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Pymm P, Saunders PM, Anand S, MacLachlan BJ, Faoro C, Hitchen C, Rossjohn J, Brooks AG, Vivian JP. The Structural Basis for Recognition of Human Leukocyte Antigen Class I Molecules by the Pan-HLA Antibody W6/32. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:876-885. [PMID: 39093013 DOI: 10.4049/jimmunol.2400328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
The central immunological role of HLA class I (HLA-I) in presenting peptide Ags to cellular components of the immune system has been the focus of intense study for >60 y. A confounding factor in the study of HLA-I has been the extreme polymorphism of these molecules. The mAb W6/32 has been a fundamental reagent bypassing the issue of polymorphism by recognizing an epitope that is conserved across diverse HLA-I allotypes. However, despite the widespread use of W6/32, the epitope of this Ab has not been definitively mapped. In this study, we present the crystal structure of the Fab fragment of W6/32 in complex with peptide-HLA-B*27:05. W6/32 bound to HLA-B*27:05 beneath the Ag-binding groove, recognizing a discontinuous epitope comprised of the α1, α2, and α3 domains of HLA-I and β2-microglobulin. The epitope comprises a region of low polymorphism reflecting the pan-HLA-I nature of the binding. Notably, the W6/32 epitope neither overlaps the HLA-I binding sites of either T cell Ag receptors or killer cell Ig-like receptors. However, it does coincide with the binding sites for leukocyte Ig-like receptors and CD8 coreceptors. Consistent with this, the use of W6/32 to block the interaction of NK cells with HLA-I only weakly impaired inhibition mediated by KIR3DL1, but impacted HLA-LILR recognition.
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Affiliation(s)
- Phillip Pymm
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Sushma Anand
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Bruce J MacLachlan
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Camilla Faoro
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Corinne Hitchen
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff
| | - Andrew G Brooks
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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Rascle P, Woolley G, Jost S, Manickam C, Reeves RK. NK cell education: Physiological and pathological influences. Front Immunol 2023; 14:1087155. [PMID: 36742337 PMCID: PMC9896005 DOI: 10.3389/fimmu.2023.1087155] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Natural killer (NK) cells represent a critical defense against viral infections and cancers. NK cells require integration of activating and inhibitory NK cell receptors to detect target cells and the balance of these NK cell inputs defines the global NK cell response. The sensitivity of the response is largely defined by interactions between self-major histocompatibility complex class I (MHC-I) molecules and specific inhibitory NK cell receptors, so-called NK cell education. Thus, NK cell education is a crucial process to generate tuned effector NK cell responses in different diseases. In this review, we discuss the relationship between NK cell education and physiologic factors (type of self-MHC-I, self-MHC-I allelic variants, variant of the self-MHC-I-binding peptides, cytokine effects and inhibitory KIR expression) underlying NK cell education profiles (effector function or metabolism). Additionally, we describe the broad-spectrum of effector educated NK cell functions on different pathologies (such as HIV-1, CMV and tumors, among others).
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Affiliation(s)
- Philippe Rascle
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Griffin Woolley
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Stephanie Jost
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Cordelia Manickam
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - R. Keith Reeves
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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3
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He Y, Chen Y, Yao L, Wang J, Sha X, Wang Y. The Inflamm-Aging Model Identifies Key Risk Factors in Atherosclerosis. Front Genet 2022; 13:865827. [PMID: 35706446 PMCID: PMC9191626 DOI: 10.3389/fgene.2022.865827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Atherosclerosis, one of the main threats to human life and health, is driven by abnormal inflammation (i.e., chronic inflammation or oxidative stress) during accelerated aging. Many studies have shown that inflamm-aging exerts a significant impact on the occurrence of atherosclerosis, particularly by inducing an immune homeostasis imbalance. However, the potential mechanism by which inflamm-aging induces atherosclerosis needs to be studied more thoroughly, and there is currently a lack of powerful prediction models.Methods: First, an improved inflamm-aging prediction model was constructed by integrating aging, inflammation, and disease markers with the help of machine learning methods; then, inflamm-aging scores were calculated. In addition, the causal relationship between aging and disease was identified using Mendelian randomization. A series of risk factors were also identified by causal analysis, sensitivity analysis, and network analysis.Results: Our results revealed an accelerated inflamm-aging pattern in atherosclerosis and suggested a causal relationship between inflamm-aging and atherosclerosis. Mechanisms involving inflammation, nutritional balance, vascular homeostasis, and oxidative stress were found to be driving factors of atherosclerosis in the context of inflamm-aging.Conclusion: In summary, we developed a model integrating crucial risk factors in inflamm-aging and atherosclerosis. Our computation pipeline could be used to explore potential mechanisms of related diseases.
