1
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Hong N, Jiang D, Wang Z, Sun H, Luo H, Bao L, Song M, Kang Y, Hou T. TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. J Chem Inf Model 2024; 64:5016-5027. [PMID: 38920330 DOI: 10.1021/acs.jcim.4c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The intricate interaction between major histocompatibility complexes (MHCs) and antigen peptides with diverse amino acid sequences plays a pivotal role in immune responses and T cell activity. In recent years, deep learning (DL)-based models have emerged as promising tools for accelerating antigen peptide screening. However, most of these models solely rely on one-dimensional amino acid sequences, overlooking crucial information required for the three-dimensional (3-D) space binding process. In this study, we propose TransfIGN, a structure-based DL model that is inspired by our previously developed framework, Interaction Graph Network (IGN), and incorporates sequence information from transformers to predict the interactions between HLA-A*02:01 and antigen peptides. Our model, trained on a comprehensive data set containing 61,816 sequences with 9051 binding affinity labels and 56,848 eluted ligand labels, achieves an area under the curve (AUC) of 0.893 on the binary data set, better than state-of-the-art sequence-based models trained on larger data sets such as NetMHCpan4.1, ANN, and TransPHLA. Furthermore, when evaluated on the IEDB weekly benchmark data sets, our predictions (AUC = 0.816) are better than those of the recommended methods like the IEDB consensus (AUC = 0.795). Notably, the interaction weight matrices generated by our method highlight the strong interactions at specific positions within peptides, emphasizing the model's ability to provide physical interpretability. This capability to unveil binding mechanisms through intricate structural features holds promise for new immunotherapeutic avenues.
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Affiliation(s)
- Nanqi Hong
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Hao Luo
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lingjie Bao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mingli Song
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
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2
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Pereira ACL, Bezerra KS, Santos JLS, I N Oliveira J, Freire VN, Fulco UL. In silico approach of modified melanoma peptides and their immunotherapeutic potential. Phys Chem Chem Phys 2021; 23:2836-2845. [PMID: 33470998 DOI: 10.1039/d0cp05322h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Melanoma is a type of skin cancer with increasing incidence worldwide and high lethality. Conventional forms of treatment are not effective in advanced cancer stages. Hence, immunotherapeutic approaches have been tested to modulate immune response against tumor cells. Some vaccine models using tumor-associated antigens (TAAs) such as glycoprotein 100 (gp100) have been studied, but their expected effectiveness has not been shown until now. Antigen immunogenicity is a crucial point to improve the immune response, and therefore mutations are inserted in peptide sequences. It is possible to understand the interactions which occur between peptides and immune system molecules through computer simulation, and this is essential in order to guide efficient vaccine models. In this work, we have calculated the interaction binding energies of crystallographic data based on modified gp100 peptides and HLA-A*0201 using density functional theory (DFT) and the molecular fractionation with conjugated caps (MFCC) approach. Our results show the most relevant residue-residue interactions, the impact of three mutations in their binding sites, and the main HLA-A*0201 amino acids for peptide-HLA binding.
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Affiliation(s)
- A C L Pereira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
| | - K S Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
| | - J L S Santos
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
| | - J I N Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
| | - V N Freire
- Departamento de Física, Universidade Federal do Ceará, 60455-760, Fortaleza-CE, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
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3
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Szeto C, Bloom JI, Sloane H, Lobos CA, Fodor J, Jayasinghe D, Chatzileontiadou DSM, Grant EJ, Buckle AM, Gras S. Impact of HLA-DR Antigen Binding Cleft Rigidity on T Cell Recognition. Int J Mol Sci 2020; 21:ijms21197081. [PMID: 32992915 PMCID: PMC7582474 DOI: 10.3390/ijms21197081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 01/22/2023] Open
Abstract
The interaction between T cell receptor (TCR) and peptide (p)-Human Leukocyte Antigen (HLA) complexes is the critical first step in determining T cell responses. X-ray crystallographic studies of pHLA in TCR-bound and free states provide a structural perspective that can help understand T cell activation. These structures represent a static “snapshot”, yet the nature of pHLAs and their interactions with TCRs are highly dynamic. This has been demonstrated for HLA class I molecules with in silico techniques showing that some interactions, thought to stabilise pHLA-I, are only transient and prone to high flexibility. Here, we investigated the dynamics of HLA class II molecules by focusing on three allomorphs (HLA-DR1, -DR11 and -DR15) that are able to present the same epitope and activate CD4+ T cells. A single TCR (F24) has been shown to recognise all three HLA-DR molecules, albeit with different affinities. Using molecular dynamics and crystallographic ensemble refinement, we investigate the molecular basis of these different affinities and uncover hidden roles for HLA polymorphic residues. These polymorphisms were responsible for the widening of the antigen binding cleft and disruption of pHLA-TCR interactions, underpinning the hierarchy of F24 TCR binding affinity, and ultimately T cell activation. We expanded this approach to all available pHLA-DR structures and discovered that all HLA-DR molecules were inherently rigid. Together with in vitro protein stability and peptide affinity measurements, our results suggest that HLA-DR1 possesses inherently high protein stability, and low HLA-DM susceptibility.
