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Zhang X, Reinsmoen NL, Kobashigawa JA. HLA Mismatches Identified by a Novel Algorithm Predict Risk of Antibody-mediated Rejection From De Novo Donor-specific Antibodies. Transplantation 2024:00007890-990000000-00829. [PMID: 39049137 DOI: 10.1097/tp.0000000000005140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
BACKGROUND The development of de novo donor-specific antibodies (dnDSA) and antibody-mediated rejection (AMR) remains a barrier to long-term graft and patient survival. Most dnDSA are directed against mismatched donor HLA-DQ antigens. Here, we describe a novel algorithm, which we have termed categorical amino acid mismatched epitope, to evaluate HLA-DQ mismatches. METHODS In this algorithm, amino acid residues of HLA-DQ protein were categorized into 4 groups based on their chemical characteristics. The likelihood of categorically mismatched peptides presented by the recipient's HLA-DRB1 was expressed as a normalized value, %Rank score. Categorical HLA-DQ mismatches were analyzed in 386 heart transplant recipients who were mismatched with their donors at the HLA-DQB1 locus. RESULTS We found that the presence of DQB1 mismatches with %Rank score ≤1 was associated with the development of dnDSA (P = 0.002). Furthermore, dnDSA increased the risk of AMR only in recipients who had DQ mismatches with %Rank score ≤1 (hazard ratio = 5.8), but the freedom from AMR was comparable between recipients with dnDSA and those without dnDSA if %Rank scores of DQ mismatching were >1. CONCLUSIONS These results suggest that HLA-DQ mismatches evaluated by the categorical amino acid mismatched epitope algorithm can stratify the risk of development of dnDSA and AMR in heart transplant recipients.
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Affiliation(s)
- Xiaohai Zhang
- HLA and Immunogenetics Laboratory, Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Nancy L Reinsmoen
- Independent HLA Consultant, Cedars-Sinai Medical Center, Scottsdale, AZ
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2
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Cho E, Han S, Eom HS, Lee SJ, Han C, Singh R, Kim SH, Park BM, Kim BG, Kim YH, Kwon BS, Nam KT, Choi BK. Cross-Activation of Regulatory T Cells by Self Antigens Limits Self-Reactive and Activated CD8 + T Cell Responses. Int J Mol Sci 2023; 24:13672. [PMID: 37761976 PMCID: PMC10530955 DOI: 10.3390/ijms241813672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The interaction between regulatory T (Treg) cells and self-reactive T cells is a crucial mechanism for maintaining immune tolerance. In this study, we investigated the cross-activation of Treg cells by self-antigens and its impact on self-reactive CD8+ T cell responses, with a focus on the P53 signaling pathway. We discovered that major histocompatibility complex (MHC) I-restricted self-peptides not only activated CD8+ T cells but also induced the delayed proliferation of Treg cells. Following HLA-A*0201-restricted Melan-A-specific (pMelan) CD8+ T cells, we observed the direct expansion of Treg cells and concurrent suppression of pMelan+CD8+ T cell proliferation upon stimulation with Melan-A peptide. Transcriptome analysis revealed no significant alterations in specific signaling pathways in pMelan+CD8+ T cells that were co-cultured with activated Treg cells. However, there was a noticeable upregulation of genes involved in P53 accumulation, a critical regulator of cell survival and apoptosis. Consistent with such observation, the blockade of P53 induced a continuous proliferation of pMelan+CD8+ T cells. The concurrent stimulation of Treg cells through self-reactive TCRs by self-antigens provides insights into the immune system's ability to control activated self-reactive CD8+ T cells as part of peripheral tolerance, highlighting the intricate interplay between Treg cells and CD8+ T cells and implicating therapeutic interventions in autoimmune diseases and cancer immunotherapy.
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Affiliation(s)
- Eunjung Cho
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
| | - Seongeun Han
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
| | - Hyeon Seok Eom
- Hematological Malignancy Center of the Hospital, National Cancer Center, Goyang 10408, Republic of Korea
| | - Sang-Jin Lee
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
| | - Chungyong Han
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
| | - Rohit Singh
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
| | - Seon-Hee Kim
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
- Department of Biomedical Laboratory Science, Catholic Kwandong University, Gangneung 25601, Republic of Korea
| | - Bo-Mi Park
- Biomedicine Production Branch, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Byoung-Gie Kim
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Young H. Kim
- Eutilex, Co., Ltd., Geumcheon-gu, Seoul 08594, Republic of Korea
| | - Byoung S. Kwon
- Eutilex, Co., Ltd., Geumcheon-gu, Seoul 08594, Republic of Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Beom K. Choi
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
- Innobationbio, Co., Ltd., Mapo-gu, Seoul 03929, Republic of Korea
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Olsson N, Jiang W, Adler LN, Mellins ED, Elias JE. Tuning DO:DM ratios modulates MHC class II immunopeptidomes. Mol Cell Proteomics 2022; 21:100204. [DOI: 10.1016/j.mcpro.2022.100204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 01/07/2022] [Accepted: 01/16/2022] [Indexed: 10/19/2022] Open
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4
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Gupta S, Li D, Ostrov DA, Nguyen CQ. Blocking IAg 7 class II major histocompatibility complex by drug-like small molecules alleviated Sjögren's syndrome in NOD mice. Life Sci 2022; 288:120182. [PMID: 34843735 PMCID: PMC8883604 DOI: 10.1016/j.lfs.2021.120182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 10/25/2022]
Abstract
BACKGROUND Sjögren's syndrome (SjS) is an autoimmune disease with a strong genetic association. To date, no vaccine or therapeutic agent exists to cure SjS, and patients must rely on lifelong therapies to treat symptoms. Human leukocyte antigens (HLA) are primary susceptibility loci that form the genetic basis for many autoimmune diseases, including SjS. In this study, we sought to determine whether blocking MHC class II IAg7 antigen presentation in the NOD mouse would alleviate SjS by preventing the recognition of autoantigens by pathogenic T cells. METHODS Mapping of the antigenic epitopes of Ro60 autoantigen to IAg7 of the NOD mice was performed using structural modeling and in-vitro stimulation. Tetraazatricyclo-dodecane (TATD) and 8-Azaguanine (8-Aza) were previously identified as potential binders to IAg7 of the NOD mice using in silico drug screening. Mice were treated with 20mgs/kg via IP every day five days/week for 23 weeks. Disease profiling was conducted. FINDINGS Specific peptides of Ro60 autoantigen were identified to bind to IAg7 and stimulated splenocytes of the NOD mice. Treating NOD mice with TATD or 8-Azaguanine alleviated SjS symptoms by improving salivary and lacrimal gland secretory function, decreasing the levels of autoantibodies, and reducing the severity of lymphocytic infiltration in the salivary and lacrimal glands. INTERPRETATION This study presents a novel therapeutic approach for SjS by identifying small molecules capable of inhibiting T cell response via antigen-specific presentation. FUNDING CQN is supported financially in part by PHS grants AI130561, DE026450, and DE028544 from the National Institutes of Health.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Danmeng Li
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - David A Ostrov
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA; Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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5
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Peereboom ETM, Matern BM, Tomosugi T, Niemann M, Drylewicz J, Joosten I, Allebes WA, van der Meer A, Hilbrands LB, Baas MC, van Reekum FE, Verhaar MC, Kamburova EG, Seelen MAJ, Sanders JS, Hepkema BG, Lambeck AJ, Bungener LB, Roozendaal C, Tilanus MGJ, Voorter CE, Wieten L, van Duijnhoven EM, Gelens MACJ, Christiaans MHL, van Ittersum FJ, Nurmohamed A, Lardy NM, Swelsen W, van der Pant KA, van der Weerd NC, Ten Berge IJM, Bemelman FJ, de Vries APJ, de Fijter JW, Betjes MGH, Roelen DL, Claas FH, Otten HG, Heidt S, van Zuilen AD, Kobayashi T, Geneugelijk K, Spierings E. T-Cell Epitopes Shared Between Immunizing HLA and Donor HLA Associate With Graft Failure After Kidney Transplantation. Front Immunol 2021; 12:784040. [PMID: 34868064 PMCID: PMC8637278 DOI: 10.3389/fimmu.2021.784040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
CD4+ T-helper cells play an important role in alloimmune reactions following transplantation by stimulating humoral as well as cellular responses, which might lead to failure of the allograft. CD4+ memory T-helper cells from a previous immunizing event can potentially be reactivated by exposure to HLA mismatches that share T-cell epitopes with the initial immunizing HLA. Consequently, reactivity of CD4+ memory T-helper cells toward T-cell epitopes that are shared between immunizing HLA and donor HLA could increase the risk of alloimmunity following transplantation, thus affecting transplant outcome. In this study, the amount of T-cell epitopes shared between immunizing and donor HLA was used as a surrogate marker to evaluate the effect of donor-reactive CD4+ memory T-helper cells on the 10-year risk of death-censored kidney graft failure in 190 donor/recipient combinations using the PIRCHE-II algorithm. The T-cell epitopes of the initial theoretical immunizing HLA and the donor HLA were estimated and the number of shared PIRCHE-II epitopes was calculated. We show that the natural logarithm-transformed PIRCHE-II overlap score, or Shared T-cell EPitopes (STEP) score, significantly associates with the 10-year risk of death-censored kidney graft failure, suggesting that the presence of pre-transplant donor-reactive CD4+ memory T-helper cells might be a strong indicator for the risk of graft failure following kidney transplantation.