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Affiliation(s)
- Yudan He
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yao Chen
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Lilin Yao
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Junyi Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Xianzheng Sha
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yin Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Yin Wang,
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Ichise H, Tsukamoto S, Hirashima T, Konishi Y, Oki C, Tsukiji S, Iwano S, Miyawaki A, Sumiyama K, Terai K, Matsuda M. Functional visualization of NK Cell-mediated killing of metastatic single tumor cells. eLife 2022; 11:76269. [PMID: 35113018 PMCID: PMC8849286 DOI: 10.7554/elife.76269] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/22/2022] [Indexed: 12/04/2022] Open
Abstract
Natural killer (NK) cells lyse invading tumor cells to limit metastatic growth in the lung, but how some cancers evade this host protective mechanism to establish a growing lesion is unknown. Here, we have combined ultra-sensitive bioluminescence imaging with intravital two-photon microscopy involving genetically encoded biosensors to examine this question. NK cells eliminated disseminated tumor cells from the lung within 24 hr of arrival, but not thereafter. Intravital dynamic imaging revealed that 50% of NK-tumor cell encounters lead to tumor cell death in the first 4 hr after tumor cell arrival, but after 24 hr of arrival, nearly 100% of the interactions result in the survival of the tumor cell. During this 24-hr period, the probability of ERK activation in NK cells upon encountering the tumor cells was decreased from 68% to 8%, which correlated with the loss of the activating ligand CD155/PVR/Necl5 from the tumor cell surface. Thus, by quantitatively visualizing, the NK-tumor cell interaction at the early stage of metastasis, we have revealed the crucial parameters of NK cell immune surveillance in the lung.
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Affiliation(s)
- Hiroshi Ichise
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shoko Tsukamoto
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Hirashima
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshinobu Konishi
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, Japan
| | - Satoshi Iwano
- Brain Science Institute, Center for Brain Science, RIKEN, Wako, Japan
| | - Atsushi Miyawaki
- Brain Science Institute, Center for Brain Science,, RIKEN, Wako, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Suita, Japan
| | - Kenta Terai
- Department of Pathology and Biology of Diseasesv Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Michiyuki Matsuda
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Pugh J, Guethlein L, Parham P. Abundant CpG-sequences in human genomes inhibit KIR3DL2-expressing NK cells. PeerJ 2021; 9:e12258. [PMID: 34760351 PMCID: PMC8574216 DOI: 10.7717/peerj.12258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/15/2021] [Indexed: 11/20/2022] Open
Abstract
Killer Immunoglobulin-like Receptors (KIR) comprise a diverse, highly polymorphic family of cell-surface glycoproteins that are principally expressed by Natural Killer (NK) cells. These innate immune lymphocytes fulfill vital functions in human reproduction and immune responses to viral infection. KIR3DL2 is an inhibitory NK cell receptor that recognizes a common epitope of the HLA-A3 and HLA-A11 class I glycoproteins of the major histocompatibility complex. KIR3DL2 also binds exogenous DNA containing the CpG motif. This interaction causes internalization of the KIR-DNA. Exogenous CpG-DNA typically activates NK cells, but the specificity of KIR3DL2-DNA binding and internalization is unclear. We hypothesized that KIR3DL2 binds exogenous DNA in a sequence-specific manner that differentiates pathogen DNA from self-DNA. In testing this hypothesis, we surveyed octameric CpG-DNA sequences in the human genome, and in reference genomes of all bacteria, fungi, viruses, and parasites, with focus on medically relevant species. Among all pathogens, the nucleotides flanking CpG motifs in the genomes of parasitic worms that infect humans are most divergent from those in the human genome. We cultured KIR3DL2+NKL cells with the commonest CpG-DNA sequences in either human or pathogen genomes. DNA uptake was negatively correlated with the most common CpG-DNA sequences in the human genome. These CpG-DNA sequences induced inhibitory signaling in KIR3DL2+NKL cells. In contrast, KIR3DL2+NKL cells lysed more malignant targets and produced more IFNγ after culture with CpG-DNA sequences prevalent in parasitic worms. By applying functional immunology to evolutionary genomics, we conclude that KIR3DL2 allows NK cells to differentiate self-DNA from pathogen DNA.
