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Chawla YM, Bajpai P, Saini K, Reddy ES, Patel AK, Murali-Krishna K, Chandele A. Regional Variation of the CD4 and CD8 T Cell Epitopes Conserved in Circulating Dengue Viruses and Shared with Potential Vaccine Candidates. Viruses 2024; 16:730. [PMID: 38793612 PMCID: PMC11126086 DOI: 10.3390/v16050730] [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: 01/30/2024] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/26/2024] Open
Abstract
As dengue expands globally and many vaccines are under trials, there is a growing recognition of the need for assessing T cell immunity in addition to assessing the functions of neutralizing antibodies during these endeavors. While several dengue-specific experimentally validated T cell epitopes are known, less is understood about which of these epitopes are conserved among circulating dengue viruses and also shared by potential vaccine candidates. As India emerges as the epicenter of the dengue disease burden and vaccine trials commence in this region, we have here aligned known dengue specific T cell epitopes, reported from other parts of the world with published polyprotein sequences of 107 dengue virus isolates available from India. Of the 1305 CD4 and 584 CD8 epitopes, we found that 24% and 41%, respectively, were conserved universally, whereas 27% and 13% were absent in any viral isolates. With these data, we catalogued epitopes conserved in circulating dengue viruses from India and matched them with each of the six vaccine candidates under consideration (TV003, TDEN, DPIV, CYD-TDV, DENVax and TVDV). Similar analyses with viruses from Thailand, Brazil and Mexico revealed regional overlaps and variations in these patterns. Thus, our study provides detailed and nuanced insights into regional variation that should be considered for itemization of T cell responses during dengue natural infection and vaccine design, testing and evaluation.
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Affiliation(s)
- Yadya M. Chawla
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (Y.M.C.); (P.B.); (K.S.); (E.S.R.)
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (Y.M.C.); (P.B.); (K.S.); (E.S.R.)
| | - Keshav Saini
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (Y.M.C.); (P.B.); (K.S.); (E.S.R.)
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (Y.M.C.); (P.B.); (K.S.); (E.S.R.)
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India;
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India;
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (Y.M.C.); (P.B.); (K.S.); (E.S.R.)
- Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30317, USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (Y.M.C.); (P.B.); (K.S.); (E.S.R.)
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Dos Santos Alves RP, Timis J, Miller R, Valentine K, Pinto PBA, Gonzalez A, Regla-Nava JA, Maule E, Nguyen MN, Shafee N, Landeras-Bueno S, Olmedillas E, Laffey B, Dobaczewska K, Mikulski Z, McArdle S, Leist SR, Kim K, Baric RS, Ollmann Saphire E, Elong Ngono A, Shresta S. Human coronavirus OC43-elicited CD4 + T cells protect against SARS-CoV-2 in HLA transgenic mice. Nat Commun 2024; 15:787. [PMID: 38278784 PMCID: PMC10817949 DOI: 10.1038/s41467-024-45043-2] [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: 08/18/2023] [Accepted: 01/10/2024] [Indexed: 01/28/2024] Open
Abstract
SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1-/- transgenic mice. We find that OC43 infection can elicit polyfunctional CD8+ and CD4+ effector T cells that cross-react with SARS-CoV-2 peptides. Furthermore, pre-exposure to OC43 reduces subsequent SARS-CoV-2 infection and disease in the lung for a short-term in HLA-DRB1*0101 Ifnar1-/- transgenic mice, and a longer-term in HLA-B*0702 Ifnar1-/- transgenic mice. Depletion of CD4+ T cells in HLA-DRB1*0101 Ifnar1-/- transgenic mice with prior OC43 exposure results in increased viral burden in the lung but no change in virus-induced lung damage following infection with SARS-CoV-2 (versus CD4+ T cell-sufficient mice), demonstrating that the OC43-elicited SARS-CoV-2 cross-reactive T cell-mediated cross-protection against SARS-CoV-2 is partially dependent on CD4+ T cells. These findings contribute to our understanding of the origin of pre-existing SARS-CoV-2-reactive T cells and their effects on SARS-CoV-2 clinical outcomes, and also carry implications for development of broadly protective betacoronavirus vaccines.
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Affiliation(s)
| | - Julia Timis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Robyn Miller
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kristen Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Microbiology and Pathology, University Center for Health Science (CUCS), University of Guadalajara, Guadalajara, 44340, Mexico
| | - Erin Maule
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Michael N Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Norazizah Shafee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brett Laffey
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Katarzyna Dobaczewska
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Kim
- Histopathology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Annie Elong Ngono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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3
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Singh P, Bajpai P, Maheshwari D, Chawla YM, Saini K, Reddy ES, Gottimukkala K, Nayak K, Gunisetty S, Aggarwal C, Jain S, Verma C, Singla P, Soneja M, Wig N, Murali-Krishna K, Chandele A. Functional and transcriptional heterogeneity within the massively expanding HLADR +CD38 + CD8 T cell population in acute febrile dengue patients. J Virol 2023; 97:e0074623. [PMID: 37855600 PMCID: PMC10688317 DOI: 10.1128/jvi.00746-23] [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: 05/23/2023] [Accepted: 09/17/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE CD8 T cells play a crucial role in protecting against intracellular pathogens such as viruses by eliminating infected cells and releasing anti-viral cytokines such as interferon gamma (IFNγ). Consequently, there is significant interest in comprehensively characterizing CD8 T cell responses in acute dengue febrile patients. Previous studies, including our own, have demonstrated that a discrete population of CD8 T cells with HLADR+ CD38+ phenotype undergoes massive expansion during the acute febrile phase of natural dengue virus infection. Although about a third of these massively expanding HLADR+ CD38+ CD8 T cells were also CD69high when examined ex vivo, only a small fraction of them produced IFNγ upon in vitro peptide stimulation. Therefore, to better understand such functional diversity of CD8 T cells responding to dengue virus infection, it is important to know the cytokines/chemokines expressed by these peptide-stimulated HLADR+CD38+ CD8 T cells and the transcriptional profiles that distinguish the CD69+IFNγ+, CD69+IFNγ-, and CD69-IFNγ- subsets.
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Affiliation(s)
- Prabhat Singh
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Deepti Maheshwari
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Yadya M. Chawla
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Keshav Saini
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kaustuv Nayak
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sivaram Gunisetty
- Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Charu Aggarwal
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shweta Jain
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Chaitanya Verma
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Paras Singla
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Soneja
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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da Silva Antunes R, Weiskopf D, Sidney J, Rubiro P, Peters B, Arlehamn CSL, Grifoni A, Sette A. The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses. Curr Protoc 2023; 3:e934. [PMID: 37966108 PMCID: PMC10662678 DOI: 10.1002/cpz1.934] [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] [Indexed: 11/16/2023]
Abstract
Epitopes recognized by T cells are a collection of short peptide fragments derived from specific antigens or proteins. Immunological research to study T cell responses is hindered by the extreme degree of heterogeneity of epitope targets, which are usually derived from multiple antigens; within a given antigen, hundreds of different T cell epitopes can be recognized, differing from one individual to the next because T cell epitope recognition is restricted by the epitopes' ability to bind to MHC molecules, which are extremely polymorphic in different individuals. Testing large pools encompassing hundreds of peptides is technically challenging because of logistical considerations regarding solvent-induced toxicity. To address this issue, we developed the MegaPool (MP) approach based on sequential lyophilization of large numbers of peptides that can be used in a variety of assays to measure T cell responses, including ELISPOT, intracellular cytokine staining, and activation-induced marker assays, and that has been validated in the study of infectious diseases, allergies, and autoimmunity. Here, we describe the procedures for generating and testing MPs, starting with peptide synthesis and lyophilization, as well as a step-by-step guide and recommendations for their handling and experimental usage. Overall, the MP approach is a powerful strategy for studying T cell responses and understanding the immune system's role in health and disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generation of peptide pools ("MegaPools") Basic Protocol 2: MegaPool testing and quantitation of antigen-specific T cell responses.
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Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | | | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
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Nemirov K, Authié P, Souque P, Moncoq F, Noirat A, Blanc C, Bourgine M, Majlessi L, Charneau P. Preclinical proof of concept of a tetravalent lentiviral T-cell vaccine against dengue viruses. Front Immunol 2023; 14:1208041. [PMID: 37654495 PMCID: PMC10466046 DOI: 10.3389/fimmu.2023.1208041] [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: 04/18/2023] [Accepted: 07/17/2023] [Indexed: 09/02/2023] Open
Abstract
Dengue virus (DENV) is responsible for approximately 100 million cases of dengue fever annually, including severe forms such as hemorrhagic dengue and dengue shock syndrome. Despite intensive vaccine research and development spanning several decades, a universally accepted and approved vaccine against dengue fever has not yet been developed. The major challenge associated with the development of such a vaccine is that it should induce simultaneous and equal protection against the four DENV serotypes, because past infection with one serotype may greatly increase the severity of secondary infection with a distinct serotype, a phenomenon known as antibody-dependent enhancement (ADE). Using a lentiviral vector platform that is particularly suitable for the induction of cellular immune responses, we designed a tetravalent T-cell vaccine candidate against DENV ("LV-DEN"). This vaccine candidate has a strong CD8+ T-cell immunogenicity against the targeted non-structural DENV proteins, without inducing antibody response against surface antigens. Evaluation of its protective potential in the preclinical flavivirus infection model, i.e., mice knockout for the receptor to the type I IFN, demonstrated its significant protective effect against four distinct DENV serotypes, based on reduced weight loss, viremia, and viral loads in peripheral organs of the challenged mice. These results provide proof of concept for the use of lentiviral vectors for the development of efficient polyvalent T-cell vaccine candidates against all DENV serotypes.
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Affiliation(s)
- Kirill Nemirov
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris, Virology Department, Paris, France
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Meng R, Yang B, Feng C, Huang J, Wang X, Zhang D. The difference in CD4+ T cell immunity between high- and low-virulence Tembusu viruses is mainly related to residues 151 and 304 in the envelope protein. Front Immunol 2022; 13:890263. [PMID: 36016955 PMCID: PMC9395619 DOI: 10.3389/fimmu.2022.890263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/20/2022] [Indexed: 11/22/2022] Open
Abstract
Tembusu virus (TMUV) can result in a severe disease affecting domestic ducks. The role of T cells in protection from TMUV infection and the molecular basis of T cell-mediated protection against TMUV remain largely uncharacterized. Here, we used the high-virulence TMUV strain Y and the low-virulence TMUV strain PS to investigate the protective role for TMUV-specific CD4+ and CD8+ T cells. When tested in a 5-day-old Pekin duck model, Y and PS induced comparable levels of neutralizing antibody, whereas Y elicited significantly stronger cellular immune response relative to PS. Using a duck adoptive transfer model, we showed that both CD4+ and CD8+ T cells provided significant protection from TMUV-related disease, with CD8+ T cell conferring more robust protection to recipient ducklings. For TMUV, CD4+ T cells mainly provided help for neutralizing antibody response, whereas CD8+ T cells mainly mediated viral clearance from infected tissues. The difference in T cell immunity between Y and PS was primarily attributed to CD4+ T cells; adoptive transfer of Y-specific CD4+ T cells resulted in significantly enhanced protective ability, neutralizing antibody response, and viral clearance from the brain relative to PS-specific CD4+ T cells. Further investigations with chimeric viruses, mutant viruses, and their parental viruses identified two mutations (T151A and R304M) in the envelope (E) protein that contributed significantly to TMUV-specific CD4+ T cell-mediated protective ability and neutralizing antibody response, with more beneficial effects being conferred by R304M. These data indicate T cell-mediated immunity is important for protection from disease, for viral clearance from tissues, and for the production of neutralizing antibodies, and that the difference in CD4+T cell immunity between high- and low-virulence TMUV strains is primarily related to residues 151 and 304 in the E protein.