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Affiliation(s)
- Emma T M Peereboom
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Benedict M Matern
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Toshihide Tomosugi
- Department of Transplant Surgery, Japanese Red Cross Aichi Medical Center Nagoya Daini Hospital, Nagoya, Japan.,Department of Kidney Diseases and Transplant Immunology, Aichi Medical University School of Medicine, Nagakute, Japan
| | | | - Julia Drylewicz
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Irma Joosten
- Laboratory Medicine, Laboratory Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wil A Allebes
- Laboratory Medicine, Laboratory Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Arnold van der Meer
- Laboratory Medicine, Laboratory Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Luuk B Hilbrands
- Department of Nephrology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marije C Baas
- Department of Nephrology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Franka E van Reekum
- Department of Nephrology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Marianne C Verhaar
- Department of Nephrology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Elena G Kamburova
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Marc A J Seelen
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jan Stephan Sanders
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bouke G Hepkema
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Annechien J Lambeck
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Laura B Bungener
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Caroline Roozendaal
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Marcel G J Tilanus
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - Christien E Voorter
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - Lotte Wieten
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - Elly M van Duijnhoven
- Department of Internal Medicine, Division of Nephrology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Mariëlle A C J Gelens
- Department of Internal Medicine, Division of Nephrology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Maarten H L Christiaans
- Department of Internal Medicine, Division of Nephrology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Frans J van Ittersum
- Department of Nephrology, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Azam Nurmohamed
- Department of Nephrology, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Neubury M Lardy
- Department of Immunogenetics/HLA Diagnostic, Sanquin Diagnostic Services, Amsterdam, Netherlands
| | - Wendy Swelsen
- Department of Immunogenetics/HLA Diagnostic, Sanquin Diagnostic Services, Amsterdam, Netherlands
| | - Karlijn A van der Pant
- Renal Transplant Unit, Department of Internal Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Neelke C van der Weerd
- Renal Transplant Unit, Department of Internal Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Ineke J M Ten Berge
- Renal Transplant Unit, Department of Internal Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Fréderike J Bemelman
- Renal Transplant Unit, Department of Internal Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Aiko P J de Vries
- Department of Nephrology, Leiden University Medical Center, Leiden, Netherlands
| | - Johan W de Fijter
- Department of Nephrology, Leiden University Medical Center, Leiden, Netherlands
| | - Michiel G H Betjes
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands.,Department of Nephrology, Erasmus MC, Rotterdam, Netherlands
| | - Dave L Roelen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Frans H Claas
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Henny G Otten
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Arjan D van Zuilen
- Department of Nephrology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Takaaki Kobayashi
- Department of Renal Transplant Surgery, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Kirsten Geneugelijk
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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6
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Ofori EA, Tetteh JKA, Frimpong A, Ganeshan H, Belmonte M, Peters B, Villasante E, Sedegah M, Ofori MF, Kusi KA. Comparison of the impact of allelic polymorphisms in PfAMA1 on the induction of T Cell responses in high and low malaria endemic communities in Ghana. Malar J 2021; 20:367. [PMID: 34507582 PMCID: PMC8431259 DOI: 10.1186/s12936-021-03900-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria eradication requires a combined effort involving all available control tools, and these efforts would be complemented by an effective vaccine. The antigen targets of immune responses may show polymorphisms that can undermine their recognition by immune effectors and hence render vaccines based on antigens from a single parasite variant ineffective against other variants. This study compared the influence of allelic polymorphisms in Plasmodium falciparum apical membrane antigen 1 (PfAMA1) peptide sequences from three strains of P. falciparum (3D7, 7G8 and FVO) on their function as immunodominant targets of T cell responses in high and low malaria transmission communities in Ghana. METHODS Peripheral blood mononuclear cells (PBMCs) from 10 subjects from a high transmission area (Obom) and 10 subjects from a low transmission area (Legon) were tested against 15 predicted CD8 + T cell minimal epitopes within the PfAMA1 antigen of multiple parasite strains using IFN-γ ELISpot assay. The peptides were also tested in similar assays against CD8 + enriched PBMC fractions from the same subjects in an effort to characterize the responding T cell subsets. RESULTS In assays using unfractionated PBMCs, two subjects from the high transmission area, Obom, responded positively to four (26.7%) of the 15 tested peptides. None of the Legon subject PBMCs yielded positive peptide responses using unfractionated PBMCs. In assays with CD8 + enriched PBMCs, three subjects from Obom made positive recall responses to six (40%) of the 15 tested peptides, while only one subject from Legon made a positive recall response to a single peptide. Overall, 5 of the 20 study subjects who had positive peptide-specific IFN-γ recall responses were from the high transmission area, Obom. Furthermore, while subjects from Obom responded to peptides in PfAMA1 from multiple parasite strains, one subject from Legon responded to a peptide from 3D7 strain only. CONCLUSIONS The current data demonstrate the possibility of a real effect of PfAMA1 polymorphisms on the induction of T cell responses in malaria exposed subjects, and this effect may be more pronounced in communities with higher parasite exposure.
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Affiliation(s)
- Ebenezer A Ofori
- West Africa Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana.,Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - John K A Tetteh
- Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Augustina Frimpong
- Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Harini Ganeshan
- Malaria Department, Naval Medical Research Center, Silver Spring, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Maria Belmonte
- Malaria Department, Naval Medical Research Center, Silver Spring, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Eileen Villasante
- Malaria Department, Naval Medical Research Center, Silver Spring, USA
| | - Martha Sedegah
- Malaria Department, Naval Medical Research Center, Silver Spring, USA
| | - Michael F Ofori
- West Africa Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana.,Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Kwadwo A Kusi
- West Africa Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana. .,Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana.
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7
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Chukwudozie OS, Gray CM, Fagbayi TA, Chukwuanukwu RC, Oyebanji VO, Bankole TT, Adewole RA, Daniel EM. Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein. PLoS One 2021; 16:e0248061. [PMID: 33730022 PMCID: PMC7968690 DOI: 10.1371/journal.pone.0248061] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022] Open
Abstract
Developing an efficacious vaccine for SARS-CoV-2 infection is critical to stemming COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in designing an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers and 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC I and II alleles, respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. With our In silico test, the vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was also characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We, therefore, propose that potential vaccine designs consider this approach.
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Affiliation(s)
| | - Clive M. Gray
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Tawakalt A. Fagbayi
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | - Rebecca C. Chukwuanukwu
- Immunology Unit, Medical Laboratory Science Department, Nnamdi Azikiwe University, Nnewi, Nigeria
| | - Victor O. Oyebanji
- Department of Veterinary Pathology, University of Ibadan, Ibadan, Nigeria
| | - Taiwo T. Bankole
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | - Richard A. Adewole
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | - Eze M. Daniel
- Public Health Biotechnology Unit, Institute of Child Health, University College Hospital, University of Ibadan, Ibadan, Nigeria
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8
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Iannuzzi R, Rossetti G, Spitaleri A, Bonnal RJP, Pagani M, Mollica L. A Simplified Amino Acidic Alphabet to Unveil the T-Cells Receptors Antigens: A Computational Perspective. Front Chem 2021; 9:598802. [PMID: 33718327 PMCID: PMC7947793 DOI: 10.3389/fchem.2021.598802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/19/2021] [Indexed: 11/15/2022] Open
Abstract
The exposure to pathogens triggers the activation of adaptive immune responses through antigens bound to surface receptors of antigen presenting cells (APCs). T cell receptors (TCR) are responsible for initiating the immune response through their physical direct interaction with antigen-bound receptors on the APCs surface. The study of T cell interactions with antigens is considered of crucial importance for the comprehension of the role of immune responses in cancer growth and for the subsequent design of immunomodulating anticancer drugs. RNA sequencing experiments performed on T cells represented a major breakthrough for this branch of experimental molecular biology. Apart from the gene expression levels, the hypervariable CDR3α/β sequences of the TCR loops can now be easily determined and modelled in the three dimensions, being the portions of TCR mainly responsible for the interaction with APC receptors. The most direct experimental method for the investigation of antigens would be based on peptide libraries, but their huge combinatorial nature, size, cost, and the difficulty of experimental fine tuning makes this approach complicated time consuming, and costly. We have implemented in silico methodology with the aim of moving from CDR3α/β sequences to a library of potentially antigenic peptides that can be used in immunologically oriented experiments to study T cells’ reactivity. To reduce the size of the library, we have verified the reproducibility of experimental benchmarks using the permutation of only six residues that can be considered representative of all ensembles of 20 natural amino acids. Such a simplified alphabet is able to correctly find the poses and chemical nature of original antigens within a small subset of ligands of potential interest. The newly generated library would have the advantage of leading to potentially antigenic ligands that would contribute to a better understanding of the chemical nature of TCR-antigen interactions. This step is crucial in the design of immunomodulators targeted towards T-cells response as well as in understanding the first principles of an immune response in several diseases, from cancer to autoimmune disorders.
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Affiliation(s)
- Raffaele Iannuzzi
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Grazisa Rossetti
- Molecular Oncology and Immunology, FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raoul J P Bonnal
- Molecular Oncology and Immunology, FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Massimiliano Pagani
- Molecular Oncology and Immunology, FIRC Institute of Molecular Oncology (IFOM), Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Luca Mollica
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
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9
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MacLachlan BJ, Dolton G, Papakyriakou A, Greenshields-Watson A, Mason GH, Schauenburg A, Besneux M, Szomolay B, Elliott T, Sewell AK, Gallimore A, Rizkallah P, Cole DK, Godkin A. Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope. J Biol Chem 2019; 294:20246-20258. [PMID: 31619516 PMCID: PMC6937582 DOI: 10.1074/jbc.ra119.009437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/18/2019] [Indexed: 01/03/2023] Open
Abstract
CD4+ T-cells recognize peptide antigens, in the context of human leukocyte antigen (HLA) class II molecules (HLA-II), which through peptide-flanking residues (PFRs) can extend beyond the limits of the HLA binding. The role of the PFRs during antigen recognition is not fully understood; however, recent studies have indicated that these regions can influence T-cell receptor (TCR) affinity and pHLA-II stability. Here, using various biochemical approaches including peptide sensitivity ELISA and ELISpot assays, peptide-binding assays and HLA-II tetramer staining, we focused on CD4+ T-cell responses against a tumor antigen, 5T4 oncofetal trophoblast glycoprotein (5T4), which have been associated with improved control of colorectal cancer. Despite their weak TCR-binding affinity, we found that anti-5T4 CD4+ T-cells are polyfunctional and that their PFRs are essential for TCR recognition of the core bound nonamer. The high-resolution (1.95 Å) crystal structure of HLA-DR1 presenting the immunodominant 20-mer peptide 5T4111-130, combined with molecular dynamic simulations, revealed how PFRs explore the HLA-proximal space to contribute to antigen reactivity. These findings advance our understanding of what constitutes an HLA-II epitope and indicate that PFRs can tune weak affinity TCR-pHLA-II interactions.
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Affiliation(s)
- Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15341 Athens, Greece
| | - Alexander Greenshields-Watson
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Georgina H Mason
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Andrea Schauenburg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Matthieu Besneux
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Barbara Szomolay
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Tim Elliott
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Centre for Cancer Immunology, University of Southampton, Faculty of Medicine, University Hospital, Southampton SO16 6YD, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Awen Gallimore
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Pierre Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Andrew Godkin
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
- Department of Gastroenterology and Hepatology, University Hospital of Wales, CF14 4XN Cardiff, United Kingdom
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10
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Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM. Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft. Immunogenetics 2019; 71:519-530. [PMID: 31520135 PMCID: PMC6790208 DOI: 10.1007/s00251-019-01129-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022]
Abstract
Human CD4+ T lymphocytes play an important role in inducing potent immune responses. T cells are activated and stimulated by peptides presented in human leucocyte antigen (HLA)-class II molecules. These HLA-class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the HLA molecule, designated as the peptide-binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different cell types, potentially harbouring different proteolytic enzymes, the ligandomes of HLA-DRB1*03:01/HLA-DRB > 1 derived from two different cell types (dendritic cells and EBV-transformed B cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues of a total of 16,568 peptides were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, the terminal conservations of these ligandomes were compared to the N- and C-terminal conservations of the ligandome acquired from dendritic cells homozygous for HLA-DRB1*04:01. Again, comparable conservations were evident with only minor differences. Taken together, these data show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.