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Affiliation(s)
- Christopher Szeto
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Joseph I. Bloom
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Hannah Sloane
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Christian A. Lobos
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - James Fodor
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| | - Dhilshan Jayasinghe
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Demetra S. M. Chatzileontiadou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Emma J. Grant
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Ashley M. Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
- Correspondence:
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4
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Joshi A, Kaushik V. In-Silico Proteomic Exploratory Quest: Crafting T-Cell Epitope Vaccine Against Whipple's Disease. Int J Pept Res Ther 2020; 27:169-179. [PMID: 32427224 PMCID: PMC7233679 DOI: 10.1007/s10989-020-10077-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 12/11/2022]
Abstract
Whipple’s disease is one of the rare maladies in terms of spread but very fatal one as it is linked with many disorders (like Gastroenteritis, Endocarditis etc.). Also, current regimens include less effective drugs which require long duration follows up. This exploratory study was conducted to commence the investigation for crafting multi target epitope vaccine against its bacterial pathogen Tropheryma whipplei. The modern bioinformatics tools like VaxiJen, NETMHCII PAN 3.2, ALLERGEN-FP, PATCH-DOCK, TOXIC-PRED, MHCPRED and IEDB were deployed, which makes the study more intensive in analyzing proteome of T. whipplei as these methods are based on robust result generating statistical algorithms ANN, HMM, and ML. This Immuno-Informatics approach leads us in the prediction of two epitopes: VLMVSAFPL and IRYLAALHL interacting with 4 and 6 HLA DRB1 alleles of MHC Class II respectively. VLMVSAFPL epitope is a part of DNA-directed RNA polymerase subunit beta, and IRYLAALHL epitope is a part of membranous protein insertase YidC of this bacterium. Molecular-Docking and Molecular-Simulation analysis yields the perfect interaction based on Atomic contact energy, binding scores along with RMSD values (0 to 1.5 Ǻ) in selection zone. The IEDB (Immune epitope database) population coverage analysis exhibits satisfactory relevance with respect to world population.
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Affiliation(s)
- Amit Joshi
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
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5
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Abstract
T cells recognize and respond to self antigens in both cancer and autoimmunity. One strategy to influence this response is to incorporate amino acid substitutions into these T cell-specific epitopes. This strategy is being reconsidered now with the goal of increasing time to regression with checkpoint blockade therapies in cancer and antigen-specific immunotherapies in autoimmunity. We discuss how these amino acid substitutions change the interactions with the MHC class I or II molecule and the responding T cell repertoire. Amino acid substitutions in epitopes that are the most effective in therapies bind more strongly to T cell receptor and/or MHC molecules and cross-react with the same repertoire of T cells as the natural antigen.
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Affiliation(s)
- Jill E Slansky
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19thAvenue, Aurora, CO 80045, USA.
| | - Maki Nakayama
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19thAvenue, Aurora, CO 80045, USA; Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, 1775 Aurora Court, Aurora, CO 80045, USA
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6
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Yang X, Xie S, Yang X, Cueva JC, Hou X, Tang Z, Yao H, Mo F, Yin S, Liu A, Lu X. Opportunities and Challenges for Antibodies against Intracellular Antigens. Am J Cancer Res 2019; 9:7792-7806. [PMID: 31695801 PMCID: PMC6831482 DOI: 10.7150/thno.35486] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Therapeutic antibodies are one most significant advances in immunotherapy, the development of antibodies against disease-associated MHC-peptide complexes led to the introduction of TCR-like antibodies. TCR-like antibodies combine the recognition of intracellular proteins with the therapeutic potency and versatility of monoclonal antibodies (mAb), offering an unparalleled opportunity to expand the repertoire of therapeutic antibodies available to treat diseases like cancer. This review details the current state of TCR-like antibodies and describes their production, mechanisms as well as their applications. In addition, it presents an insight on the challenges that they must overcome in order to become commercially and clinically validated.
