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Kelly JJ, Bloodworth N, Shao Q, Shabanowitz J, Hunt D, Meiler J, Pires MM. A Chemical Approach to Assess the Impact of Post-translational Modification on MHC Peptide Binding and Effector Cell Engagement. ACS Chem Biol 2024; 19:1991-2001. [PMID: 39150956 PMCID: PMC11420952 DOI: 10.1021/acschembio.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
The human major histocompatibility complex (MHC) plays a pivotal role in the presentation of peptidic fragments from proteins, which can originate from self-proteins or from nonhuman antigens, such as those produced by viruses or bacteria. To prevent cytotoxicity against healthy cells, thymocytes expressing T cell receptors (TCRs) that recognize self-peptides are removed from circulation (negative selection), thus leaving T cells that recognize nonself-peptides. Current understanding suggests that post-translationally modified (PTM) proteins and the resulting peptide fragments they generate following proteolysis are largely excluded from negative selection; this feature means that PTMs can generate nonself-peptides that potentially contribute to the development of autoreactive T cells and subsequent autoimmune diseases. Although it is well-established that PTMs are prevalent in peptides present on MHCs, the precise mechanisms by which PTMs influence the antigen presentation machinery remain poorly understood. In the present work, we introduce chemical modifications mimicking PTMs on synthetic peptides. This is the first systematic study isolating the impact of PTMs on MHC binding and also their impact on TCR recognition. Our findings reveal various ways PTMs alter antigen presentation, which could have implications for tumor neoantigen presentation.
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Affiliation(s)
- Joey J Kelly
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Nathaniel Bloodworth
- Division of Clinical Pharmacology, Department of MedicineVanderbilt University Medical Center, Nashville, Tennessee 37240, United States
| | - Qianqian Shao
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Donald Hunt
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Jens Meiler
- Division of Clinical Pharmacology, Department of MedicineVanderbilt University Medical Center, Nashville, Tennessee 37240, United States
- Institute of Drug Discovery, Faculty of MedicineUniversity of Leipzig, Leipzig, SAC 04103, Germany
- Center for Structural Biology Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Marcos M Pires
- Department of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
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2
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Jiang D, Zhang J, Shen W, Sun Y, Wang Z, Wang J, Zhang J, Zhang G, Zhang G, Wang Y, Cai S, Zhang J, Wang Y, Liu R, Bai T, Sun Y, Yang S, Ma Z, Li Z, Li J, Ma C, Cheng L, Sun B, Yang K. DNA Vaccines Encoding HTNV GP-Derived Th Epitopes Benefited from a LAMP-Targeting Strategy and Established Cellular Immunoprotection. Vaccines (Basel) 2024; 12:928. [PMID: 39204051 PMCID: PMC11359959 DOI: 10.3390/vaccines12080928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
Vaccines has long been the focus of antiviral immunotherapy research. Viral epitopes are thought to be useful biomarkers for immunotherapy (both antibody-based and cellular). In this study, we designed a novel vaccine molecule, the Hantaan virus (HTNV) glycoprotein (GP) tandem Th epitope molecule (named the Gnc molecule), in silico. Subsequently, computer analysis was used to conduct a comprehensive and in-depth study of the various properties of the molecule and its effects as a vaccine molecule in the body. The Gnc molecule was designed for DNA vaccines and optimized with a lysosomal-targeting membrane protein (LAMP) strategy. The effects of GP-derived Th epitopes and multiepitope vaccines were initially verified in animals. Our research has resulted in the design of two vaccines based on effective antiviral immune targets. The effectiveness of molecular therapies has also been preliminarily demonstrated in silico and in laboratory animals, which lays a foundation for the application of a vaccines strategy in the field of antivirals.
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Affiliation(s)
- Dongbo Jiang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
- Department of Microbiology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China;
| | - Junqi Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Wenyang Shen
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Yubo Sun
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Zhenjie Wang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Jiawei Wang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Jinpeng Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Guanwen Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Gefei Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Yueyue Wang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Sirui Cai
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Jiaxing Zhang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Yongkai Wang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Ruibo Liu
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Tianyuan Bai
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Yuanjie Sun
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Shuya Yang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Zilu Ma
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Zhikui Li
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Jijin Li
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Chenjin Ma
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
| | - Linfeng Cheng
- Department of Microbiology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China;
| | - Baozeng Sun
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
- Yingtan Detachment, Jiangxi General Hospital, Chinese People’s Armed Police Force, Nanchang 330001, China
| | - Kun Yang
- Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (D.J.); (J.Z.); (W.S.); (Y.S.); (Z.W.); (J.W.); (J.Z.); (G.Z.); (G.Z.); (Y.W.); (S.C.); (J.Z.); (Y.W.); (R.L.); (T.B.); (Y.S.); (S.Y.); (Z.M.); (Z.L.); (J.L.); (C.M.)