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Affiliation(s)
- Jason Pugh
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Lisbeth Guethlein
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States
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Leijonhufvud C, Reger R, Segerberg F, Theorell J, Schlums H, Bryceson YT, Childs RW, Carlsten M. LIR-1 educates expanded human NK cells and defines a unique antitumor NK cell subset with potent antibody-dependent cellular cytotoxicity. Clin Transl Immunology 2021; 10:e1346. [PMID: 34631057 PMCID: PMC8491220 DOI: 10.1002/cti2.1346] [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: 12/08/2020] [Revised: 09/01/2021] [Accepted: 09/16/2021] [Indexed: 11/07/2022] Open
Abstract
Objective KIR and NKG2A receptors educate human NK cells to stay responsive to cells with diminished HLA class I. Here, we addressed whether the HLA class I-binding receptor LIR-1 (LILRB1/ILT2/CD85j), which is widely expressed on human NK cells, can mediate education and contribute to antitumor functions of NK cells. Methods Healthy donor NK cells either unstimulated, overnight cytokine-activated or ex vivo-expanded were used to target human cell lines. Phenotype and function were analysed using flow cytometry and 51Cr-release assays. Results We found that the inhibitory receptor LIR-1 can mediate NK cell education under specific conditions. This novel finding was exclusive to expanded NK cells and further characterisation of the cells revealed high expression of granzyme B and DNAM-1, which both previously have been linked to NK cell education. Corroborating the rheostat education model, LIR-1 co-expression with an educating KIR further increased the responsiveness of expanded NK cells. Inversely, antibody masking of LIR-1 decreased the responsiveness. LIR-1+ expanded NK cells displayed high intrinsic ADCC that, in contrast to KIR and NKG2A, was not inhibited by HLA class I. Conclusion These findings identify a unique NK cell subset attractive for adoptive cell therapy to treat cancer. Given that LIR-1 binds most HLA class I molecules, this subset may be explored in both autologous and allogeneic settings to innately reject HLA class I- tumor cells as well as HLA class I+ target cells when combined with antitumor antibodies. Further studies are warranted to address the potential of this subset in vivo.
