1
|
Waanders L, van der Donk LEH, Ates LS, Maaskant J, van Hamme JL, Eldering E, van Bruggen JAC, Rietveld JM, Bitter W, Geijtenbeek TBH, Kuijl CP. Ectopic expression of cGAS in Salmonella typhimurium enhances STING-mediated IFN-β response in human macrophages and dendritic cells. J Immunother Cancer 2023; 11:jitc-2022-005839. [PMID: 37072345 PMCID: PMC10124277 DOI: 10.1136/jitc-2022-005839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Interferon (IFN)-β induction via activation of the stimulator of interferon genes (STING) pathway has shown promising results in tumor models. STING is activated by cyclic dinucleotides such as cyclic GMP-AMP dinucleotides with phosphodiester linkages 2'-5' and 3'-5' (cGAMPs), that are produced by cyclic GMP-AMP synthetase (cGAS). However, delivery of STING pathway agonists to the tumor site is a challenge. Bacterial vaccine strains have the ability to specifically colonize hypoxic tumor tissues and could therefore be modified to overcome this challenge. Combining high STING-mediated IFN-β levels with the immunostimulatory properties of Salmonella typhimurium could have potential to overcome the immune suppressive tumor microenvironment. METHODS We have engineered S. typhimurium to produce cGAMP by expression of cGAS. The ability of cGAMP to induce IFN-β and its IFN-stimulating genes was addressed in infection assays of THP-I macrophages and human primary dendritic cells (DCs). Expression of catalytically inactive cGAS is used as a control. DC maturation and cytotoxic T-cell cytokine and cytotoxicity assays were conducted to assess the potential antitumor response in vitro. Finally, by making use of different S. typhimurium type III secretion (T3S) mutants, the mode of cGAMP transport was elucidated. RESULTS Expression of cGAS in S. typhimurium results in a 87-fold stronger IFN-β response in THP-I macrophages. This effect was mediated by cGAMP production and is STING dependent. Interestingly, the needle-like structure of the T3S system was necessary for IFN-β induction in epithelial cells. DC activation included upregulation of maturation markers and induction of type I IFN response. Coculture of challenged DCs with cytotoxic T cells revealed an improved cGAMP-mediated IFN-γ response. In addition, coculture of cytotoxic T cells with challenged DCs led to improved immune-mediated tumor B-cell killing. CONCLUSION S. typhimurium can be engineered to produce cGAMPs that activate the STING pathway in vitro. Furthermore, they enhanced the cytotoxic T-cell response by improving IFN-γ release and tumor cell killing. Thus, the immune response triggered by S. typhimurium can be enhanced by ectopic cGAS expression. These data show the potential of S. typhimurium-cGAS in vitro and provides rationale for further research in vivo.
Collapse
Affiliation(s)
- Lisette Waanders
- Department of Medical Microbiology and Infection Control, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Immunology, Amsterdam, Netherlands
| | - Lieve E H van der Donk
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Louis S Ates
- Department of Experimental Immunology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Janneke Maaskant
- Department of Medical Microbiology and Infection Control, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - John L van Hamme
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Eric Eldering
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Immunology, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Cancer Immunology, Amsterdam, Netherlands
- The Lymphoma and Myeloma Center Amsterdam, LYMMCARE, Amsterdam, Netherlands
| | - Jaco A C van Bruggen
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Immunology, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Cancer Immunology, Amsterdam, Netherlands
| | - Joanne M Rietveld
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Immunology, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Cancer Immunology, Amsterdam, Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Amsterdam institute for Life and Environment, Vrije Universiteit, Amsterdam, Netherlands
| | - Teunis B H Geijtenbeek
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Coenraad P Kuijl
- Department of Medical Microbiology and Infection Control, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Immunology, Amsterdam, Netherlands
| |
Collapse
|
2
|
van der Donk LEH, van der Spek J, van Duivenvoorde T, Ten Brink MS, Geijtenbeek TBH, Kuijl CP, van Heijst JWJ, Ates LS. An optimized retroviral toolbox for overexpression and genetic perturbation of primary lymphocytes. Biol Open 2022; 11:274579. [PMID: 35229875 PMCID: PMC8905627 DOI: 10.1242/bio.059032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/11/2022] [Indexed: 11/20/2022] Open
Abstract
Genetic manipulation of primary lymphocytes is crucial for both clinical purposes and fundamental research. Despite their broad use, we encountered a paucity of data on systematic comparison and optimization of retroviral vectors, the workhorses of genetic modification of primary lymphocytes. Here, we report the construction and validation of a versatile range of retroviral expression vectors. These vectors can be used for the knockdown or overexpression of genes of interest in primary human and murine lymphocytes, in combination with a wide choice of selection and reporter strategies. By streamlining the vector backbone and insert design, these publicly available vectors allow easy interchangeability of the independent building blocks, such as different promoters, fluorescent proteins, surface markers and antibiotic resistance cassettes. We validated these vectors and tested the optimal promoters for in vitro and in vivo overexpression and knockdown of the murine T cell antigen receptor. By publicly sharing these vectors and the data on their optimization, we aim to facilitate genetic modification of primary lymphocytes for researchers entering this field. Summary: Viral transduction is generally the method of choice for genetic manipulation of primary lymphocytes. Here, the authors systematically compared different genetic components and created and shared an optimized set of vectors that can be used in all aspects of research on T cells.