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7
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Clancy-Thompson E, Devlin CA, Tyler PM, Servos MM, Ali LR, Ventre KS, Bhuiyan MA, Bruck PT, Birnbaum ME, Dougan SK. Altered Binding of Tumor Antigenic Peptides to MHC Class I Affects CD8 + T Cell-Effector Responses. Cancer Immunol Res 2018; 6:1524-1536. [PMID: 30352798 DOI: 10.1158/2326-6066.cir-18-0348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/03/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022]
Abstract
T-cell priming occurs when a naïve T cell recognizes cognate peptide-MHC complexes on an activated antigen-presenting cell. The circumstances of this initial priming have ramifications on the fate of the newly primed T cell. Newly primed CD8+ T cells can embark onto different trajectories, with some becoming short-lived effector cells and others adopting a tissue resident or memory cell fate. To determine whether T-cell priming influences the quality of the effector T-cell response to tumors, we used transnuclear CD8+ T cells that recognize the melanoma antigen TRP1 using TRP1high or TRP1low TCRs that differ in both affinity and fine specificity. From a series of altered peptide ligands, we identified a point mutation (K8) in a nonanchor residue that, when analyzed crystallographically and biophysically, destabilized the peptide interaction with the MHC binding groove. In vitro, the K8 peptide induced robust proliferation of both TRP1high and TRP1low CD8+ T cells but did not induce expression of PD-1. Cytokine production from K8-stimulated TRP1 cells was minimal, whereas cytotoxicity was increased. Upon transfer into B16 tumor-bearing mice, the reference peptide (TRP1-M9)- and K8-stimulated TRP1 cells were equally effective at controlling tumor growth but accomplished this through different mechanisms. TRP1-M9-stimulated cells produced more IFNγ, whereas K8-stimulated cells accumulated to higher numbers and were more cytotoxic. We, therefore, conclude that TCR recognition of weakly binding peptides during priming can skew the effector function of tumor-specific CD8+ T cells.
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Affiliation(s)
- Eleanor Clancy-Thompson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Christine A Devlin
- Department of Biological Engineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts
| | - Paul M Tyler
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mariah M Servos
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lestat R Ali
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Katherine S Ventre
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - M Aladdin Bhuiyan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patrick T Bruck
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts.
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
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8
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Lindgren C, Tyagi M, Viljanen J, Toms J, Ge C, Zhang N, Holmdahl R, Kihlberg J, Linusson A. Dynamics Determine Signaling in a Multicomponent System Associated with Rheumatoid Arthritis. J Med Chem 2018; 61:4774-4790. [PMID: 29727183 DOI: 10.1021/acs.jmedchem.7b01880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Strategies that target multiple components are usually required for treatment of diseases originating from complex biological systems. The multicomponent system consisting of the DR4 major histocompatibility complex type II molecule, the glycopeptide CII259-273 from type II collagen, and a T-cell receptor is associated with development of rheumatoid arthritis (RA). We introduced non-native amino acids and amide bond isosteres into CII259-273 and investigated the effect on binding to DR4 and the subsequent T-cell response. Molecular dynamics simulations revealed that complexes between DR4 and derivatives of CII259-273 were highly dynamic. Signaling in the overall multicomponent system was found to depend on formation of an appropriate number of dynamic intramolecular hydrogen bonds between DR4 and CII259-273, together with the positioning of the galactose moiety of CII259-273 in the DR4 binding groove. Interestingly, the system tolerated modifications at several positions in CII259-273, indicating opportunities to use analogues to increase our understanding of how rheumatoid arthritis develops and for evaluation as vaccines to treat RA.
