Systems analysis of immune responses to attenuated P. falciparum malaria sporozoite vaccination reveals excessive inflammatory signatures correlating with impaired immunity

Immunization with radiation-attenuated sporozoites (RAS) can confer sterilizing protection against malaria, although the mechanisms behind this protection are incompletely understood. We performed a systems biology analysis of samples from the Immunization by Mosquito with Radiation Attenuated Sporozoites IMRAS) trial, which comprised P. falciparum RAS-immunized (PfRAS), malaria-naive participants whose protection from malaria infection was subsequently assessed by controlled human malaria infection (CHMI). Blood samples collected after initial PfRAS immunization were analyzed to compare immune responses between protected and non-protected volunteers leveraging integrative analysis of whole blood RNA-seq, high parameter flow cytometry, and single cell CITEseq of PBMCs. This analysis revealed differences in early innate immune responses indicating divergent paths associated with protection. In particular, elevated levels of inflammatory responses early after the initial immunization were detrimental for the development of protective adaptive immunity. Specifically, non-classical monocytes and early type I interferon responses induced within 1 day of PfRAS vaccination correlated with impaired immunity. Non-protected individuals also showed an increase in Th2 polarized T cell responses whereas we observed a trend towards increased Th1 and T-bet+ CD8 T cell responses in protected individuals. Temporal differences in genes associated with natural killer cells suggest an important role in immune regulation by these cells. These findings give insight into the immune responses that confer protection against malaria and may guide further malaria vaccine development.

[1]  P. Alonso,et al.  Meeting report: WHO consultation on malaria vaccine development, Geneva, 15-16 July 2019. , 2021, Vaccine.

[2]  O. Traoré,et al.  High Efficacy of a Low Dose Candidate Malaria Vaccine, R21 in 1 Adjuvant Matrix-M™, with Seasonal Administration to Children in Burkina Faso , 2021 .

[3]  D. Kyle,et al.  Altered cleavage of Caspase-1 in hepatocytes limits control of malaria in the liver , 2021, bioRxiv.

[4]  Kenneth G. C. Smith,et al.  A CD8+ NK cell transcriptomic signature associated with clinical outcome in relapsing remitting multiple sclerosis , 2021, Nature Communications.

[5]  Indirect Effects , 2020, Do Running Mates Matter?.

[6]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[7]  David L. Smith,et al.  Indirect effects of the COVID-19 pandemic on malaria intervention coverage, morbidity, and mortality in Africa: a geospatial modelling analysis , 2020, The Lancet Infectious Diseases.

[8]  Santosh Kumar Singh.  COVID-19— A Study , 2020, Volume 5 - 2020, Issue 9 - September.

[9]  J. C. Cohen Tervaert,et al.  Natural Killer Cell Dysfunction and Its Role in COVID-19 , 2020, International journal of molecular sciences.

[10]  S. Chaudhury,et al.  IMRAS—A clinical trial of mosquito-bite immunization with live, radiation-attenuated P. falciparum sporozoites: Impact of immunization parameters on protective efficacy and generation of a repository of immunologic reagents , 2020, PloS one.

[11]  K. Stuart,et al.  OMIP‐064: A 27‐Color Flow Cytometry Panel to Detect and Characterize Human NK Cells and Other Innate Lymphoid Cell Subsets, MAIT Cells, and γδ T Cells , 2020, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[12]  S. Shekhar,et al.  NK cells modulate T cell responses via interaction with dendritic cells in Chlamydophila pneumoniae infection. , 2020, Cellular immunology.

[13]  You Chen,et al.  Immune dysfunction leads to mortality and organ injury in patients with COVID-19 in China: insights from ERS-COVID-19 study , 2020, Signal Transduction and Targeted Therapy.

[14]  Z. Tian,et al.  Functional exhaustion of antiviral lymphocytes in COVID-19 patients , 2020, Cellular & Molecular Immunology.

[15]  P. Mehta,et al.  COVID-19: consider cytokine storm syndromes and immunosuppression , 2020, The Lancet.

[16]  R. Zambello,et al.  NK cells and CD38: Implication for (Immuno)Therapy in Plasma Cell Dyscrasias , 2020, Cells.

[17]  Chemokine Receptor , 2020, Definitions.

[18]  Gennady Korotkevich,et al.  Fast gene set enrichment analysis , 2019, bioRxiv.