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Reguzova A, Fischer N, Müller M, Salomon F, Jaenisch T, Amann R. A Novel Orf Virus D1701-VrV-Based Dengue Virus (DENV) Vaccine Candidate Expressing HLA-Specific T Cell Epitopes: A Proof-of-Concept Study. Biomedicines 2021; 9:biomedicines9121862. [PMID: 34944678 PMCID: PMC8698572 DOI: 10.3390/biomedicines9121862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/02/2022] Open
Abstract
Although dengue virus (DENV) affects almost half of the world’s population there are neither preventive treatments nor any long-lasting and protective vaccines available at this time. The complexity of the protective immune response to DENV is still not fully understood. The most advanced vaccine candidates focus specifically on humoral immune responses and the production of virus-neutralizing antibodies. However, results from several recent studies have revealed the protective role of T cells in the immune response to DENV. Hence, in this study, we generated a novel and potent DENV vaccine candidate based on an Orf virus (ORFV, genus Parapoxvirus) vector platform engineered to encode five highly conserved or cross-reactive DENV human leukocyte antigen (HLA)-A*02- or HLA-B*07-restricted epitopes as minigenes (ORFV-DENV). We showed that ORFV-DENV facilitates the in vitro priming of CD8+ T cells from healthy blood donors based on responses to each of the encoded immunogenic peptides. Moreover, we demonstrated that peripheral blood mononuclear cells isolated from clinically confirmed DENV-positive donors stimulated with ORFV-DENV generate cytotoxic T cell responses to at least three of the expressed DENV peptides. Finally, we showed that ORFV-DENV could activate CD8+ T cells isolated from donors who had recovered from Zika virus (ZIKV) infection. ZIKV belongs to the same virus family (Flaviviridae) and has epitope sequences that are homologous to those of DENV. We found that highly conserved HLA-B*07-restricted ZIKV and DENV epitopes induced functional CD8+ T cell responses in PBMCs isolated from confirmed ZIKV-positive donors. In summary, this proof-of-concept study characterizes a promising new ORFV D1701-VrV-based DENV vaccine candidate that induces broad and functional epitope-specific CD8+ T cell responses.
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Affiliation(s)
- Alena Reguzova
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Nico Fischer
- Department of Infectious Diseases, Heidelberg Institute of Global Health (HIGH) & Tropical Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany; (N.F.); (T.J.)
| | - Melanie Müller
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Ferdinand Salomon
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Thomas Jaenisch
- Department of Infectious Diseases, Heidelberg Institute of Global Health (HIGH) & Tropical Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany; (N.F.); (T.J.)
| | - Ralf Amann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
- Correspondence: ; Tel.: +49-707-1298-7614
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Abstract
The composition of the gut microbiota is affected by a number of factors, including the innate and adaptive immune system. The major histocompatibility complex (MHC), or the human leukocyte antigen (HLA) in humans, performs an essential role in vertebrate immunity and is very polymorphic in different populations. HLA determines the specificity of T lymphocyte and natural killer (NK) cell responses, including those against the commensal bacteria present in the human gut. Thus, it is likely that our HLA molecules, and thereby the adaptive immune response, can shape the composition of our microbiota. Here, we investigated the effect of HLA haplotype on the microbiota composition. We performed HLA typing and microbiota composition analyses on 3,002 public human gut microbiome data sets. We found that individuals with functionally similar HLA molecules are also similar in their microbiota composition. Our results show a statistical association between host HLA haplotype and gut microbiota composition. Because the HLA haplotype is a readily measurable parameter of the human immune system, these results open the door to incorporating the genetics of the immune system into predictive microbiome models. IMPORTANCE The microorganisms that live in the digestive tracts of humans, known as the gut microbiota, are essential for hosts' survival, as they support crucial functions. For example, they support the host in facilitating the uptake of nutrients and give colonization resistance against pathogens. The composition of the gut microbiota varies among humans. Studies have proposed multiple factors driving the observed variation, including diet, lifestyle, and health condition. Another major influence on the microbiota is the host's genetic background. We hypothesized the immune system to be one of the most important genetic factors driving the differences observed between gut microbiotas. Therefore, we searched for a link between the polymorphic molecules that shape human immune responses and the composition of the microbiota. HLA molecules are the most polymorphic molecules in our genome and therefore makes an excellent candidate to test such an association. To our knowledge for the first time, our results indicate a significant impact of the HLA on the human gut microbiota.
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9
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CD4 + T Cells Cross-Reactive with Dengue and Zika Viruses Protect against Zika Virus Infection. Cell Rep 2021; 31:107566. [PMID: 32348763 PMCID: PMC7261136 DOI: 10.1016/j.celrep.2020.107566] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 02/06/2020] [Accepted: 04/02/2020] [Indexed: 12/31/2022] Open
Abstract
The underlying mechanisms by which prior immunity to dengue virus (DENV) affords cross-protection against the related flavivirus Zika virus (ZIKV) are poorly understood. Here, we examine the ability of DENV/ZIKV-cross-reactive CD4+ T cells to protect against versus exacerbate ZIKV infection by using a histocompatibility leukocyte antigen (HLA)-DRB1*0101 transgenic, interferon α/β receptor-deficient mouse model that supports robust DENV and ZIKV replication. By mapping the HLA-DRB1*0101-restricted T cell response, we identify DENV/ZIKV-cross-reactive CD4+ T cell epitopes that stimulate interferon gamma (IFNγ) and/or tumor necrosis factor (TNF) production. Vaccination of naive HLA-DRB1*0101 transgenic mice with these peptides induces a CD4+ T cell response sufficient to reduce tissue viral burden following ZIKV infection. Notably, this protective response requires IFNγ and/or TNF secretion but not anti-ZIKV immunoglobulin G (IgG) production. Thus, DENV/ZIKV-cross-reactive CD4+ T cells producing canonical Th1 cytokines can suppress ZIKV replication in an antibody-independent manner. These results may have important implications for increasing the efficacy and safety of DENV/ZIKV vaccines and for developing pan-flavivirus vaccines.
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Schmidt J, Smith AR, Magnin M, Racle J, Devlin JR, Bobisse S, Cesbron J, Bonnet V, Carmona SJ, Huber F, Ciriello G, Speiser DE, Bassani-Sternberg M, Coukos G, Baker BM, Harari A, Gfeller D. Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting. CELL REPORTS MEDICINE 2021; 2:100194. [PMID: 33665637 PMCID: PMC7897774 DOI: 10.1016/j.xcrm.2021.100194] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 12/11/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
CD8+ T cell recognition of peptide epitopes plays a central role in immune responses against pathogens and tumors. However, the rules that govern which peptides are truly recognized by existing T cell receptors (TCRs) remain poorly understood, precluding accurate predictions of neo-epitopes for cancer immunotherapy. Here, we capitalize on recent (neo-)epitope data to train a predictor of immunogenic epitopes (PRIME), which captures molecular properties of both antigen presentation and TCR recognition. PRIME not only improves prioritization of neo-epitopes but also correlates with T cell potency and unravels biophysical determinants of TCR recognition that we experimentally validate. Analysis of cancer genomics data reveals that recurrent mutations tend to be less frequent in patients where they are predicted to be immunogenic, providing further evidence for immunoediting in human cancer. PRIME will facilitate identification of pathogen epitopes in infectious diseases and neo-epitopes in cancer immunotherapy.
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Affiliation(s)
- Julien Schmidt
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Angela R Smith
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Morgane Magnin
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Jason R Devlin
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Sara Bobisse
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Julien Cesbron
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | | | - Santiago J Carmona
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Florian Huber
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Giovanni Ciriello
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Daniel E Speiser
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Alexandre Harari
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland.,Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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11
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Lim HX, Lim J, Poh CL. Identification and selection of immunodominant B and T cell epitopes for dengue multi-epitope-based vaccine. Med Microbiol Immunol 2021; 210:1-11. [PMID: 33515283 DOI: 10.1007/s00430-021-00700-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/08/2021] [Indexed: 12/27/2022]
Abstract
Dengue virus (DENV) comprises four serotypes (DENV1-4) which cause 390 million global infections with 500,000 hospitalizations and 25,000 fatalities annually. Currently, the only FDA approved DENV vaccine is the chimeric live-attenuated vaccine, Dengvaxia®, which is based on the yellow fever virus (YFV) genome that carries the prM and E genes of the respective DENV 1, 2, 3, and 4 serotypes. However, it has lower efficacies against serotypes DENV1 (51%) and DENV2 (34%) when compared with DENV3 (75%) and DENV4 (77%). The absence of T cell epitopes from non-structural (NS) and capsid (C) proteins of the yellow fever vaccine strain might have prevented Dengvaxia® to elicit robust cellular immune responses, as CD8+ T cell epitopes are mainly localized in the NS3 and NS5 regions. Multi-epitope-based peptide vaccines carrying CD4+, CD8+ T cell and B cell epitopes represent a novel approach to generate specific immune responses. Therefore, assessing and selecting epitopes that can induce robust B and T cell responses is a prerequisite for constructing an efficient multi-epitope peptide vaccine. Potent B and T cell epitopes can be identified by utilizing immunoinformatic analysis, but the immunogenicity of the epitopes have to be experimentally validated. In this review, we presented T cell epitopes that have been predicted by bioinformatic approaches as well as recent experimental validations of CD4+ and CD8+ T cell epitopes by ex-vivo stimulation of PBMCs with specific peptides. Immunoproteomic analysis could be utilized to uncover HLA-specific epitopes presented by DENV-infected cells. Based on various approaches, immunodominant epitopes capable of inducing strong immune responses could be selected and incorporated to form a universally applicable multi-epitope-based peptide dengue vaccine.
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Affiliation(s)
- Hui Xuan Lim
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Kuala Lumpur, Selangor, Malaysia
| | - Jianhua Lim
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Kuala Lumpur, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Kuala Lumpur, Selangor, Malaysia.
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12
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Advances in Transgenic Mouse Models to Study Infections by Human Pathogenic Viruses. Int J Mol Sci 2020; 21:ijms21239289. [PMID: 33291453 PMCID: PMC7730764 DOI: 10.3390/ijms21239289] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 02/08/2023] Open
Abstract
Medical research is changing into direction of precision therapy, thus, sophisticated preclinical models are urgently needed. In human pathogenic virus research, the major technical hurdle is not only to translate discoveries from animals to treatments of humans, but also to overcome the problem of interspecies differences with regard to productive infections and comparable disease development. Transgenic mice provide a basis for research of disease pathogenesis after infection with human-specific viruses. Today, humanized mice can be found at the very heart of this forefront of medical research allowing for recapitulation of disease pathogenesis and drug mechanisms in humans. This review discusses progress in the development and use of transgenic mice for the study of virus-induced human diseases towards identification of new drug innovations to treat and control human pathogenic infectious diseases.
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13
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Identification of Novel Yellow Fever Class II Epitopes in YF-17D Vaccinees. Viruses 2020; 12:v12111300. [PMID: 33198381 PMCID: PMC7697718 DOI: 10.3390/v12111300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/27/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
Yellow fever virus (YFV) is a mosquito-borne member of the genus flavivirus, including other important human-pathogenic viruses, such as dengue, Japanese encephalitis, and Zika. Herein, we report identifying 129 YFV Class II epitopes in donors vaccinated with the live attenuated YFV vaccine (YFV-17D). A total of 1156 peptides predicted to bind 17 different common HLA-DRB1 allelic variants were tested using IFNγ ELISPOT assays in vitro re-stimulated peripheral blood mononuclear cells from twenty-six vaccinees. Overall, we detected responses against 215 YFV epitopes. We found that the capsid and envelope proteins, as well as the non-structural (NS) proteins NS3 and NS5, were the most targeted proteins by CD4+ T cells from YF-VAX vaccinated donors. In addition, we designed and validated by flow cytometry a CD4+ mega pool (MP) composed of structural and non-structural epitopes in an independent cohort of vaccinated donors. Overall, this study provides a comprehensive prediction and validation of YFV epitopes in a cohort of YF-17D vaccinated individuals. With the design of a CD4 epitope MP, we further provide a useful tool to detect ex vivo responses of YFV-specific CD4 T cells in small sample volumes.