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Affiliation(s)
- Cecilia Lindgren
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | - Mohit Tyagi
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | - Johan Viljanen
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | - Johannes Toms
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | - Changrong Ge
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics , Karolinska Institute , SE-171 77 Stockholm , Sweden
| | - Naru Zhang
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics , Karolinska Institute , SE-171 77 Stockholm , Sweden.,School of Pharmaceutical Science , Southern Medical University , Guangzhou , China
| | - Rikard Holmdahl
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics , Karolinska Institute , SE-171 77 Stockholm , Sweden.,School of Pharmaceutical Science , Southern Medical University , Guangzhou , China
| | - Jan Kihlberg
- Department of Chemistry-BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| | - Anna Linusson
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
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9
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Antunes DA, Abella JR, Devaurs D, Rigo MM, Kavraki LE. Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes. Curr Top Med Chem 2018; 18:2239-2255. [PMID: 30582480 PMCID: PMC6361695 DOI: 10.2174/1568026619666181224101744] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/29/2018] [Accepted: 12/08/2018] [Indexed: 12/26/2022]
Abstract
Understanding the mechanisms involved in the activation of an immune response is essential to many fields in human health, including vaccine development and personalized cancer immunotherapy. A central step in the activation of the adaptive immune response is the recognition, by T-cell lymphocytes, of peptides displayed by a special type of receptor known as Major Histocompatibility Complex (MHC). Considering the key role of MHC receptors in T-cell activation, the computational prediction of peptide binding to MHC has been an important goal for many immunological applications. Sequence- based methods have become the gold standard for peptide-MHC binding affinity prediction, but structure-based methods are expected to provide more general predictions (i.e., predictions applicable to all types of MHC receptors). In addition, structural modeling of peptide-MHC complexes has the potential to uncover yet unknown drivers of T-cell activation, thus allowing for the development of better and safer therapies. In this review, we discuss the use of computational methods for the structural modeling of peptide-MHC complexes (i.e., binding mode prediction) and for the structure-based prediction of binding affinity.
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Affiliation(s)
| | - Jayvee R. Abella
- Computer Science Department, Rice University, Houston, Texas, USA
| | - Didier Devaurs
- Computer Science Department, Rice University, Houston, Texas, USA
| | - Maurício M. Rigo
- School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Lydia E. Kavraki
- Computer Science Department, Rice University, Houston, Texas, USA
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10
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Capasso C, Magarkar A, Cervera-Carrascon V, Fusciello M, Feola S, Muller M, Garofalo M, Kuryk L, Tähtinen S, Pastore L, Bunker A, Cerullo V. A novel in silico framework to improve MHC-I epitopes and break the tolerance to melanoma. Oncoimmunology 2017; 6:e1319028. [PMID: 28932628 DOI: 10.1080/2162402x.2017.1319028] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/21/2022] Open
Abstract
Tolerance toward tumor antigens, which are shared by normal tissues, have often limited the efficacy of cancer vaccines. However, wild type epitopes can be tweaked to activate cross-reactive T-cell clones, resulting in antitumor activity. The design of these analogs (i.e., heteroclitic peptides) can be difficult and time-consuming since no automated in silico tools are available. Hereby we describe the development of an in silico framework to improve the selection of heteroclitic peptides. The Epitope Discovery and Improvement System (EDIS) was first validated by studying the model antigen SIINFEKL. Based on artificial neural network (ANN) predictions, we selected two mutant analogs that are characterized by an increased MHC-I binding affinity (SIINFAKL) or increased TCR stimulation (SIIWFEKL). Therapeutic vaccination using optimized peptides resulted in enhanced antitumor activity and against B16.OVA melanomas in vivo. The translational potential of the EDIS platform was further demonstrated by studying the melanoma-associated antigen tyrosinase related protein 2 (TRP2). Following therapeutic immunization with the EDIS-derived epitope SVYDFFAWL, a significant reduction in the growth of established B16.F10 tumors was observed, suggesting a break in the tolerance toward the wild type epitope. Finally, we tested a multi vaccine approach, demonstrating that combination of wild type and mutant epitopes targeting both TRP2 and OVA antigens increases the antitumor response. In conclusion, by taking advantage of available prediction servers and molecular dynamics simulations, we generated an innovative platform for studying the initial sequences and selecting lead candidates with improved immunological features. Taken together, EDIS is the first automated algorithm-driven platform to speed up the design of heteroclitic peptides that can be publicly queried online.