[19]  E. Latz,et al.  Platelets Fuel the Inflammasome Activation of Innate Immune Cells , 2019, bioRxiv.

[20]  A. Vaughan,et al.  Innate immunity limits protective adaptive immune responses against pre-erythrocytic malaria parasites , 2019, Nature Communications.

[21]  Peter D. Crompton,et al.  Whole-blood transcriptomic signatures induced during immunization by chloroquine prophylaxis and Plasmodium falciparum sporozoites , 2019, Scientific Reports.

[22]  Peter D. Crompton,et al.  Adaptive NK cells in people exposed to Plasmodium falciparum correlate with protection from malaria , 2019, The Journal of experimental medicine.

[23]  J. Alferink,et al.  Sources of Type I Interferons in Infectious Immunity: Plasmacytoid Dendritic Cells Not Always in the Driver's Seat , 2019, Front. Immunol..

[24]  R. Vijay,et al.  Monocyte-Derived CD11c+ Cells Acquire Plasmodium from Hepatocytes to Prime CD8 T Cell Immunity to Liver-Stage Malaria. , 2019, Cell host & microbe.

[25]  M. Leboyer,et al.  Immune Dysfunction , 2018, Immunopsychiatry.

[26]  S. Pallikkuth,et al.  Circulating inflammatory monocytes contribute to impaired influenza vaccine responses in HIV-infected participants , 2018, AIDS.

[27]  Florian Mair,et al.  OMIP‐044: 28‐color immunophenotyping of the human dendritic cell compartment , 2018, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[28]  R. Zemans,et al.  Neutrophil-mediated T-Cell Suppression in Influenza: Novel Finding Raising Additional Questions. , 2018, American journal of respiratory cell and molecular biology.

[29]  Byoungjae Kim,et al.  Fundamental role of dendritic cells in inducing Th2 responses , 2018, The Korean journal of internal medicine.

[30]  Matthew Collin,et al.  Human dendritic cell subsets: an update , 2018, Immunology.

[31]  Gerard Tromp,et al.  Host blood RNA signatures predict the outcome of tuberculosis treatment , 2017, Tuberculosis.

[32]  P. Duffy,et al.  Advances in malaria vaccine development: report from the 2017 malaria vaccine symposium , 2017, npj Vaccines.

[33]  M. Jordana,et al.  Inflammatory monocytes require type I interferon receptor signaling to activate NK cells via IL-18 during a mucosal viral infection , 2017, The Journal of experimental medicine.

[34]  V. V. Ganusov,et al.  Up-regulation of LFA-1 allows liver-resident memory T cells to patrol and remain in the hepatic sinusoids , 2017, Science Immunology.

[35]  Eva K. Lee,et al.  Systems analysis of protective immune responses to RTS,S malaria vaccination in humans , 2017, Proceedings of the National Academy of Sciences.

[36]  D. Saunders,et al.  Chemoprophylaxis with sporozoite immunization in P. knowlesi rhesus monkeys confers protection and elicits sporozoite-specific memory T cells in the liver , 2017, PloS one.

[37]  Sumana Chakravarty,et al.  Protection against Plasmodium falciparum malaria by PfSPZ Vaccine. , 2017, JCI insight.

[38]  Scott N. Mueller,et al.  Liver-Resident Memory CD8+ T Cells Form a Front-Line Defense against Malaria Liver-Stage Infection. , 2016, Immunity.

[39]  M. Degli-Esposti,et al.  “Natural Regulators”: NK Cells as Modulators of T Cell Immunity , 2016, Front. Immunol..

[40]  Mario Roederer,et al.  Protection against malaria at 1 year and immune correlates following PfSPZ vaccination , 2016, Nature Medicine.

[41]  D. Golenbock,et al.  Type I Interferon Transcriptional Signature in Neutrophils and Low-Density Granulocytes Are Associated with Tissue Damage in Malaria. , 2015, Cell reports.

[42]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[43]  Peter D. Crompton,et al.  Circulating Th1-Cell-type Tfh Cells that Exhibit Impaired B Cell Help Are Preferentially Activated during Acute Malaria in Children. , 2015, Cell reports.

[44]  T. Lamb,et al.  Interferon-γ: The Jekyll and Hyde of Malaria , 2015, PLoS pathogens.