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Affiliation(s)
- Arieke S B Kampstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Jurgen van Heemst
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - George M Janssen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Menno van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
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11
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Chen J, Lu S, Weng X, Liang Z, Wu X. Heterogeneity of antigen specificity between HLA-A*02:01 and other frequent Chinese HLA-A2 subtypes detected by a modified autologous lymphocyte-monocyte coculture. Mol Immunol 2019; 114:389-394. [PMID: 31454596 DOI: 10.1016/j.molimm.2019.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/18/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
Abstract
HLA-A2 is the most common serological HLA type among all ethnic groups. Through advances in DNA typing, more than 800 subtypes of HLA-A2 have been identified, and the existence of heterogeneity of antigen specificity among the HLA-A2 subtypes has been suggested by retrospective analyses of allogeneic transplantation patients and by studies of antigen amino acid structure. However, prior to this study, the antigenicity of a given subtype or the mismatch extent between two given subtypes could not be studied in vitro. Here, we used a modified autologous lymphocyte-monocyte coculture method to reveal heterogeneity of antigen specificity among HLA-A2 subtypes. The coculture was set up with HLA-A2 (non-A*02:01) lymphocytes and monocytes, and the monocytes were coated with an HLA-A*02:01/IgG1-Fc fusion protein (dimer) by high-affinity binding of the IgG1-Fc to FcgRI. Lymphocyte proliferation following coculture indicated that HLA-A*02:01 showed antigenicity against the HLA-A2 (non-A*02:01) subtype. Among the most frequent HLA-A2 subtypes in the Chinese population (HLA-A*02:01, -A*02:03, -A*02:06 and -A*02:07), we identified significant -A*02:01 antigenicity for T cells from -A*02:03 or -A*02:06 but not -A*02:07 individuals. Our findings were consistent with retrospective studies of allograft patients with a limited number of involved subtypes, indicating that this modified coculture method provides a practical and reliable means to study the antigenicity of HLA allele subtypes in vitro.
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Affiliation(s)
- Jun Chen
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Afilliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Shengjun Lu
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiufang Weng
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhihui Liang
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Xiongwen Wu
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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12
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Prasasty VD, Grazzolie K, Rosmalena R, Yazid F, Ivan FX, Sinaga E. Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches. Microorganisms 2019; 7:E226. [PMID: 31370224 PMCID: PMC6722788 DOI: 10.3390/microorganisms7080226] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
The Zika virus disease, also known as Zika fever is an arboviral disease that became epidemic in the Pacific Islands and had spread to 18 territories of the Americas in 2016. Zika virus disease has been linked to several health problems such as microcephaly and the Guillain-Barré syndrome, but to date, there has been no vaccine available for Zika. Problems related to the development of a vaccine include the vaccination target, which covers pregnant women and children, and the antibody dependent enhancement (ADE), which can be caused by non-neutralizing antibodies. The peptide vaccine was chosen as a focus of this study as a safer platform to develop the Zika vaccine. In this study, a collection of Zika proteomes was used to find the best candidates for T- and B-cell epitopes using the immunoinformatics approach. The most promising T-cell epitopes were mapped using the selected human leukocyte antigen (HLA) alleles, and further molecular docking and dynamics studies showed a good peptide-HLA interaction for the best major histocompatibility complex-II (MHC-II) epitope. The most promising B-cell epitopes include four linear peptides predicted to be cross-reactive with T-cells, and conformational epitopes from two proteins accessible by antibodies in their native biological assembly. It is believed that the use of immunoinformatics methods is a promising strategy against the Zika viral infection in designing an efficacious multiepitope vaccine.
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Affiliation(s)
- Vivitri Dewi Prasasty
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta 12930, Indonesia.
| | - Karel Grazzolie
- Department of Biology, Faculty of Life Science, Surya University, Tangerang, Banten 15143, Indonesia
| | - Rosmalena Rosmalena
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Depok 16424, Indonesia
| | - Fatmawaty Yazid
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Depok 16424, Indonesia
| | - Fransiskus Xaverius Ivan
- Department of Biology, Faculty of Life Science, Surya University, Tangerang, Banten 15143, Indonesia
| | - Ernawati Sinaga
- Faculty of Biology, Universitas Nasional, Jakarta 12520, Indonesia
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13
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Magnin M, Guillaume P, Coukos G, Harari A, Schmidt J. High-throughput identification of human antigen-specific CD8 + and CD4 + T cells using soluble pMHC multimers. Methods Enzymol 2019; 631:21-42. [PMID: 31948548 DOI: 10.1016/bs.mie.2019.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Peptide major histocompatibility complex (pMHC) multimers have been used since decades to identify, isolate and analyze antigen-specific T cells by flow (and more recently mass) cytometry. Yet well established as a standard technology, improvements are still required to face the growing needs of personalized immune monitoring. Here we review the latest developments about (i) the quality of pMHC class I and II monomers, (ii) the importance of the multimeric scaffold, (iii) the staining conditions and (iv) the high-throughput synthesis of pMHC monomers. Finally, innovative multiplexed, combinatorial strategies for parallel detection of antigen-specific T cells in a single sample are discussed.
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Affiliation(s)
- Morgane Magnin
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland.
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
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14
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Dhanda SK, Karosiene E, Edwards L, Grifoni A, Paul S, Andreatta M, Weiskopf D, Sidney J, Nielsen M, Peters B, Sette A. Predicting HLA CD4 Immunogenicity in Human Populations. Front Immunol 2018; 9:1369. [PMID: 29963059 PMCID: PMC6010533 DOI: 10.3389/fimmu.2018.01369] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/01/2018] [Indexed: 12/12/2022] Open
Abstract
Background Prediction of T cell immunogenicity is a topic of considerable interest, both in terms of basic understanding of the mechanisms of T cells responses and in terms of practical applications. HLA binding affinity is often used to predict T cell epitopes, since HLA binding affinity is a key requisite for human T cell immunogenicity. However, immunogenicity at the population it is complicated by the high level of variability of HLA molecules, potential other factors beyond HLA as well as the frequent lack of HLA typing data. To overcome those issues, we explored an alternative approach to identify the common characteristics able to distinguish immunogenic peptides from non-recognized peptides. Methods Sets of dominant epitopes derived from peer-reviewed published papers were used in conjunction with negative peptides from the same experiments/donors to train neural networks and generate an “immunogenicity score.” We also compared the performance of the immunogenicity score with previously described method for immunogenicity prediction based on HLA class II binding at the population level. Results The immunogenicity score was validated on a series of independent datasets derived from the published literature, representing 57 independent studies where immunogenicity in human populations was assessed by testing overlapping peptides spanning different antigens. Overall, these testing datasets corresponded to over 2,000 peptides and tested in over 1,600 different human donors. The 7-allele method prediction and the immunogenicity score were associated with similar performance [average area under the ROC curve (AUC) values of 0.703 and 0.702, respectively] while the combined methods reached an average AUC of 0.725. This increase in average AUC value is significant compared with the immunogenicity score (p = 0.0135) and a strong trend toward significance is observed when compared to the 7-allele method (p = 0.0938). The new immunogenicity score method is now freely available using CD4 T cell immunogenicity prediction tool on the Immune Epitope Database website (http://tools.iedb.org/CD4episcore). Conclusion The new immunogenicity score predicts CD4 T cell immunogenicity at the population level starting from protein sequences and with no need for HLA typing. Its efficacy has been validated in the context of different antigen sources, ethnicities, and disparate techniques for epitope identification.
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Affiliation(s)
- Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Edita Karosiene
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Lindy Edwards
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.,Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
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15
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Lopes MD, Oliveira FM, Coelho IEV, Passos MJF, Alves CC, Taranto AG, Júnior MC, Santos LL, Fonseca CT, Villar JAFP, Lopes DO. Epitopes rationally selected through computational analyses induce T‐cell proliferation in mice and are recognized by serum from individuals infected with
Schistosoma mansoni. Biotechnol Prog 2017; 33:804-814. [DOI: 10.1002/btpr.2463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/03/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Marcelo D. Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del‐Rei, Rua Sebastião Gonçalves CoelhoDivinópolis MG Brasil
| | - Flávio M. Oliveira
- Laboratório de Biologia Molecular, Universidade Federal de São João del‐Rei, Rua Sebastião Gonçalves CoelhoDivinópolis MG Brasil
| | - Ivan E. V. Coelho
- Laboratório de Química Farmacêutica, Universidade Federal de São João del‐ReiDivinópolis MGBrasil
| | - Maria J. F. Passos
- Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del‐ReiDivinópolis MG Brasil
| | - Clarice C. Alves
- Grupo de Pesquisa em Biologia Parasitária e Imunologia, Centro de Pesquisas René Rachou, Fundação Oswaldo CruzBelo Horizonte MG30190‐002 Brasil
| | - Alex G. Taranto
- Laboratório de Química Farmacêutica, Universidade Federal de São João del‐ReiDivinópolis MGBrasil
| | - Moacyr C. Júnior
- Laboratório de Química Farmacêutica, Universidade Federal de São João del‐ReiDivinópolis MGBrasil
| | - Luciana L. Santos
- Laboratório de Biologia Molecular, Universidade Federal de São João del‐Rei, Rua Sebastião Gonçalves CoelhoDivinópolis MG Brasil
| | - Cristina T. Fonseca
- Grupo de Pesquisa em Biologia Parasitária e Imunologia, Centro de Pesquisas René Rachou, Fundação Oswaldo CruzBelo Horizonte MG30190‐002 Brasil
| | - José A. F. P. Villar
- Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del‐ReiDivinópolis MG Brasil
| | - Débora O. Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del‐Rei, Rua Sebastião Gonçalves CoelhoDivinópolis MG Brasil
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16
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Kanduc D, Shoenfeld Y. From HBV to HPV: Designing vaccines for extensive and intensive vaccination campaigns worldwide. Autoimmun Rev 2016; 15:1054-1061. [DOI: 10.1016/j.autrev.2016.07.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 07/12/2016] [Indexed: 12/12/2022]
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17
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Malek Abrahimians E, Vander Elst L, Carlier VA, Saint-Remy JM. Thioreductase-Containing Epitopes Inhibit the Development of Type 1 Diabetes in the NOD Mouse Model. Front Immunol 2016; 7:67. [PMID: 26973647 PMCID: PMC4773585 DOI: 10.3389/fimmu.2016.00067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/12/2016] [Indexed: 01/01/2023] Open
Abstract
Autoreactive CD4+ T cells recognizing islet-derived antigens play a primary role in type 1 diabetes. Specific suppression of such cells therefore represents a strategic target for the cure of the disease. We have developed a methodology by which CD4+ T cells acquire apoptosis-inducing properties on antigen-presenting cells after cognate recognition of natural sequence epitopes. We describe here that inclusion of a thiol-disulfide oxidoreductase (thioreductase) motif within the flanking residues of a single MHC class II-restricted GAD65 epitope induces GAD65-specific cytolytic CD4+ T cells (cCD4+ T). The latter, obtained either in vitro or by active immunization, acquire an effector memory phenotype and lyse APCs by a Fas–FasL interaction. Furthermore, cCD4+ T cells eliminate by apoptosis activated bystander CD4+ T cells recognizing alternative epitopes processed by the same APC. Active immunization with a GAD65 class II-restricted thioreductase-containing T cell epitope protects mice from diabetes and abrogates insulitis. Passive transfer of in vitro-elicited cCD4+ T cells establishes that such cells are efficient in suppressing autoimmunity. These findings provide strong evidence for a new vaccination strategy to prevent type 1 diabetes.