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Affiliation(s)
- Cristian Capasso
- Laboratory of Immunovirotherapy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Aniket Magarkar
- Centre for Drug Research at the Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
| | - Victor Cervera-Carrascon
- TILT Biotherapeutics, Helsinki, Finland.,Cancer Gene Therapy Group, Department of Oncology, Faculty of Medicine, University Helsinki, Helsinki, Finland
| | - Manlio Fusciello
- Laboratory of Immunovirotherapy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Sara Feola
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Martin Muller
- Department of Pharmacy - Center for Drug Research, Pharmaceutical Biology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Mariangela Garofalo
- Centre for Drug Research at the Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | | | - Siri Tähtinen
- Laboratory of Immunovirotherapy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Lucio Pastore
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy.,CEINGE-Biotecnologie Avanzate S.C. a R.L., Naples, Italy
| | - Alex Bunker
- Laboratory of Immunovirotherapy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Vincenzo Cerullo
- Laboratory of Immunovirotherapy, Drug Research Program, University of Helsinki, Helsinki, Finland
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11
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The Immunogenicity of HLA Class II Mismatches: The Predicted Presentation of Nonself Allo-HLA-Derived Peptide by the HLA-DR Phenotype of the Recipient Is Associated with the Formation of DSA. J Immunol Res 2017; 2017:2748614. [PMID: 28331856 PMCID: PMC5346368 DOI: 10.1155/2017/2748614] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 01/17/2017] [Accepted: 02/02/2017] [Indexed: 12/02/2022] Open
Abstract
The identification of permissible HLA class II mismatches can prevent DSA in mismatched transplantation. The HLA-DR phenotype of recipients contributes to DSA formation by presenting allo-HLA-derived peptides to T-helper cells, which induces the differentiation of B cells into plasma cells. Comparing the binding affinity of self and nonself allo-HLA-derived peptides for recipients' HLA class II antigens may distinguish immunogenic HLA mismatches from nonimmunogenic ones. The binding affinities of allo-HLA-derived peptides to recipients' HLA-DR and HLA-DQ antigens were predicted using the NetMHCIIpan 3.1 server. HLA class II mismatches were classified based on whether they induced DSA and whether self or nonself peptide was predicted to bind with highest affinity to recipients' HLA-DR and HLA-DQ. Other mismatch characteristics (eplet, hydrophobic, electrostatic, and amino acid mismatch scores and PIRCHE-II) were evaluated. A significant association occurred between DSA formation and the predicted HLA-DR presentation of nonself peptides (P = 0.0169; accuracy = 80%; sensitivity = 88%; specificity = 63%). In contrast, mismatch characteristics did not differ significantly between mismatches that induced DSA and the ones that did not, except for PIRCHE-II (P = 0.0094). This methodology predicts DSA formation based on HLA mismatches and recipients' HLA-DR phenotype and may identify permissible HLA mismatches to help optimize HLA matching and guide donor selection.
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Candia M, Kratzer B, Pickl WF. On Peptides and Altered Peptide Ligands: From Origin, Mode of Action and Design to Clinical Application (Immunotherapy). Int Arch Allergy Immunol 2016; 170:211-233. [PMID: 27642756 PMCID: PMC7058415 DOI: 10.1159/000448756] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
T lymphocytes equipped with clonotypic T cell antigen receptors (TCR) recognize immunogenic peptides only when presented in the context of their own major histocompatibility complex (MHC) molecules. Peptide loading to MHC molecules occurs in intracellular compartments (ER for class I and MIIC for class II molecules) and relies on the interaction of the respective peptides and peptide binding pockets on MHC molecules. Those peptide residues not engaged in MHC binding point towards the TCR screening for possible peptide MHC complex binding partners. Natural or intentional modification of both MHC binding registers and TCR interacting residues of peptides - leading to the formation of altered peptide ligands (APLs) - might alter the way peptides interact with TCRs and hence influence subsequent T cell activation events, and consequently T cell effector functions. This review article summarizes how APLs were detected and first described, current concepts of how APLs modify T cellular signaling, which biological mechanisms might force the generation of APLs in vivo, and how peptides and APLs might be used for the benefit of patients suffering from allergic or autoimmune diseases.