[45]  M. Kaplan,et al.  Integrated Transcriptomics Establish Macrophage Polarization Signatures and have Potential Applications for Clinical Health and Disease , 2015, Scientific Reports.

[46]  S. C. T. P. Rts.  Efficacy and safety of RTS,S/AS01 malaria vaccine with or without a booster dose in infants and children in Africa: final results of a phase 3, individually randomised, controlled trial , 2015, The Lancet.

[47]  Peter D. Crompton,et al.  Malaria-associated atypical memory B cells exhibit markedly reduced B cell receptor signaling and effector function , 2015, eLife.

[48]  A. Sher,et al.  Type I interferons in infectious disease , 2015, Nature Reviews Immunology.

[49]  M. Mota,et al.  Innate Immunity Induced by Plasmodium Liver Infection Inhibits Malaria Reinfections , 2015, Infection and Immunity.

[50]  J. Langhorne,et al.  CD4 T-Cell Subsets in Malaria: TH1/TH2 Revisited , 2015, Front. Immunol..

[51]  S. Schwab,et al.  Interferon Beta and Vitamin D Synergize to Induce Immunoregulatory Receptors on Peripheral Blood Monocytes of Multiple Sclerosis Patients , 2014, PloS one.

[52]  A. Sperling,et al.  Distinct dendritic cell subsets actively induce Th2 polarization. , 2014, Current opinion in immunology.

[53]  Andrea J. Radtke,et al.  The chemokine receptor CXCR6 is required for the maintenance of liver memory CD8⁺ T cells specific for infectious pathogens. , 2014, The Journal of infectious diseases.

[54]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[55]  D. Bates,et al.  Fitting Linear Mixed-Effects Models Using lme4 , 2014, 1406.5823.

[56]  L. Rénia,et al.  Type I IFN signaling in CD8- DCs impairs Th1-dependent malaria immunity. , 2014, The Journal of clinical investigation.

[57]  A. Vaughan,et al.  Interferon-mediated innate immune responses against malaria parasite liver stages. , 2014, Cell reports.

[58]  Peter D. Crompton,et al.  Exposure-Dependent Control of Malaria-Induced Inflammation in Children , 2014, PLoS pathogens.

[59]  G. Superti-Furga,et al.  Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection , 2013, Nature Medicine.

[60]  Sandra Romero-Steiner,et al.  Molecular signatures of antibody responses derived from a systems biological study of 5 human vaccines , 2013, Nature Immunology.

[61]  Shuzhao Li,et al.  Systems biological approaches to measure and understand vaccine immunity in humans. , 2013, Seminars in immunology.

[62]  Mario Roederer,et al.  Protection Against Malaria by Intravenous Immunization with a Nonreplicating Sporozoite Vaccine , 2013, Science.

[63]  S. Kappe,et al.  Malaria parasite liver stages render host hepatocytes susceptible to mitochondria-initiated apoptosis , 2013, Cell Death and Disease.

[64]  Andrea J. Radtke,et al.  In vivo imaging of CD8+ T cell-mediated elimination of malaria liver stages , 2013, Proceedings of the National Academy of Sciences.

[65]  M. Kubo,et al.  Basophils are required for the induction of Th2 immunity to haptens and peptide antigens , 2013, Nature Communications.

[66]  J. V. van Dissel,et al.  Inhibition of the type I immune responses of human monocytes by IFN-α and IFN-β. , 2013, Cytokine.

[67]  S. Dow,et al.  Suppression of Vaccine Immunity by Inflammatory Monocytes , 2012, The Journal of Immunology.

[68]  A. Kim,et al.  Identification of human NK cells that are deficient for signaling adaptor FcRγ and specialized for antibody-dependent immune functions. , 2012, International immunology.

[69]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[70]  Leo Koenderman,et al.  A subset of neutrophils in human systemic inflammation inhibits T cell responses through Mac-1. , 2012, The Journal of clinical investigation.

[71]  D. Choubey,et al.  IFI16 Protein Mediates the Anti-inflammatory Actions of the Type-I Interferons through Suppression of Activation of Caspase-1 by Inflammasomes , 2011, PloS one.

[72]  E. R. James,et al.  Live Attenuated Malaria Vaccine Designed to Protect Through Hepatic CD8+ T Cell Immunity , 2011, Science.

[73]  Alberto Mantovani,et al.  Neutrophils in the activation and regulation of innate and adaptive immunity , 2011, Nature Reviews Immunology.

