1
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Yin R, Melton S, Huseby ES, Kardar M, Chakraborty AK. How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease. Proc Natl Acad Sci U S A 2024; 121:e2318599121. [PMID: 38446856 PMCID: PMC10945823 DOI: 10.1073/pnas.2318599121] [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: 10/24/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
T cells help orchestrate immune responses to pathogens, and their aberrant regulation can trigger autoimmunity. Recent studies highlight that a threshold number of T cells (a quorum) must be activated in a tissue to mount a functional immune response. These collective effects allow the T cell repertoire to respond to pathogens while suppressing autoimmunity due to circulating autoreactive T cells. Our computational studies show that increasing numbers of pathogenic peptides targeted by T cells during persistent or severe viral infections increase the probability of activating T cells that are weakly reactive to self-antigens (molecular mimicry). These T cells are easily re-activated by the self-antigens and contribute to exceeding the quorum threshold required to mount autoimmune responses. Rare peptides that activate many T cells are sampled more readily during severe/persistent infections than in acute infections, which amplifies these effects. Experiments in mice to test predictions from these mechanistic insights are suggested.
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Affiliation(s)
- Rose Yin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Samuel Melton
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eric S. Huseby
- Basic Pathology, Department of Pathology, University of Massachusetts Medical School, Worcester, MA01655
| | - Mehran Kardar
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
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2
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Musunuri S, Weidenbacher PAB, Kim PS. Bringing immunofocusing into focus. NPJ Vaccines 2024; 9:11. [PMID: 38195562 PMCID: PMC10776678 DOI: 10.1038/s41541-023-00792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Immunofocusing is a strategy to create immunogens that redirect humoral immune responses towards a targeted epitope and away from non-desirable epitopes. Immunofocusing methods often aim to develop "universal" vaccines that provide broad protection against highly variant viruses such as influenza virus, human immunodeficiency virus (HIV-1), and most recently, severe acute respiratory syndrome coronavirus (SARS-CoV-2). We use existing examples to illustrate five main immunofocusing strategies-cross-strain boosting, mosaic display, protein dissection, epitope scaffolding, and epitope masking. We also discuss obstacles for immunofocusing like immune imprinting. A thorough understanding, advancement, and application of the methods we outline here will enable the design of high-resolution vaccines that protect against future viral outbreaks.
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Affiliation(s)
- Sriharshita Musunuri
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Payton A B Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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3
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Han Y, Yang Y, Tian Y, Fattah FJ, von Itzstein MS, Hu Y, Zhang M, Kang X, Yang DM, Liu J, Xue Y, Liang C, Raman I, Zhu C, Xiao O, Dowell JE, Homsi J, Rashdan S, Yang S, Gwin ME, Hsiehchen D, Gloria-McCutchen Y, Pan K, Wu F, Gibbons D, Wang X, Yee C, Huang J, Reuben A, Cheng C, Zhang J, Gerber DE, Wang T. pan-MHC and cross-Species Prediction of T Cell Receptor-Antigen Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569599. [PMID: 38105939 PMCID: PMC10723300 DOI: 10.1101/2023.12.01.569599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Profiling the binding of T cell receptors (TCRs) of T cells to antigenic peptides presented by MHC proteins is one of the most important unsolved problems in modern immunology. Experimental methods to probe TCR-antigen interactions are slow, labor-intensive, costly, and yield moderate throughput. To address this problem, we developed pMTnet-omni, an Artificial Intelligence (AI) system based on hybrid protein sequence and structure information, to predict the pairing of TCRs of αβ T cells with peptide-MHC complexes (pMHCs). pMTnet-omni is capable of handling peptides presented by both class I and II pMHCs, and capable of handling both human and mouse TCR-pMHC pairs, through information sharing enabled this hybrid design. pMTnet-omni achieves a high overall Area Under the Curve of Receiver Operator Characteristics (AUROC) of 0.888, which surpasses competing tools by a large margin. We showed that pMTnet-omni can distinguish binding affinity of TCRs with similar sequences. Across a range of datasets from various biological contexts, pMTnet-omni characterized the longitudinal evolution and spatial heterogeneity of TCR-pMHC interactions and their functional impact. We successfully developed a biomarker based on pMTnet-omni for predicting immune-related adverse events of immune checkpoint inhibitor (ICI) treatment in a cohort of 57 ICI-treated patients. pMTnet-omni represents a major advance towards developing a clinically usable AI system for TCR-pMHC pairing prediction that can aid the design and implementation of TCR-based immunotherapeutics.
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4
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Mavi AK, Gaur S, Gaur G, Babita, Kumar N, Kumar U. CAR T-cell therapy: Reprogramming patient's immune cell to treat cancer. Cell Signal 2023; 105:110638. [PMID: 36822565 DOI: 10.1016/j.cellsig.2023.110638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Chimeric antigen receptor (CAR)-T cell therapy is a game changer in cancer treatment. Although CAR-T cell therapy has achieved significant clinical responses in specific subgroups of B cell leukaemia or lymphoma, various difficulties restrict CAR-T cell therapy's therapeutic effectiveness in solid tumours and haematological malignancies. Severe life-threatening toxicities, poor anti-tumour effectiveness, antigen escape, restricted trafficking, and limited tumour penetration are all barriers to successful CAR-T cell treatment. Furthermore, CAR-T cell interactions with the host and tumour microenvironment have a significant impact on their activity. Furthermore, developing and implementing these therapies necessitates a complicated staff. Innovative methodologies and tactics to engineering more potent CAR-T cells with greater anti-tumour activity and less toxicity are required to address these important difficulties.
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Affiliation(s)
- Anil Kumar Mavi
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India
| | - Sonal Gaur
- Department of Biosciences and Biotechnology, Banasthali Vidyapith, Jaipur, Rajasthan 304022, India
| | - Gauri Gaur
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana 133203, India
| | - Babita
- Department of Pharmacology, Sharda School of Allied Health Sciences, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India
| | - Neelesh Kumar
- Department of Aquaculture, College of Fisheries, GB Pant University of Agriculture & Technology, Pantnagar, Udham Singh Nagar, Uttarakhand 263145, India
| | - Umesh Kumar
- School of Biosciences, Institute of Management Studies Ghaziabad (University Courses Campus), NH09, Adhyatmik Nagar, Ghaziabad, Uttar Pradesh 201015, India.
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5
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Shrock EL, Timms RT, Kula T, Mena EL, West AP, Guo R, Lee IH, Cohen AA, McKay LGA, Bi C, Keerti, Leng Y, Fujimura E, Horns F, Li M, Wesemann DR, Griffiths A, Gewurz BE, Bjorkman PJ, Elledge SJ. Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses. Science 2023; 380:eadc9498. [PMID: 37023193 PMCID: PMC10273302 DOI: 10.1126/science.adc9498] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023]
Abstract
Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant "public epitopes" at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition. Systematic analysis of antibody-antigen structures uncovered 18 human and 21 partially overlapping mouse germline-encoded amino acid-binding (GRAB) motifs within heavy and light V gene segments that in case studies proved critical for public epitope recognition. GRAB motifs represent a fundamental component of the immune system's architecture that promotes recognition of pathogens and leads to species-specific public antibody responses that can exert selective pressure on pathogens.
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Affiliation(s)
- Ellen L. Shrock
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
| | - Richard T. Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
- Present address: Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Elijah L. Mena
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rui Guo
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - I-Hsiu Lee
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lindsay G. A. McKay
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Caihong Bi
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Keerti
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric Fujimura
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Felix Horns
- Department of Bioengineering, Department of Applied Physics, Chan Zuckerberg Biohub and Stanford University, Stanford, CA 94305, USA
| | - Mamie Li
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Duane R. Wesemann
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139 USA
| | - Anthony Griffiths
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Benjamin E. Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
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6
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Yin Q, Luo W, Mallajosyula V, Bo Y, Guo J, Xie J, Sun M, Verma R, Li C, Constantz CM, Wagar LE, Li J, Sola E, Gupta N, Wang C, Kask O, Chen X, Yuan X, Wu NC, Rao J, Chien YH, Cheng J, Pulendran B, Davis MM. A TLR7-nanoparticle adjuvant promotes a broad immune response against heterologous strains of influenza and SARS-CoV-2. NATURE MATERIALS 2023; 22:380-390. [PMID: 36717665 PMCID: PMC9981462 DOI: 10.1038/s41563-022-01464-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/12/2022] [Indexed: 06/01/2023]
Abstract
The ideal vaccine against viruses such as influenza and SARS-CoV-2 must provide a robust, durable and broad immune protection against multiple viral variants. However, antibody responses to current vaccines often lack robust cross-reactivity. Here we describe a polymeric Toll-like receptor 7 agonist nanoparticle (TLR7-NP) adjuvant, which enhances lymph node targeting, and leads to persistent activation of immune cells and broad immune responses. When mixed with alum-adsorbed antigens, this TLR7-NP adjuvant elicits cross-reactive antibodies for both dominant and subdominant epitopes and antigen-specific CD8+ T-cell responses in mice. This TLR7-NP-adjuvanted influenza subunit vaccine successfully protects mice against viral challenge of a different strain. This strategy also enhances the antibody response to a SARS-CoV-2 subunit vaccine against multiple viral variants that have emerged. Moreover, this TLR7-NP augments antigen-specific responses in human tonsil organoids. Overall, we describe a nanoparticle adjuvant to improve immune responses to viral antigens, with promising implications for developing broadly protective vaccines.
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Affiliation(s)
- Qian Yin
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Wei Luo
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Yang Bo
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jing Guo
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jinghang Xie
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Meng Sun
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Rohit Verma
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Christian M Constantz
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Lisa E Wagar
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Jing Li
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Elsa Sola
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Neha Gupta
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Chunlin Wang
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Oliver Kask
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xin Chen
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xue Yuan
- Department of Otolaryngology-Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jianghong Rao
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Yueh-Hsiu Chien
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jianjun Cheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA.
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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7
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Gong HR, Hu YF, Li X, Yau T, Zhang BZ, Huang JD. Non-Neutralizing Epitopes Shade Neutralizing Epitopes against Omicron in a Multiple Epitope-Based Vaccine. ACS Infect Dis 2022; 8:2586-2593. [PMID: 36357959 PMCID: PMC9662650 DOI: 10.1021/acsinfecdis.2c00488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Indexed: 11/13/2022]
Abstract
The ongoing coronavirus disease 2019 pandemic has raised concerns about the risk of re-infection. Non-neutralizing epitopes are one of the major reasons for antibody-dependent enhancement. Past studies on the ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have revealed an infectivity-enhancing site on the ancestral SARS-CoV-2 spike protein. However, infection enhancement associated with the SARS-CoV-2 Omicron strain remains elusive. In this study, we examined the antibodies induced by a multiple epitope-based vaccine, which showed infection enhancement for the Omicron strain but not for the ancestral SARS-CoV-2 or Delta strain. By examining the antibodies induced by single epitope-based vaccines, we identified a conserved epitope, IDf (450-469), with neutralizing activity against ancestral SARS-CoV-2, Delta, and Omicron. Although neutralizing epitopes are present in the multiple epitope-based vaccine, other immunodominant non-neutralizing epitopes such as IDg (480-499) can shade their neutralizing activity, leading to infection enhancement of Omicron. Our study provides up-to-date epitope information on SARS-CoV-2 variants to help design better vaccines or antibody-based therapeutics against future variants.
