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Beelen NA, Molenbroeck SJJ, Groeneveld L, Voorter CE, Bos GMJ, Wieten L. HLA class I NK-epitopes and KIR diversities in patients with multiple myeloma. Immunogenetics 2024; 76:155-164. [PMID: 38478091 PMCID: PMC11087314 DOI: 10.1007/s00251-024-01336-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/22/2024] [Indexed: 05/12/2024]
Abstract
Multiple myeloma (MM) is a hematological malignancy caused by the clonal expansion of malignant plasma cells in the bone marrow. Myeloma cells are susceptible to killing by natural killer (NK) cells, but NK cells fail to control disease progression, suggesting immunosuppression. The activation threshold of NK-effector function is regulated by interaction between KIRs and self-HLA class I, during a process called "education" to ensure self-tolerance. NK cells can respond to diseased cells based on the absence of HLA class I expression ("Missing-self" hypothesis). The HLA and KIR repertoire is extremely diverse; thus, the present study aimed to characterize potential variances in genotypic composition of HLA Class I NK-epitopes and KIRs between MM patients and healthy controls. Genotypic expression of KIR and HLA (HLA-C group-C1/C2 and Bw4 motifs (including HLA-A*23, A*24, A*32) were analyzed in 172 MM patients and 195 healthy controls. Compared to healthy controls, we did not observe specific KIR genes or genotypes, or HLA NK-epitopes with higher prevalence among MM patients. The presence of all three HLA NK-epitopes (C1+C2+Bw4+) was not associated with MM occurrence. However, MM patients were more likely to be C1-/C2+/Bw4+ (p = 0.049, OR 1.996). In line with this, there was a trend of increased genetic co-occurrence of Bw4 and KIR3DL1 in MM patients (p = 0.05, OR 1.557). Furthermore, MM patients were more likely to genetically express both C2/KIR2DL1 and Bw4/KIR3DL1 (p = 0.019, OR 2.453). Our results reveal an HLA NK-epitope combination that is associated with the occurrence of MM. No specific KIR genotypes were associated with MM.
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Affiliation(s)
- Nicky A Beelen
- Division of Hematology, Department of Internal Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands
- GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Stefan J J Molenbroeck
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Lisette Groeneveld
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Christien E Voorter
- GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Gerard M J Bos
- Division of Hematology, Department of Internal Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands
- GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands
| | - Lotte Wieten
- GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands.
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center+, Maastricht, the Netherlands.
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2
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Hibler W, Merlino G, Yu Y. CAR NK Cell Therapy for the Treatment of Metastatic Melanoma: Potential & Prospects. Cells 2023; 12:2750. [PMID: 38067178 PMCID: PMC10706172 DOI: 10.3390/cells12232750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Melanoma is among the most lethal forms of cancer, accounting for 80% of deaths despite comprising just 5% of skin cancer cases. Treatment options remain limited due to the genetic and epigenetic mechanisms associated with melanoma heterogeneity that underlie the rapid development of secondary drug resistance. For this reason, the development of novel treatments remains paramount to the improvement of patient outcomes. Although the advent of chimeric antigen receptor-expressing T (CAR-T) cell immunotherapies has led to many clinical successes for hematological malignancies, these treatments are limited in their utility by their immune-induced side effects and a high risk of systemic toxicities. CAR natural killer (CAR-NK) cell immunotherapies are a particularly promising alternative to CAR-T cell immunotherapies, as they offer a more favorable safety profile and have the capacity for fine-tuned cytotoxic activity. In this review, the discussion of the prospects and potential of CAR-NK cell immunotherapies touches upon the clinical contexts of melanoma, the immunobiology of NK cells, the immunosuppressive barriers preventing endogenous immune cells from eliminating tumors, and the structure and design of chimeric antigen receptors, then finishes with a series of proposed design innovations that could improve the efficacy CAR-NK cell immunotherapies in future studies.