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Affiliation(s)
- Elin Malek Abrahimians
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; ImCyse SA, Leuven, Belgium
| | - Luc Vander Elst
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; ImCyse SA, Leuven, Belgium
| | - Vincent A Carlier
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; ImCyse SA, Leuven, Belgium
| | - Jean-Marie Saint-Remy
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; ImCyse SA, Leuven, Belgium
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18
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Kanduc D. Measles virus hemagglutinin epitopes are potential hotspots for crossreactions with immunodeficiency-related proteins. Future Microbiol 2016; 10:503-15. [PMID: 25865190 DOI: 10.2217/fmb.14.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIMS Measles virus (MV) infection induces a protective immunity that is accompanied by a transient pathologic suppression of the immune system. This immunologic paradox remains unexplained in spite of the numerous hypotheses that have been advanced (i.e., cytokine production, soluble immunosuppressive factor, cell cycle block, signaling lymphocyte activation molecule receptor and MV infection of dendritic cells, among others). METHODS Searching for molecular link(s) between MV infection and host immunodeficiency, this study used the Immune Epitope DataBase to analyze the peptide sharing between the antigenic MV hemagglutinin (H) protein and human proteins associated with immunodeficiency. RESULTS It was found that the majority of MVH derived epitopes share several exact pentapeptide sequences with numerous human proteins involved in immune functions and immunodeficiency, such as B- and T-cell antigens, and complement components. CONCLUSION The data suggest that crossreactivity might contribute to our understanding of the link between MV immunogenicity and MV-induced immunosuppression, and highlight peptides unique to MV as a basis for developing effective and safe anti-MV vaccines.
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19
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Major histocompatibility complex linked databases and prediction tools for designing vaccines. Hum Immunol 2015; 77:295-306. [PMID: 26585361 DOI: 10.1016/j.humimm.2015.11.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/29/2015] [Accepted: 11/09/2015] [Indexed: 12/19/2022]
Abstract
Presently, the major histocompatibility complex (MHC) is receiving considerable interest owing to its remarkable role in antigen presentation and vaccine design. The specific databases and prediction approaches related to MHC sequences, structures and binding/nonbinding peptides have been aggressively developed in the past two decades with their own benchmarks and standards. Before using these databases and prediction tools, it is important to analyze why and how the tools are constructed along with their strengths and limitations. The current review presents insights into web-based immunological bioinformatics resources that include searchable databases of MHC sequences, epitopes and prediction tools that are linked to MHC based vaccine design, including population coverage analysis. In T cell epitope forecasts, MHC class I binding predictions are very accurate for most of the identified MHC alleles. However, these predictions could be further improved by integrating proteasome cleavage (in conjugation with transporter associated with antigen processing (TAP) binding) prediction, as well as T cell receptor binding prediction. On the other hand, MHC class II restricted epitope predictions display relatively low accuracy compared to MHC class I. To date, pan-specific tools have been developed, which not only deliver significantly improved predictions in terms of accuracy, but also in terms of the coverage of MHC alleles and supertypes. In addition, structural modeling and simulation systems for peptide-MHC complexes enable the molecular-level investigation of immune processes. Finally, epitope prediction tools, and their assessments and guidelines, have been presented to immunologist for the design of novel vaccine and diagnostics.
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20
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Capone G, Fasano C, Lucchese G, Calabrò M, Kanduc D. EBV-Associated Cancer and Autoimmunity: Searching for Therapies. Vaccines (Basel) 2015; 3:74-89. [PMID: 26344947 PMCID: PMC4494242 DOI: 10.3390/vaccines3010074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/12/2014] [Accepted: 01/27/2015] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) infects B-, T-, and NK cells and has been associated not only with a wide range of lymphoid malignancies but also with autoimmune diseases such as lupus erythematosus, rheumatoid arthritis and, in particular, multiple sclerosis. Hence, effective immunotherapeutic approaches to eradicate EBV infection might overthrow cancer and autoimmunity incidence. However, currently no effective anti-EBV immunotherapy is available. Here we use the concept that protein immunogenicity is allocated in rare peptide sequences and search the Epstein-Barr nuclear antigen 1 (EBNA1) sequence for peptides unique to the viral protein and absent in the human host. We report on a set of unique EBV EBNA1 peptides that might be used in designing peptide-based therapies able to specifically hitting the virus or neutralizing pathogenic autoantibodies.
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Affiliation(s)
- Giovanni Capone
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Candida Fasano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Guglielmo Lucchese
- Brain and Language Laboratory, Free University of Berlin, 14195 Berlin, Germany.
| | - Michele Calabrò
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
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Huber A, Diedrichs-Möhring M, Wildner G. Spontaneously relapsing-remitting experimental autoimmune uveitis in rats allows successful therapeutic oral tolerance induction in ongoing disease. Mol Immunol 2014; 63:215-26. [PMID: 25085538 DOI: 10.1016/j.molimm.2014.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/02/2014] [Accepted: 07/05/2014] [Indexed: 10/25/2022]
Abstract
Antigen-specific tolerance induction is a desired therapy for uveitis patients. Our relapsing-remitting rat model of experimental autoimmune uveitis (EAU) induced with IRBP peptide R14 enables us to test the effect of oral tolerance on the prevention of relapsing uveitis. We investigated several peptides overlapping the sequence of R14 for prevention and different doses of R14 for therapy to determine the tolerogenic epitope and the most effective therapeutic regimen for uveitis. Lewis rats were immunized with R14-CFA to induce EAU. Oral tolerance was induced prior to immunization (prevention) or after onset of EAU to prevent relapses (therapy). Therapeutic feeding was performed with high and/or low doses of oral antigen for clonal deletion of effector and induction of regulatory T cells. Uveitis was determined clinically and histologically; mesenteric lymph node (mLN) cells of tolerized rats were tested for surface markers, cytokines and Foxp3 expression. Preventive feeding of R14 and its major epitope R16, but none of the overlapping peptides significantly suppressed EAU and also prevented relapses, irrespective of their pathogenicity. Therapeutic feeding with R14 dramatically reduced relapses, while only the consecutive feeding of high and low-dose R14 had an ameliorating effect on the first course of disease. IL-10-producing T cells from mLN decreased after oral tolerization, and with R14-stimulation in vitro the TCRαβ+/Foxp3+ population increased in the low-dose fed group. No mLN population could be clearly assigned to successful oral tolerance induction during active autoimmune uveitis.
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Affiliation(s)
- Andrea Huber
- Section of Immunobiology, Department of Ophthalmology, Klinikum der Universität, Mathildenstr. 8, 80336 München, Germany
| | - Maria Diedrichs-Möhring
- Section of Immunobiology, Department of Ophthalmology, Klinikum der Universität, Mathildenstr. 8, 80336 München, Germany
| | - Gerhild Wildner
- Section of Immunobiology, Department of Ophthalmology, Klinikum der Universität, Mathildenstr. 8, 80336 München, Germany.
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The Peptide Network between Tetanus Toxin and Human Proteins Associated with Epilepsy. EPILEPSY RESEARCH AND TREATMENT 2014; 2014:236309. [PMID: 24982805 PMCID: PMC4058587 DOI: 10.1155/2014/236309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/24/2014] [Accepted: 05/13/2014] [Indexed: 11/17/2022]
Abstract
Sequence matching analyses show that Clostridium tetani neurotoxin shares numerous pentapeptides (68, including multiple occurrences) with 42 human proteins that, when altered, have been associated with epilepsy. Such a peptide sharing is higher than expected, nonstochastic, and involves tetanus toxin-derived epitopes that have been validated as immunopositive in the human host. Of note, an unexpected high level of peptide matching is found in mitogen-activated protein kinase 10 (MK10), a protein selectively expressed in hippocampal areas. On the whole, the data indicate a potential for cross-reactivity between the neurotoxin and specific epilepsy-associated proteins and may help evaluate the potential risk for epilepsy following immune responses induced by tetanus infection. Moreover, this study may contribute to clarifying the etiopathogenesis of the different types of epilepsy.
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23
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Predicting alloreactivity in transplantation. J Immunol Res 2014; 2014:159479. [PMID: 24868561 PMCID: PMC4020392 DOI: 10.1155/2014/159479] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/13/2014] [Indexed: 01/10/2023] Open
Abstract
Human leukocyte Antigen (HLA) mismatching leads to severe complications after solid-organ transplantation and hematopoietic stem-cell transplantation. The alloreactive responses underlying the posttransplantation complications include both direct recognition of allogeneic HLA by HLA-specific alloantibodies and T cells and indirect T-cell recognition. However, the immunogenicity of HLA mismatches is highly variable; some HLA mismatches lead to severe clinical B-cell- and T-cell-mediated alloreactivity, whereas others are well tolerated. Definition of the permissibility of HLA mismatches prior to transplantation allows selection of donor-recipient combinations that will have a reduced chance to develop deleterious host-versus-graft responses after solid-organ transplantation and graft-versus-host responses after hematopoietic stem-cell transplantation. Therefore, several methods have been developed to predict permissible HLA-mismatch combinations. In this review we aim to give a comprehensive overview about the current knowledge regarding HLA-directed alloreactivity and several developed in vitro and in silico tools that aim to predict direct and indirect alloreactivity.
