1
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Fiore-Gartland A, Srivastava H, Seese A, Day T, Penn-Nicholson A, Luabeya AKK, Du Plessis N, Loxton AG, Bekker LG, Diacon A, Walzl G, Sagawa ZK, Reed SG, Scriba TJ, Hatherill M, Coler R. Co-regulation of innate and adaptive immune responses induced by ID93+GLA-SE vaccination in humans. Front Immunol 2024; 15:1441944. [PMID: 39381003 PMCID: PMC11458388 DOI: 10.3389/fimmu.2024.1441944] [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: 05/31/2024] [Accepted: 09/02/2024] [Indexed: 10/10/2024] Open
Abstract
Introduction Development of an effective vaccine against tuberculosis is a critical step towards reducing the global burden of disease. A therapeutic vaccine might also reduce the high rate of TB recurrence and help address the challenges of drug-resistant strains. ID93+GLA-SE is a candidate subunit vaccine that will soon be evaluated in a phase 2b efficacy trial for prevention of recurrent TB among patients undergoing TB treatment. ID93+GLA-SE vaccination was shown to elicit robust CD4+ T cell and IgG antibody responses among recently treated TB patients in the TBVPX-203 Phase 2a study (NCT02465216), but the mechanisms underlying these responses are not well understood. Methods In this study we used specimens from TBVPX-203 participants to describe the changes in peripheral blood gene expression that occur after ID93+GLA-SE vaccination. Results Analyses revealed several distinct modules of co-varying genes that were either up- or down-regulated after vaccination, including genes associated with innate immune pathways at 3 days post-vaccination and genes associated with lymphocyte expansion and B cell activation at 7 days post-vaccination. Notably, the regulation of these gene modules was affected by the dose schedule and by participant sex, and early innate gene signatures were correlated with the ID93-specific CD4+ T cell response. Discussion The results provide insight into the complex interplay of the innate and adaptive arms of the immune system in developing responses to vaccination with ID93+GLA-SE and demonstrate how dosing and schedule can affect vaccine responses.
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Affiliation(s)
- Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Himangi Srivastava
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Aaron Seese
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Tracey Day
- Infectious Diseases and Vaccines, Innovative Medicine, Johnson & Johnson, Leiden, Netherlands
| | | | - Angelique Kany Kany Luabeya
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nelita Du Plessis
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre G. Loxton
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Linda-Gail Bekker
- The Desmond Tutu Human Immunodeficiency Virus (HIV) Centre, University of Cape Town, Cape Town, South Africa
| | | | - Gerhard Walzl
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | | | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Rhea Coler
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle Children’s, Seattle, WA, United States
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
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2
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Apps R, Biancotto A, Candia J, Kotliarov Y, Perl S, Cheung F, Farmer R, Mulè MP, Rachmaninoff N, Chen J, Martins AJ, Shi R, Zhou H, Bansal N, Schum P, Olnes MJ, Milanez-Almeida P, Han KL, Sellers B, Cortese M, Hagan T, Rouphael N, Pulendran B, King L, Manischewitz J, Khurana S, Golding H, van der Most RG, Dickler HB, Germain RN, Schwartzberg PL, Tsang JS. Acute and persistent responses after H5N1 vaccination in humans. Cell Rep 2024; 43:114706. [PMID: 39235945 DOI: 10.1016/j.celrep.2024.114706] [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: 01/16/2024] [Revised: 04/14/2024] [Accepted: 08/16/2024] [Indexed: 09/07/2024] Open
Abstract
To gain insight into how an adjuvant impacts vaccination responses, we use systems immunology to study human H5N1 influenza vaccination with or without the adjuvant AS03, longitudinally assessing 14 time points including multiple time points within the first day after prime and boost. We develop an unsupervised computational framework to discover high-dimensional response patterns, which uncover adjuvant- and immunogenicity-associated early response dynamics, including some that differ post prime versus boost. With or without adjuvant, some vaccine-induced transcriptional patterns persist to at least 100 days after initial vaccination. Single-cell profiling of surface proteins, transcriptomes, and chromatin accessibility implicates transcription factors in the erythroblast-transformation-specific (ETS) family as shaping these long-lasting signatures, primarily in classical monocytes but also in CD8+ naive-like T cells. These cell-type-specific signatures are elevated at baseline in high-antibody responders in an independent vaccination cohort, suggesting that antigen-agnostic baseline immune states can be modulated by vaccine antigens alone to enhance future responses.
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Affiliation(s)
- Richard Apps
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | | | - Julián Candia
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA; Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD, USA
| | - Shira Perl
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; NIH Oxford-Cambridge Scholars Program, Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, UCB2 0QQ Cambridge, UK
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Rongye Shi
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Huizhi Zhou
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Paula Schum
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Matthew J Olnes
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | | | - Kyu Lee Han
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Brian Sellers
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Mario Cortese
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Thomas Hagan
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Decatur, GA 30030, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA; Hope Clinic of the Emory Vaccine Center, Decatur, GA 30030, USA
| | - Lisa King
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20993 USA
| | - Jody Manischewitz
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20993 USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20993 USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20993 USA
| | | | | | - Ronald N Germain
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Pamela L Schwartzberg
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA; Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - John S Tsang
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA; Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Center for Systems and Engineering Immunology, Departments of Immunobiology and Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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3
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Alonso-Rodríguez N, Vianello E, van Veen S, Jenum S, Tonby K, van Riessen R, Lai X, Mortensen R, Ottenhoff THM, Dyrhol-Riise AM. Whole blood RNA signatures in tuberculosis patients receiving H56:IC31 vaccine as adjunctive therapy. Front Immunol 2024; 15:1350593. [PMID: 38433842 PMCID: PMC10904528 DOI: 10.3389/fimmu.2024.1350593] [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: 12/05/2023] [Accepted: 01/25/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction Therapeutic vaccination in tuberculosis (TB) represents a Host Directed Therapy strategy which enhances immune responses in order to improve clinical outcomes and shorten TB treatment. Previously, we have shown that the subunit H56:IC31 vaccine induced both humoral and cellular immune responses when administered to TB patients adjunctive to standard TB treatment (TBCOX2 study, NCT02503839). Here we present the longitudinal whole blood gene expression patterns in H56:IC31 vaccinated TB patients compared to controls receiving standard TB treatment only. Methods The H56:IC31 group (N=11) and Control group (N=7) underwent first-line TB treatment for 182 days. The H56:IC31 group received 5 micrograms of the H56:IC31 vaccine (Statens Serum Institut; SSI, Valneva Austria GmbH) intramuscularly at day 84 and day 140. Total RNA was extracted from whole blood samples collected in PAXgene tubes on days 0, 84, 98, 140, 154, 182 and 238. The expression level of 183 immune-related genes was measured by high-throughput microfluidic qPCR (Biomark HD system, Standard BioTools). Results The targeted gene expression profiling unveiled the upregulation of modules such as interferon (IFN) signalling genes, pattern recognition receptors and small nucleotide guanosine triphosphate (GTP)-ases in the vaccinated group compared to controls two weeks after administration of the first H56:IC31 vaccine. Additionally, the longitudinal analysis of the Adolescent Cohort Study-Correlation of Risk (ACS-COR) signature showed a progressive downregulation in both study arms towards the end of TB treatment, in congruence with reported treatment responses and clinical improvements. Still, two months after the end of TB treatment, vaccinated patients, and especially those developing both cellular and humoral vaccine responses, showed a lower expression of the ACS-COR genes compared to controls. Discussion Our data report gene expression patterns following H56:IC31 vaccination which might be interpreted as a lower risk of relapse in therapeutically vaccinated patients. Further studies are needed to conclude if these gene expression patterns could be used as prognostic biosignatures for therapeutic TB vaccine responses.