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Flender D, Vilenne F, Adams C, Boonen K, Valkenborg D, Baggerman G. Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39152539 DOI: 10.1002/mas.21905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/19/2024]
Abstract
Immunopeptidomics is becoming an increasingly important field of study. The capability to identify immunopeptides with pivotal roles in the human immune system is essential to shift the current curative medicine towards personalized medicine. Throughout the years, the field has matured, giving insight into the current pitfalls. Nowadays, it is commonly accepted that generalizing shotgun proteomics workflows is malpractice because immunopeptidomics faces numerous challenges. While many of these difficulties have been addressed, the road towards the ideal workflow remains complicated. Although the presence of Posttranslational modifications (PTMs) in the immunopeptidome has been demonstrated, their identification remains highly challenging despite their significance for immunotherapies. The large number of unpredictable modifications in the immunopeptidome plays a pivotal role in the functionality and these challenges. This review provides a comprehensive overview of the current advancements in immunopeptidomics. We delve into the challenges associated with identifying PTMs within the immunopeptidome, aiming to address the current state of the field.
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Affiliation(s)
- Daniel Flender
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- Health Unit, VITO, Mol, Belgium
| | - Frédérique Vilenne
- Health Unit, VITO, Mol, Belgium
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- ImmuneSpec, Niel, Belgium
| | - Dirk Valkenborg
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Geert Baggerman
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
- ImmuneSpec, Niel, Belgium
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4
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Fasoulis R, Rigo MM, Lizée G, Antunes DA, Kavraki LE. APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. J Chem Inf Model 2024; 64:1730-1750. [PMID: 38415656 PMCID: PMC10936522 DOI: 10.1021/acs.jcim.3c01667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
The recognition of peptides bound to class I major histocompatibility complex (MHC-I) receptors by T-cell receptors (TCRs) is a determinant of triggering the adaptive immune response. While the exact molecular features that drive the TCR recognition are still unknown, studies have suggested that the geometry of the joint peptide-MHC (pMHC) structure plays an important role. As such, there is a definite need for methods and tools that accurately predict the structure of the peptide bound to the MHC-I receptor. In the past few years, many pMHC structural modeling tools have emerged that provide high-quality modeled structures in the general case. However, there are numerous instances of non-canonical cases in the immunopeptidome that the majority of pMHC modeling tools do not attend to, most notably, peptides that exhibit non-standard amino acids and post-translational modifications (PTMs) or peptides that assume non-canonical geometries in the MHC binding cleft. Such chemical and structural properties have been shown to be present in neoantigens; therefore, accurate structural modeling of these instances can be vital for cancer immunotherapy. To this end, we have developed APE-Gen2.0, a tool that improves upon its predecessor and other pMHC modeling tools, both in terms of modeling accuracy and the available modeling range of non-canonical peptide cases. Some of the improvements include (i) the ability to model peptides that have different types of PTMs such as phosphorylation, nitration, and citrullination; (ii) a new and improved anchor identification routine in order to identify and model peptides that exhibit a non-canonical anchor conformation; and (iii) a web server that provides a platform for easy and accessible pMHC modeling. We further show that structures predicted by APE-Gen2.0 can be used to assess the effects that PTMs have in binding affinity in a more accurate manner than just using solely the sequence of the peptide. APE-Gen2.0 is freely available at https://apegen.kavrakilab.org.
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Affiliation(s)
- Romanos Fasoulis
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Mauricio M. Rigo
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Gregory Lizée
- Department
of Melanoma Medical Oncology—Research, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Dinler A. Antunes
- Department
of Biology and Biochemistry, University
of Houston, Houston, Texas 77004, United States
| | - Lydia E. Kavraki
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
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Imani S, Tagit O, Pichon C. Neoantigen vaccine nanoformulations based on Chemically synthesized minimal mRNA (CmRNA): small molecules, big impact. NPJ Vaccines 2024; 9:14. [PMID: 38238340 PMCID: PMC10796345 DOI: 10.1038/s41541-024-00807-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Recently, chemically synthesized minimal mRNA (CmRNA) has emerged as a promising alternative to in vitro transcribed mRNA (IVT-mRNA) for cancer therapy and immunotherapy. CmRNA lacking the untranslated regions and polyadenylation exhibits enhanced stability and efficiency. Encapsulation of CmRNA within lipid-polymer hybrid nanoparticles (LPPs) offers an effective approach for personalized neoantigen mRNA vaccines with improved control over tumor growth. LPP-based delivery systems provide superior pharmacokinetics, stability, and lower toxicity compared to viral vectors, naked mRNA, or lipid nanoparticles that are commonly used for mRNA delivery. Precise customization of LPPs in terms of size, surface charge, and composition allows for optimized cellular uptake, target specificity, and immune stimulation. CmRNA-encoded neo-antigens demonstrate high translational efficiency, enabling immune recognition by CD8+ T cells upon processing and presentation. This perspective highlights the potential benefits, challenges, and future directions of CmRNA neoantigen vaccines in cancer therapy compared to Circular RNAs and IVT-mRNA. Further research is needed to optimize vaccine design, delivery, and safety assessment in clinical trials. Nevertheless, personalized LPP-CmRNA vaccines hold great potential for advancing cancer immunotherapy, paving the way for personalized medicine.