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Affiliation(s)
- Caroline Leijonhufvud
- Department of Medicine Center for Hematology and Regenerative Medicine Karolinska Institutet Stockholm Sweden
| | - Robert Reger
- Cellular and Molecular Therapeutics Branch National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD USA
| | - Filip Segerberg
- Department of Medicine Center for Hematology and Regenerative Medicine Karolinska Institutet Stockholm Sweden
| | - Jakob Theorell
- Department of Medicine Center for Hematology and Regenerative Medicine Karolinska Institutet Stockholm Sweden.,Oxford Autoimmune Neurology Group Nuffield Department of Clinical Neurosciences University of Oxford Oxford UK.,Department of Clinical Neuroscience Centre for Molecular Medicine Karolinska Institute Karolinska University Hospital Stockholm Sweden
| | - Heinrich Schlums
- Department of Medicine Center for Hematology and Regenerative Medicine Karolinska Institutet Stockholm Sweden
| | - Yenan T Bryceson
- Department of Medicine Center for Hematology and Regenerative Medicine Karolinska Institutet Stockholm Sweden
| | - Richard W Childs
- Cellular and Molecular Therapeutics Branch National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD USA
| | - Mattias Carlsten
- Department of Medicine Center for Hematology and Regenerative Medicine Karolinska Institutet Stockholm Sweden.,Center for Cell Therapy and Allogeneic Stem Cell Transplantation Karolinska University Hospital Sweden
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Tian Q, Gao H, Zhao W, Zhou Y, Yang J. Development and validation of an immune gene set-based prognostic signature in cutaneous melanoma. Future Oncol 2021; 17:4115-4129. [PMID: 34291650 DOI: 10.2217/fon-2021-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We aimed to fully understand the landscape of the skin cutaneous melanoma (SKCM) microenvironment and develop an immune prognostic signature that can predict the prognosis for SKCM patients. RNA sequencing data and clinical information were downloaded from the Cancer Genome Atlas and Gene Expression Omnibus databases. The immune-prognostic signature was constructed by LASSO Cox regression analysis. We calculated the relative abundance of 29 immune-related gene sets based on the mRNA expression profiles of 314 SKCM patients in the Cancer Genome Atlas training set. Hierarchical clustering was performed to classify SKCM patients into three clusters: immunity-high, -medium and -low. The values of our prognostic model in predicting disease progression, metastasis and immunotherapeutic responses were also validated. In conclusion, the prognostic model demonstrated a powerful ability to distinguish and predict SKCM patients' prognosis.
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Affiliation(s)
- Qi Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wen Zhao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yan Zhou
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Jin Yang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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Amorim LM, Augusto DG, Nemat-Gorgani N, Montero-Martin G, Marin WM, Shams H, Dandekar R, Caillier S, Parham P, Fernández-Viña MA, Oksenberg JR, Norman PJ, Hollenbach JA. High-Resolution Characterization of KIR Genes in a Large North American Cohort Reveals Novel Details of Structural and Sequence Diversity. Front Immunol 2021; 12:674778. [PMID: 34025673 PMCID: PMC8137979 DOI: 10.3389/fimmu.2021.674778] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
The KIR (killer-cell immunoglobulin-like receptor) region is characterized by structural variation and high sequence similarity among genes, imposing technical difficulties for analysis. We undertook the most comprehensive study to date of KIR genetic diversity in a large population sample, applying next-generation sequencing in 2,130 United States European-descendant individuals. Data were analyzed using our custom bioinformatics pipeline specifically designed to address technical obstacles in determining KIR genotypes. Precise gene copy number determination allowed us to identify a set of uncommon gene-content KIR haplotypes accounting for 5.2% of structural variation. In this cohort, KIR2DL4 is the framework gene that most varies in copy number (6.5% of all individuals). We identified phased high-resolution alleles in large multi-locus insertions and also likely founder haplotypes from which they were deleted. Additionally, we observed 250 alleles at 5-digit resolution, of which 90 have frequencies ≥1%. We found sequence patterns that were consistent with the presence of novel alleles in 398 (18.7%) individuals and contextualized multiple orphan dbSNPs within the KIR complex. We also identified a novel KIR2DL1 variant, Pro151Arg, and demonstrated by molecular dynamics that this substitution is predicted to affect interaction with HLA-C. No previous studies have fully explored the full range of structural and sequence variation of KIR as we present here. We demonstrate that pairing high-throughput sequencing with state-of-art computational tools in a large cohort permits exploration of all aspects of KIR variation including determination of population-level haplotype diversity, improving understanding of the KIR system, and providing an important reference for future studies.
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Affiliation(s)
- Leonardo M. Amorim
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danillo G. Augusto
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | - Gonzalo Montero-Martin
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Wesley M. Marin
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Hengameh Shams
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Ravi Dandekar
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Stacy Caillier
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Peter Parham
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | | | - Jorge R. Oksenberg
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, CA, United States
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