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14
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Elong Ngono A, Syed T, Nguyen AV, Regla-Nava JA, Susantono M, Spasova D, Aguilar A, West M, Sparks J, Gonzalez A, Branche E, DeHart JL, Vega JB, Karmali PP, Chivukula P, Kamrud K, Aliahmad P, Wang N, Shresta S. CD8 + T cells mediate protection against Zika virus induced by an NS3-based vaccine. SCIENCE ADVANCES 2020; 6:eabb2154. [PMID: 33148638 PMCID: PMC7673678 DOI: 10.1126/sciadv.abb2154] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/21/2020] [Indexed: 05/07/2023]
Abstract
Zika virus (ZIKV) is associated with congenital malformations in infants born to infected mothers, and with Guillain-Barré syndrome in infected adults. Development of ZIKV vaccines has focused predominantly on the induction of neutralizing antibodies, although a suboptimal antibody response may theoretically enhance disease severity through antibody-dependent enhancement (ADE). Here, we report induction of a protective anti-ZIKV CD8+ T cell response in the HLA-B*0702 Ifnar1-/- transgenic mice using an alphavirus-based replicon RNA vaccine expressing ZIKV nonstructural protein NS3, a potent T cell antigen. The NS3 vaccine did not induce a neutralizing antibody response but elicited polyfunctional CD8+ T cells that were necessary and sufficient for preventing death in lethally infected adult mice and fetal growth restriction in infected pregnant mice. These data identify CD8+ T cells as the major mediators of ZIKV NS3 vaccine-induced protection and suggest a new strategy to develop safe and effective anti-flavivirus vaccines.
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Affiliation(s)
- Annie Elong Ngono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Thasneem Syed
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Anh-Viet Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Mercylia Susantono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Darina Spasova
- Synthetic Genomics Inc., 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Allison Aguilar
- Synthetic Genomics Inc., 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Melissa West
- Synthetic Genomics Inc., 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Jessica Sparks
- Synthetic Genomics Inc., 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Emilie Branche
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Jason L DeHart
- Synthetic Genomics Inc., 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Jerel Boyd Vega
- Arcturus Therapeutics Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Priya Prakash Karmali
- Arcturus Therapeutics Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Padmanabh Chivukula
- Arcturus Therapeutics Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Kurt Kamrud
- Synthetic Genomics Inc., 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Parinaz Aliahmad
- Synthetic Genomics Inc., 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Nathaniel Wang
- Synthetic Genomics Inc., 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
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15
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Alves RPDS, Andreata-Santos R, de Freitas CL, Pereira LR, Fabris-Maeda DLN, Rodrigues-Jesus MJ, Pereira SS, Carvalho AAVB, Sales NS, Peron JPS, Amorim JH, Ferreira LCDS. Protective Immunity to Dengue Virus Induced by DNA Vaccines Encoding Nonstructural Proteins in a Lethal Challenge Immunocompetent Mouse Model. FRONTIERS IN MEDICAL TECHNOLOGY 2020; 2:558984. [PMID: 35047876 PMCID: PMC8757693 DOI: 10.3389/fmedt.2020.558984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/30/2020] [Indexed: 11/29/2022] Open
Abstract
Dengue virus represents the main arbovirus affecting humans, but there are no effective drugs or available worldwide licensed vaccine formulations capable of conferring full protection against the infection. Experimental studies and results generated after the release of the licensed anti-DENV vaccine demonstrated that induction of high-titer neutralizing antibodies does not represent the sole protection correlate and that, indeed, T cell-based immune responses plays a relevant role in the establishment of an immune protective state. In this context, this study aimed to further demonstrate protective features of immune responses elicited in immunocompetent C57BL/6 mice immunized with three plasmids encoding DENV2 nonstructural proteins (NS1, NS3, and NS5), which were subsequently challenged with a DENV2 strain naturally capable of inducing lethal encephalitis in immunocompetent mouse strains. The animals were immunized intramuscularly with the DNA vaccine mix and complete protection was observed among vaccinated mice. Vaccine induced protection correlated with the cytokine profiles expressed by spleen cells and brain-infiltrating mononuclear cells. The results confirm the pivotal role of cellular immune responses targeting nonstructural DENV proteins and validate the experimental model based on a DENV2 strain capable of infecting and killing immunocompetent mice as a tool for the evaluation of protective immunity induced by anti-DENV vaccines.
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Affiliation(s)
- Rúbens Prince dos Santos Alves
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Robert Andreata-Santos
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Carla Longo de Freitas
- Laboratório de Interações Neuroimunes, Departamento de Imunologia, Universidade de São Paulo, São Paulo, Brazil
| | - Lennon Ramos Pereira
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Denicar Lina Nascimento Fabris-Maeda
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Mônica Josiane Rodrigues-Jesus
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Samuel Santos Pereira
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Natiely Silva Sales
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Jaime Henrique Amorim
- Laboratório de Microbiologia, Centro das Ciências Biológicas e da Saúde, Universidade Federal Do Oeste da Bahia, Barreiras, Brazil
| | - Luís Carlos de Souza Ferreira
- Laboratório de Desenvolvimento de Vacinas, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- *Correspondence: Luís Carlos de Souza Ferreira
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16
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Kalia A, Agrawal M, Gupta N. CD8 + T cells are crucial for humoral immunity establishment by SA14-14-2 live attenuated Japanese encephalitis vaccine in mice. Eur J Immunol 2020; 51:368-379. [PMID: 32749679 DOI: 10.1002/eji.202048745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/06/2020] [Indexed: 11/09/2022]
Abstract
The live attenuated SA14-14-2 Japanese encephalitis (JE) vaccine is a historical vaccine that protects against JE. Despite its extensive use, the mechanism of protective immunity conferred by the SA14-14-2 vaccine is not well established. Here, we used mouse models to understand the mechanism of the development of humoral immunity against the vaccine. The vaccine induces robust GC responses within a week postimmunization. In lethal virus challenge, we show that CD4+ T cells alone, but not CD8+ T cells, are sufficient to confer vaccine-mediated protection. However, the CD4-mediated protection was potentiated in the presence of vaccine-primed CD8+ T cells. Employing CD8-deficient mice, we show that both the protective traits of CD4+ T cells and the quality of antibody response to the vaccine are impaired in absence of CD8+ T cells. We further demonstrate that the poor protective immune response induced by the vaccine in absence of CD8+ T cells is mainly due to the impaired differentiation and function of follicular Th cells, leading to suboptimal GC reaction. Our study highlights an unprecedented role of CD8+ T cells in the establishment of humoral responses to the vaccine. By elucidating underlying cellular determinants of vaccine-induced protective immunity, our work has implications for rational design of vaccines against JE virus and related flaviviruses.
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Affiliation(s)
- Anurag Kalia
- Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, India
| | - Mona Agrawal
- Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, India
| | - Nimesh Gupta
- Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, India
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17
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Wolf D, Gerhardt T, Winkels H, Michel NA, Pramod AB, Ghosheh Y, Brunel S, Buscher K, Miller J, McArdle S, Baas L, Kobiyama K, Vassallo M, Ehinger E, Dileepan T, Ali A, Schell M, Mikulski Z, Sidler D, Kimura T, Sheng X, Horstmann H, Hansen S, Mitre LS, Stachon P, Hilgendorf I, Gaddis DE, Hedrick C, Benedict CA, Peters B, Zirlik A, Sette A, Ley K. Pathogenic Autoimmunity in Atherosclerosis Evolves From Initially Protective Apolipoprotein B 100-Reactive CD4 + T-Regulatory Cells. Circulation 2020; 142:1279-1293. [PMID: 32703007 PMCID: PMC7515473 DOI: 10.1161/circulationaha.119.042863] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Throughout the inflammatory response that accompanies atherosclerosis, autoreactive CD4+ T-helper cells accumulate in the atherosclerotic plaque. Apolipoprotein B100 (apoB), the core protein of low-density lipoprotein, is an autoantigen that drives the generation of pathogenic T-helper type 1 (TH1) cells with proinflammatory cytokine secretion. Clinical data suggest the existence of apoB-specific CD4+ T cells with an atheroprotective, regulatory T cell (Treg) phenotype in healthy individuals. Yet, the function of apoB-reactive Tregs and their relationship with pathogenic TH1 cells remain unknown. METHODS To interrogate the function of autoreactive CD4+ T cells in atherosclerosis, we used a novel tetramer of major histocompatibility complex II to track T cells reactive to the mouse self-peptide apo B978-993 (apoB+) at the single-cell level. RESULTS We found that apoB+ T cells build an oligoclonal population in lymph nodes of healthy mice that exhibit a Treg-like transcriptome, although only 21% of all apoB+ T cells expressed the Treg transcription factor FoxP3 (Forkhead Box P3) protein as detected by flow cytometry. In single-cell RNA sequencing, apoB+ T cells formed several clusters with mixed TH signatures that suggested overlapping multilineage phenotypes with pro- and anti-inflammatory transcripts of TH1, T helper cell type 2 (TH2), and T helper cell type 17 (TH17), and of follicular-helper T cells. ApoB+ T cells were increased in mice and humans with atherosclerosis and progressively converted into pathogenic TH1/TH17-like cells with proinflammatory properties and only a residual Treg transcriptome. Plaque T cells that expanded during progression of atherosclerosis consistently showed a mixed TH1/TH17 phenotype in single-cell RNA sequencing. In addition, we observed a loss of FoxP3 in a fraction of apoB+ Tregs in lineage tracing of hyperlipidemic Apoe-/- mice. In adoptive transfer experiments, converting apoB+ Tregs failed to protect from atherosclerosis. CONCLUSIONS Our results demonstrate an unexpected mixed phenotype of apoB-reactive autoimmune T cells in atherosclerosis and suggest an initially protective autoimmune response against apoB with a progressive derangement in clinical disease. These findings identify apoB autoreactive Tregs as a novel cellular target in atherosclerosis.
