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Uncovering novel MHC alleles from RNA-Seq data: expanding the spectrum of MHC class I alleles in sheep. BMC Genom Data 2023; 24:1. [PMID: 36597020 PMCID: PMC9809118 DOI: 10.1186/s12863-022-01102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Major histocompatibility complex (MHC) class I glycoproteins present selected peptides or antigens to CD8 + T cells that control the cytotoxic immune response. The MHC class I genes are among the most polymorphic loci in the vertebrate genome, with more than twenty thousand alleles known in humans. In sheep, only a very small number of alleles have been described to date, making the development of genotyping systems or functional studies difficult. A cost-effective way to identify new alleles could be to use already available RNA-Seq data from sheep. Current strategies for aligning RNA-Seq reads against annotated genome sequences or transcriptomes fail to detect the majority of class I alleles. Here, I combine the alignment of RNA-Seq reads against a specific reference database with de novo assembly to identify alleles. The method allows the comprehensive discovery of novel MHC class I alleles from RNA-Seq data (DinoMfRS). RESULTS Using DinoMfRS, virtually all expressed MHC class I alleles could be determined. From 18 animals 75 MHC class I alleles were identified, of which 69 were novel. In addition, it was shown that DinoMfRS can be used to improve the annotation of MHC genes in the sheep genome sequence. CONCLUSIONS DinoMfRS allows for the first time the annotation of unknown, more divergent MHC alleles from RNA-Seq data. Successful application to RNA-Seq data from 16 animals has approximately doubled the number of known alleles in sheep. By using existing data, alleles can now be determined very inexpensively for populations that have not been well studied. In addition, MHC expression studies or evolutionary studies, for example, can be greatly improved in this way, and the method should be applicable to a broader spectrum of other multigene families or highly polymorphic genes.
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Waters S, Lee S, Ariyanto I, Leary S, Munyard K, Gaudieri S, Irish A, Allcock RJN, Price P. Variants of HCMV UL18 Sequenced Directly from Clinical Specimens Associate with Antibody and T-Cell Responses to HCMV. Int J Mol Sci 2022; 23:ijms232112911. [PMID: 36361707 PMCID: PMC9658343 DOI: 10.3390/ijms232112911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/28/2022] Open
Abstract
Around 80% of adults worldwide carry human cytomegaloviris (HCMV). The HCMV gene UL18 is a homolog of HLA class I genes and encodes a protein with high affinity for the NK and T-cell cytotoxicity inhibitor LIR-1. UL18 was deep sequenced from blood, saliva or urine from Indonesian people with HIV (PWH) (n = 28), Australian renal transplant recipients (RTR) (n = 21), healthy adults (n = 7) and neonates (n = 4). 95% of samples contained more than one variant of HCMV UL18, as defined by carriage of nonsynonymous variations. When aligned with immunological markers of the host’s burden of HCMV, the S318N variation associated with high levels of antibody reactive with HCMV lysate in PWH over 12 months on antiretroviral therapy. The A107T variation associated with HCMV antibody levels and inflammatory biomarkers in PWH at early timepoints. Variants D32G, D248N, V250A and E252D aligned with elevated HCMV antibody levels in RTR, while M191K, E196Q and F165L were associated with HCMV-reactive T-cells and proportions of Vδ2− γδ T-cells—populations linked with high burdens of HCMV. We conclude that UL18 is a highly variable gene, where variation may alter the persistent burden of HCMV and/or the host response to that burden.
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Affiliation(s)
- Shelley Waters
- Curtin Health Innovation Research Institute, Curtin Medical School, Curtin University, Bentley 6102, Australia
- Correspondence:
| | - Silvia Lee
- Curtin Health Innovation Research Institute, Curtin Medical School, Curtin University, Bentley 6102, Australia
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands 6009, Australia
| | - Ibnu Ariyanto
- Virology and Cancer Pathobiology Research Center, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch 6150, Australia
| | - Kylie Munyard
- Curtin Health Innovation Research Institute, Curtin Medical School, Curtin University, Bentley 6102, Australia
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch 6150, Australia
- School of Human Sciences, University of Western Australia, Nedlands 6009, Australia
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ashley Irish
- Department of Nephrology, Fiona Stanley Hospital, Murdoch 6150, Australia
| | - Richard J. N. Allcock
- School of Biomedical Sciences, University of Western Australia, Nedlands 6009, Australia
- PathWest Laboratory Medicine WA, Department of Diagnostic Genomics, Nedlands 6009, Australia
| | - Patricia Price
- Curtin Health Innovation Research Institute, Curtin Medical School, Curtin University, Bentley 6102, Australia
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3
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Siepe DH, Henneberg LT, Wilson SC, Hess GT, Bassik MC, Zinn K, Garcia KC. Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform. eLife 2022; 11:e81398. [PMID: 36178190 PMCID: PMC9578707 DOI: 10.7554/elife.81398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Secreted proteins, which include cytokines, hormones, and growth factors, are extracellular ligands that control key signaling pathways mediating cell-cell communication within and between tissues and organs. Many drugs target secreted ligands and their cell surface receptors. Still, there are hundreds of secreted human proteins that either have no identified receptors ('orphans') or are likely to act through cell surface receptors that have not yet been characterized. Discovery of secreted ligand-receptor interactions by high-throughput screening has been problematic, because the most commonly used high-throughput methods for protein-protein interaction (PPI) screening are not optimized for extracellular interactions. Cell-based screening is a promising technology for the deorphanization of ligand-receptor interactions, because multimerized ligands can enrich for cells expressing low affinity cell surface receptors, and such methods do not require purification of receptor extracellular domains. Here, we present a proteo-genomic cell-based CRISPR activation (CRISPRa) enrichment screening platform employing customized pooled cell surface receptor sgRNA libraries in combination with a magnetic bead selection-based enrichment workflow for rapid, parallel ligand-receptor deorphanization. We curated 80 potentially high-value orphan secreted proteins and ultimately screened 20 secreted ligands against two cell sgRNA libraries with targeted expression of all single-pass (TM1) or multi-pass transmembrane (TM2+) receptors by CRISPRa. We identified previously unknown interactions in 12 of these screens, and validated several of them using surface plasmon resonance and/or cell binding assays. The newly deorphanized ligands include three receptor protein tyrosine phosphatase (RPTP) ligands and a chemokine-like protein that binds to killer immunoglobulin-like receptors (KIRs). These new interactions provide a resource for future investigations of interactions between the human-secreted and membrane proteomes.
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Affiliation(s)
- Dirk H Siepe
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Lukas T Henneberg
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Gaelen T Hess
- Stanford ChEM-H, Department of Genetics, Stanford UniversityStanfordUnited States
| | - Michael C Bassik
- Stanford ChEM-H, Department of Genetics, Stanford UniversityStanfordUnited States
| | - Kai Zinn
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
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4
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Pontarotti P, Paganini J. COVID-19 Pandemic: Escape of Pathogenic Variants and MHC Evolution. Int J Mol Sci 2022; 23:ijms23052665. [PMID: 35269808 PMCID: PMC8910380 DOI: 10.3390/ijms23052665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
We propose a new hypothesis that explains the maintenance and evolution of MHC polymorphism. It is based on two phenomena: the constitution of the repertoire of naive T lymphocytes and the evolution of the pathogen and its impact on the immune memory of T lymphocytes. Concerning the latter, pathogen evolution will have a different impact on reinfection depending on the MHC allomorph. If a mutation occurs in a given region, in the case of MHC allotypes, which do not recognize the peptide in this region, the mutation will have no impact on the memory repertoire. In the case where the MHC allomorph binds to the ancestral peptides and not to the mutated peptide, that individual will have a higher chance of being reinfected. This difference in fitness will lead to a variation of the allele frequency in the next generation. Data from the SARS-CoV-2 pandemic already support a significant part of this hypothesis and following up on these data may enable it to be confirmed. This hypothesis could explain why some individuals after vaccination respond less well than others to variants and leads to predict the probability of reinfection after a first infection depending upon the variant and the HLA allomorph.
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Affiliation(s)
- Pierre Pontarotti
- Evolutionary Biology Team, MEPHI, Aix Marseille Université, IRD, APHM, IHU MI, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- SNC 5039 CNRS, 13005 Marseille, France
- Xegen, 15 Rue Dominique Piazza, 13420 Gemenos, France
- Correspondence: (P.P.); (J.P.)
| | - Julien Paganini
- Xegen, 15 Rue Dominique Piazza, 13420 Gemenos, France
- Correspondence: (P.P.); (J.P.)
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5
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SARS-CoV-2 peptides bind to NKG2D and increase NK cell activity. Cell Immunol 2021; 371:104454. [PMID: 34773897 PMCID: PMC8577527 DOI: 10.1016/j.cellimm.2021.104454] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/05/2021] [Accepted: 10/31/2021] [Indexed: 12/18/2022]
Abstract
Immune dysregulation is commonly
observed in patients with coronavirus disease 2019 (COVID-19). Severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces severe lung
inflammation and innate immune cell dysregulation. However, the precise
interaction between SARS-CoV-2 and the innate immune system is currently
unknown. To understand the interaction between SARS-CoV-2 and natural
killer (NK) cells, several SARS-CoV-2 S protein peptides capable of
binding to the NKG2D receptor were screened by in
silico analysis. Among them, two peptides, cov1 and cov2,
bound to NK cells and NKG2D receptors. These cov peptides increased NK
cytotoxicity toward lung cancer cells, stimulated interferon gamma
(IFN-γ) production by NK cells, and likely mediated these responses
through the phosphorylation of Vav1, a key downstream-signaling molecule
of NKG2D and NK activation genes. The direct interaction between
SARS-CoV-2 and NK cells is a novel finding, and modulation of this
interaction has potential clinical application as a therapeutic target
for COVID-19.