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Affiliation(s)
| | - Eleonora Vianello
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Suzanne van Veen
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Synne Jenum
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Kristian Tonby
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rosalie van Riessen
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Xiaoran Lai
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rasmus Mortensen
- Deptartment of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Anne Ma Dyrhol-Riise
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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4
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Imbratta C, Gela A, Bilek N, Mabwe S, Cloete Y, Mortensen R, Borges ÁH, Maenetje P, Mlotshwa M, Churchyard G, Sudi L, Sabi I, Meewes P, Wallis CL, Hatherill M, Scriba TJ, Nemes E. Qualification of the differential leukocyte count and immunophenotyping in cryopreserved ex vivo whole blood assay. Cytometry A 2023; 103:992-1003. [PMID: 37675607 DOI: 10.1002/cyto.a.24793] [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: 02/07/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/08/2023]
Abstract
We developed a flow cytometry-based assay, termed Differential Leukocyte Counting and Immunophenotyping in Cryopreserved Ex vivo whole blood (DLC-ICE), that allows quantification of absolute counts and frequencies of leukocyte subsets and measures expression of activation, phenotypic and functional markers. We evaluated the performance of the DLC-ICE assay by determining inter-operator variability for processing fresh whole blood (WB) from healthy donors collected at multiple clinical sites. In addition, we assessed inter-operator variability for staining of fixed cells and robustness across different anticoagulants. Accuracy was evaluated by comparing DLC-ICE measurements to real-time cell enumeration using an accredited hematology analyzer. Finally, we developed and tested the performance of a 27-colour immunophenotyping panel on cryopreserved fixed WB and compared results to matched fresh WB. Overall, we observed <20% variability in absolute counts and frequencies of granulocytes, monocytes and lymphocytes (T, B and NK cells) when fresh WB was collected in different anti-coagulant tubes, processed or stained by independent operators. Absolute cell counts measured across operators and anti-coagulants using the DLC-ICE method exhibited excellent correlation with the reference method, complete blood count (CBC) with differential, measured using a hematology analyzer (r2 > 0.9 for majority of measurements). A comparison of leukocyte immunophenotyping on fresh WB versus DLC-ICE processed blood yielded equivalent and linear results over a wide dynamic range (r2 = 0.94 over 10-104 cells/μL). These results demonstrate low variability across trained operators, high robustness, linearity and accuracy, supporting utility of the DLC-ICE assay for large cohort studies involving multiple clinical research sites.
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Affiliation(s)
- Claire Imbratta
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anele Gela
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Simbarashe Mabwe
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Yolundi Cloete
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Rasmus Mortensen
- Department of Infectious Diseases Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Álvaro H Borges
- Department of Infectious Diseases Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Pholo Maenetje
- Aurum Institute, Parktown, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Mandla Mlotshwa
- Aurum Institute, Parktown, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Gavin Churchyard
- Aurum Institute, Parktown, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Lwitiho Sudi
- Mbeya Medical Research Centre, National Institute for Medical Research (NIMR), Mbeya, Tanzania
| | - Issa Sabi
- Mbeya Medical Research Centre, National Institute for Medical Research (NIMR), Mbeya, Tanzania
| | | | - Carole L Wallis
- BARC, South Africa
- Lancet Laboratories, Johannesburg, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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5
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Ouaked N, Demoitié MA, Godfroid F, Mortier MC, Vanloubbeeck Y, Temmerman ST. Non-clinical evaluation of local and systemic immunity induced by different vaccination strategies of the candidate tuberculosis vaccine M72/AS01. Tuberculosis (Edinb) 2023; 143:102425. [PMID: 38180028 DOI: 10.1016/j.tube.2023.102425] [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: 07/04/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 01/06/2024]
Abstract
A new efficacious tuberculosis vaccine targeting adolescents/adults represents an urgent medical need. The M72/AS01E vaccine candidate protected half of the latently-infected adults against progression to pulmonary tuberculosis in a Phase IIb trial (NCT01755598). We report that three immunizations of mice, two weeks apart, with AS01-adjuvanted M72 induced polyfunctional, Th1-cytokine-expressing M72-specific CD4+/CD8+ T cells in blood and lungs, with the highest frequencies in lungs. Antigen-dose reductions across the three vaccinations skewed pulmonary CD4+ T-cell profiles towards IL-17 expression. In blood, reducing antigen and adjuvant doses of only the third injection (to 1/5th or 1/25th of those of the first injections) did not significantly alter CD4+ T-cell/antibody responses; applying a 10-week delay for the fractional third dose enhanced antibody titers. Delaying a full-dose booster enhanced systemic CD4+ T-cell and antibody responses. Cross-reactivity with PPE and non-PPE proteins was assessed, as Mycobacterium tuberculosis (Mtb) virulence factors and evasion mechanisms are often associated with PE/PPE proteins, to which Mtb39a (contained in M72) belongs. In silico/in vivo analyses revealed that M72/AS01 induced cross-reactive systemic CD4+ T-cell responses to epitopes in a non-vaccine antigen (putative latency-associated Mtb protein PPE24/Rv1753c). These preclinical data describing novel mechanisms of M72/AS01-induced immunity could guide future clinical development of the vaccine.
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Affiliation(s)
- Nadia Ouaked
- GSK, Rue de l'Institut 89, 1330, Rixensart, Belgium
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6
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Kim H, Choi HG, Shin SJ. Bridging the gaps to overcome major hurdles in the development of next-generation tuberculosis vaccines. Front Immunol 2023; 14:1193058. [PMID: 37638056 PMCID: PMC10451085 DOI: 10.3389/fimmu.2023.1193058] [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: 03/24/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Although tuberculosis (TB) remains one of the leading causes of death from an infectious disease worldwide, the development of vaccines more effective than bacille Calmette-Guérin (BCG), the only licensed TB vaccine, has progressed slowly even in the context of the tremendous global impact of TB. Most vaccine candidates have been developed to strongly induce interferon-γ (IFN-γ)-producing T-helper type 1 (Th1) cell responses; however, accumulating evidence has suggested that other immune factors are required for optimal protection against Mycobacterium tuberculosis (Mtb) infection. In this review, we briefly describe the five hurdles that must be overcome to develop more effective TB vaccines, including those with various purposes and tested in recent promising clinical trials. In addition, we discuss the current knowledge gaps between preclinical experiments and clinical studies regarding peripheral versus tissue-specific immune responses, different underlying conditions of individuals, and newly emerging immune correlates of protection. Moreover, we propose how recently discovered TB risk or susceptibility factors can be better utilized as novel biomarkers for the evaluation of vaccine-induced protection to suggest more practical ways to develop advanced TB vaccines. Vaccines are the most effective tools for reducing mortality and morbidity from infectious diseases, and more advanced technologies and a greater understanding of host-pathogen interactions will provide feasibility and rationale for novel vaccine design and development.