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Affiliation(s)
- Dennis Wolf
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA.,Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Teresa Gerhardt
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA.,Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Department of Cardiology, Charité - University Medicine Berlin (Campus Benjamin Franklin), Germany (T.G.)
| | - Holger Winkels
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Nathaly Anto Michel
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Department of Cardiology, Medical University Graz, Austria (N.A.M., A.Z.)
| | - Akula Bala Pramod
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA.,Department of Psychiatry, University of California San Diego, La Jolla (A.B.P.)
| | - Yanal Ghosheh
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Simon Brunel
- Division of Immune Regulation (S.B., D.S., C.A.B.), La Jolla Institute for Immunology, CA
| | - Konrad Buscher
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Jacqueline Miller
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Sara McArdle
- Microscopy Core Facility (S.M.), La Jolla Institute for Immunology, CA
| | - Livia Baas
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Kouji Kobiyama
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Melanie Vassallo
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Erik Ehinger
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | | | - Amal Ali
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Maximilian Schell
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Zbigniew Mikulski
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Daniel Sidler
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Takayuki Kimura
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Xia Sheng
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Hauke Horstmann
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Sophie Hansen
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Lucia Sol Mitre
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Peter Stachon
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Ingo Hilgendorf
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Dalia E Gaddis
- Center for Autoimmunity and Inflammation (D.E.G., C.H., K.L.), La Jolla Institute for Immunology, CA
| | - Catherine Hedrick
- Center for Autoimmunity and Inflammation (D.E.G., C.H., K.L.), La Jolla Institute for Immunology, CA
| | - Chris A Benedict
- Division of Immune Regulation (S.B., D.S., C.A.B.), La Jolla Institute for Immunology, CA
| | - Bjoern Peters
- Division of Vaccine Discovery (B.P., A.S.), La Jolla Institute for Immunology, CA
| | - Andreas Zirlik
- Department of Cardiology, Medical University Graz, Austria (N.A.M., A.Z.)
| | - Alessandro Sette
- Division of Vaccine Discovery (B.P., A.S.), La Jolla Institute for Immunology, CA
| | - Klaus Ley
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA.,Center for Autoimmunity and Inflammation (D.E.G., C.H., K.L.), La Jolla Institute for Immunology, CA
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18
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Grifoni A, Voic H, Dhanda SK, Kidd CK, Brien JD, Buus S, Stryhn A, Durbin AP, Whitehead S, Diehl SA, De Silva AD, Balmaseda A, Harris E, Weiskopf D, Sette A. T Cell Responses Induced by Attenuated Flavivirus Vaccination Are Specific and Show Limited Cross-Reactivity with Other Flavivirus Species. J Virol 2020; 94:e00089-20. [PMID: 32132233 PMCID: PMC7199411 DOI: 10.1128/jvi.00089-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/25/2020] [Indexed: 12/14/2022] Open
Abstract
Members of the flavivirus genus share a high level of sequence similarity and often circulate in the same geographical regions. However, whether T cells induced by one viral species cross-react with other related flaviviruses has not been globally addressed. In this study, we tested pools of epitopes derived from dengue (DENV), Zika (ZIKV), Japanese encephalitis (JEV), West Nile (WNV), and yellow fever (YFV) viruses by intracellular cytokine staining (ICS) using peripheral blood mononuclear cells (PBMCs) of individuals naturally exposed to DENV or immunized with DENV (TV005) or YF17D vaccine. CD8 T cell responses recognized epitopes from multiple flaviviruses; however, the magnitude of cross-reactive responses was consistently severalfold lower than those to the autologous epitope pools and was associated with lower expression of activation markers such as CD40L, CD69, and CD137. Next, we characterized the antigen sensitivity of short-term T cell lines (TCL) representing 29 different individual epitope/donor combinations. TCL derived from DENV monovalent vaccinees induced CD8 and CD4 T cells that cross-reacted within the DENV serocomplex but were consistently associated with >100-fold-lower antigen sensitivity for most other flaviviruses, with no cross-recognition of YFV-derived peptides. CD8 and CD4 TCL from YF17D vaccinees were associated with very limited cross-reactivity with any other flaviviruses and in five out of eight cases >1,000-fold-lower antigen sensitivity. Overall, our data suggest limited cross-reactivity for both CD4 and CD8 T cell responses between flaviviruses and have implications for understanding immunity elicited by natural infection and strategies to develop live attenuated vaccines against flaviviral species.IMPORTANCE The envelope (E) protein is the dominant target of neutralizing antibodies for dengue virus (DENV) and yellow fever virus (YFV). Accordingly, several DENV vaccine constructs use the E protein in a live attenuated vaccine format, utilizing a backbone derived from a heterologous flavivirus (such as YF) as a delivery vector. This backbone comprises the nonstructural (NS) and capsid (C) antigens, which are dominant targets of T cell responses. Here, we demonstrate that cross-reactivity at the level of T cell responses among different flaviviruses is very limited, despite high levels of sequence homology. Thus, the use of heterologous flavivirus species as a live attenuated vaccine vector is not likely to generate optimal T cell responses and might thus impair vaccine performance.
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Affiliation(s)
- Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Hannah Voic
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Conner K Kidd
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Søren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anette Stryhn
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna P Durbin
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Stephen Whitehead
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sean A Diehl
- University of Vermont School of Medicine, Burlington, Vermont, USA
| | - Aruna D De Silva
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Paraclinical Sciences, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Angel Balmaseda
- National Virology Laboratory, National Center for Diagnosis and Reference, Ministry of Health, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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19
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Subramaniam KS, Lant S, Goodwin L, Grifoni A, Weiskopf D, Turtle L. Two Is Better Than One: Evidence for T-Cell Cross-Protection Between Dengue and Zika and Implications on Vaccine Design. Front Immunol 2020; 11:517. [PMID: 32269575 PMCID: PMC7109261 DOI: 10.3389/fimmu.2020.00517] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Dengue virus (DENV, family Flaviviridae, genus Flavivirus) exists as four distinct serotypes. Generally, immunity after infection with one serotype is protective and lifelong, though exceptions have been described. However, secondary infection with a different serotype can result in more severe disease for a minority of patients. Host responses to the first DENV infection involve the development of both cross-reactive antibody and T cell responses, which, depending upon their precise balance, may mediate protection or enhance disease upon secondary infection with a different serotype. Abundant evidence now exists that responses elicited by DENV infection can cross-react with other members of the genus Flavivirus, particularly Zika virus (ZIKV). Cohort studies have shown that prior DENV immunity is associated with protection against Zika. Cross-reactive antibody responses may enhance infection with flaviviruses, which likely accounts for the cases of severe disease seen during secondary DENV infections. Data for T cell responses are contradictory, and even though cross-reactive T cell responses exist, their clinical significance is uncertain. Recent mouse experiments, however, show that cross-reactive T cells are capable of mediating protection against ZIKV. In this review, we summarize and discuss the evidence that T cell responses may, at least in part, explain the cross-protection seen against ZIKV from DENV infection, and that T cell antigens should therefore be included in putative Zika vaccines.
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Affiliation(s)
- Krishanthi S Subramaniam
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Suzannah Lant
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Lynsey Goodwin
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Tropical and Infectious Disease Unit, Liverpool University Hospitals, Liverpool, United Kingdom
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20
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Blight J, Alves E, Reyes-Sandoval A. Considering Genomic and Immunological Correlates of Protection for a Dengue Intervention. Vaccines (Basel) 2019; 7:E203. [PMID: 31816907 PMCID: PMC6963661 DOI: 10.3390/vaccines7040203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 01/18/2023] Open
Abstract
Over three billion are at risk of dengue infection with more than 100 million a year presenting with symptoms that can lead to deadly haemorrhagic disease. There are however no treatments available and the only licensed vaccine shows limited efficacy and is able to enhance the disease in some cases. These failures have mainly been due to the complex pathology and lack of understanding of the correlates of protection for dengue virus (DENV) infection. With increasing data suggesting both a protective and detrimental effect for antibodies and CD8 T-cells whilst having complex environmental dynamics. This review discusses the roles of genomic and immunological aspects of DENV infection, providing both a historical interpretation and fresh discussion on how this information can be used for the next generation of dengue interventions.
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Affiliation(s)
- Joshua Blight
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK; (J.B.); (E.A.)
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Eduardo Alves
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK; (J.B.); (E.A.)
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arturo Reyes-Sandoval
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
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21
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Dos Santos Franco L, Gushi LT, Luiz WB, Amorim JH. Seeking Flavivirus Cross-Protective Immunity. Front Immunol 2019; 10:2260. [PMID: 31616432 PMCID: PMC6763598 DOI: 10.3389/fimmu.2019.02260] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/06/2019] [Indexed: 01/04/2023] Open
Abstract
The Flavivirus genus is composed by viral serocomplexes with relevant global epidemiological impact. Many areas of the world present both, vector fauna and geographical conditions compatible with co-circulation, importing, emergence, and epidemics of flaviviruses of different serocomplexes. In this study, we aimed to identify both, immunological determinants and patterns of immune response possibly involved in flavivirus serocomplex cross-protection. We searched B and T cells epitopes which were thoroughly shown to be involved in flavivirus immunological control. Such epitopes were analyzed regarding their conservation, population coverage, and location along flavivirus polyprotein. We found that epitopes capable of eliciting flavivirus cross-protective immunity to a wide range of human populations are concentrated in proteins E, NS3, and NS5. Such identification of both, immunological determinants and patterns of immune response involved in flavivirus cross-protective immunity should be considered in future vaccine development. Moreover, cross-reactive epitopes presented in this work may be involved in dynamics of diseases caused by flaviviruses worldwide.
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Affiliation(s)
- Lorrany Dos Santos Franco
- Laboratório de Agentes Infecciosos e Vetores, Programa de Pós-graduação em Patologia Investigativa, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Bahia, Brazil
| | - Letícia Tsieme Gushi
- Laboratório de Agentes Infecciosos e Vetores, Programa de Pós-graduação em Patologia Investigativa, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Bahia, Brazil
| | - Wilson Barros Luiz
- Programa de Pós-graduação em Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz, Bahia, Brazil
| | - Jaime Henrique Amorim
- Laboratório de Agentes Infecciosos e Vetores, Programa de Pós-graduação em Patologia Investigativa, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Bahia, Brazil.,Programa de Pós-graduação em Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz, Bahia, Brazil
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22
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Tian Y, Grifoni A, Sette A, Weiskopf D. Human T Cell Response to Dengue Virus Infection. Front Immunol 2019; 10:2125. [PMID: 31552052 PMCID: PMC6737489 DOI: 10.3389/fimmu.2019.02125] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/23/2019] [Indexed: 12/28/2022] Open
Abstract
DENV is a major public health problem worldwide, thus underlining the overall significance of the proposed Program. The four dengue virus (DENV) serotypes (1-4) cause the most common mosquito-borne viral disease of humans, with 3 billion people at risk for infection and up to 100 million cases each year, most often affecting children. The protective role of T cells during viral infection is well-established. Generally, CD8 T cells can control viral infection through several mechanisms, including direct cytotoxicity, and production of pro-inflammatory cytokines such as IFN-γ and TNF-α. Similarly, CD4 T cells are thought to control viral infection through multiple mechanisms, including enhancement of B and CD8 T cell responses, production of inflammatory and anti-viral cytokines, cytotoxicity, and promotion of memory responses. To probe the phenotype of virus-specific T cells, epitopes derived from viral sequences need to be known. Here we discuss the identification of CD4 and CD8 T cell epitopes derived from DENV and how these epitopes have been used by researchers to interrogate the phenotype and function of DENV-specific T cell populations.
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Affiliation(s)
- Yuan Tian
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
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23
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Pinto PBA, Assis ML, Vallochi AL, Pacheco AR, Lima LM, Quaresma KRL, Pereira BAS, Costa SM, Alves AMB. T Cell Responses Induced by DNA Vaccines Based on the DENV2 E and NS1 Proteins in Mice: Importance in Protection and Immunodominant Epitope Identification. Front Immunol 2019; 10:1522. [PMID: 31333657 PMCID: PMC6617960 DOI: 10.3389/fimmu.2019.01522] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/18/2019] [Indexed: 01/04/2023] Open
Abstract
The importance of the cellular immune response against DENV has been increasingly highlighted in the past few years, in particular for vaccine development. We have previously constructed two plasmids, pE1D2, and pcTPANS1, encoding the envelope (E) ectodomain (domains I, II, and III) and the non-structural 1 (NS1) protein of dengue virus serotype 2 (DENV2), respectively. In the present work, we analyzed the induction of the cellular response in mice immunized with these DNA vaccines and identified the immunogenic peptides. Vaccinated BALB/c mice became protected against a lethal challenge of DENV2. Depletion of CD4+ cells in vaccinated animals almost completely abolished protection elicited by both vaccines. In contrast, a significant number of pE1D2- and pcTPANS1-immunized mice survived virus challenge after depletion of CD8+ cells, although some animals presented morbidity. To identify immunogenic peptides recognized by T cells, we stimulated splenocytes with overlapping peptide libraries covering the E and NS1 proteins and evaluated the production of IFN-γ by ELISPOT. We detected two and three immunodominant epitopes in the E and NS1 proteins, respectively, and four additional NS1-derived peptides after virus challenge. Characterization by intracellular cytokine staining (ICS) revealed that both CD4+ and CD8+ T cells were involved in IFN-γ and TNF-α production. The IFN-γ ICS confirmed reaction of almost all E-derived peptides before challenge and identified other epitopes after infection. All NS1-derived peptides were able to elicit IFN-γ production in CD4+ cells, while only a few peptides induced expression of this cytokine in CD8+ T lymphocytes. Interestingly, we observed an increase in the frequency of either CD4+ or CD8+ T cells producing TNF-α after immunization with the pE1D2 and challenge with DENV2, while lymphocytes from pcTPANS1-vaccinated animals maintained ordinary TNF-α production after virus infection. We also assessed the recognition of E and NS1 immunogenic peptides in C57BL/6 mice due to the difference in MHC haplotype expression. Two NS1-derived epitopes featured prominently in the IFN-γ response with cells from both animal strains. Overall, our results emphasize the importance of the T cell response involved in protection against dengue induced by E and NS1 based DNA vaccines.
