1
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Viard M, O'hUigin C, Yuki Y, Bashirova AA, Collins DR, Urbach JM, Wolinsky S, Buchbinder S, Kirk GD, Goedert JJ, Michael NL, Haas DW, Deeks SG, Walker BD, Yu X, Carrington M. Impact of HLA class I functional divergence on HIV control. Science 2024; 383:319-325. [PMID: 38236978 DOI: 10.1126/science.adk0777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024]
Abstract
Heterozygosity of Human leukocyte antigen (HLA) class I genes is linked to beneficial outcomes after HIV infection, presumably through greater breadth of HIV epitope presentation and cytotoxic T cell response. Distinct allotype pairs, however, differ in the extent to which they bind shared sets of peptides. We developed a functional divergence metric that measures pairwise complementarity of allotype-associated peptide binding profiles. Greater functional divergence for pairs of HLA-A and/or HLA-B allotypes was associated with slower AIDS progression and independently with enhanced viral load control. The metric predicts immune breadth at the peptide level rather than gene level and redefines HLA heterozygosity as a continuum differentially affecting disease outcome. Functional divergence may affect response to additional infections, vaccination, immunotherapy, and other diseases where HLA heterozygote advantage occurs.
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Affiliation(s)
- Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - David R Collins
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jonathan M Urbach
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Steven Wolinsky
- Division of Infectious Diseases, Department of Medicine, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
- Department of Medicine, Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Gregory D Kirk
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xu Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
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2
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Wang Y, Fenyö D. Proteogenomics Reveal the Overexpression of HLA-I in Cancer. J Proteome Res 2023; 22:3625-3639. [PMID: 37857377 PMCID: PMC10629274 DOI: 10.1021/acs.jproteome.3c00491] [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: 08/06/2023] [Indexed: 10/21/2023]
Abstract
An accurate quantification of HLA class I gene expression is important in understanding the interplay with the tumor microenvironment of antitumor cytotoxic T cell activities. Because HLA-I sequences are highly variable, standard RNAseq and mass spectrometry-based quantification workflows using common genome and protein sequence references do not provide HLA-I allele specific quantifications. Here, we used personalized HLA-I nucleotide and protein reference sequences based on the subjects' HLA-I genotypes and surveyed tumor and adjacent normal samples from patients across nine cancer types. Mass spectrometry using data dependent acquisition data was validated to be sufficient to estimate HLA-A protein expression at the allele level. We found that HLA-I proteins were present in significantly higher levels in tumors compared to adjacent normal tissues from 41 to 63% of head and neck squamous cell carcinoma, uterine corpus endometrial carcinoma, and clear cell renal cell carcinoma patients, and this was driven by increased levels of HLA-I gene transcripts. Most immune cell types are universally enriched in HLA-I high tumors, while endothelial and neuronal cells showed divergent relationships with HLA-I. Pathway analysis revealed that tumor senescence and autophagy activity influence the level of HLA-I proteins in glioblastoma. Genes correlated to HLA-I protein expression are mostly the ones directly involved in HLA-I function in immune response and cell death, while glycosylation genes are exclusively co-expressed with HLA-I at the protein level.
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Affiliation(s)
- Ying Wang
- Institute
for Systems Genetics, NYU Grossman School
of Medicine, New York, New York 10016, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - David Fenyö
- Institute
for Systems Genetics, NYU Grossman School
of Medicine, New York, New York 10016, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
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3
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Czaja AJ. Introducing Molecular Chaperones into the Causality and Prospective Management of Autoimmune Hepatitis. Dig Dis Sci 2023; 68:4098-4116. [PMID: 37755606 PMCID: PMC10570239 DOI: 10.1007/s10620-023-08118-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
Molecular chaperones influence the immunogenicity of peptides and the activation of effector T cells, and their pathogenic roles in autoimmune hepatitis are unclear. Heat shock proteins are pivotal in the processing and presentation of peptides that activate CD8+ T cells. They can also induce regulatory B and T cells and promote immune tolerance. Tapasin and the transporter associated with antigen processing-binding protein influence the editing and loading of high-affinity peptides for presentation by class I molecules of the major histocompatibility complex. Their over-expression could enhance the autoimmune response, and their deficiency could weaken it. The lysosome-associated membrane protein-2a isoform in conjunction with heat shock cognate 70 supports the importation of cytosolic proteins into lysosomes. Chaperone-mediated autophagy can then process the peptides for activation of CD4+ T cells. Over-expression of autophagy in T cells may also eliminate negative regulators of their activity. The human leukocyte antigen B-associated transcript three facilitates the expression of class II peptide receptors, inhibits T cell apoptosis, prevents T cell exhaustion, and sustains the immune response. Immunization with heat shock proteins has induced immune tolerance in experimental models and humans with autoimmune disease by inducing regulatory T cells. Therapeutic manipulation of other molecular chaperones may promote T cell exhaustion and induce tolerogenic dendritic cells. In conclusion, molecular chaperones constitute an under-evaluated family of ancillary proteins that could affect the occurrence, severity, and outcome of autoimmune hepatitis. Clarification of their contributions to the immune mechanisms and clinical activity of autoimmune hepatitis could have therapeutic implications.
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Affiliation(s)
- Albert J Czaja
- Mayo Clinic College of Medicine and Science, 200 First Street S.W., Rochester, MN, 55905, USA.
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4
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Kaur A, Surnilla A, Zaitouna AJ, Mumphrey MB, Basrur V, Grigorova I, Cieslik M, Carrington M, Nesvizhskii AI, Raghavan M. Mass Spectrometric Profiling of HLA-B44 Peptidomes Provides Evidence for Tapasin-Mediated Tryptophan Editing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1298-1307. [PMID: 37737643 PMCID: PMC10592002 DOI: 10.4049/jimmunol.2300232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/29/2023] [Indexed: 09/23/2023]
Abstract
The extreme polymorphisms of HLA class I proteins result in structural variations in their peptide binding sites to achieve diversity in Ag presentation. External factors could independently constrict or alter HLA class I peptide repertoires. Such effects of the assembly factor tapasin were assessed for HLA-B*44:05 (Y116) and a close variant, HLA-B*44:02 (D116), which have low and high tapasin dependence, respectively, for their cell surface expression. Analyses of the HLA-B*44:05 peptidomes in the presence and absence of tapasin reveal that peptides with C-terminal tryptophans and higher predicted affinities are preferentially selected by tapasin, coincident with reduced frequencies of peptides with other C-terminal amino acids, including leucine. Comparisons of the HLA-B*44:05 and HLA-B*44:02 peptidomes indicate the expected structure-based alterations near the peptide C termini, but also C-terminal amino acid frequency and predicted affinity changes among the unique and shared peptide groups for B*44:02 and B*44:05. Overall, these findings indicate that the presence of tapasin and the tapasin dependence of assembly alter HLA class I peptide-binding preferences at the peptide C terminus. The particular C-terminal amino acid preferences that are altered by tapasin are expected to be determined by the intrinsic peptide-binding specificities of HLA class I allotypes. Additionally, the findings suggest that tapasin deficiency and reduced tapasin dependence expand the permissive affinities of HLA class I-bound peptides, consistent with prior findings that HLA class I allotypes with low tapasin dependence have increased breadth of CD8+ T cell epitope presentation and are more protective in HIV infections.
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Affiliation(s)
- Amanpreet Kaur
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Avrokin Surnilla
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anita J. Zaitouna
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael B. Mumphrey
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Irina Grigorova
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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5
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Olson E, Raghavan M. Major histocompatibility complex class I assembly within endolysosomal pathways. Curr Opin Immunol 2023; 84:102356. [PMID: 37379719 DOI: 10.1016/j.coi.2023.102356] [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: 12/11/2022] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 06/30/2023]
Abstract
Major histocompatibility complex class I (MHC class I) molecules facilitate subcellular immune surveillance by presenting peptides on the cell surface. MHC class I assembly with peptides generally happens in the endoplasmic reticulum (ER). Peptides are processed in the cytosol, transported into the ER, and assembled with MHC class I heavy and light chains. However, as many pathogens reside within multiple subcellular organelles, peptide sampling across non-cytosolic compartments is also important. MHC class I molecules internalize from the cell surface into endosomes and constitutively traffic between endosomes and the cell surface. Within endosomes, MHC class I molecules assemble with both exogenous and endogenous antigens processed within these compartments. Human MHC classI polymorphisms, well known to affect ER assembly modes, also influence endosomal assembly outcomes, an area of current interest to the field.
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Affiliation(s)
- Eli Olson
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicine, Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Graduate Program In Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
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6
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van Hateren A, Elliott T. Visualising tapasin- and TAPBPR-assisted editing of major histocompatibility complex class-I immunopeptidomes. Curr Opin Immunol 2023; 83:102340. [PMID: 37245412 DOI: 10.1016/j.coi.2023.102340] [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: 11/29/2022] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/30/2023]
Abstract
Which peptides are selected for presentation by major histocompatibility complex class-I (MHC-I) molecules is a key determinant of successful immune responses. Peptide selection is co-ordinated by the tapasin and TAP Binding PRotein (TAPBPR) proteins, which ensure MHC-I molecules preferentially acquire high-affinity-binding peptides. New structural analyses have offered insight into how tapasin achieves this function within the peptide-loading complex (PLC) (comprising the Transporter associated with Antigen Presentation (TAP) peptide transporter, tapasin-ERp57, MHC-I and calreticulin), and how TAPBPR performs a peptide editing function independently of other molecules. The new structures reveal nuances in how tapasin and TAPBPR interact with MHC-I, and how calreticulin and ERp57 complement tapasin to exploit the plasticity of MHC-I molecules to achieve peptide editing.
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Affiliation(s)
- Andy van Hateren
- Institute for Life Sciences and Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Building 85, Southampton SO17 1BJ, UK
| | - Tim Elliott
- Centre for Immuno-oncology and CAMS-Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK.
