayer-Barber KD. Granulocytes subsets and their divergent functions in host resistance to Mycobacterium tuberculosis - a 'tipping-point' model of disease exacerbation. Curr Opin Immunol 2023; 84:102365. [PMID: 37437471 PMCID: PMC10543468 DOI: 10.1016/j.coi.2023.102365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/29/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Granulocytes are innate immune effector cells with essential functions in host resistance to bacterial infections. I will discuss emerging evidence that during Mycobacterium tuberculosis infection, counter-intuitively, eosinophils are host-protective while neutrophils are host detrimental. Additionally, I will propose a 'tipping-point' model in which neutrophils are an integral part of a feedforward loop driving tuberculosis disease exacerbation.
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Affiliation(s)
- Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, 20892, USA.
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19
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Bloom BR. A half-century of research on tuberculosis: Successes and challenges. J Exp Med 2023; 220:e20230859. [PMID: 37552470 PMCID: PMC10407785 DOI: 10.1084/jem.20230859] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/09/2023] Open
Abstract
Great progress has been made over the past half-century, but TB remains a formidable global health problem, particularly in low- and middle-income countries. Understanding the mechanisms of pathogenesis and necessary and sufficient conditions for protection are critical. The need for inexpensive and sensitive point-of-care diagnostic tests for earlier detection of infection and disease, shorter and less-toxic drug regimens for drug-sensitive and -resistant TB, and a more effective vaccine than BCG is immense. New and better tools, greater support for international research, collaborations, and training will be required to dramatically reduce the burden of this devastating disease which still kills 1.6 million people annually.
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Affiliation(s)
- Barry R. Bloom
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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20
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Meade RK, Long JE, Jinich A, Rhee KY, Ashbrook DG, Williams RW, Sassetti CM, Smith CM. Genome-wide screen identifies host loci that modulate Mycobacterium tuberculosis fitness in immunodivergent mice. G3 (BETHESDA, MD.) 2023; 13:jkad147. [PMID: 37405387 PMCID: PMC10468300 DOI: 10.1093/g3journal/jkad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/05/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023]
Abstract
Genetic differences among mammalian hosts and among strains of Mycobacterium tuberculosis (Mtb) are well-established determinants of tuberculosis (TB) patient outcomes. The advent of recombinant inbred mouse panels and next-generation transposon mutagenesis and sequencing approaches has enabled dissection of complex host-pathogen interactions. To identify host and pathogen genetic determinants of Mtb pathogenesis, we infected members of the highly diverse BXD family of strains with a comprehensive library of Mtb transposon mutants (TnSeq). Members of the BXD family segregate for Mtb-resistant C57BL/6J (B6 or B) and Mtb-susceptible DBA/2J (D2 or D) haplotypes. The survival of each bacterial mutant was quantified within each BXD host, and we identified those bacterial genes that were differentially required for Mtb fitness across BXD genotypes. Mutants that varied in survival among the host family of strains were leveraged as reporters of "endophenotypes," each bacterial fitness profile directly probing specific components of the infection microenvironment. We conducted quantitative trait loci (QTL) mapping of these bacterial fitness endophenotypes and identified 140 host-pathogen QTL (hpQTL). We located a QTL hotspot on chromosome 6 (75.97-88.58 Mb) associated with the genetic requirement of multiple Mtb genes: Rv0127 (mak), Rv0359 (rip2), Rv0955 (perM), and Rv3849 (espR). Together, this screen reinforces the utility of bacterial mutant libraries as precise reporters of the host immunological microenvironment during infection and highlights specific host-pathogen genetic interactions for further investigation. To enable downstream follow-up for both bacterial and mammalian genetic research communities, all bacterial fitness profiles have been deposited into GeneNetwork.org and added into the comprehensive collection of TnSeq libraries in MtbTnDB.
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Affiliation(s)
- Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Jarukit E Long
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01655, USA
- Research Animal Diagnostic Services, Charles River Laboratories, Wilmington, MA 01887, USA
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10021, USA
| | - David G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
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21
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Bobak CA, Botha M, Workman L, Hill JE, Nicol MP, Holloway JW, Stein DJ, Martinez L, Zar HJ. Gene Expression in Cord Blood and Tuberculosis in Early Childhood: A Nested Case-Control Study in a South African Birth Cohort. Clin Infect Dis 2023; 77:438-449. [PMID: 37144357 PMCID: PMC10425199 DOI: 10.1093/cid/ciad268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 04/29/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Transcriptomic profiling of adults with tuberculosis (TB) has become increasingly common, predominantly for diagnostic and risk prediction purposes. However, few studies have evaluated signatures in children, particularly in identifying those at risk for developing TB disease. We investigated the relationship between gene expression obtained from umbilical cord blood and both tuberculin skin test conversion and incident TB disease through the first 5 years of life. METHODS We conducted a nested case-control study in the Drakenstein Child Health Study, a longitudinal, population-based birth cohort in South Africa. We applied transcriptome-wide screens to umbilical cord blood samples from neonates born to a subset of selected mothers (N = 131). Signatures identifying tuberculin conversion and risk of subsequent TB disease were identified from genome-wide analysis of RNA expression. RESULTS Gene expression signatures revealed clear differences predictive of tuberculin conversion (n = 26) and TB disease (n = 10); 114 genes were associated with tuberculin conversion and 30 genes were associated with the progression to TB disease among children with early infection. Coexpression network analysis revealed 6 modules associated with risk of TB infection or disease, including a module associated with neutrophil activation in immune response (P < .0001) and defense response to bacterium (P < .0001). CONCLUSIONS These findings suggest multiple detectable differences in gene expression at birth that were associated with risk of TB infection or disease throughout early childhood. Such measures may provide novel insights into TB pathogenesis and susceptibility.
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Affiliation(s)
- Carly A Bobak
- Department of Biomedical Data Science, Dartmouth College, Hanover, New Hampshire
| | - Maresa Botha
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
| | - Jane E Hill
- School of Biomedical Engineering and the School of Chemical and Biological Engineering, University of British Columbia, Vancouver, Canada
| | - Mark P Nicol
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Division of Medical Microbiology, University of Cape Town, South Africa
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton
- National Institute for Health and Care Research Southampton Biomedical Research Center, University Hospital Southampton, United Kingdom
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town
- Unit on Risk and Resilience in Mental Disorders, South African Medical Research Council
- Neuroscience Institute, University of Cape Town, South Africa
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Massachusetts
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
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22
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Corleis B, Bastian M, Hoffmann D, Beer M, Dorhoi A. Animal models for COVID-19 and tuberculosis. Front Immunol 2023; 14:1223260. [PMID: 37638020 PMCID: PMC10451089 DOI: 10.3389/fimmu.2023.1223260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Respiratory infections cause tremendous morbidity and mortality worldwide. Amongst these diseases, tuberculosis (TB), a bacterial illness caused by Mycobacterium tuberculosis which often affects the lung, and coronavirus disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), stand out as major drivers of epidemics of global concern. Despite their unrelated etiology and distinct pathology, these infections affect the same vital organ and share immunopathogenesis traits and an imperative demand to model the diseases at their various progression stages and localizations. Due to the clinical spectrum and heterogeneity of both diseases experimental infections were pursued in a variety of animal models. We summarize mammalian models employed in TB and COVID-19 experimental investigations, highlighting the diversity of rodent models and species peculiarities for each infection. We discuss the utility of non-human primates for translational research and emphasize on the benefits of non-conventional experimental models such as livestock. We epitomize advances facilitated by animal models with regard to understanding disease pathophysiology and immune responses. Finally, we highlight research areas necessitating optimized models and advocate that research of pulmonary infectious diseases could benefit from cross-fertilization between studies of apparently unrelated diseases, such as TB and COVID-19.