Collapse
Affiliation(s)
- Lieve E H van der Donk
- Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
| | - Jet van der Spek
- Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
| | - Tom van Duivenvoorde
- Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
| | - Marieke S Ten Brink
- Division of Infectious Diseases and Center of Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
| | - Coenraad P Kuijl
- Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam 1081 HV, the Netherlands
| | - Jeroen W J van Heijst
- Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands
| | - Louis S Ates
- Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands.,Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam 1081 HV, the Netherlands
| |
Collapse
|
3
|
Orgeur M, Frigui W, Pawlik A, Clark S, Williams A, Ates LS, Ma L, Bouchier C, Parkhill J, Brodin P, Brosch R. Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts. Microb Genom 2021; 7:000505. [PMID: 33529148 PMCID: PMC8208694 DOI: 10.1099/mgen.0.000505] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/16/2020] [Indexed: 01/03/2023] Open
Abstract
Mycobacterium microti is an animal-adapted member of the Mycobacterium tuberculosis complex (MTBC), which was originally isolated from voles, but has more recently also been isolated from other selected mammalian hosts, including occasionally from humans. Here, we have generated and analysed the complete genome sequences of five representative vole and clinical M. microti isolates using PacBio- and Illumina-based technologies, and have tested their virulence and vaccine potential in SCID (severe combined immune deficient) mouse and/or guinea pig infection models. We show that the clinical isolates studied here cluster separately in the phylogenetic tree from vole isolates and other clades from publicly available M. microti genome sequences. These data also confirm that the vole and clinical M. microti isolates were all lacking the specific RD1mic region, which in other tubercle bacilli encodes the ESX-1 type VII secretion system. Biochemical analysis further revealed marked phenotypic differences between isolates in type VII-mediated secretion of selected PE and PPE proteins, which in part were attributed to specific genetic polymorphisms. Infection experiments in the highly susceptible SCID mouse model showed that the clinical isolates were significantly more virulent than the tested vole isolates, but still much less virulent than the M. tuberculosis H37Rv control strain. The strong attenuation of the ATCC 35872 vole isolate in immunocompromised mice, even compared to the attenuated BCG (bacillus Calmette-Guérin) vaccine, and its historic use in human vaccine trials encouraged us to test this strain's vaccine potential in a guinea pig model, where it demonstrated similar protective efficacy as a BCG control, making it a strong candidate for vaccination of immunocompromised individuals in whom BCG vaccination is contra-indicated. Overall, we provide new insights into the genomic and phenotypic variabilities and particularities of members of an understudied clade of the MTBC, which all share a recent common ancestor that is characterized by the deletion of the RD1mic region.