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Affiliation(s)
- Paolla B. A. Pinto
- Laboratory of Biotechnology and Physiology of Viral Infections, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Maysa L. Assis
- Laboratory of Biotechnology and Physiology of Viral Infections, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Adriana L. Vallochi
- Laboratory of Immunopharmacology, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Agatha R. Pacheco
- Laboratory of Biotechnology and Physiology of Viral Infections, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Lauro M. Lima
- Laboratory of Biotechnology and Physiology of Viral Infections, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Kátia R. L. Quaresma
- Laboratory of Biotechnology and Physiology of Viral Infections, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Bernardo A. S. Pereira
- Laboratory of Biotechnology and Physiology of Viral Infections, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Simone M. Costa
- Laboratory of Biotechnology and Physiology of Viral Infections, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Ada M. B. Alves
- Laboratory of Biotechnology and Physiology of Viral Infections, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
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24
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Roth C, Cantaert T, Colas C, Prot M, Casadémont I, Levillayer L, Thalmensi J, Langlade-Demoyen P, Gerke C, Bahl K, Ciaramella G, Simon-Loriere E, Sakuntabhai A. A Modified mRNA Vaccine Targeting Immunodominant NS Epitopes Protects Against Dengue Virus Infection in HLA Class I Transgenic Mice. Front Immunol 2019; 10:1424. [PMID: 31293584 PMCID: PMC6598640 DOI: 10.3389/fimmu.2019.01424] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/05/2019] [Indexed: 11/13/2022] Open
Abstract
Dengue virus (DENV) induces strong T and B cell responses upon infection. Hence, it is difficult to determine the contribution of cell-mediated immunity alone in the long lasting protection against DENV infection and disease. Numerous CD4+ and CD8+ T cell epitopes have been identified, mainly in the non-structural proteins of DENV. Taking into account the immunogenicity and peptide sequence conservation among the different DENV serotypes, a minimal DENV antigen, called DENV1-NS, has been designed. This antigen is enriched in conserved and highly antigenic epitopes located in the NS3, NS4B, and NS5 regions of DENV1. To evaluate the ability of the DENV1-NS poly-epitope to express the antigenic peptides in the context of different HLA class I molecules, we established its in vivo immunogenicity by measuring, after DNA immunization and electroporation, the activation of DENV-specific CD8 T cells in transgenic mice expressing the human HLA-A*0201, -A*2402, -B*0702, and -B*3502 class I alleles. We then engineered a lipid nanoparticle (LNP) encapsulated modified mRNA vaccine encoding DENV1-NS and tested immunogenicity and protection in these human HLA class I transgenic mice, after transient blockade of the interferon (IFN) type I receptor. Significant protection was observed, after two injections of the mRNA vaccine. Collectively, these data strongly support the development of T cell-based vaccines targeting immunodominant T cell epitopes that generate potent virus-specific T cell responses conferring immunity against DENV infection.
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Affiliation(s)
- Claude Roth
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | | | - Chloé Colas
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - Matthieu Prot
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - Isabelle Casadémont
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - Laurine Levillayer
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | | | | | | | - Kapil Bahl
- Moderna, Inc., Cambridge, MA, United States
| | | | - Etienne Simon-Loriere
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
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25
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Elong Ngono A, Shresta S. Cross-Reactive T Cell Immunity to Dengue and Zika Viruses: New Insights Into Vaccine Development. Front Immunol 2019; 10:1316. [PMID: 31244855 PMCID: PMC6579874 DOI: 10.3389/fimmu.2019.01316] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/23/2019] [Indexed: 11/25/2022] Open
Abstract
Dengue virus (DENV) is a member of the Flavivirus family that includes Zika virus (ZIKV), West Nile virus, Japanese encephalitis virus, and yellow fever virus. As the most prevalent of the flaviviruses, DENV is responsible for tens of millions of infections each year. The clinical manifestations of infection with one of the four DENV serotypes (DENV1–4) range from no symptoms to hemorrhagic fever and shock (“severe dengue”), which is fatal in ~25,000 patients annually. Many factors contribute to the development of severe dengue, including the DENV serotype and host expression of certain HLA alleles; however, it now seems clear that pre-existing immunity to DENV—and possibly other flaviviruses—is a major precipitating factor. While primary infection with one DENV serotype elicits strong cellular and humoral immune responses that likely confer long-lived protection against the same serotype, subsequent infection with a different serotype carries an increased risk of developing severe dengue. Thus, primary DENV infection elicits cross-reactive immunity that may be protective or pathogenic, depending on the context of the subsequent infection. Many flaviviruses share high sequence homology, raising the possibility that cross-reactive immunity to one virus may contribute to protection against or pathogenesis of a second virus in a similar manner. In addition, several flaviviruses are now endemic in overlapping geographic regions, underscoring the need to gain more knowledge about the mechanisms underlying cross-reactive immunity to different DENV serotypes and flaviviruses. Here, we review our current understanding of T cell immunity to DENV, focusing on cross-reactivity with other serotypes and flaviviruses such as ZIKV, and the role of DENV-elicited CD4+ and CD8+ T cells in protection. Recent work in this area supports a beneficial role for cross-reactive T cells and provides new insights into the design of safe and efficient flavivirus/pan-flavivirus vaccines.
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Affiliation(s)
- Annie Elong Ngono
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, United States
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26
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Wen J, Shresta S. Antigenic cross-reactivity between Zika and dengue viruses: is it time to develop a universal vaccine? Curr Opin Immunol 2019; 59:1-8. [PMID: 30884384 DOI: 10.1016/j.coi.2019.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/06/2019] [Indexed: 12/22/2022]
Abstract
Zika and the four serotypes of dengue are closely related flaviviruses that share a high degree of structural and sequence homology and co-circulate in many regions of the world. Here, we review recent studies investigating antigenic cross-reactivity between the two viruses. We discuss the pathogenic and protective roles of cross-reactive anti-viral antibody and T cell responses, respectively, in modulating the outcome of secondary dengue or Zika infection. Based on recent findings and increased incidence of severe disease in seronegative recipients of the first dengue vaccine to be licensed, we propose that the time has come to focus on developing pan-flavivirus vaccines that protect against Zika and four dengue serotypes by eliciting protective cross-reactive T cell responses while concomitantly reducing production of cross-reactive antibodies that can exacerbate disease.
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Affiliation(s)
- Jinsheng Wen
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Department of Microbiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
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Krishnakumar V, Durairajan SSK, Alagarasu K, Li M, Dash AP. Recent Updates on Mouse Models for Human Immunodeficiency, Influenza, and Dengue Viral Infections. Viruses 2019; 11:v11030252. [PMID: 30871179 PMCID: PMC6466164 DOI: 10.3390/v11030252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/09/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Well-developed mouse models are important for understanding the pathogenesis and progression of immunological response to viral infections in humans. Moreover, to test vaccines, anti-viral drugs and therapeutic agents, mouse models are fundamental for preclinical investigations. Human viruses, however, seldom infect mice due to differences in the cellular receptors used by the viruses for entry, as well as in the innate immune responses in mice and humans. In other words, a species barrier exists when using mouse models for investigating human viral infections. Developing transgenic (Tg) mice models expressing the human genes coding for viral entry receptors and knock-out (KO) mice models devoid of components involved in the innate immune response have, to some extent, overcome this barrier. Humanized mouse models are a third approach, developed by engrafting functional human cells and tissues into immunodeficient mice. They are becoming indispensable for analyzing human viral diseases since they nearly recapitulate the human disease. These mouse models also serve to test the efficacy of vaccines and antiviral agents. This review provides an update on the Tg, KO, and humanized mouse models that are used in studies investigating the pathogenesis of three important human-specific viruses, namely human immunodeficiency (HIV) virus 1, influenza, and dengue.
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Affiliation(s)
- Vinodhini Krishnakumar
- Department of Microbiology, School of Life Sciences, Central University of Tamilnadu, Tiruvarur 610 005, India.
| | | | - Kalichamy Alagarasu
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India.
| | - Min Li
- Neuroscience Research Laboratory, Mr. & Mrs. Ko Chi-Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, HKSAR, China.
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Monette A, Mouland AJ. T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 342:175-263. [PMID: 30635091 PMCID: PMC7104940 DOI: 10.1016/bs.ircmb.2018.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Continuous epidemiological surveillance of existing and emerging viruses and their associated disorders is gaining importance in light of their abilities to cause unpredictable outbreaks as a result of increased travel and vaccination choices by steadily growing and aging populations. Close surveillance of outbreaks and herd immunity are also at the forefront, even in industrialized countries, where previously eradicated viruses are now at risk of re-emergence due to instances of strain recombination, contractions in viral vector geographies, and from their potential use as agents of bioterrorism. There is a great need for the rational design of current and future vaccines targeting viruses, with a strong focus on vaccine targeting of adaptive immune effector memory T cells as the gold standard of immunity conferring long-lived protection against a wide variety of pathogens and malignancies. Here, we review viruses that have historically caused large outbreaks and severe lethal disorders, including respiratory, gastric, skin, hepatic, neurologic, and hemorrhagic fevers. To observe trends in vaccinology against these viral disorders, we describe viral genetic, replication, transmission, and tropism, host-immune evasion strategies, and the epidemiology and health risks of their associated syndromes. We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates.
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Zhao D, Han K, Zhang L, Wang H, Tian Y, Huang X, Liu Q, Yang J, Liu Y, Li Y. Identification and immunogenic evaluation of T cell epitopes based on tembusu virus envelope protein in ducks. Virus Res 2018; 257:74-81. [DOI: 10.1016/j.virusres.2018.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/06/2018] [Accepted: 09/17/2018] [Indexed: 10/28/2022]
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Manet C, Roth C, Tawfik A, Cantaert T, Sakuntabhai A, Montagutelli X. Host genetic control of mosquito-borne Flavivirus infections. Mamm Genome 2018; 29:384-407. [PMID: 30167843 PMCID: PMC7614898 DOI: 10.1007/s00335-018-9775-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022]
Abstract
Flaviviruses are arthropod-borne viruses, several of which represent emerging or re-emerging pathogens responsible for widespread infections with consequences ranging from asymptomatic seroconversion to severe clinical diseases and congenital developmental deficits. This variability is due to multiple factors including host genetic determinants, the role of which has been investigated in mouse models and human genetic studies. In this review, we provide an overview of the host genes and variants which modify susceptibility or resistance to major mosquito-borne flaviviruses infections in mice and humans.