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Affiliation(s)
- Hua-Rui Gong
- School of Biomedical Sciences, Li Ka Shing Faculty of
Medicine, University of Hong Kong, 3/F, Laboratory Block, 21
Sassoon Road, Hong kong999077, China
| | - Ye-fan Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of
Medicine, University of Hong Kong, 3/F, Laboratory Block, 21
Sassoon Road, Hong kong999077, China
- Department of Medicine, School of Clinical Medicine,
University of Hong Kong, 4/F Professional Block, Queen Mary
Hospital, 102 Pokfulam Road, Hong Kong999077, China
| | - Xuechen Li
- Department of Chemistry, University of Hong
Kong, Pokfulam Road, Hong Kong999077, China
| | - Thomas Yau
- Department of Medicine, School of Clinical Medicine,
University of Hong Kong, 4/F Professional Block, Queen Mary
Hospital, 102 Pokfulam Road, Hong Kong999077, China
| | - Bao-Zhong Zhang
- Chinese Academy of Sciences (CAS) Key
Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences,
Shenzhen518055, China
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of
Medicine, University of Hong Kong, 3/F, Laboratory Block, 21
Sassoon Road, Hong kong999077, China
- Chinese Academy of Sciences (CAS) Key
Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences,
Shenzhen518055, China
- Department of Clinical Oncology, Shenzhen Key Laboratory
for Cancer Metastasis and Personalized Therapy, The University of Hong
Kong-Shenzhen Hospital, Shenzhen518055, China
- Guangdong-Hong Kong Joint Laboratory for RNA Medicine,
Sun Yat-Sen University, Guangzhou510120,
China
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8
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Multiple instance neural networks based on sparse attention for cancer detection using T-cell receptor sequences. BMC Bioinformatics 2022; 23:469. [PMID: 36348271 PMCID: PMC9644450 DOI: 10.1186/s12859-022-05012-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
Early detection of cancers has been much explored due to its paramount importance in biomedical fields. Among different types of data used to answer this biological question, studies based on T cell receptors (TCRs) are under recent spotlight due to the growing appreciation of the roles of the host immunity system in tumor biology. However, the one-to-many correspondence between a patient and multiple TCR sequences hinders researchers from simply adopting classical statistical/machine learning methods. There were recent attempts to model this type of data in the context of multiple instance learning (MIL). Despite the novel application of MIL to cancer detection using TCR sequences and the demonstrated adequate performance in several tumor types, there is still room for improvement, especially for certain cancer types. Furthermore, explainable neural network models are not fully investigated for this application. In this article, we propose multiple instance neural networks based on sparse attention (MINN-SA) to enhance the performance in cancer detection and explainability. The sparse attention structure drops out uninformative instances in each bag, achieving both interpretability and better predictive performance in combination with the skip connection. Our experiments show that MINN-SA yields the highest area under the ROC curve scores on average measured across 10 different types of cancers, compared to existing MIL approaches. Moreover, we observe from the estimated attentions that MINN-SA can identify the TCRs that are specific for tumor antigens in the same T cell repertoire.
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9
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Layton DS, Butler J, Stewart C, Stevens V, Payne J, Rootes C, Deffrasnes C, Walker S, Shan S, Gough TJ, Cowled C, Bruce K, Wang J, Kedzierska K, Wong FYK, Bean AGD, Bingham J, Williams DT. H7N9 bearing a mutation in the nucleoprotein leads to increased pathology in chickens. Front Immunol 2022; 13:974210. [PMID: 36275684 PMCID: PMC9583263 DOI: 10.3389/fimmu.2022.974210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
The zoonotic H7N9 avian influenza (AI) virus first emerged in 2013 as a low pathogenic (LPAI) strain, and has repeatedly caused human infection resulting in severe respiratory illness and a mortality of ~39% (>600 deaths) across five epidemic waves. This virus has circulated in poultry with little to no discernible clinical signs, making detection and control difficult. Contrary to published data, our group has observed a subset of specific pathogen free chickens infected with the H7N9 virus succumb to disease, showing clinical signs consistent with highly pathogenic AI (HPAI). Viral genome sequencing revealed two key mutations had occurred following infection in the haemagglutinin (HA 226 L>Q) and nucleoprotein (NP 373 A>T) proteins. We further investigated the impact of the NP mutation and demonstrated that only chickens bearing a single nucleotide polymorphism (SNP) in their IFITM1 gene were susceptible to the H7N9 virus. Susceptible chickens demonstrated a distinct loss of CD8+ T cells from the periphery as well as a dysregulation of IFNγ that was not observed for resistant chickens, suggesting a role for the NP mutation in altered T cell activation. Alternatively, it is possible that this mutation led to altered polymerase activity, as the mutation occurs in the NP 360-373 loop which has been previously show to be important in RNA binding. These data have broad ramifications for our understanding of the pathobiology of AI in chickens and humans and provide an excellent model for investigating the role of antiviral genes in a natural host species.
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Affiliation(s)
- Daniel S. Layton
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
- *Correspondence: Daniel S. Layton, ; David T. Williams,
| | - Jeffrey Butler
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Cameron Stewart
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Vicky Stevens
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Jean Payne
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Christina Rootes
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Celine Deffrasnes
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Som Walker
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Songhua Shan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Parkville, VIC, Australia
| | - Tamara J. Gough
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Christopher Cowled
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Kerri Bruce
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Jianning Wang
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Parkville, VIC, Australia
| | - Frank Y. K. Wong
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Andrew G. D. Bean
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - John Bingham
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - David T. Williams
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
- *Correspondence: Daniel S. Layton, ; David T. Williams,
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10
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Biavasco R, De Giovanni M. The Relative Positioning of B and T Cell Epitopes Drives Immunodominance. Vaccines (Basel) 2022; 10:vaccines10081227. [PMID: 36016115 PMCID: PMC9413633 DOI: 10.3390/vaccines10081227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 12/05/2022] Open
Abstract
Humoral immunity is crucial for protection against invading pathogens. Broadly neutralizing antibodies (bnAbs) provide sterilizing immunity by targeting conserved regions of viral variants and represent the goal of most vaccination approaches. While antibodies can be selected to bind virtually any region of a given antigen, the consistent induction of bnAbs in the context of influenza and HIV has represented a major roadblock. Many possible explanations have been considered; however, none of the arguments proposed to date seem to fully recapitulate the observed counter-selection for broadly protective antibodies. Antibodies can influence antigen presentation by enhancing the processing of CD4 epitopes adjacent to the binding region while suppressing the overlapping ones. We analyze the relative positioning of dominant B and T cell epitopes in published antigens that elicit strong and poor humoral responses. In strong immunogenic antigens, regions bound by immunodominant antibodies are frequently adjacent to CD4 epitopes, potentially boosting their presentation. Conversely, poorly immunogenic regions targeted by bnAbs in HIV and influenza overlap with clusters of dominant CD4 epitopes, potentially conferring an intrinsic disadvantage for bnAb-bearing B cells in germinal centers. Here, we propose the theory of immunodominance relativity, according to which the relative positioning of immunodominant B and CD4 epitopes within a given antigen drives immunodominance. Thus, we suggest that the relative positioning of B-T epitopes may be one additional mechanism that cooperates with other previously described processes to influence immunodominance. If demonstrated, this theory can improve the current understanding of immunodominance, provide a novel explanation for HIV and influenza escape from humoral responses, and pave the way for a new rational design of universal vaccines.
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Affiliation(s)
- Riccardo Biavasco
- Department of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Marco De Giovanni
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Correspondence:
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11
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Combination therapy with CAR T cells and oncolytic viruses: a new era in cancer immunotherapy. Cancer Gene Ther 2022; 29:647-660. [PMID: 34158626 DOI: 10.1038/s41417-021-00359-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/16/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Chimeric antigen receptor (CAR) T-cell therapy is an encouraging and fast-growing platform used for the treatment of various types of tumors in human body. Despite the recent success of CAR T-cell therapy in hematologic malignancies, especially in B-cell lymphoma and acute lymphoblastic leukemia, the application of this treatment approach in solid tumors faced several obstacles resulted from the heterogeneous expression of antigens as well as the induction of immunosuppressive tumor microenvironment. Oncolytic virotherapy (OV) is a new cancer treatment modality by the use of competent or genetically engineered viruses to replicate in tumor cells selectively. OVs represent potential candidates to synergize the current setbacks of CAR T-cell application in solid tumors and then and overcome them. As well, the application of OVs gives researches the ability to engineer the virus with payloads in the way that it selectively deliver a specific therapeutic agents in tumor milieu to reinforce the cytotoxic activity of CAR T cells. Herein, we made a comprehensive review on the outcomes resulted from the combination of CAR T-cell immunotherapy and oncolytic virotherapy for the treatment of solid cancers. In the current study, we also provided brief details on some challenges that remained in this field and attempted to shed a little light on the future perspectives.
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12
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Mardi A, Shirokova AV, Mohammed RN, Keshavarz A, Zekiy AO, Thangavelu L, Mohamad TAM, Marofi F, Shomali N, Zamani A, Akbari M. Biological causes of immunogenic cancer cell death (ICD) and anti-tumor therapy; Combination of Oncolytic virus-based immunotherapy and CAR T-cell therapy for ICD induction. Cancer Cell Int 2022; 22:168. [PMID: 35488303 PMCID: PMC9052538 DOI: 10.1186/s12935-022-02585-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 04/11/2022] [Indexed: 12/22/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy is a promising and rapidly expanding therapeutic option for a wide range of human malignancies. Despite the ongoing progress of CAR T-cell therapy in hematologic malignancies, the application of this therapeutic strategy in solid tumors has encountered several challenges due to antigen heterogeneity, suboptimal CAR T-cell trafficking, and the immunosuppressive features of the tumor microenvironment (TME). Oncolytic virotherapy is a novel cancer therapy that employs competent or genetically modified oncolytic viruses (OVs) to preferentially proliferate in tumor cells. OVs in combination with CAR T-cells are promising candidates for overcoming the current drawbacks of CAR T-cell application in tumors through triggering immunogenic cell death (ICD) in cancer cells. ICD is a type of cellular death in which danger-associated molecular patterns (DAMPs) and tumor-specific antigens are released, leading to the stimulation of potent anti-cancer immunity. In the present review, we discuss the biological causes of ICD, different types of ICD, and the synergistic combination of OVs and CAR T-cells to reach potent tumor-specific immunity.