Collapse
Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
| | - Wafa Frigui
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
| | - Alexandre Pawlik
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
| | - Simon Clark
- Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Ann Williams
- Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Louis S. Ates
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
- Amsterdam UMC, University of Amsterdam, Department of Experimental Immunology, Amsterdam institute for Infection & Immunity, Meibergdreef 9, Amsterdam, Netherlands
| | - Laurence Ma
- Institut Pasteur, Biomics, C2RT, Paris 75015, France
| | | | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Priscille Brodin
- CIIL - Center for Infection and Immunity of Lille, Université de Lille/CNRS UMR 9017/INSERM U1019/CHU Lille/Institut Pasteur de Lille, Lille 59000, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
| |
Collapse
|
4
|
van der Donk LEH, Ates LS, van der Spek J, Tukker LM, Geijtenbeek TBH, van Heijst JWJ. Separate signaling events control TCR downregulation and T cell activation in primary human T cells. Immun Inflamm Dis 2020; 9:223-238. [PMID: 33350598 PMCID: PMC7860602 DOI: 10.1002/iid3.383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/27/2020] [Accepted: 11/17/2020] [Indexed: 12/02/2022]
Abstract
Introduction T‐cell antigen receptor (TCR) interaction with cognate peptide:MHC complexes trigger clustering of TCR:CD3 complexes and signal transduction. Triggered TCR:CD3 complexes are rapidly internalized and degraded in a process called ligand‐induced TCR downregulation. Classic studies in immortalized T‐cell lines have revealed a major role for the Src family kinase Lck in TCR downregulation. However, to what extent a similar mechanism operates in primary human T cells remains unclear. Methods Here, we developed an anti‐CD3‐mediated TCR downregulation assay, in which T‐cell gene expression in primary human T cells can be knocked down by microRNA constructs. In parallel, we used CRISPR/Cas9‐mediated knockout in Jurkat cells for validation experiments. Results We efficiently knocked down the expression of tyrosine kinases Lck, Fyn, and ZAP70, and found that, whereas this impaired T cell activation and effector function, TCR downregulation was not affected. Although TCR downregulation was marginally inhibited by the simultaneous knockdown of Lck and Fyn, its full abrogation required broad‐acting tyrosine kinase inhibitors. Conclusions These data suggest that there is substantial redundancy in the contribution of individual tyrosine kinases to TCR downregulation in primary human T cells. Our results highlight that TCR downregulation and T cell activation are controlled by different signaling events and illustrate the need for further research to untangle these processes.
Collapse
Affiliation(s)
- Lieve E H van der Donk
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Louis S Ates
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jet van der Spek
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura M Tukker
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeroen W J van Heijst
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Neogene Therapeutics, Amsterdam, The Netherlands
| |
Collapse
|
5
|
Abstract
The PE and PPE proteins of Mycobacterium tuberculosis have been studied with great interest since their discovery. Named after the conserved proline (P) and glutamic acid (E) residues in their N-terminal domains, these proteins are postulated to perform wide-ranging roles in virulence and immune modulation. However, technical challenges in studying these proteins and their encoding genes have hampered the elucidation of molecular mechanisms and leave many open questions regarding the biological functions mediated by these proteins. Here, I review the shared and unique characteristics of PE and PPE proteins from a molecular perspective linking this information to their functions in mycobacterial virulence. I discuss how the different subgroups (PE_PGRS, PPE-PPW, PPE-SVP and PPE-MPTR) are defined and why this classification of paramount importance to understand the PE and PPE proteins as individuals and or groups. The goal of this MicroReview is to summarize and structure the existing information on this gene family into a simplified framework of thinking about PE and PPE proteins and genes. Thereby, I hope to provide helpful starting points in studying these genes and proteins for researchers with different backgrounds. This has particular implications for the design and monitoring of novel vaccine candidates and in understanding the evolution of the M. tuberculosis complex.