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Affiliation(s)
- Björn Corleis
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Max Bastian
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Anca Dorhoi
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Faculty of Mathematics and Natural Sciences, University of Greifswald, Greifswald, Germany
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23
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Kurtz SL, Rydén P, Elkins KL. Transcriptional signatures measured in whole blood correlate with protection against tuberculosis in inbred and outbred mice. PLoS One 2023; 18:e0289358. [PMID: 37535648 PMCID: PMC10399789 DOI: 10.1371/journal.pone.0289358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Abstract
Although BCG has been used for almost 100 years to immunize against Mycobacterium tuberculosis, TB remains a global public health threat. Numerous clinical trials are underway studying novel vaccine candidates and strategies to improve or replace BCG, but vaccine development still lacks a well-defined set of immune correlates to predict vaccine-induced protection against tuberculosis. This study aimed to address this gap by examining transcriptional responses to BCG vaccination in C57BL/6 inbred mice, coupled with protection studies using Diversity Outbred mice. We evaluated relative gene expression in blood obtained from vaccinated mice, because blood is easily accessible, and data can be translated to human studies. We first determined that the average peak time after vaccination is 14 days for gene expression of a small subset of immune-related genes in inbred mice. We then performed global transcriptomic analyses using whole blood samples obtained two weeks after mice were vaccinated with BCG. Using comparative bioinformatic analyses and qRT-PCR validation, we developed a working correlate panel of 18 genes that were highly correlated with administration of BCG but not heat-killed BCG. We then tested this gene panel using BCG-vaccinated Diversity Outbred mice and revealed associations between the expression of a subset of genes and disease outcomes after aerosol challenge with M. tuberculosis. These data therefore demonstrate that blood-based transcriptional immune correlates measured within a few weeks after vaccination can be derived to predict protection against M. tuberculosis, even in outbred populations.
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Affiliation(s)
- Sherry L Kurtz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
| | - Karen L Elkins
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
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24
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Kinsella RL, Kimmey JM, Smirnov A, Woodson R, Gaggioli MR, Chavez SM, Kreamalmeyer D, Stallings CL. Autophagy prevents early proinflammatory responses and neutrophil recruitment during Mycobacterium tuberculosis infection without affecting pathogen burden in macrophages. PLoS Biol 2023; 21:e3002159. [PMID: 37319285 DOI: 10.1371/journal.pbio.3002159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023] Open
Abstract
The immune response to Mycobacterium tuberculosis infection determines tuberculosis disease outcomes, yet we have an incomplete understanding of what immune factors contribute to a protective immune response. Neutrophilic inflammation has been associated with poor disease prognosis in humans and in animal models during M. tuberculosis infection and, therefore, must be tightly regulated. ATG5 is an essential autophagy protein that is required in innate immune cells to control neutrophil-dominated inflammation and promote survival during M. tuberculosis infection; however, the mechanistic basis for how ATG5 regulates neutrophil recruitment is unknown. To interrogate what innate immune cells require ATG5 to control neutrophil recruitment during M. tuberculosis infection, we used different mouse strains that conditionally delete Atg5 in specific cell types. We found that ATG5 is required in CD11c+ cells (lung macrophages and dendritic cells) to control the production of proinflammatory cytokines and chemokines during M. tuberculosis infection, which would otherwise promote neutrophil recruitment. This role for ATG5 is autophagy dependent, but independent of mitophagy, LC3-associated phagocytosis, and inflammasome activation, which are the most well-characterized ways that autophagy proteins regulate inflammation. In addition to the increased proinflammatory cytokine production from macrophages during M. tuberculosis infection, loss of ATG5 in innate immune cells also results in an early induction of TH17 responses. Despite prior published in vitro cell culture experiments supporting a role for autophagy in controlling M. tuberculosis replication in macrophages, the effects of autophagy on inflammatory responses occur without changes in M. tuberculosis burden in macrophages. These findings reveal new roles for autophagy proteins in lung resident macrophages and dendritic cells that are required to suppress inflammatory responses that are associated with poor control of M. tuberculosis infection.
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Affiliation(s)
- Rachel L Kinsella
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jacqueline M Kimmey
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Asya Smirnov
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Reilly Woodson
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Margaret R Gaggioli
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sthefany M Chavez
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Darren Kreamalmeyer
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
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25
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Thirunavukkarasu S, Ahmed M, Rosa BA, Boothby M, Cho SH, Rangel-Moreno J, Mbandi SK, Schreiber V, Gupta A, Zuniga J, Mitreva M, Kaushal D, Scriba TJ, Khader SA. Poly(ADP-ribose) polymerase 9 mediates early protection against Mycobacterium tuberculosis infection by regulating type I IFN production. J Clin Invest 2023; 133:e158630. [PMID: 37200107 PMCID: PMC10266794 DOI: 10.1172/jci158630] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/19/2023] [Indexed: 05/20/2023] Open
Abstract
The ADP ribosyltransferases (PARPs 1-17) regulate diverse cellular processes, including DNA damage repair. PARPs are classified on the basis of their ability to catalyze poly-ADP-ribosylation (PARylation) or mono-ADP-ribosylation (MARylation). Although PARP9 mRNA expression is significantly increased in progressive tuberculosis (TB) in humans, its participation in host immunity to TB is unknown. Here, we show that PARP9 mRNA encoding the MARylating PARP9 enzyme was upregulated during TB in humans and mice and provide evidence of a critical modulatory role for PARP9 in DNA damage, cyclic GMP-AMP synthase (cGAS) expression, and type I IFN production during TB. Thus, Parp9-deficient mice were susceptible to Mycobacterium tuberculosis infection and exhibited increased TB disease, cGAS and 2'3'-cyclic GMP-AMP (cGAMP) expression, and type I IFN production, along with upregulation of complement and coagulation pathways. Enhanced M. tuberculosis susceptibility is type I IFN dependent, as blockade of IFN α receptor (IFNAR) signaling reversed the enhanced susceptibility of Parp9-/- mice. Thus, in sharp contrast to PARP9 enhancement of type I IFN production in viral infections, this member of the MAR family plays a protective role by limiting type I IFN responses during TB.
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Affiliation(s)
| | | | - Bruce A. Rosa
- McDonnell Genome Institute, and
- Division of Infectious Diseases, Department of Internal Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Mark Boothby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sung Hoon Cho
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Javier Rangel-Moreno
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Stanley K. Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Valérie Schreiber
- Biotechnology and Cell Signaling, CNRS UMR7242, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | | | - Joaquin Zuniga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Makedonka Mitreva
- McDonnell Genome Institute, and
- Division of Infectious Diseases, Department of Internal Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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26
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Maceiras AR, Silvério D, Gonçalves R, Cardoso MS, Saraiva M. Infection with hypervirulent Mycobacterium tuberculosis triggers emergency myelopoiesis but not trained immunity. Front Immunol 2023; 14:1211404. [PMID: 37383236 PMCID: PMC10296772 DOI: 10.3389/fimmu.2023.1211404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/30/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction During infection, bone marrow (BM) hematopoiesis is reprogrammed toward myeloid cell production, a mechanism named emergency myelopoiesis. In addition to replenishing myeloid cells, emergency myelopoiesis has been linked to trained immunity, a process that allows enhanced innate immune responses to secondary challenges. Although hematopoietic alterations during tuberculosis (TB) have been described and Mycobacterium tuberculosis may colonize the BM, studies using the mouse model of infection and the laboratory reference strain M. tuberculosis H37Rv have demonstrated limited emergency myelopoiesis and trained immunity. Methods To further address this issue, we aerosol- infected C57BL/6 mice with high doses of the hypervirulent M. tuberculosis isolate HN878 and monitored alterations to the BM. This experimental model better resembles the human blood immune signature of TB. Results and discussion We found increased frequencies of lineage-Sca-1+cKit+ (LSK) cells and the granulocyte/macrophage progenitor (GMP) population. At the mature cell level, we observed an increase of monocytes and neutrophils in the blood and lung, likely reflecting the increased BM myeloid output. Monocytes or monocyte-derived macrophages recovered from the BM of M. tuberculosis HN878-infected mice did not show signs of trained immunity, suggesting an uncoupling of emergency myelopoiesis and trained immunity in the BM. Surprisingly, M. tuberculosis HN878-induced emergency myelopoiesis was not fully dependent on IFNγ, as mice lacking this cytokine and infected under the same conditions as wild-type mice still presented BM alterations. These data expand our understanding of the immune response to M. tuberculosis and raise awareness of pathogen strain-imposed differences to host responses.