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Affiliation(s)
- Amirhossein Mardi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anastasia V Shirokova
- Department of Prosthetic Dentistry, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Rebar N Mohammed
- Medical Laboratory Analysis Department, College of Health Science, Cihan University of Sulaimaniya, Suleimanyah, Kurdistan region, Iraq.,College of. Veterinary Medicine, University of Sulaimani, Suleimanyah, Iraq
| | - Ali Keshavarz
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Angelina O Zekiy
- Department of Prosthetic Dentistry, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Lakshmi Thangavelu
- Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Saveetha University, Chennai, India
| | - Talar Ahmad Merza Mohamad
- Department of Pharmacology and Toxicology, Clinical Pharmacy, Hawler Medical University, College of Pharmacy, Kurdistan Region-Erbil, Iraq
| | - Faroogh Marofi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Navid Shomali
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Zamani
- Shiraz Transplant Center, Abu Ali Sina Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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13
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Antonarelli G, Corti C, Tarantino P, Ascione L, Cortes J, Romero P, Mittendorf E, Disis M, Curigliano G. Therapeutic cancer vaccines revamping: technology advancements and pitfalls. Ann Oncol 2021; 32:1537-1551. [PMID: 34500046 PMCID: PMC8420263 DOI: 10.1016/j.annonc.2021.08.2153] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/21/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer vaccines (CVs) represent a long-sought therapeutic and prophylactic immunotherapy strategy to obtain antigen (Ag)-specific T-cell responses and potentially achieve long-term clinical benefit. However, historically, most CV clinical trials have resulted in disappointing outcomes, despite promising signs of immunogenicity across most formulations. In the past decade, technological advances regarding vaccine delivery platforms, tools for immunogenomic profiling, and Ag/epitope selection have occurred. Consequently, the ability of CVs to induce tumor-specific and, in some cases, remarkable clinical responses have been observed in early-phase clinical trials. It is notable that the record-breaking speed of vaccine development in response to the coronavirus disease-2019 pandemic mainly relied on manufacturing infrastructures and technological platforms already developed for CVs. In turn, research, clinical data, and infrastructures put in place for the severe acute respiratory syndrome coronavirus 2 pandemic can further speed CV development processes. This review outlines the main technological advancements as well as major issues to tackle in the development of CVs. Possible applications for unmet clinical needs will be described, putting into perspective the future of cancer vaccinology.
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Affiliation(s)
- G. Antonarelli
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy,Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - C. Corti
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy,Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - P. Tarantino
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy,Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - L. Ascione
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy,Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - J. Cortes
- International Breast Cancer Center (IBCC), Quironsalud Group, Barcelona, Spain,Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - P. Romero
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland
| | - E.A. Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, USA,Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, USA
| | - M.L. Disis
- UW Medicine Cancer Vaccine Institute, University of Washington, Seattle, USA
| | - G. Curigliano
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy,Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy,Correspondence to: Prof. Giuseppe Curigliano, Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Via Ripamonti 435, 20141 Milan, Italy. Tel: +39-0257489599
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14
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Duan L, Zhang J, Chen Z, Gou Q, Xiong Q, Yuan Y, Jing H, Zhu J, Ni L, Zheng Y, Liu Z, Zhang X, Zeng H, Zou Q, Zhao Z. Antibiotic Combined with Epitope-Specific Monoclonal Antibody Cocktail Protects Mice Against Bacteremia and Acute Pneumonia from Methicillin-Resistant Staphylococcus aureus Infection. J Inflamm Res 2021; 14:4267-4282. [PMID: 34511967 PMCID: PMC8415768 DOI: 10.2147/jir.s325286] [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: 06/25/2021] [Accepted: 08/20/2021] [Indexed: 12/19/2022] Open
Abstract
Purpose We previously reported that monoclonal antibody (mAb) cocktail improves survival in Staphylococcus aureus infection. In this study, we used acute pneumonia model and lethal sepsis model to investigate the efficacy of antibiotic combined with epitope-specific mAb cocktail in treating MRSA252 infection. Methods MRSA252 was challenged by tail vein injection or tracheal intubation to establish sepsis model or pneumonia model. One hour after infection, the mice received a single intravenous injection of normal saline, vancomycin, and vancomycin combined monoclonal antibody, linezolid alone or linezolid combined monoclonal antibody. Daily record survival rate (total 7 days), bacterial load, histology, cytokine analysis of serum and alveolar lavage fluid, and in vitro determination of the neutralizing ability of antibodies to SEB toxin and Hla toxin explained the mechanism of antibody action. Results The mAb cocktail combined with low doses of vancomycin or linezolid improved survival rates in acute pneumonia model (70%, 80%) and lethal sepsis model (80%, 80%). Epitope-specific monoclonal antibodies reduced bacterial colonization in the kidneys and lungs of mice and inhibited the biological functions of the toxins Hla and SEB in vitro. Compared to the antibiotic alone or PBS groups, the combination group had higher levels of IL-1α, IL-1β and IFN-γ and lower levels of IL-6, IL-10, TNF-α. Further, the combination of antibiotic and mAb cocktail improved infection survival against the clinical MRSA isolates in a lethal sepsis model. Conclusion This study demonstrates a novel method to treat people with low immunity against drug-resistant S. aureus infections.
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Affiliation(s)
- LianLi Duan
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Jinyong Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Zhifu Chen
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Qiang Gou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Qingshan Xiong
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Yue Yuan
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Haiming Jing
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Jiang Zhu
- Department of Pathology, Southwest Hospital, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Li Ni
- Obstetrics and Gynecology, The First People's Hospital of Jiulongpo District, Chongqing, 400050, People's Republic of China
| | - Yuling Zheng
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Zhiyong Liu
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Xiaokai Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Hao Zeng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Zhuo Zhao
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, People's Republic of China
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15
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Billiard S, Castric V, Llaurens V. The integrative biology of genetic dominance. Biol Rev Camb Philos Soc 2021; 96:2925-2942. [PMID: 34382317 PMCID: PMC9292577 DOI: 10.1111/brv.12786] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022]
Abstract
Dominance is a basic property of inheritance systems describing the link between a diploid genotype at a single locus and the resulting phenotype. Models for the evolution of dominance have long been framed as an opposition between the irreconcilable views of Fisher in 1928 supporting the role of largely elusive dominance modifiers and Wright in 1929, who viewed dominance as an emerging property of the structure of enzymatic pathways. Recent theoretical and empirical advances however suggest that these opposing views can be reconciled, notably using models investigating the regulation of gene expression and developmental processes. In this more comprehensive framework, phenotypic dominance emerges from departures from linearity between any levels of integration in the genotype‐to‐phenotype map. Here, we review how these different models illuminate the emergence and evolution of dominance. We then detail recent empirical studies shedding new light on the diversity of molecular and physiological mechanisms underlying dominance and its evolution. By reconciling population genetics and functional biology, we hope our review will facilitate cross‐talk among research fields in the integrative study of dominance evolution.
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Affiliation(s)
- Sylvain Billiard
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Vincent Castric
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité, CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, CP50, 57 rue Cuvier, 75005, Paris, France
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16
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Broad-Based Influenza-Specific CD8 + T Cell Response without the Typical Immunodominance Hierarchy and Its Potential Implication. Viruses 2021; 13:v13061080. [PMID: 34198851 PMCID: PMC8229067 DOI: 10.3390/v13061080] [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: 04/29/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Syngeneic murine systems have pre-fixed MHC, making them an imperfect model for investigating the impact of MHC polymorphism on immunodominance in influenza A virus (IAV) infections. To date, there are few studies focusing on MHC allelic differences and its impact on immunodominance even though it is well documented that an individual’s HLA plays a significant role in determining immunodominance hierarchy. Here, we describe a broad-based CD8+ T cell response in a healthy individual to IAV infection rather than a typical immunodominance hierarchy. We used a systematic antigen screen approach combined with epitope prediction to study such a broad CD8+ T cell response to IAV infection. We show CD8+ T cell responses to nine IAV proteins and identify their minimal epitope sequences. These epitopes are restricted to HLA-B*44:03, HLA-A*24:02 and HLA-A*33:03 and seven out of the nine epitopes are novel (NP319–330# (known and demonstrated minimal epitope positions are subscripted; otherwise, amino acid positions are shown as normal text (for example NP 319–330 or NP 313–330)), M1124–134, M27–15, NA337–346, PB239–49, HA445–453 and NS1195–203). Additionally, most of these novel epitopes are highly conserved among H1N1 and H3N2 strains that circulated in Australia and other parts of the world.
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17
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Blair TC, Alice AF, Zebertavage L, Crittenden MR, Gough MJ. The Dynamic Entropy of Tumor Immune Infiltrates: The Impact of Recirculation, Antigen-Specific Interactions, and Retention on T Cells in Tumors. Front Oncol 2021; 11:653625. [PMID: 33968757 PMCID: PMC8101411 DOI: 10.3389/fonc.2021.653625] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Analysis of tumor infiltration using conventional methods reveals a snapshot view of lymphocyte interactions with the tumor environment. However, lymphocytes have the unique capacity for continued recirculation, exploring varied tissues for the presence of cognate antigens according to inflammatory triggers and chemokine gradients. We discuss the role of the inflammatory and cellular makeup of the tumor environment, as well as antigen expressed by cancer cells or cross-presented by stromal antigen presenting cells, on recirculation kinetics of T cells. We aim to discuss how current cancer therapies may manipulate lymphocyte recirculation versus retention to impact lymphocyte exclusion in the tumor.
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Affiliation(s)
- Tiffany C Blair
- Molecular Microbiology and Immunology, Oregon Health and Sciences University (OHSU), Portland, OR, United States.,Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Alejandro F Alice
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Lauren Zebertavage
- Molecular Microbiology and Immunology, Oregon Health and Sciences University (OHSU), Portland, OR, United States.,Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Marka R Crittenden
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States.,The Oregon Clinic, Portland, OR, United States
| | - Michael J Gough
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
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18
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Abstract
As one of the most important weapons against infectious diseases, vaccines have saved countless lives since their first use in the late eighteenth century. Antibodies produced by effector B cells upon vaccination play a critical role in mediating protection. The past several decades of research have led to a revolution in our understanding of B cell response to vaccination. Vaccines against SARS-CoV-2 coronavirus were developed at an unprecedented speed to power our global fight against COVID-19 pandemic. Nevertheless, we still face many challenges in the development of vaccines against many other deadly viruses, such as human immunodeficiency virus (HIV) and influenza virus. In this review, we summarize the latest findings on B cell response to vaccination and pathogen infection. We also discuss the current challenges in the field and the potential strategies targeting B cell response to improve vaccine efficacy.Key abbreviations box: BCR: B cell receptor; bNAb: broadly neutralizing antibody; DC: dendritic cells; DZ: dark zone; EF response: extrafollicular response; FDC: follicular dendritic cell; GC: germinal center; HIV: human immunodeficiency virus; IC: immune complex; LLPC: long-lived plasma cell; LZ: light zone; MBC: memory B cell; SLPB: short-lived plasmablast; TFH: T follicular helper cells; TLR: Toll-like receptor.