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Lucchese G, Capone G, Kanduc D. Peptide sharing between influenza A H1N1 hemagglutinin and human axon guidance proteins. Schizophr Bull 2014; 40:362-75. [PMID: 23378012 PMCID: PMC3932078 DOI: 10.1093/schbul/sbs197] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epidemiologic data suggest that maternal microbial infections may cause fetal neurodevelopmental disorders, potentially increasing susceptibility to heavy psychopathologies such as schizophrenia, schizophreniform disorder, autism, pervasive developmental disorders, bipolar disorders, psychosis, epilepsy, language and speech disorders, and cognitive impairment in adult offspring. However, the molecular pathomechanisms underlying such a relationship are not clear. Here we analyze the potential role of the maternal immune response to viral infection in determining fetal brain injuries that increase the risk of neurological disorders in the adult. We use influenza infection as a disease model and human axon guidance pathway, a key process in the formation of neural network during midgestation, as a potential fetal target of immune insults. Specifically, we examined influenza A H1N1 hemagglutinin (HA), an antigenic viral protein, for amino acid sequence similarity to a random library of 188 axon guidance proteins. We obtain the results that (1) contrary to any theoretical expectations, 45 viral pentapeptide matches are distributed throughout a subset of 36 guidance molecules; (2) in 24 guidance proteins, the peptide sharing with HA antigen involves already experimentally validated influenza HA epitopes; and (3) most of the axon guidance vs HA peptide overlap is conserved among influenza A viral strains and subsets. Taken together, our data indicate that immune cross-reactivity between influenza HA and axon guidance molecules is possible and may well represent a pathologic mechanism capable of determining neurodevelopmental disruption in the fetus.
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Affiliation(s)
- Guglielmo Lucchese
- To whom correspondence should be addressed; tel: +39.080.544.3321, fax: +39.080.544.3317, e-mail:
| | - Giovanni Capone
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy
| | - Darja Kanduc
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy,To whom correspondence should be addressed; tel: +39.080.544.3321, fax: +39.080.544.3317, e-mail:
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25
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Spinosa JP, Kanduc D. Ovarian cancer: designing effective vaccines and specific diagnostic tools. Immunotherapy 2014; 6:35-41. [DOI: 10.2217/imt.13.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: Notwithstanding a renewed interest in the application of immunotherapy as an alternative to chemotherapy and radiotherapy for the treatment of ovarian cancer (OC), and in spite of the available knowledge about ovarian tumor-associated-antigens, the search for a vaccine against OC remains a scientific and clinical challenge. Likewise, immunodiagnostics can detect only a late stage of the disease. Thus, the development of new therapeutic and diagnostic options is highly desirable. Methods: Based on the low-similarity hypothesis, which supports the concept that immunogenicity is preferentially associated to sequences with no/low-similarity to the host proteome, and using Protein Information Resource peptide match program, we searched the ovarian tumor antigen CA125 for amino acid sequences unique to CA125 and absent in the remaining human proteins. Results & conclusion: We identified a set of 159 pentapeptides unique to CA125 that might be used to design specific and effective immunological tools for diagnosis and treatment of OC.
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Affiliation(s)
- Jean Pierre Spinosa
- Department Biosciences, Biotechnologies & Biopharmaceutics, University of Bari, Bari, Italy
- Faculty of Biology & Medicine, University of Lausanne, Lausanne, Switzerland
| | - Darja Kanduc
- Department Biosciences, Biotechnologies & Biopharmaceutics, University of Bari, Bari, Italy
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26
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Determining the breadth of the respiratory syncytial virus-specific T cell response. J Virol 2013; 88:3135-43. [PMID: 24371055 DOI: 10.1128/jvi.02139-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Respiratory syncytial virus (RSV) is the most common cause of viral lower respiratory tract infections in infants and children under the age of 5. Studies examining RSV infection in susceptible BALB/c mice indicate that both CD4 and CD8 T cells not only contribute to viral clearance but also facilitate RSV-induced disease. However, efforts to understand the mechanisms by which RSV-specific T cells mediate disease following acute RSV infection have been hampered by the lack of defined RSV-specific T cell epitopes. Using an overlapping peptide library spanning each of the RSV-derived proteins, intracellular cytokine staining for gamma interferon was utilized to identify novel RSV-specific CD4 and CD8 T cell epitopes. Five novel CD8 T cell epitopes were revealed within the RSV fusion (F) protein and glycoprotein (G). In addition, five previously unidentified CD4 T cell epitopes were discovered, including epitopes in the phosphoprotein (P), polymerase protein (L), M2-1 protein, and nucleoprotein (N). Though the initial CD4 T cell epitopes were 15 amino acids in length, synthesis of longer peptides increased the frequency of responding CD4 T cells. Our results indicate that CD4 T cell epitopes that are 17 amino acids in length result in more optimal CD4 T cell stimulation than the commonly used 15-mer peptides. IMPORTANCE Respiratory syncytial virus (RSV) is the leading cause of hospitalization for lower respiratory tract infection in children. T cells play a critical role in clearing an acute RSV infection, as well as contributing to RSV-induced disease. Here we examined the breadth of the RSV-specific T cell response, using for the first time an overlapping peptide library spanning the entire viral genome. We identified 5 new CD4 and 5 new CD8 T cell epitopes, including a CD8 T cell epitope within the G protein that was previously believed not to elicit a CD8 T cell response. Importantly, we also demonstrated that the use of longer, 17-mer peptides elicits a higher frequency of responding CD4 T cells than the more commonly used 15-mer peptides. Our results demonstrate the breadth of the CD4 and CD8 T cell response to RSV and demonstrate the importance of using longer peptides when stimulating CD4 T cell responses.
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27
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Schmidt J, Dojcinovic D, Guillaume P, Luescher I. Analysis, Isolation, and Activation of Antigen-Specific CD4(+) and CD8(+) T Cells by Soluble MHC-Peptide Complexes. Front Immunol 2013; 4:218. [PMID: 23908656 PMCID: PMC3726995 DOI: 10.3389/fimmu.2013.00218] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/15/2013] [Indexed: 11/24/2022] Open
Abstract
T cells constitute the core of adaptive cellular immunity and protect higher organisms against pathogen infections and cancer. Monitoring of disease progression as well as prophylactic or therapeutic vaccines and immunotherapies call for conclusive detection, analysis, and sorting of antigen-specific T cells. This is possible by means of soluble recombinant ligands for T cells, i.e., MHC class I-peptide (pMHC I) complexes for CD8(+) T cells and MHC class II-peptide (pMHC II) complexes for CD4(+) T cells and flow cytometry. Here we review major developments in the development of pMHC staining reagents and their diverse applications and discuss perspectives of their use for basic and clinical investigations.
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Affiliation(s)
- Julien Schmidt
- Ludwig Center, University of Lausanne, Epalinges, Switzerland
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28
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Holland CJ, Cole DK, Godkin A. Re-Directing CD4(+) T Cell Responses with the Flanking Residues of MHC Class II-Bound Peptides: The Core is Not Enough. Front Immunol 2013; 4:172. [PMID: 23847615 PMCID: PMC3696884 DOI: 10.3389/fimmu.2013.00172] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/14/2013] [Indexed: 11/17/2022] Open
Abstract
Recombinant αβ T cell receptors, expressed on T cell membranes, recognize short peptides presented at the cell surface in complex with MHC molecules. There are two main subsets of αβ T cells: CD8(+) T cells that recognize mainly cytosol-derived peptides in the context of MHC class I (pMHC-I), and CD4(+) T cells that recognize peptides usually derived from exogenous proteins presented by MHC class II (pMHC-II). Unlike the more uniform peptide lengths (usually 8-13mers) bound in the MHC-I closed groove, MHC-II presented peptides are of a highly variable length. The bound peptides consist of a core bound 9mer (reflecting the binding motif for the particular MHC-II type) but with variable peptide flanking residues (PFRs) that can extend from both the N- and C-terminus of the MHC-II binding groove. Although pMHC-I and pMHC-II play a virtually identical role during T cell responses (T cell antigen presentation) and are very similar in overall conformation, there exist a number of subtle but important differences that may govern the functional dichotomy observed between CD8(+) and CD4(+) T cells. Here, we provide an overview of the impact of structural differences between pMHC-I and pMHC-II and the molecular interactions with the T cell receptor including the functional importance of MHC-II PFRs. We consider how factors such as anatomical location, inflammatory milieu, and particular types of antigen presenting cell might, in theory, contribute to the quantitative (i.e., pMHC ligand frequency) as well as qualitative (i.e., variable PFR) nature of peptide epitopes, and hence offer a means of control and influence of a CD4(+) T cell response. Lastly, we review our recent findings showing how modifications to MHC-II PFRs can modify CD4(+) T cell antigen recognition. These findings may have novel applications for the development of CD4(+) T cell peptide vaccines and diagnostics.
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Affiliation(s)
| | - David K. Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Andrew Godkin
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Department of Integrated Medicine, University Hospital of Wales, Cardiff, UK
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29
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Capone G, Lucchese G, Calabrò M, Kanduc D. West Nile virus diagnosis and vaccination: using unique viral peptide sequences to evoke specific immune responses. Immunopharmacol Immunotoxicol 2012; 35:64-70. [DOI: 10.3109/08923973.2012.736521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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30
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Carlier VA, VanderElst L, Janssens W, Jacquemin MG, Saint-Remy JMR. Increased synapse formation obtained by T cell epitopes containing a CxxC motif in flanking residues convert CD4+ T cells into cytolytic effectors. PLoS One 2012; 7:e45366. [PMID: 23056200 PMCID: PMC3467281 DOI: 10.1371/journal.pone.0045366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 08/21/2012] [Indexed: 11/25/2022] Open
Abstract
The nature of MHC class II-binding epitopes not only determines the specificity of T cell responses, but may also alter effector cell functions. Cytolytic CD4+ T cells have been observed primarily in anti-viral responses, but very little is known about the conditions under which they can be elicited. Their potential as regulators of immune responses, however, deserves investigations. We describe here that inclusion of a thiol-disulfide oxidoreductase motif within flanking residues of class II-restricted epitopes results, both in vitro and in vivo, in elicitation of antigen-specific cytolytic CD4+ T cells through increased synapse formation. We show that both naïve and polarized CD4+ T cells, including Th17 cells, can be converted by cognate recognition of such modified epitopes. Cytolytic CD4+ T cells induce apoptosis on APCs by Fas-FasL interaction. These findings potentially open the way towards a novel form of antigen-specific immunosuppression.