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Affiliation(s)
- Ana Raquel Maceiras
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Diogo Silvério
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Rute Gonçalves
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Marcos S. Cardoso
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Margarida Saraiva
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
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27
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Sadee W, Cheeseman IH, Papp A, Pietrzak M, Seweryn M, Zhou X, Lin S, Williams AM, Wewers MD, Curry HM, Zhang H, Cai H, Kunsevi-Kilola C, Tshivhula H, Walzl G, Restrepo BI, Kleynhans L, Ronacher K, Wang Y, Arnett E, Azad AK, Schlesinger LS. Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability. RESEARCH SQUARE 2023:rs.3.rs-2986649. [PMID: 37333188 PMCID: PMC10275041 DOI: 10.21203/rs.3.rs-2986649/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Mycobacterium tuberculosis (M.tb), the causative bacterium of tuberculosis (TB), establishes residence and grows in human alveolar macrophages (AMs). Inter-individual variation in M.tb-human AM interactions can indicate TB risk and the efficacy of therapies and vaccines; however, we currently lack an understanding of the gene and protein expression programs that dictate this variation in the lungs. Results Herein, we systematically analyze interactions of a virulent M.tb strain H37Rv with freshly isolated human AMs from 28 healthy adult donors, measuring host RNA expression and secreted candidate proteins associated with TB pathogenesis over 72h. A large set of genes possessing highly variable inter-individual expression levels are differentially expressed in response to M.tb infection. Eigengene modules link M.tb growth rate with host transcriptional and protein profiles at 24 and 72h. Systems analysis of differential RNA and protein expression identifies a robust network with IL1B, STAT1, and IDO1 as hub genes associated with M.tb growth. RNA time profiles document stimulation towards an M1-type macrophage gene expression followed by emergence of an M2-type profile. Finally, we replicate these results in a cohort from a TB-endemic region, finding a substantial portion of significant differentially expressed genes overlapping between studies. Conclusions We observe large inter-individual differences in bacterial uptake and growth, with tenfold variation in M.tb load by 72h.The fine-scale resolution of this work enables the identification of genes and gene networks associated with early M.tb growth dynamics in defined donor clusters, an important step in developing potential biological indicators of individual susceptibility to M.tb infection and response to therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Hong Cai
- University of Texas at San Antonio
| | | | | | | | - Blanca I Restrepo
- University of Texas Rio Grande Valley, South Texas Diabetes and Obesity Institute
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Yu F, Teng Y, Li J, Yang S, Zhang Z, He Y, Yang H, Ding CF, Zhou P. Effects of a Ganoderma lucidum Proteoglycan on Type 2 Diabetic Rats and the Recovery of Rat Pancreatic Islets. ACS OMEGA 2023; 8:17304-17316. [PMID: 37214729 PMCID: PMC10193549 DOI: 10.1021/acsomega.3c02200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023]
Abstract
Type 2 diabetes (T2D) results from both insulin resistance and pancreatic β-cell dysfunction. A natural proteoglycan extracted from Ganoderma lucidum, namely, FYGL, has been demonstrated to be capable of ameliorating insulin resistance in previous work. In this work, a T2D rat model induced by streptozocin (STZ) and a high-fat diet was used to investigate the effects of FYGL on pancreatic functions, and the transcriptomics of the rat pancreas was used to investigate the biological processes (BP) and signal pathways influenced by FYGL on the gene basis. Furthermore, the results of transcriptomics were verified both by histopathological analyses and protein expression. The studies showed that FYGL positively regulated T2D-related BP and signaling pathways and recovered the pancreatic function, therefore ameliorating hyperglycemia and hyperlipidemia in vivo. Importantly, the recovery of the pancreatic function suggested a crucial strategy to radically treat T2D.
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Affiliation(s)
- Fanzhen Yu
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Yilong Teng
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Jiaqi Li
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Shutong Yang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Zeng Zhang
- Yueyang
Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, P. R. China
| | - Yanming He
- Yueyang
Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, P. R. China
| | - Hongjie Yang
- Yueyang
Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, P. R. China
| | - Chuan-Fan Ding
- Zhejiang
Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular
Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Ping Zhou
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
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29
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Wang N, Liang Y, Ma Q, Mi J, Xue Y, Yang Y, Wang L, Wu X. Mechanisms of ag85a/b DNA vaccine conferred immunotherapy and recovery from Mycobacterium tuberculosis-induced injury. Immun Inflamm Dis 2023; 11:e854. [PMID: 37249284 DOI: 10.1002/iid3.854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Our previous research developed a novel tuberculosis (TB) DNA vaccine ag85a/b that showed a significant therapeutic effect on the mouse tuberculosis model by intramuscular injection (IM) and electroporation (EP). However, the action mechanisms between these two vaccine immunization methods remain unclear. In a previous study, 96 Mycobacterium tuberculosis (MTB) H37 Rv-infected BALB/c mice were treated with phosphate-buffered saline, 10, 50, 100, and 200 μg ag85a/b DNA vaccine delivered by IM and EP three times at 2-week intervals, respectively. In this study, peripheral blood mononuclear cells (PBMCs) from three mice in each group were isolated to extract total RNA. The gene expression profiles were analyzed using gene microarray technology to obtain differentially expressed (DE) genes. Finally, DE genes were validated by real-time reverse transcription-quantitive polymerase chain reaction and the GEO database. After MTB infection, most of the upregulated DE genes were related to the digestion and absorption of nutrients or neuroendocrine (such as Iapp, Scg2, Chga, Amy2a5), and most of the downregulated DE genes were related to cellular structural and functional proteins, especially the structure and function proteins of the alveolar epithelial cell (such as Sftpc, Sftpd, Pdpn). Most of the abnormally upregulated or downregulated DE genes in the TB model group were recovered in the 100 and 200 μg ag85a/b DNA IM groups and four DNA EP groups. The pancreatic secretion pathway downregulated and the Rap1 signal pathway upregulated had particularly significant changes during the immunotherapy of the ag85a/b DNA vaccine on the mouse TB model. The action targets and mechanisms of IM and EP are highly consistent. Tuberculosis infection causes rapid catabolism and slow anabolism in mice. For the first time, we found that the effective dose of the ag85a/b DNA vaccine immunized whether by IM or EP could significantly up-regulate immune-related pathways and recover the metabolic disorder and the injury caused by MTB.
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Affiliation(s)
- Nan Wang
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, PLA General Hospital, Beijing, China
| | - Yan Liang
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, PLA General Hospital, Beijing, China
| | - Qianqian Ma
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, PLA General Hospital, Beijing, China
| | - Jie Mi
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, PLA General Hospital, Beijing, China
| | - Yong Xue
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, PLA General Hospital, Beijing, China
| | - Yourong Yang
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, PLA General Hospital, Beijing, China
| | - Lan Wang
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, PLA General Hospital, Beijing, China
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, PLA General Hospital, Beijing, China
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30
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Wei ZY, Wang ZX, Li JH, Wen YS, Gao D, Xia SY, Li YN, Pan XB, Liu YS, Jin YY, Chen JH. Host A-to-I RNA editing signatures in intracellular bacterial and single-strand RNA viral infections. Front Immunol 2023; 14:1121096. [PMID: 37081881 PMCID: PMC10112020 DOI: 10.3389/fimmu.2023.1121096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
BackgroundMicrobial infection is accompanied by remodeling of the host transcriptome. Involvement of A-to-I RNA editing has been reported during viral infection but remains to be elucidated during intracellular bacterial infections.ResultsHerein we analyzed A-to-I RNA editing during intracellular bacterial infections based on 18 RNA-Seq datasets of 210 mouse samples involving 7 tissue types and 8 intracellular bacterial pathogens (IBPs), and identified a consensus signature of RNA editing for IBP infections, mainly involving neutrophil-mediated innate immunity and lipid metabolism. Further comparison of host RNA editing patterns revealed remarkable similarities between pneumonia caused by IBPs and single-strand RNA (ssRNA) viruses, such as altered editing enzyme expression, editing site numbers, and levels. In addition, functional enrichment analysis of genes with RNA editing highlighted that the Rab GTPase family played a common and vital role in the host immune response to IBP and ssRNA viral infections, which was indicated by the consistent up-regulated RNA editing of Ras-related protein Rab27a. Nevertheless, dramatic differences between IBP and viral infections were also observed, and clearly distinguished the two types of intracellular infections.ConclusionOur study showed transcriptome-wide host A-to-I RNA editing alteration during IBP and ssRNA viral infections. By identifying and comparing consensus signatures of host A-to-I RNA editing, our analysis implicates the importance of host A-to-I RNA editing during these infections and provides new insights into the diagnosis and treatment of infectious diseases.