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Affiliation(s)
- Wei Luo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Qian Yin
- Institute for Immunity, Transplantation & Infection, Stanford University School of Medicine, Stanford, California, USA
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19
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Medler TR, Blair TC, Crittenden MR, Gough MJ. Defining Immunogenic and Radioimmunogenic Tumors. Front Oncol 2021; 11:667075. [PMID: 33816320 PMCID: PMC8017281 DOI: 10.3389/fonc.2021.667075] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
In the cancer literature tumors are inconsistently labeled as ‘immunogenic’, and experimental results are occasionally dismissed since they are only tested in known ‘responsive’ tumor models. The definition of immunogenicity has moved from its classical definition based on the rejection of secondary tumors to a more nebulous definition based on immune infiltrates and response to immunotherapy interventions. This review discusses the basis behind tumor immunogenicity and the variation between tumor models, then moves to discuss how these principles apply to the response to radiation therapy. In this way we can identify radioimmunogenic tumor models that are particularly responsive to immunotherapy only when combined with radiation, and identify the interventions that can convert unresponsive tumors so that they can also respond to these treatments.
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Affiliation(s)
- Terry R Medler
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Tiffany C Blair
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States.,Molecular Microbiology and Immunology, OHSU, Portland, OR, United States
| | - Marka R Crittenden
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States.,Molecular Microbiology and Immunology, OHSU, Portland, OR, United States.,The Oregon Clinic, Portland, OR, United States
| | - Michael J Gough
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States.,Molecular Microbiology and Immunology, OHSU, Portland, OR, United States
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20
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Xiang Y, Sang Z, Bitton L, Xu J, Liu Y, Schneidman-Duhovny D, Shi Y. Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies. Cell Syst 2021; 12:220-234.e9. [PMID: 33592195 PMCID: PMC7979497 DOI: 10.1016/j.cels.2021.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. Here, we developed a proteomic strategy to survey, at an unprecedented scale, the landscape of antigen-engaged, circulating camelid heavy-chain antibodies, whose minimal binding fragments are called VHH antibodies or nanobodies. The sensitivity and robustness of this approach were validated with three antigens spanning orders of magnitude in immune responses; thousands of distinct, high-affinity nanobody families were reliably identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of >100,000 antigen-nanobody complexes. Our results revealed a surprising diversity of ultrahigh-affinity camelid nanobodies for specific antigen binding on various dominant epitope clusters. Nanobodies utilize both shape and charge complementarity to enable highly selective antigen binding. Interestingly, we found that nanobody-antigen binding can mimic conserved intracellular protein-protein interactions. A record of this paper's Transparent Peer Review process is included in the Supplemental information.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
| | - Lirane Bitton
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Jianquan Xu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA.
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21
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Schoeder CT, Schmitz S, Adolf-Bryfogle J, Sevy AM, Finn JA, Sauer MF, Bozhanova NG, Mueller BK, Sangha AK, Bonet J, Sheehan JH, Kuenze G, Marlow B, Smith ST, Woods H, Bender BJ, Martina CE, Del Alamo D, Kodali P, Gulsevin A, Schief WR, Correia BE, Crowe JE, Meiler J, Moretti R. Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design. Biochemistry 2021; 60:825-846. [PMID: 33705117 PMCID: PMC7992133 DOI: 10.1021/acs.biochem.0c00912] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
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Structure-based antibody
and antigen design has advanced greatly
in recent years, due not only to the increasing availability of experimentally
determined structures but also to improved computational methods for
both prediction and design. Constant improvements in performance within
the Rosetta software suite for biomolecular modeling have given rise
to a greater breadth of structure prediction, including docking and
design application cases for antibody and antigen modeling. Here,
we present an overview of current protocols for antibody and antigen
modeling using Rosetta and exemplify those by detailed tutorials originally
developed for a Rosetta workshop at Vanderbilt University. These tutorials
cover antibody structure prediction, docking, and design and antigen
design strategies, including the addition of glycans in Rosetta. We
expect that these materials will allow novice users to apply Rosetta
in their own projects for modeling antibodies and antigens.
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Affiliation(s)
- Clara T Schoeder
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Alexander M Sevy
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0417, United States
| | - Jessica A Finn
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0417, United States.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Marion F Sauer
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0417, United States
| | - Nina G Bozhanova
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Benjamin K Mueller
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Amandeep K Sangha
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jonathan H Sheehan
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Institute for Drug Discovery, University Leipzig Medical School, 04103 Leipzig, Germany
| | - Brennica Marlow
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States
| | - Shannon T Smith
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States
| | - Hope Woods
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States
| | - Brian J Bender
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Cristina E Martina
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Diego Del Alamo
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States
| | - Pranav Kodali
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Alican Gulsevin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0417, United States.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Institute for Drug Discovery, University Leipzig Medical School, 04103 Leipzig, Germany
| | - Rocco Moretti
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
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22
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Oyarzun P, Kashyap M, Fica V, Salas-Burgos A, Gonzalez-Galarza FF, McCabe A, Jones AR, Middleton D, Kobe B. A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach. Front Immunol 2021; 12:598778. [PMID: 33717077 PMCID: PMC7952308 DOI: 10.3389/fimmu.2021.598778] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/11/2021] [Indexed: 01/06/2023] Open
Abstract
Emerging infectious diseases (EIDs) caused by viruses are increasing in frequency, causing a high disease burden and mortality world-wide. The COVID-19 pandemic caused by the novel SARS-like coronavirus (SARS-CoV-2) underscores the need to innovate and accelerate the development of effective vaccination strategies against EIDs. Human leukocyte antigen (HLA) molecules play a central role in the immune system by determining the peptide repertoire displayed to the T-cell compartment. Genetic polymorphisms of the HLA system thus confer a strong variability in vaccine-induced immune responses and may complicate the selection of vaccine candidates, because the distribution and frequencies of HLA alleles are highly variable among different ethnic groups. Herein, we build on the emerging paradigm of rational epitope-based vaccine design, by describing an immunoinformatics tool (Predivac-3.0) for proteome-wide T-cell epitope discovery that accounts for ethnic-level variations in immune responsiveness. Predivac-3.0 implements both CD8+ and CD4+ T-cell epitope predictions based on HLA allele frequencies retrieved from the Allele Frequency Net Database. The tool was thoroughly assessed, proving comparable performances (AUC ~0.9) against four state-of-the-art pan-specific immunoinformatics methods capable of population-level analysis (NetMHCPan-4.0, Pickpocket, PSSMHCPan and SMM), as well as a strong accuracy on proteome-wide T-cell epitope predictions for HIV-specific immune responses in the Japanese population. The utility of the method was investigated for the COVID-19 pandemic, by performing in silico T-cell epitope mapping of the SARS-CoV-2 spike glycoprotein according to the ethnic context of the countries where the ChAdOx1 vaccine is currently initiating phase III clinical trials. Potentially immunodominant CD8+ and CD4+ T-cell epitopes and population coverages were predicted for each population (the Epitope Discovery mode), along with optimized sets of broadly recognized (promiscuous) T-cell epitopes maximizing coverage in the target populations (the Epitope Optimization mode). Population-specific epitope-rich regions (T-cell epitope clusters) were further predicted in protein antigens based on combined criteria of epitope density and population coverage. Overall, we conclude that Predivac-3.0 holds potential to contribute in the understanding of ethnic-level variations of vaccine-induced immune responsiveness and to guide the development of epitope-based next-generation vaccines against emerging pathogens, whose geographic distributions and populations in need of vaccinations are often well-defined for regional epidemics.
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Affiliation(s)
- Patricio Oyarzun
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | - Manju Kashyap
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | - Victor Fica
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | | | - Faviel F Gonzalez-Galarza
- Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico
| | - Antony McCabe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Derek Middleton
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
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23
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Teymournejad O, Montgomery CP. Evasion of Immunological Memory by S. aureus Infection: Implications for Vaccine Design. Front Immunol 2021; 12:633672. [PMID: 33692805 PMCID: PMC7937817 DOI: 10.3389/fimmu.2021.633672] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
Recurrent S. aureus infections are common, suggesting that natural immune responses are not protective. All candidate vaccines tested thus far have failed to protect against S. aureus infections, highlighting an urgent need to better understand the mechanisms by which the bacterium interacts with the host immune system to evade or prevent protective immunity. Although there is evidence in murine models that both cellular and humoral immune responses are important for protection against S. aureus, human studies suggest that T cells are critical in determining susceptibility to infection. This review will use an “anatomic” approach to systematically outline the steps necessary in generating a T cell-mediated immune response against S. aureus. Through the processes of bacterial uptake by antigen presenting cells, processing and presentation of antigens to T cells, and differentiation and proliferation of memory and effector T cell subsets, the ability of S. aureus to evade or inhibit each step of the T-cell mediated response will be reviewed. We hypothesize that these interactions result in the redirection of immune responses away from protective antigens, thereby precluding the establishment of “natural” memory and potentially inhibiting the efficacy of vaccination. It is anticipated that this approach will reveal important implications for future design of vaccines to prevent these infections.
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Affiliation(s)
- Omid Teymournejad
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Christopher P Montgomery
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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24
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Dorigatti E, Schubert B. Graph-theoretical formulation of the generalized epitope-based vaccine design problem. PLoS Comput Biol 2020; 16:e1008237. [PMID: 33095790 PMCID: PMC7652351 DOI: 10.1371/journal.pcbi.1008237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 11/09/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Epitope-based vaccines have revolutionized vaccine research in the last decades. Due to their complex nature, bioinformatics plays a pivotal role in their development. However, existing algorithms address only specific parts of the design process or are unable to provide formal guarantees on the quality of the solution. We present a unifying formalism of the general epitope vaccine design problem that tackles all phases of the design process simultaneously and combines all prevalent design principles. We then demonstrate how to formulate the developed formalism as an integer linear program, which guarantees optimality of the designs. This makes it possible to explore new regions of the vaccine design space, analyze the trade-offs between the design phases, and balance the many requirements of vaccines.
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Affiliation(s)
- Emilio Dorigatti
- Department of Statistics, Ludwig Maximilian Universität, München, Germany
- Institute of Computational Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Benjamin Schubert
- Institute of Computational Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching bei München, Germany
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25
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Zeng H, Zhang J, Song X, Zeng J, Yuan Y, Chen Z, Xu L, Gou Q, Yang F, Zeng N, Zhang Y, Peng L, Zhao L, Zhu J, Liu Y, Luo P, Zou Q, Zhao Z. An Immunodominant Epitope-Specific Monoclonal Antibody Cocktail Improves Survival in a Mouse Model of Staphylococcus aureus Bacteremia. J Infect Dis 2020; 223:1743-1752. [PMID: 32959055 DOI: 10.1093/infdis/jiaa602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/18/2020] [Indexed: 01/22/2023] Open
Abstract
To date, no vaccine or monoclonal antibody (mAb) against Staphylococcus aureus has been approved for use in humans. Our laboratory has developed a 5-antigen S. aureus vaccine (rFSAV), which is now under efficacy evaluation in a phase 2 clinical trial. In the current study, using overlapping peptides and antiserum from rFSAV-immunized volunteers, we identified 7 B-cell immunodominant epitopes on 4 antigens in rFSAV, including 5 novel epitopes (Hla48-65, IsdB402-419, IsdB432-449, SEB78-95, and MntC7-24). Ten immunodominant epitope mAbs were generated against these epitopes, and all of them exhibited partial protection in a mouse sepsis model. Four robust mAbs were used together as an mAb cocktail to prevent methicillin-resistant S. aureus strain 252 infection. The results showed that the mAb cocktail was efficient in combating S. aureus infection and that its protective efficacy correlated with a reduced bacterial burden and decreased infection pathology, which demonstrates that the mAb cocktail is a promising S. aureus vaccine candidate.