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6
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Dhusia K, Wu Y. Classification of protein-protein association rates based on biophysical informatics. BMC Bioinformatics 2021; 22:408. [PMID: 34404340 PMCID: PMC8371850 DOI: 10.1186/s12859-021-04323-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 08/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins form various complexes to carry out their versatile functions in cells. The dynamic properties of protein complex formation are mainly characterized by the association rates which measures how fast these complexes can be formed. It was experimentally observed that the association rates span an extremely wide range with over ten orders of magnitudes. Identification of association rates within this spectrum for specific protein complexes is therefore essential for us to understand their functional roles. RESULTS To tackle this problem, we integrate physics-based coarse-grained simulations into a neural-network-based classification model to estimate the range of association rates for protein complexes in a large-scale benchmark set. The cross-validation results show that, when an optimal threshold was selected, we can reach the best performance with specificity, precision, sensitivity and overall accuracy all higher than 70%. The quality of our cross-validation data has also been testified by further statistical analysis. Additionally, given an independent testing set, we can successfully predict the group of association rates for eight protein complexes out of ten. Finally, the analysis of failed cases suggests the future implementation of conformational dynamics into simulation can further improve model. CONCLUSIONS In summary, this study demonstrated that a new modeling framework that combines biophysical simulations with bioinformatics approaches is able to identify protein-protein interactions with low association rates from those with higher association rates. This method thereby can serve as a useful addition to a collection of existing experimental approaches that measure biomolecular recognition.
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Affiliation(s)
- Kalyani Dhusia
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
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7
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Truong HV, Sgourakis NG. Dynamics of MHC-I molecules in the antigen processing and presentation pathway. Curr Opin Immunol 2021; 70:122-128. [PMID: 34153556 PMCID: PMC8622473 DOI: 10.1016/j.coi.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 01/07/2023]
Abstract
The endogenous antigen processing and presentation (APP) is a fundamental pathway found in jawed vertebrates, which allows for a set of epitope peptides sampled from the intracellular proteome to be assembled and displayed on class I proteins of the major histocompatibility complex (MHC-I). Peptide/MHC-I antigens enable different aspects of adaptive immunity to emerge, by providing a basis for recognition of self vs. non-self by T cells and Natural Killer (NK) cells. Pioneering studies of pMHC-I molecules and their higher-order protein complexes with molecular chaperones and membrane receptors have gleaned important insights into the peptide loading and antigen recognition mechanisms. While X-ray and cryoEM structures have provided us with static snapshots of different MHC-I assembly stages, complementary biophysical techniques have revealed that MHC-I molecules are highly mobile on a range of biologically relevant timescales, which bears importance for their assembly, peptide repertoire selection, membrane display and turnover. This review summarizes insights gained from experimental and simulation studies aimed at investigating MHC-I dynamics, and their functional implications.
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Affiliation(s)
- Hau V Truong
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA.
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8
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Ma J, Ayres CM, Hellman LM, Devlin JR, Baker BM. Dynamic allostery controls the peptide sensitivity of the Ly49C natural killer receptor. J Biol Chem 2021; 296:100686. [PMID: 33891944 PMCID: PMC8138769 DOI: 10.1016/j.jbc.2021.100686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
Using a variety of activating and inhibitory receptors, natural killer (NK) cells protect against disease by eliminating cells that have downregulated class I major histocompatibility complex (MHC) proteins, such as in response to cell transformation or viral infection. The inhibitory murine NK receptor Ly49C specifically recognizes the class I MHC protein H-2Kb. Unusual among NK receptors, Ly49C exhibits a peptide-dependent sensitivity to H-2Kb recognition, which has not been explained despite detailed structural studies. To gain further insight into Ly49C peptide sensitivity, we examined Ly49C recognition biochemically and through the lens of dynamic allostery. We found that the peptide sensitivity of Ly49C arises through small differences in H-2Kb-binding affinity. Although molecular dynamics simulations supported a role for peptide-dependent protein dynamics in producing these differences in binding affinity, calorimetric measurements indicated an enthalpically as opposed to entropically driven process. A quantitative linkage analysis showed that this emerges from peptide-dependent dynamic tuning of electrostatic interactions across the Ly49C–H-2Kb interface. We propose a model whereby different peptides alter the flexibility of H-2Kb, which in turn changes the strength of electrostatic interactions across the protein–protein interface. Our results provide a quantitative assessment of how peptides alter Ly49C-binding affinity, suggest the underlying mechanism, and demonstrate peptide-driven allostery at work in class I MHC proteins. Lastly, our model provides a solution for how dynamic allostery could impact binding of some, but not all, class I MHC partners depending on the structural and chemical composition of the interfaces.
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Affiliation(s)
- Jiaqi Ma
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, Nevada, USA
| | - Jason R Devlin
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA.
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9
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Hagelstein I, Lutz MS, Schmidt M, Heitmann JS, Malenke E, Zhou Y, Clar KL, Kopp HG, Jung G, Salih HR, Märklin M, Hinterleitner C. Bispecific NKG2D-CD3 and NKG2D-CD16 Fusion Proteins as Novel Treatment Option in Advanced Soft Tissue Sarcomas. Front Immunol 2021; 12:653081. [PMID: 33936075 PMCID: PMC8079770 DOI: 10.3389/fimmu.2021.653081] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
Soft tissue sarcoma (STS) constitutes a rare group of heterogeneous malignancies. Effective treatment options for most subtypes of STS are still limited. As a result, especially in metastatic disease, prognosis is still dismal. The ligands for the activating immunoreceptor NKG2D (NKG2DL) are commonly expressed in STS, but generally absent in healthy tissues. This provides the rationale for utilization of NKG2DL as targets for immunotherapeutic approaches. We here report on the preclinical characterization of bispecific fusion proteins (BFP) consisting of the extracellular domain of the NKG2D receptor fused to Fab-fragments directed against CD3 (NKG2D-CD3) or CD16 (NKG2D-CD16) for treatment of STS. After characterization of NKG2DL expression patterns on various STS cell lines, we demonstrated that both NKG2D-CD16 and NKG2D-CD3 induce profound T and NK cell reactivity as revealed by analysis of activation, degranulation and secretion of IFNγ as well as granule associated proteins, resulting in potent target cell lysis. In addition, the stimulatory capacity of the constructs to induce T and NK cell activation was analyzed in heavily pretreated STS patients and found to be comparable to healthy donors. Our results emphasize the potential of NKG2D-CD3 and NKG2D-CD16 BFP to target STS even in an advanced disease.
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Affiliation(s)
- Ilona Hagelstein
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany
| | - Martina S Lutz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany
| | - Moritz Schmidt
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany.,Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany
| | - Elke Malenke
- Department of Hematology and Oncology, Eberhard Karls University Tuebingen, Children's Hospital, Tuebingen, Germany
| | - Yanjun Zhou
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany
| | - Kim L Clar
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany
| | - Hans-Georg Kopp
- Robert Bosch Center for Tumor Diseases (RBCT) Robert Bosch Cancer Center, Stuttgart, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Tuebingen, Germany
| | - Gundram Jung
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany.,Department for Immunology, Eberhard Karls University, Tuebingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany
| | - Clemens Hinterleitner
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tübingen, Germany.,Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen, Germany
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10
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Bruijnesteijn J, de Groot NG, Bontrop RE. The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates. Front Immunol 2020; 11:582804. [PMID: 33013938 PMCID: PMC7516082 DOI: 10.3389/fimmu.2020.582804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/18/2020] [Indexed: 12/26/2022] Open
Abstract
The activity and function of natural killer (NK) cells are modulated through the interactions of multiple receptor families, of which some recognize MHC class I molecules. The high level of MHC class I polymorphism requires their ligands either to interact with conserved epitopes, as is utilized by the NKG2A receptor family, or to co-evolve with the MHC class I allelic variation, which task is taken up by the killer cell immunoglobulin-like receptor (KIR) family. Multiple molecular mechanisms are responsible for the diversification of the KIR gene system, and include abundant chromosomal recombination, high mutation rates, alternative splicing, and variegated expression. The combination of these genetic mechanisms generates a compound array of diversity as is reflected by the contraction and expansion of KIR haplotypes, frequent birth of fusion genes, allelic polymorphism, structurally distinct isoforms, and variegated expression, which is in contrast to the mainly allelic nature of MHC class I polymorphism in humans. A comparison of the thoroughly studied human and macaque KIR gene repertoires demonstrates a similar evolutionarily conserved toolbox, through which selective forces drove and maintained the diversified nature of the KIR gene cluster. This hypothesis is further supported by the comparative genetics of KIR haplotypes and genes in other primate species. The complex nature of the KIR gene system has an impact upon the education, activity, and function of NK cells in coherence with an individual’s MHC class I repertoire and pathogenic encounters. Although selection operates on an individual, the continuous diversification of the KIR gene system in primates might protect populations against evolving pathogens.