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Affiliation(s)
- Zhi-Yuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Zhi-Xin Wang
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Jia-Huan Li
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yan-Shuo Wen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Di Gao
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Shou-Yue Xia
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yu-Ning Li
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Xu-Bin Pan
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Wuxi Children’s Hospital, Wuxi, Jiangsu, China
| | - Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- *Correspondence: Jian-Huan Chen, ; Yun-Yun Jin,
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- *Correspondence: Jian-Huan Chen, ; Yun-Yun Jin,
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31
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Meade RK, Long JE, Jinich A, Rhee KY, Ashbrook DG, Williams RW, Sassetti CM, Smith CM. Genome-wide screen identifies host loci that modulate M. tuberculosis fitness in immunodivergent mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.528534. [PMID: 36945430 PMCID: PMC10028809 DOI: 10.1101/2023.03.05.528534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Genetic differences among mammalian hosts and Mycobacterium tuberculosis ( Mtb ) strains determine diverse tuberculosis (TB) patient outcomes. The advent of recombinant inbred mouse panels and next-generation transposon mutagenesis and sequencing approaches has enabled dissection of complex host- pathogen interactions. To identify host and pathogen genetic determinants of Mtb pathogenesis, we infected members of the BXD family of mouse strains with a comprehensive library of Mtb transposon mutants (TnSeq). Members of the BXD family segregate for Mtb -resistant C57BL/6J (B6 or B ) and Mtb -susceptible DBA/2J (D2 or D ) haplotypes. The survival of each bacterial mutant was quantified within each BXD host, and we identified those bacterial genes that were differentially required for Mtb fitness across BXD genotypes. Mutants that varied in survival among the host family of strains were leveraged as reporters for "endophenotypes", each bacterial fitness profile directly probing specific components of the infection microenvironment. We conducted QTL mapping of these bacterial fitness endophenotypes and identified 140 h ost- p athogen quantitative trait loci ( hp QTL). We identified a QTL hotspot on chromosome 6 (75.97-88.58 Mb) associated with the genetic requirement of multiple Mtb genes; Rv0127 ( mak ), Rv0359 ( rip2 ), Rv0955 ( perM ), and Rv3849 ( espR ). Together, this screen reinforces the utility of bacterial mutant libraries as precise reporters of the host immunological microenvironment during infection and highlights specific host-pathogen genetic interactions for further investigation. To enable downstream follow-up for both bacterial and mammalian genetic research communities, all bacterial fitness profiles have been deposited into GeneNetwork.org and added into the comprehensive collection of TnSeq libraries in MtbTnDB.
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Affiliation(s)
- Rachel K. Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Jarukit E. Long
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Charles River Laboratories, Research Animal Diagnostic Services, Wilmington, MA, USA
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Cornell Medical College, NY, USA
| | - Kyu Y. Rhee
- Division of Infectious Diseases, Weill Cornell Medical College, NY, USA
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
| | - Clare M. Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
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32
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Wallis RS, O'Garra A, Sher A, Wack A. Host-directed immunotherapy of viral and bacterial infections: past, present and future. Nat Rev Immunol 2023; 23:121-133. [PMID: 35672482 PMCID: PMC9171745 DOI: 10.1038/s41577-022-00734-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 02/06/2023]
Abstract
The advent of COVID-19 and the persistent threat of infectious diseases such as tuberculosis, malaria, influenza and HIV/AIDS remind us of the marked impact that infections continue to have on public health. Some of the most effective protective measures are vaccines but these have been difficult to develop for some of these infectious diseases even after decades of research. The development of drugs and immunotherapies acting directly against the pathogen can be equally challenging, and such pathogen-directed therapeutics have the potential disadvantage of selecting for resistance. An alternative approach is provided by host-directed therapies, which interfere with host cellular processes required for pathogen survival or replication, or target the host immune response to infection (immunotherapies) to either augment immunity or ameliorate immunopathology. Here, we provide a historical perspective of host-directed immunotherapeutic interventions for viral and bacterial infections and then focus on SARS-CoV-2 and Mycobacterium tuberculosis, two major human pathogens of the current era, to indicate the key lessons learned and discuss candidate immunotherapeutic approaches, with a focus on drugs currently in clinical trials.
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Affiliation(s)
- Robert S Wallis
- The Aurum Institute, Johannesburg, South Africa.
- Vanderbilt University, Nashville, TN, USA.
- Rutgers University, Newark, NJ, USA.
- Case Western Reserve University, Cleveland, OH, USA.
| | - Anne O'Garra
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, London, UK.
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33
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Prolonged B-Lymphocyte-Mediated Immune and Inflammatory Responses to Tuberculosis Infection in the Lungs of TB-Resistant Mice. Int J Mol Sci 2023; 24:ijms24021140. [PMID: 36674664 PMCID: PMC9861759 DOI: 10.3390/ijms24021140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/25/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
During tuberculosis (TB) infection, B-lymphocytes migrate to the lungs and form B-cell follicles (BCFs) in the vicinity of TB granulomata. B-cell-lacking mice display enhanced susceptibility to TB infection, and early B-cell depletion in infected non-human primates alters T-lymphocyte cytokine responses and increases bacterial burdens in the lungs. However, the role of B cells during late TB stages remained unaddressed. Here, we demonstrate that B cells and BCFs persist up to weeks 25-45 post-challenge in the lungs of TB-resistant C57BL/6 (B6) mice. In hyper-susceptible I/St mice, B-cell content markedly drops between weeks 12-16 post-infection, paralleled by diffuse lung tissue inflammation and elevated gene expression levels for pro-inflammatory cytokines IL-1, IL-11, IL-17a, and TNF-α. To check whether B-cells/BCFs control TB infection at advanced stages, we specifically depleted B-cells from B6 mice by administrating anti-CD20 mAbs at week 16 post-infection. This resulted in more rapid cachexia, a shortened lifespan of the infected animals, an increase in (i) lung-infiltrating CD8+ T cells, (ii) IL-6 production by F4/80+ macrophages, (iii) expression levels of genes for neutrophil-attracting factors CXCL1 and IL-17, and tissue-damaging factors MMP8, MMP9, and S100A8. Taken together, our results suggest that lung B cells and BCFs are moderately protective against chronic TB infection.
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34
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Immune cell interactions in tuberculosis. Cell 2022; 185:4682-4702. [PMID: 36493751 DOI: 10.1016/j.cell.2022.10.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
Abstract
Despite having been identified as the organism that causes tuberculosis in 1882, Mycobacterium tuberculosis has managed to still evade our understanding of the protective immune response against it, defying the development of an effective vaccine. Technology and novel experimental models have revealed much new knowledge, particularly with respect to the heterogeneity of the bacillus and the host response. This review focuses on certain immunological elements that have recently yielded exciting data and highlights the importance of taking a holistic approach to understanding the interaction of M. tuberculosis with the many host cells that contribute to the development of protective immunity.
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35
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Amaral EP, Foreman TW, Namasivayam S, Hilligan KL, Kauffman KD, Barbosa Bomfim CC, Costa DL, Barreto-Duarte B, Gurgel-Rocha C, Santana MF, Cordeiro-Santos M, Du Bruyn E, Riou C, Aberman K, Wilkinson RJ, Barber DL, Mayer-Barber KD, Andrade BB, Sher A. GPX4 regulates cellular necrosis and host resistance in Mycobacterium tuberculosis infection. J Exp Med 2022; 219:e20220504. [PMID: 36069923 PMCID: PMC9458471 DOI: 10.1084/jem.20220504] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/23/2022] [Accepted: 08/11/2022] [Indexed: 01/15/2023] Open
Abstract
Cellular necrosis during Mycobacterium tuberculosis (Mtb) infection promotes both immunopathology and bacterial dissemination. Glutathione peroxidase-4 (Gpx4) is an enzyme that plays a critical role in preventing iron-dependent lipid peroxidation-mediated cell death (ferroptosis), a process previously implicated in the necrotic pathology seen in Mtb-infected mice. Here, we document altered GPX4 expression, glutathione levels, and lipid peroxidation in patients with active tuberculosis and assess the role of this pathway in mice genetically deficient in or overexpressing Gpx4. We found that Gpx4-deficient mice infected with Mtb display substantially increased lung necrosis and bacterial burdens, while transgenic mice overexpressing the enzyme show decreased bacterial loads and necrosis. Moreover, Gpx4-deficient macrophages exhibited enhanced necrosis upon Mtb infection in vitro, an outcome suppressed by the lipid peroxidation inhibitor, ferrostatin-1. These findings provide support for the role of ferroptosis in Mtb-induced necrosis and implicate the Gpx4/GSH axis as a target for host-directed therapy of tuberculosis.