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Affiliation(s)
- Hongmin Kim
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Han-Gyu Choi
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
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7
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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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8
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Liu YE, Darrah PA, Zeppa JJ, Kamath M, Laboune F, Douek DC, Maiello P, Roederer M, Flynn JL, Seder RA, Khatri P. Blood transcriptional correlates of BCG-induced protection against tuberculosis in rhesus macaques. Cell Rep Med 2023; 4:101096. [PMID: 37390827 PMCID: PMC10394165 DOI: 10.1016/j.xcrm.2023.101096] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/29/2023] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Blood-based correlates of vaccine-induced protection against tuberculosis (TB) are urgently needed. Here, we analyze the blood transcriptome of rhesus macaques immunized with varying doses of intravenous (i.v.) BCG followed by Mycobacterium tuberculosis (Mtb) challenge. We use high-dose i.v. BCG recipients for "discovery" and validate our findings in low-dose recipients and in an independent cohort of macaques receiving BCG via different routes. We identify seven vaccine-induced gene modules, including an innate module (module 1) enriched for type 1 interferon and RIG-I-like receptor signaling pathways. Module 1 on day 2 post-vaccination highly correlates with lung antigen-responsive CD4 T cells at week 8 and with Mtb and granuloma burden following challenge. Parsimonious signatures within module 1 at day 2 post-vaccination predict protection following challenge with area under the receiver operating characteristic curve (AUROC) ≥0.91. Together, these results indicate that the early innate transcriptional response to i.v. BCG in peripheral blood may provide a robust correlate of protection against TB.
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Affiliation(s)
- Yiran E Liu
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA; PhD Program in Epidemiology and Clinical Research, Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patricia A Darrah
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph J Zeppa
- Department of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Farida Laboune
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Sciences, Stanford University, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
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9
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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 PMCID: PMC10187016 DOI: 10.1002/iid3.854] [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: 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 HospitalPLA General HospitalBeijingChina
| | - 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 HospitalPLA General HospitalBeijingChina
| | - 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 HospitalPLA General HospitalBeijingChina
| | - 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 HospitalPLA General HospitalBeijingChina
| | - 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 HospitalPLA General HospitalBeijingChina
| | - 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 HospitalPLA General HospitalBeijingChina
| | - 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 HospitalPLA General HospitalBeijingChina
| | - 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 HospitalPLA General HospitalBeijingChina
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10
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Subsequent AS01-adjuvanted vaccinations induce similar transcriptional responses in populations with different disease statuses. PLoS One 2022; 17:e0276505. [DOI: 10.1371/journal.pone.0276505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/07/2022] [Indexed: 11/12/2022] Open
Abstract
Transcriptional responses to adjuvanted vaccines can vary substantially among populations. Interindividual diversity in levels of pathogen exposure, and thus of cell-mediated immunological memory at baseline, may be an important determinant of population differences in vaccine responses. Adjuvant System AS01 is used in licensed or candidate vaccines for several diseases and populations, yet the impact of pre-existing immunity on its adjuvanticity remains to be elucidated. In this exploratory post-hoc analysis of clinical trial samples (clinicalTrials.gov: NCT01424501), we compared gene expression patterns elicited by two immunizations with the candidate tuberculosis (TB) vaccine M72/AS01, between three groups of individuals with different levels of memory responses to TB antigens before vaccination. Analyzed were one group of TB-disease-treated individuals, and two groups of TB-disease-naïve individuals who were (based on purified protein derivative [PPD] skin-test results) stratified into PPD-positive and PPD-negative groups. Although TB-disease-treated individuals displayed slightly stronger transcriptional responses after each vaccine dose, functional gene signatures were overall not distinctly different between groups. Considering the similarities with the signatures found previously for other AS01-adjuvanted vaccines, many features of the response appeared to be adjuvant-driven. Across groups, cell proliferation-related signals at 7 days post-dose 1 were associated with increased anti-M72 antibody response magnitudes. These early signals were stronger in the TB-disease-treated group as compared to both TB-disease-naïve groups. Interindividual homogeneity in gene expression levels was also higher for TB-disease-treated individuals post-dose 1, but increased in all groups post-dose 2 to attain similar levels between the three groups. Altogether, strong cell-mediated memory responses at baseline accelerated and amplified transcriptional responses to a single dose of this AS01-adjuvanted vaccine, resulting in more homogenous gene expression levels among the highly-primed individuals as compared to the disease-naïve individuals. However, after a second vaccination, response heterogeneity decreased and was similar across groups, irrespective of the degree of immune memory acquired at baseline. This information can support the design and analysis of future clinical trials evaluating AS01-adjuvanted vaccines.
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11
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Gómez-Aguado I, Rodríguez-Castejón J, Beraza-Millor M, Rodríguez-Gascón A, Del Pozo-Rodríguez A, Solinís MÁ. mRNA delivery technologies: Toward clinical translation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 372:207-293. [PMID: 36064265 DOI: 10.1016/bs.ircmb.2022.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Messenger RNA (mRNA)-therapies have recently taken a huge step toward clinic thanks to the first mRNA-based medicinal products marketed. mRNA features for clinical purposes are improved by chemical modifications, but the inclusion in a delivery system is a regular requirement. mRNA nanomedicines must be designed for the specific therapeutic purpose, protecting the nucleic acid and facilitating the overcoming of biological barriers. Polymers, polypeptides, and cationic lipids are the main used materials to design mRNA delivery systems. Among them, lipid nanoparticles (LNPs) are the most advanced ones, and currently they are at the forefront of preclinical and clinical evaluation in several fields, including immunotherapy (against infectious diseases and cancer), protein replacement, gene editing and regenerative medicine. This chapter includes an overview on mRNA delivery technologies, with special interest in LNPs, and the most recent advances in their clinical application. Liposomes are the mRNA delivery technology with the highest clinical translation among LNPs, whereas the first clinical trial of a therapeutic mRNA formulated in exosomes has been recently approved for protein replacement therapy. The first mRNA products approved by the regulatory agencies worldwide are LNP-based mRNA vaccines against viral infections, specifically against the 2019 coronavirus disease (COVID-19). The clinical translation of mRNA-therapies for cancer is mainly focused on three strategies: anti-cancer vaccination by means of delivering cancer antigens or acting as an adjuvant, mRNA-engineered chimeric antigen receptors (CARs) and T-cell receptors (TCRs), and expression of antibodies and immunomodulators. Cancer immunotherapy and, more recently, COVID-19 vaccines spearhead the advance of mRNA clinical use.
