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Senkpeil L, Bhardwaj J, Little MR, Holla P, Upadhye A, Fusco EM, Swanson Ii PA, Wiegand RE, Macklin MD, Bi K, Flynn BJ, Yamamoto A, Gaskin EL, Sather DN, Oblak AL, Simpson E, Gao H, Haining WN, Yates KB, Liu X, Murshedkar T, Richie TL, Sim BKL, Otieno K, Kariuki S, Xuei X, Liu Y, Polidoro RB, Hoffman SL, Oneko M, Steinhardt LC, Schmidt NW, Seder RA, Tran TM. Innate immune activation restricts priming and protective efficacy of the radiation-attenuated PfSPZ malaria vaccine. JCI Insight 2024:e167408. [PMID: 38687615 DOI: 10.1172/jci.insight.167408] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
A systems analysis was conducted to determine the potential molecular mechanisms underlying differential immunogenicity and protective efficacy results of a clinical trial of the radiation-attenuated whole sporozoite PfSPZ Vaccine in African infants. Innate immune activation and myeloid signatures at pre-vaccination baseline correlated with protection from Pf parasitemia in placebo controls. These same signatures were associated with susceptibility to parasitemia among infants who received the highest and most protective PfSPZ Vaccine dose. Machine learning identified spliceosome, proteosome, and resting dendritic cell signatures as pre-vaccination features predictive of protection after highest-dose PfSPZ vaccination, whereas baseline CSP-specific IgG predicted non-protection. Pre-vaccination innate inflammatory and myeloid signatures were associated with higher sporozoite-specific IgG Ab response but undetectable PfSPZ-specific CD8+ T-cell responses post-vaccination. Consistent with these human data, innate stimulation in vivo conferred protection against infection by sporozoite injection in malaria-naïve mice while diminishing the CD8+ T-cell response to radiation-attenuated sporozoites. These data suggest a dichotomous role of innate stimulation for malaria protection and induction of protective immunity of whole-sporozoite malaria vaccines. The uncoupling of vaccine-induced protective immunity achieved by Abs from more protective CD8+ T cell responses suggest that PfSPZ Vaccine efficacy in malaria-endemic settings may be constrained by opposing antigen presentation pathways.
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Affiliation(s)
- Leetah Senkpeil
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America
| | - Jyoti Bhardwaj
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America
| | - Morgan R Little
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Depa, Indiana University School of Medicine, Indianapolis, United States of America
| | - Prasida Holla
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Depa, Indiana University School of Medicine, Indianapolis, United States of America
| | - Aditi Upadhye
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America
| | - Elizabeth M Fusco
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, United States of America
| | - Phillip A Swanson Ii
- Cellular Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, NIH, Bethesda, United States of America
| | - Ryan E Wiegand
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Glob, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Michael D Macklin
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America
| | - Kevin Bi
- Broad Institute of MIT Harvard, Cambridge, United States of America
| | - Barbara J Flynn
- Cellular Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, NIH, Bethesda, United States of America
| | - Ayako Yamamoto
- Cellular Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, NIH, Bethesda, United States of America
| | - Erik L Gaskin
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America
| | - D Noah Sather
- Center for Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States of America
| | - Adrian L Oblak
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, United States of America
| | - Edward Simpson
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, United States of America
| | - Hongyu Gao
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, United States of America
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Kathleen B Yates
- Broad Institute of MIT Harvard, Cambridge, United States of America
| | - Xiaowen Liu
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, United States of America
| | | | | | - B Kim Lee Sim
- Manufacturing, Sanaria Inc., Rockville, United States of America
| | - Kephas Otieno
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Simon Kariuki
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Xiaoling Xuei
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, United States of America
| | - Yunlong Liu
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, United States of America
| | - Rafael B Polidoro
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Depa, Indiana University School of Medicine, Indianapolis, United States of America
| | | | - Martina Oneko
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Laura C Steinhardt
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Glob, Center for Disease Control and Prevention, Atlanta, United States of America
| | - Nathan W Schmidt
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Depa, Indiana University School of Medicine, Indianapolis, United States of America
| | - Robert A Seder