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Affiliation(s)
- Eduardo P. Amaral
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Taylor W. Foreman
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Sivaranjani Namasivayam
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Kerry L. Hilligan
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Keith D. Kauffman
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Caio Cesar Barbosa Bomfim
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Diego L. Costa
- Departmento de Bioquímica e Imunologia, Programa de Pós-Graduação em Imunologia Básica e Aplicada, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Beatriz Barreto-Duarte
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Salvador, Brazil
- Curso de Medicina, Universidade Salvador, Laureate Universities, Salvador, Brazil
| | - Clarissa Gurgel-Rocha
- Department of Pathology, School of Medicine of the Federal University of Bahia, Salvador, Bahia, Brazil
- Center for Biotechnology and Cell Therapy, D’Or Institute for Research and Education, Sao Rafael Hospital, Salvador, Bahia, Brazil
| | - Monique Freire Santana
- Departmento de Ensino e Pesquisa, Fundação Centro de Controle de Oncologia do Estado do Amazonas, Manaus, Brazil
- Fundação Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Marcelo Cordeiro-Santos
- Fundação Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Brazil
- Faculdade de Medicina, Universidade Nilton Lins, Manaus, Brazil
| | - Elsa Du Bruyn
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Catherine Riou
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Kate Aberman
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Robert John Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- The Francis Crick Institute, London, Northwick Park Hospital, Harrow, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Daniel L. Barber
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Bruno B. Andrade
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Salvador, Brazil
- Curso de Medicina, Universidade Salvador, Laureate Universities, Salvador, Brazil
- Curso de Medicina, Escola Bahiana de Medicina e Saúde Pública, Salvador, Bahia, Brazil
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador, Brazil
- Curso de Medicina, Universidade Faculdade de Tecnologia e Ciências, Salvador, Bahia, Brazil
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
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Seto S, Nakamura H, Guo TC, Hikichi H, Wakabayashi K, Miyabayashi A, Nagata T, Hijikata M, Keicho N. Spatial multiomic profiling reveals the novel polarization of foamy macrophages within necrotic granulomatous lesions developed in lungs of C3HeB/FeJ mice infected with Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:968543. [PMID: 36237431 PMCID: PMC9551193 DOI: 10.3389/fcimb.2022.968543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/26/2022] [Indexed: 11/29/2022] Open
Abstract
Infection with Mycobacterium tuberculosis leads to the development of tuberculosis (TB) with the formation of granulomatous lesions. Foamy macrophages (FM) are a hallmark of TB granulomas, because they provide the primary platform of M. tuberculosis proliferation and the main source of caseous necrosis. In this study, we applied spatial multiomic profiling to identify the signatures of FM within the necrotic granulomas developed in a mouse model resembling human TB histopathology. C3HeB/FeJ mice were infected with M. tuberculosis to induce the formation of necrotic granulomas in the lungs. Using laser microdissection, necrotic granulomas were fractionated into three distinct regions, including the central caseous necrosis, the rim containing FM, and the peripheral layer of macrophages and lymphocytes, and subjected to proteomic and transcriptomic analyses. Comparison of proteomic and transcriptomic analyses of three distinct granulomatous regions revealed that four proteins/genes are commonly enriched in the rim region. Immunohistochemistry confirmed the localization of identified signatures to the rim of necrotic granulomas. We also investigated the localization of the representative markers for M1 macrophages in granulomas because the signatures of the rim included M2 macrophage markers. The localization of both macrophage markers suggests that FM in necrotic granulomas possessed the features of M1 or M2 macrophages. Gene set enrichment analysis of transcriptomic profiling revealed the upregulation of genes related to M2 macrophage activation and mTORC1 signaling in the rim. These results will provide new insights into the process of FM biogenesis, leading to further understanding of the pathophysiology of TB granulomas.
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Affiliation(s)
- Shintaro Seto
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
- *Correspondence: Shintaro Seto,
| | - Hajime Nakamura
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Tz-Chun Guo
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Haruka Hikichi
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Keiko Wakabayashi
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Akiko Miyabayashi
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Toshi Nagata
- Department of Health Science, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Minako Hijikata
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Naoto Keicho
- Vice Director, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Mata-Espinosa DA, Bini EI, Barrios-Payan J, Zatarain-Barrón ZL, Anzola JM, Cornejo-Granados F, Ochoa-Leyva A, Del Portillo P, Murcia MI, Hernández-Pando R. Close Related Drug-Resistance Beijing Isolates of Mycobacterium tuberculosis Reveal a Different Transcriptomic Signature in a Murine Disease Progression Model. Int J Mol Sci 2022; 23:ijms23095157. [PMID: 35563545 PMCID: PMC9100210 DOI: 10.3390/ijms23095157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) lineage 2/Beijing is associated with high virulence and drug resistance worldwide. In Colombia, the Beijing genotype has circulated since 1997, predominantly on the pacific coast, with the Beijing-Like SIT-190 being more prevalent. This genotype conforms to a drug-resistant cluster and shows a fatal outcome in patients. To better understand virulence determinants, we performed a transcriptomic analysis with a Beijing-Like SIT-190 isolate (BL-323), and Beijing-Classic SIT-1 isolate (BC-391) in progressive tuberculosis (TB) murine model. Bacterial RNA was extracted from mice lungs on days 3, 14, 28, and 60. On average, 0.6% of the total reads mapped against MTB genomes and of those, 90% against coding genes. The strains were independently associated as determined by hierarchical cluster and multidimensional scaling analysis. Gene ontology showed that in strain BL-323 enriched functions were related to host immune response and hypoxia, while proteolysis and protein folding were enriched in the BC-391 strain. Altogether, our results suggested a differential bacterial transcriptional program when evaluating these two closely related strains. The data presented here could potentially impact the control of this emerging, highly virulent, and drug-resistant genotype.
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Affiliation(s)
- María Irene Cerezo-Cortés
- Laboratorio de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (M.I.C.-C.); (J.G.R.-C.)
| | - Juan Germán Rodríguez-Castillo
- Laboratorio de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (M.I.C.-C.); (J.G.R.-C.)
| | - Dulce Adriana Mata-Espinosa
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
| | - Estela Isabel Bini
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
| | - Jorge Barrios-Payan
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
| | - Zyanya Lucia Zatarain-Barrón
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
| | - Juan Manuel Anzola
- Grupo de Biotecnología Molecular, Grupo de Bioinformática y Biología Computacional, Corporación CorpoGen, Bogotá 110311, Colombia; (J.M.A.); (P.D.P.)
- Universidad Central, Facultad de Ingeniería y Ciencias Básicas Bogotá, Bogotá 100270, Colombia
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (F.C.-G.); (A.O.-L.)
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (F.C.-G.); (A.O.-L.)
| | - Patricia Del Portillo
- Grupo de Biotecnología Molecular, Grupo de Bioinformática y Biología Computacional, Corporación CorpoGen, Bogotá 110311, Colombia; (J.M.A.); (P.D.P.)
| | - Martha Isabel Murcia
- Laboratorio de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (M.I.C.-C.); (J.G.R.-C.)
- Correspondence: (M.I.M.); (R.H.-P.)
| | - Rogelio Hernández-Pando
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
- Correspondence: (M.I.M.); (R.H.-P.)
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Gilbertson SE, Walter HC, Gardner K, Wren SN, Vahedi G, Weinmann AS. Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans. Cell Rep 2022; 39:110769. [PMID: 35508135 PMCID: PMC9142060 DOI: 10.1016/j.celrep.2022.110769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 12/11/2022] Open
Abstract
Distinguishing between conserved and divergent regulatory mechanisms is
essential for translating preclinical research from mice to humans, yet there is
a lack of information about how evolutionary genome rearrangements affect the
regulation of the immune response, a rapidly evolving system. The current model
is topologically associating domains (TADs) are conserved between species,
buffering evolutionary rearrangements and conserving long-range interactions
within a TAD. However, we find that TADs frequently span evolutionary
translocation and inversion breakpoints near genes with species-specific
expression in immune cells, creating unique enhancer-promoter interactions
exclusive to the mouse or human genomes. This includes TADs encompassing
immune-related transcription factors, cytokines, and receptors. For example, we
uncover an evolutionary rearrangement that created a shared LPS-inducible
regulatory module between OASL and P2RX7 in
human macrophages that is absent in mice. Therefore, evolutionary genome
rearrangements disrupt TAD boundaries, enabling sequence-conserved enhancer
elements from divergent genomic locations between species to create unique
regulatory modules. It is currently unclear how evolutionary genome rearrangements affecting
the mouse and human genomes influence the expression of genes important in
immunity. Gilbertson et al. report that evolutionary genome rearrangements
disrupt topologically associating domain boundaries, enabling sequence-conserved
enhancer elements from divergent locations between species to create unique
regulatory modules.