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7
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Silva NDSB, Souza ADS, Andrade HDS, Pereira RN, Castro CFB, Vince N, Limou S, Naslavsky MS, Zatz M, Duarte YADO, Mendes-Junior CT, Castelli EDC. Immunogenetics of HLA-B: SNP, allele, and haplotype diversity in populations from different continents and ancestry backgrounds. HLA 2023; 101:634-646. [PMID: 37005006 DOI: 10.1111/tan.15043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/04/2023]
Abstract
HLA-B is among the most variable gene in the human genome. This gene encodes a key molecule for antigen presentation to CD8+ T lymphocytes and NK cell modulation. Despite the myriad of studies evaluating its coding region (with an emphasis on exons 2 and 3), few studies evaluated introns and regulatory sequences in real population samples. Thus, HLA-B variability is probably underestimated. We applied a bioinformatics pipeline tailored for HLA genes on 5347 samples from 80 different populations, which includes more than 1000 admixed Brazilians, to evaluate the HLA-B variability (SNPs, indels, MNPs, alleles, and haplotypes) in exons, introns, and regulatory regions. We observed 610 variable sites throughout HLA-B; the most frequent variants are shared worldwide. However, the haplotype distribution is geographically structured. We detected 920 full-length haplotypes (exons, introns, and untranslated regions) encoding 239 different protein sequences. HLA-B gene diversity is higher in admixed populations and Europeans while lower in African ancestry individuals. Each HLA-B allele group is associated with specific promoter sequences. This HLA-B variation resource may improve HLA imputation accuracy and disease-association studies and provide evolutionary insights regarding HLA-B genetic diversity in human populations.
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Affiliation(s)
- Nayane Dos Santos Brito Silva
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Andreia da Silva Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
| | - Heloisa de Souza Andrade
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
| | - Raphaela Neto Pereira
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
| | - Camila Ferreira Bannwart Castro
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
- UniFSP, Centro Universitário Sudoeste Paulista, Itapetininga, São Paulo, Brazil
| | - Nicolas Vince
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Sophie Limou
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Michel Satya Naslavsky
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Celso Teixeira Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Erick da Cruz Castelli
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
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8
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Han L, Wu S, Zhang T, Peng W, Zhao M, Yue C, Wen W, Cai W, Li M, Wallny HJ, Avila DW, Mwangi W, Nair V, Ternette N, Guo Y, Zhao Y, Chai Y, Qi J, Liang H, Gao GF, Kaufman J, Liu WJ. A Wider and Deeper Peptide-Binding Groove for the Class I Molecules from B15 Compared with B19 Chickens Correlates with Relative Resistance to Marek's Disease. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:668-680. [PMID: 36695776 PMCID: PMC7614295 DOI: 10.4049/jimmunol.2200211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023]
Abstract
The chicken MHC is known to confer decisive resistance or susceptibility to various economically important pathogens, including the iconic oncogenic herpesvirus that causes Marek's disease (MD). Only one classical class I gene, BF2, is expressed at a high level in chickens, so it was relatively easy to discern a hierarchy from well-expressed thermostable fastidious specialist alleles to promiscuous generalist alleles that are less stable and expressed less on the cell surface. The class I molecule BF2*1901 is better expressed and more thermostable than the closely related BF2*1501, but the peptide motif was not simpler as expected. In this study, we confirm for newly developed chicken lines that the chicken MHC haplotype B15 confers resistance to MD compared with B19. Using gas phase sequencing and immunopeptidomics, we find that BF2*1901 binds a greater variety of amino acids in some anchor positions than does BF2*1501. However, by x-ray crystallography, we find that the peptide-binding groove of BF2*1901 is narrower and shallower. Although the self-peptides that bound to BF2*1901 may appear more various than those of BF2*1501, the structures show that the wider and deeper peptide-binding groove of BF2*1501 allows stronger binding and thus more peptides overall, correlating with the expected hierarchies for expression level, thermostability, and MD resistance. Our study provides a reasonable explanation for greater promiscuity for BF2*1501 compared with BF2*1901, corresponding to the difference in resistance to MD.
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Affiliation(s)
- Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- National Poultry Laboratory Animal Resource Center, Harbin 150001, China
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin 150069, China
| | - Shaolian Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Zhang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Weiyu Peng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Min Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Can Yue
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanxin Wen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Wenbo Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Min Li
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | | | - David W. Avila
- The Basel Institute for Immunology, Basel CH4001, Switzerland
| | - William Mwangi
- The Pirbright Institute, Pirbright GU24 0NF, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute, Pirbright GU24 0NF, United Kingdom
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Headington OX37BN, United Kingdom
| | - Yaxin Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Yingze Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Liang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Jim Kaufman
- The Basel Institute for Immunology, Basel CH4001, Switzerland
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Department of Veterinary Science, University of Cambridge, Cambridge CB3 0ES, United Kingdom
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - William J. Liu
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
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9
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Kaur A, Surnilla A, Zaitouna AJ, Basrur V, Mumphrey MB, Grigorova I, Cieslik M, Carrington M, Nesvizhskii AI, Raghavan M. Mass spectrometric profiling of HLA-B44 peptidomes provides evidence for tapasin-mediated tryptophan editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.530125. [PMID: 36909546 PMCID: PMC10002704 DOI: 10.1101/2023.02.26.530125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Activation of CD8 + T cells against pathogens and cancers involves the recognition of antigenic peptides bound to human leukocyte antigen (HLA) class-I proteins. Peptide binding to HLA class I proteins is coordinated by a multi-protein complex called the peptide loading complex (PLC). Tapasin, a key PLC component, facilitates the binding and optimization of HLA class I peptides. However, different HLA class I allotypes have variable requirements for tapasin for their assembly and surface expression. HLA-B*44:02 and HLA-B*44:05, which differ only at residue 116 of their heavy chain sequences, fall at opposite ends of the tapasin-dependency spectrum. HLA-B*44:02 (D116) is highly tapasin-dependent, whereas HLA-B*44:05 (Y116) is highly tapasinindependent. Mass spectrometric comparisons of HLA-B*4405 and HLA-B*44:02 peptidomes were undertaken to better understand the influences of tapasin upon HLA-B44 peptidome compositions. Analyses of the HLA-B*44:05 peptidomes in the presence and absence of tapasin reveal that peptides with the C-terminal tryptophan residues and those with higher predicted binding affinities are selected in the presence of tapasin. Additionally, when tapasin is present, C-terminal tryptophans are also more highly represented among peptides unique to B*44:02 and those shared between B*44:02 and B*44:05, compared with peptides unique to B*44:05. Overall, our findings demonstrate that tapasin influences the C-terminal composition of HLA class I-bound peptides and favors the binding of higher affinity peptides. For the HLA-B44 family, the presence of tapasin or high tapasin-dependence of an allotype results in better binding of peptides with C-terminal tryptophans, consistent with a role for tapasin in stabilizing an open conformation to accommodate bulky C-terminal residues.
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Affiliation(s)
- Amanpreet Kaur
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Avrokin Surnilla
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anita J. Zaitouna
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael B. Mumphrey
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Irina Grigorova
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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10
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Sun Y, Papadaki GF, Devlin CA, Danon JN, Young MC, Winters TJ, Burslem GM, Procko E, Sgourakis NG. Xeno interactions between MHC-I proteins and molecular chaperones enable ligand exchange on a broad repertoire of HLA allotypes. SCIENCE ADVANCES 2023; 9:eade7151. [PMID: 36827371 PMCID: PMC9956121 DOI: 10.1126/sciadv.ade7151] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/19/2023] [Indexed: 06/01/2023]
Abstract
Immunological chaperones tapasin and TAP binding protein, related (TAPBPR) play key roles in antigenic peptide optimization and quality control of nascent class I major histocompatibility complex (MHC-I) molecules. The polymorphic nature of MHC-I proteins leads to a range of allelic dependencies on chaperones for assembly and cell-surface expression, limiting chaperone-mediated peptide exchange to a restricted set of human leukocyte antigen (HLA) allotypes. Here, we demonstrate and characterize xeno interactions between a chicken TAPBPR ortholog and a complementary repertoire of HLA allotypes, relative to its human counterpart. We find that TAPBPR orthologs recognize empty MHC-I with broader allele specificity and facilitate peptide exchange by maintaining a reservoir of receptive molecules. Deep mutational scanning of human TAPBPR further identifies gain-of-function mutants, resembling the chicken sequence, which can enhance HLA-A*01:01 expression in situ and promote peptide exchange in vitro. These results highlight that polymorphic sites on MHC-I and chaperone surfaces can be engineered to manipulate their interactions, enabling chaperone-mediated peptide exchange on disease-relevant HLA alleles.
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Affiliation(s)
- Yi Sun
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Georgia F. Papadaki
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Christine A. Devlin
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61820, USA
| | - Julia N. Danon
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Michael C. Young
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Trenton J. Winters
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - George M. Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61820, USA
| | - Nikolaos G. Sgourakis
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
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11
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Lan BH, Becker M, Freund C. The mode of action of tapasin on major histocompatibility class I (MHC-I) molecules. J Biol Chem 2023; 299:102987. [PMID: 36758805 PMCID: PMC10040737 DOI: 10.1016/j.jbc.2023.102987] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Tapasin (Tsn) plays a critical role in antigen processing and presentation by major histocompatibility complex class I (MHC-I) molecules. The mechanism of Tsn-mediated peptide loading and exchange hinges on the conformational dynamics governing the interaction of Tsn and MHC-I with recent structural and functional studies pinpointing the critical sites of direct or allosteric regulation. In this review, we highlight these recent findings and relate them to the extensive molecular and cellular data that are available for these evolutionary interdependent proteins. Furthermore, allotypic differences of MHC-I with regard to the editing and chaperoning function of Tsn are reviewed and related to the mechanistic observations. Finally, evolutionary aspects of the mode of action of Tsn will be discussed, a short comparison with the Tsn-related molecule TAPBPR (Tsn-related protein) will be given, and the impact of Tsn on noncanonical MHC-I molecules will be described.
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Affiliation(s)
- By Huan Lan
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Moritz Becker
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany.
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12
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Olson E, Ceccarelli T, Raghavan M. Endo-lysosomal assembly variations among human leukocyte antigen class I (HLA class I) allotypes. eLife 2023; 12:e79144. [PMID: 36722462 PMCID: PMC9917446 DOI: 10.7554/elife.79144] [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: 03/31/2022] [Accepted: 01/13/2023] [Indexed: 02/02/2023] Open
Abstract
The extreme polymorphisms of human leukocyte antigen class I (HLA class I) proteins enable the presentation of diverse peptides to cytotoxic T lymphocytes. The canonical endoplasmic reticulum (ER) HLA class I assembly pathway enables presentation of cytosolic peptides, but effective intracellular surveillance requires multi-compartmental antigen sampling. Endo-lysosomes are generally sites of HLA class II assembly, but human monocytes and monocyte-derived dendritic cells (moDCs) also contain significant reserves of endo-lysosomal HLA class I molecules. We hypothesized variable influences of HLA class I polymorphisms upon outcomes of endo-lysosomal trafficking, as the stabilities and peptide occupancies of cell surface HLA class I molecules are variable. Consistent with this model, when the endo-lysosomal pH of moDCs is disrupted, HLA-B allotypes display varying propensities for reductions in surface expression, with HLA-B*08:01 or HLA-B*35:01 being among the most resistant or sensitive, respectively, among eight tested HLA-B allotypes. Perturbations of moDC endo-lysosomal pH result in accumulation of HLA-B*35:01 in LAMP1+ compartments and increase HLA-B*35:01 peptide receptivity. These findings reveal the intersection of the vacuolar cross-presentation pathway with a constitutive assembly pathway for some HLA-B allotypes. Notably, cross-presentation of epitopes derived from two soluble antigens was also more efficient for B*35:01 compared to B*08:01, even when matched for T cell response sensitivity, and more affected by cathepsin inhibition. Thus, HLA class I polymorphisms dictate the degree of endo-lysosomal assembly, which can supplement ER assembly for constitutive HLA class I expression and increase the efficiency of cross-presentation.