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Affiliation(s)
- Itziar Gómez-Aguado
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - Julen Rodríguez-Castejón
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - Marina Beraza-Millor
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - Alicia Rodríguez-Gascón
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - Ana Del Pozo-Rodríguez
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - María Ángeles Solinís
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain.
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12
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2021 White Paper on Recent Issues in Bioanalysis: TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness ( Part 3 - Recommendations on Gene Therapy, Cell Therapy, Vaccine Assays; Immunogenicity of Biotherapeutics and Novel Modalities; Integrated Summary of Immunogenicity Harmonization). Bioanalysis 2022; 14:737-793. [PMID: 35578991 DOI: 10.4155/bio-2022-0081] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The 15th edition of the Workshop on Recent Issues in Bioanalysis (15th WRIB) was held on 27 September to 1 October 2021. Even with a last-minute move from in-person to virtual, an overwhelmingly high number of nearly 900 professionals representing pharma and biotech companies, contract research organizations (CROs), and multiple regulatory agencies still eagerly convened to actively discuss the most current topics of interest in bioanalysis. The 15th WRIB included 3 Main Workshops and 7 Specialized Workshops that together spanned 1 week in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on biomarker assay development and validation (BAV) (focused on clarifying the confusion created by the increased use of the term "Context of Use - COU"); mass spectrometry of proteins (therapeutic, biomarker and transgene); state-of-the-art cytometry innovation and validation; and, critical reagent and positive control generation were the special features of the 15th edition. This 2021 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2021 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations on TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness. Part 1A (Endogenous Compounds, Small Molecules, Complex Methods, Regulated Mass Spec of Large Molecules, Small Molecule, PoC), Part 1B (Regulatory Agencies' Inputs on Bioanalysis, Biomarkers, Immunogenicity, Gene & Cell Therapy and Vaccine) and Part 2 (ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry) are published in volume 14 of Bioanalysis, issues 9 and 10 (2022), respectively.
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13
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A century of attempts to develop an effective tuberculosis vaccine: Why they failed? Int Immunopharmacol 2022; 109:108791. [PMID: 35487086 DOI: 10.1016/j.intimp.2022.108791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 11/23/2022]
Abstract
Tuberculosis (TB) remains a major global health problem despite widespread use of the Bacillus BCG vaccine. This situation is worsened by co-infection with HIV, and the development of multidrug-resistant Mycobacterium tuberculosis (Mtb) strains. Thus, novel vaccine candidates and improved vaccination strategies are urgently needed in order to reduce the incidence of TB and even to eradicate TB by 2050. Over the last few decades, 23 novel TB vaccines have entered into clinical trials, more than 13 new vaccines have reached various stages of preclinical development, and more than 50 potential candidates are in the discovery stage as next-generation vaccines. Nevertheless, why has a century of attempts to introduce an effective TB vaccine failed? Who should be blamed -scientists, human response, or Mtb strategies? Literature review reveals that the elimination of latent or active Mtb infections in a given population seems to be an epigenetic process. With a better understanding of the connections between bacterial infections and gene expression conditions in epigenetic events, opportunities arise in designing protective vaccines or therapeutic agents, particularly as epigenetic processes can be reversed. Therefore, this review provides a brief overview of different approaches towards novel vaccination strategies and the mechanisms underlying these approaches.
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14
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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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15
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Larsen SE, Williams BD, Rais M, Coler RN, Baldwin SL. It Takes a Village: The Multifaceted Immune Response to Mycobacterium tuberculosis Infection and Vaccine-Induced Immunity. Front Immunol 2022; 13:840225. [PMID: 35359957 PMCID: PMC8960931 DOI: 10.3389/fimmu.2022.840225] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Despite co-evolving with humans for centuries and being intensely studied for decades, the immune correlates of protection against Mycobacterium tuberculosis (Mtb) have yet to be fully defined. This lapse in understanding is a major lag in the pipeline for evaluating and advancing efficacious vaccine candidates. While CD4+ T helper 1 (TH1) pro-inflammatory responses have a significant role in controlling Mtb infection, the historically narrow focus on this cell population may have eclipsed the characterization of other requisite arms of the immune system. Over the last decade, the tuberculosis (TB) research community has intentionally and intensely increased the breadth of investigation of other immune players. Here, we review mechanistic preclinical studies as well as clinical anecdotes that suggest the degree to which different cell types, such as NK cells, CD8+ T cells, γ δ T cells, and B cells, influence infection or disease prevention. Additionally, we categorically outline the observed role each major cell type plays in vaccine-induced immunity, including Mycobacterium bovis bacillus Calmette-Guérin (BCG). Novel vaccine candidates advancing through either the preclinical or clinical pipeline leverage different platforms (e.g., protein + adjuvant, vector-based, nucleic acid-based) to purposefully elicit complex immune responses, and we review those design rationales and results to date. The better we as a community understand the essential composition, magnitude, timing, and trafficking of immune responses against Mtb, the closer we are to reducing the severe disease burden and toll on human health inflicted by TB globally.
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Affiliation(s)
- Sasha E. Larsen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA, United States
| | - Brittany D. Williams
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA, United States,Department of Global Health, University of Washington, Seattle, WA, United States
| | - Maham Rais
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA, United States
| | - Rhea N. Coler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA, United States,Department of Global Health, University of Washington, Seattle, WA, United States,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - Susan L. Baldwin
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA, United States,*Correspondence: Susan L. Baldwin,
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16
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Enriquez AB, Izzo A, Miller SM, Stewart EL, Mahon RN, Frank DJ, Evans JT, Rengarajan J, Triccas JA. Advancing Adjuvants for Mycobacterium tuberculosis Therapeutics. Front Immunol 2021; 12:740117. [PMID: 34759923 PMCID: PMC8572789 DOI: 10.3389/fimmu.2021.740117] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/26/2021] [Indexed: 01/15/2023] Open
Abstract
Tuberculosis (TB) remains one of the leading causes of death worldwide due to a single infectious disease agent. BCG, the only licensed vaccine against TB, offers limited protection against pulmonary disease in children and adults. TB vaccine research has recently been reinvigorated by new data suggesting alternative administration of BCG induces protection and a subunit/adjuvant vaccine that provides close to 50% protection. These results demonstrate the need for generating adjuvants in order to develop the next generation of TB vaccines. However, development of TB-targeted adjuvants is lacking. To help meet this need, NIAID convened a workshop in 2020 titled “Advancing Vaccine Adjuvants for Mycobacterium tuberculosis Therapeutics”. In this review, we present the four areas identified in the workshop as necessary for advancing TB adjuvants: 1) correlates of protective immunity, 2) targeting specific immune cells, 3) immune evasion mechanisms, and 4) animal models. We will discuss each of these four areas in detail and summarize what is known and what we can advance on in order to help develop more efficacious TB vaccines.