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Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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11
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Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association. Biomolecules 2020; 10:biom10071056. [PMID: 32679892 PMCID: PMC7407674 DOI: 10.3390/biom10071056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/22/2022] Open
Abstract
The formation of functionally versatile protein complexes underlies almost every biological process. The estimation of how fast these complexes can be formed has broad implications for unravelling the mechanism of biomolecular recognition. This kinetic property is traditionally quantified by association rates, which can be measured through various experimental techniques. To complement these time-consuming and labor-intensive approaches, we developed a coarse-grained simulation approach to study the physical processes of protein–protein association. We systematically calibrated our simulation method against a large-scale benchmark set. By combining a physics-based force field with a statistically-derived potential in the simulation, we found that the association rates of more than 80% of protein complexes can be correctly predicted within one order of magnitude relative to their experimental measurements. We further showed that a mixture of force fields derived from complementary sources was able to describe the process of protein–protein association with mechanistic details. For instance, we show that association of a protein complex contains multiple steps in which proteins continuously search their local binding orientations and form non-native-like intermediates through repeated dissociation and re-association. Moreover, with an ensemble of loosely bound encounter complexes observed around their native conformation, we suggest that the transition states of protein–protein association could be highly diverse on the structural level. Our study also supports the idea in which the association of a protein complex is driven by a “funnel-like” energy landscape. In summary, these results shed light on our understanding of how protein–protein recognition is kinetically modulated, and our coarse-grained simulation approach can serve as a useful addition to the existing experimental approaches that measure protein–protein association rates.
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12
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Panda AK, Gangaplara A, Buszko M, Natarajan K, Boyd LF, Sharma S, Margulies DH, Shevach EM. Cutting Edge: Inhibition of the Interaction of NK Inhibitory Receptors with MHC Class I Augments Antiviral and Antitumor Immunity. THE JOURNAL OF IMMUNOLOGY 2020; 205:567-572. [PMID: 32601097 DOI: 10.4049/jimmunol.2000412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/22/2020] [Indexed: 01/10/2023]
Abstract
NK cells recognize MHC class I (MHC-I) Ags via stochastically expressed MHC-I-specific inhibitory receptors that prevent NK cell activation via cytoplasmic ITIM. We have identified a pan anti-MHC-I mAb that blocks NK cell inhibitory receptor binding at a site distinct from the TCR binding site. Treatment of unmanipulated mice with this mAb disrupted immune homeostasis, markedly activated NK and memory phenotype T cells, enhanced immune responses against transplanted tumors, and augmented responses to acute and chronic viral infection. mAbs of this type represent novel checkpoint inhibitors in tumor immunity, potent tools for the eradication of chronic infection, and may function as adjuvants for the augmentation of the immune response to weak vaccines.
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Affiliation(s)
- Abir K Panda
- Cellular Immunology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Arunakumar Gangaplara
- Laboratory of Early Sickle Mortality Prevention, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Maja Buszko
- Cellular Immunology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Suveena Sharma
- Cellular Immunology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Ethan M Shevach
- Cellular Immunology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892;
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13
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Shaffer TM, Aalipour A, Schürch CM, Gambhir SS. PET Imaging of the Natural Killer Cell Activation Receptor NKp30. J Nucl Med 2020; 61:1348-1354. [PMID: 32532927 PMCID: PMC7456168 DOI: 10.2967/jnumed.119.233163] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 05/20/2020] [Indexed: 12/15/2022] Open
Abstract
Redirecting the immune system in cancer treatment has led to remarkable responses in a subset of patients. Natural killer (NK) cells are innate lymphoid cells being explored as they engage tumor cells in different mechanisms compared with T cells, which could be exploited for treatment of nonresponders to current immunotherapies. NK cell therapies are monitored through measuring peripheral NK cell concentrations or changes in tumor volume over time. The former does not detect NK cells at the tumor site, and the latter is inaccurate for immunotherapies because of pseudoprogression. Therefore, new imaging methods are required as companion diagnostics for optimizing immunotherapies. Methods: In this study, we developed and completed preclinical in vivo validation of 2 antibody-based PET probes specific for NKp30, an activation natural cytotoxicity receptor expressed by human NK cells. Quantitative, multicolor flow cytometry during a variety of NK cell activation conditions was completed on primary human NK cells and the NK92MI cell line. Human renal cell carcinoma (RCC) tumors were stained for the NK cell receptors CD56, NKp30, and NKp46 to determine expression on tumor-infiltrating NK cells. An NKp30 antibody was radiolabeled with 64Cu or 89Zr and evaluated in subcutaneous xenografts and adoptive cell transfer mouse models. Results: Quantitative flow cytometry showed consistent expression of the NKp30 receptor during different activation conditions. NKp30 and NKp46 costained in RCC samples, demonstrating the expression of these receptors on tumor-infiltrating NK cells in human tumors, whereas tumor cells in one RCC sample expressed the peripheral NK marker CD56. Both PET tracers showed high stability and specificity in vitro and in vivo. Notably, 89Zr-NKp30Ab had higher on-target contrast than 64Cu-NKp30Ab at their respective terminal time points. 64Cu-NKp30Ab delineated NK cell trafficking to the liver and spleen in an adoptive cell transfer model. Conclusion: The consistent expression of NKp30 on NK cells makes it an attractive target for quantitative imaging. Immunofluorescence staining on human RCC samples demonstrated the advantages of NKp30 targeting versus CD56 for detection of tumor infiltrating NK cells. This work advances PET imaging of NK cells and supports the translation of imaging agents for immunotherapy monitoring.
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Affiliation(s)
- Travis M Shaffer
- Department of Radiology, Stanford University, Stanford, California
| | - Amin Aalipour
- Department of Bioengineering, Stanford University, Stanford, California
| | - Christian M Schürch
- Department of Microbiology and Immunology, Stanford University, Stanford, California; and
| | - Sanjiv S Gambhir
- Department of Radiology, Stanford University, Stanford, California .,Department of Bioengineering, Stanford University, Stanford, California.,Bio-X Program and Molecular Imaging Program at Stanford, Stanford University, Stanford, California
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14
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Serçinoğlu O, Ozbek P. Sequence-structure-function relationships in class I MHC: A local frustration perspective. PLoS One 2020; 15:e0232849. [PMID: 32421728 PMCID: PMC7233585 DOI: 10.1371/journal.pone.0232849] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, human MHC (Human Leukocyte Antigen, HLA) is the most polymorphic protein in humans. This allelic diversity provides a wide coverage of peptide sequence space, yet does not affect the three-dimensional structure of the complex. Moreover, TCRs mostly interact with HLA in a common diagonal binding mode, and KIR-HLA interaction is allele-dependent. With the aim of establishing a framework for understanding the relationships between polymorphism (sequence), structure (conserved fold) and function (protein interactions) of the human MHC, we performed here a local frustration analysis on pMHC homology models covering 1436 HLA I alleles. An analysis of local frustration profiles indicated that (1) variations in MHC fold are unlikely due to minimally-frustrated and relatively conserved residues within the HLA peptide-binding groove, (2) high frustration patches on HLA helices are either involved in or near interaction sites of MHC with the TCR, KIR, or tapasin of the PLC, and (3) peptide ligands mainly stabilize the F-pocket of HLA binding groove.
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Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Recep Tayyip Erdogan University, Faculty of Engineering, Fener, Rize, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Faculty of Engineering, Goztepe, Istanbul, Turkey
- * E-mail:
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15
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Liu Y, Cuendet MA, Goffin L, Šachl R, Cebecauer M, Cariolato L, Guillaume P, Reichenbach P, Irving M, Coukos G, Luescher IF. CD8 Binding of MHC-Peptide Complexes in cis or trans Regulates CD8 + T-cell Responses. J Mol Biol 2019; 431:4941-4958. [PMID: 31704286 DOI: 10.1016/j.jmb.2019.10.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 11/19/2022]
Abstract
The coreceptor CD8αβ can greatly promote activation of T cells by strengthening T-cell receptor (TCR) binding to cognate peptide-MHC complexes (pMHC) on antigen presenting cells and by bringing p56Lck to TCR/CD3. Here, we demonstrate that CD8 can also bind to pMHC on the T cell (in cis) and that this inhibits their activation. Using molecular modeling, fluorescence resonance energy transfer experiments on living cells, biochemical and mutational analysis, we show that CD8 binding to pMHC in cis involves a different docking mode and is regulated by posttranslational modifications including a membrane-distal interchain disulfide bond and negatively charged O-linked glycans near positively charged sequences on the CD8β stalk. These modifications distort the stalk, thus favoring CD8 binding to pMHC in cis. Differential binding of CD8 to pMHC in cis or trans is a means to regulate CD8+ T-cell responses and provides new translational opportunities.
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Affiliation(s)
- Yang Liu
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
| | - Michel A Cuendet
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA
| | - Laurence Goffin
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
| | - Radek Šachl
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, 18223 Prague, Czech Republic
| | - Marek Cebecauer
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, 18223 Prague, Czech Republic
| | - Luca Cariolato
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
| | - Patrick Reichenbach
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
| | - Immanuel F Luescher
- Ludwig Institute for Cancer Research, University of Lausanne, and Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland.