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Affiliation(s)
- Eli Olson
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
- Graduate Program in Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
| | - Theadora Ceccarelli
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
- Graduate Program in Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
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13
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Relationship of HLA-B alleles on susceptibility to and protection from HIV infection in Turkish population. North Clin Istanb 2023; 10:67-73. [PMID: 36910436 PMCID: PMC9996654 DOI: 10.14744/nci.2021.00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/19/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Many human leukocyte antigen (HLA)-B alleles are associated with an increased risk of Acquired Immune Deficiency Syndrome (AIDS) and Human Immunodeficiency Virus (HIV) progression; however, their distribution varies among different racial/ethnic groups. Abacavir used in the treatment of AIDS significantly increases the risk of hypersensitivity reactions in patients with HLA-B*57:01. The aim of this study was to determine the distribution of HIV-associated HLA-B subgroups (high and low resolution) and HLA-B*57:01 associated with Abacavir sensitivity in Turkiye. METHODS This retrospective case-control study consisted of 416 (F/M:111/305) HIV positive patients and 416 (F/M:111/305) healthy controls. HLA-B alleles were identified using Luminex based low-resolution method and further subgrouped by sequence-based high-resolution typing. RESULTS Our data showed that in patients with HIV-1 infection, HLA-B*15, *35, and *51 allele frequencies were higher, while the HLA-B*07, *14 and *55 allele frequencies were lower as compared to the controls. It was determined that HLA-B*15:01, *35:01, *35:08, and *51:01 alleles frequencies were higher in the patients with HIV-1 infection compared to the controls as HLA-B*07:02, *14:01, *44:01, and *55:01 allele frequencies were detected low. HLA-B*57:01 allele positivity, which is important in Abacavir hypersensitivity, was lower than controls, and this difference was not statistically significant. CONCLUSION Our results suggest that, HLA-B*07, *14, and *55 alleles and HLA-B*07:02, *14:01, *44:01, and *55:01 subgroups might have a protective effect, while HLA-B*15, *35, and *51 alleles and HLA-B*15:01, *35:01, *35:08, and *51:01 subgroups might play a role in susceptibility to HIV-1 infection.
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14
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Boulanger DSM, Douglas LR, Duriez PJ, Kang Y, Dalchau N, James E, Elliott T. Tapasin-mediated editing of the MHC I immunopeptidome is epitope specific and dependent on peptide off-rate, abundance, and level of tapasin expression. Front Immunol 2022; 13:956603. [PMID: 36389776 PMCID: PMC9659924 DOI: 10.3389/fimmu.2022.956603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Tapasin, a component of the major histocompatibility complex (MHC) I peptide loading complex, edits the repertoire of peptides that is presented at the cell surface by MHC I and thereby plays a key role in shaping the hierarchy of CD8+ T-cell responses to tumors and pathogens. We have developed a system that allows us to tune the level of tapasin expression and independently regulate the expression of competing peptides of different off-rates. By quantifying the relative surface expression of peptides presented by MHC I molecules, we show that peptide editing by tapasin can be measured in terms of “tapasin bonus,” which is dependent on both peptide kinetic stability (off-rate) and peptide abundance (peptide supply). Each peptide has therefore an individual tapasin bonus fingerprint. We also show that there is an optimal level of tapasin expression for each peptide in the immunopeptidome, dependent on its off-rate and abundance. This is important, as the level of tapasin expression can vary widely during different stages of the immune response against pathogens or cancer and is often the target for immune escape.
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Affiliation(s)
- Denise S. M. Boulanger
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- *Correspondence: Denise S. M. Boulanger, ; Tim Elliott,
| | - Leon R. Douglas
- Cancer Research UK (CR-UK) Protein Core Facility, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Patrick J. Duriez
- Cancer Research UK (CR-UK) Protein Core Facility, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Yoyel Kang
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Edd James
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tim Elliott
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- *Correspondence: Denise S. M. Boulanger, ; Tim Elliott,
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15
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Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation. Nat Commun 2022; 13:5470. [PMID: 36115831 PMCID: PMC9482634 DOI: 10.1038/s41467-022-33153-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/26/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractLoading of MHC-I molecules with peptide by the catalytic chaperone tapasin in the peptide loading complex plays a critical role in antigen presentation and immune recognition. Mechanistic insight has been hampered by the lack of detailed structural information concerning tapasin–MHC-I. We present here crystal structures of human tapasin complexed with the MHC-I molecule HLA-B*44:05, and with each of two anti-tapasin antibodies. The tapasin-stabilized peptide-receptive state of HLA-B*44:05 is characterized by distortion of the peptide binding groove and destabilization of the β2-microglobulin interaction, leading to release of peptide. Movements of the membrane proximal Ig-like domains of tapasin, HLA-B*44:05, and β2-microglobulin accompany the transition to a peptide-receptive state. Together this ensemble of crystal structures provides insights into a distinct mechanism of tapasin-mediated peptide exchange.
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16
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Müller IK, Winter C, Thomas C, Spaapen RM, Trowitzsch S, Tampé R. Structure of an MHC I–tapasin–ERp57 editing complex defines chaperone promiscuity. Nat Commun 2022; 13:5383. [PMID: 36104323 PMCID: PMC9474470 DOI: 10.1038/s41467-022-32841-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Adaptive immunity depends on cell surface presentation of antigenic peptides by major histocompatibility complex class I (MHC I) molecules and on stringent ER quality control in the secretory pathway. The chaperone tapasin in conjunction with the oxidoreductase ERp57 is crucial for MHC I assembly and for shaping the epitope repertoire for high immunogenicity. However, how the tapasin–ERp57 complex engages MHC I clients has not yet been determined at atomic detail. Here, we present the 2.7-Å crystal structure of a tapasin–ERp57 heterodimer in complex with peptide-receptive MHC I. Our study unveils molecular details of client recognition by the multichaperone complex and highlights elements indispensable for peptide proofreading. The structure of this transient ER quality control complex provides the mechanistic basis for the selector function of tapasin and showcases how the numerous MHC I allomorphs are chaperoned during peptide loading and editing. Adaptive immunity depends on cellular chaperone and quality control systems that are decisive for an effective presentation of foreign antigens via MHC I molecules. Here, the authors present the structure of a key chaperone-MHC I complex.
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17
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Halabi S, Kaufman J. New vistas unfold: Chicken MHC molecules reveal unexpected ways to present peptides to the immune system. Front Immunol 2022; 13:886672. [PMID: 35967451 PMCID: PMC9372762 DOI: 10.3389/fimmu.2022.886672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/07/2022] [Indexed: 11/27/2022] Open
Abstract
The functions of a wide variety of molecules with structures similar to the classical class I and class II molecules encoded by the major histocompatibility complex (MHC) have been studied by biochemical and structural studies over decades, with many aspects for humans and mice now enshrined in textbooks as dogma. However, there is much variation of the MHC and MHC molecules among the other jawed vertebrates, understood in the most detail for the domestic chicken. Among the many unexpected features in chickens is the co-evolution between polymorphic TAP and tapasin genes with a dominantly-expressed class I gene based on a different genomic arrangement compared to typical mammals. Another important discovery was the hierarchy of class I alleles for a suite of properties including size of peptide repertoire, stability and cell surface expression level, which is also found in humans although not as extreme, and which led to the concept of generalists and specialists in response to infectious pathogens. Structural studies of chicken class I molecules have provided molecular explanations for the differences in peptide binding compared to typical mammals. These unexpected phenomena include the stringent binding with three anchor residues and acidic residues at the peptide C-terminus for fastidious alleles, and the remodelling binding sites, relaxed binding of anchor residues in broad hydrophobic pockets and extension at the peptide C-terminus for promiscuous alleles. The first few studies for chicken class II molecules have already uncovered unanticipated structural features, including an allele that binds peptides by a decamer core. It seems likely that the understanding of how MHC molecules bind and present peptides to lymphocytes will broaden considerably with further unexpected discoveries through biochemical and structural studies for chickens and other non-mammalian vertebrates.
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Affiliation(s)
- Samer Halabi
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Jim Kaufman,
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18
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Walker-Sperling V, Digitale JC, Viard M, Martin MP, Bashirova A, Yuki Y, Ramsuran V, Kulkarni S, Naranbhai V, Li H, Anderson SK, Yum L, Clifford R, Kibuuka H, Ake J, Thomas R, Rowland-Jones S, Rek J, Arinaitwe E, Kamya M, Rodriguez-Barraquer I, Feeney ME, Carrington M. Genetic variation that determines TAPBP expression levels associates with the course of malaria in an HLA allotype-dependent manner. Proc Natl Acad Sci U S A 2022; 119:e2205498119. [PMID: 35858344 PMCID: PMC9303992 DOI: 10.1073/pnas.2205498119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022] Open
Abstract
HLA class I (HLA-I) allotypes vary widely in their dependence on tapasin (TAPBP), an integral component of the peptide-loading complex, to present peptides on the cell surface. We identified two single-nucleotide polymorphisms that regulate TAPBP messenger RNA (mRNA) expression in Africans, rs111686073 (G/C) and rs59097151 (A/G), located in an AP-2α transcription factor binding site and a microRNA (miR)-4486 binding site, respectively. rs111686073G and rs59097151A induced significantly higher TAPBP mRNA expression relative to the alternative alleles due to higher affinity for AP-2α and abrogation of miR-4486 binding, respectively. These variants associated with lower Plasmodium falciparum parasite prevalence and lower incidence of clinical malaria specifically among individuals carrying tapasin-dependent HLA-I allotypes, presumably by augmenting peptide loading, whereas tapasin-independent allotypes associated with relative protection, regardless of imputed TAPBP mRNA expression levels. Thus, an attenuated course of malaria may occur through enhanced breadth and/or magnitude of antigen presentation, an important consideration when evaluating vaccine efficacy.