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Affiliation(s)
- Hao Zeng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Jinyong Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Xu Song
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Jiangmin Zeng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Yue Yuan
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Zhifu Chen
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Limin Xu
- Chengdu Olymvax Biotechnology Co, Ltd, Chengdu, Sichuan, People's Republic of China
| | - Qiang Gou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Feng Yang
- Chengdu Olymvax Biotechnology Co, Ltd, Chengdu, Sichuan, People's Republic of China
| | - Ni Zeng
- Chengdu Olymvax Biotechnology Co, Ltd, Chengdu, Sichuan, People's Republic of China
| | - Yi Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Liusheng Peng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Liqun Zhao
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Jiang Zhu
- Department of Pathology, Southwest Hospital, Army Medical University, Chongqing, People's Republic of China
| | - Yuanyuan Liu
- Medical Corps Department, Unit 69016, Chinese People's Liberation Army, Xinjiang, People's Republic of China
| | - Ping Luo
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
| | - Zhuo Zhao
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, People's Republic of China
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26
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Sant S, Quiñones-Parra SM, Koutsakos M, Grant EJ, Loudovaris T, Mannering SI, Crowe J, van de Sandt CE, Rimmelzwaan GF, Rossjohn J, Gras S, Loh L, Nguyen THO, Kedzierska K. HLA-B*27:05 alters immunodominance hierarchy of universal influenza-specific CD8+ T cells. PLoS Pathog 2020; 16:e1008714. [PMID: 32750095 PMCID: PMC7428290 DOI: 10.1371/journal.ppat.1008714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/14/2020] [Accepted: 06/18/2020] [Indexed: 12/15/2022] Open
Abstract
Seasonal influenza virus infections cause 290,000–650,000 deaths annually and severe morbidity in 3–5 million people. CD8+ T-cell responses towards virus-derived peptide/human leukocyte antigen (HLA) complexes provide the broadest cross-reactive immunity against human influenza viruses. Several universally-conserved CD8+ T-cell specificities that elicit prominent responses against human influenza A viruses (IAVs) have been identified. These include HLA-A*02:01-M158-66 (A2/M158), HLA-A*03:01-NP265-273, HLA-B*08:01-NP225-233, HLA-B*18:01-NP219-226, HLA-B*27:05-NP383-391 and HLA-B*57:01-NP199-207. The immunodominance hierarchies across these universal CD8+ T-cell epitopes were however unknown. Here, we probed immunodominance status of influenza-specific universal CD8+ T-cells in HLA-I heterozygote individuals expressing two or more universal HLAs for IAV. We found that while CD8+ T-cell responses directed towards A2/M158 were generally immunodominant, A2/M158+CD8+ T-cells were markedly diminished (subdominant) in HLA-A*02:01/B*27:05-expressing donors following ex vivo and in vitro analyses. A2/M158+CD8+ T-cells in non-HLA-B*27:05 individuals were immunodominant, contained optimal public TRBV19/TRAV27 TCRαβ clonotypes and displayed highly polyfunctional and proliferative capacity, while A2/M158+CD8+ T cells in HLA-B*27:05-expressing donors were subdominant, with largely distinct TCRαβ clonotypes and consequently markedly reduced avidity, proliferative and polyfunctional efficacy. Our data illustrate altered immunodominance patterns and immunodomination within human influenza-specific CD8+ T-cells. Accordingly, our work highlights the importance of understanding immunodominance hierarchies within individual donors across a spectrum of prominent virus-specific CD8+ T-cell specificities prior to designing T cell-directed vaccines and immunotherapies, for influenza and other infectious diseases. Annual influenza infections cause significant morbidity and morbidity globally. Established T-cell immunity directed at conserved viral regions provides some protection against influenza viruses and promotes rapid recovery, leading to better clinical outcomes. Killer CD8+ T-cells recognising viral peptides in a context of HLA-I glycoproteins, provide the broadest ever reported immunity across distinct influenza strains and subtypes. We asked whether the expression of certain HLA-I alleles affects CD8+ T cells responses. Our study clearly illustrates altered immunodominance hierarchies and immunodomination within broadly-cross-reactive influenza-specific CD8+ T-cells in individuals expressing two or more universal HLA-I alleles, key for T cell-directed vaccines and immunotherapies.
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Affiliation(s)
- Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Sergio M. Quiñones-Parra
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Emma J. Grant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Stuart I. Mannering
- Immunology and Diabetes Unit, St Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, Victoria, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Guus F. Rimmelzwaan
- National Influenza Center and Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Thi H. O. Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail: (THON); (KK)
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail: (THON); (KK)
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27
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Wang Y, Xiang Y, Xin VW, Wang XW, Peng XC, Liu XQ, Wang D, Li N, Cheng JT, Lyv YN, Cui SZ, Ma Z, Zhang Q, Xin HW. Dendritic cell biology and its role in tumor immunotherapy. J Hematol Oncol 2020; 13:107. [PMID: 32746880 PMCID: PMC7397618 DOI: 10.1186/s13045-020-00939-6] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
As crucial antigen presenting cells, dendritic cells (DCs) play a vital role in tumor immunotherapy. Taking into account the many recent advances in DC biology, we discuss how DCs (1) recognize pathogenic antigens with pattern recognition receptors through specific phagocytosis and through non-specific micropinocytosis, (2) process antigens into small peptides with proper sizes and sequences, and (3) present MHC-peptides to CD4+ and CD8+ T cells to initiate immune responses against invading microbes and aberrant host cells. During anti-tumor immune responses, DC-derived exosomes were discovered to participate in antigen presentation. T cell microvillar dynamics and TCR conformational changes were demonstrated upon DC antigen presentation. Caspase-11-driven hyperactive DCs were recently reported to convert effectors into memory T cells. DCs were also reported to crosstalk with NK cells. Additionally, DCs are the most important sentinel cells for immune surveillance in the tumor microenvironment. Alongside DC biology, we review the latest developments for DC-based tumor immunotherapy in preclinical studies and clinical trials. Personalized DC vaccine-induced T cell immunity, which targets tumor-specific antigens, has been demonstrated to be a promising form of tumor immunotherapy in patients with melanoma. Importantly, allogeneic-IgG-loaded and HLA-restricted neoantigen DC vaccines were discovered to have robust anti-tumor effects in mice. Our comprehensive review of DC biology and its role in tumor immunotherapy aids in the understanding of DCs as the mentors of T cells and as novel tumor immunotherapy cells with immense potential.
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Affiliation(s)
- Yingying Wang
- State Key Laboratory of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China.,Department of Gynaecology, Comprehensive Cancer Center, Hannover Medical School, 30625, Hannover, Germany
| | - Ying Xiang
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China
| | | | - Xian-Wang Wang
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China.,Department of Laboratory Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China
| | - Xiao-Chun Peng
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China.,Department of Pathophysiology, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Xiao-Qin Liu
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China.,Department of Medical Imaging, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Dong Wang
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Na Li
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Jun-Ting Cheng
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Yan-Ning Lyv
- Institute for Infectious Diseases and Endemic Diseases Prevention and Control, Beijing Center for Diseases Prevention and Control, Beijing, 100013, China
| | - Shu-Zhong Cui
- State Key Laboratory of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Zhaowu Ma
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China. .,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China.
| | - Qing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China.
| | - Hong-Wu Xin
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Faculty of Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, 434023, Hubei, China. .,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Faculty of Medicine, Yangtze University, Jingzhou, 434023, Hubei, China. .,People's Hospital of Lianjiang, Lianjiang, 524400, Guangdong, China.
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Park S, Wang X, Lim J, Xiao G, Lu T, Wang T. Bayesian multiple instance regression for modeling immunogenic neoantigens. Stat Methods Med Res 2020; 29:3032-3047. [PMID: 32401701 DOI: 10.1177/0962280220914321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The relationship between tumor immune responses and tumor neoantigens is one of the most fundamental and unsolved questions in tumor immunology, and is the key to understanding the inefficiency of immunotherapy observed in many cancer patients. However, the properties of neoantigens that can elicit immune responses remain unclear. This biological problem can be represented and solved under a multiple instance learning framework, which seeks to model multiple instances (neoantigens) within each bag (patient specimen) with the continuous response (T cell infiltration) observed for each bag. To this end, we develop a Bayesian multiple instance regression method, named BMIR, using a Gaussian distribution to address continuous responses and latent binary variables to model primary instances in bags. By means of such Bayesian modeling, BMIR can learn a function for predicting the bag-level responses and for identifying the primary instances within bags, as well as give access to Bayesian statistical inference, which are elusive in existing works. We demonstrate the superiority of BMIR over previously proposed optimization-based methods for multiple instance regression through simulation and real data analyses. Our method is implemented in R package entitled "BayesianMIR" and is available at https://github.com/inmybrain/BayesianMIR.
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Affiliation(s)
- Seongoh Park
- Department of Statistics, Seoul National University, Seoul, Korea
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, Dallas, TX, USA
| | - Johan Lim
- Department of Statistics, Seoul National University, Seoul, Korea
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tianshi Lu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Cai L, Caraballo Galva LD, Peng Y, Luo X, Zhu W, Yao Y, Ji Y, He Y. Preclinical Studies of the Off-Target Reactivity of AFP 158-Specific TCR Engineered T Cells. Front Immunol 2020; 11:607. [PMID: 32395117 PMCID: PMC7196607 DOI: 10.3389/fimmu.2020.00607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/17/2020] [Indexed: 01/27/2023] Open
Abstract
Autologous T cells engineered with T receptor genes (TCR) are being studied to treat cancers. We have recently identified a panel of mouse TCRs specific for the HLA-A0201/alpha fetoprotein epitope (AFP158) complex and have shown that human T cells engineered with these TCR genes (TCR-Ts) can eradicate hepatocellular carcinoma (HCC) xenografts in NSG mice. However, due to TCR’s promiscuity, their off-target cross-reactivity must be studied prior to conducting clinical trials. In this study, we conducted in vitro X-scan assay and in silico analysis to determine the off-target cross-reactivity of 3 AFP158-specific TCR-Ts. We found that the 3 AFP158-specific TCR-Ts could be cross-activated by ENPP1436 peptide and that the TCR3-Ts could also be activated by another off-target peptide, RCL1215. However, compared to AFP158, it requires 250 times more ENPP1436 and 10,000 times more RCL1215 peptides to achieve the same level of activation. The EC50 of ENPP1436 peptide for activating TCR-Ts is approximately 17–33 times higher than AFP158. Importantly, the ENPP1+ tumor cells did not activate TCR1-Ts and TCR2-Ts, and only weakly activated TCR3-Ts. The IFNγ produced by TCR3-Ts after ENPP1+ cell stimulation was >22x lower than that after HepG2 cells. And, all TCR-Ts did not kill ENPP1 + tumor cells. Furthermore, ectopic over-expression of ENPP1 protein in HLA-A2+ tumor cells did not activate TCR-Ts. In silico analysis showed that the ENPP1436 peptide affinity for HLA-A0201 was ranked 40 times lower than AFP158 and the chance of ENPP1436 peptide being processed and presented by HLA-A0201 was 100 times less likely than AFP158. In contrast, the two off-targets (Titin and MAGE-A3) that did cause severe toxicity in previous trials have the same or higher MHC-binding affinity and the same or higher chance of being processed and presented. In conclusion, our data shows that TCR-Ts can be activated by off-target ENPP1436 peptide. But, compared to target AFP158, it requires at least 250 times more ENPP1436 to achieve the same level of activation. Importantly, ENPP1436 peptide in human cells is not processed and presented to a sufficient level to activate the AFP158-specific TCR-Ts. Thus, these TCR-Ts, especially the TCR1-Ts and TCR2-Ts, will unlikely cause significant off-target toxicity.