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Affiliation(s)
- Caroline Manet
- Mouse Genetics Laboratory, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Claude Roth
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- CNRS, UMR 2000-Génomique Evolutive, Modélisation et Santé, Institut Pasteur, 75015, Paris, France
| | - Ahmed Tawfik
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- CNRS, UMR 2000-Génomique Evolutive, Modélisation et Santé, Institut Pasteur, 75015, Paris, France
| | - Tineke Cantaert
- Immunology Group, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, Phnom Penh, 12201, Cambodia
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
- CNRS, UMR 2000-Génomique Evolutive, Modélisation et Santé, Institut Pasteur, 75015, Paris, France.
| | - Xavier Montagutelli
- Mouse Genetics Laboratory, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
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Gfeller D, Bassani-Sternberg M. Predicting Antigen Presentation-What Could We Learn From a Million Peptides? Front Immunol 2018; 9:1716. [PMID: 30090105 PMCID: PMC6068240 DOI: 10.3389/fimmu.2018.01716] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/12/2018] [Indexed: 12/30/2022] Open
Abstract
Antigen presentation lies at the heart of immune recognition of infected or malignant cells. For this reason, important efforts have been made to predict which peptides are more likely to bind and be presented by the human leukocyte antigen (HLA) complex at the surface of cells. These predictions have become even more important with the advent of next-generation sequencing technologies that enable researchers and clinicians to rapidly determine the sequences of pathogens (and their multiple variants) or identify non-synonymous genetic alterations in cancer cells. Here, we review recent advances in predicting HLA binding and antigen presentation in human cells. We argue that the very large amount of high-quality mass spectrometry data of eluted (mainly self) HLA ligands generated in the last few years provides unprecedented opportunities to improve our ability to predict antigen presentation and learn new properties of HLA molecules, as demonstrated in many recent studies of naturally presented HLA-I ligands. Although major challenges still lie on the road toward the ultimate goal of predicting immunogenicity, these experimental and computational developments will facilitate screening of putative epitopes, which may eventually help decipher the rules governing T cell recognition.
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Affiliation(s)
- David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
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Abstract
The 2015-2016 Zika virus (ZIKV) outbreak in the Americas has brought this relatively unknown flavivirus into the spotlight as the etiologic agent of congenital Zika syndrome in newborns and, potentially, of Guillain-Barré syndrome in adults. ZIKV shares a high degree of amino acid sequence homology with the closely related flavivirus Dengue virus (DENV). Due to the paucity of research investigating T cell-mediated immune responses to ZIKV, the precise roles of T cells in protection against and pathogenesis of ZIKV infection are unclear. Nevertheless, knowledge gained from studies of T cell responses to other flaviviruses, such as the four DENV serotypes, provides a framework for investigating and understanding anti-ZIKV T cell responses. In this review, we summarize our current understanding of how T cells respond to primary and secondary infections with DENV and ZIKV. A thorough understanding of the role of ZIKV-specific and DENV cross-reactive T cells in controlling infection is essential for developing ZIKV- and DENV-specific vaccines with maximal safety and efficacy.
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Affiliation(s)
- Jinsheng Wen
- 1 Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology , La Jolla, California.,2 Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University , Wenzhou, China
| | - Sujan Shresta
- 1 Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology , La Jolla, California.,2 Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University , Wenzhou, China
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Moodie Z, Juraska M, Huang Y, Zhuang Y, Fong Y, Carpp LN, Self SG, Chambonneau L, Small R, Jackson N, Noriega F, Gilbert PB. Neutralizing Antibody Correlates Analysis of Tetravalent Dengue Vaccine Efficacy Trials in Asia and Latin America. J Infect Dis 2018; 217:742-753. [PMID: 29194547 PMCID: PMC5854020 DOI: 10.1093/infdis/jix609] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/07/2017] [Indexed: 01/16/2023] Open
Abstract
Background In the CYD14 and CYD15 Phase 3 trials of the CYD-TDV dengue vaccine, estimated vaccine efficacy (VE) against symptomatic, virologically confirmed dengue (VCD) occurring between months 13 and 25 was 56.5% and 60.8%, respectively. Methods Neutralizing antibody titers to the 4 dengue serotypes in the CYD-TDV vaccine insert were measured at month 13 in a randomly sampled immunogenicity subcohort and in all VCD cases through month 25 (2848 vaccine, 1574 placebo) and studied for their association with VCD and with the level of VE to prevent VCD. Results For each trial and serotype, vaccinees with higher month 13 titer to the serotype had significantly lower risk of VCD with that serotype (hazard ratios, 0.19-0.43 per 10-fold increase). Moreover, for each trial, vaccinees with higher month 13 average titer to the 4 serotypes had significantly higher VE against VCD of any serotype (P < .001). Conclusions Neutralizing antibody titers postdose 3 correlate with CYD-TDV VE to prevent dengue. High titers associate with high VE for all serotypes, baseline serostatus groups, age groups, and both trials. However, lowest titers do not fully correspond to zero VE, indicating that other factors influence VE.
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Affiliation(s)
- Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | - Yingying Zhuang
- Department of Biostatistics, University of Washington, Seattle
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Steven G Self
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | | | | | | | | | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
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Abstract
Flaviviruses such as dengue (DENV), yellow fever (YFV), West Nile (WNV), and Zika (ZIKV) are human pathogens of global significance. In particular, DENV causes the most prevalent mosquito-borne viral diseases in humans, and ZIKV emerged from obscurity into the spotlight in 2016 as the etiologic agent of congenital Zika syndrome. Owing to the recent emergence of ZIKV as a global pandemic threat, the roles of the immune system during ZIKV infections are as yet unclear. In contrast, decades of DENV research implicate a dual role for the immune system in protection against and pathogenesis of DENV infection. As DENV and ZIKV are closely related, knowledge based on DENV studies has been used to prioritize investigation of ZIKV immunity and pathogenesis, and to accelerate ZIKV diagnostic, therapeutic, and vaccine design. This review discusses the following topics related to innate and adaptive immune responses to DENV and ZIKV: the interferon system as the key mechanism of host defense and viral target for immune evasion, antibody-mediated protection versus antibody-dependent enhancement, and T cell-mediated protection versus original T cell antigenic sin. Understanding the mechanisms that regulate the balance between immune-mediated protection and pathogenesis during DENV and ZIKV infections is critical toward development of safe and effective DENV and ZIKV therapeutics and vaccines.
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Affiliation(s)
- Annie Elong Ngono
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA;
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA;
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Reginald K, Chan Y, Plebanski M, Poh CL. Development of Peptide Vaccines in Dengue. Curr Pharm Des 2018; 24:1157-1173. [PMID: 28914200 PMCID: PMC6040172 DOI: 10.2174/1381612823666170913163904] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/30/2017] [Accepted: 09/06/2017] [Indexed: 12/11/2022]
Abstract
Dengue is one of the most important arboviral infections worldwide, infecting up to 390 million people and causing 25,000 deaths annually. Although a licensed dengue vaccine is available, it is not efficacious against dengue serotypes that infect people living in South East Asia, where dengue is an endemic disease. Hence, there is an urgent need to develop an efficient dengue vaccine for this region. Data from different clinical trials indicate that a successful dengue vaccine must elicit both neutralizing antibodies and cell mediated immunity. This can be achieved by designing a multi-epitope peptide vaccine comprising B, CD8+ and CD4+ T cell epitopes. As recognition of T cell epitopes are restricted by human leukocyte antigens (HLA), T cell epitopes which are able to recognize several major HLAs will be preferentially included in the vaccine design. While peptide vaccines are safe, biocompatible and cost-effective, it is poorly immunogenic. Strategies to improve its immunogenicity by the use of long peptides, adjuvants and nanoparticle delivery mechanisms are discussed.
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Affiliation(s)
| | | | | | - Chit Laa Poh
- Address correspondence to this author at the Research Centre for Biomedical Sciences, School of Science and Technology, Sunway University, 5 Jalan University, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia; Tel: +60-3-7491 8622 ext. 7338; E-mail:
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Dhanda SK, Usmani SS, Agrawal P, Nagpal G, Gautam A, Raghava GPS. Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeutics. Brief Bioinform 2017; 18:467-478. [PMID: 27016393 DOI: 10.1093/bib/bbw025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 12/19/2022] Open
Abstract
The conventional approach for designing vaccine against a particular disease involves stimulation of the immune system using the whole pathogen responsible for the disease. In the post-genomic era, a major challenge is to identify antigenic regions or epitopes that can stimulate different arms of the immune system. In the past two decades, numerous methods and databases have been developed for designing vaccine or immunotherapy against various pathogen-causing diseases. This review describes various computational resources important for designing subunit vaccines or epitope-based immunotherapy. First, different immunological databases are described that maintain epitopes, antigens and vaccine targets. This is followed by in silico tools used for predicting linear and conformational B-cell epitopes required for activating humoral immunity. Finally, information on T-cell epitope prediction methods is provided that includes indirect methods like prediction of Major Histocompatibility Complex and transporter-associated protein binders. Different studies for validating the predicted epitopes are also examined critically. This review enlists novel in silico resources and tools available for predicting humoral and cell-mediated immune potential. These predicted epitopes could be used for designing epitope-based vaccines or immunotherapy as they may activate the adaptive immunity. Authors emphasized the need to develop tools for the prediction of adjuvants to activate innate and adaptive immune system simultaneously. In addition, attention has also been given to novel prediction methods to predict general therapeutic properties of peptides like half-life, cytotoxicity and immune toxicity.
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Wen J, Elong Ngono A, Regla-Nava JA, Kim K, Gorman MJ, Diamond MS, Shresta S. Dengue virus-reactive CD8 + T cells mediate cross-protection against subsequent Zika virus challenge. Nat Commun 2017; 8:1459. [PMID: 29129917 PMCID: PMC5682281 DOI: 10.1038/s41467-017-01669-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/05/2017] [Indexed: 01/28/2023] Open
Abstract
Zika virus (ZIKV) and dengue virus (DENV) are antigenically related flaviviruses that share cross-reactivity in antibody and T cell responses, and co-circulate in increasing numbers of countries. Whether pre-existing DENV immunity can cross-protect or enhance ZIKV infection during sequential infection of the same host is unknown. Here, we show that DENV-immune Ifnar1−/− or wild-type C57BL/6 mice infected with ZIKV have cross-reactive immunity to subsequent ZIKV infection and pathogenesis. Adoptive transfer and cell depletion studies demonstrate that DENV-immune CD8+ T cells predominantly mediate cross-protective responses to ZIKV. In contrast, passive transfer studies suggest that DENV-immune serum does not protect against ZIKV infection. Thus, CD8+ T cell immunity generated during primary DENV infection can confer protection against secondary ZIKV infection in mice. Further optimization of current DENV vaccines for T cell responses might confer cross-protection and prevent antibody-mediated enhancement of ZIKV infection. Dengue virus-specific antibody and CD8+ T cells that cross-react with Zika virus have been described. Here, the authors establish a functionally protective role for cross-reactive dengue virus-specific CD8+ T cells during challenge with Zika virus.
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Affiliation(s)
- Jinsheng Wen
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA.,Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Annie Elong Ngono
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Jose Angel Regla-Nava
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Kenneth Kim
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Matthew J Gorman
- Department of Medicine, Molecular Microbiology, Pathology and Immunology, The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael S Diamond
- Department of Medicine, Molecular Microbiology, Pathology and Immunology, The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA. .,Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China. .,Department of Medicine, School of Medicine, University of California, La Jolla, San Diego, CA, 92037, USA.