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31
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Hatzioannou A, Alevizaki M, Carayanniotis G, Lymberi P. Fine epitope mapping within the pathogenic thyroglobulin peptide 2340-2359: minimal epitopes retaining antigenicity across various MHC haplotypes are not necessarily immunogenic. Immunology 2011; 135:245-53. [PMID: 22098450 DOI: 10.1111/j.1365-2567.2011.03538.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We have previously reported that the 20-mer peptide p2340 (amino acids 2340-2359), of human thyroglobulin (Tg) has the unique feature that it causes experimental autoimmune thyroiditis (EAT) in mouse strains bearing high-responder (HR) or low-responder (LR) MHC haplotypes in Tg-induced EAT. In this study, we have employed fine epitope mapping to examine whether this property of p2340 is the result of recognition of distinct or shared minimal T-cell epitopes in the context of HR or LR MHC class II molecules. Use of overlapping peptides showed that a core minimal 9-mer epitope (LTWVQTHIR, amino acids 2344-2352) was recognized by p2340-primed T cells from both HR (H2(k,s) ) and LR (H2(b,d) ) strains, whereas a second 9-mer epitope (HIRGFGGDP, amino acids 2350-2358) was antigenic only in H2(s) hosts. Truncation analysis of LTWVQTHIR and HIRGFGGDP peptides delineated them as the minimal epitopes recognized by p2340-primed T cells from the above strains. Subcutaneous challenge of all mouse strains with the 9-mer core peptide LTWVQTHIR in adjuvant elicited specific lymph node cell proliferative responses and mild EAT only in HR hosts, highlighting this sequence as a minimal pathogenic Tg peptide in EAT. The 9-mer peptide HIRGFGGDP was not found to be immunogenic in H2(s) hosts. These data demonstrate that minimal T-cell epitopes, defined as autoantigenic in hosts of various MHC haplotypes, are not intrinsically immunogenic. Activation of naive autoreactive T cells may require contributions from flanking residues within longer peptide sequences encompassing these epitopes.
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Jahn-Schmid B, Pickl WF, Bohle B. Interaction of allergens, major histocompatibility complex molecules, and T cell receptors: a 'ménage à trois' that opens new avenues for therapeutic intervention in type I allergy. Int Arch Allergy Immunol 2011; 156:27-42. [PMID: 21447957 DOI: 10.1159/000321904] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
T cells are major players in the initiation and perpetuation of the allergic immune response. In this review, we summarize the current knowledge on allergen recognition by T lymphocytes and address the components of the trimeric recognition complex: T cell receptors, major histocompatibility complex molecules, and allergen-derived peptides. Furthermore, possible implications of this scientific background for future therapeutic developments are discussed.
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Affiliation(s)
- Beatrice Jahn-Schmid
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria. beatrice.jahn-schmid @ meduniwien.ac.at
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33
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Lozano JM, Lesmes LP, Carreño LF, Gallego GM, Patarroyo ME. Development of designed site-directed pseudopeptide-peptido-mimetic immunogens as novel minimal subunit-vaccine candidates for malaria. Molecules 2010; 15:8856-89. [PMID: 21135800 PMCID: PMC6259129 DOI: 10.3390/molecules15128856] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Accepted: 10/28/2010] [Indexed: 11/16/2022] Open
Abstract
Synthetic vaccines constitute the most promising tools for controlling and preventing infectious diseases. When synthetic immunogens are designed from the pathogen native sequences, these are normally poorly immunogenic and do not induce protection, as demonstrated in our research. After attempting many synthetic strategies for improving the immunogenicity properties of these sequences, the approach consisting of identifying high binding motifs present in those, and then performing specific changes on amino-acids belonging to such motifs, has proven to be a workable strategy. In addition, other strategies consisting of chemically introducing non-natural constraints to the backbone topology of the molecule and modifying the α-carbon asymmetry are becoming valuable tools to be considered in this pursuit. Non-natural structural constraints to the peptide backbone can be achieved by introducing peptide bond isosters such as reduced amides, partially retro or retro-inverso modifications or even including urea motifs. The second can be obtained by strategically replacing L-amino-acids with their enantiomeric forms for obtaining both structurally site-directed designed immunogens as potential vaccine candidates and their Ig structural molecular images, both having immuno-therapeutic effects for preventing and controlling malaria.
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MESH Headings
- Animals
- Haplorhini
- Humans
- Malaria Vaccines/chemical synthesis
- Malaria Vaccines/chemistry
- Malaria Vaccines/immunology
- Malaria Vaccines/pharmacology
- Malaria, Falciparum/immunology
- Malaria, Falciparum/prevention & control
- Mice
- Mice, Inbred BALB C
- Peptidomimetics/chemical synthesis
- Peptidomimetics/chemistry
- Peptidomimetics/immunology
- Peptidomimetics/pharmacology
- Vaccines, Subunit/chemical synthesis
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
- Vaccines, Subunit/pharmacology
- Vaccines, Synthetic/chemistry
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/pharmacology
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Affiliation(s)
- José Manuel Lozano
- Fundación Instituto de Inmunología de Colombia (FIDIC), Universidad del Rosario and Universidad Nacional de Colombia, Bogotá DC, Colombia.
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Cecconi V, Moro M, Del Mare S, Sidney J, Bachi A, Longhi R, Sette A, Protti MP, Dellabona P, Casorati G. The CD4+ T-cell epitope-binding register is a critical parameter when generating functional HLA-DR tetramers with promiscuous peptides. Eur J Immunol 2010; 40:1603-16. [PMID: 20306469 DOI: 10.1002/eji.200940123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Detection of CD4(+) T cells specific for tumor-associated antigens is critical to investigate the spontaneous tumor immunosurveillance and to monitor immunotherapy protocols in patients. We investigated the ability of HLA-DR 1101 multimers to detect CD4(+) T cells specific for three highly promiscuous MAGE-A3 derived peptides: MAGE-A3(191-205) (p39), MAGE-A3(281-295) (p57) and MAGE-A3(286-300) (p58). Tetramers stained specific CD4(+) T cells only when loaded with p39, although all peptides activated the specific T cells when presented by plastic-bound HLA-DR 1101 monomers. This suggested that tetramer staining ability was determined by the mode rather than the affinity of peptide binding to HLA-DR 1101. We hypothesized that peptides should bear a single P1 anchor residue to bind all arms of the multimer in a homogeneous register to generate peptide-HLA-DR conformers with maximal avidity. Bioinformatics analysis indicated that p39 contained one putative P1 anchor residue, whereas the other two peptides contained multiple ones. Designing p57 and p58 analogues containing a single anchor residue generated HLA-DR 1101 tetramers that stained specific CD4(+) T cells. Producing HLA-DR 1101 monomers linked with the optimized MAGE-A3 analogues, but not with the original epitopes, further improved tetramer efficiency. Optimization of CD4(+) T-cell epitope-binding registers is thus critical to generate functional HLA-DR tetramers.
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Affiliation(s)
- Virginia Cecconi
- Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
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35
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36
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Knapp B, Omasits U, Bohle B, Maillere B, Ebner C, Schreiner W, Jahn-Schmid B. 3-Layer-based analysis of peptide-MHC interaction: in silico prediction, peptide binding affinity and T cell activation in a relevant allergen-specific model. Mol Immunol 2009; 46:1839-44. [PMID: 19232439 DOI: 10.1016/j.molimm.2009.01.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 01/08/2009] [Accepted: 01/09/2009] [Indexed: 10/21/2022]
Abstract
CD4+ T cells recognize peptides bound to major histocompatibility complex (MHC) class II molecules on the surface of antigen presenting cells by their T cell receptor (TCR). Using a well-characterized allergen-specific model we studied peptide/MHC (pMHC) interactions by combining computational methods with experimental analyses. A 12-mer and an 18-mer peptide, both containing the human leukocyte antigen (HLA)-DR1-restricted, immunodominant T cell epitope of Art v 1, the major mugwort pollen allergen, were compared. A Molecular Dynamics simulation for a real time of 20 ns using GROMACS was performed. To this aim, the peptides were modelled into the binding groove of HLA-DRB1*0101 using different amino acid substitution tools. Binding of synthetic peptides to purified HLA-DRB1*0101 molecules was analysed in competition assays. The potency of the peptides to activate Art v 1-specific T cells was assessed using oligo- and monoclonal Art v 1-specific T cell cultures expanded from mugwort allergic individuals. All approaches revealed that the 18-mer peptide possessed higher HLA DR affinity as compared to the 12-mer. Computer modelling indicated that a loop-like structure within the additional N-terminal peptide flanking region of the 18-mer contributed to the pMHC interaction. Our approach, to combine computational methods validated by experimental results, demonstrates that Molecular Dynamics simulation may be a useful tool for the prediction of pMHC interactions in the future with possible applications in T cell-based immunotherapy e.g. in Type I allergy.
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Affiliation(s)
- Bernhard Knapp
- Department for Biomedical Computersimulation and Bioinformatics, Medical University of Vienna, Austria.
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37
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Moran E, Simmons C, Chau NV, Luhn K, Wills B, Phuong Dung N, Thao LTT, Hien TT, Farrar J, Rowland-Jones S, Dong T. Preservation of a critical epitope core region is associated with the high degree of flaviviral cross-reactivity exhibited by a dengue-specific CD4+ T cell clone. Eur J Immunol 2008; 38:1050-1057. [PMID: 18383038 PMCID: PMC4333208 DOI: 10.1002/eji.200737699] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Dengue is a member of the Flaviviridae, a large group of related viruses some of which co-circulate in certain regions (e.g. dengue and Yellow fever in South America). Immune responses cross-reactive between different dengue serotypes are important in the pathogenesis of dengue disease but it is not known whether previous infection with one flavivirus might affect the clinical course of subsequent infections with other members of the family. CD4+ T cells have been shown to be important in the production of cytokines in response to dengue infection and can demonstrate significant epitope cross-reactivity. Here, we describe the generation and characterisation of CD4+ T cell clones from a patient experiencing acute dengue infection. These clones were DRB1*15+ and recognised epitope variants not only within other dengue viruses but certain other flaviviruses. This cross-reactivity was dependent upon the presence of a five-amino acid core region, consistent with structural observations of class II MHC binding to TCR demonstrating that only a subset of residues within an epitope bound to a class II molecule are "read out" by the TCR. This capacity of CD4+ T cell clones to recognise a given epitope despite considerable variation between viruses may be of pathological significance, particularly in regions where related viruses co-circulate.