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16
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Karade SS, Mariuzza RA. How Natural Killer Cell Receptors Stick to Cell-Cell Adhesion Proteins. Structure 2019; 27:209-210. [PMID: 30726753 DOI: 10.1016/j.str.2019.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The cytolytic activity of NK cells is regulated by activating and inhibitory receptors, including ones that recognize cell-cell adhesion molecules. In this issue of Structure, Deuss et al. (2019) report the structure of nectin-like protein-5 bound to the NK inhibitory receptor CD96, a promising new target for cancer immunotherapy.
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Affiliation(s)
- Sharanbasappa S Karade
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Roy A Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.
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17
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Adámková L, Kvíčalová Z, Rozbeský D, Kukačka Z, Adámek D, Cebecauer M, Novák P. Oligomeric Architecture of Mouse Activating Nkrp1 Receptors on Living Cells. Int J Mol Sci 2019; 20:ijms20081884. [PMID: 30995786 PMCID: PMC6515139 DOI: 10.3390/ijms20081884] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/04/2019] [Accepted: 04/10/2019] [Indexed: 12/03/2022] Open
Abstract
Mouse activating Nkrp1 proteins are commonly described as type II transmembrane receptors with disulfide-linked homodimeric structure. Their function and the manner in which Nkrp1 proteins of mouse strain (C57BL/6) oligomerize are still poorly understood. To assess the oligomerization state of Nkrp1 proteins, mouse activating EGFP-Nkrp1s were expressed in mammalian lymphoid cells and their oligomerization evaluated by Förster resonance energy transfer (FRET). Alternatively, Nkrp1s oligomers were detected by Western blotting to specify the ratio between monomeric and dimeric forms. We also performed structural characterization of recombinant ectodomains of activating Nkrp1 receptors. Nkrp1 isoforms c1, c2 and f were expressed prevalently as homodimers, whereas the Nkrp1a displays larger proportion of monomers on the cell surface. Cysteine-to-serine mutants revealed the importance of all stalk cysteines for protein dimerization in living cells with a major influence of cysteine at position 74 in two Nkrp1 protein isoforms. Our results represent a new insight into the oligomerization of Nkrp1 receptors on lymphoid cells, which will help to determine their function.
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Affiliation(s)
- Ljubina Adámková
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic.
| | - Zuzana Kvíčalová
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 2155/3, 18223 Prague 8, Czech Republic.
| | - Daniel Rozbeský
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic.
| | - Zdeněk Kukačka
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic.
| | - David Adámek
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic.
| | - Marek Cebecauer
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 2155/3, 18223 Prague 8, Czech Republic.
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic.
- Department of Biochemistry, Charles University, Hlavova 8, 12843 Prague 2, Czech Republic.
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18
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Evidence of functional Cd94 polymorphism in a free-living house mouse population. Immunogenetics 2018; 71:321-333. [PMID: 30535636 DOI: 10.1007/s00251-018-01100-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023]
Abstract
The CD94 receptor, expressed on natural killer (NK) and CD8+ T cells, is known as a relatively non-polymorphic receptor with orthologues in humans, other primates, cattle, and rodents. In the house mouse (Mus musculus), a single allele is highly conserved among laboratory strains, and reports of allelic variation in lab- or wild-living mice are lacking, except for deficiency in one lab strain (DBA/2J). The non-classical MHC-I molecule Qa-1b is the ligand for mouse CD94/NKG2A, presenting alternative non-americ fragment of leader peptides (Qa-1 determinant modifier (Qdm)) from classical MHC-I molecules. Here, we report a novel allele identified in free-living house mice captured in Norway, living among individuals carrying the canonical Cd94 allele. The novel Cd94LocA allele encodes 12 amino acid substitutions in the extracellular lectin-like domain. Flow cytometric analysis of primary NK cells and transfected cells indicates that the substitutions prevent binding of CD94 mAb and Qa-1b/Qdm tetramers. Our data further indicate correlation of Cd94 polymorphism with the two major subspecies of house mice in Europe. Together, these findings suggest that the Cd94LocA/NKG2A heterodimeric receptor is widely expressed among M. musculus subspecies musculus, with ligand-binding properties different from mice of subspecies domesticus, such as the C57BL/6 strain.
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19
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Wang B, Xie ZR, Chen J, Wu Y. Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells. Structure 2018; 26:1414-1424.e3. [PMID: 30174150 DOI: 10.1016/j.str.2018.07.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/12/2018] [Accepted: 07/24/2018] [Indexed: 02/07/2023]
Abstract
The information of how two proteins interact is embedded in the atomic details of their binding interfaces. These interactions, spatial-temporally coordinating each other as a network in a variable cytoplasmic environment, dominate almost all biological functions. A feasible and reliable computational model is highly demanded to realistically simulate these cellular processes and unravel the complexities beneath them. We therefore present a multiscale framework that integrates simulations on two different scales. The higher-resolution model incorporates structural information of proteins and energetics of their binding, while the lower-resolution model uses a highly simplified representation of proteins to capture the long-time-scale dynamics of a system with multiple proteins. Through a systematic benchmark test and two practical applications of biomolecular systems with specific cellular functions, we demonstrated that this method could be a powerful approach to understand molecular mechanisms of dynamic interactions between biomolecules and their functional impacts with high computational efficiency.
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Affiliation(s)
- Bo Wang
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA
| | - Zhong-Ru Xie
- College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Jiawen Chen
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA.
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20
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Natarajan K, Jiang J, May NA, Mage MG, Boyd LF, McShan AC, Sgourakis NG, Bax A, Margulies DH. The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling. Front Immunol 2018; 9:1657. [PMID: 30065727 PMCID: PMC6056622 DOI: 10.3389/fimmu.2018.01657] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/04/2018] [Indexed: 01/20/2023] Open
Abstract
Antigen presentation is a cellular process that involves a number of steps, beginning with the production of peptides by proteolysis or aberrant synthesis and the delivery of peptides to cellular compartments where they are loaded on MHC class I (MHC-I) or MHC class II (MHC-II) molecules. The selective loading and editing of high-affinity immunodominant antigens is orchestrated by molecular chaperones: tapasin/TAP-binding protein, related for MHC-I and HLA-DM for MHC-II. Once peptide/MHC (pMHC) complexes are assembled, following various steps of quality control, they are delivered to the cell surface, where they are available for identification by αβ receptors on CD8+ or CD4+ T lymphocytes. In addition, recognition of cell surface peptide/MHC-I complexes by natural killer cell receptors plays a regulatory role in some aspects of the innate immune response. Many of the components of the pathways of antigen processing and presentation and of T cell receptor (TCR)-mediated signaling have been studied extensively by biochemical, genetic, immunological, and structural approaches over the past several decades. Until recently, however, dynamic aspects of the interactions of peptide with MHC, MHC with molecular chaperones, or of pMHC with TCR have been difficult to address experimentally, although computational approaches such as molecular dynamics (MD) simulations have been illuminating. Studies exploiting X-ray crystallography, cryo-electron microscopy, and multidimensional nuclear magnetic resonance (NMR) spectroscopy are beginning to reveal the importance of molecular flexibility as it pertains to peptide loading onto MHC molecules, the interactions between pMHC and TCR, and subsequent TCR-mediated signals. In addition, recent structural and dynamic insights into how molecular chaperones define peptide selection and fine-tune the MHC displayed antigen repertoire are discussed. Here, we offer a review of current knowledge that highlights experimental data obtained by X-ray crystallography and multidimensional NMR methodologies. Collectively, these findings strongly support a multifaceted role for protein plasticity and conformational dynamics throughout the antigen processing and presentation pathway in dictating antigen selection and recognition.
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Affiliation(s)
- Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Nathan A May
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael G Mage
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew C McShan
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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21
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Shemesh A, Brusilovsky M, Hadad U, Teltsh O, Edri A, Rubin E, Campbell KS, Rosental B, Porgador A. Survival in acute myeloid leukemia is associated with NKp44 splice variants. Oncotarget 2018; 7:32933-45. [PMID: 27102296 PMCID: PMC5078064 DOI: 10.18632/oncotarget.8782] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/27/2016] [Indexed: 11/25/2022] Open
Abstract
NKp44 is a receptor encoded by the NCR2 gene, which is expressed by cytokine-activated natural killer (NK) cells that are involved in anti-AML immunity. NKp44 has three splice variants corresponding to NKp44ITIM+ (NKp44-1) and NKp44ITIM− (NKp44-2, and NKp44-3) isoforms. RNAseq data of AML patients revealed similar survival of NKp46+NKp44+ and NKp46+NKp44− patients. However, if grouped according to the NKp44 splice variant profile, NKp44-1 expression was significantly associated with poor survival of AML patients. Moreover, activation of PBMC from healthy controls showed co-dominant expression of NKp44-1 and NKp44-3, while primary NK clones show more diverse NKp44 splice variant profiles. Cultured primary NK cells resulted in NKp44-1 dominance and impaired function associated with PCNA over-expression by target cells. This impaired functional phenotype could be rescued by blocking of NKp44 receptor. Human NK cell lines revealed co-dominant expression of NKp44-1 and NKp44-3 and showed a functional phenotype that was not inhibited by PCNA over-expression. Furthermore, transfection-based overexpression of NKp44-1, but not NKp44-2/NKp44-3, reversed the endogenous resistance of NK-92 cells to PCNA-mediated inhibition, and resulted in poor formation of stable lytic immune synapses. This research contributes to the understanding of AML prognosis by shedding new light on the functional implications of differential splicing of NKp44.