Collapse
Affiliation(s)
- Louis S. Ates
- Department of Experimental ImmunologyAmsterdam Infection & Immunity InstituteAmsterdam UMCUniversity of AmsterdamMeibergdreef 9Amsterdamthe Netherlands
| |
Collapse
|
6
|
Burggraaf MJ, Ates LS, Speer A, van der Kuij K, Kuijl C, Bitter W. Optimization of secretion and surface localization of heterologous OVA protein in mycobacteria by using LipY as a carrier. Microb Cell Fact 2019; 18:44. [PMID: 30841891 PMCID: PMC6402100 DOI: 10.1186/s12934-019-1093-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium bovis Bacille Calmette-Guérin (BCG) is not only used as a vaccine against tuberculosis but also protects against leprosy and is used as part of bladder cancer treatment to induce a protective immune response. However, protection by BCG vaccination is not optimal. To improve vaccine efficacy, recombinant BCG expressing heterologous antigens has been put forward to elicit antigen-specific cellular and humoral responses. Cell surface localized or secreted antigens induce better immune responses than their cytosolic counterparts. Optimizing secretion of heterologous proteins or protein fragments holds therefore unexplored potential for improving the efficacy of recombinant BCG vaccine candidates. Secretion of heterologous antigens requires crossing the mycobacterial inner and outer membrane. Mycobacteria have specialized ESX or type VII secretion systems that enable translocation of proteins across both membranes. Probing this secretion system could therefore be a valid approach to surface localize heterologous antigens. RESULTS We show that ESX-5 substrate LipY, a lipase, can be used as a carrier for heterologous secretion of an ovalbumin fragment (OVA). LipY contains a PE domain and a lipase domain, separated by a linker region. This linker domain is processed upon secretion. Fusion of the PE and linker domains of LipY to OVA enabled ESX-5-dependent secretion of the fusion construct LipY-OVA in M. marinum, albeit with low efficiency. Subsequent random mutagenesis of LipY-OVA and screening for increased secretion resulted in mutants with improved heterologous secretion. Detailed analysis identified two mutations in OVA that improved secretion, i.e. an L280P mutation and a protein-extending frameshift mutation. Finally, deletion of the linker domain of LipY enhanced secretion of LipY-OVA, although this mutation also reduced surface association. Further analysis in wild type LipY showed that the linker domain is required for surface association. CONCLUSION We show that the ESX-5 system can be used for heterologous secretion. Furthermore, minor mutations in the substrate can enhance secretion. Especially the C-terminal region seems to be important for this. The linker domain of LipY is involved in surface association. These findings show that non-biased screening approaches aid in optimization of heterologous secretion, which can contribute to heterologous vaccine development.
Collapse
Affiliation(s)
- Maroeska J Burggraaf
- Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Louis S Ates
- Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands.,Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Alexander Speer
- Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Kim van der Kuij
- Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Coen Kuijl
- Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Wilbert Bitter
- Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands. .,Molecular Microbiology, Vrije Universiteit Amsterdam, de Boelelaan 1105, Amsterdam, Netherlands.
| |
Collapse
|
7
|
Ates LS, Dippenaar A, Sayes F, Pawlik A, Bouchier C, Ma L, Warren RM, Sougakoff W, Majlessi L, van Heijst JWJ, Brossier F, Brosch R. Unexpected Genomic and Phenotypic Diversity of Mycobacterium africanum Lineage 5 Affects Drug Resistance, Protein Secretion, and Immunogenicity. Genome Biol Evol 2018; 10:1858-1874. [PMID: 30010947 PMCID: PMC6071665 DOI: 10.1093/gbe/evy145] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium africanum consists of Lineages L5 and L6 of the Mycobacterium tuberculosis complex (MTBC) and causes human tuberculosis in specific regions of Western Africa, but is generally not transmitted in other parts of the world. Since M. africanum is evolutionarily closely placed between the globally dispersed Mycobacterium tuberculosis and animal-adapted MTBC-members, these lineages provide valuable insight into M. tuberculosis evolution. Here, we have collected 15 M. africanum L5 strains isolated in France over 4 decades. Illumina sequencing and phylogenomic analysis revealed a previously underappreciated diversity within L5, which consists of distinct sublineages. L5 strains caused relatively high levels of extrapulmonary tuberculosis and included multi- and extensively drug-resistant isolates, especially in the newly defined sublineage L5.2. The specific L5 sublineages also exhibit distinct phenotypic characteristics related to in vitro growth, protein secretion and in vivo immunogenicity. In particular, we identified a PE_PGRS and PPE-MPTR secretion defect specific for sublineage L5.2, which was independent of PPE38. Furthermore, L5 isolates were able to efficiently secrete and induce immune responses against ESX-1 substrates contrary to previous predictions. These phenotypes of Type VII protein secretion and immunogenicity provide valuable information to better link genome sequences to phenotypic traits and thereby understand the evolution of the MTBC.