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Affiliation(s)
- Edward Moran
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Cameron Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | | | - Kerstin Luhn
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Bridget Wills
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | - Nguyen Phuong Dung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | | | - Tran Tinh Hien
- Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | - Sarah Rowland-Jones
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
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Muixí L, Alvarez I, Jaraquemada D. Peptides presented in vivo by HLA-DR in thyroid autoimmunity. Adv Immunol 2008; 99:165-209. [PMID: 19117535 DOI: 10.1016/s0065-2776(08)00606-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The association of the major histocompatibility complex (MHC) genes with autoimmune diseases together with the ectopic expression of class II molecules by epithelial cells of the target tissue gives to these molecules a central role in the pathogenesis of the disease, in its regulation and in the persistence of the immune response in situ. HLA-DR molecules expressed by thyroid follicular cells in thyroid autoimmune diseases are compact molecules stably associated with peptides. The nature of these peptides is of vital importance in the understanding of the disease, since these MHC-II-peptide complexes are going to be recognized by both effector and regulatory T cells in situ. In this chapter, we review the current state of the analysis of naturally processed peptides presented by MHC class II molecules in the context of autoimmunity and we discuss our data of natural HLA-DR ligands eluted from Graves' disease affected thyroid glands, from where autoantigen-derived peptides have been identified.
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Affiliation(s)
- Laia Muixí
- Immunology Unit, Institut de Biotechnologia i Biomedicina, Universitat Autònoma de Barcelona, Campus de Bellaterra, Barcelona, Spain
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Differential role of gamma interferon in inhibiting pulmonary eosinophilia and exacerbating systemic disease in fusion protein-immunized mice undergoing challenge infection with respiratory syncytial virus. J Virol 2007; 82:2196-207. [PMID: 18094193 DOI: 10.1128/jvi.01949-07] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Secondary exposure to respiratory syncytial virus (RSV) can lead to immunopathology and enhanced disease in vaccinated individuals. Vaccination with individual RSV proteins influences the type of secondary RSV-specific immune response that develops upon challenge RSV infection, as well as the extent of immunopathology. RSV-specific memory CD4 T cells can directly contribute to immunopathology through their cytokine production. Immunization of BALB/c mice with a recombinant vaccinia virus (vv) expressing the attachment (G) protein of RSV results in pulmonary eosinophilia upon RSV challenge, whereas immunization of mice with a vv expressing the fusion (F) protein does not. We analyzed the CD4 T-cell response to an I-E(d)-restricted CD4 T-cell epitope within the F protein of RSV corresponding to amino acids 51 to 66 in an effort to better understand the similarities and differences in the immune response elicited by the G versus the F protein. Vaccination with the G protein induces a mixture of RSV G-specific Th1 and Th2 cells with a restricted T-cell receptor repertoire. In contrast, we demonstrate here that immunization with the F protein elicits a broad repertoire of RSV F-specific CD4 T cells that predominantly exhibit a Th1 phenotype. However, in the absence of gamma interferon (IFN-gamma), RSV F(51-66)-specific CD4 T cells secreted interleukin-5, and mice developed pulmonary eosinophilia after RSV challenge. IFN-gamma-deficient mice exhibited decreased weight loss compared to wild-type controls, suggesting that IFN-gamma exacerbates systemic disease. These data demonstrate that IFN-gamma can have both beneficial and detrimental effects during a secondary RSV infection.
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40
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Aggerbeck H, Madsen SM. Safety of ESAT-6. Tuberculosis (Edinb) 2006; 86:363-73. [PMID: 16352469 DOI: 10.1016/j.tube.2005.08.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 08/12/2005] [Accepted: 08/22/2005] [Indexed: 11/23/2022]
Abstract
A recombinant dimer of the Mycobacterium tuberculosis (MTb) 6 kDa early secreted antigenic target (ESAT-6) was produced in Lactococcus lactis. Pharmacodynamic and safety studies were carried out in guinea pigs, rats, mice and dogs with intradermal (id), subcutaneous (sc) and intravenous (iv) administration of the antigen. In contrast to tuberculin purified protein derivative (PPD) the recombinant dimer (rdESAT-6) was able to discriminate MTb infection from BCG vaccination in vivo. In guinea pigs sensitized by infection with MTb, 1 microg rdESAT-6 gave a mean delayed-type hypersensitivity (DTH) response of 22 mm, a significantly stronger reaction than in animals sensitised by the environmental mycobacteria M. kansasii, M. szulgai and M. marinum. rdESAT-6 proved to be a safe tuberculin reagent in a dose range of 1-1000 microg with no or only minor local reactions.
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Affiliation(s)
- Henrik Aggerbeck
- Statens Serum Institut, Department of Vaccine Development, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
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41
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Soeria-Atmadja D, Lundell T, Gustafsson MG, Hammerling U. Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning. Nucleic Acids Res 2006; 34:3779-93. [PMID: 16977698 PMCID: PMC1540723 DOI: 10.1093/nar/gkl467] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The placing of novel or new-in-the-context proteins on the market, appearing in genetically modified foods, certain bio-pharmaceuticals and some household products leads to human exposure to proteins that may elicit allergic responses. Accurate methods to detect allergens are therefore necessary to ensure consumer/patient safety. We demonstrate that it is possible to reach a new level of accuracy in computational detection of allergenic proteins by presenting a novel detector, Detection based on Filtered Length-adjusted Allergen Peptides (DFLAP). The DFLAP algorithm extracts variable length allergen sequence fragments and employs modern machine learning techniques in the form of a support vector machine. In particular, this new detector shows hitherto unmatched specificity when challenged to the Swiss-Prot repository without appreciable loss of sensitivity. DFLAP is also the first reported detector that successfully discriminates between allergens and non-allergens occurring in protein families known to hold both categories. Allergenicity assessment for specific protein sequences of interest using DFLAP is possible via ulfh@slv.se.
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Affiliation(s)
| | | | - M. G. Gustafsson
- Department of Engineering Sciences, Uppsala UniversityPO Box 534, SE-751 21 Uppsala, Sweden
- Department of Genetics and Pathology, Uppsala University, Rudbeck LaboratorySE-751 85 Uppsala, Sweden
- Correspondence may also be addressed to M. G. Gustafsson. Tel: +46 18 4713229; Fax: +46 18 555096; Present address: M. G. Gustafsson, Department of Medical Sciences, Uppsala University, Uppsala University Hospital, SE-751 85 Uppsala, Sweden
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42
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Durinovic-Belló I, Rosinger S, Olson JA, Congia M, Ahmad RC, Rickert M, Hampl J, Kalbacher H, Drijfhout JW, Mellins ED, Al Dahouk S, Kamradt T, Maeurer MJ, Nhan C, Roep BO, Boehm BO, Polychronakos C, Nepom GT, Karges W, McDevitt HO, Sønderstrup G. DRB1*0401-restricted human T cell clone specific for the major proinsulin73-90 epitope expresses a down-regulatory T helper 2 phenotype. Proc Natl Acad Sci U S A 2006; 103:11683-8. [PMID: 16868084 PMCID: PMC1544230 DOI: 10.1073/pnas.0603682103] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Recently, we have identified proinsulin (P-Ins)(73-90) as an immunodominant T cell epitope of HLA-DRB1*0401 (DR4) subjects with beta-islet cell autoimmunity and of HLA-DR4/CD4 double-transgenic mice immunized with human P-Ins. We have compared the fine specificities of one human CD4 T cell clone and two mouse T cell hybridoma clones recognizing this epitope, and, although these three clones all recognized the same core region (LALEGSLQK), there were major differences in how they interacted with the peptide (p)/HLA complex, reflecting the fact that human P-Ins is a foreign antigen in the mouse and an autoantigen in the type 1 diabetes patient. The human T cell clone was forkhead transcription factor 3 (Foxp3)-positive, a marker for regulatory T cell lineages, and secreted predominantly IL-5, IL-10, and low levels of IFNgamma in response to P-Ins(73-90). This finding is compatible with the previously detected regulatory cytokine pattern in subjects with beta-cell autoimmunity. However, added N- or C-terminal amino acids drastically changed HLA and tetramer binding capacity as well as T cell reactivity and the cytokine phenotype of the P-Ins(73-90)-specific human CD4 T cell clone, suggesting a potential for this P-Ins epitope as a target for therapeutic intervention in HLA-DR4-positive humans with beta-islet cell autoimmunity or recent-onset type 1 diabetes.
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Affiliation(s)
- Ivana Durinovic-Belló
- Department of Internal Medicine I, Division of Endocrinology, University of Ulm, D-89081 Ulm, Germany
- Departments of Microbiology and Immunology and
| | - Silke Rosinger
- Department of Internal Medicine I, Division of Endocrinology, University of Ulm, D-89081 Ulm, Germany
| | | | - Mauro Congia
- Departments of Microbiology and Immunology and
- Department of Biomedical Sciences and Biotechnology, University of Cagliari, I-09121 Cagliari, Italy
| | | | | | - Johannes Hampl
- Biomedical Research Division, Beckman Coulter, Inc., San Diego, CA 92196
| | - Hubert Kalbacher
- Medical Scientific Center, University of Tuebingen, D-72072 Tuebingen, Germany
| | - Jan W. Drijfhout
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands
| | | | - Sascha Al Dahouk
- Department of Internal Medicine I, Division of Endocrinology, University of Ulm, D-89081 Ulm, Germany
| | - Thomas Kamradt
- Institut of Immunology, Friedrich Schiller University Clinic, D-07740 Jena, Germany
| | - Markus J. Maeurer
- Department of Medical Microbiology, University of Mainz, D-55101 Mainz, Germany
| | - Carol Nhan
- Endocrine Genetics Laboratory, McGill University Health Center, Montreal, QC, Canada H3H 1P3; and
| | - Bart O. Roep
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands
| | - Bernhard O. Boehm
- Department of Internal Medicine I, Division of Endocrinology, University of Ulm, D-89081 Ulm, Germany
| | - Constantin Polychronakos
- Endocrine Genetics Laboratory, McGill University Health Center, Montreal, QC, Canada H3H 1P3; and
| | - Gerald T. Nepom
- Virginia Mason Research Center, Benaroya Research Institute, Seattle, WA 98101-2795
| | - Wolfram Karges
- Department of Internal Medicine I, Division of Endocrinology, University of Ulm, D-89081 Ulm, Germany
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Hattotuwagama CK, Toseland CP, Guan P, Taylor DJ, Hemsley SL, Doytchinova IA, Flower DR. Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique. J Chem Inf Model 2006; 46:1491-502. [PMID: 16711768 DOI: 10.1021/ci050380d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide-MHC binding affinity. The ISC-PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide-MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms--q2, SEP, and NC--ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).