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Zeng Y, Gao T, Zhao G, Jiang Y, Yang Y, Yu H, Kou Z, Lone Y, Sun S, Zhou Y. Generation of human MHC (HLA-A11/DR1) transgenic mice for vaccine evaluation. Hum Vaccin Immunother 2017; 12:829-36. [PMID: 26479036 DOI: 10.1080/21645515.2015.1103405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The rapid occurrence of emerging infectious diseases demonstrates an urgent need for a new preclinical experimental model that reliably replicates human immune responses. Here, a new homozygous humanized human leukocyte antigen (HLA)-A11/DR1 transgenic mouse (HLA-A11(+/+)/DR01(+/+)/H-2-β2m(-/-)/IAβ(-/-)) was generated by crossing HLA-A11 transgenic (Tg) mice with HLA-A2(+/+)/DR01(+/+)/H-2-β2m(-/-)/IAβ(-/-) mice. The HLA-A11-restricted immune response of this mouse model was then examined. HLA-A11 Tg mice expressing a chimeric major histocompatibility complex (MHC) molecule comprising the α1, α2, and β2m domains of human HLA-A11 and the α3 transmembrane and cytoplasmic domains of murine H-2D(b) were generated. The correct integration of HLA-A11 and HLA-DR1 into the genome of the HLA-A11/DR1 Tg mice (which lacked the expression of endogenous H-2-I/II molecules) was then confirmed. Immunizing mice with a recombinant HBV vaccine or a recombinant HIV-1 protein resulted in the generation of IFN-γ-producing cytotoxic T lymphocyte (CTL) and antigen-specific antibodies. The HLA-A11-restricted CTL response was directed at HLA immunodominant epitopes. These mice represent a versatile animal model for studying the immunogenicity of HLA CTL epitopes in the absence of a murine MHC response. The established animal model will also be useful for evaluating and optimizing T cell-based vaccines and for studying differences in antigen processing between mice and humans.
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Affiliation(s)
- Yang Zeng
- a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China.,b INSERM U1197 (ex U1014), University of Paris-Sud, Hospital Paul Brousse , Villejuif , France
| | | | - Guangyu Zhao
- a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Yuting Jiang
- a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Yi Yang
- a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Hong Yu
- a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Zhihua Kou
- a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Yuchun Lone
- b INSERM U1197 (ex U1014), University of Paris-Sud, Hospital Paul Brousse , Villejuif , France
| | - Shihui Sun
- a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Yusen Zhou
- a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China.,c Wenzhou Medical University , Zhejiang , China
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39
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T Cell Immunity and Zika Virus Vaccine Development. Trends Immunol 2017; 38:594-605. [DOI: 10.1016/j.it.2017.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/08/2017] [Accepted: 05/09/2017] [Indexed: 12/30/2022]
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Boldescu V, Behnam MAM, Vasilakis N, Klein CD. Broad-spectrum agents for flaviviral infections: dengue, Zika and beyond. Nat Rev Drug Discov 2017; 16:565-586. [PMID: 28473729 PMCID: PMC5925760 DOI: 10.1038/nrd.2017.33] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Infections with flaviviruses, such as dengue, West Nile virus and the recently re-emerging Zika virus, are an increasing and probably lasting global risk. This Review summarizes and comments on the opportunities for broad-spectrum agents that are active against multiple flaviviruses. Broad-spectrum activity is particularly desirable to prepare for the next flaviviral epidemic, which could emerge from as-yet unknown or neglected viruses. Potential molecular targets for broad-spectrum antiflaviviral compounds include viral proteins, such as the viral protease or polymerase, and host targets that are exploited by these viruses during entry and replication, including α-glucosidase and proteins involved in nucleoside biosynthesis. Numerous compounds with broad-spectrum antiviral activity have already been identified by target-specific or phenotypic assays. For other compounds, broad-spectrum activity can be anticipated because of their mode of action and molecular targets.
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Affiliation(s)
- Veaceslav Boldescu
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry of the Academy of Sciences of Moldova, Academiei 3, 2028 Chisinau, Moldova
| | - Mira A. M. Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nikos Vasilakis
- Dept. of Pathology and Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases and Institute for Human Infections and Immunity, 2.138D Keiller Bldg, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555–0609, USA
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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Collins MH, Metz SW. Progress and Works in Progress: Update on Flavivirus Vaccine Development. Clin Ther 2017; 39:1519-1536. [PMID: 28754189 DOI: 10.1016/j.clinthera.2017.07.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/30/2022]
Abstract
Most areas of the globe are endemic for at least one flavivirus, putting billions at risk for infection. This diverse group of viral pathogens causes a range of manifestations in humans from asymptomatic infection to hemorrhagic fever to encephalitis to birth defects and even death. Many flaviviruses are transmitted by mosquitos and have expanded in geographic distribution in recent years, with dengue virus being the most prevalent, infecting approximately 400 million people each year. The explosive emergence of Zika virus in Latin America in 2014 refocused international attention on this medically important group of viruses. Meanwhile, yellow fever has caused major outbreaks in Africa and South America since 2015 despite a reliable vaccine. There is no vaccine for Zika yet, and the only licensed dengue vaccine performs suboptimally in certain contexts. Further lessons are found when considering the experience with Japanese encephalitis virus, West Nile virus, and tickborne encephalitis virus, all of which now have protective vaccination in human or veterinary populations. Thus, vaccination is a mainstay of public health strategy for combating flavivirus infections; however, numerous challenges exist along the path from development to delivery of a tolerable and effective vaccine. Nevertheless, intensification of investment and effort in this area holds great promise for significantly reducing the global burden of disease attributable to flavivirus infection.
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Affiliation(s)
- Matthew H Collins
- Department of Medicine, Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina.
| | - Stefan W Metz
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina
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42
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Affiliation(s)
- Matthew Collins
- Division of Infectious Diseases in the Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Aravinda de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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Chen XY, Li DZ, Zhong XZ, Chen B, Duan ZL, Wen JS. Induction of multiple cytotoxic T lymphocyte responses in mice by a multiepitope DNA vaccine against dengue virus serotype 1. Microbiol Immunol 2017; 60:835-845. [PMID: 27981613 DOI: 10.1111/1348-0421.12457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/14/2016] [Accepted: 12/02/2016] [Indexed: 12/20/2022]
Abstract
Dengue virus (DENV) is still a major threat to human health in most tropical and subtropical countries and regions. In the present study, a multi-epitope DNA vaccine that encodes 15 immunogenic and conserved HLA-A*0201-, HLA-A*1101-, HLA-A*2402-restricted CTL epitopes from DENV serotype 1 (DENV-1) was constructed based on the eukaryotic expressing plasmid pcDNATM 3.1/myc-His(-) A. Immunization of HLA-A*0201, HLA-A*1101 and HLA-A*2402 transgenic mice with the recombinant plasmid pcDNATM 3.1/myc-His(-) A-DENV-1-Meg resulted in significantly greater IFN-γ-secreting T-cell responses against most (14/15) CTL epitopes than occurred in mice immunized with the empty plasmid pcDNATM 3.1/myc-His(-) A. Additionally, the epitope-specific T cells directed to some epitopes secreted not only IFN-γ but also IL-6 and/or TNF-α. Finally, the induced epitope-specific T cells also efficiently lysed epitope-pulsed splenocytes and DENV-1-infected splenic monocytes. The present study confirms the immunogenicity of multi-epitope DENV vaccine, suggesting that it may contribute to the development of a universal DENV vaccine.
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Affiliation(s)
- Xin Yu Chen
- Department of Clinical Laboratory, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Xueyuan West Road, Wenzhou 325000
| | - De Zhou Li
- Department of Liver, The Second Hospital of Ningbo, Ningbo 315010, China
| | - Xiao Zhi Zhong
- Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Chashan, Wenzhou 32500
| | - Bokun Chen
- Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Chashan, Wenzhou 32500
| | - Zhi Liang Duan
- Department of Clinical Laboratory, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Xueyuan West Road, Wenzhou 325000
| | - Jin Sheng Wen
- Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Chashan, Wenzhou 32500
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Patterns of Cellular Immunity Associated with Experimental Infection with rDEN2Δ30 (Tonga/74) Support Its Suitability as a Human Dengue Virus Challenge Strain. J Virol 2017; 91:JVI.02133-16. [PMID: 28148797 DOI: 10.1128/jvi.02133-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/28/2017] [Indexed: 11/20/2022] Open
Abstract
A deletion variant of the dengue virus (DENV) serotype 2 (DENV2) Tonga/74 strain lacking 30 nucleotides from its 3' untranslated region (rDEN2Δ30) has previously been established for use in a controlled human DENV challenge model. To evaluate if this model is appropriate for the derivation of correlates of protection for DENV vaccines on the basis of cellular immunity, we wanted to compare the cellular immune response to this challenge strain to the response induced by natural infection. To achieve this, we predicted HLA class I- and class II-restricted peptides from rDEN2Δ30 and used them in a gamma interferon enzyme-linked immunosorbent spot assay to interrogate CD8+ and CD4+ T cell responses in healthy volunteers infected with rDEN2Δ30. At the level of CD8 responses, vigorous ex vivo responses were detected in approximately 80% of donors. These responses were similar in terms of the magnitude and the numbers of epitopes recognized to the responses previously observed in peripheral blood mononuclear cells from donors from regions where DENV is hyperendemic. The similarity extended to the immunodominance hierarchy of the DENV nonstructural proteins, with NS3, NS5, and NS1 being dominant in both donor cohorts. At the CD4 level, the responses to rDEN2Δ30 vaccination were less vigorous than those to natural DENV infection and were more focused on nonstructural proteins. The epitopes recognized following rDEN2Δ30 infection and natural infection were largely overlapping for both the CD8 (100%) and CD4 (85%) responses. Finally, rDEN2Δ30 induced stronger CD8 responses than other, more attenuated DENV isolates.IMPORTANCE The lack of a known correlate of protection and the failure of a neutralizing antibody to correlate with protection against dengue virus have highlighted the need for a human DENV challenge model to better evaluate the candidate live attenuated dengue vaccines. In this study, we sought to characterize the immune profiles of rDEN2Δ30-infected subjects and to compare the profiles with those for subjects from areas where DENV is hyperendemic. Our data demonstrate that T cell responses to rDENV2Δ30 are largely similar to those to natural infection in terms of specificity, highlighting that the response to this virus in humans is appropriate as a model for the T cell response to primary DENV2 infection.
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Wen J, Tang WW, Sheets N, Ellison J, Sette A, Kim K, Shresta S. Identification of Zika virus epitopes reveals immunodominant and protective roles for dengue virus cross-reactive CD8 + T cells. Nat Microbiol 2017; 2:17036. [PMID: 28288094 DOI: 10.1038/nmicrobiol.2017.36] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/17/2017] [Indexed: 01/10/2023]
Abstract
CD8+ T cells play an important role in controlling Flavivirus infection, including Zika virus (ZIKV). Here, we have identified 25 HLA-B*0702-restricted epitopes and 1 HLA-A*0101-restricted epitope using interferon (IFN)-γ enzyme-linked immunospot (ELISPOT) and intracellular cytokine staining (ICS) in ZIKV-infected IFN-α/β receptor-deficient HLA transgenic mice. The cross-reactivity of ZIKV epitopes to dengue virus (DENV) was tested using IFN-γ-ELISPOT and IFN-γ-ICS on CD8+ T cells from DENV-infected mice, and five cross-reactive HLA-B*0702-binding peptides were identified by both assays. ZIKV/DENV cross-reactive CD8+ T cells in DENV-immune mice expanded post ZIKV challenge and dominated in the subsequent CD8+ T cell response. ZIKV challenge following immunization of mice with ZIKV-specific and ZIKV/DENV cross-reactive epitopes elicited CD8+ T cell responses that reduced infectious ZIKV levels, and CD8+ T cell depletions confirmed that CD8+ T cells mediated this protection. These results identify ZIKV-specific and ZIKV/DENV cross-reactive epitopes and demonstrate both an altered immunodominance pattern in the DENV-immune setting relative to naive, as well as a protective role for epitope-specific CD8+ T cells against ZIKV. These results have important implications for ZIKV vaccine development and provide a mouse model for evaluating anti-ZIKV CD8+ T cell responses of human relevance.