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Affiliation(s)
- Sarah E Gilbertson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hannah C Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Katherine Gardner
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Spencer N Wren
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Golnaz Vahedi
- Department of Genetics, Institute of Immunology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Kwon KW, Kim LH, Kang SM, Lee JM, Choi E, Park J, Hong JJ, Shin SJ. Host-directed antimycobacterial activity of colchicine, an anti-gout drug, via strengthened host innate resistance reinforced by the IL-1β/PGE 2 axis. Br J Pharmacol 2022; 179:3951-3969. [PMID: 35301712 DOI: 10.1111/bph.15838] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND AND PURPOSE To diversify and expand possible tuberculosis (TB) drug candidates and maximize limited global resources, we investigated the effect of colchicine, an FDA-approved anti-gout drug, against Mycobacterium tuberculosis (Mtb) infection because of its immune-modulating effect. EXPERIMENTAL APPROACH We evaluated the intracellular anti-Mtb activity of different concentrations of colchicine in murine bone marrow-derived macrophages (BMDMs). To elucidate the underlying mechanism, RNA sequencing, biological and chemical inhibition assays, and Western blot, quantitative real-time PCR, enzyme-linked immunosorbent assay (ELISA) and immunohistochemical analyses were employed. Finally, type I interferon-dependent highly TB-susceptible A/J mice were challenged with virulent Mtb H37Rv, and the host-directed therapeutic effect of oral colchicine administration on bacterial burdens and lung inflammation was assessed 30 days post-infection (2.5 mg·kg-1 every two days). KEY RESULTS Colchicine reinforced the anti-Mtb activity of BMDMs without affecting cell viability, indicating that colchicine facilitated macrophage immune activation upon Mtb infection. The results from RNA sequencing, NLRP3 knockout BMDM, IL-1 receptor blockade, and immunohistochemistry analyses revealed that this unexpected intracellular anti-Mtb activity of colchicine was mediated through NLRP3-dependent IL-1β signalling and Cox-2-regulated PGE2 production in macrophages. Consequently, the TB-susceptible A/J mouse model showed remarkable protection, with decreased bacterial loads in both the lungs and spleens of oral colchicine-treated mice, with significantly elevated Cox-2 expression at infection sites. CONCLUSIONS AND IMPLICATIONS The repurposing of colchicine against Mtb infection in this study highlights its unique function in macrophages upon Mtb infection and its novel potential use in treating TB as host-directed or adjunctive therapy.
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Affiliation(s)
- Kee Woong Kwon
- Department of Microbiology and Institute for Immunology and Immunological Disease, Brain Korea 21 Project for the Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Lee-Han Kim
- Department of Microbiology and Institute for Immunology and Immunological Disease, Brain Korea 21 Project for the Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Soon Myung Kang
- Department of Microbiology and Institute for Immunology and Immunological Disease, Brain Korea 21 Project for the Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Ju Mi Lee
- Department of Microbiology and Institute for Immunology and Immunological Disease, Brain Korea 21 Project for the Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Eunsol Choi
- Department of Microbiology and Institute for Immunology and Immunological Disease, Brain Korea 21 Project for the Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jiyun Park
- Department of Microbiology and Institute for Immunology and Immunological Disease, Brain Korea 21 Project for the Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jung Joo Hong
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Sung Jae Shin
- Department of Microbiology and Institute for Immunology and Immunological Disease, Brain Korea 21 Project for the Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
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Martínez-Pérez A, Estévez O, González-Fernández Á. Contribution and Future of High-Throughput Transcriptomics in Battling Tuberculosis. Front Microbiol 2022; 13:835620. [PMID: 35283833 PMCID: PMC8908424 DOI: 10.3389/fmicb.2022.835620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
While Tuberculosis (TB) infection remains a serious challenge worldwide, big data and “omic” approaches have greatly contributed to the understanding of the disease. Transcriptomics have been used to tackle a wide variety of queries including diagnosis, treatment evolution, latency and reactivation, novel target discovery, vaccine response or biomarkers of protection. Although a powerful tool, the elevated cost and difficulties in data interpretation may hinder transcriptomics complete potential. Technology evolution and collaborative efforts among multidisciplinary groups might be key in its exploitation. Here, we discuss the main fields explored in TB using transcriptomics, and identify the challenges that need to be addressed for a real implementation in TB diagnosis, prevention and therapy.
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Affiliation(s)
- Amparo Martínez-Pérez
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
| | - Olivia Estévez
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
| | - África González-Fernández
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
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41
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Evaluation of Myeloperoxidase as Target for Host-Directed Therapy in Tuberculosis In Vivo. Int J Mol Sci 2022; 23:ijms23052554. [PMID: 35269694 PMCID: PMC8910451 DOI: 10.3390/ijms23052554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022] Open
Abstract
Due to the rise of tuberculosis cases infected with multi and extensively drug-resistant Mycobacterium tuberculosis strains and the emergence of isolates resistant to antibiotics newly in clinical use, host-directed therapies targeting pathogenesis-associated immune pathways adjunct to antibiotics may ameliorate disease and bacterial clearance. Active tuberculosis is characterized by neutrophil-mediated lung pathology and tissue destruction. Previously, we showed that preventing M. tuberculosis induced necrosis in human neutrophils by inhibition of myeloperoxidase (MPO) promoted default apoptosis and subsequent control of mycobacteria by macrophages taking up the mycobacteria-infected neutrophils. To translate our findings in an in vivo model, we tested the MPO inhibitor 4-aminobenzoic acid hydrazide (ABAH) in C3HeB/FeJ mice, which are highly susceptible to M. tuberculosis infection manifesting in neutrophil-associated necrotic granulomas. MPO inhibition alone or as co-treatment with isoniazid, a first-line antibiotic in tuberculosis treatment, did not result in reduced bacterial burden, improved pathology, or altered infiltrating immune cell compositions. MPO inhibition failed to prevent M. tuberculosis induced neutrophil necrosis in C3Heb/FeJ mice in vivo as well as in murine neutrophils in vitro. In contrast to human neutrophils, murine neutrophils do not respond to M. tuberculosis infection in an MPO-dependent manner. Thus, the murine C3HeB/FeJ model does not fully resemble the pathomechanisms in active human tuberculosis. Consequently, murine infection models of tuberculosis are not necessarily adequate to evaluate host-directed therapies targeting neutrophils in vivo.
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42
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López-Agudelo VA, Baena A, Barrera V, Cabarcas F, Alzate JF, Beste DJV, Ríos-Estepa R, Barrera LF. Dual RNA Sequencing of Mycobacterium tuberculosis-Infected Human Splenic Macrophages Reveals a Strain-Dependent Host-Pathogen Response to Infection. Int J Mol Sci 2022; 23:ijms23031803. [PMID: 35163725 PMCID: PMC8836425 DOI: 10.3390/ijms23031803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), leading to pulmonary and extrapulmonary TB, whereby Mtb is disseminated to many other organs and tissues. Dissemination occurs early during the disease, and bacteria can be found first in the lymph nodes adjacent to the lungs and then later in the extrapulmonary organs, including the spleen. The early global gene expression response of human tissue macrophages and intracellular clinical isolates of Mtb has been poorly studied. Using dual RNA-seq, we have explored the mRNA profiles of two closely related clinical strains of the Latin American and Mediterranean (LAM) family of Mtb in infected human splenic macrophages (hSMs). This work shows that these pathogens mediate a distinct host response despite their genetic similarity. Using a genome-scale host–pathogen metabolic reconstruction to analyze the data further, we highlight that the infecting Mtb strain also determines the metabolic response of both the host and pathogen. Thus, macrophage ontogeny and the genetic-derived program of Mtb direct the host–pathogen interaction.
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Affiliation(s)
- Víctor A. López-Agudelo
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
- Grupo de Bioprocesos, Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
| | - Vianey Barrera
- Programa de Ingeniería Biológica, Universidad Nacional de Colombia, Sede Medellín, Medellín 050010, Colombia;
| | - Felipe Cabarcas
- Grupo Sistemas Embebidos e Inteligencia Computacional (SISTEMIC), Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica (CNSG), Sede de Investigación Universitaria (SIU), Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Dany J. V. Beste
- Department of Microbial Sciences, Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7XH, UK;
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
- Correspondence:
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Smith CM, Baker RE, Proulx MK, Mishra BB, Long JE, Park SW, Lee HN, Kiritsy MC, Bellerose MM, Olive AJ, Murphy KC, Papavinasasundaram K, Boehm FJ, Reames CJ, Meade RK, Hampton BK, Linnertz CL, Shaw GD, Hock P, Bell TA, Ehrt S, Schnappinger D, Pardo-Manuel de Villena F, Ferris MT, Ioerger TR, Sassetti CM. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. eLife 2022; 11:74419. [PMID: 35112666 PMCID: PMC8846590 DOI: 10.7554/elife.74419] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/27/2022] [Indexed: 11/21/2022] Open
Abstract
The outcome of an encounter with Mycobacterium tuberculosis (Mtb) depends on the pathogen’s ability to adapt to the variable immune pressures exerted by the host. Understanding this interplay has proven difficult, largely because experimentally tractable animal models do not recapitulate the heterogeneity of tuberculosis disease. We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to create a resource for associating bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection and produce qualitatively distinct immune states. Global analysis of Mtb transposon mutant fitness (TnSeq) across the CC panel revealed that many virulence pathways are only required in specific host microenvironments, identifying a large fraction of the pathogen’s genome that has been maintained to ensure fitness in a diverse population. Both immunological and bacterial traits can be associated with genetic variants distributed across the mouse genome, making the CC a unique population for identifying specific host-pathogen genetic interactions that influence pathogenesis.