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Affiliation(s)
- Victoria Walker-Sperling
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
| | - Jean C. Digitale
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, 94143
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Maureen P. Martin
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Arman Bashirova
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Yuko Yuki
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Smita Kulkarni
- Texas Biomedical Research Institute, Host Pathogen Interaction Program, San Antonio, Texas, 78227
| | - Vivek Naranbhai
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
- Dana Farber Cancer Institute, Department of Medical Oncology, Boston, Massachusetts, 02215
- MGH Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, 02114
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, 4041, South Africa
| | - Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Stephen K. Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Lauren Yum
- U.S. Military HIV Research Program,, Walter Reed Army Institute of Research, Silver Spring, Maryland, 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, 20817
| | - Robert Clifford
- U.S. Military HIV Research Program,, Walter Reed Army Institute of Research, Silver Spring, Maryland, 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, 20817
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Julie Ake
- U.S. Military HIV Research Program,, Walter Reed Army Institute of Research, Silver Spring, Maryland, 20910
| | - Rasmi Thomas
- U.S. Military HIV Research Program,, Walter Reed Army Institute of Research, Silver Spring, Maryland, 20910
| | - Sarah Rowland-Jones
- Viral Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University, Kampala, Uganda
| | | | - Margaret E. Feeney
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158
- Department of Pediatrics, University of California San Francisco, San Francisco, California, 94158
| | - Mary Carrington
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, 02139
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19
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Shirayanagi T, Kazaoka A, Watanabe K, Qu L, Sakamoto N, Hoshino T, Ito K, Aoki S. Weak complex formation of adverse drug reaction-associated HLAB57, B58, and B15 molecules. Toxicol In Vitro 2022; 82:105383. [PMID: 35568130 DOI: 10.1016/j.tiv.2022.105383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 10/18/2022]
Abstract
The combination of certain human leukocyte antigen (HLA) polymorphisms with administration of certain drugs shows a strong correlation with developing drug hypersensitivity. Examples of typical combinations are HLA-B*57:01 with abacavir and HLA-B*15:02 with carbamazepine. However, despite belonging to the same serotype, HLA-B*57:03 and HLA-B*15:01 are not associated with drug hypersensitivity. Recent studies have shown that several HLA polymorphisms are associated with multiple drugs rather than a single drug, all resulting in drug hypersensitivity. In this study, we compared the molecular structures and intracellular localization of HLA-B*57:01, HLA-B*58:01, and HLA-B*15:02, which pose risks for developing drug hypersensitivity, as well as HLA-B*57:03 and HLA-B*15:01 that do not present such risks. We found that HLA molecules posing risks have a low affinity for the subunit β2-microglobulin; notably, the weak hydrogen bond formed via Gln96 of the HLA molecule contributes to this behavior. We also clarified that these HLA molecules are easily accumulated in the endoplasmic reticulum, exhibiting a low expression on the cell surface. Considering that these hypersensitivity risk-associated HLA molecules form complexes with β2-microglobulin and peptides in the endoplasmic reticulum, we assumed that their low complex formation ability in the endoplasmic reticulum facilitates the interaction with multiple drugs.
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Affiliation(s)
- Tomohiro Shirayanagi
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-city, Chiba 260-8675, Japan
| | - Akira Kazaoka
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-city, Chiba 260-8675, Japan
| | - Kenji Watanabe
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-city, Chiba 260-8675, Japan
| | - Liang Qu
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-city, Chiba 260-8675, Japan
| | - Naoki Sakamoto
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-city, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-city, Chiba 260-8675, Japan
| | - Kousei Ito
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-city, Chiba 260-8675, Japan
| | - Shigeki Aoki
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-city, Chiba 260-8675, Japan.
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20
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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21
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The role of MHC I protein dynamics in tapasin and TAPBPR-assisted immunopeptidome editing. Curr Opin Immunol 2021; 70:138-143. [PMID: 34265495 DOI: 10.1016/j.coi.2021.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 11/23/2022]
Abstract
Major Histocompatibility Complex class I (MHC I) molecules are highly polymorphic, with allotypes differing in peptide binding preferences, and in their dependence upon tapasin for optimal peptide selection. The tapasin dependence of MHC allotypes is inversely correlated with their self-editing ability, and underpinned by conformational plasticity. Recently, TAPBPR has been shown to enhance MHC I assembly via a chaperone-like function, and by editing the peptide repertoire of some MHC I allotypes. Structural analysis has shown TAPBPR binding changes the conformation and dynamics of MHC I, with MHC protein dynamics likely to determine the prevailing TAPBPR function: generically enhancing MHC I assembly by stabilising highly dynamic peptide-empty MHC I; and by editing the peptide repertoire of highly dynamic MHC I allotypes.
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22
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Lan H, Abualrous ET, Sticht J, Fernandez LMA, Werk T, Weise C, Ballaschk M, Schmieder P, Loll B, Freund C. Exchange catalysis by tapasin exploits conserved and allele-specific features of MHC-I molecules. Nat Commun 2021; 12:4236. [PMID: 34244493 PMCID: PMC8271027 DOI: 10.1038/s41467-021-24401-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
The repertoire of peptides presented by major histocompatibility complex class I (MHC-I) molecules on the cell surface is tailored by the ER-resident peptide loading complex (PLC), which contains the exchange catalyst tapasin. Tapasin stabilizes MHC-I molecules and promotes the formation of stable peptide-MHC-I (pMHC-I) complexes that serve as T cell antigens. Exchange of suboptimal by high-affinity ligands is catalyzed by tapasin, but the underlying mechanism is still elusive. Here we analyze the tapasin-induced changes in MHC-I dynamics, and find the catalyst to exploit two essential features of MHC-I. First, tapasin recognizes a conserved allosteric site underneath the α2-1-helix of MHC-I, ‘loosening’ the MHC-I F-pocket region that accomodates the C-terminus of the peptide. Second, the scoop loop11–20 of tapasin relies on residue L18 to target the MHC-I F-pocket, enabling peptide exchange. Meanwhile, tapasin residue K16 plays an accessory role in catalysis of MHC-I allotypes bearing an acidic F-pocket. Thus, our results provide an explanation for the observed allele-specificity of catalyzed peptide exchange. Tapasin is part of the peptide loading complex necessary for presenting antigenic peptides on MHC-I for the induction of adaptive immunity. Here the authors show that tapasin interacts with MHC-I in both conserved and allele-specific regions to promote antigen presentation, with tapasin L18 and K16 residues both implicated in this molecular interaction.
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Affiliation(s)
- Huan Lan
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Esam T Abualrous
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Artificial Intelligence for the Sciences, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Jana Sticht
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Core Facility BioSupraMol, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Laura Maria Arroyo Fernandez
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tamina Werk
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christoph Weise
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Core Facility BioSupraMol, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martin Ballaschk
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Bernhard Loll
- Laboratory of Structural Biology, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.
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23
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Tregaskes CA, Kaufman J. Chickens as a simple system for scientific discovery: The example of the MHC. Mol Immunol 2021; 135:12-20. [PMID: 33845329 PMCID: PMC7611830 DOI: 10.1016/j.molimm.2021.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 01/07/2023]
Abstract
Chickens have played many roles in human societies over thousands of years, most recently as an important model species for scientific discovery, particularly for embryology, virology and immunology. In the last few decades, biomedical models like mice have become the most important model organism for understanding the mechanisms of disease, but for the study of outbred populations, they have many limitations. Research on humans directly addresses many questions about disease, but frank experiments into mechanisms are limited by practicality and ethics. For research into all levels of disease simultaneously, chickens combine many of the advantages of humans and of mice, and could provide an independent, integrated and overarching system to validate and/or challenge the dogmas that have arisen from current biomedical research. Moreover, some important systems are simpler in chickens than in typical mammals. An example is the major histocompatibility complex (MHC) that encodes the classical MHC molecules, which play crucial roles in the innate and adaptive immune systems. Compared to the large and complex MHCs of typical mammals, the chicken MHC is compact and simple, with single dominantly-expressed MHC molecules that can determine the response to infectious pathogens. As a result, some fundamental principles have been easier to discover in chickens, with the importance of generalist and specialist MHC alleles being the latest example.
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Affiliation(s)
- Clive A Tregaskes
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom; University of Edinburgh, Institute for Immunology and Infection Research, Ashworth Laboratories, Kings Buildings, Edinburgh, EH9 3FL, United Kingdom.
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24
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Aflalo A, Boyle LH. Polymorphisms in MHC class I molecules influence their interactions with components of the antigen processing and presentation pathway. Int J Immunogenet 2021; 48:317-325. [PMID: 34176210 DOI: 10.1111/iji.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
MHC class I (MHC-I) molecules undergo an intricate folding process in order to pick up antigenic peptide to present to the immune system. In recent years, the discovery of a new peptide editor for MHC-I has added an extra level of complexity in our understanding of how peptide presentation is regulated. On top of this, the incredible diversity in MHC-I molecules leads to significant variation in the interaction between MHC-I and components of the antigen processing and presentation pathway. Here, we review our current understanding regarding how polymorphisms in human leukocyte antigen class I molecules influence their interactions with key components of the antigen processing and presentation pathway. A deeper understanding of this may offer new insights regarding how apparently subtle variation in MHC-I can have a significant impact on susceptibility to disease.
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Affiliation(s)
- Aure Aflalo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, UK
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25
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Saikia A, Springer S. Peptide-MHC I complex stability measured by nanoscale differential scanning fluorimetry reveals molecular mechanism of thermal denaturation. Mol Immunol 2021; 136:73-81. [PMID: 34091103 DOI: 10.1016/j.molimm.2021.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/08/2021] [Accepted: 04/29/2021] [Indexed: 12/22/2022]
Abstract
Recombinant major histocompatibility complex class I molecules are used in diagnostic and therapeutic approaches in cancer immunotherapy, with many studies exploring their binding to antigenic peptides. Current techniques for kinetic peptide binding studies are hampered by high sample consumption, low throughput, interference with protein stability, and/or high background signal. Here, we validate nanoscale differential scanning fluorimetry (nanoDSF), a method using the tryptophan fluorescence of class I molecules, for class I/peptide binding, and we use it to determine the molecular mechanism of the thermal denaturation of HLA-A*02:01.
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Affiliation(s)
- Ankur Saikia
- Department of Life Science and Chemistry, Jacobs University Bremen, Germany
| | - Sebastian Springer
- Department of Life Science and Chemistry, Jacobs University Bremen, Germany.