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Affiliation(s)
- Jinsheng Wen
- Division of Inflammation Biology, La Jolla Institute for Allergy &Immunology, La Jolla, California 92037, USA.,Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - William Weihao Tang
- Division of Inflammation Biology, La Jolla Institute for Allergy &Immunology, La Jolla, California 92037, USA
| | - Nicholas Sheets
- Division of Inflammation Biology, La Jolla Institute for Allergy &Immunology, La Jolla, California 92037, USA
| | - Julia Ellison
- Division of Inflammation Biology, La Jolla Institute for Allergy &Immunology, La Jolla, California 92037, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy &Immunology, La Jolla, California 92037, USA
| | - Kenneth Kim
- Division of Inflammation Biology, La Jolla Institute for Allergy &Immunology, La Jolla, California 92037, USA
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Allergy &Immunology, La Jolla, California 92037, USA
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Rivino L, Lim MQ. CD4 + and CD8 + T-cell immunity to Dengue - lessons for the study of Zika virus. Immunology 2016; 150:146-154. [PMID: 27763656 DOI: 10.1111/imm.12681] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 12/11/2022] Open
Abstract
Dengue virus (DENV) and Zika virus (ZIKV) are rapidly emerging mosquito-borne flaviviruses that represent a public health concern. Understanding host protective immunity to these viruses is critical for the design of optimal vaccines. Over a decade of research has highlighted a significant contribution of the T-cell response to both protection and/or disease enhancement during DENV infection, the latter being mainly associated with sub-optimal cross-reactive T-cell responses during secondary infections. Phase IIb/III clinical trials of the first licensed tetravalent dengue vaccine highlight increased vaccine efficacy in dengue-immune as opposed to dengue-naive vaccinees, suggesting a possible immunoprotective role of pre-existing DENV-specific T cells that are boosted upon vaccination. No vaccine is available for ZIKV and little is known about the T-cell response to this virus. ZIKV and DENV are closely related viruses with a sequence identity ranging from 44% and 56% for the structural proteins capsid and envelope to 68% for the more conserved non-structural proteins NS3/NS5, which represent the main targets of the CD4+ and CD8+ T-cell response to DENV, respectively. In this review we discuss our current knowledge of T-cell immunity to DENV and what it can teach us for the study of ZIKV. The extent of T-cell cross-reactivity towards ZIKV of pre-existing DENV-specific memory T cells and its potential impact on protective immunity and/or immunopathology will also be discussed.
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Affiliation(s)
- Laura Rivino
- Emerging Infectious Disease Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Mei Qiu Lim
- Emerging Infectious Disease Programme, Duke-NUS Medical School, Singapore 169857, Singapore
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Xu X, Vaughan K, Weiskopf D, Grifoni A, Diamond MS, Sette A, Peters B. Identifying Candidate Targets of Immune Responses in Zika Virus Based on Homology to Epitopes in Other Flavivirus Species. PLOS CURRENTS 2016; 8. [PMID: 28018746 PMCID: PMC5145810 DOI: 10.1371/currents.outbreaks.9aa2e1fb61b0f632f58a098773008c4b] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Introduction: The current outbreak of Zika virus has resulted in a massive effort to accelerate the development of ZIKV-specific diagnostics and vaccines. These efforts would benefit greatly from the definition of the specific epitope targets of immune responses in ZIKV, but given the relatively recent emergence of ZIKV as a pandemic threat, few such data are available. Methods: We used a large body of epitope data for other Flaviviruses that was available from the IEDB for a comparative analysis against the ZIKV proteome in order to project targets of immune responses in ZIKV. Results: We found a significant level of overlap between known antigenic sites from other Flavivirus proteins with residues on the ZIKV polyprotein. The E and NS1 proteins shared functional antibody epitope sites, whereas regions of T cell reactivity were conserved within NS3 and NS5 for ZIKV. Discussion: Our epitope based analysis provides guidance for which regions of the ZIKV polyprotein are most likely unique targets of ZIKV-specific antibodies, and which targets in ZIKV are most likely to be cross-reactive with other Flavivirus species. These data may therefore provide insights for the development of antibody- and T cell-based ZIKV-specific diagnostics, therapeutics and prophylaxis.
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Affiliation(s)
- Xiaojun Xu
- Division of Vaccine Discovery, La Jolla Institute for Allergy And Immunology, San Diego, California, USA
| | - Kerrie Vaughan
- Division of Vaccine Discovery, La Jolla Institute for Allergy And Immunology, San Diego, California, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy And Immunology, San Diego, California, USA
| | | | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA; The Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy And Immunology, San Diego, California, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy And Immunology, San Diego, California, USA
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Oseroff C, Christensen LH, Westernberg L, Pham J, Lane J, Paul S, Greenbaum J, Stranzl T, Lund G, Hoof I, Holm J, Würtzen PA, Meno KH, Frazier A, Schulten V, Andersen PS, Peters B, Sette A. Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity. Clin Exp Allergy 2016; 47:577-592. [PMID: 27684489 DOI: 10.1111/cea.12829] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/11/2016] [Accepted: 08/30/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND House dust mite (HDM) allergens are a common cause of allergy and allergic asthma. A comprehensive analysis of proteins targeted by T cells, which are implicated in the development and regulation of allergic disease independent of their antibody reactivity, is still lacking. OBJECTIVE To comprehensively analyse the HDM-derived protein targets of T cell responses in HDM-allergic individuals, and investigate their correlation with IgE/IgG responses and protein function. METHODS Proteomic analysis (liquid chromatography-tandem mass spectrometry) of HDM extracts identified 90 distinct protein clusters, corresponding to 29 known allergens and 61 novel proteins. Peripheral blood mononuclear cells (PBMC) from 20 HDM-allergic individuals were stimulated with HDM extracts and assayed with a set of ~2500 peptides derived from these 90 protein clusters and predicted to bind the most common HLA class II types. 2D immunoblots were made in parallel to elucidate IgE and IgG reactivity, and putative function analyses were performed in silico according to Gene Ontology annotations. RESULTS Analysis of T cell reactivity revealed a large number of T cell epitopes. Overall response magnitude and frequency was comparable for known and novel proteins, with 15 antigens (nine of which were novel) dominating the total T cell response. Most of the known allergens that were dominant at the T cell level were also IgE reactive, as expected, while few novel dominant T cell antigens were IgE reactive. Among known allergens, hydrolase activity and detectable IgE/IgG reactivity are strongly correlated, while no protein function correlates with immunogenicity of novel proteins. A total of 106 epitopes accounted for half of the total T cell response, underlining the heterogeneity of T cell responses to HDM allergens. CONCLUSIONS AND CLINICAL RELEVANCE Herein, we define the T cell targets for both known allergens and novel proteins, which may inform future diagnostics and immunotherapeutics for allergy to HDM.
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Affiliation(s)
- Carla Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | - Luise Westernberg
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - John Pham
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Jerome Lane
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Sinu Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Jason Greenbaum
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | - Gitte Lund
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - Ilka Hoof
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - Jens Holm
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | | | - Kåre H Meno
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - April Frazier
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | | | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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Elong Ngono A, Chen HW, Tang WW, Joo Y, King K, Weiskopf D, Sidney J, Sette A, Shresta S. Protective Role of Cross-Reactive CD8 T Cells Against Dengue Virus Infection. EBioMedicine 2016; 13:284-293. [PMID: 27746192 PMCID: PMC5264312 DOI: 10.1016/j.ebiom.2016.10.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 01/27/2023] Open
Abstract
Infection with one of the four dengue virus serotypes (DENV1-4) presumably leads to lifelong immunity against the infecting serotype but not against heterotypic reinfection, resulting in a greater risk of developing Dengue Hemorrhagic Fever/Dengue Shock Syndrome (DHF/DSS) during secondary infection. Both antibodies and T cell responses have been implicated in DHF/DSS pathogenesis. According to the T cell-based hypothesis termed “original antigenic sin,” secondary DENV infection is dominated by non-protective, cross-reactive T cells that elicit an aberrant immune response. The goal of our study was to compare the roles of serotype-specific and cross-reactive T cells in protection vs. pathogenesis during DENV infection in vivo. Specifically, we utilized IFN-α/βR−/− HLA*B0702 transgenic mice in the context of peptide vaccination with relevant human CD8 T cell epitopes. IFN-α/βR−/− HLA*B0702 transgenic mice were immunized with DENV serotype 2 (DENV2)-specific epitopes or variants found in any of the other three serotypes (DENV1, DENV3 or DENV4), followed by challenge with DENV. Although cross-reactive T cell responses were lower than responses elicited by serotype-specific T cells, immunization with either serotype-specific or variant peptide epitopes enhanced viral clearance, demonstrating that both serotype-specific and cross-reactive T cells can contribute to protection in vivo against DENV infection. Serotype-cross-reactive CD8 T cells elicit a polyfunctional immune response similar to the response elicited by serotype-specific CD8 T cells. Serotype cross-reactive CD8 T cells play a role in protection against DENV infection in a HLA-B*0702 Transgenic IFN-α/βR−/− mouse model.
There are four major subtypes (serotypes) of the mosquito-borne Dengue virus. Infection with a first serotype is generally asymptomatic, but secondary infection with a different serotype is capable of causing severe disease. T cells previously exposed to a first serotype and which produce an immune response to a second serotype are said to be cross-reactive. Using a mouse model engineered with human T cell features, we characterized the cross-reactive T cell response to live dengue virus serotypes and viral protein fragments. Our results suggested cross-reactive T cells contribute to control of and protection against infection by a second dengue serotype, rather than leading to more severe disease.
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Affiliation(s)
- Annie Elong Ngono
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Hui-Wen Chen
- Department of Veterinary Medicine, National Taiwan University, Taiwan
| | - William W Tang
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Yunichel Joo
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Kevin King
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.
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50
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Hinz D, Oseroff C, Pham J, Sidney J, Peters B, Sette A. Definition of a pool of epitopes that recapitulates the T cell reactivity against major house dust mite allergens. Clin Exp Allergy 2016; 45:1601-12. [PMID: 25652035 DOI: 10.1111/cea.12507] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Allergens from house dust mites (HDM) are a common cause of asthma. Der p and Der f from Dermatophagoides sp. are strong immunogens in humans. Allergen extracts are used to study T helper (Th2) cell responses to HDM, which are implicated in the development and regulation of allergic disease. OBJECTIVE To define an epitope mixture that recapitulates, and might substitute for, HDM extract in terms of detecting and characterizing Th2 cell responses. METHODS Peripheral blood mononuclear cells (PBMC) from 52 HDM allergic and 10 non-allergic individuals were stimulated with HDM extracts and assayed with a set of 178 peptides spanning mite allergens group Der p 1, 2, 23 and Der f group 1 and 2 allergens. A pool of the most dominant T cell epitopes identified in the present study and from published literature was assembled and tested for ex vivo T cell responses. Correlation with HDM-specific IgE titres was examined. RESULTS Patterns of T cell reactivity to Der p and Der f - derived peptides revealed a large number of epitopes. Clear patterns of immunodominance were apparent, with HDM allergen group 1 and 2 dominant over group 23. Furthermore, within a given antigen, 6-11 epitopes accounted for the vast majority of responses. Based on these results and published data, a comprehensive dust mite pool (DMP) of epitopes was designed and found to allow detection of ex vivo T cell responses. DMP ex vivo reactivity correlated with HDM-specific IgE titres and was similar to that detected with commonly used HDM extracts. Ex vivo DMP stimulation was associated with a predominant Th2 response in allergic donors, and minor reactivity of T cells producing IFNγ, IL17 and IL10. CONCLUSIONS & CLINICAL RELEVANCE A detailed map of Der p and Der f antigens defined a pool of epitopes that can be used to detect ex vivo HDM responses.
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Affiliation(s)
- D Hinz
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - C Oseroff
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - J Pham
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - J Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - B Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - A Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
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