- Cellular Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, NIH, Bethesda, United States of America
| | - Tuan M Tran
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America
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3
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Gutierrez-Arcelus M, Teslovich N, Mola AR, Polidoro RB, Nathan A, Kim H, Hannes S, Slowikowski K, Watts GFM, Korsunsky I, Brenner MB, Raychaudhuri S, Brennan PJ. Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions. Nat Commun 2019; 10:687. [PMID: 30737409 PMCID: PMC6368609 DOI: 10.1038/s41467-019-08604-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 01/21/2019] [Indexed: 02/06/2023] Open
Abstract
How innate T cells (ITC), including invariant natural killer T (iNKT) cells, mucosal-associated invariant T (MAIT) cells, and γδ T cells, maintain a poised effector state has been unclear. Here we address this question using low-input and single-cell RNA-seq of human lymphocyte populations. Unbiased transcriptomic analyses uncover a continuous ‘innateness gradient’, with adaptive T cells at one end, followed by MAIT, iNKT, γδ T and natural killer cells at the other end. Single-cell RNA-seq reveals four broad states of innateness, and heterogeneity within canonical innate and adaptive populations. Transcriptional and functional data show that innateness is characterized by pre-formed mRNA encoding effector functions, but impaired proliferation marked by decreased baseline expression of ribosomal genes. Together, our data shed new light on the poised state of ITC, in which innateness is defined by a transcriptionally-orchestrated trade-off between rapid cell growth and rapid effector function. Innate T cells (ITC) contain many subsets and are poised to promptly respond to antigens and pathogens, but how this poised state is maintained is still unclear. Here the authors perform single-cell RNA-seq to align the various ITC subsets along an ‘innateness gradient’ that is associated with changes in proliferation and effector functions.
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Affiliation(s)
- Maria Gutierrez-Arcelus
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Nikola Teslovich
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alex R Mola
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rafael B Polidoro
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Aparna Nathan
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hyun Kim
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Susan Hannes
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kamil Slowikowski
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerald F M Watts
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ilya Korsunsky
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael B Brenner
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Soumya Raychaudhuri
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115. .,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA. .,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Faculty of Medical and Human Sciences, University of Manchester, Manchester, M13 9PL, UK.
| | - Patrick J Brennan
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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5
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Belew AT, Junqueira C, Rodrigues-Luiz GF, Valente BM, Oliveira AER, Polidoro RB, Zuccherato LW, Bartholomeu DC, Schenkman S, Gazzinelli RT, Burleigh BA, El-Sayed NM, Teixeira SMR. Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection. PLoS Pathog 2017; 13:e1006767. [PMID: 29240831 PMCID: PMC5746284 DOI: 10.1371/journal.ppat.1006767] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 06/17/2017] [Revised: 12/28/2017] [Accepted: 11/22/2017] [Indexed: 01/23/2023] Open
Abstract
Trypanosoma cruzi, the protozoan that causes Chagas disease, has a complex life cycle involving several morphologically and biochemically distinct stages that establish intricate interactions with various insect and mammalian hosts. It has also a heterogeneous population structure comprising strains with distinct properties such as virulence, sensitivity to drugs, antigenic profile and tissue tropism. We present a comparative transcriptome analysis of two cloned T. cruzi strains that display contrasting virulence phenotypes in animal models of infection: CL Brener is a virulent clone and CL-14 is a clone that is neither infective nor pathogenic in in vivo models of infection. Gene expression analysis of trypomastigotes and intracellular amastigotes harvested at 60 and 96 hours post-infection (hpi) of human fibroblasts revealed large differences that reflect the parasite’s adaptation to distinct environments during the infection of mammalian cells, including changes in energy sources, oxidative stress responses, cell cycle control and cell surface components. While extensive transcriptome remodeling was observed when trypomastigotes of both strains were compared to 60 hpi amastigotes, differences in gene expression were much less pronounced when 96 hpi amastigotes and trypomastigotes of CL Brener were compared. In contrast, the differentiation of the avirulent CL-14 from 96 hpi amastigotes to extracellular trypomastigotes was associated with considerable changes in gene expression, particularly in gene families encoding surface proteins such as trans-sialidases, mucins and the mucin associated surface proteins (MASPs). Thus, our comparative transcriptome analysis indicates that the avirulent phenotype of CL-14 may be due, at least in part, to a reduced or delayed expression of genes encoding surface proteins that are associated with the transition of amastigotes to trypomastigotes, an essential step in the establishment of the infection in the mammalian host. Confirming the role of members of the trans-sialidase family of surface proteins for parasite differentiation, transfected CL-14 constitutively expressing a trans-sialidase gene displayed faster kinetics of trypomastigote release in the supernatant of infected cells compared to wild type CL-14. Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, is an infection that occurs in several Latin American countries, resulting in a mild illness or in severe damage of the heart and intestinal tract. Such a broad spectrum of clinical manifestations observed in Chagas disease patients is likely due to differences in host susceptibility as well as to a large heterogeneity among T. cruzi isolates. The identification of virulence factors that are differentially expressed in the parasite population is a valuable strategy for understanding of the distinct interactions that occur between this pathogen and its host, which may or may not lead to pathogenesis. By comparing the gene expression profiles of two T. cruzi strains that display contrasting virulence phenotypes in animal models of infection, we identified a central role for genes encoding surface proteins that is associated with the differentiation from intracellular replicative amastigotes to infective trypomastigotes. We showed that the expression of these genes occurs differentially within the two strains and this difference may be a factor that impacts parasite survival and dissemination in the mammalian host.
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Affiliation(s)
- A. Trey Belew
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Caroline Junqueira
- Centro de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriela F. Rodrigues-Luiz
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruna M. Valente
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Antonio Edson R. Oliveira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rafael B. Polidoro
- Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Luciana W. Zuccherato
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Daniella C. Bartholomeu
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sergio Schenkman
- Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Ricardo T. Gazzinelli
- Centro de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Barbara A. Burleigh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Najib M. El-Sayed
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (SMRT); (NES)
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail: (SMRT); (NES)
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6
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Padmanabhan PK, Polidoro RB, Barteneva NS, Gazzinelli RT, Burleigh BA. Transient transfection and expression of foreign and endogenous genes in the intracellular stages of Trypanosoma cruzi. Mol Biochem Parasitol 2015; 198:100-3. [PMID: 25712770 DOI: 10.1016/j.molbiopara.2015.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/06/2015] [Accepted: 02/14/2015] [Indexed: 11/17/2022]
Abstract
The capacity for rapid localization of epitope-tagged or fluorescent fusion proteins in cells is an important tool for biological discovery and functional analysis. For Trypanosoma cruzi, the protozoan parasite that causes human Chagas disease, visualization of ectopically-expressed proteins in the clinically-relevant mammalian stages is hindered by the necessity to first perform transfection and lengthy selection procedures in the insect vector form of the parasite. Here, we demonstrate the ability to by-pass the insect stage with the delivery of plasmid DNA to non-dividing, tissue culture trypomastigotes such that upon host cell infection, transgenes are expressed and rapidly localized in intracellular T. cruzi amastigotes. The inclusion of a sorting step prior to host cell infection by trypomastigotes greatly enriches (>90%) the number of transgene-expressing amastigotes observed in mammalian host cells. This is a significant methodological advance that has the potential to accelerate the pace of discovery in the Chagas disease field.
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Affiliation(s)
- Prasad K Padmanabhan
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Ave, Boston, MA 02115, United States
| | - Rafael B Polidoro
- Departamento de Bioquímica e Imunologia and Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Natasha S Barteneva
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, United States
| | - Ricardo T Gazzinelli
- Departamento de Bioquímica e Imunologia and Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Minas Gerais, Brazil; Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, 30190-002 Belo Horizonte, MG, Brazil; Division of Infectious Disease and Immunology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, United States
| | - Barbara A Burleigh
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Ave, Boston, MA 02115, United States.
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