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Affiliation(s)
- Ana B Enriquez
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Angelo Izzo
- Tuberculosis Research Program, Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Shannon M Miller
- Center for Translational Medicine, University of Montana, Missoula, MT, United States.,Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT, United States
| | - Erica L Stewart
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases and Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Robert N Mahon
- Division of AIDS, Columbus Technologies & Services Inc., Contractor to National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Daniel J Frank
- Division of AIDS, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States
| | - Jay T Evans
- Center for Translational Medicine, University of Montana, Missoula, MT, United States.,Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT, United States
| | - Jyothi Rengarajan
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States.,Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - James A Triccas
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases and Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
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17
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Moita D, Nunes-Cabaço H, Mendes AM, Prudêncio M. A guide to investigating immune responses elicited by whole-sporozoite pre-erythrocytic vaccines against malaria. FEBS J 2021; 289:3335-3359. [PMID: 33993649 DOI: 10.1111/febs.16016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/19/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022]
Abstract
In the last few decades, considerable efforts have been made toward the development of efficient vaccines against malaria. Whole-sporozoite (Wsp) vaccines, which induce efficient immune responses against the pre-erythrocytic (PE) stages (sporozoites and liver forms) of Plasmodium parasites, the causative agents of malaria, are among the most promising immunization strategies tested until present. Several Wsp PE vaccination approaches are currently under evaluation in the clinic, including radiation- or genetically-attenuated Plasmodium sporozoites, live parasites combined with chemoprophylaxis, or genetically modified rodent Plasmodium parasites. In addition to the assessment of their protective efficacy, clinical trials of Wsp PE vaccine candidates inevitably involve the thorough investigation of the immune responses elicited by vaccination, as well as the identification of correlates of protection. Here, we review the main methodologies employed to dissect the humoral and cellular immune responses observed in the context of Wsp PE vaccine clinical trials and discuss future strategies to further deepen the knowledge generated by these studies, providing a toolbox for the in-depth analysis of vaccine-induced immunogenicity.
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Affiliation(s)
- Diana Moita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Helena Nunes-Cabaço
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - António M Mendes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Miguel Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
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18
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Mottram L, Lundgren A, Svennerholm AM, Leach S. A Systems Biology Approach Identifies B Cell Maturation Antigen (BCMA) as a Biomarker Reflecting Oral Vaccine Induced IgA Antibody Responses in Humans. Front Immunol 2021; 12:647873. [PMID: 33828557 PMCID: PMC8019727 DOI: 10.3389/fimmu.2021.647873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
Vaccines against enteric diseases could improve global health. Despite this, only a few oral vaccines are currently available for human use. One way to facilitate such vaccine development could be to identify a practical and relatively low cost biomarker assay to assess oral vaccine induced primary and memory IgA immune responses in humans. Such an IgA biomarker assay could complement antigen-specific immune response measurements, enabling more oral vaccine candidates to be tested, whilst also reducing the work and costs associated with early oral vaccine development. With this in mind, we take a holistic systems biology approach to compare the transcriptional signatures of peripheral blood mononuclear cells isolated from volunteers, who following two oral priming doses with the oral cholera vaccine Dukoral®, had either strong or no vaccine specific IgA responses. Using this bioinformatical method, we identify TNFRSF17, a gene encoding the B cell maturation antigen (BCMA), as a candidate biomarker of oral vaccine induced IgA immune responses. We then assess the ability of BCMA to reflect oral vaccine induced primary and memory IgA responses using an ELISA BCMA assay on a larger number of samples collected in clinical trials with Dukoral® and the oral enterotoxigenic Escherichia coli vaccine candidate ETVAX. We find significant correlations between levels of BCMA and vaccine antigen-specific IgA in antibodies in lymphocyte secretion (ALS) specimens, as well as with proportions of circulating plasmablasts detected by flow cytometry. Importantly, our results suggest that levels of BCMA detected early after primary mucosal vaccination may be a biomarker for induction of long-lived vaccine specific memory B cell responses, which are otherwise difficult to measure in clinical vaccine trials. In addition, we find that ALS-BCMA responses in individuals vaccinated with ETVAX plus the adjuvant double mutant heat-labile toxin (dmLT) are significantly higher than in subjects given ETVAX only. We therefore propose that as ALS-BCMA responses may reflect the total vaccine induced IgA responses to oral vaccination, this BCMA ELISA assay could also be used to estimate the total adjuvant effect on vaccine induced-antibody responses, independently of antigen specificity, further supporting the usefulness of the assay.
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Affiliation(s)
- Lynda Mottram
- Gothenburg University Vaccine Research Institute (GUVAX), Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Lundgren
- Gothenburg University Vaccine Research Institute (GUVAX), Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ann-Mari Svennerholm
- Gothenburg University Vaccine Research Institute (GUVAX), Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Susannah Leach
- Gothenburg University Vaccine Research Institute (GUVAX), Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pharmacology, Sahlgrenska University Hospital, Gothenburg, Sweden
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19
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Baldwin SL, Reese VA, Larsen SE, Beebe E, Guderian J, Orr MT, Fox CB, Reed SG, Coler RN. Prophylactic efficacy against Mycobacterium tuberculosis using ID93 and lipid-based adjuvant formulations in the mouse model. PLoS One 2021; 16:e0247990. [PMID: 33705411 PMCID: PMC7951850 DOI: 10.1371/journal.pone.0247990] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/17/2021] [Indexed: 11/19/2022] Open
Abstract
An estimated 10 million people developed tuberculosis (TB) disease in 2019 which underscores the need for a vaccine that prevents disease and reduces transmission. The aim of our current studies is to characterize and test a prophylactic tuberculosis vaccine comprised of ID93, a polyprotein fusion antigen, and a liposomal formulation [including a synthetic TLR4 agonist (glucopyranosyl lipid adjuvant, GLA) and QS-21] in a preclinical mouse model of TB disease. Comparisons of the ID93+GLA-LSQ vaccines are also made to the highly characterized ID93+GLA-SE oil-in-water emulsion adjuvant, which are also included these studies. The recent success of vaccine candidate M72 combined with adjuvant AS01E (GlaxoSmithKline Biologicals) in reducing progression to active disease is promising and has renewed excitement for experimental vaccines currently in the TB vaccine pipeline. The AS01E adjuvant contains monophosphoryl lipid A (MPL) and QS-21 (a saponin) in a liposomal formulation. While AS01E has demonstrated potent adjuvant activity as a component of both approved and experimental vaccines, developing alternatives to this adjuvant system will become important to fill the high demand envisioned for future vaccine needs. Furthermore, replacement sources of potent adjuvants will help to supply the demand of a TB vaccine [almost one-quarter of the world's population are estimated to have latent Mycobacterium tuberculosis (Mtb) according to the WHO 2019 global TB report], addressing (a) cost of goods, (b) supply of goods, and (c) improved efficacy of subunit vaccines against Mtb. We show that both ID93+GLA-SE (containing an emulsion adjuvant) and ID93+GLA-LSQ (containing a liposomal adjuvant) induce ID93-specific TH1 cellular immunity including CD4+CD44+ T cells expressing IFNγ, TNF, and IL-2 (using flow cytometry and intracellular cytokine staining) and vaccine-specific IgG2 antibody responses (using an ELISA). In addition, both ID93+GLA-SE and ID93+GLA-LSQ effectively decrease the bacterial load within the lungs of mice infected with Mtb. Formulations based on this liposomal adjuvant formulation may provide an alternative to AS01 adjuvant systems.