Collapse
Affiliation(s)
- Louis S Ates
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Anzaan Dippenaar
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Fadel Sayes
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Alexandre Pawlik
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Christiane Bouchier
- Department of Genomes and Genetics, Institut Pasteur, Genomics Platform, Paris, France
| | - Laurence Ma
- Department of Genomes and Genetics, Institut Pasteur, Genomics Platform, Paris, France
| | - Robin M Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wladimir Sougakoff
- Sorbonne Universités, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Team 13 (Bacteriology), Paris, France
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries (NRC MyRMA), Hôpitaux Universitaires Pitié-Salpêtrière – Charles Foix, Paris, France
| | - Laleh Majlessi
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Jeroen W J van Heijst
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Florence Brossier
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Sorbonne Universités, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Team 13 (Bacteriology), Paris, France
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries (NRC MyRMA), Hôpitaux Universitaires Pitié-Salpêtrière – Charles Foix, Paris, France
| | - Roland Brosch
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| |
Collapse
|
8
|
Ates LS, Sayes F, Frigui W, Ummels R, Damen MPM, Bottai D, Behr MA, van Heijst JWJ, Bitter W, Majlessi L, Brosch R. RD5-mediated lack of PE_PGRS and PPE-MPTR export in BCG vaccine strains results in strong reduction of antigenic repertoire but little impact on protection. PLoS Pathog 2018; 14:e1007139. [PMID: 29912964 PMCID: PMC6023246 DOI: 10.1371/journal.ppat.1007139] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/28/2018] [Accepted: 06/05/2018] [Indexed: 01/03/2023] Open
Abstract
Tuberculosis is the deadliest infectious disease worldwide. Although the BCG vaccine is widely used, it does not efficiently protect against pulmonary tuberculosis and an improved tuberculosis vaccine is therefore urgently needed. Mycobacterium tuberculosis uses different ESX/Type VII secretion (T7S) systems to transport proteins important for virulence and host immune responses. We recently reported that secretion of T7S substrates belonging to the mycobacteria-specific Pro-Glu (PE) and Pro-Pro-Glu (PPE) proteins of the PGRS (polymorphic GC-rich sequences) and MPTR (major polymorphic tandem repeat) subfamilies required both a functional ESX-5 system and a functional PPE38/71 protein for secretion. Inactivation of ppe38/71 and the resulting loss of PE_PGRS/PPE-MPTR secretion were linked to increased virulence of M. tuberculosis strains. Here, we show that a predicted total of 89 PE_PGRS/PPE-MPTR surface proteins are not exported by certain animal-adapted strains of the M. tuberculosis complex including M. bovis. This Δppe38/71-associated secretion defect therefore also occurs in the M. bovis-derived tuberculosis vaccine BCG and could be partially restored by introduction of the M. tuberculosis ppe38-locus. Epitope mapping of the PPE-MPTR protein PPE10, further allowed us to monitor T-cell responses in splenocytes from BCG/M. tuberculosis immunized mice, confirming the dependence of PPE10-specific immune-induction on ESX-5/PPE38-mediated secretion. Restoration of PE_PGRS/PPE-MPTR secretion in recombinant BCG neither altered global antigenic presentation or activation of innate immune cells, nor protective efficacy in two different mouse vaccination-infection models. This unexpected finding stimulates a reassessment of the immunomodulatory properties of PE_PGRS/PPE-MPTR proteins, some of which are contained in vaccine formulations currently in clinical evaluation. One of the major findings of the pioneering Mycobacterium tuberculosis H37Rv genome sequencing project was the identification of the highly abundant PE and PPE proteins, named after their N-terminal motifs Pro–Glu (PE) or Pro–Pro–Glu (PPE). Within the 20 years of research since then, many claims were made that PE/PPE proteins, including the two large subgroups encoded by repetitive sequences with very high GC content (PE_PGRS and PPE-MPTR families), are exported to the bacterial surface or beyond, and show broad immunomodulatory impact on host-pathogen interaction. We thus screened strains from different branches of the M. tuberculosis complex, including the attenuated Mycobacterium bovis BCG vaccine strains, for their capacity to export PE_PGRS/PPE-MPTR proteins. Strikingly, we found that BCG strains were unable to export the plethora of PE_PGRS/PPE-MPTR proteins due to the absence of the region of difference RD5, which in M. tuberculosis encodes PPE38, required for PE_PGRS/PPE-MPTR export. Surprisingly, the restoration of PE_PGRS/PPE-MPTR export by genetic complementation in recombinant BCG did not result in immunomodulatory changes or altered protection in mouse models. Our results thus put into perspective the numerous reports on virulence-associated immunomodulatory impact of individual PE_PGRS and PPE-MPTR proteins and open novel questions on their biological function(s).