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Affiliation(s)
- Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Megan K Proulx
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Bibhuti B Mishra
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Jarukit E Long
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Michael C Kiritsy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Michelle M Bellerose
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Andrew J Olive
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Frederick J Boehm
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Charlotte J Reames
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Morrisville, United States
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Timothy A Bell
- Department of Genetics,, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | | | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, United States
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
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44
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Wilburn KM, Montague CR, Qin B, Woods AK, Love MS, McNamara CW, Schultz PG, Southard TL, Huang L, Petrassi HM, VanderVen BC. Pharmacological and genetic activation of cAMP synthesis disrupts cholesterol utilization in Mycobacterium tuberculosis. PLoS Pathog 2022; 18:e1009862. [PMID: 35134095 PMCID: PMC8856561 DOI: 10.1371/journal.ppat.1009862] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/18/2022] [Accepted: 01/18/2022] [Indexed: 01/27/2023] Open
Abstract
There is a growing appreciation for the idea that bacterial utilization of host-derived lipids, including cholesterol, supports Mycobacterium tuberculosis (Mtb) pathogenesis. This has generated interest in identifying novel antibiotics that can disrupt cholesterol utilization by Mtb in vivo. Here we identify a novel small molecule agonist (V-59) of the Mtb adenylyl cyclase Rv1625c, which stimulates 3', 5'-cyclic adenosine monophosphate (cAMP) synthesis and inhibits cholesterol utilization by Mtb. Similarly, using a complementary genetic approach that induces bacterial cAMP synthesis independent of Rv1625c, we demonstrate that inducing cAMP synthesis is sufficient to inhibit cholesterol utilization in Mtb. Although the physiological roles of individual adenylyl cyclase enzymes in Mtb are largely unknown, here we demonstrate that the transmembrane region of Rv1625c is required during cholesterol metabolism. Finally, the pharmacokinetic properties of Rv1625c agonists have been optimized, producing an orally-available Rv1625c agonist that impairs Mtb pathogenesis in infected mice. Collectively, this work demonstrates a role for Rv1625c and cAMP signaling in controlling cholesterol metabolism in Mtb and establishes that cAMP signaling can be pharmacologically manipulated for the development of new antibiotic strategies.
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Affiliation(s)
- Kaley M. Wilburn
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - Christine R. Montague
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - Bo Qin
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Ashley K. Woods
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Melissa S. Love
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Case W. McNamara
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Peter G. Schultz
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Teresa L. Southard
- Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Lu Huang
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - H. Michael Petrassi
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Brian C. VanderVen
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
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Jong RM, Van Dis E, Berry SB, Nguyenla X, Baltodano A, Pastenkos G, Xu C, Fox D, Yosef N, McWhirter SM, Stanley SA. Mucosal Vaccination with Cyclic Dinucleotide Adjuvants Induces Effective T Cell Homing and IL-17-Dependent Protection against Mycobacterium tuberculosis Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:407-419. [PMID: 34965963 PMCID: PMC8755605 DOI: 10.4049/jimmunol.2100029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/10/2021] [Indexed: 01/17/2023]
Abstract
Tuberculosis consistently causes more deaths worldwide annually than any other single pathogen, making new effective vaccines an urgent priority for global public health. Among potential adjuvants, STING-activating cyclic dinucleotides (CDNs) uniquely stimulate a cytosolic sensing pathway activated only by pathogens. Recently, we demonstrated that a CDN-adjuvanted protein subunit vaccine robustly protects against tuberculosis infection in mice. In this study, we delineate the mechanistic basis underlying the efficacy of CDN vaccines for tuberculosis. CDN vaccines elicit CD4 T cells that home to lung parenchyma and penetrate into macrophage lesions in the lung. Although CDNs, like other mucosal vaccines, generate B cell-containing lymphoid structures in the lungs, protection is independent of B cells. Mucosal vaccination with a CDN vaccine induces Th1, Th17, and Th1-Th17 cells, and protection is dependent upon both IL-17 and IFN-γ. Single-cell RNA sequencing experiments reveal that vaccination enhances a metabolic state in Th17 cells reflective of activated effector function and implicate expression of Tnfsf8 (CD153) in vaccine-induced protection. Finally, we demonstrate that simply eliciting Th17 cells via mucosal vaccination with any adjuvant is not sufficient for protection. A vaccine adjuvanted with deacylated monophosphoryl lipid A (MPLA) failed to protect against tuberculosis infection when delivered mucosally, despite eliciting Th17 cells, highlighting the unique promise of CDNs as adjuvants for tuberculosis vaccines.
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Affiliation(s)
- Robyn M Jong
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Erik Van Dis
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Samuel B Berry
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Xammy Nguyenla
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Alexander Baltodano
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Gabrielle Pastenkos
- Comparative Pathology Laboratory, University of California, Davis, Davis, CA
| | - Chenling Xu
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA
| | - Douglas Fox
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA; and
| | | | - Sarah A Stanley
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA;
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA
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46
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Li XY, Corvino D, Nowlan B, Aguilera AR, Ng SS, Braun M, Cillo AR, Bald T, Smyth MJ, Engwerda CR. NKG7 Is Required for Optimal Antitumor T-cell Immunity. Cancer Immunol Res 2022; 10:154-161. [PMID: 35013002 DOI: 10.1158/2326-6066.cir-20-0649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/12/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Tumor antigen-specific CD8+ T cells play a critical role in antitumor immunity. Clinical trials reinvigorating the immune system via immune checkpoint blockade (ICB) have shown remarkable clinical promise. Numerous studies have identified an association between NKG7 expression and patient outcome across different malignancies. However, aside from these correlative observations, very little is known about NKG7 and its role in antitumor immunity. Herein, we utilized single-cell RNA sequencing (scRNA-seq) datasets, NKG7-deficient mice, NKG7-reporter mice, and mouse tumor models to investigate the role of NKG7 in neoantigen-mediated tumor rejection and ICB immunotherapy. scRNA-seq of tumors from patients with metastatic melanoma or head and neck squamous cell carcinoma revealed that NKG7 expression is highly associated with cytotoxicity and specifically expressed by CD8+ T cells and natural killer (NK) cells. Furthermore, we identified a key role for NKG7 in controlling intratumor T-cell accumulation and activation. NKG7 was upregulated on intratumor antigen-specific CD8+ T cells and NK cells and required for the accumulation of T cells in the tumor microenvironment. Accordingly, neoantigen-expressing mouse tumors grew faster in Nkg7-deficient mice. Strikingly, efficacy of single or combination ICB was significantly reduced in Nkg7-deficient mice.
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Affiliation(s)
- Xian-Yang Li
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Zhuhai Precision Medical Center, Zhuhai People's Hospital, Jinan University, Zhuhai, Guangdong, P.R. China
| | - Dillon Corvino
- Oncology and Cellular Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Bianca Nowlan
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Amelia Roman Aguilera
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Susanna S Ng
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
- Immunology and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Griffith University, School of Environment and Science, Nathan, Queensland, Australia
| | - Matthias Braun
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Oncology and Cellular Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Tobias Bald
- Oncology and Cellular Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Christian R Engwerda
- Immunology and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
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47
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Gilbertson SE, Weinmann AS. Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis. Trends Immunol 2021; 42:1077-1087. [PMID: 34740529 DOI: 10.1016/j.it.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023]
Abstract
Model organisms such as mice are important for basic research and serve as valuable tools in preclinical translational studies. A challenge with translating findings from mice to humans is identifying and separating evolutionarily conserved mechanisms in the immune system from those diverging between species. A significant emphasis has been placed on defining conserved gene regulation principles, with divergent mechanisms often overlooked. We put forward the perspective that both conserved and divergent mechanisms that regulate gene expression programs are of equal importance. With recent advances and availability of datasets, immunologists should take a closer look at the role for genetic diversity in altering gene expression programs between mouse and human immune cells.