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Affiliation(s)
- Susan L. Baldwin
- Seattle Children’s Research Institute, Seattle, WA, United States of America
- * E-mail:
| | - Valerie A. Reese
- Seattle Children’s Research Institute, Seattle, WA, United States of America
| | - Sasha E. Larsen
- Seattle Children’s Research Institute, Seattle, WA, United States of America
| | - Elyse Beebe
- Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Jeff Guderian
- Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Mark T. Orr
- Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Christopher B. Fox
- Infectious Disease Research Institute, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Steven G. Reed
- Infectious Disease Research Institute, Seattle, WA, United States of America
| | - Rhea N. Coler
- Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
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20
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De Mot L, Bechtold V, Bol V, Callegaro A, Coccia M, Essaghir A, Hasdemir D, Ulloa-Montoya F, Siena E, Smilde A, van den Berg RA, Didierlaurent AM, Burny W, van der Most RG. Transcriptional profiles of adjuvanted hepatitis B vaccines display variable interindividual homogeneity but a shared core signature. Sci Transl Med 2020; 12:12/569/eaay8618. [DOI: 10.1126/scitranslmed.aay8618] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/23/2020] [Indexed: 12/19/2022]
Abstract
The current routine use of adjuvants in human vaccines provides a strong incentive to increase our understanding of how adjuvants differ in their ability to stimulate innate immunity and consequently enhance vaccine immunogenicity. Here, we evaluated gene expression profiles in cells from whole blood elicited in naive subjects receiving the hepatitis B surface antigen formulated with different adjuvants. We identified a core innate gene signature emerging 1 day after the second vaccination and that was shared by the recipients of vaccines formulated with adjuvant systems AS01B, AS01E, or AS03. This core signature associated with the magnitude of the hepatitis B surface-specific antibody response and was characterized by positive regulation of genes associated with interferon-related responses or the innate cell compartment and by negative regulation of natural killer cell–associated genes. Analysis at the individual subject level revealed that the higher immunogenicity of AS01B-adjuvanted vaccine was linked to its ability to induce this signature in most vaccinees even after the first vaccination. Therefore, our data suggest that adjuvanticity is not strictly defined by the nature of the receptors or signaling pathways it activates but by the ability of the adjuvant to consistently induce a core inflammatory signature across individuals.
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Affiliation(s)
| | | | | | | | | | | | - Dicle Hasdemir
- Bioinformatics Laboratory, University of Amsterdam, 1012 WX Amsterdam, Netherlands
- Biosystems Data Analysis Group, University of Amsterdam, 1012 WX Amsterdam, Netherlands
| | | | | | - Age Smilde
- Biosystems Data Analysis Group, University of Amsterdam, 1012 WX Amsterdam, Netherlands
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21
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Bouwman W, Verhaegh W, Holtzer L, van de Stolpe A. Measurement of Cellular Immune Response to Viral Infection and Vaccination. Front Immunol 2020; 11:575074. [PMID: 33193365 PMCID: PMC7604353 DOI: 10.3389/fimmu.2020.575074] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022] Open
Abstract
Combined cellular and humoral host immune response determine the clinical course of a viral infection and effectiveness of vaccination, but currently the cellular immune response cannot be measured on simple blood samples. As functional activity of immune cells is determined by coordinated activity of signaling pathways, we developed mRNA-based JAK-STAT signaling pathway activity assays to quantitatively measure the cellular immune response on Affymetrix expression microarray data of various types of blood samples from virally infected patients (influenza, RSV, dengue, yellow fever, rotavirus) or vaccinated individuals, and to determine vaccine immunogenicity. JAK-STAT1/2 pathway activity was increased in blood samples of patients with viral, but not bacterial, infection and was higher in influenza compared to RSV-infected patients, reflecting known differences in immunogenicity. High JAK-STAT3 pathway activity was associated with more severe RSV infection. In contrast to inactivated influenza virus vaccine, live yellow fever vaccine did induce JAK-STAT1/2 pathway activity in blood samples, indicating superior immunogenicity. Normal (healthy) JAK-STAT1/2 pathway activity was established, enabling assay interpretation without the need for a reference sample. The JAK-STAT pathway assays enable measurement of cellular immune response for prognosis, therapy stratification, vaccine development, and clinical testing.
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22
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Ullah I, Bibi S, Ul Haq I, Safia, Ullah K, Ge L, Shi X, Bin M, Niu H, Tian J, Zhu B. The Systematic Review and Meta-Analysis on the Immunogenicity and Safety of the Tuberculosis Subunit Vaccines M72/AS01 E and MVA85A. Front Immunol 2020; 11:1806. [PMID: 33133057 PMCID: PMC7578575 DOI: 10.3389/fimmu.2020.01806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/06/2020] [Indexed: 01/30/2023] Open
Abstract
Background: Tuberculosis (TB) is a severe infectious disease with devastating effects on global public health. No TB vaccine has yet been approved for use on latent TB infections and healthy adults. In this study, we performed a systematic review and meta-analysis to evaluate the immunogenicity and safety of the M72/AS01E and MVA85A subunit vaccines. The M72/AS01E is a novel peptide-based vaccine currently in progress, which may increase the protection level against TB infection. The MVA85A was a viral vector-based TB subunit vaccine being used in the clinical trials. The vaccines mentioned above have been studied in various phase I/II clinical trials. Immunogenicity and safety is the first consideration for TB vaccine development. Methods: The PubMed, Embase, and Cochrane Library databases were searched for published studies (until October 2019) to find out information on the M72/AS01E and MVA85A candidate vaccines. The meta-analysis was conducted by applying the standard methods and processes established by the Cochrane Collaboration. Results: Five eligible randomized clinical trials (RCTs) were selected for the meta-analysis of M72/AS01E candidate vaccines. The analysis revealed that the M72/AS01E subunit vaccine had an abundance of polyfunctional M72-specific CD4+ T cells [standardized mean difference (SMD) = 2.37] in the vaccine group versus the control group, the highest seropositivity rate [relative risk (RR) = 5.09]. The M72/AS01E vaccinated group were found to be at high risk of local injection site redness (RR = 2.64), headache (RR = 1.59), malaise (RR = 3.55), myalgia (RR = 2.27), fatigue (RR = 2.16), pain (RR = 3.99), swelling (RR = 5.09), and fever (RR = 2.04) compared to the control groups. The incidences of common adverse events of M72/AS01E were local injection site redness, headache, malaise, myalgia, fatigue, pain, swelling, fever, etc. Six eligible RCTs were selected for the meta-analysis on MVA85A candidate vaccines. The analysis revealed that the subunit vaccine MVA85A had a higher abundance of overall pooled proportion polyfunctional MVA85A-specific CD4+ T cells SMD = 2.41 in the vaccine group vs. the control group, with the highest seropositivity rate [estimation rate (ER) = 0.55]. The MVA85A vaccinated group were found to be at high risk of local injection site redness (ER = 0.55), headache (ER = 0.40), malaise (ER = 0.29), pain (ER = 0.54), myalgia (ER = 0.31), and fever (ER = 0.20). The incidences of common adverse events of MVA85A were local injection site redness, headache, malaise, pain, myalgia, fever, etc. Conclusion: The M72/AS01E and MVA85A vaccines against TB are safe and had immunogenicity in diverse clinical trials. The M72/AS01E and MVA85A vaccines are associated with a mild adverse reaction. The meta-analysis on immunogenicity and safety of M72/AS01E and MVA85A vaccines provides useful information for the evaluation of available subunit vaccines in the clinic.