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Affiliation(s)
- Avishai Shemesh
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michael Brusilovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Uzi Hadad
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Omri Teltsh
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Avishay Edri
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Kerry S Campbell
- Immune Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Benyamin Rosental
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine and the Hopkins Marine Station, Stanford, CA, USA
| | - Angel Porgador
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
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22
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Burley SK, Berman HM, Christie C, Duarte JM, Feng Z, Westbrook J, Young J, Zardecki C. RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. Protein Sci 2018; 27:316-330. [PMID: 29067736 PMCID: PMC5734314 DOI: 10.1002/pro.3331] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 01/27/2023]
Abstract
The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical SchoolNew BrunswickNew Jersey08903
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of California, San DiegoLa JollaCalifornia92093
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
| | - Cole Christie
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of California, San DiegoLa JollaCalifornia92093
| | - Jose M. Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of California, San DiegoLa JollaCalifornia92093
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
| | - John Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
| | - Jasmine Young
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
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Anti-NKG2D mAb: A New Treatment for Crohn's Disease? Int J Mol Sci 2017; 18:ijms18091997. [PMID: 28926962 PMCID: PMC5618646 DOI: 10.3390/ijms18091997] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/24/2017] [Accepted: 09/11/2017] [Indexed: 01/09/2023] Open
Abstract
Crohn’s disease (CD) and ulcerative colitis (UC) are immunologically-mediated, debilitating conditions resulting from destructive inflammation of the gastrointestinal tract. The pathogenesis of IBD is incompletely understood, but is considered to be the result of an abnormal immune response with a wide range of cell types and proteins involved. Natural Killer Group 2D (NKG2D) is an activating receptor constitutively expressed on human Natural Killer (NK), γδ T, mucosal-associated invariant T (MAIT), CD56+ T, and CD8+ T cells. Activation of NKG2D triggers cellular proliferation, cytokine production, and target cell killing. Research into the NKG2D mechanism of action has primarily been focused on cancer and viral infections where cytotoxicity evasion is a concern. In human inflammatory bowel disease (IBD) this system is less characterized, but the ligands have been shown to be highly expressed during intestinal inflammation and the following receptor activation may contribute to tissue degeneration. A recent phase II clinical trial showed that an antibody against NKG2D induced clinical remission of CD in some patients, suggesting NKG2D and its ligands to be of importance in the pathogenesis of CD. This review will describe the receptor and its ligands in intestinal tissues and the clinical potential of blocking NKG2D in Crohn’s disease.
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Carrillo-Bustamante P, de Boer RJ, Keşmir C. Specificity of inhibitory KIRs enables NK cells to detect changes in an altered peptide environment. Immunogenetics 2017; 70:87-97. [PMID: 28695292 PMCID: PMC5775373 DOI: 10.1007/s00251-017-1019-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/20/2017] [Indexed: 12/12/2022]
Abstract
The activity of natural killer (NK) cells is tightly regulated by inhibitory and activating receptors. Inhibitory killer immunoglobulin-like receptors (iKIRs) survey the surface of target cells by monitoring the expression of human leukocyte antigen (HLA) class I. The binding of iKIRs has been shown to be sensitive to the peptides presented by HLA class I, implying that iKIRs have the ability to detect the changes in the repertoire of peptide-HLA class I complexes (pHLA), a process occurring during viral infection and in tumor cells. To study how the pHLA repertoire changes upon infection, and whether an iKIR is able to detect these changes, we study peptides eluted from cells prior and after infection with measles virus (MV). Remarkably, most changes in the repertoire of potential iKIR ligands are predicted to be caused by the altered expression of self-peptides. We show that an iKIR can detect these changes in the presented peptides only if it is sufficiently specific, e.g., if iKIRs can distinguish between different amino acids in the contact residues (e.g., position 7 and 8). Our analysis further indicates that one single iKIR per host is not sufficient to detect changes in the peptide repertoire, suggesting that a multigene family encoding for different iKIRs is required for successful peptide recognition.
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Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands. .,Center for Modeling and Simulation in the Biosciences (BIOMS/IWR), Max Planck Institute, Heidelberg, Germany.
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Can Keşmir
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
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25
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CIK Cells and HDAC Inhibitors in Multiple Myeloma. Int J Mol Sci 2017; 18:ijms18050945. [PMID: 28468247 PMCID: PMC5454858 DOI: 10.3390/ijms18050945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/07/2017] [Accepted: 04/25/2017] [Indexed: 12/01/2022] Open
Abstract
Multiple myeloma is the second most common hematological malignancy. Despite all the progress made in treating multiple myeloma, it still remains an incurable disease. Patients are left with a median survival of 4–5 years. The combined treatment of multiple myeloma with histone deacetylase inhibitors and cytokine-induced killer cells provides a promising targeted treatment option for patients. This study investigated the impact of a combined treatment compared to treatment with histone deacetylase inhibitors. The experiments revealed that a treatment with histone deacetylase (HDAC) inhibitors could reduce cell viability to 59% for KMS 18 cell line and 46% for the U-266 cell line. The combined treatment led to a decrease of cell viability to 33% for KMS 18 and 27% for the U-266 cell line, thus showing a significantly better efficacy than the single treatment.
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26
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Waide EH, Tuggle CK, Serão NVL, Schroyen M, Hess A, Rowland RRR, Lunney JK, Plastow G, Dekkers JCM. Genomewide association of piglet responses to infection with one of two porcine reproductive and respiratory syndrome virus isolates. J Anim Sci 2017; 95:16-38. [PMID: 28177360 DOI: 10.2527/jas.2016.0874] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease in the swine industry. Identification of host genetic factors that enable selection for improved performance during PRRS virus (PRRSV) infection would reduce the impact of this disease on animal welfare and production efficiency. We conducted genomewide association study (GWAS) analyses of data from 13 trials of approximately 200 commercial crossbred nursery-age piglets that were experimentally infected with 1 of 2 type 2 isolates of PRRSV (NVSL 97-7985 [NVSL] and KS2006-72109 [KS06]). Phenotypes analyzed were viral load (VL) in blood during the first 21 d after infection (dpi) and weight gain (WG) from 0 to 42 dpi. We accounted for the previously identified QTL in the region on SSC4 in our models to increase power to identify additional regions. Many regions identified by single-SNP analyses were not identified using Bayes-B, but both analyses identified the same regions on SSC3 and SSC5 to be associated with VL in the KS06 trials and on SSC6 in the NVSL trials ( < 5 × 10); for WG, regions on SSC5 and SSC17 were associated in the NVSL trials ( < 3 × 10). No regions were identified with either method for WG in the KS06 trials. Except for the region on SSC4, which was associated with VL for both isolates (but only with WG for NVSL), identified regions did not overlap between the 2 PRRSV isolate data sets, despite high estimates of the genetic correlation between isolates for traits based on these data. We also identified genomic regions whose associations with VL or WG interacted with either PRRSV isolate or with genotype at the SSC4 QTL. Gene ontology (GO) annotation terms for genes located near moderately associated SNP ( < 0.003) were enriched for multiple immunologically (VL) and metabolism- (WG) related GO terms. The biological relevance of these regions suggests that, although it may increase the number of false positives, the use of single-SNP analyses and a relaxed threshold also increased the identification of true positives. In conclusion, although only the SSC4 QTL was associated with response to both PRRSV isolates, genes near associated SNP were enriched for the same GO terms across PRRSV isolates, suggesting that host responses to these 2 isolates are affected by the actions of many genes that function together in similar biological processes.
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27
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Abstract
Triggering of cell-mediated immunity is largely dependent on the recognition of foreign or abnormal molecules by a myriad of cell surface-bound receptors. Many activating immune receptors do not possess any intrinsic signaling capacity but instead form noncovalent complexes with one or more dimeric signaling modules that communicate with a common set of kinases to initiate intracellular information-transfer pathways. This modular architecture, where the ligand binding and signaling functions are detached from one another, is a common theme that is widely employed throughout the innate and adaptive arms of immune systems. The evolutionary advantages of this highly adaptable platform for molecular recognition are visible in the variety of ligand-receptor interactions that can be linked to common signaling pathways, the diversification of receptor modules in response to pathogen challenges, and the amplification of cellular responses through incorporation of multiple signaling motifs. Here we provide an overview of the major classes of modular activating immune receptors and outline the current state of knowledge regarding how these receptors assemble, recognize their ligands, and ultimately trigger intracellular signal transduction pathways that activate immune cell effector functions.