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26
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Hafstrand I, Aflalo A, Boyle LH. Why TAPBPR? Implications of an additional player in MHC class I peptide presentation. Curr Opin Immunol 2021; 70:90-94. [PMID: 34052734 DOI: 10.1016/j.coi.2021.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The peptide editor TAPBPR is the newest member of the major histocompatibility complex class I (MHC-I) antigen processing and presentation pathway. Since 2013, studies have explored the functions and mechanisms of action of this tapasin homolog. Here, we review the key insights gained from structural studies of the TAPBPR:MHC-I complex and the involvement of the TAPBPR loop in peptide exchange. However, despite recent advances, the question still remains: why do we need TAPBPR? The recent appreciation that different MHC-I allotypes vary in their ability to interact with TAPBPR, together with a role for TAPBPR in alternative presentation pathways highlights that much remains unknown concerning the biological need for TAPBPR.
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Affiliation(s)
- Ida Hafstrand
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Aure Aflalo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom.
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27
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Jongsma MLM, Neefjes J, Spaapen RM. Playing hide and seek: Tumor cells in control of MHC class I antigen presentation. Mol Immunol 2021; 136:36-44. [PMID: 34082257 DOI: 10.1016/j.molimm.2021.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/07/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
MHC class I (MHC-I) molecules present a blueprint of the intracellular proteome to T cells allowing them to control infection or malignant transformation. As a response, pathogens and tumor cells often downmodulate MHC-I mediated antigen presentation to escape from immune surveillance. Although the fundamental rules of antigen presentation are known in detail, the players in this system are not saturated and new modules of regulation have recently been uncovered. Here, we update the understanding of antigen presentation by MHC-I molecules and how this can be exploited by tumors to prevent exposure of the intracellular proteome. This knowledge can provide new ways to improve immune responses against tumors and pathogens.
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Affiliation(s)
- M L M Jongsma
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - J Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - R M Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands.
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28
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Abualrous ET, Sticht J, Freund C. Major histocompatibility complex (MHC) class I and class II proteins: impact of polymorphism on antigen presentation. Curr Opin Immunol 2021; 70:95-104. [PMID: 34052735 DOI: 10.1016/j.coi.2021.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 01/01/2023]
Abstract
The major histocompatibility complex (MHC) loci are amongst the most polymorphic regions in the genomes of vertebrates. In the human population, thousands of MHC gene variants (alleles) exist that translate into distinct allotypes equipped with overlapping but unique peptide binding profiles. Understanding the differential structural and dynamic properties of MHC alleles and their interaction with critical regulators of peptide exchange bears the potential for more personalized strategies of immune modulation in the context of HLA-associated diseases.
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Affiliation(s)
- Esam T Abualrous
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.
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29
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Illing PT, van Hateren A, Darley R, Croft NP, Mifsud NA, King S, Kostenko L, Bharadwaj M, McCluskey J, Elliott T, Purcell AW. Kinetics of Abacavir-Induced Remodelling of the Major Histocompatibility Complex Class I Peptide Repertoire. Front Immunol 2021; 12:672737. [PMID: 34093574 PMCID: PMC8170132 DOI: 10.3389/fimmu.2021.672737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022] Open
Abstract
Abacavir hypersensitivity syndrome can occur in individuals expressing the HLA-B*57:01 major histocompatibility complex class I allotype when utilising the drug abacavir as a part of their anti-retroviral regimen. The drug is known to bind within the HLA-B*57:01 antigen binding cleft, leading to the selection of novel self-peptide ligands, thus provoking life-threatening immune responses. However, the sub-cellular location of abacavir binding and the mechanics of altered peptide selection are not well understood. Here, we probed the impact of abacavir on the assembly of HLA-B*57:01 peptide complexes. We show that whilst abacavir had minimal impact on the maturation or average stability of HLA-B*57:01 molecules, abacavir was able to differentially enhance the formation, selectively decrease the dissociation, and alter tapasin loading dependency of certain HLA-B*57:01-peptide complexes. Our data reveals a spectrum of abacavir mediated effects on the immunopeptidome which reconciles the heterogeneous functional T cell data reported in the literature.
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Affiliation(s)
- Patricia T. Illing
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Andy van Hateren
- Institute for Life Sciences and Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Rachel Darley
- Institute for Life Sciences and Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nathan P. Croft
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nicole A. Mifsud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Samuel King
- Institute for Life Sciences and Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Lyudmila Kostenko
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Mandvi Bharadwaj
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Tim Elliott
- Institute for Life Sciences and Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anthony W. Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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30
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Geng J, Raghavan M. Conformational sensing of major histocompatibility complex (MHC) class I molecules by immune receptors and intracellular assembly factors. Curr Opin Immunol 2021; 70:67-74. [PMID: 33857912 DOI: 10.1016/j.coi.2021.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Major histocompatibility complex class I (MHC-I) molecules play a critical role in both innate and adaptive immune responses. The heterodimeric complex of a polymorphic MHC-I heavy chain and a conserved light chain binds to a diverse set of peptides which are presented at the cell surface. Peptide-free (empty) versions of MHC-I molecules are typically retained intracellularly due to their low stability and bound by endoplasmic reticulum chaperones and assembly factors. However, emerging evidence suggests that at least some MHC-I allotypes are relatively stable and detectable at the cell-surface as peptide-deficient conformers, under some conditions. Such MHC-I conformers interact with multiple immune receptors to mediate various immunological functions. Furthermore, conformational sensing of MHC-I molecules by intracellular assembly factors and endoplasmic reticulum chaperones influences the peptide repertoire, with profound consequences for immunity. In this review, we discuss recent advances relating to MHC-I conformational variations and their pathophysiological implications.
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Affiliation(s)
- Jie Geng
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
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31
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Wei X, Wang S, Li Z, Li Z, Qu Z, Wang S, Zou B, Liang R, Xia C, Zhang N. Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism. Front Immunol 2021; 12:592447. [PMID: 33717070 PMCID: PMC7952875 DOI: 10.3389/fimmu.2021.592447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/13/2021] [Indexed: 01/24/2023] Open
Abstract
The micropolymorphism of major histocompatibility complex class I (MHC-I) can greatly alter the plasticity of peptide presentation, but elucidating the underlying mechanism remains a challenge. Here we investigated the impact of the micropolymorphism on peptide presentation of swine MHC-I (termed swine leukocyte antigen class I, SLA-I) molecules via immunopeptidomes that were determined by our newly developed random peptide library combined with the mass spectrometry (MS) de novo sequencing method (termed RPLD–MS) and the corresponding crystal structures. The immunopeptidomes of SLA-1*04:01, SLA-1*13:01, and their mutants showed that mutations of residues 156 and 99 could expand and narrow the ranges of peptides presented by SLA-I molecules, respectively. R156A mutation of SLA-1*04:01 altered the charge properties and enlarged the volume size of pocket D, which eliminated the harsh restriction to accommodate the third (P3) anchor residue of the peptide and expanded the peptide binding scope. Compared with 99Tyr of SLA-1*0401, 99Phe of SLA-1*13:01 could not form a conservative hydrogen bond with the backbone of the P3 residues, leading to fewer changes in the pocket properties but a significant decrease in quantitative of immunopeptidomes. This absent force could be compensated by the salt bridge formed by P1-E and 170Arg. These data illustrate two distinguishing manners that show how micropolymorphism alters the peptide-binding plasticity of SLA-I alleles, verifying the sensitivity and accuracy of the RPLD-MS method for determining the peptide binding characteristics of MHC-I in vitro and helping to more accurately predict and identify MHC-I restricted epitopes.
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Affiliation(s)
- Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Song Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhuolin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zibin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zehui Qu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Suqiu Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Baohua Zou
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruiying Liang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
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32
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Kaufman J. From Chickens to Humans: The Importance of Peptide Repertoires for MHC Class I Alleles. Front Immunol 2020; 11:601089. [PMID: 33381122 PMCID: PMC7767893 DOI: 10.3389/fimmu.2020.601089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/30/2020] [Indexed: 12/21/2022] Open
Abstract
In humans, killer immunoglobulin-like receptors (KIRs), expressed on natural killer (NK) and thymus-derived (T) cells, and their ligands, primarily the classical class I molecules of the major histocompatibility complex (MHC) expressed on nearly all cells, are both polymorphic. The variation of this receptor-ligand interaction, based on which alleles have been inherited, is known to play crucial roles in resistance to infectious disease, autoimmunity, and reproduction in humans. However, not all the variation in response is inherited, since KIR binding can be affected by a portion of the peptide bound to the class I molecules, with the particular peptide presented affecting the NK response. The extent to which the large multigene family of chicken immunoglobulin-like receptors (ChIRs) is involved in functions similar to KIRs is suspected but not proven. However, much is understood about the two MHC-I molecules encoded in the chicken MHC. The BF2 molecule is expressed at a high level and is thought to be the predominant ligand of cytotoxic T lymphocytes (CTLs), while the BF1 molecule is expressed at a much lower level if at all and is thought to be primarily a ligand for NK cells. Recently, a hierarchy of BF2 alleles with a suite of correlated properties has been defined, from those expressed at a high level on the cell surface but with a narrow range of bound peptides to those expressed at a lower level on the cell surface but with a very wide repertoire of bound peptides. Interestingly, there is a similar hierarchy for human class I alleles, although the hierarchy is not as wide. It is a question whether KIRs and ChIRs recognize class I molecules with bound peptide in a similar way, and whether fastidious to promiscuous hierarchy of class I molecules affect both T and NK cell function. Such effects might be different from those predicted by the similarities of peptide-binding based on peptide motifs, as enshrined in the idea of supertypes. Since the size of peptide repertoire can be very different for alleles with similar peptide motifs from the same supertype, the relative importance of these two properties may be testable.