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Affiliation(s)
- Inayat Ullah
- Lanzhou Center for Tuberculosis Research and Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, China
| | - Shaheen Bibi
- Lanzhou Center for Tuberculosis Research and Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, China.,School of Life Science, Northwest Normal University, Lanzhou, China
| | - Ijaz Ul Haq
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, China
| | - Safia
- Pakistan Institute of Community Ophthalmology (PICO), Hayatabad Medical Complex, KMU, Peshawar, Pakistan
| | - Kifayat Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Long Ge
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Xintong Shi
- Lanzhou Center for Tuberculosis Research and Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, China
| | - Ma Bin
- Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, China
| | - Hongxia Niu
- Lanzhou Center for Tuberculosis Research and Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, China
| | - Jinhui Tian
- Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, China
| | - Bingdong Zhu
- Lanzhou Center for Tuberculosis Research and Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, China
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23
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Noé A, Cargill TN, Nielsen CM, Russell AJC, Barnes E. The Application of Single-Cell RNA Sequencing in Vaccinology. J Immunol Res 2020; 2020:8624963. [PMID: 32802896 PMCID: PMC7411487 DOI: 10.1155/2020/8624963] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA sequencing allows highly detailed profiling of cellular immune responses from limited-volume samples, advancing prospects of a new era of systems immunology. The power of single-cell RNA sequencing offers various opportunities to decipher the immune response to infectious diseases and vaccines. Here, we describe the potential uses of single-cell RNA sequencing methods in prophylactic vaccine development, concentrating on infectious diseases including COVID-19. Using examples from several diseases, we review how single-cell RNA sequencing has been used to evaluate the immunological response to different vaccine platforms and regimens. By highlighting published and unpublished single-cell RNA sequencing studies relevant to vaccinology, we discuss some general considerations how the field could be enriched with the widespread adoption of this technology.
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MESH Headings
- Animals
- Betacoronavirus/immunology
- COVID-19
- Cell Line
- Clinical Trials as Topic
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Disease Models, Animal
- Drug Evaluation, Preclinical
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Immunity, Cellular/genetics
- Immunity, Innate/genetics
- Immunogenicity, Vaccine
- Pandemics/prevention & control
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- RNA, Viral/isolation & purification
- RNA-Seq/methods
- SARS-CoV-2
- Single-Cell Analysis
- Vaccinology/methods
- Viral Vaccines/administration & dosage
- Viral Vaccines/immunology
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Affiliation(s)
- Andrés Noé
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Tamsin N. Cargill
- Peter Medawar Building for Pathogen Research and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Carolyn M. Nielsen
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | | | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
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24
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Scriba TJ, Netea MG, Ginsberg AM. Key recent advances in TB vaccine development and understanding of protective immune responses against Mycobacterium tuberculosis. Semin Immunol 2020; 50:101431. [PMID: 33279383 PMCID: PMC7786643 DOI: 10.1016/j.smim.2020.101431] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/02/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022]
Abstract
Tuberculosis is the leading infectious disease killer globally due to a single pathogen. Despite wide deployment of standard drug regimens, modern diagnostics and a vaccine (bacille Calmette Guerin, BCG), the global tuberculosis epidemic is inadequately controlled. Novel, effective vaccine(s) are a crucial element of the World Health Organization End TB Strategy. TB vaccine research and development has recently been catalysed by several factors, including a revised strategy focused first on preventing pulmonary TB in adolescents and adults who are the main source of transmission, and encouraging evaluations of novel efficacy endpoints. Renewed enthusiasm for TB vaccine research has also been stimulated by recent preclinical and clinical advancements. These include new insights into underlying protective immune responses, including potential roles for 'trained' innate immunity and Th1/Th17 CD4+ (and CD8+) T cells. The field has been further reinvigorated by two positive proof of concept efficacy trials: one evaluating a potential new use of BCG in preventing high risk populations from sustained Mycobacterium tuberculosis infection and the second evaluating a novel, adjuvanted, recombinant protein vaccine candidate (M72/AS01E) for prevention of disease in adults already infected. Fourteen additional candidates are currently in various phases of clinical evaluation and multiple approaches to next generation vaccines are in discovery and preclinical development. The two positive efficacy trials and recent studies in nonhuman primates have enabled the first opportunities to discover candidate vaccine-induced correlates of protection, an effort being undertaken by a broad research consortium.
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Affiliation(s)
- 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.
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, Geert Grooteplein 8, 6525 GA Nijmegen, the Netherlands; Department of Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Germany.
| | - Ann M Ginsberg
- Bill & Melinda Gates Foundation, Division of Global Health, Washington DC, United States.