Collapse
Affiliation(s)
- Louis S. Ates
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- * E-mail: (LSA); (RB)
| | - Fadel Sayes
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Wafa Frigui
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Roy Ummels
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | - Merel P. M. Damen
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicine & Systems, Vrije Universiteit, Amsterdam, the Netherlands
| | - Daria Bottai
- University of Pisa, Department of Biology, Pisa, Italy
| | - Marcel A. Behr
- McGill International TB Centre, Infectious Diseases and Immunity in Global Health Program at the McGill University Health Centre Research Institute, Montreal, Canada
| | - Jeroen W. J. van Heijst
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicine & Systems, Vrije Universiteit, Amsterdam, the Netherlands
| | - Laleh Majlessi
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- * E-mail: (LSA); (RB)
| |
Collapse
|
9
|
Ates LS, Dippenaar A, Ummels R, Piersma SR, van der Woude AD, van der Kuij K, Le Chevalier F, Mata-Espinosa D, Barrios-Payán J, Marquina-Castillo B, Guapillo C, Jiménez CR, Pain A, Houben ENG, Warren RM, Brosch R, Hernández-Pando R, Bitter W. Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis. Nat Microbiol 2018; 3:181-188. [DOI: 10.1038/s41564-017-0090-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/29/2017] [Indexed: 12/30/2022]
|
10
|
Abstract
Mycobacterium tuberculosis, the etiological agent of human tuberculosis, harbours five ESAT-6/type VII secretion (ESX/T7S) systems. The first esx gene clusters were identified during the genome-sequencing project of M. tuberculosis H37Rv. Follow-up studies revealed additional genes playing important roles in ESX/T7S systems. Among the latter genes, one can find those that encode Pro-Glu (PE) and Pro-Pro-Glu (PPE) proteins as well as a gene cluster that is encoded >260 kb upstream of the esx-1 locus and encodes ESX-1 secretion-associated proteins EspA (Rv3616c), EspC (Rv3615c) and EspD (Rv3614c). The espACD cluster has been suggested to have an important function in ESX-1 secretion since EspA-EspC and EsxA-EsxB are mutually co-dependent on each other for secretion. However, the molecular mechanism of this co-dependence and interaction between the substrates remained unknown. In this issue of Molecular Microbiology, Lou and colleagues show that EspC forms high-molecular weight polymerization complexes that resemble selected components of type II, III and/or IV secretion systems of Gram-negative bacteria. Indeed, EspC-multimeric complexes form filamentous structures that could well represent a secretion needle of ESX-1 type VII secretion systems. This exciting observation opens new avenues for research to discover and characterize ESX/T7S components and elucidates the co-dependence of EsxA/B secretion with EspA/C.
Collapse
Affiliation(s)
- Louis S Ates
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75724 Paris Cedex 15, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75724 Paris Cedex 15, France
| |
Collapse
|
11
|
Ates LS, van der Woude AD, Bestebroer J, van Stempvoort G, Musters RJP, Garcia-Vallejo JJ, Picavet DI, Weerd RVD, Maletta M, Kuijl CP, van der Wel NN, Bitter W. The ESX-5 System of Pathogenic Mycobacteria Is Involved In Capsule Integrity and Virulence through Its Substrate PPE10. PLoS Pathog 2016; 12:e1005696. [PMID: 27280885 PMCID: PMC4900558 DOI: 10.1371/journal.ppat.1005696] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/20/2016] [Indexed: 11/18/2022] Open
Abstract
Mycobacteria produce a capsule layer, which consists of glycan-like polysaccharides and a number of specific proteins. In this study, we show that, in slow-growing mycobacteria, the type VII secretion system ESX-5 plays a major role in the integrity and stability of the capsule. We have identified PPE10 as the ESX-5 substrate responsible for this effect. Mutants in esx-5 and ppe10 both have impaired capsule integrity as well as reduced surface hydrophobicity. Electron microscopy, immunoblot and flow cytometry analyses demonstrated reduced amounts of surface localized proteins and glycolipids, and morphological differences in the capsular layer. Since capsular proteins secreted by the ESX-1 system are important virulence factors, we tested the effect of the mutations that cause capsular defects on virulence mechanisms. Both esx-5 and ppe10 mutants of Mycobacterium marinum were shown to be impaired in ESX-1-dependent hemolysis. In agreement with this, the ppe10 and esx5 mutants showed reduced recruitment of ubiquitin in early macrophage infection and intermediate attenuation in zebrafish embryos. These results provide a pivotal role for the ESX-5 secretion system and its substrate PPE10, in the capsular integrity of pathogenic mycobacteria. These findings open up new roads for research on the mycobacterial capsule and its role in virulence and immune modulation.