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Affiliation(s)
- Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University , Clayton, Victoria 3800, Australia
| | - Matthew E Call
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne , Parkville, Victoria 3052, Australia
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28
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Kinetic and thermodynamic studies of the interaction between activating and inhibitory Ly49 natural killer receptors and MHC class I molecules. Biochem J 2017; 474:179-194. [PMID: 27831490 DOI: 10.1042/bcj20160876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/01/2016] [Accepted: 11/09/2016] [Indexed: 11/17/2022]
Abstract
Natural killer (NK) cells are lymphocytes of the innate immune system that eliminate virally infected or malignantly transformed cells. NK cell function is regulated by diverse surface receptors that are both activating and inhibitory. Among them, the homodimeric Ly49 receptors control NK cell cytotoxicity by sensing major histocompatibility complex class I molecules (MHC-I) on target cells. Although crystal structures have been reported for Ly49/MHC-I complexes, the underlying binding mechanism has not been elucidated. Accordingly, we carried out thermodynamic and kinetic experiments on the interaction of four NK Ly49 receptors (Ly49G, Ly49H, Ly49I and Ly49P) with two MHC-I ligands (H-2Dd and H-2Dk). These Ly49s embrace the structural and functional diversity of the highly polymorphic Ly49 family. Combining surface plasmon resonance, fluorescence anisotropy and far-UV circular dichroism (CD), we determined that the best model to describe both inhibitory and activating Ly49/MHC-I interactions is one in which the two MHC-I binding sites of the Ly49 homodimer present similar binding constants for the two sites (∼106 M-1) with a slightly positive co-operativity in some cases, and without far-UV CD observable conformational changes. Furthermore, Ly49/MHC-I interactions are diffusion-controlled and enthalpy-driven. These features stand in marked contrast with the activation-controlled and entropy-driven interaction of Ly49s with the viral immunoevasin m157, which is characterized by strong positive co-operativity and conformational selection. These differences are explained by the distinct structures of Ly49/MHC-I and Ly49/m157 complexes. Moreover, they reflect the opposing roles of NK cells to rapidly scan for virally infected cells and of viruses to escape detection using immunoevasins such as m157.
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29
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Kim M, Kim CH. Colonization and effector functions of innate lymphoid cells in mucosal tissues. Microbes Infect 2016; 18:604-614. [PMID: 27365193 PMCID: PMC5050099 DOI: 10.1016/j.micinf.2016.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/11/2016] [Accepted: 06/13/2016] [Indexed: 02/07/2023]
Abstract
Innate lymphoid cells (ILCs) protect mucosal barrier tissues to fight infection and maintain tissue integrity. ILCs and their progenitors are developmentally programmed to migrate, differentiate and populate various mucosal tissues and associated lymphoid tissues. Functionally mature ILC subsets respond to diverse pathogens such as bacteria, viruses, fungi and parasites in subset-specific manners. In this review, we will discuss how ILCs populate mucosal tissues and regulate immune responses to distinct pathogens to protect the host and maintain tissue integrity.
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Affiliation(s)
- Myunghoo Kim
- Laboratory of Immunology and Hematopoiesis, Department of Comparative Pathobiology, Weldon School of Biomedical Engineering, Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Chang H Kim
- Laboratory of Immunology and Hematopoiesis, Department of Comparative Pathobiology, Weldon School of Biomedical Engineering, Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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30
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Xu X, Narni-Mancinelli E, Cantoni C, Li Y, Guia S, Gauthier L, Chen Q, Moretta A, Vély F, Eisenstein E, Rangarajan S, Vivier E, Mariuzza RA. Structural Insights into the Inhibitory Mechanism of an Antibody against B7-H6, a Stress-Induced Cellular Ligand for the Natural Killer Cell Receptor NKp30. J Mol Biol 2016; 428:4457-4466. [PMID: 27663271 DOI: 10.1016/j.jmb.2016.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/15/2016] [Accepted: 09/14/2016] [Indexed: 01/08/2023]
Abstract
Antibodies have been shown to block signaling through cell surface receptors using several mechanisms. The two most common are binding to the ligand-binding site of the receptor and, conversely, binding to the receptor-binding site of the ligand. Here, we investigated the inhibitory mechanism of an antibody (17B1.3) against human B7-H6, a stress-induced cellular ligand for the natural killer (NK) cell receptor NKp30. Binding of this antibody to B7-H6, a transmembrane protein expressed on tumor and other stressed cells, but not on normal cells, prevents NK cell activation via NKp30. We determined the crystal structure of antibody 17B1.3 in complex with the ectodomain of B7-H6 to 2.5Å resolution. Surprisingly, 17B1.3 binds to a site on B7-H6 that is completely distinct from the binding site for NKp30, such that 17B1.3 does not block the NKp30-B7-H6 interaction. We then asked whether 17B1.3 prevents signaling by binding to a putative site for B7-H6 dimerization. However, structure-based mutations designed to disrupt potential B7-H6 dimerization through this site did not diminish NKp30-mediated cell activation. We conclude that the bulky 17B1.3 antibody most likely acts by sterically interfering with close cell-cell contacts at the NK cell-target cell interface that are required for NK cell activation. A similar inhibitory mechanism may apply to other antibodies, including therapeutic antibodies that block signaling through cell surface receptors whose ligands are also cell surface proteins.
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Affiliation(s)
- Xiaoping Xu
- University of Maryland Institute for Bioscience and Biotechnology Research, W.M. Keck Laboratory for Structural Biology, Rockville, MD 20850, USA; State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Sichuan 610041, People's Republic of China
| | - Emilie Narni-Mancinelli
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, Inserm, U1104, CNRS UMR7280, Marseille 13288, France
| | - Claudia Cantoni
- Dipartimento di Medicina Sperimentale, Università degli Studi di Genova, Genova 16132, Italy; Centro di Eccellenza per le Ricerche Biomediche, Università degli Studi di Genova, Genova 16132, Italy; Istituto Giannina Gaslini, Genova 16147, Italy
| | - Yili Li
- University of Maryland Institute for Bioscience and Biotechnology Research, W.M. Keck Laboratory for Structural Biology, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sophie Guia
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, Inserm, U1104, CNRS UMR7280, Marseille 13288, France
| | | | - Qianming Chen
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Sichuan 610041, People's Republic of China
| | - Alessandro Moretta
- Dipartimento di Medicina Sperimentale, Università degli Studi di Genova, Genova 16132, Italy; Centro di Eccellenza per le Ricerche Biomediche, Università degli Studi di Genova, Genova 16132, Italy
| | - Frédéric Vély
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, Inserm, U1104, CNRS UMR7280, Marseille 13288, France; Immunologie, Hôpital de la Conception, Assistance Publique - Hôpitaux de Marseille, Aix-Marseille Université, Marseille 13005, France
| | - Edward Eisenstein
- University of Maryland Institute for Bioscience and Biotechnology Research, W.M. Keck Laboratory for Structural Biology, Rockville, MD 20850, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Sneha Rangarajan
- University of Maryland Institute for Bioscience and Biotechnology Research, W.M. Keck Laboratory for Structural Biology, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, Inserm, U1104, CNRS UMR7280, Marseille 13288, France.
| | - Roy A Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, W.M. Keck Laboratory for Structural Biology, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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31
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Chalan P, van den Berg A, Kroesen BJ, Brouwer L, Boots A. Rheumatoid Arthritis, Immunosenescence and the Hallmarks of Aging. Curr Aging Sci 2016. [PMID: 26212057 PMCID: PMC5388800 DOI: 10.2174/1874609808666150727110744] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Age is the most important risk factor for the development of infectious diseases, cancer and chronic inflammatory diseases including rheumatoid arthritis (RA). The very act of living causes damage to cells. A network of molecular, cellular and physiological maintenance and repair systems creates a buffering capacity against these damages. Aging leads to progressive shrinkage of the buffering capacity and increases vulnerability. In order to better understand the complex mammalian aging processes, nine hallmarks of aging and their interrelatedness were recently put forward. RA is a chronic autoimmune disease affecting the joints. Although RA may develop at a young age, the incidence of RA increases with age. It has been suggested that RA may develop as a consequence of premature aging (immunosenescence) of the immune system. Alternatively, premature aging may be the consequence of the inflammatory state in RA. In an effort to answer this chicken and egg conundrum, we here outline and discuss the nine hallmarks of aging, their contribution to the pre-aged phenotype and the effects of treatment on the reversibility of immunosenescence in RA.
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Affiliation(s)
| | | | | | | | - Annemieke Boots
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, P.O Box 30.001, 9700 RB, Groningen, The Netherlands.
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32
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Frietze KK, Pappy AL, Melson JW, O'Driscoll EE, Tyler CM, Perlman DH, Boulanger LM. Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins. BMC Immunol 2016; 17:24. [PMID: 27435737 PMCID: PMC4950430 DOI: 10.1186/s12865-016-0154-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 05/27/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Major histocompatibility complex class I (MHCI) proteins present antigenic peptides for immune surveillance and play critical roles in nervous system development and plasticity. Most MHCI are transmembrane proteins. The extracellular domain of MHCI interacts with immunoreceptors, peptides, and co-receptors to mediate immune signaling. While the cytoplasmic domain also plays important roles in endocytic trafficking, cross-presentation of extracellularly derived antigens, and CTL priming, the molecular mediators of cytoplasmic signaling by MHCI remain largely unknown. RESULTS Here we show that the cytoplasmic domain of MHCI contains putative protein-protein interaction domains known as PDZ (PSD95/disc large/zonula occludens-1) ligands. PDZ ligands are motifs that bind to PDZ domains to organize and mediate signaling at cell-cell contacts. PDZ ligands are short, degenerate motifs, and are therefore difficult to identify via sequence homology alone, but several lines of evidence suggest that putative PDZ ligand motifs in MHCI are under positive selective pressure. Putative PDZ ligands are found in all of the 99 MHCI proteins examined from diverse species, and are enriched in the cytoplasmic domain, where PDZ interactions occur. Both the position of the PDZ ligand and the class of ligand motif are conserved across species, as well as among genes within a species. Non-synonymous substitutions, when they occur, frequently preserve the motif. Of the many specific possible PDZ ligand motifs, a handful are strikingly and selectively overrepresented in MHCI's cytoplasmic domain, but not elsewhere in the same proteins. Putative PDZ ligands in MHCI encompass conserved serine and tyrosine residues that are targets of phosphorylation, a post-translational modification that can regulate PDZ interactions. Finally, proof-of-principle in vitro interaction assays demonstrate that the cytoplasmic domains of particular MHCI proteins can bind directly and specifically to PDZ1 and PDZ4&5 of MAGI-1, and identify a conserved PDZ ligand motif in the classical MHCI H2-K that is required for this interaction. CONCLUSIONS These results identify cryptic protein interaction motifs in the cytoplasmic domain of MHCI. In so doing, they suggest that the cytoplasmic domain of MHCI could participate in previously unsuspected PDZ mediated protein-protein interactions at neuronal as well as immunological synapses.