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25
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Zyla J, Marczyk M, Domaszewska T, Kaufmann SHE, Polanska J, Weiner J. Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. Bioinformatics 2019; 35:5146-5154. [PMID: 31165139 PMCID: PMC6954644 DOI: 10.1093/bioinformatics/btz447] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/08/2019] [Accepted: 06/10/2019] [Indexed: 01/12/2023] Open
Abstract
MOTIVATION Analysis of gene set (GS) enrichment is an essential part of functional omics studies. Here, we complement the established evaluation metrics of GS enrichment algorithms with a novel approach to assess the practical reproducibility of scientific results obtained from GS enrichment tests when applied to related data from different studies. RESULTS We evaluated eight established and one novel algorithm for reproducibility, sensitivity, prioritization, false positive rate and computational time. In addition to eight established algorithms, we also included Coincident Extreme Ranks in Numerical Observations (CERNO), a flexible and fast algorithm based on modified Fisher P-value integration. Using real-world datasets, we demonstrate that CERNO is robust to ranking metrics, as well as sample and GS size. CERNO had the highest reproducibility while remaining sensitive, specific and fast. In the overall ranking Pathway Analysis with Down-weighting of Overlapping Genes, CERNO and over-representation analysis performed best, while CERNO and GeneSetTest scored high in terms of reproducibility. AVAILABILITY AND IMPLEMENTATION tmod package implementing the CERNO algorithm is available from CRAN (cran.r-project.org/web/packages/tmod/index.html) and an online implementation can be found at http://tmod.online/. The datasets analyzed in this study are widely available in the KEGGdzPathwaysGEO, KEGGandMetacoreDzPathwaysGEO R package and GEO repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joanna Zyla
- Data Mining Group, Faculty of Automatic Control, Electronic and Computer Science, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Michal Marczyk
- Data Mining Group, Faculty of Automatic Control, Electronic and Computer Science, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
- Yale School of Medicine, Yale Cancer Center, New Haven, CT 06510, USA
| | - Teresa Domaszewska
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Joanna Polanska
- Data Mining Group, Faculty of Automatic Control, Electronic and Computer Science, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
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26
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Khader SA, Divangahi M, Hanekom W, Hill PC, Maeurer M, Makar KW, Mayer-Barber KD, Mhlanga MM, Nemes E, Schlesinger LS, van Crevel R, Vankayalapati R(K, Xavier RJ, Netea MG. Targeting innate immunity for tuberculosis vaccination. J Clin Invest 2019; 129:3482-3491. [PMID: 31478909 PMCID: PMC6715374 DOI: 10.1172/jci128877] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vaccine development against tuberculosis (TB) is based on the induction of adaptive immune responses endowed with long-term memory against mycobacterial antigens. Memory B and T cells initiate a rapid and robust immune response upon encounter with Mycobacterium tuberculosis, thus achieving long-lasting protection against infection. Recent studies have shown, however, that innate immune cell populations such as myeloid cells and NK cells also undergo functional adaptation after infection or vaccination, a de facto innate immune memory that is also termed trained immunity. Experimental and epidemiological data have shown that induction of trained immunity contributes to the beneficial heterologous effects of vaccines such as bacille Calmette-Guérin (BCG), the licensed TB vaccine. Moreover, increasing evidence argues that trained immunity also contributes to the anti-TB effects of BCG vaccination. An interaction among immunological signals, metabolic rewiring, and epigenetic reprogramming underlies the molecular mechanisms mediating trained immunity in myeloid cells and their bone marrow progenitors. Future studies are warranted to explore the untapped potential of trained immunity to develop a future generation of TB vaccines that would combine innate and adaptive immune memory induction.
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Affiliation(s)
- Shabaana A. Khader
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, and Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, Quebec, Canada
| | - Willem Hanekom
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Philip C. Hill
- Centre for International Health, Department of Preventive and Social Medicine, University of Otago Medical School, Dunedin, New Zealand
| | - Markus Maeurer
- Department of Oncology/Haematology, Krankenhaus Nordwest (KHNW), Frankfurt, Germany
- ImmunoSurgery Unit, Champalimaud Foundation, Lisbon, Portugal
| | - Karen W. Makar
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Musa M. Mhlanga
- Division of Chemical Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Faculty of Health Sciences, Department of Integrative Biomedical Sciences, and
| | - Elisa Nemes
- 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
| | | | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Raman (Krishna) Vankayalapati
- Department of Pulmonary Immunology, Center for Biomedical Research, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Computational and Integrative Biology and
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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27
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Ji Z, Jian M, Chen T, Luo L, Li L, Dai X, Bai R, Ding Z, Bi Y, Wen S, Zhou G, Abi ME, Liu A, Bao F. Immunogenicity and Safety of the M72/AS01 E Candidate Vaccine Against Tuberculosis: A Meta-Analysis. Front Immunol 2019; 10:2089. [PMID: 31552037 PMCID: PMC6735267 DOI: 10.3389/fimmu.2019.02089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Background: Currently, there is no tuberculosis (TB) vaccine recommended for use in latent TB infections and healthy adults. M72/AS01E is a new peptide vaccine currently under development, which may improve protection against TB disease. This vaccine has been investigated in several phase I/II clinical trials. We conducted a meta-analysis to clarify the immunogenicity and safety of the M72/AS01E peptide vaccine. Methods: We searched the PubMed, Embase, and Cochrane Library databases for published studies (until December 2018) investigating this candidate vaccine. A meta-analysis was performed using the standard methods and procedures established by the Cochrane Collaboration. Results: Seven eligible studies—involving 4,590 participants—were selected. The analysis revealed a vaccine efficacy was 57.0%, significantly higher abundance of polyfunctional M72-specific CD4+ T cells [standardized mean difference (SMD) = 2.58] in the vaccine group vs. the control group, the highest seropositivity rate [relative risk (RR) = 74.87] at 1 month after the second dose of vaccination (Day 60), and sustained elevated anti-M72 IgG geometric mean concentration at study end (Day 210) (SWD = 4.94). Compared with the control, participants who received vaccination were at increased risk of local injection site redness [relative risk (RR) = 5.99], local swelling (RR = 7.57), malaise (RR = 3.01), and fatigue (RR = 3.17). However, they were not at increased risk of headache (RR = 1.57), myalgia (RR = 0.97), and pain (RR = 3.02). Conclusion: The M72/AS01E vaccine against TB is safe and effective. Although the vaccine is associated with a mild adverse reaction, it is promising for the prevention of TB in healthy adults.
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Affiliation(s)
- Zhenhua Ji
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Miaomiao Jian
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Taigui Chen
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Lisha Luo
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Lianbao Li
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Xiting Dai
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Ruolan Bai
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Zhe Ding
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Yunfeng Bi
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Shiyuan Wen
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Guozhong Zhou
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Manzama-Esso Abi
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Aihua Liu
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China.,Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Yunnan Province Key Laboratory for Major Childhood Diseases, Kunming Medical University, Kunming, China
| | - Fukai Bao
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China.,Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Yunnan Province Key Laboratory for Major Childhood Diseases, Kunming Medical University, Kunming, China
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Raeven RHM, van Riet E, Meiring HD, Metz B, Kersten GFA. Systems vaccinology and big data in the vaccine development chain. Immunology 2018; 156:33-46. [PMID: 30317555 PMCID: PMC6283655 DOI: 10.1111/imm.13012] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/03/2018] [Indexed: 02/06/2023] Open
Abstract
Systems vaccinology has proven a fascinating development in the last decade. Where traditionally vaccine development has been dominated by trial and error, systems vaccinology is a tool that provides novel and comprehensive understanding if properly used. Data sets retrieved from systems‐based studies endorse rational design and effective development of safe and efficacious vaccines. In this review we first describe different omics‐techniques that form the pillars of systems vaccinology. In the second part, the application of systems vaccinology in the different stages of vaccine development is described. Overall, this review shows that systems vaccinology has become an important tool anywhere in the vaccine development chain.
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Affiliation(s)
- René H M Raeven
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Elly van Riet
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Hugo D Meiring
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Bernard Metz
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Gideon F A Kersten
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands.,Leiden Academic Center for Drug Research, Division of Biotherapeutics, Leiden University, Leiden, The Netherlands
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