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Affiliation(s)
- Saber Imani
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China.
| | - Oya Tagit
- Institute of Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Chantal Pichon
- Center of Molecular Biophysics, CNRS, Orléans, France.
- ART-ARNm, National Institute of Health and Medical Research (Inserm) and University of Orléans, Orléans, France.
- Institut Universitaire de France, Paris, France.
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6
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Parizi FM, Marzella DF, Ramakrishnan G, ‘t Hoen PAC, Karimi-Jafari MH, Xue LC. PANDORA v2.0: Benchmarking peptide-MHC II models and software improvements. Front Immunol 2023; 14:1285899. [PMID: 38143769 PMCID: PMC10739464 DOI: 10.3389/fimmu.2023.1285899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
T-cell specificity to differentiate between self and non-self relies on T-cell receptor (TCR) recognition of peptides presented by the Major Histocompatibility Complex (MHC). Investigations into the three-dimensional (3D) structures of peptide:MHC (pMHC) complexes have provided valuable insights of MHC functions. Given the limited availability of experimental pMHC structures and considerable diversity of peptides and MHC alleles, it calls for the development of efficient and reliable computational approaches for modeling pMHC structures. Here we present an update of PANDORA and the systematic evaluation of its performance in modelling 3D structures of pMHC class II complexes (pMHC-II), which play a key role in the cancer immune response. PANDORA is a modelling software that can build low-energy models in a few minutes by restraining peptide residues inside the MHC-II binding groove. We benchmarked PANDORA on 136 experimentally determined pMHC-II structures covering 44 unique αβ chain pairs. Our pipeline achieves a median backbone Ligand-Root Mean Squared Deviation (L-RMSD) of 0.42 Å on the binding core and 0.88 Å on the whole peptide for the benchmark dataset. We incorporated software improvements to make PANDORA a pan-allele framework and improved the user interface and software quality. Its computational efficiency allows enriching the wealth of pMHC binding affinity and mass spectrometry data with 3D models. These models can be used as a starting point for molecular dynamics simulations or structure-boosted deep learning algorithms to identify MHC-binding peptides. PANDORA is available as a Python package through Conda or as a source installation at https://github.com/X-lab-3D/PANDORA.
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Affiliation(s)
- Farzaneh M. Parizi
- Medical BioSciences Department, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Dario F. Marzella
- Medical BioSciences Department, Radboud University Medical Center, Nijmegen, Netherlands
| | - Gayatri Ramakrishnan
- Medical BioSciences Department, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter A. C. ‘t Hoen
- Medical BioSciences Department, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Li C. Xue
- Medical BioSciences Department, Radboud University Medical Center, Nijmegen, Netherlands
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Goodson H, Kawahara R, Chatterjee S, Goncalves G, Fehring J, Purcell AW, Croft NP, Thaysen-Andersen M. Profound N-glycan remodelling accompanies MHC-II immunopeptide presentation. Front Immunol 2023; 14:1258518. [PMID: 38022636 PMCID: PMC10663315 DOI: 10.3389/fimmu.2023.1258518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Immunopeptidomics, the study of peptide antigens presented on the cell surface by the major histocompatibility complex (MHC), offers insights into how our immune system recognises self/non-self in health and disease. We recently discovered that hyper-processed (remodelled) N-glycans are dominant features decorating viral spike immunopeptides presented via MHC-class II (MHC-II) molecules by dendritic cells pulsed with SARS-CoV-2 spike protein, but it remains unknown if endogenous immunopeptides also undergo N-glycan remodelling. Taking a multi-omics approach, we here interrogate published MHC-II immunopeptidomics datasets of cultured monocyte-like (THP-1) and breast cancer-derived (MDA-MB-231) cell lines for overlooked N-glycosylated peptide antigens, which we compare to their source proteins in the cellular glycoproteome using proteomics and N-glycomics data from matching cell lines. Hyper-processed chitobiose core and paucimannosidic N-glycans alongside under-processed oligomannosidic N-glycans were found to prevalently modify MHC-II-bound immunopeptides isolated from both THP-1 and MDA-MB-231, while complex/hybrid-type N-glycans were (near-)absent in the immunopeptidome as supported further by new N-glycomics data generated from isolated MHC-II-bound peptides derived from MDA-MB-231 cells. Contrastingly, the cellular proteomics and N-glycomics data from both cell lines revealed conventional N-glycosylation rich in complex/hybrid-type N-glycans, which, together with the identification of key lysosomal glycosidases, suggest that MHC-II peptide antigen processing is accompanied by extensive N-glycan trimming. N-glycan remodelling appeared particularly dramatic for cell surface-located glycoproteins while less remodelling was observed for lysosomal-resident glycoproteins. Collectively, our findings indicate that both under- and hyper-processed N-glycans are prevalent features of endogenous MHC-II immunopeptides, an observation that demands further investigation to enable a better molecular-level understanding of immune surveillance.