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Affiliation(s)
- Martín Candia
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Bernhard Kratzer
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Winfried F. Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Immunomodulation, Vienna, Austria
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Abstract
UNLABELLED Conjugate vaccines are known to be one of the most effective and safest types of vaccines against bacterial pathogens. Previously, vaccine biosynthesis has been performed by using N-linked glycosylation systems. However, the structural specificity of these systems for sugar substrates has hindered their application. Here, we report a novel protein glycosylation system (O-linked glycosylation via Neisseria meningitidis) that can transfer virtually any glycan to produce a conjugate vaccine. We successfully established this system in Shigella spp., avoiding the construction of an expression vector for polysaccharide synthesis. We further found that different protein substrates can be glycosylated using this system and that the O-linked glycosylation system can also effectively function in other Gram-negative bacteria, including some strains whose polysaccharide structure was not suitable for conjugation using the N-linked glycosylation system. The results from a series of animal experiments show that the conjugate vaccine produced by this O-linked glycosylation system offered a potentially protective antibody response. Furthermore, we elucidated and optimized the recognition motif, named MOOR, for the O-glycosyltransferase PglL. Finally, we demonstrated that the fusion of other peptides recognized by major histocompatibility complex class II around MOOR had no adverse effects on substrate glycosylation, suggesting that this optimized system will be useful for future vaccine development. Our results expand the glycoengineering toolbox and provide a simpler and more robust strategy for producing bioconjugate vaccines against a variety of pathogens. IMPORTANCE Recently, the rapid development of synthetic biology has allowed bioconjugate vaccines with N-linked protein glycosylation to become a reality. However, the difficulty of reestablishing the exogenous polysaccharide synthetic pathway in Escherichia coli hinders their application. Here, we show that an O-linked protein glycosylation system from Neisseria meningitidis, which has a lower structure specificity for sugar substrates, could be engineered directly in attenuated pathogens to produce effective conjugate vaccines. To facilitate the further design of next-generation bioconjugate vaccines, we optimized a novel short motif consisting of 8 amino acids that is sufficient for glycosylation. Our results expand the application potential of O-linked protein glycosylation and demonstrate a simpler and more robust strategy for producing bioconjugate vaccines against different pathogens. In the future, bacterial antigenic polysaccharides could be attached to major histocompatibility complex binding peptides to improve immunological memory or attached to protein subunit vaccine candidates to provide double immune stimulation.
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Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10. PLoS One 2016; 11:e0153939. [PMID: 27100390 PMCID: PMC4839630 DOI: 10.1371/journal.pone.0153939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 04/06/2016] [Indexed: 01/26/2023] Open
Abstract
Blockade of IL-10 signalling clears chronic viral and bacterial infections. Immunization together with blockade of IL-10 signalling or relatively low level of IL-10 further enhances viral and bacterial clearance. IL-10 functions through binding to interleukin 10 receptor (IL-10R). Here we showed that peptides P1 and P2 with the hydrophobic and hydrophilic pattern of the IL10R-binding helix in IL-10 could bind with either IL-10R1 or IL-10, and inhibit inflammatory signals with long duration and negligible cytotoxicity in vitro. Furthermore, P2 can enhance antigen specific CD8+ T cell responses in mice induced by the vaccine based on a long peptide of protein E7 in a human papillomavirus type 16.
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15
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Zuidscherwoude M, Göttfert F, Dunlock VME, Figdor CG, van den Bogaart G, van Spriel AB. The tetraspanin web revisited by super-resolution microscopy. Sci Rep 2015; 5:12201. [PMID: 26183063 PMCID: PMC4505338 DOI: 10.1038/srep12201] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 06/17/2015] [Indexed: 12/19/2022] Open
Abstract
The spatial organization of membrane proteins in the plasma membrane is critical for signal transduction, cell communication and membrane trafficking. Tetraspanins organize functional higher-order protein complexes called ‘tetraspanin-enriched microdomains (TEMs)’ via interactions with partner molecules and other tetraspanins. Still, the nanoscale organization of TEMs in native plasma membranes has not been resolved. Here, we elucidated the size, density and distribution of TEMs in the plasma membrane of human B cells and dendritic cells using dual color stimulated emission depletion (STED) microscopy. We demonstrate that tetraspanins form individual nanoclusters smaller than 120 nm and quantified that a single tetraspanin CD53 cluster contains less than ten CD53 molecules. CD53 and CD37 domains were adjacent to and displayed only minor overlap with clusters containing tetraspanins CD81 or CD82. Moreover, CD53 and CD81 were found in closer proximity to their partners MHC class II and CD19 than to other tetraspanins. Although these results indicate that tetraspanin domains are adjacently positioned in the plasma membrane, they challenge the current view of the tetraspanin web of multiple tetraspanin species organized into a single domain. This study increases the molecular understanding of TEMs at the nanoscale level which is essential for comprehending tetraspanin function in cell biology.