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Affiliation(s)
- Lun Cai
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States
| | - Leidy D Caraballo Galva
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States.,The Graduate School, Augusta University, Augusta, GA, United States
| | - Yibing Peng
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States
| | - Xiaobing Luo
- Cellular Biomedicine Group (CBMG), Gaithersburg, MD, United States
| | - Wei Zhu
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States
| | - Yihong Yao
- Cellular Biomedicine Group (CBMG), Gaithersburg, MD, United States
| | - Yun Ji
- Cellular Biomedicine Group (CBMG), Gaithersburg, MD, United States
| | - Yukai He
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States.,The Graduate School, Augusta University, Augusta, GA, United States.,Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States.,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, United States
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Saulle I, Vicentini C, Clerici M, Biasin M. An Overview on ERAP Roles in Infectious Diseases. Cells 2020; 9:E720. [PMID: 32183384 PMCID: PMC7140696 DOI: 10.3390/cells9030720] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/12/2022] Open
Abstract
Endoplasmic reticulum (ER) aminopeptidases ERAP1 and ERAP2 (ERAPs) are crucial enzymes shaping the major histocompatibility complex I (MHC I) immunopeptidome. In the ER, these enzymes cooperate in trimming the N-terminal residues from precursors peptides, so as to generate optimal-length antigens to fit into the MHC class I groove. Alteration or loss of ERAPs function significantly modify the repertoire of antigens presented by MHC I molecules, severely affecting the activation of both NK and CD8+ T cells. It is, therefore, conceivable that variations affecting the presentation of pathogen-derived antigens might result in an inadequate immune response and onset of disease. After the first evidence showing that ERAP1-deficient mice are not able to control Toxoplasma gondii infection, a number of studies have demonstrated that ERAPs are control factors for several infectious organisms. In this review we describe how susceptibility, development, and progression of some infectious diseases may be affected by different ERAPs variants, whose mechanism of action could be exploited for the setting of specific therapeutic approaches.
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Affiliation(s)
- Irma Saulle
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
- Cattedra di Immunologia, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti Università degli Studi di Milano, 20122 Milan, Italy;
| | - Chiara Vicentini
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
| | - Mario Clerici
- Cattedra di Immunologia, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti Università degli Studi di Milano, 20122 Milan, Italy;
- IRCCS Fondazione Don Carlo Gnocchi, 20157 Milan, Italy
| | - Mara Biasin
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
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Kochneva GV, Sivolobova GF, Tkacheva AV, Gorchakov AA, Kulemzin SV. Combination of Oncolytic Virotherapy and CAR T/NK Cell Therapy for the Treatment of Cancer. Mol Biol 2020; 54:3-16. [DOI: 10.1134/s0026893320010100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 12/28/2022]
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Wickström SL, Lövgren T, Volkmar M, Reinhold B, Duke-Cohan JS, Hartmann L, Rebmann J, Mueller A, Melief J, Maas R, Ligtenberg M, Hansson J, Offringa R, Seliger B, Poschke I, Reinherz EL, Kiessling R. Cancer Neoepitopes for Immunotherapy: Discordance Between Tumor-Infiltrating T Cell Reactivity and Tumor MHC Peptidome Display. Front Immunol 2019; 10:2766. [PMID: 31921104 PMCID: PMC6918724 DOI: 10.3389/fimmu.2019.02766] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Tumor-infiltrating lymphocytes (TIL) are considered enriched for T cells recognizing shared tumor antigens or mutation-derived neoepitopes. We performed exome sequencing and HLA-A*02:01 epitope prediction from tumor cell lines from two HLA-A2-positive melanoma patients whose TIL displayed strong tumor reactivity. The potential neoepitopes were screened for recognition using autologous TIL by immunological assays and presentation on tumor major histocompatibility complex class I (MHC-I) molecules by Poisson detection mass spectrometry (MS). TIL from the patients recognized 5/181 and 3/49 of the predicted neoepitopes, respectively. MS screening detected 3/181 neoepitopes on tumor MHC-I from the first patient but only one was also among those recognized by TIL. Consequently, TIL enriched for neoepitope specificity failed to recognize tumor cells, despite being activated by peptides. For the second patient, only after IFN-γ treatment of the tumor cells was one of 49 predicted neoepitopes detected by MS, and this coincided with recognition by TIL sorted for the same specificity. Importantly, specific T cells could be expanded from patient and donor peripheral blood mononuclear cells (PBMC) for all neoepitopes recognized by TIL and/or detected on tumor MHC-I. In summary, stimulating the appropriate inflammatory environment within tumors may promote neoepitope MHC presentation while expanding T cells in blood may circumvent lack of specific TIL. The discordance in detection between physical and functional methods revealed here can be rationalized and used to improve neoantigen-targeted T cell immunotherapy.
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Affiliation(s)
- Stina L Wickström
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Tanja Lövgren
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Michael Volkmar
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bruce Reinhold
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Jonathan S Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Laura Hartmann
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Janina Rebmann
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jeroen Melief
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Roeltje Maas
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Maarten Ligtenberg
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Hansson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rienk Offringa
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Isabel Poschke
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,DKTK Immune Monitoring Unit, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Rolf Kiessling
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
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Lou H, Li X, Guo F, Ding M, Hu Y, Chen H, Yan J. Evaluations of Alkyl hydroperoxide reductase B cell antigen epitope as a potential epitope vaccine against Campylobacter jejuni. Saudi J Biol Sci 2019; 26:1117-1122. [PMID: 31516338 PMCID: PMC6734151 DOI: 10.1016/j.sjbs.2019.05.011] [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: 01/05/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 11/18/2022] Open
Abstract
Objective The present study aimed to screen and find alkyl hydroperoxide reductase (AhpC) B cell dominant epitope of Campylobacter jejuni (C. jejuni). Materials and methods Bio-informatic algorithms were used to predict B cell epitopes of AhpC. The AhpC protein and chemically synthesized antigenic epitopes of C. jejuni were considered as antigens, and the AhpC antibody was used as the primary antibody, ELISA and dot blot were used to analyze and screen the dominant epitope. The specific IgG of mice serum and IL-4 in splenocyte culture supernatant were detected by ELISA. The protective efficacy was evaluated by animal disease index and tissue histopathological staining of the jejunum. Results Seven epitopes of AhpC were predicted, one epitope (AhpC4–16) was found to recognize the antibodies of AhpC and had strong antigenicity by ELISA and dot blot analysis. In epitope AhpC4–16 immunized mice, specific IgG of serum and IL-4 in splenocyte culture supernatant were significantly higher. The illness index decreased significantly, the protective rate was 66.67%. Histopathology displayed that the jejunum morphology was better than the control group. Conclusions These findings suggested that epitope AhpC4–16 showed effective protective role against C. jejuni and is a candidate epitope of vaccine against this pathogen.
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Affiliation(s)
- Hongqiang Lou
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua 321000, China
| | - Xusheng Li
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua 321000, China
| | - Fangming Guo
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua 321000, China
| | - Mingxing Ding
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua 321000, China
| | - Ye Hu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua 321000, China
| | - Haohao Chen
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua 321000, China
- Corresponding authors.
| | - Jie Yan
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Corresponding authors.
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34
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Impact of epitope density on CD8+ T cell development and function. Mol Immunol 2019; 113:120-125. [DOI: 10.1016/j.molimm.2019.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/17/2019] [Accepted: 03/21/2019] [Indexed: 11/23/2022]
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Hassert M, Brien JD, Pinto AK. Mouse Models of Heterologous Flavivirus Immunity: A Role for Cross-Reactive T Cells. Front Immunol 2019; 10:1045. [PMID: 31143185 PMCID: PMC6520664 DOI: 10.3389/fimmu.2019.01045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022] Open
Abstract
Most of the world is at risk of being infected with a flavivirus such as dengue virus, West Nile virus, yellow fever virus, Japanese encephalitis virus, tick-borne encephalitis virus, and Zika virus, significantly impacting millions of lives. Importantly, many of these genetically similar viruses co-circulate within the same geographic regions, making it likely for individuals living in areas of high flavivirus endemicity to be infected with multiple flaviviruses during their lifetime. Following a flavivirus infection, a robust virus-specific T cell response is generated and the memory recall of this response has been demonstrated to provide long-lasting immunity, protecting against reinfection with the same pathogen. However, multiple studies have shown that this flavivirus specific T cell response can be cross-reactive and active during heterologous flavivirus infection, leading to the question: How does immunity to one flavivirus shape immunity to the next, and how does this impact disease? It has been proposed that in some cases unfavorable disease outcomes may be caused by lower avidity cross-reactive memory T cells generated during a primary flavivirus infection that preferentially expand during a secondary heterologous infection and function sub optimally against the new pathogen. While in other cases, these cross-reactive cells still have the potential to facilitate cross-protection. In this review, we focus on cross-reactive T cell responses to flaviviruses and the concepts and consequences of T cell cross-reactivity, with particular emphasis linking data generated using murine models to our new understanding of disease outcomes following heterologous flavivirus infection.