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Kallinteris NL, Wu S, Lu X, Humphreys RE, von Hofe E, Xu M. Enhanced CD4+ T-cell response in DR4-transgenic mice to a hybrid peptide linking the Ii-Key segment of the invariant chain to the melanoma gp100(48-58) MHC class II epitope. J Immunother 2005; 28:352-8. [PMID: 16000953 DOI: 10.1097/01.cji.0000170362.45456.00] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Linking the Ii-Key functional group LRMK, through a simple polymethylene linker, to the melanoma gp100(48-58) MHC class II epitope significantly enhances the vaccine response to that epitope in DR4-IE transgenic mice. A homologous series of Ii-Key/gp100(46-58) hybrids was synthesized to test the influence of spacer length (between Ii-Key and the gp100(48-58) epitope) on in vivo enhancement of gp100(48-58)-specific CD4+ T-lymphocyte responses. As measured by IFN-gamma and IL-4 ELISPOT cytokine assays, the most effective vaccine hybrid was the one with a shorter linker between Ii-Key and the epitope. Mechanistic reasons for this observation are considered. This structure-activity relationship was seen with bulk and CD4+ purified T cells, and both primary and secondary in vitro restimulation assays. CFA augmented the IFN-gamma response and to a lesser extent the IL-4 response. CpG enhanced a strong IFN-gamma response, with a negligible IL-4 response. The 3- to 5-times enhancement of the total ELISPOT responses (number of spots x mean spot area) observed after vaccination with peptides consisting of an MHC class II epitope engineered into an Ii-Key hybrid indicates a potent vaccine effect. Such constructs can be applied to many diagnostic and therapeutic uses.
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45
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Schulze zur Wiesch J, Lauer GM, Day CL, Kim AY, Ouchi K, Duncan JE, Wurcel AG, Timm J, Jones AM, Mothe B, Allen TM, McGovern B, Lewis-Ximenez L, Sidney J, Sette A, Chung RT, Walker BD. Broad repertoire of the CD4+ Th cell response in spontaneously controlled hepatitis C virus infection includes dominant and highly promiscuous epitopes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2005; 175:3603-13. [PMID: 16148104 DOI: 10.4049/jimmunol.175.6.3603] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A vigorous hepatitis C virus (HCV)-specific Th cell response is regarded as essential to the immunological control of HCV viremia. The aim of this study was to comprehensively define the breadth and specificity of dominant HCV-specific CD4(+) T cell epitopes in large cohorts of subjects with chronic and spontaneously resolved HCV viremia. Following in vitro stimulation of PBMC, HCV-specific cell cultures from each subject were screened with an overlapping panel of synthetic 20-mer peptides spanning the entire HCV polyprotein. Of 22 subjects who spontaneously controlled HCV viremia, all recognized at least one of a group of six epitopes situated within the nonstructural (NS) proteins NS3, NS4, and NS5, each of which was detected by >30% of subjects, but most subjects recognized additional, more heterogeneous specificities. In contrast, none of the most frequently targeted epitopes was detected by >5% of persons with chronic infection. The most frequently recognized peptides showed promiscuous binding to multiple HLA-DR molecules in in vitro binding assays and were restricted by different HLA-DR molecules in functional assays in different persons. These data demonstrate that predominant CD4(+) T cell epitopes in persons with resolved HCV infection are preferentially located in the nonstructural proteins and are immunogenic in the context of multiple class II molecules. This comprehensive characterization of CD4(+) T cell epitopes in resolved HCV infection provides important information to facilitate studies of immunopathogenesis and HCV vaccine design and evaluation.
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Affiliation(s)
- Julian Schulze zur Wiesch
- Partners AIDS Research Center and Infectious Disease Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
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Cheunsuk S, Lian ZX, Yang GX, Gershwin ME, Gruen JR, Bowlus CL. Prss16 is not required for T-cell development. Mol Cell Biol 2005; 25:789-96. [PMID: 15632078 PMCID: PMC543420 DOI: 10.1128/mcb.25.2.789-796.2005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
PRSS16 is a serine protease expressed exclusively in cortical thymic epithelial cells (cTEC) of the thymus, suggesting that it plays a role in the processing of peptide antigens during the positive selection of T cells. Moreover, the human PRSS16 gene is encoded in a region near the class I major histocompatibility complex (MHC) that has been linked to type 1 diabetes mellitus susceptibility. The mouse orthologue Prss16 is conserved in genetic structure, sequence, and pattern of expression. To study the role of Prss16 in thymic development, we generated a deletion mutant of Prss16 and characterized T-lymphocyte populations and MHC class II expression on cortical thymic epithelial cells. Prss16-deficient mice develop normally, are fertile, and show normal thymic morphology, cellularity, and anatomy. The total numbers and frequencies of thymocytes and splenic T-cell populations did not differ from those of wild-type controls. Surface expression of MHC class II on cTEC was also similar in homozygous mutant and wild-type animals, and invariant chain degradation was not impaired by deletion of Prss16. These findings suggest that Prss16 is not required for quantitatively normal T-cell development.
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Affiliation(s)
- Saijai Cheunsuk
- Division of Gastroenterology, Department of Internal Medicine, UC Davis Medical Center, 4150 V St., PSSB 3500, Sacramento, CA 95817, USA
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Zavala-Ruiz Z, Strug I, Walker BD, Norris PJ, Stern LJ. A hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition. Proc Natl Acad Sci U S A 2004; 101:13279-84. [PMID: 15331779 PMCID: PMC516560 DOI: 10.1073/pnas.0403371101] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2004] [Indexed: 11/18/2022] Open
Abstract
T cells generally recognize peptide antigens bound to MHC proteins through contacts with residues found within or immediately flanking the seven- to nine-residue sequence accommodated in the MHC peptide-binding groove. However, some T cells require peptide residues outside this region for activation, the structural basis for which is unknown. Here, we have investigated a HIV Gag-specific T cell clone that requires an unusually long peptide antigen for activation. The crystal structure of a minimally antigenic 16-mer bound to HLA-DR1 shows that the peptide C-terminal region bends sharply into a hairpin turn as it exits the binding site, orienting peptide residues outside the MHC-binding region in position to interact with a T cell receptor. Peptide truncation and substitution studies show that both the hairpin turn and the extreme C-terminal residues are required for T cell activation. These results demonstrate a previously unrecognized mode of MHC-peptide-T cell receptor interaction.
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Affiliation(s)
- Zarixia Zavala-Ruiz
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Reche PA, Glutting JP, Zhang H, Reinherz EL. Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics 2004; 56:405-19. [PMID: 15349703 DOI: 10.1007/s00251-004-0709-7] [Citation(s) in RCA: 252] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Revised: 07/12/2004] [Indexed: 01/07/2023]
Abstract
We introduced previously an on-line resource, RANKPEP that uses position specific scoring matrices (PSSMs) or profiles for the prediction of peptide-MHC class I (MHCI) binding as a basis for CD8 T-cell epitope identification. Here, using PSSMs that are structurally consistent with the binding mode of MHC class II (MHCII) ligands, we have extended RANKPEP to prediction of peptide-MHCII binding and anticipation of CD4 T-cell epitopes. Currently, 88 and 50 different MHCI and MHCII molecules, respectively, can be targeted for peptide binding predictions in RANKPEP. Because appropriate processing of antigenic peptides must occur prior to major histocompatibility complex (MHC) binding, cleavage site prediction methods are important adjuncts for T-cell epitope discovery. Given that the C-terminus of most MHCI-restricted epitopes results from proteasomal cleavage, we have modeled the cleavage site from known MHCI-restricted epitopes using statistical language models. The RANKPEP server now determines whether the C-terminus of any predicted MHCI ligand may result from such proteasomal cleavage. Also implemented is a variability masking function. This feature focuses prediction on conserved rather than highly variable protein segments encoded by infectious genomes, thereby offering identification of invariant T-cell epitopes to thwart mutation as an immune evasion mechanism.
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Affiliation(s)
- Pedro A Reche
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.
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Hall FC, Visconti KC, Ahmad RC, Parry SL, Miltenburg AMM, McConnell HM, Mellins ED, Sønderstrup G. Cytokines elicited by T cell epitopes from a synovial autoantigen: altered peptide ligands can reduce interferon-gamma and interleukin-10 production. ARTHRITIS AND RHEUMATISM 2003; 48:2375-85. [PMID: 12905493 DOI: 10.1002/art.11132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To explore the cytokine responses associated with T cell epitopes from human cartilage glycoprotein 39 (HC gp-39) and the potential for modifying cytokine secretion using altered peptide ligands (APLs). METHODS Draining lymph node cells were harvested from HLA-DR*0401 transgenic mice that had been immunized with HC gp-39. Cytokine responses to 5 previously identified HLA-DR*0401-restricted HC gp-39 T cell epitopes were studied in vitro. The anchor and T cell receptor (TCR) contact residues of peptide 322-337 were identified, and this information was used to design alanine-substituted APLs. T cells were primed in vivo with wild-type peptide 322-337, restimulated with wild-type peptide or APLs, and the cytokine profiles were compared. RESULTS Restimulation with individual peptides elicited distinct cytokine profiles. HC gp-39 (peptide 322-337) elicited a dominant interferon-gamma (IFNgamma) response. Residues within the core (positions P1-P9) 322-337 peptide sequence were critical for T cell recognition. Surprisingly, the N-terminal flanking region was also important for recognition by 6 of 10 specific T cell hybridomas. Substitutions of charged TCR contact residues in the 322-337 core epitope (E332A and K335A) were associated with a significant reduction in the IFNgamma and interleukin-10 (IL-10) stimulation indices. Restimulation with peptides W325A and V326A was also associated with a trend toward reduced IFNgamma and IL-10 secretion. In contrast, restimulation with peptide D330N elicited cytokine profiles more comparable with those resulting from restimulation with wild-type peptide. CONCLUSION This study indicates that APLs of a proinflammatory HC gp-39 T cell epitope may be used to alter the cytokine response from a memory T cell population.
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Affiliation(s)
- Frances C Hall
- Stanford University School of medicine, 299 Campus Drive, Stanford, CA 94305, USA
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