[74]  Matthew A. Kayala,et al.  Sterile Protective Immunity to Malaria is Associated with a Panel of Novel P. falciparum Antigens* , 2011, Molecular & Cellular Proteomics.

[75]  Pedro Romero,et al.  Type I interferon inhibits interleukin-1 production and inflammasome activation. , 2011, Immunity.

[76]  M. Cassatella,et al.  The defensive alliance between neutrophils and NK cells as a novel arm of innate immunity , 2011, Journal of leukocyte biology.

[77]  R. Maizels,et al.  CD11c depletion severely disrupts Th2 induction and development in vivo , 2010, The Journal of experimental medicine.

[78]  T. Kepler,et al.  The T helper type 2 response to cysteine proteases requires dendritic cell–basophil cooperation via ROS-mediated signaling , 2010, Nature Immunology.

[79]  L. Lenz,et al.  The Journal of Experimental Medicine CORRESPONDENCE , 2005 .

[80]  M. Jensen,et al.  Immunoglobulin-like transcript 3, an inhibitor of T cell activation, is reduced on blood monocytes during multiple sclerosis relapses and is induced by interferon β-1b , 2010, Multiple sclerosis.

[81]  Virginia Pascual,et al.  A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. , 2008, Immunity.

[82]  Eric Vivier,et al.  Functions of natural killer cells , 2008, Nature Immunology.

[83]  E. Wherry,et al.  Molecular Signature of CD8+ T Cell Exhaustion during Chronic Viral Infection (DOI:10.1016/j.immuni.2007.09.006) , 2007 .

[84]  E. Wherry,et al.  Molecular signature of CD8+ T cell exhaustion during chronic viral infection. , 2007, Immunity.

[85]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[86]  V. Bronte,et al.  High-Dose Granulocyte-Macrophage Colony-Stimulating Factor-Producing Vaccines Impair the Immune Response through the Recruitment of Myeloid Suppressor Cells , 2004, Cancer Research.

[87]  A. Hill,et al.  A CD4+ T-cell immune response to a conserved epitope in the circumsporozoite protein correlates with protection from natural Plasmodium falciparum infection and disease , 2004, Nature Medicine.

[88]  D. Gabrilovich,et al.  Antigen-Specific Inhibition of CD8+ T Cell Response by Immature Myeloid Cells in Cancer Is Mediated by Reactive Oxygen Species1 , 2004, The Journal of Immunology.

[89]  H. Ljunggren,et al.  NK Cell TRAIL Eliminates Immature Dendritic Cells In Vivo and Limits Dendritic Cell Vaccination Efficacy 1 , 2004, The Journal of Immunology.

[90]  S. Szabo,et al.  Antigen-driven effector CD8 T cell function regulated by T-bet , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[91]  T. Mueller,et al.  Timing of IFN-β Exposure during Human Dendritic Cell Maturation and Naive Th Cell Stimulation Has Contrasting Effects on Th1 Subset Generation: A Role for IFN-β-Mediated Regulation of IL-12 Family Cytokines and IL-18 in Naive Th Cell Differentiation1 , 2003, The Journal of Immunology.

[92]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[93]  Diego Piccioli,et al.  Contact-dependent Stimulation and Inhibition of Dendritic Cells by Natural Killer Cells , 2002, The Journal of experimental medicine.

[94]  S. Hoffman,et al.  The Complexity of Protective Immunity Against Liver-Stage Malaria1 2 , 2000, The Journal of Immunology.

[95]  A. Berger.  Protection against malaria , 1998, BMJ.

[96]  Chris Sugden,et al.  Partnership , 1997, The Fairchild Books Dictionary of Fashion.

[97]  D. N. Carss,et al.  Meeting report , 1975, Appetite.

[98]  R. L. Thorndike.  Who belongs in the family? , 1953 .

[99]  J. Mesirov,et al.  The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.

[100]  S. Ing,et al.  Follicular helper T cells: new insights into mechanisms of autoimmune diseases. , 2013, The Ochsner journal.

[101]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[102]  Charles A Tilford,et al.  Gene set enrichment analysis. , 2009, Methods in molecular biology.

[103]  Sandra Romero-Steiner,et al.  Molecular signatures of antibody responses derived from a systems biology study of five human vaccines , 2022 .