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Affiliation(s)
- Jim Kaufman
- School of Biological Sciences, Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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33
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Ivanova M, Tsvetkova G, Lukanov T, Stoimenov A, Hadjiev E, Shivarov V. Probable HLA-mediated immunoediting of JAK2 V617F-driven oncogenesis. Exp Hematol 2020; 92:75-88.e10. [DOI: 10.1016/j.exphem.2020.09.200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/13/2022]
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34
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Bashirova AA, Viard M, Naranbhai V, Grifoni A, Garcia-Beltran W, Akdag M, Yuki Y, Gao X, O'hUigin C, Raghavan M, Wolinsky S, Bream JH, Duggal P, Martinson J, Michael NL, Kirk GD, Buchbinder SP, Haas D, Goedert JJ, Deeks SG, Fellay J, Walker B, Goulder P, Cresswell P, Elliott T, Sette A, Carlson J, Carrington M. HLA tapasin independence: broader peptide repertoire and HIV control. Proc Natl Acad Sci U S A 2020; 117:28232-28238. [PMID: 33097667 PMCID: PMC7668082 DOI: 10.1073/pnas.2013554117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human leukocyte antigen (HLA) class I allotypes vary in their ability to present peptides in the absence of tapasin, an essential component of the peptide loading complex. We quantified tapasin dependence of all allotypes that are common in European and African Americans (n = 97), which revealed a broad continuum of values. Ex vivo examination of cytotoxic T cell responses to the entire HIV-1 proteome from infected subjects indicates that tapasin-dependent allotypes present a more limited set of distinct peptides than do tapasin-independent allotypes, data supported by computational predictions. This suggests that variation in tapasin dependence may impact the strength of the immune responses by altering peptide repertoire size. In support of this model, we observed that individuals carrying HLA class I genotypes characterized by greater tapasin independence progress more slowly to AIDS and maintain lower viral loads, presumably due to increased breadth of peptide presentation. Thus, tapasin dependence level, like HLA zygosity, may serve as a means to restrict or expand breadth of the HLA-I peptide repertoire across humans, ultimately influencing immune responses to pathogens and vaccines.
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Affiliation(s)
- Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Vivek Naranbhai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Wilfredo Garcia-Beltran
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Marjan Akdag
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Xiaojiang Gao
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Steven Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Jay H Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Susan P Buchbinder
- HIV Research Section, San Francisco Department of Public Health, San Francisco, CA 94102
| | - David Haas
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37204
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA 94110
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bruce Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, OX1 4AJ, United Kingdom
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Tim Elliott
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
- Centre for Cancer Immunology, University of Southampton, Southampton SO16 6YD, United Kingdom
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702;
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
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35
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Zaitoua AJ, Kaur A, Raghavan M. Variations in MHC class I antigen presentation and immunopeptidome selection pathways. F1000Res 2020; 9. [PMID: 33014341 PMCID: PMC7525337 DOI: 10.12688/f1000research.26935.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Major histocompatibility class I (MHC-I) proteins mediate immunosurveillance against pathogens and cancers by presenting antigenic or mutated peptides to antigen receptors of CD8+ T cells and by engaging receptors of natural killer (NK) cells. In humans, MHC-I molecules are highly polymorphic. MHC-I variations permit the display of thousands of distinct peptides at the cell surface. Recent mass spectrometric studies have revealed unique and shared characteristics of the peptidomes of individual MHC-I variants. The cell surface expression of MHC-I–peptide complexes requires the functions of many intracellular assembly factors, including the transporter associated with antigen presentation (TAP), tapasin, calreticulin, ERp57, TAP-binding protein related (TAPBPR), endoplasmic reticulum aminopeptidases (ERAPs), and the proteasomes. Recent studies provide important insights into the structural features of these factors that govern MHC-I assembly as well as the mechanisms underlying peptide exchange. Conformational sensing of MHC-I molecules mediates the quality control of intracellular MHC-I assembly and contributes to immune recognition by CD8 at the cell surface. Recent studies also show that several MHC-I variants can follow unconventional assembly routes to the cell surface, conferring selective immune advantages that can be exploited for immunotherapy.
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Affiliation(s)
- Anita J Zaitoua
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amanpreet Kaur
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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36
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Ilca FT, Drexhage LZ, Brewin G, Peacock S, Boyle LH. Distinct Polymorphisms in HLA Class I Molecules Govern Their Susceptibility to Peptide Editing by TAPBPR. Cell Rep 2020; 29:1621-1632.e3. [PMID: 31693900 PMCID: PMC7057265 DOI: 10.1016/j.celrep.2019.09.074] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/28/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022] Open
Abstract
Understanding how peptide selection is controlled on different major histocompatibility complex class I (MHC I) molecules is pivotal for determining how variations in these proteins influence our predisposition to infectious diseases, cancer, and autoinflammatory conditions. Although the intracellular chaperone TAPBPR edits MHC I peptides, it is unclear which allotypes are subjected to TAPBPR-mediated peptide editing. Here, we examine the ability of 97 different human leukocyte antigen (HLA) class I allotypes to interact with TAPBPR. We reveal a striking preference of TAPBPR for HLA-A, particularly for supertypes A2 and A24, over HLA-B and -C molecules. We demonstrate that the increased propensity of these HLA-A molecules to undergo TAPBPR-mediated peptide editing is determined by molecular features of the HLA-A F pocket, specifically residues H114 and Y116. This work reveals that specific polymorphisms in MHC I strongly influence their susceptibility to chaperone-mediated peptide editing, which may play a significant role in disease predisposition.
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Affiliation(s)
- F Tudor Ilca
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Linnea Z Drexhage
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Gemma Brewin
- Tissue Typing Laboratory, Box 209, Level 6 ATC, Cambridge University Hospitals, NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Sarah Peacock
- Tissue Typing Laboratory, Box 209, Level 6 ATC, Cambridge University Hospitals, NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
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37
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Wingbermühle S, Schäfer LV. Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques. J Chem Theory Comput 2020; 16:4615-4630. [PMID: 32497432 DOI: 10.1021/acs.jctc.9b01150] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Enhanced sampling techniques are a promising approach to obtain reliable binding free-energy profiles for flexible protein-ligand complexes from molecular dynamics (MD) simulations. To put four popular enhanced sampling techniques to a biologically relevant and challenging test, we studied the partial dissociation of an antigenic peptide from the Major Histocompatibility Complex I (MHC I) HLA-B*35:01 to systematically investigate the performance of umbrella sampling (US), replica exchange with solute tempering 2 (REST2), bias exchange umbrella sampling (BEUS, or replica-exchange umbrella sampling), and well-tempered metadynamics (MTD). With regard to the speed of sampling and convergence, the peptide-MHC I complex (pMHC I) under study showcases intrinsic strengths and weaknesses of the four enhanced sampling techniques used. We found that BEUS can best handle the sampling challenges that arise from the coexistence of an enthalpically and an entropically stabilized free-energy minimum in the pMHC I under study. These findings might also be relevant for other flexible biomolecular systems with competing enthalpically and entropically stabilized minima.
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Affiliation(s)
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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38
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Olson E, Geng J, Raghavan M. Polymorphisms of HLA-B: influences on assembly and immunity. Curr Opin Immunol 2020; 64:137-145. [PMID: 32619904 PMCID: PMC7772265 DOI: 10.1016/j.coi.2020.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/22/2020] [Indexed: 01/07/2023]
Abstract
The major histocompatibility class I (MHC-I) complex functions in innate and adaptive immunity, mediating surveillance of the subcellular environment. In humans, MHC-I heavy chains are encoded by three genes: the human leukocyte antigen (HLA)-A, HLA-B, and HLA-C. These genes are highly polymorphic, which results in the expression, typically, of six different HLA class I (HLA-I) proteins on the cell surface, and the presentation of diverse peptide antigens to CD8+ T cells for broad surveillance against many pathogenic conditions. Recent studies of HLA-B allotypes show that the polymorphisms, not surprisingly, also significantly impact protein folding and assembly pathways. The use of non-canonical assembly routes and the generation of non-canonical HLA-B conformers has consequences for immune receptor interactions and disease therapies.
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Affiliation(s)
- Eli Olson
- Graduate Program in Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Geng
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
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39
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High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange. Nat Commun 2020; 11:1909. [PMID: 32312993 PMCID: PMC7170893 DOI: 10.1038/s41467-020-15710-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/23/2020] [Indexed: 12/31/2022] Open
Abstract
Peptide exchange technologies are essential for the generation of pMHC-multimer libraries used to probe diverse, polyclonal TCR repertoires in various settings. Here, using the molecular chaperone TAPBPR, we develop a robust method for the capture of stable, empty MHC-I molecules comprising murine H2 and human HLA alleles, which can be readily tetramerized and loaded with peptides of choice in a high-throughput manner. Alternatively, catalytic amounts of TAPBPR can be used to exchange placeholder peptides with high affinity peptides of interest. Using the same system, we describe high throughput assays to validate binding of multiple candidate peptides on empty MHC-I/TAPBPR complexes. Combined with tetramer-barcoding via a multi-modal cellular indexing technology, ECCITE-seq, our approach allows a combined analysis of TCR repertoires and other T cell transcription profiles together with their cognate antigen specificities in a single experiment. The new approach allows TCR/pMHC interactions to be interrogated easily at large scale. Peptide-MHC (pMHC) tetramers are important tools for probing T cell repertoire and adaptive immune responses. Here the authors use a molecular chaperone, TAPBPR, to develop a high-throughput, multiplexible platform for pMHC tetramer generation to facilitate simultaneous assessments of T cell repertoire/antigen specificity and transcriptome.
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40
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Del Val M, Antón LC, Ramos M, Muñoz-Abad V, Campos-Sánchez E. Endogenous TAP-independent MHC-I antigen presentation: not just the ER lumen. Curr Opin Immunol 2020; 64:9-14. [PMID: 31935516 DOI: 10.1016/j.coi.2019.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/11/2019] [Indexed: 11/30/2022]
Abstract
Altered and infected cells are eliminated by CD8+ cytotoxic T lymphocytes. This requires production of antigenic peptides mostly in the cytosol, transport to the endoplasmic reticulum (ER) by the transporter associated with antigen processing (TAP), and cell surface presentation by major histocompatibility complex class I (MHC-I). Strikingly, antigen presentation occurs without TAP, although it is inefficient and associated to human pathology. TAP-independent peptides derive both from membrane and secreted proteins, as well as cytosolic ones. The efficiency of TAP-independent presentation may be impacted by the availability of receptive MHC-I, and in turn by the functional presence in the ER of the peptide-loading complex, itself anchored on TAP. Without TAP, surface expression of human leukocyte antigen (HLA)-B allotypes varies widely, with those presenting a broader peptide repertoire among the most TAP-independent. Much remains to be learned on the alternative cellular pathways for antigen presentation in the absence of TAP.