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Affiliation(s)
- Sarah E Gilbertson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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48
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Tabone O, Verma R, Singhania A, Chakravarty P, Branchett WJ, Graham CM, Lee J, Trang T, Reynier F, Leissner P, Kaiser K, Rodrigue M, Woltmann G, Haldar P, O'Garra A. Blood transcriptomics reveal the evolution and resolution of the immune response in tuberculosis. J Exp Med 2021; 218:212624. [PMID: 34491266 PMCID: PMC8493863 DOI: 10.1084/jem.20210915] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/08/2021] [Accepted: 08/05/2021] [Indexed: 12/02/2022] Open
Abstract
Blood transcriptomics have revealed major characteristics of the immune response in active TB, but the signature early after infection is unknown. In a unique clinically and temporally well-defined cohort of household contacts of active TB patients that progressed to TB, we define minimal changes in gene expression in incipient TB increasing in subclinical and clinical TB. While increasing with time, changes in gene expression were highest at 30 d before diagnosis, with heterogeneity in the response in household TB contacts and in a published cohort of TB progressors as they progressed to TB, at a bulk cohort level and in individual progressors. Blood signatures from patients before and during anti-TB treatment robustly monitored the treatment response distinguishing early and late responders. Blood transcriptomics thus reveal the evolution and resolution of the immune response in TB, which may help in clinical management of the disease.
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Affiliation(s)
- Olivier Tabone
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | - Raman Verma
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, UK
| | - Akul Singhania
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | | | - William J Branchett
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | - Christine M Graham
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | - Jo Lee
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, UK
| | - Tran Trang
- Bioaster Microbiology Technology Institute, Lyon, France
| | | | | | - Karine Kaiser
- Medical Diagnostic Discovery Department, bioMérieux SA, Marcy l'Etoile, France
| | - Marc Rodrigue
- Global Medical Affairs, bioMérieux SA, Marcy l'Etoile, France
| | - Gerrit Woltmann
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, UK
| | - Pranabashis Haldar
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, UK
| | - Anne O'Garra
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK
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49
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Koyuncu D, Niazi MKK, Tavolara T, Abeijon C, Ginese ML, Liao Y, Mark C, Specht A, Gower AC, Restrepo BI, Gatti DM, Kramnik I, Gurcan M, Yener B, Beamer G. CXCL1: A new diagnostic biomarker for human tuberculosis discovered using Diversity Outbred mice. PLoS Pathog 2021; 17:e1009773. [PMID: 34403447 PMCID: PMC8423361 DOI: 10.1371/journal.ppat.1009773] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/07/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
More humans have died of tuberculosis (TB) than any other infectious disease and millions still die each year. Experts advocate for blood-based, serum protein biomarkers to help diagnose TB, which afflicts millions of people in high-burden countries. However, the protein biomarker pipeline is small. Here, we used the Diversity Outbred (DO) mouse population to address this gap, identifying five protein biomarker candidates. One protein biomarker, serum CXCL1, met the World Health Organization’s Targeted Product Profile for a triage test to diagnose active TB from latent M.tb infection (LTBI), non-TB lung disease, and normal sera in HIV-negative, adults from South Africa and Vietnam. To find the biomarker candidates, we quantified seven immune cytokines and four inflammatory proteins corresponding to highly expressed genes unique to progressor DO mice. Next, we applied statistical and machine learning methods to the data, i.e., 11 proteins in lungs from 453 infected and 29 non-infected mice. After searching all combinations of five algorithms and 239 protein subsets, validating, and testing the findings on independent data, two combinations accurately diagnosed progressor DO mice: Logistic Regression using MMP8; and Gradient Tree Boosting using a panel of 4: CXCL1, CXCL2, TNF, IL-10. Of those five protein biomarker candidates, two (MMP8 and CXCL1) were crucial for classifying DO mice; were above the limit of detection in most human serum samples; and had not been widely assessed for diagnostic performance in humans before. In patient sera, CXCL1 exceeded the triage diagnostic test criteria (>90% sensitivity; >70% specificity), while MMP8 did not. Using Area Under the Curve analyses, CXCL1 averaged 94.5% sensitivity and 88.8% specificity for active pulmonary TB (ATB) vs LTBI; 90.9% sensitivity and 71.4% specificity for ATB vs non-TB; and 100.0% sensitivity and 98.4% specificity for ATB vs normal sera. Our findings overall show that the DO mouse population can discover diagnostic-quality, serum protein biomarkers of human TB. More humans die of tuberculosis (TB) than any other infectious disease, yet diagnostic tools remain limited. Here, we used the Diversity Outbred mouse population to discover candidate protein biomarkers of human TB. By applying statistical methods and machine learning to multidimensional data, we identified CXCL1 and MMP8 as the two most promising protein biomarker candidates. When evaluated in samples from human patients, CXCL1 achieved the World Health Organization’s targeted profile for a triage diagnostic test, discriminating active TB from important clinical differential diagnoses: latent Mtb infection and non-TB lung disease in HIV-negative adults. Overall, our studies show how a translationally relevant animal population model can accelerate TB biomarker discovery, validation, and testing for humans.
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Affiliation(s)
- Deniz Koyuncu
- Rensselaer Polytechnic Institute, Department of Electrical, Computer, and Systems Engineering, Troy, New York, United States of America
| | - Muhammad Khalid Khan Niazi
- Wake Forest School of Medicine, Bowman Gray Center for Medical Education, Winston-Salem, North Carolina, United States of America
| | - Thomas Tavolara
- Wake Forest School of Medicine, Bowman Gray Center for Medical Education, Winston-Salem, North Carolina, United States of America
| | - Claudia Abeijon
- Tufts University, Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Melanie L. Ginese
- Tufts University, Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | | | - Carolyn Mark
- Kansas State University, College of Veterinary Medicine, Manhattan, Kansas, United States of America
| | - Aubrey Specht
- Tufts University, Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Adam C. Gower
- Boston University Clinical and Translational Science Institute, Boston, Massachusetts, United States of America
| | - Blanca I. Restrepo
- The University of Texas Health Science Center at Houston School of Public Health in Brownsville, Texas, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Igor Kramnik
- Boston University, National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, United States of America
| | - Metin Gurcan
- Wake Forest School of Medicine, Bowman Gray Center for Medical Education, Winston-Salem, North Carolina, United States of America
| | - Bülent Yener
- Rensselaer Polytechnic Institute, Department of Computer Science, Troy, New York, United States of America
| | - Gillian Beamer
- Tufts University, Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
- * E-mail:
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50
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Borah P, Deb PK, Venugopala KN, Al-Shar'i NA, Singh V, Deka S, Srivastava A, Tiwari V, Mailavaram RP. Tuberculosis: An Update on Pathophysiology, Molecular Mechanisms of Drug Resistance, Newer Anti-TB Drugs, Treatment Regimens and Host- Directed Therapies. Curr Top Med Chem 2021; 21:547-570. [PMID: 33319660 DOI: 10.2174/1568026621999201211200447] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/16/2020] [Accepted: 11/19/2020] [Indexed: 11/22/2022]
Abstract
Human tuberculosis (TB) is primarily caused by Mycobacterium tuberculosis (Mtb) that inhabits inside and amidst immune cells of the host with adapted physiology to regulate interdependent cellular functions with intact pathogenic potential. The complexity of this disease is attributed to various factors such as the reactivation of latent TB form after prolonged persistence, disease progression specifically in immunocompromised patients, advent of multi- and extensivelydrug resistant (MDR and XDR) Mtb strains, adverse effects of tailor-made regimens, and drug-drug interactions among anti-TB drugs and anti-HIV therapies. Thus, there is a compelling demand for newer anti-TB drugs or regimens to overcome these obstacles. Considerable multifaceted transformations in the current TB methodologies and molecular interventions underpinning hostpathogen interactions and drug resistance mechanisms may assist to overcome the emerging drug resistance. Evidently, recent scientific and clinical advances have revolutionised the diagnosis, prevention, and treatment of all forms of the disease. This review sheds light on the current understanding of the pathogenesis of TB disease, molecular mechanisms of drug-resistance, progress on the development of novel or repurposed anti-TB drugs and regimens, host-directed therapies, with particular emphasis on underlying knowledge gaps and prospective for futuristic TB control programs.
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Affiliation(s)
- Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Pran K Deb
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, PO Box 1, Amman 19392, Jordan
| | - Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Nizar A Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, 7701, South Africa
| | - Satyendra Deka
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Amavya Srivastava
- Neuroscience and Pain Research Lab, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221 005, India
| | - Vinod Tiwari
- Neuroscience and Pain Research Lab, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221 005, India
| | - Raghu P Mailavaram
- Department of Pharmaceutical Chemistry, Shri Vishnu College of Pharmacy, Vishnupur, Bhimavaram - 534 202, West Godavari Dist., Andhra Pradesh, India
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