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Affiliation(s)
- Malou Zuidscherwoude
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Fabian Göttfert
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vera Marie E Dunlock
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annemiek B van Spriel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Lipson EJ, Sharfman WH, Chen S, McMiller TL, Pritchard TS, Salas JT, Sartorius-Mergenthaler S, Freed I, Ravi S, Wang H, Luber B, Sproul JD, Taube JM, Pardoll DM, Topalian SL. Safety and immunologic correlates of Melanoma GVAX, a GM-CSF secreting allogeneic melanoma cell vaccine administered in the adjuvant setting. J Transl Med 2015; 13:214. [PMID: 26143264 PMCID: PMC4491237 DOI: 10.1186/s12967-015-0572-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/11/2015] [Indexed: 02/04/2023] Open
Abstract
Background Limited adjuvant treatment options exist for patients with high-risk surgically resected melanoma. This first-in-human study investigated the safety, tolerability and immunologic correlates of Melanoma GVAX, a lethally irradiated granulocyte–macrophage colony stimulating factor (GM-CSF)-secreting allogeneic whole-cell melanoma vaccine, administered in the adjuvant setting. Methods Patients with stage IIB-IV melanoma were enrolled following complete surgical resection. Melanoma GVAX was administered intradermally once every 28 days for four cycles, at 5E7 cells/cycle (n = 3), 2E8 cells/cycle (n = 9), or 2E8 cells/cycle preceded by cyclophosphamide 200 mg/m2 to deplete T regulatory cells (Tregs; n = 8). Blood was collected before each vaccination and at 4 and 6 months after treatment initiation for immunologic studies. Vaccine injection site biopsies and additional blood samples were obtained 2 days after the 1st and 4th vaccines. Results Among 20 treated patients, 18 completed 4 vaccinations. Minimal treatment-related toxicity was observed. One patient developed vitiligo and patches of white hair during the treatment and follow-up period. Vaccine site biopsies demonstrated complex inflammatory infiltrates, including significant increases in eosinophils and PD-1+ lymphocytes from cycle 1 to cycle 4 (P < 0.05). Serum GM-CSF concentrations increased significantly in a dose-dependent manner 48 h after vaccination (P = 0.0086), accompanied by increased numbers of activated circulating monocytes (P < 0.0001) and decreased percentages of myeloid-derived suppressor cells among monocytes (CD14+ , CD11b+ , HLA-DR low or negative; P = 0.002). Cyclophosphamide did not affect numbers of circulating Tregs. No significant changes in anti-melanoma immunity were observed in peripheral T cells by interferon-gamma ELIPSOT, or immunoglobulins by serum Western blotting. Conclusion Melanoma GVAX was safe and tolerable in the adjuvant setting. Pharmacodynamic testing revealed complex vaccine site immune infiltrates and an immune-reactive profile in circulating monocytic cell subsets. These findings support the optimization of Melanoma GVAX with additional monocyte and dendritic cell activators, and the potential development of combinatorial treatment regimens with synergistic agents. Trial registration: NCT01435499 Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0572-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evan J Lipson
- Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, 1550 Orleans Street, Room 507, Baltimore, MD, 21287, USA.
| | - William H Sharfman
- Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
| | - Shuming Chen
- Department of Surgery, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Tracee L McMiller
- Department of Surgery, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Theresa S Pritchard
- Department of Surgery, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
| | - January T Salas
- Department of Surgery, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Susan Sartorius-Mergenthaler
- Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
| | - Irwin Freed
- Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
| | - Sowmya Ravi
- Department of Dermatology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Hao Wang
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Brandon Luber
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Janice Davis Sproul
- Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
| | - Janis M Taube
- Department of Dermatology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA. .,Department of Pathology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
| | - Suzanne L Topalian
- Department of Surgery, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
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17
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Abstract
One of the most consistent findings in multiple sclerosis (MS) is that development of MS is linked with carriage of the class II human leucocyte antigen (HLA) molecule HLA-DRB1*15:01; around 60 % of Caucasian MS patients carry this allele compared to 25-30 % of ethnically matched healthy individuals. However, other HLA molecules have also been linked to the development of MS. In this chapter, the association between different HLA types and susceptibility to MS will be reviewed, and other linkages between the carriage of specific HLA molecules and clinical and experimental findings in MS will be considered.
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Affiliation(s)
- Judith M Greer
- The University of Queensland, UQ Centre for Clinical Research, Building 71/918 Riyal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia.
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