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Affiliation(s)
- Margarita Del Val
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain.
| | - Luis C Antón
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Manuel Ramos
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Víctor Muñoz-Abad
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Elena Campos-Sánchez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
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41
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Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection. Proc Natl Acad Sci U S A 2019; 116:25602-25613. [PMID: 31796585 PMCID: PMC6926029 DOI: 10.1073/pnas.1915562116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The interplay between a highly polymorphic set of MHC-I alleles and molecular chaperones shapes the repertoire of peptide antigens displayed on the cell surface for T cell surveillance. Here, we demonstrate that the molecular chaperone TAP-binding protein related (TAPBPR) associates with a broad range of partially folded MHC-I species inside the cell. Bimolecular fluorescence complementation and deep mutational scanning reveal that TAPBPR recognition is polarized toward the α2 domain of the peptide-binding groove, and depends on the formation of a conserved MHC-I disulfide epitope in the α2 domain. Conversely, thermodynamic measurements of TAPBPR binding for a representative set of properly conformed, peptide-loaded molecules suggest a narrower MHC-I specificity range. Using solution NMR, we find that the extent of dynamics at "hotspot" surfaces confers TAPBPR recognition of a sparsely populated MHC-I state attained through a global conformational change. Consistently, restriction of MHC-I groove plasticity through the introduction of a disulfide bond between the α1/α2 helices abrogates TAPBPR binding, both in solution and on a cellular membrane, while intracellular binding is tolerant of many destabilizing MHC-I substitutions. Our data support parallel TAPBPR functions of 1) chaperoning unstable MHC-I molecules with broad allele-specificity at early stages of their folding process, and 2) editing the peptide cargo of properly conformed MHC-I molecules en route to the surface, which demonstrates a narrower specificity. Our results suggest that TAPBPR exploits localized structural adaptations, both near and distant to the peptide-binding groove, to selectively recognize discrete conformational states sampled by MHC-I alleles, toward editing the repertoire of displayed antigens.
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42
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Abstract
Cluster of differentiation 8 (CD8) is a cell surface glycoprotein, which is expressed as 2 forms, αα homodimer or αβ heterodimer. Peptide-loaded major histocompatibility complex class I (pMHC-I) molecules are major ligands for both forms of CD8. CD8αβ is a coreceptor for the T cell receptor (TCR) and binds to the same cognate pMHC-I as the TCR, thus enabling or augmenting T cell responses. The function of CD8αα homodimers is largely unknown. While CD8αβ heterodimer is expressed exclusively on CD8+ T cells, the CD8αα homodimer is present in subsets of T cells and human natural killer (NK) cells. Here, we report that the CD8αα homodimer functions as a coreceptor for KIR3DL1, an inhibitory receptor of NK cells that is specific for certain MHC-I allotypes. CD8αα enhances binding of pMHC-I to KIR3DL1, increases KIR3DL1 clustering at the immunological synapse, and augments KIR3DL1-mediated inhibition of NK cell activation. Additionally, interactions between pMHC-I and CD8αα homodimers regulate KIR3DL1+ NK cell education. Together, these findings reveal another dimension to the modulation of NK cell activity.
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43
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Carey BS, Poulton KV, Poles A. Factors affecting HLA expression: A review. Int J Immunogenet 2019; 46:307-320. [PMID: 31183978 DOI: 10.1111/iji.12443] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022]
Abstract
The detection and semiquantitative measurement of circulating human leucocyte antigen (HLA)-specific antibodies is essential for the management of patients before and after transplantation. In addition, the pretransplant cross-match to assess the reactivity of recipient HLA antibody against donor lymphocytes has long been the gold standard to prevent hyperacute rejection. Whilst both of these tests assume that recipient HLA-specific antibody is the only variable in the assessment of transplant risk, this is not the case. Transplant immunologists recognize that some HLA antigens are expressed at levels a magnitude lower than others (e.g., HLA-C, HLA-DQ), but within loci, and between different cell types there are many factors that influence HLA expression in both resting and activated cells. HLA is not usually expressed without the specific promoter proteins NLRC5, for HLA class I, and CIITA, for class II. The quantity of HLA protein production is then affected by factors including promoter region polymorphisms, alternative exon splice sites, methylation and microRNA-directed degradation. Different loci are influenced by multiple combinations of these control mechanisms making prediction of HLA regulation difficult, but an ability to measure the cellular expression of each HLA antigen, in conjunction with knowledge of circulating HLA-specific antibody, would lead to a more informed algorithm to assess transplant risk.
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Affiliation(s)
- B Sean Carey
- Histocompatibility and Immunogenetics, Combined Laboratory, University Hospitals Plymouth, Plymouth, UK
| | | | - Anthony Poles
- Histocompatibility and Immunogenetics, Combined Laboratory, University Hospitals Plymouth, Plymouth, UK
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44
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Natarajan K, Jiang J, Margulies DH. Structural aspects of chaperone-mediated peptide loading in the MHC-I antigen presentation pathway. Crit Rev Biochem Mol Biol 2019; 54:164-173. [PMID: 31084439 DOI: 10.1080/10409238.2019.1610352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recognition of foreign and dysregulated antigens by the cellular innate and adaptive immune systems is in large part dependent on the cell surface display of peptide/MHC (pMHC) complexes. The formation of such complexes requires the generation of antigenic peptides, proper folding of MHC molecules, loading of peptides onto MHC molecules, glycosylation, and transport to the plasma membrane. This complex series of biosynthetic, biochemical, and cell biological reactions is known as "antigen processing and presentation". Here, we summarize recent work, focused on the structural and functional characterization of the key MHC-I-dedicated chaperones, tapasin, and TAPBPR. The mechanisms reflect the ability of conformationally flexible molecules to adapt to their ligands, and are comparable to similar processes that are exploited in peptide antigen loading in the MHC-II pathway.
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Affiliation(s)
- Kannan Natarajan
- a Molecular Biology Section, Laboratory of Immune System Biology , National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda , MD , USA
| | - Jiansheng Jiang
- a Molecular Biology Section, Laboratory of Immune System Biology , National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda , MD , USA
| | - David H Margulies
- a Molecular Biology Section, Laboratory of Immune System Biology , National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda , MD , USA
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45
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Raghavan M, Yarzabek B, Zaitouna AJ, Krishnakumar S, Ramon DS. Strategies for the measurements of expression levels and half-lives of HLA class I allotypes. Hum Immunol 2019; 80:221-227. [PMID: 30735755 DOI: 10.1016/j.humimm.2019.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/05/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
Abstract
HLA class I molecules are highly polymorphic cell surface proteins that trigger immune responses by CD8+ T cells and natural killer (NK) cells. Most humans express six different HLA class I proteins encoded by the HLA-A, HLA-B and HLA-C genes. HLA class I molecules bind to peptide antigens and present these antigens to T cell receptors (TCR) of CD8+ T cells. HLA class I expression levels also regulate NK cell activation. The presence of individual HLA class I genes is linked to many different disease, transplantation and therapy outcomes. An understanding of HLA class I expression and stability patterns is fundamentally important towards a better understanding of the associations of HLA class I genes with disease and treatment outcomes, and towards HLA class I targeting for vaccine development. Quantitative flow cytometry allows for assessments of variations in expression levels of HLA class I molecules in cells from a single blood donor over time, as well as averaged measurements across donors for the same allotype. Since all HLA class I molecules are structurally-related, cellular measurements of the HLA class I expression levels and stabilities of individual variants in human cells require careful choices of donors and antibodies, which are discussed here.
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Affiliation(s)
- Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Brogan Yarzabek
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anita J Zaitouna
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sujatha Krishnakumar
- Sirona Genomics, Immucor Inc, Suite A, 1916 Old Middlefield Way Mountain View, CA 94043, USA
| | - Daniel S Ramon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ 85054, USA
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46
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Kennedy PR, Barthen C, Williamson DJ, Davis DM. HLA-B and HLA-C Differ in Their Nanoscale Organization at Cell Surfaces. Front Immunol 2019; 10:61. [PMID: 30761133 PMCID: PMC6362897 DOI: 10.3389/fimmu.2019.00061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/11/2019] [Indexed: 12/30/2022] Open
Abstract
The particular HLA class I variants an individual carries influences their resistance and susceptibility to a multitude of diseases. Expression level and variation in the peptide binding region correlates with, for example, a person's progression to AIDS after HIV infection. One factor which has not yet been addressed is whether or not different HLA class I proteins organize differently in the cell membrane on a nanoscale. Here, we examined the organization of three HLA-B allotypes (B*2705, B*5301, and B*5701) and two HLA-C allotypes (C*0602 and C*0702) in the membrane of 721.221 cells which otherwise lack expression of HLA-B or HLA-C. All these allotypes are ligands for the T cell receptor and leukocyte immunoglobulin-like receptors, but additionally, the HLA-B allotypes are ligands for the killer-cell immunoglobulin-like receptor family member KIR3DL1, HLA-C*0602 is a ligand for KIR2DL1, and HLA-C*0702 is a ligand for KIR2DL2/3. Using super-resolution microscopy, we found that both HLA-B and HLA-C formed more clusters and a greater proportion of HLA contributed to clusters, when expressed at lower levels. Thus, HLA class I organization is a covariate in genetic association studies of HLA class I expression level with disease progression. Surprisingly, we also found that HLA-C was more clustered than HLA-B when expression level was controlled. HLA-C consistently formed larger and more numerous clusters than HLA-B and a greater proportion of HLA-C contributed to clusters than for HLA-B. We also found that the organization of HLA class I proteins varied with cell type. T cells exhibited a particularly clustered organization of HLA class I while B cells expressed a more uniform distribution. In summary, HLA class I variants are organized differently in the cell surface membrane which may impact their functions.
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Affiliation(s)
- Philippa R Kennedy
- Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, United Kingdom
| | - Charlotte Barthen
- Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, United Kingdom.,Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom
| | - David J Williamson
- Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, United Kingdom
| | - Daniel M Davis
- Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, United Kingdom
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47
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Illing PT, Pymm P, Croft NP, Hilton HG, Jojic V, Han AS, Mendoza JL, Mifsud NA, Dudek NL, McCluskey J, Parham P, Rossjohn J, Vivian JP, Purcell AW. HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome. Nat Commun 2018; 9:4693. [PMID: 30410026 PMCID: PMC6224591 DOI: 10.1038/s41467-018-07109-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
Immunophenotypic differences between closely related human leukocyte antigen (HLA) alleles have been associated with divergent clinical outcomes in infection, autoimmunity, transplantation and drug hypersensitivity. Here we explore the impact of micropolymorphism on peptide antigen presentation by three closely related HLA molecules, HLA-B*57:01, HLA-B*57:03 and HLA-B*58:01, that are differentially associated with the HIV elite controller phenotype and adverse drug reactions. For each allotype, we mine HLA ligand data sets derived from the same parental cell proteome to define qualitative differences in peptide presentation using classical peptide binding motifs and an unbiased statistical approach. The peptide repertoires show marked qualitative overlap, with 982 peptides presented by all allomorphs. However, differences in peptide abundance, HLA-peptide stability, and HLA-bound conformation demonstrate that HLA micropolymorphism impacts more than simply the range of peptide ligands. These differences provide grounds for distinct immune reactivity and insights into the capacity of micropolymorphism to diversify immune outcomes. Human leukocyte antigens (HLA) are multi-allelic and polymorphic genes that present antigens to immune cells for inducing protective immunity. Here, using systems biology and structural approaches, the authors show that micropolymorphism of three HLA has effects beyond the modulation of antigen diversity.