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Affiliation(s)
- Karla K Frietze
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Adlai L Pappy
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jack W Melson
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Emily E O'Driscoll
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Carolyn M Tyler
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA
| | - David H Perlman
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Lisa M Boulanger
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. .,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA.
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33
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Guethlein LA, Norman PJ, Hilton HG, Parham P. Co-evolution of MHC class I and variable NK cell receptors in placental mammals. Immunol Rev 2016; 267:259-82. [PMID: 26284483 DOI: 10.1111/imr.12326] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Shaping natural killer (NK) cell functions in human immunity and reproduction are diverse killer cell immunoglobulin-like receptors (KIRs) that recognize polymorphic MHC class I determinants. A survey of placental mammals suggests that KIRs serve as variable NK cell receptors only in certain primates and artiodactyls. Divergence of the functional and variable KIRs in primates and artiodactyls predates placental reproduction. Among artiodactyls, cattle but not pigs have diverse KIRs. Catarrhine (humans, apes, and Old World monkeys) and platyrrhine (New World monkeys) primates, but not prosimians, have diverse KIRs. Platyrrhine and catarrhine systems of KIR and MHC class I are highly diverged, but within the catarrhines, a stepwise co-evolution of MHC class I and KIR is discerned. In Old World monkeys, diversification focuses on MHC-A and MHC-B and their cognate lineage II KIR. With evolution of C1-bearing MHC-C from MHC-B, as informed by orangutan, the focus changes to MHC-C and its cognate lineage III KIR. Evolution of C2 from C1 and fixation of MHC-C drove further elaboration of MHC-C-specific KIR, as exemplified by chimpanzee. In humans, the evolutionary trajectory changes again. Emerging from reorganization of the KIR locus and selective attenuation of KIR avidity for MHC class I are the functionally distinctive KIR A and KIR B haplotypes.
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Affiliation(s)
- Lisbeth A Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J Norman
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Hugo G Hilton
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
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Abstract
NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8(+) T cells, and subsets of CD4(+) T cells, invariant NKT cells (iNKT), and γδ T cells. In humans, NKG2D transmits signals by its association with the DAP10 adapter subunit, and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least eight genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and posttranslation. In general, healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyperproliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves as a mechanism for the immune system to detect and eliminate cells that have undergone "stress." Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system, and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases.
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Affiliation(s)
- Lewis L Lanier
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California.
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35
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Abstract
Natural killer (NK) cells are immune cells that play a crucial role against viral infections and tumors. To be tolerant against healthy tissue and simultaneously attack infected cells, the activity of NK cells is tightly regulated by a sophisticated array of germline-encoded activating and inhibiting receptors. The best characterized mechanism of NK cell activation is “missing self” detection, i.e., the recognition of virally infected or transformed cells that reduce their MHC expression to evade cytotoxic T cells. To monitor the expression of MHC-I on target cells, NK cells have monomorphic inhibitory receptors which interact with conserved MHC molecules. However, there are other NK cell receptors (NKRs) encoded by gene families showing a remarkable genetic diversity. Thus, NKR haplotypes contain several genes encoding for receptors with activating and inhibiting signaling, and that vary in gene content and allelic polymorphism. But if missing-self detection can be achieved by a monomorphic NKR system why have these polygenic and polymorphic receptors evolved? Here, we review the expansion of NKR receptor families in different mammal species, and we discuss several hypotheses that possibly underlie the diversification of the NK cell receptor complex, including the evolution of viral decoys, peptide sensitivity, and selective MHC-downregulation.
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36
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Raghavan M, Geng J. HLA-B polymorphisms and intracellular assembly modes. Mol Immunol 2015; 68:89-93. [PMID: 26239417 DOI: 10.1016/j.molimm.2015.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/29/2015] [Accepted: 07/07/2015] [Indexed: 02/08/2023]
Abstract
Human leukocyte antigen (HLA) class I molecules are ligands for antigen receptors of cytotoxic T cells (CTL) and inhibitory receptors of natural killer (NK) cells. The high degree of HLA class I polymorphism allows for the selection of distinct and diverse sets of antigenic peptide ligands for presentation to CTL. The extensive polymorphisms of the HLA class I genes also result in large variations in their intracellular folding and assembly characteristics. Recent findings indicate that North American HLA-B variants differ significantly in the stabilities of their peptide-deficient forms and in the requirements for the endoplasmic reticulum (ER)-resident factor tapasin for proper assembly. In HIV-infected individuals, the presence of tapasin-independent HLA-B allotypes links to more rapid progression to death. Further studies are important to better understand how the intrinsic structural characteristics of HLA class I folding intermediates affect immune responses mediated by CTL and NK cells.
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Affiliation(s)
- Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Jie Geng
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Biassoni R, Malnati M, Vanni I, Raso A, Sironi F, Broccolo F, Garbarino L, Mazzocco M, Montera M, Larghero P, Di Marco E, Ugolotti E. An improved method for HLA-B and -C supratyping. J Immunol Methods 2015; 426:29-34. [PMID: 26232127 DOI: 10.1016/j.jim.2015.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/16/2015] [Accepted: 07/16/2015] [Indexed: 01/26/2023]
Abstract
A growing body of evidence links the analysis of the KIR genotype and the presence of their HLA-B and -C ligands to a wide repertoire of human diseases. We noticed that, using a panel of 184 Caucasoid donors, a limited number of HLA alleles were incorrectly supratyped by previously described pyrosequence-based assays. Here we describe a simple implementation of the reported methods that corrects all the discrepancies found with HLA-B and -C molecular typing and allows establishing a quick and high-throughput method for the determination of HLA-Bw4 I(80), Bw4T(80), Bw6 and HLA-C1 or -C2 supratype.
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Affiliation(s)
- R Biassoni
- Istituto Giannina Gaslini, Genova, Italy.
| | - M Malnati
- Human Virology Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy
| | - I Vanni
- Istituto Giannina Gaslini, Genova, Italy
| | - A Raso
- Istituto Giannina Gaslini, Genova, Italy
| | - F Sironi
- Human Virology Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy
| | - F Broccolo
- Department of Health Sciences, University of Milano-Bicocca, Milano, Italy
| | - L Garbarino
- Histocompatibility Laboratory, Galliera Hospital, Genova, Italy
| | - M Mazzocco
- Histocompatibility Laboratory, Galliera Hospital, Genova, Italy
| | - M Montera
- Istituto Giannina Gaslini, Genova, Italy
| | - P Larghero
- Istituto Giannina Gaslini, Genova, Italy
| | - E Di Marco
- Istituto Giannina Gaslini, Genova, Italy
| | - E Ugolotti
- Istituto Giannina Gaslini, Genova, Italy
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Angelo LS, Banerjee PP, Monaco-Shawver L, Rosen JB, Makedonas G, Forbes LR, Mace EM, Orange JS. Practical NK cell phenotyping and variability in healthy adults. Immunol Res 2015; 62:341-56. [PMID: 26013798 PMCID: PMC4470870 DOI: 10.1007/s12026-015-8664-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human natural killer (NK) cells display a wide array of surface and intracellular markers that indicate various states of differentiation and/or levels of effector function. These NK cell subsets exist simultaneously in peripheral blood and may vary among individuals. We examined variety among selected NK cell receptors expressed by NK cells from normal donors, as well as the distribution of select NK cell subsets and NK cell receptor expression over time in several individual donors. Peripheral blood mononuclear cells were evaluated using flow cytometry via fluorochrome-conjugated antibodies against a number of NK cell receptors. Results were analyzed for both mean fluorescence intensity (MFI) and the percent positive cells for each receptor. CD56(bright) and CD56(dim) NK cell subsets were also considered separately, as was variation in receptor expression in NK cell subsets over time in selected individuals. Through this effort, we provide ranges of NK cell surface receptor expression for a local adult population as well as provide insight into intra-individual variation.