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Affiliation(s)
- Mariah Hassert
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, MO, United States
| | - James D Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, MO, United States
| | - Amelia K Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, MO, United States
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Chen Y, Batra H, Dong J, Chen C, Rao VB, Tao P. Genetic Engineering of Bacteriophages Against Infectious Diseases. Front Microbiol 2019; 10:954. [PMID: 31130936 PMCID: PMC6509161 DOI: 10.3389/fmicb.2019.00954] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/15/2019] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages (phages) are the most abundant and widely distributed organisms on Earth, constituting a virtually unlimited resource to explore the development of biomedical therapies. The therapeutic use of phages to treat bacterial infections (“phage therapy”) was conceived by Felix d’Herelle nearly a century ago. However, its power has been realized only recently, largely due to the emergence of multi-antibiotic resistant bacterial pathogens. Progress in technologies, such as high-throughput sequencing, genome editing, and synthetic biology, further opened doors to explore this vast treasure trove. Here, we review some of the emerging themes on the use of phages against infectious diseases. In addition to phage therapy, phages have also been developed as vaccine platforms to deliver antigens as part of virus-like nanoparticles that can stimulate immune responses and prevent pathogen infections. Phage engineering promises to generate phage variants with unique properties for prophylactic and therapeutic applications. These approaches have created momentum to accelerate basic as well as translational phage research and potential development of therapeutics in the near future.
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Affiliation(s)
- Yibao Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Himanshu Batra
- Department of Biology, The Catholic University of America, Washington, DC, United States
| | - Junhua Dong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Cen Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, United States
| | - Pan Tao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.,Department of Biology, The Catholic University of America, Washington, DC, United States
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Guedan S, Alemany R. CAR-T Cells and Oncolytic Viruses: Joining Forces to Overcome the Solid Tumor Challenge. Front Immunol 2018; 9:2460. [PMID: 30405639 PMCID: PMC6207052 DOI: 10.3389/fimmu.2018.02460] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/04/2018] [Indexed: 12/28/2022] Open
Abstract
Adoptive transfer of chimeric antigen receptor (CAR)-modified T cells has resulted in unprecedented rates of long-lasting complete responses in patients with leukemia and lymphoma. However, despite the impressive results in patients with hematologic malignancies, CAR-T cells have showed limited effect against solid cancers. New approaches will need to simultaneously overcome the multiple challenges that CAR-T cells encounter in solid tumors, including the immunosuppressive tumor microenvironment and heterogeneity of antigen expression. Oncolytic viruses are lytic and immunogenic anti-cancer agents with the potential to synergize with CAR-T cells for the treatment of solid tumors. In addition, viruses can be further modified to deliver therapeutic transgenes selectively to the tumor microenvironment, which could enhance the effector functions of tumor-specific T cells. This review summarizes the major limitations of CAR-T cells in solid tumors and discusses the potential role for oncolytic viruses as partners for CAR-T cells in the fight against cancer.
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Affiliation(s)
- Sonia Guedan
- Department of Hematology and Oncology, Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Ramon Alemany
- ProCure Program, IDIBELL-Institut Catala d'Oncologia, L'Hospitalet de Llobregat, Spain
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Cerqueira-Rodrigues B, Mendes A, Correia-Neves M, Nobrega C. Ag85-focused T-cell immune response controls Mycobacterium avium chronic infection. PLoS One 2018; 13:e0193596. [PMID: 29499041 PMCID: PMC5834192 DOI: 10.1371/journal.pone.0193596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/14/2018] [Indexed: 01/09/2023] Open
Abstract
CD4+ T cells are essential players for the control of mycobacterial infections. Several mycobacterial antigens have been identified for eliciting a relevant CD4+ T cell mediated-immune response, and numerous studies explored this issue in the context of Mycobacterium tuberculosis infection. Antigen 85 (Ag85), a highly conserved protein across Mycobacterium species, is secreted at the early phase of M. tuberculosis infection leading to the proliferation of Ag85-specific CD4+ T cells. However, in the context of Mycobacterium avium infection, little is known about the expression of this antigen and the elicited immune response. In the current work, we investigated if a T cell receptor (TCR) repertoire mostly, but not exclusively, directed at Ag85 is sufficient to mount a protective immune response against M. avium. We show that P25 mice, whose majority of T cells express a transgenic TCR specific for Ag85, control M. avium infection at the same level as wild type (WT) mice up to 20 weeks post-infection (wpi). During M. avium infection, Ag85 antigen is easily detected in the liver of 20 wpi mice by immunohistochemistry. In spite of the propensity of P25 CD4+ T cells to produce higher amounts of interferon-gamma (IFNγ) upon ex vivo stimulation, no differences in serum IFNγ levels are detected in P25 compared to WT mice, nor enhanced immunopathology is detected in P25 mice. These results indicate that a T cell response dominated by Ag85-specific T cells is appropriate to control M. avium infection with no signs of immunopathology.
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Affiliation(s)
- Bruno Cerqueira-Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ana Mendes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Claudia Nobrega
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail:
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Newell EW, Becht E. High-Dimensional Profiling of Tumor-Specific Immune Responses: Asking T Cells about What They “See” in Cancer. Cancer Immunol Res 2018; 6:2-9. [DOI: 10.1158/2326-6066.cir-17-0519] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/18/2017] [Accepted: 12/04/2017] [Indexed: 11/16/2022]
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Abstract
Safe and efficacious vaccines are arguably the most successful medical interventions of all time. Yet the ongoing discovery of new pathogens, along with emergence of antibiotic-resistant pathogens and a burgeoning population at risk of such infections, imposes unprecedented public health challenges. To meet these challenges, innovative strategies to discover and develop new or improved anti-infective vaccines are necessary. These approaches must intersect the most meaningful insights into protective immunity and advanced technologies with capabilities to deliver immunogens for optimal immune protection. This goal is considered through several recent advances in host-pathogen relationships, conceptual strides in vaccinology, and emerging technologies. Given a clear and growing risk of pandemic disease should the threat of infection go unmet, developing vaccines that optimize protective immunity against high-priority and antibiotic-resistant pathogens represents an urgent and unifying imperative.
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Affiliation(s)
- Michael R Yeaman
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California 90024.,Division of Molecular Medicine, Department of Medicine, Harbor-UCLA Medical Center, Torrance, California 90509; .,Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, California 90509.,Los Angeles Biomedical Research Institute, Torrance, California 90502
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Determining T-cell specificity to understand and treat disease. Nat Biomed Eng 2017; 1:784-795. [DOI: 10.1038/s41551-017-0143-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/05/2017] [Indexed: 02/06/2023]
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Fehlings M, Simoni Y, Penny HL, Becht E, Loh CY, Gubin MM, Ward JP, Wong SC, Schreiber RD, Newell EW. Checkpoint blockade immunotherapy reshapes the high-dimensional phenotypic heterogeneity of murine intratumoural neoantigen-specific CD8 + T cells. Nat Commun 2017; 8:562. [PMID: 28916749 PMCID: PMC5601925 DOI: 10.1038/s41467-017-00627-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 07/16/2017] [Indexed: 12/20/2022] Open
Abstract
The analysis of neoantigen-specific CD8+ T cells in tumour-bearing individuals is challenging due to the small pool of tumour antigen-specific T cells. Here we show that mass cytometry with multiplex combinatorial tetramer staining can identify and characterize neoantigen-specific CD8+ T cells in mice bearing T3 methylcholanthrene-induced sarcomas that are susceptible to checkpoint blockade immunotherapy. Among 81 candidate antigens tested, we identify T cells restricted to two known neoantigens simultaneously in tumours, spleens and lymph nodes in tumour-bearing mice. High-dimensional phenotypic profiling reveals that antigen-specific, tumour-infiltrating T cells are highly heterogeneous. We further show that neoantigen-specific T cells display a different phenotypic profile in mice treated with anti-CTLA-4 or anti-PD-1 immunotherapy, whereas their peripheral counterparts are not affected by the treatments. Our results provide insights into the nature of neoantigen-specific T cells and the effects of checkpoint blockade immunotherapy. Immune checkpoint blockade (ICB) therapies can unleash anti-tumour T-cell responses. Here the authors show, by integrating MHC tetramer multiplexing, mass cytometry and high-dimensional analyses, that neoantigen-specific, tumour-infiltrating T cells are highly heterogeneous and are subjected to ICB modulations.
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Affiliation(s)
- M Fehlings
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore
| | - Y Simoni
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore
| | - H L Penny
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore
| | - E Becht
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore
| | - C Y Loh
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore
| | - M M Gubin
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - J P Ward
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - S C Wong
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore
| | - R D Schreiber
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - E W Newell
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore.
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Faham M, Carlton V, Moorhead M, Zheng J, Klinger M, Pepin F, Asbury T, Vignali M, Emerson RO, Robins HS, Ireland J, Baechler-Gillespie E, Inman RD. Discovery of T Cell Receptor β Motifs Specific to HLA-B27-Positive Ankylosing Spondylitis by Deep Repertoire Sequence Analysis. Arthritis Rheumatol 2017; 69:774-784. [PMID: 28002888 DOI: 10.1002/art.40028] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Ankylosing spondylitis (AS), a chronic inflammatory disorder, has a notable association with HLA-B27. One hypothesis suggests that a common antigen that binds to HLA-B27 is important for AS disease pathogenesis. This study was undertaken to determine sequences and motifs that are shared among HLA-B27-positive AS patients, using T cell repertoire next-generation sequencing. METHODS To identify motifs enriched among B27-positive AS patients, we performed T cell receptor β (TCRβ) repertoire sequencing on samples from 191 B27-positive AS patients, 43 B27-negative AS patients, and 227 controls, and we obtained >77 million TCRβ clonotype sequences. First, we assessed whether any of 50 previously published sequences were enriched in B27-positive AS patients. We then used training and test cohorts to identify discovered motifs that were enriched in B27-positive AS patients versus controls. RESULTS Six previously published and 11 discovered motifs were enriched in the B27-positive AS samples as compared to controls. After combining motifs related by sequence, we identified a total of 15 independent motifs. Both the full set of 15 motifs and a set of 6 published motifs were enriched in the B27-positive AS patients as compared to B27-positive healthy individuals (P = 0.049 and P = 0.001, respectively). Using an independent cohort, we validated that at least some of these motifs were associated with AS, and not simply with B27-positive status. CONCLUSION We identified TCRβ motifs that are enriched in B27-positive AS patients as compared to B27-positive healthy controls. This suggests that a common antigen, presented by HLA-B27 and detected by CD8+ T cells, may be associated with AS disease pathogenesis.
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Affiliation(s)
- Malek Faham
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Victoria Carlton
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Martin Moorhead
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Jianbiao Zheng
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Mark Klinger
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Francois Pepin
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Thomas Asbury
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Marissa Vignali
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Ryan O Emerson
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation, Seattle, Washington
| | - Harlan S Robins
- Adaptive Biotechnologies Corporation, South San Francisco, California, and Adaptive Biotechnologies Corporation and Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | - Robert D Inman
- Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada
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44
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Zhu W, Wang C, Wang BZ. From Variation of Influenza Viral Proteins to Vaccine Development. Int J Mol Sci 2017; 18:ijms18071554. [PMID: 28718801 PMCID: PMC5536042 DOI: 10.3390/ijms18071554] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/10/2017] [Accepted: 07/14/2017] [Indexed: 11/19/2022] Open
Abstract
Recurrent influenza epidemics and occasional pandemics are one of the most important global public health concerns and are major causes of human morbidity and mortality. Influenza viruses can evolve through antigen drift and shift to overcome the barriers of human immunity, leading to host adaption and transmission. Mechanisms underlying this viral evolution are gradually being elucidated. Vaccination is an effective method for the prevention of influenza virus infection. However, the emergence of novel viruses, including the 2009 pandemic influenza A (H1N1), the avian influenza A virus (H7N9), and the highly pathogenic avian influenza A virus (HPAI H5N1), that have infected human populations frequently in recent years reveals the tremendous challenges to the current influenza vaccine strategy. A better vaccine that provides protection against a wide spectrum of various influenza viruses and long-lasting immunity is urgently required. Here, we review the evolutionary changes of several important influenza proteins and the influence of these changes on viral antigenicity, host adaption, and viral pathogenicity. Furthermore, we discuss the development of a potent universal influenza vaccine based on this knowledge.
