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Mura M, Misganaw B, Gautam A, Robinson T, Chaudhury S, Bansal N, Martins AJ, Tsang J, Hammamieh R, Bergmann-Leitner E. Human transcriptional signature of protection after Plasmodium falciparum immunization and infectious challenge via mosquito bites. Hum Vaccin Immunother 2023; 19:2282693. [PMID: 38010150 PMCID: PMC10760396 DOI: 10.1080/21645515.2023.2282693] [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: 09/14/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
The identification of immune correlates of protection against infectious pathogens will accelerate the design and optimization of recombinant and subunit vaccines. Systematic analyses such as immunoprofiling including serological, cellular, and molecular assessments supported by computational tools are key to not only identify correlates of protection but also biomarkers of disease susceptibility. The current study expands our previous cellular and serological profiling of vaccine-induced responses to a whole parasite malaria vaccine. The irradiated sporozoite model was chosen as it is considered the most effective vaccine against malaria. In contrast to whole blood transcriptomics analysis, we stimulated peripheral blood mononuclear cells (PBMC) with sporozoites and enriched for antigen-specific cells prior to conducting transcriptomics analysis. By focusing on transcriptional events triggered by antigen-specific stimulation, we were able to uncover quantitative and qualitative differences between protected and non-protected individuals to controlled human malaria infections and identified differentially expressed genes associated with sporozoite-specific responses. Further analyses including pathway and gene set enrichment analysis revealed that vaccination with irradiated sporozoites induced a transcriptomic profile associated with Th1-responses, Interferon-signaling, antigen-presentation, and inflammation. Analyzing longitudinal time points not only post-vaccination but also post-controlled human malaria infection further revealed that the transcriptomic profile of protected vs non-protected individuals was not static but continued to diverge over time. The results lay the foundation for comparing protective immune signatures induced by various vaccine platforms to uncover immune correlates of protection that are common across platforms.
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Affiliation(s)
- Marie Mura
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Host-Pathogen Interactions, Microbiology and Infectious Diseases, IRBA-Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Burook Misganaw
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Vysnova Inc, Landover, MD, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Tanisha Robinson
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sidhartha Chaudhury
- Center of Enabling Capabilties, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - John Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Elke Bergmann-Leitner
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Oyong DA, Duffy FJ, Neal ML, Du Y, Carnes J, Schwedhelm KV, Hertoghs N, Jun SH, Miller H, Aitchison JD, De Rosa SC, Newell EW, McElrath MJ, McDermott SM, Stuart KD. Distinct immune responses associated with vaccination status and protection outcomes after malaria challenge. PLoS Pathog 2023; 19:e1011051. [PMID: 37195999 PMCID: PMC10228810 DOI: 10.1371/journal.ppat.1011051] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/30/2023] [Accepted: 04/26/2023] [Indexed: 05/19/2023] Open
Abstract
Understanding immune mechanisms that mediate malaria protection is critical for improving vaccine development. Vaccination with radiation-attenuated Plasmodium falciparum sporozoites (PfRAS) induces high level of sterilizing immunity against malaria and serves as a valuable tool for the study of protective mechanisms. To identify vaccine-induced and protection-associated responses during malarial infection, we performed transcriptome profiling of whole blood and in-depth cellular profiling of PBMCs from volunteers who received either PfRAS or noninfectious mosquito bites, followed by controlled human malaria infection (CHMI) challenge. In-depth single-cell profiling of cell subsets that respond to CHMI in mock-vaccinated individuals showed a predominantly inflammatory transcriptome response. Whole blood transcriptome analysis revealed that gene sets associated with type I and II interferon and NK cell responses were increased in prior to CHMI while T and B cell signatures were decreased as early as one day following CHMI in protected vaccinees. In contrast, non-protected vaccinees and mock-vaccinated individuals exhibited shared transcriptome changes after CHMI characterized by decreased innate cell signatures and inflammatory responses. Additionally, immunophenotyping data showed different induction profiles of vδ2+ γδ T cells, CD56+ CD8+ T effector memory (Tem) cells, and non-classical monocytes between protected vaccinees and individuals developing blood-stage parasitemia, following treatment and resolution of infection. Our data provide key insights in understanding immune mechanistic pathways of PfRAS-induced protection and infective CHMI. We demonstrate that vaccine-induced immune response is heterogenous between protected and non-protected vaccinees and that inducted-malaria protection by PfRAS is associated with early and rapid changes in interferon, NK cell and adaptive immune responses. Trial Registration: ClinicalTrials.gov NCT01994525.
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Affiliation(s)
- Damian A. Oyong
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Fergal J. Duffy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ying Du
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Katharine V. Schwedhelm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Nina Hertoghs
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Seong-Hwan Jun
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Helen Miller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - John D. Aitchison
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Evan W. Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Suzanne M. McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Kenneth D. Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
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Duffy FJ, Hertoghs N, Du Y, Neal ML, Oyong D, McDermott S, Minkah N, Carnes J, Schwedhelm KV, McElrath MJ, De Rosa SC, Newell E, Aitchison JD, Stuart K. Longitudinal immune profiling after radiation-attenuated sporozoite vaccination reveals coordinated immune processes correlated with malaria protection. Front Immunol 2022; 13:1042741. [PMID: 36591224 PMCID: PMC9798120 DOI: 10.3389/fimmu.2022.1042741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Background Identifying immune processes required for liver-stage sterilizing immunity to malaria remains an open problem. The IMRAS trial comprised 5x immunizations with radiation-attenuated sporozoites resulting in 55% protection from subsequent challenge. Methods To identify correlates of vaccination and protection, we performed detailed systems immunology longitudinal profiling of the entire trial time course including whole blood transcriptomics, detailed PBMC cell phenotyping and serum antigen array profiling of 11 IMRAS radiation-attenuated sporozoite (RAS) vaccinees at up to 21 timepoints each. Results RAS vaccination induced serum antibody responses to CSP, TRAP, and AMA1 in all vaccinees. We observed large numbers of differentially expressed genes associated with vaccination response and protection, with distinctly differing transcriptome responses elicited after each immunization. These included inflammatory and proliferative responses, as well as increased abundance of monocyte and DC subsets after each immunization. Increases in Vδ2 γδ; T cells and MAIT cells were observed in response to immunization over the course of study, and CD1c+ CD40+ DC abundance was significantly associated with protection. Interferon responses strongly differed between protected and non-protected individuals with high interferon responses after the 1st immunization, but not the 2nd-5th. Blood transcriptional interferon responses were correlated with abundances of different circulating classical and non-classical monocyte populations. Conclusions This study has revealed multiple coordinated immunological processes induced by vaccination and associated with protection. Our work represents the most detailed immunological profiling of a RAS vaccine trial performed to date and will guide the design and interpretation of future malaria vaccine trials.
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Affiliation(s)
- Fergal J. Duffy
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States,*Correspondence: Fergal J. Duffy, ; Ken Stuart,
| | - Nina Hertoghs
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States
| | - Ying Du
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States
| | - Damian Oyong
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States
| | - Suzanne McDermott
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States
| | - Nana Minkah
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States
| | - Jason Carnes
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States
| | - Katharine V. Schwedhelm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Evan Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States
| | - Ken Stuart
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States,*Correspondence: Fergal J. Duffy, ; Ken Stuart,
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