Collapse
Affiliation(s)
- Louis S Ates
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | - Aniek D van der Woude
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands.,Department of Molecular Microbiology, VU University, Amsterdam, the Netherlands
| | - Jovanka Bestebroer
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | | | - René J P Musters
- Department of Physiology and Cardiology, VU University Medical Center, Amsterdam, the Netherlands
| | - Juan J Garcia-Vallejo
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, the Netherlands
| | - Daisy I Picavet
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Amsterdam the Netherlands
| | - Robert van de Weerd
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Coenraad P Kuijl
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | - Nicole N van der Wel
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Amsterdam the Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands.,Department of Molecular Microbiology, VU University, Amsterdam, the Netherlands
| |
Collapse
|
12
|
Ates LS, Ummels R, Commandeur S, van der Weerd R, Sparrius M, Weerdenburg E, Alber M, Kalscheuer R, Piersma SR, Abdallah AM, Abd El Ghany M, Abdel-Haleem AM, Pain A, Jiménez CR, Bitter W, Houben EN. Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria. PLoS Genet 2015; 11:e1005190. [PMID: 25938982 PMCID: PMC4418733 DOI: 10.1371/journal.pgen.1005190] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 04/02/2015] [Indexed: 12/03/2022] Open
Abstract
Mycobacteria possess different type VII secretion (T7S) systems to secrete proteins across their unusual cell envelope. One of these systems, ESX-5, is only present in slow-growing mycobacteria and responsible for the secretion of multiple substrates. However, the role of ESX-5 substrates in growth and/or virulence is largely unknown. In this study, we show that esx-5 is essential for growth of both Mycobacterium marinum and Mycobacterium bovis. Remarkably, this essentiality can be rescued by increasing the permeability of the outer membrane, either by altering its lipid composition or by the introduction of the heterologous porin MspA. Mutagenesis of the first nucleotide-binding domain of the membrane ATPase EccC5 prevented both ESX-5-dependent secretion and bacterial growth, but did not affect ESX-5 complex assembly. This suggests that the rescuing effect is not due to pores formed by the ESX-5 membrane complex, but caused by ESX-5 activity. Subsequent proteomic analysis to identify crucial ESX-5 substrates confirmed that all detectable PE and PPE proteins in the cell surface and cell envelope fractions were routed through ESX-5. Additionally, saturated transposon-directed insertion-site sequencing (TraDIS) was applied to both wild-type M. marinum cells and cells expressing mspA to identify genes that are not essential anymore in the presence of MspA. This analysis confirmed the importance of esx-5, but we could not identify essential ESX-5 substrates, indicating that multiple of these substrates are together responsible for the essentiality. Finally, examination of phenotypes on defined carbon sources revealed that an esx-5 mutant is strongly impaired in the uptake and utilization of hydrophobic carbon sources. Based on these data, we propose a model in which the ESX-5 system is responsible for the transport of cell envelope proteins that are required for nutrient uptake. These proteins might in this way compensate for the lack of MspA-like porins in slow-growing mycobacteria.
Collapse
Affiliation(s)
- Louis S. Ates
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Susanna Commandeur
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Robert van der Weerd
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Marion Sparrius
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Eveline Weerdenburg
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Marina Alber
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Rainer Kalscheuer
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sander R. Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, the Netherlands
| | - Abdallah M. Abdallah
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Moataz Abd El Ghany
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Alyaa M. Abdel-Haleem
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Connie R. Jiménez
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, the Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicine & Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Edith N.G. Houben
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicine & Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|