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Affiliation(s)
- Wandi Zhu
- Center for Inflammation, Immunity & Infection, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA.
| | - Chao Wang
- Center for Inflammation, Immunity & Infection, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA.
| | - Bao-Zhong Wang
- Center for Inflammation, Immunity & Infection, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA.
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45
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Kousted TM, Kalliokoski O, Christensen SK, Winther JR, Hau J. Exploring the antigenic response to multiplexed immunizations in a chicken model of antibody production. Heliyon 2017; 3:e00267. [PMID: 28367512 PMCID: PMC5362046 DOI: 10.1016/j.heliyon.2017.e00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 02/22/2017] [Accepted: 03/09/2017] [Indexed: 11/28/2022] Open
Abstract
Hens have a tremendous capacity for producing polyclonal antibodies that can subsequently be isolated in high concentrations from their eggs. An approach for further maximizing their potential is to produce multiple antisera in the same individual through multiplexed (multiple simultaneous) immunizations. An unknown with this approach is how many immunogens a single bird is capable of mounting a sizeable antigenic response toward. At what point does it become counter-productive to add more immunogens to the same immunization regimen? In the present study we were able to demonstrate that the competing effects of co-administering multiple immunogens effectively limit the antibody specificities that can be raised in a single individual to a fairly low number. Two potent model immunogens, KLH and CRM197, were administered together with competing antigens in various concentrations and complexities. With an upper limit of 1 mg protein material recommended for chicken immunizations, we found that the maximum number of immunogens that can be reliably used is most likely in the low double digits. The limiting factor for a response to an immunogen could not be related to the number of splenic plasma cells producing antibodies against it. When administering KLH alone, up to 70% of the IgY-producing splenic plasma cells were occupied with producing anti-KLH antibodies; but when simultaneously being exposed to a plethora of other antigens, a response of a comparable magnitude could be mounted with a splenic plasma cell involvement of less than 5%. Two breeds of egg-layers were compared with respect to antibody production in an initial experiment, but differences in antibody productivity were negligible. Although our findings support the use of multiplexed immunizations in the hen, we find that the number of immunogens cannot be stretched much higher than the handful that has been used in mammalian models to date.
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Affiliation(s)
- Tina M. Kousted
- Department of Experimental Medicine, University of Copenhagen, Denmark
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark
| | - Otto Kalliokoski
- Department of Experimental Medicine, University of Copenhagen, Denmark
- Corresponding author at: Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
| | | | - Jakob R. Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark
| | - Jann Hau
- Department of Experimental Medicine, University of Copenhagen, Denmark
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46
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Du L, Tai W, Yang Y, Zhao G, Zhu Q, Sun S, Liu C, Tao X, Tseng CTK, Perlman S, Jiang S, Zhou Y, Li F. Introduction of neutralizing immunogenicity index to the rational design of MERS coronavirus subunit vaccines. Nat Commun 2016; 7:13473. [PMID: 27874853 PMCID: PMC5121417 DOI: 10.1038/ncomms13473] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/06/2016] [Indexed: 12/13/2022] Open
Abstract
Viral subunit vaccines often contain immunodominant non-neutralizing epitopes that divert host immune responses. These epitopes should be eliminated in vaccine design, but there is no reliable method for evaluating an epitope's capacity to elicit neutralizing immune responses. Here we introduce a new concept 'neutralizing immunogenicity index' (NII) to evaluate an epitope's neutralizing immunogenicity. To determine the NII, we mask the epitope with a glycan probe and then assess the epitope's contribution to the vaccine's overall neutralizing immunogenicity. As proof-of-concept, we measure the NII for different epitopes on an immunogen comprised of the receptor-binding domain from MERS coronavirus (MERS-CoV). Further, we design a variant form of this vaccine by masking an epitope that has a negative NII score. This engineered vaccine demonstrates significantly enhanced efficacy in protecting transgenic mice from lethal MERS-CoV challenge. Our study may guide the rational design of highly effective subunit vaccines to combat MERS-CoV and other life-threatening viruses.
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Affiliation(s)
- Lanying Du
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York 10065, USA
| | - Wanbo Tai
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York 10065, USA
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yang Yang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qing Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Chang Liu
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Xinrong Tao
- Department of Microbiology and Immunology and Center for Biodefense and Emerging Disease, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology and Center for Biodefense and Emerging Disease, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Shibo Jiang
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York 10065, USA
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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Arcia D, Acevedo-Sáenz L, Rugeles MT, Velilla PA. Role of CD8 + T Cells in the Selection of HIV-1 Immune Escape Mutations. Viral Immunol 2016; 30:3-12. [PMID: 27805477 DOI: 10.1089/vim.2016.0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) infection represents one of the biggest public health problems worldwide. The immune response, mainly the effector mechanisms mediated by CD8+ T cells, induces the selection of mutations that allows the virus to escape the immune control. These mutations are generally selected within CD8+ T cell epitopes restricted to human leukocyte antigen class I (HLA-I), leading to a decrease in the presentation and recognition of the epitope, decreasing the activation of CD8+ T cells. However, these mutations may also affect cellular processing of the peptide or recognition by the T cell receptor. Escape mutations often carry a negative impact in viral fitness that is partially or totally compensated by the selection of compensatory mutations. The selection of either escape mutations or compensatory mutations may negatively affect the course of the infection. In addition, these mutations are a major barrier for the development of new therapeutic strategies focused on the induction of specific CD8+ T cell responses.
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Affiliation(s)
- David Arcia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - Liliana Acevedo-Sáenz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - Paula A Velilla
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
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Kaabinejadian S, McMurtrey CP, Kim S, Jain R, Bardet W, Schafer FB, Davenport JL, Martin AD, Diamond MS, Weidanz JA, Hansen TH, Hildebrand WH. Immunodominant West Nile Virus T Cell Epitopes Are Fewer in Number and Fashionably Late. THE JOURNAL OF IMMUNOLOGY 2016; 196:4263-73. [PMID: 27183642 DOI: 10.4049/jimmunol.1501821] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/20/2016] [Indexed: 12/23/2022]
Abstract
Class I HLA molecules mark infected cells for immune targeting by presenting pathogen-encoded peptides on the cell surface. Characterization of viral peptides unique to infected cells is important for understanding CD8(+) T cell responses and for the development of T cell-based immunotherapies. Having previously reported a series of West Nile virus (WNV) epitopes that are naturally presented by HLA-A*02:01, in this study we generated TCR mimic (TCRm) mAbs to three of these peptide/HLA complexes-the immunodominant SVG9 (E protein), the subdominant SLF9 (NS4B protein), and the immunorecessive YTM9 (NS3 protein)-and used these TCRm mAbs to stain WNV-infected cell lines and primary APCs. TCRm staining of WNV-infected cells demonstrated that the immunorecessive YTM9 appeared several hours earlier and at 5- to 10-fold greater density than the more immunogenic SLF9 and SVG9 ligands, respectively. Moreover, staining following inhibition of the TAP demonstrated that all three viral ligands were presented in a TAP-dependent manner despite originating from different cellular compartments. To our knowledge, this study represents the first use of TCRm mAbs to define the kinetics and magnitude of HLA presentation for a series of epitopes encoded by one virus, and the results depict a pattern whereby individual epitopes differ considerably in abundance and availability. The observations that immunodominant ligands can be found at lower levels and at later time points after infection suggest that a reevaluation of the factors that combine to shape T cell reactivity may be warranted.
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Affiliation(s)
- Saghar Kaabinejadian
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Curtis P McMurtrey
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Sojung Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - Rinki Jain
- Center for Immunotherapeutic Research, Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX 79601; Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX 79601; Receptor Logic, Inc., Abilene, TX 79601
| | - Wilfried Bardet
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Fredda B Schafer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | | | | | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110; Department of Medicine, Washington University School of Medicine, St Louis, MO 63110; and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110
| | - Jon A Weidanz
- Center for Immunotherapeutic Research, Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX 79601; Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX 79601; Receptor Logic, Inc., Abilene, TX 79601
| | - Ted H Hansen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104;
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49
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What Makes A Bacterial Oral Vaccine a Strong Inducer of High-Affinity IgA Responses? Antibodies (Basel) 2015. [DOI: 10.3390/antib4040295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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50
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Acevedo-Sáenz L, Carmona-Pérez L, Velilla-Hernández PA, Delgado JC, Rugeles L MT. The APPEESFRS Peptide, Restricted by the HLA-B*35:01 Molecule, and the APPEESFRF Variant Derived from an Autologous HIV-1 Strain Induces Polyfunctional Responses in CD8+ T Cells. Biores Open Access 2015; 4:115-20. [PMID: 26309788 PMCID: PMC4497628 DOI: 10.1089/biores.2014.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Numerous reports have focused on consensus peptides to determine CD8+ T-cell responses; however, few studies evaluated the functional profile using peptides derived from circulating strains of a specific region. We determined the effector profile and maturation phenotype of CD8+ T-cells targeting the consensus APPEESFRS (AS9) epitope and its variant APPEESFRF (AF9), previously identified. The free energy of binding, maturation phenotype, and polyfunctional profile of both peptides were similar. The magnitude of CD8+ T-cell responses to AF9 was greater than the one elicited by AS9, although the difference was not significant. The polyfunctional profile of AF9 was characterized by CD107a/interleukin-2 (IL-2)/macrophage inflammatory protein beta (MIP1β) and by interferon gamma (IFNγ)/MIP1β/tumor necrosis factor alpha (TNFα) in response to AS9. TNFα production was significantly higher in response to AF9 than to AS9, and there was a negative correlation between the absolute number of CD8+ T-cell-producing TNFα and the plasma human immunodeficiency virus (HIV) load, suggesting a role of this cytokine in the control of HIV replication.
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Affiliation(s)
- Liliana Acevedo-Sáenz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA) , Medellín, Colombia
| | - Liseth Carmona-Pérez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA) , Medellín, Colombia
| | | | - Julio C Delgado
- ARUP Institute for Clinical and Experimental Pathology, Department of Pathology, University of Utah School of Medicine , Salt Lake City, Utah
| | - María Teresa Rugeles L
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA) , Medellín, Colombia
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