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Affiliation(s)
- Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Phillip Pymm
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia
| | - Nathan P Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, School of Medicine, Stanford University, Stanford, 94305, CA, USA.,Calico Life Sciences LLC, South San Francisco, 94080, CA, USA
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, 94080, CA, USA
| | - Alex S Han
- Department of Genetics, School of Medicine, Stanford University, Stanford, 94305, CA, USA
| | - Juan L Mendoza
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, 94305, CA, USA.,Institute for Molecular Engineering and Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, 60637, IL, USA
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Nadine L Dudek
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, School of Medicine, Stanford University, Stanford, 94305, CA, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. .,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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The role of polymorphic ERAP1 in autoinflammatory disease. Biosci Rep 2018; 38:BSR20171503. [PMID: 30054427 PMCID: PMC6131210 DOI: 10.1042/bsr20171503] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/19/2018] [Accepted: 07/23/2018] [Indexed: 01/29/2023] Open
Abstract
Autoimmune and autoinflammatory conditions represent a group of disorders characterized by self-directed tissue damage due to aberrant changes in innate and adaptive immune responses. These disorders possess widely varying clinical phenotypes and etiology; however, they share a number of similarities in genetic associations and environmental influences. Whilst the pathogenic mechanisms of disease remain poorly understood, genome wide association studies (GWAS) have implicated a number of genetic loci that are shared between several autoimmune and autoinflammatory conditions. Association of particular HLA alleles with disease susceptibility represents one of the strongest genetic associations. Furthermore, recent GWAS findings reveal strong associations with single nucleotide polymorphisms in the endoplasmic reticulum aminopeptidase 1 (ERAP1) gene and susceptibility to a number of these HLA-associated conditions. ERAP1 plays a major role in regulating the repertoire of peptides presented on HLA class I alleles at the cell surface, with the presence of single nucleotide polymorphisms in ERAP1 having a significant impact on peptide processing function and the repertoire of peptides presented. The impact of this dysfunctional peptide generation on CD8+ T-cell responses has been proposed as a mechanism of pathogenesis diseases where HLA and ERAP1 are associated. More recently, studies have highlighted a role for ERAP1 in innate immune-mediated pathways involved in inflammatory responses. Here, we discuss the role of polymorphic ERAP1 in various immune cell functions, and in the context of autoimmune and autoinflammatory disease pathogenesis.
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49
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Geng J, Zaitouna AJ, Raghavan M. Selected HLA-B allotypes are resistant to inhibition or deficiency of the transporter associated with antigen processing (TAP). PLoS Pathog 2018; 14:e1007171. [PMID: 29995954 PMCID: PMC6056074 DOI: 10.1371/journal.ppat.1007171] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/23/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Major histocompatibility complex class I (MHC-I) molecules present antigenic peptides to CD8+ T cells, and are also important for natural killer (NK) cell immune surveillance against infections and cancers. MHC-I molecules are assembled via a complex assembly pathway in the endoplasmic reticulum (ER) of cells. Peptides present in the cytosol of cells are transported into the ER via the transporter associated with antigen processing (TAP). In the ER, peptides are assembled with MHC-I molecules via the peptide-loading complex (PLC). Components of the MHC-I assembly pathway are frequently targeted by viruses, in order to evade host immunity. Many viruses encode inhibitors of TAP, which is thought to be a central source of peptides for the assembly of MHC-I molecules. However, human MHC-I (HLA-I) genes are highly polymorphic, and it is conceivable that several variants can acquire peptides via TAP-independent pathways, thereby conferring resistance to pathogen-derived inhibitors of TAP. To broadly assess TAP-independent expression within the HLA-B locus, expression levels of 27 frequent HLA-B alleles were tested in cells with deficiencies in TAP. Approximately 15% of tested HLA-B allotypes are expressed at relatively high levels on the surface of TAP1 or TAP2-deficient cells and occur in partially peptide-receptive forms and Endoglycosidase H sensitive forms on the cell surface. Synergy between high peptide loading efficiency, broad specificity for peptides prevalent within unconventional sources and high intrinsic stability of the empty form allows for deviations from the conventional HLA-I assembly pathway for some HLA-B*35, HLA-B*57 and HLA-B*15 alleles. Allotypes that display higher expression in TAP-deficient cells are more resistant to viral TAP inhibitor-induced HLA-I down-modulation, and HLA-I down-modulation-induced NK cell activation. Conversely, the same allotypes are expected to mediate stronger CD8+ T cell responses under TAP-inhibited conditions. Thus, the degree of resistance to TAP inhibition functionally separates specific HLA-B allotypes. Human leukocyte antigen (HLA) class I molecules present pathogen-derived components (peptides) to cytotoxic T cells, thereby inducing the T cells to kill virus-infected cells. A complex cellular pathway involving the transporter associated with antigen processing (TAP) is typically required for the loading of peptides onto HLA class I molecules, and for effective anti-viral immunity mediated by cytotoxic T cells. Many viruses encode inhibitors of TAP as a means to evade anti-viral immunity by cytotoxic T cells. In humans, there are three sets of genes encoding HLA class I molecules, which are the HLA-A, HLA-B and HLA-C genes. These genes are highly variable, with thousands of allelic variants in human populations. Most individuals typically express two variants of each gene, one inherited from each parent. We demonstrate that about 15% of tested HLA-B allotypes have higher resistance to viral inhibitors of TAP or deficiency of TAP, compared to other HLA-B variants. HLA-B allotypes that are more resistant to TAP inhibition are expected to induce stronger CD8+ T cell responses against pathogens that inhibit TAP. Thus, unconventional TAP-independent assembly pathways are broadly prevalent among HLA-B variants. Such pathways provide mechanisms to effectively combat viruses that evade the conventional TAP-dependent HLA-B assembly pathway.
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Affiliation(s)
- Jie Geng
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Anita J. Zaitouna
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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50
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Yarzabek B, Zaitouna AJ, Olson E, Silva GN, Geng J, Geretz A, Thomas R, Krishnakumar S, Ramon DS, Raghavan M. Variations in HLA-B cell surface expression, half-life and extracellular antigen receptivity. eLife 2018; 7:34961. [PMID: 29989547 PMCID: PMC6039183 DOI: 10.7554/elife.34961] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022] Open
Abstract
The highly polymorphic human leukocyte antigen (HLA) class I molecules present peptide antigens to CD8+ T cells, inducing immunity against infections and cancers. Quality control mediated by peptide loading complex (PLC) components is expected to ensure the cell surface expression of stable peptide-HLA class I complexes. This is exemplified by HLA-B*08:01 in primary human lymphocytes, with both expression level and half-life at the high end of the measured HLA-B expression and stability hierarchies. Conversely, low expression on lymphocytes is measured for three HLA-B allotypes that bind peptides with proline at position 2, which are disfavored by the transporter associated with antigen processing. Surprisingly, these lymphocyte-specific expression and stability differences become reversed or altered in monocytes, which display larger intracellular pools of HLA class I than lymphocytes. Together, the findings indicate that allele and cell-dependent variations in antigen acquisition pathways influence HLA-B surface expression levels, half-lives and receptivity to exogenous antigens. Most cells in the body make proteins called human leukocyte antigen class I (or HLA-I). These proteins sit on the cell surface, where they help the immune system distinguish between healthy and diseased cells. A groove in each HLA-I protein holds a fragment of a protein chain, called a peptide, from inside the cell. In healthy cells, all the peptides come from normal proteins. Yet in diseased or infected cells, the peptides may come from abnormal or foreign proteins – those encoded by viruses, for example. When the immune system sees these abnormal peptides, it responds by killing the cell. Across the human population, there are thousands of types of HLA-I, each able to carry a different set of peptides. Any individual person can only make a maximum of six types of the HLA-I, meaning we each show a different combination of peptides to our immune cells. This difference will change the way different people respond to the same disease. Before a peptide can be assembled into HLA-I, it must be moved to the correct part of the cell by a transporter known as TAP. This transport favors peptides with certain characteristics, but these characteristics do not always match the preferences of the individual's HLA-I proteins. For example, TAP is less likely to transport peptides where the second building block in the chain is a proline, but these peptides will still fit into the binding grooves of some HLA-I variants. Here, Yarzabek, Zaitouna, Olson et al. obtained blood from healthy human donors to answer questions about what happens when TAP and HLA-I have different preferences. Specifically, how many HLA-I molecules reach the surface, how long do they last, and which peptides do they carry? This analysis revealed that, when there was a mismatch between HLA-I and TAP, the amount of some HLA-I types on the surface of white blood cells called lymphocytes dropped. These HLA-I types were also able to pick up new peptides from their environment, indicating that some HLA-I were at the surface of the cell without a peptide. The role of these empty HLA-I remains to be fully defined. The reverse was true for other white blood cells called monocytes; HLA-I variants that were mismatched with TAP became more abundant on the cell surface. Monocytes also had more HLA-I molecules inside and did not pick up peptides from the environment. This suggests that monocytes may load peptides via new pathways, filling grooves left empty in lymphocytes, although other mechanisms might also explain the differences between the two types of white blood cells. Taken together, the findings reveal that HLA-I on the surface of cells depends on both the type of HLA-I and the type of immune cell. HLA-I proteins play a key role in the immune system’s ability to recognize and kill diseased cells. A better knowledge of how HLA-I variants differ could help us to understand why people respond differently to the same disease. A better grasp of HLA-I could in the future lead to improved drug and vaccine design.
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Affiliation(s)
- Brogan Yarzabek
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Michigan, United States
| | - Anita J Zaitouna
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Michigan, United States
| | - Eli Olson
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Michigan, United States.,Graduate Program in Immunology, Michigan Medicine, University of Michigan, Michigan, United States
| | - Gayathri N Silva
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Michigan, United States
| | - Jie Geng
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Michigan, United States
| | - Aviva Geretz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | | | - Daniel S Ramon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Arizona, United States
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Michigan, United States
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