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Affiliation(s)
- Hayley Goodson
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Sayantani Chatterjee
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
| | - Gabriel Goncalves
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Joshua Fehring
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nathan P. Croft
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
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Conundrum for Psoriasis and Thyroid Involvement. Int J Mol Sci 2023; 24:ijms24054894. [PMID: 36902323 PMCID: PMC10003398 DOI: 10.3390/ijms24054894] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Strategies concerning thyroid anomalies in patients confirmed with psoriasis, either on clinical level or molecular levels, and their genetic findings remain an open issue. Identification of the exact subgroup of individuals that are candidates to endocrine assessments is also controversial. Our purpose in this work was to overview clinical and pathogenic data concerning psoriasis and thyroid comorbidities from a dual perspective (dermatologic and endocrine). This was a narrative review of English literature between January 2016 and January 2023. We included clinically relevant, original articles with different levels of statistical evidence published on PubMed. We followed four clusters of conditions: thyroid dysfunction, autoimmunity, thyroid cancer, and subacute thyroiditis. A new piece of information in this field was the fact that psoriasis and autoimmune thyroid diseases (ATD) have been shown to be related to the immune-based side effects of modern anticancer drugs-namely, immune checkpoint inhibitors (ICP). Overall, we identified 16 confirmatory studies, but with heterogeneous data. Psoriatic arthritis had a higher risk of positive antithyroperoxidase antibodies (TPOAb) (25%) compared to cutaneous psoriasis or control. There was an increased risk of thyroid dysfunction versus control, and hypothyroidism was the most frequent type of dysfunction (subclinical rather than clinical), among thyroid anomalies correlated with >2-year disease duration, peripheral > axial and polyarticular involvement. With a few exceptions, there was a female predominance. Hormonal imbalance included, most frequently, low thyroxine (T4) and/or triiodothyronine (T3) with normal thyroid stimulating hormone (TSH), followed by high TSH (only one study had higher total T3). The highest ratio of thyroid involvement concerning dermatologic subtypes was 59% for erythrodermic psoriasis. Most studies found no correlation between thyroid anomalies and psoriasis severity. Statistically significant odds ratios were as follows: hypothyroidism: 1.34-1.38; hyperthyroidism: 1.17-1.32 (fewer studies than hypo); ATD: 1.42-2.05; Hashimoto's thyroiditis (HT): 1.47-2.09; Graves' disease: 1.26-1.38 (fewer studies than HT). A total of 8 studies had inconsistent or no correlations, while the lowest rate of thyroid involvement was 8% (uncontrolled studies). Other data included 3 studies on patients with ATD looking for psoriasis, as well as 1 study on psoriasis and thyroid cancer. ICP was shown to potentially exacerbate prior ATD and psoriasis or to induce them both de novo (5 studies). At the case report level, data showed subacute thyroiditis due to biological medication (ustekinumab, adalimumab, infliximab). Thyroid involvement in patients with psoriasis thus remained puzzling. We observed significant data that confirmed a higher risk of identifying positive antibodies and/or thyroid dysfunction, especially hypothyroidism, in these subjects. Awareness will be necessary to improve overall outcomes. The exact profile of individuals diagnosed with psoriasis who should be screened by the endocrinology team is still a matter of debate, in terms of dermatological subtype, disease duration, activity, and other synchronous (especially autoimmune) conditions.
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