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Affiliation(s)
- Laura S. Angelo
- Center for Human Immunobiology, Department of Allergy, Immunology and Rheumatology, The Feigin Center, Texas Children’s Hospital, 1102 Bates Street, Suite 330, Houston, TX, USA 77030 and Baylor College of Medicine
| | - Pinaki P. Banerjee
- Center for Human Immunobiology, Department of Allergy, Immunology and Rheumatology, The Feigin Center, Texas Children’s Hospital, 1102 Bates Street, Suite 330, Houston, TX, USA 77030 and Baylor College of Medicine
| | - Linda Monaco-Shawver
- Children’s Hospital of Philadelphia Research Institute, 3615 Civic Center Boulevard, Philadelphia, PA USA 19104
| | - Joshua B. Rosen
- Drexel University College of Medicine, 245 N. 15 Street, Philadelphia, PA USA 19102
| | - George Makedonas
- Center for Human Immunobiology, Department of Allergy, Immunology and Rheumatology, The Feigin Center, Texas Children’s Hospital, 1102 Bates Street, Suite 330, Houston, TX, USA 77030 and Baylor College of Medicine
| | - Lisa R. Forbes
- Center for Human Immunobiology, Department of Allergy, Immunology and Rheumatology, The Feigin Center, Texas Children’s Hospital, 1102 Bates Street, Suite 330, Houston, TX, USA 77030 and Baylor College of Medicine
| | - Emily M. Mace
- Center for Human Immunobiology, Department of Allergy, Immunology and Rheumatology, The Feigin Center, Texas Children’s Hospital, 1102 Bates Street, Suite 330, Houston, TX, USA 77030 and Baylor College of Medicine
| | - Jordan S. Orange
- Center for Human Immunobiology, Department of Allergy, Immunology and Rheumatology, The Feigin Center, Texas Children’s Hospital, 1102 Bates Street, Suite 330, Houston, TX, USA 77030 and Baylor College of Medicine
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Xu X, Li Y, Gauthier L, Chen Q, Vivier E, Mariuzza RA. Expression, crystallization and X-ray diffraction analysis of a complex between B7-H6, a tumor cell ligand for the natural cytotoxicity receptor NKp30, and an inhibitory antibody. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:697-701. [PMID: 26057798 DOI: 10.1107/s2053230x15006755] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 04/03/2015] [Indexed: 12/13/2022]
Abstract
Natural killer (NK) cells are essential components of the innate immune response to tumors and viral infections. In humans, the activating natural cytotoxicity receptor NKp30 plays a major role in NK cell-mediated tumor cell lysis. NKp30 recognizes the cell-surface protein B7-H6, which is expressed on tumor, but not healthy, cells. A mouse monoclonal antibody (17B1.3) against human B7-H6 has been developed (Kd = 0.2 µM) to investigate NKp30-mediated NK cell activation and to target tumors expressing B7-H6. Surprisingly, 17B1.3 blocks NK cell activation without interfering with the binding of B7-H6 to NKp30. Understanding the inhibitory mechanism of this antibody will require knowing the structure of 17B1.3 bound to B7-H6. The antigen-binding fragment (Fab) of 17B1.3 was expressed by in vitro folding from bacterial inclusion bodies. The extracellular domain of B7-H6 was produced by secretion from baculovirus-infected insect cells. Crystals of the Fab 17B1.3-B7-H6 complex grown by macro-seeding diffracted to 2.5 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 89.6, b = 138.0, c = 171.4 Å, α = β = γ = 90°. Comparison of the Fab 17B1.3-B7-H6 structure with the known NKp30-B7-H6 structure will elucidate the inhibitory mechanism of 17B1.3.
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Affiliation(s)
- Xiaoping Xu
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Yili Li
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Laurent Gauthier
- Innate Pharma S.A., 117 Avenue de Luminy, 13009 Marseille, France
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Institut National de la Santé et de la Recherche Médical U1104, 13288 Marseille, France
| | - Roy A Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
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40
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Goldberg AC, Rizzo LV. MHC structure and function – antigen presentation. Part 1. ACTA ACUST UNITED AC 2015; 13:153-6. [PMID: 25807245 PMCID: PMC4977602 DOI: 10.1590/s1679-45082015rb3122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/26/2014] [Indexed: 11/22/2022]
Abstract
The setting for the occurrence of an immune response is that of the need to cope with a vast array of different antigens from both pathogenic and non-pathogenic sources. When the first barriers against infection and innate defense fail, adaptive immune response enters the stage for recognition of the antigens by means of extremely variable molecules, namely immunoglobulins and T-cell receptors. The latter recognize the antigen exposed on cell surfaces, in the form of peptides presented by the HLA molecule. The first part of this review details the central role played by these molecules, establishing the close connection existing between their structure and their antigen presenting function.
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Sivori S, Olive D, López-Botet M, Vitale M. NK receptors: tools for a polyvalent cell family. Front Immunol 2014; 5:617. [PMID: 25520722 PMCID: PMC4253963 DOI: 10.3389/fimmu.2014.00617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/18/2014] [Indexed: 12/22/2022] Open
Affiliation(s)
- Simona Sivori
- Dipartimento di Medicina Sperimentale (DI.ME.S.), Centro di Eccellenza per le Ricerche Biomediche (CEBR), Università degli Studi di Genova , Genova , Italy
| | - Daniel Olive
- U1068, CRCM, Immunity and Cancer, INSERM , Marseille , France ; Institut Paoli-Calmettes , Marseille , France ; UM 105, Aix-Marseille Université , Marseille , France ; UMR7258, CNRS , Marseille , France
| | - Miguel López-Botet
- Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra , Barcelona , Spain
| | - Massimo Vitale
- IRCCS Azienda Ospedaliera Universitaria S.Martino-IST , Genova , Italy
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Steinle A. Transferrin' activation: bonding with transferrin receptors tunes KLRG1 function. Eur J Immunol 2014; 44:1600-3. [PMID: 24752778 DOI: 10.1002/eji.201444670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 04/07/2014] [Accepted: 04/15/2014] [Indexed: 11/10/2022]
Abstract
The inhibitory C-type lectin-like immunoreceptor KLRG1 enables mature NK cells and differentiated T cells to sense cadherin-expressing cells by ligating "classical" cadherins. Upon engagement of the KLRG1 ectodomain, an inhibitory signal emanates from the cytoplasmic immunoreceptor-tyrosine-based inhibition motif (ITIM), dampening functional responses of these lymphocytes. Malignancy-associated loss of cadherins has been proposed to relieve KLRG1-mediated inhibition of cytotoxic lymphocytes and thereby to contribute to tumor surveillance by an alternate mode of "missing self-recognition". In this issue of the European Journal of Immunology, Schweier et al. [Eur. J. Immunol. 2014. 44: 1851-1856] propose another intriguing mechanism that may relieve KLRG1-mediated inhibition in the course of lymphocyte activation. Subsequent to identification of the transferrin receptor (TfR) as a component of a high molecular mass KLRG1 complex, they demonstrate that a fraction of mouse KLRG1 molecules undergoes disulfide-bonding with TfRs and colocalises with the latter at the cell surface. In functional terms, high levels of TfRs such as those found on activated lymphocytes were found to be associated with decreased KLRG1 inhibitory function, indicating that TfRs may sequester KLRG1 from interacting with cadherins. Hence, this unexpected liaison between KLRG1 and TfR may represent a regulatory link between metabolic activation and responses of lymphocytes.
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Affiliation(s)
- Alexander Steinle
- Institute for Molecular Medicine, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
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43
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Heil M, Land WG. Danger signals - damaged-self recognition across the tree of life. FRONTIERS IN PLANT SCIENCE 2014; 5:578. [PMID: 25400647 PMCID: PMC4215617 DOI: 10.3389/fpls.2014.00578] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 10/07/2014] [Indexed: 05/15/2023]
Abstract
Multicellular organisms suffer injury and serve as hosts for microorganisms. Therefore, they require mechanisms to detect injury and to distinguish the self from the non-self and the harmless non-self (microbial mutualists and commensals) from the detrimental non-self (pathogens). Danger signals are "damage-associated molecular patterns" (DAMPs) that are released from the disrupted host tissue or exposed on stressed cells. Seemingly ubiquitous DAMPs are extracellular ATP or extracellular DNA, fragmented cell walls or extracellular matrices, and many other types of delocalized molecules and fragments of macromolecules that are released when pre-existing precursors come into contact with enzymes from which they are separated in the intact cell. Any kind of these DAMPs enable damaged-self recognition, inform the host on tissue disruption, initiate processes aimed at restoring homeostasis, such as sealing the wound, and prepare the adjacent tissues for the perception of invaders. In mammals, antigen-processing and -presenting cells such as dendritic cells mature to immunostimulatory cells after the perception of DAMPs, prime naïve T-cells and elicit a specific adaptive T-/B-cell immune response. We discuss molecules that serve as DAMPs in multiple organisms and their perception by pattern recognition receptors (PRRs). Ca(2+)-fluxes, membrane depolarization, the liberation of reactive oxygen species and mitogen-activated protein kinase (MAPK) signaling cascades are the ubiquitous molecular mechanisms that act downstream of the PRRs in organisms across the tree of life. Damaged-self recognition contains both homologous and analogous elements and is likely to have evolved in all eukaryotic kingdoms, because all organisms found the same solutions for the same problem: damage must be recognized without depending on enemy-derived molecules and responses to the non-self must be directed specifically against detrimental invaders.
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Affiliation(s)
- Martin Heil
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-IrapuatoIrapuato, México
- *Correspondence: Martin Heil, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Irapuato, Km 9.6 Libramiento Norte, Carretera Irapuato- León, Irapuato, Guanajuato, Mexico e-mail:
| | - Walter G. Land
- Molecular ImmunoRheumatology, INSERM UMR S1109, Laboratory of Excellence Transplantex, Faculty of Medicine, University of StrasbourgStrasbourg, France
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