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Affiliation(s)
| | | | - Yanlin Yu
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Nersesian S, Carter EB, Lee SN, Westhaver LP, Boudreau JE. Killer instincts: natural killer cells as multifactorial cancer immunotherapy. Front Immunol 2023; 14:1269614. [PMID: 38090565 PMCID: PMC10715270 DOI: 10.3389/fimmu.2023.1269614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
Natural killer (NK) cells integrate heterogeneous signals for activation and inhibition using germline-encoded receptors. These receptors are stochastically co-expressed, and their concurrent engagement and signaling can adjust the sensitivity of individual cells to putative targets. Against cancers, which mutate and evolve under therapeutic and immunologic pressure, the diversity for recognition provided by NK cells may be key to comprehensive cancer control. NK cells are already being trialled as adoptive cell therapy and targets for immunotherapeutic agents. However, strategies to leverage their naturally occurring diversity and agility have not yet been developed. In this review, we discuss the receptors and signaling pathways through which signals for activation or inhibition are generated in NK cells, focusing on their roles in cancer and potential as targets for immunotherapies. Finally, we consider the impacts of receptor co-expression and the potential to engage multiple pathways of NK cell reactivity to maximize the scope and strength of antitumor activities.
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Affiliation(s)
- Sarah Nersesian
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Emily B. Carter
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Stacey N. Lee
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | | | - Jeanette E. Boudreau
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
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4
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Philippon C, Tao S, Clement D, Haroun-Izquierdo A, Kichula KM, Netskar H, Brandt L, Oei VS, Kanaya M, Lanuza PM, Schaffer M, Goodridge JP, Horowitz A, Zhu F, Hammer Q, Sohlberg E, Majhi RK, Kveberg L, Önfelt B, Norman PJ, Malmberg KJ. Allelic variation of KIR and HLA tunes the cytolytic payload and determines functional hierarchy of NK cell repertoires. Blood Adv 2023; 7:4492-4504. [PMID: 37327114 PMCID: PMC10440473 DOI: 10.1182/bloodadvances.2023009827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/18/2023] [Accepted: 06/04/2023] [Indexed: 06/18/2023] Open
Abstract
The functionality of natural killer (NK) cells is tuned during education and is associated with remodeling of the lysosomal compartment. We hypothesized that genetic variation in killer cell immunoglobulin-like receptor (KIR) and HLA, which is known to influence the functional strength of NK cells, fine-tunes the payload of effector molecules stored in secretory lysosomes. To address this possibility, we performed a high-resolution analysis of KIR and HLA class I genes in 365 blood donors and linked genotypes to granzyme B loading and functional phenotypes. We found that granzyme B levels varied across individuals but were stable over time in each individual and genetically determined by allelic variation in HLA class I genes. A broad mapping of surface receptors and lysosomal effector molecules revealed that DNAM-1 and granzyme B levels served as robust metric of the functional state in NK cells. Variation in granzyme B levels at rest was tightly linked to the lytic hit and downstream killing of major histocompatibility complex-deficient target cells. Together, these data provide insights into how variation in genetically hardwired receptor pairs tunes the releasable granzyme B pool in NK cells, resulting in predictable hierarchies in global NK cell function.
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Affiliation(s)
- Camille Philippon
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Sudan Tao
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Dennis Clement
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Alvaro Haroun-Izquierdo
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Katherine M. Kichula
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Herman Netskar
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Ludwig Brandt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincent Sheng Oei
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Minoru Kanaya
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Pilar Maria Lanuza
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marie Schaffer
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Amir Horowitz
- Department of Oncological Sciences, The Marc and Jennifer Lipshultz Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Faming Zhu
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Quirin Hammer
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ebba Sohlberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rakesh Kumar Majhi
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Lise Kveberg
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Björn Önfelt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Paul J. Norman
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Karl-Johan Malmberg
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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5
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Palmer WH, Leaton LA, Codo AC, Crute B, Roest J, Zhu S, Petersen J, Tobin RP, Hume PS, Stone M, van Bokhoven A, Gerich ME, McCarter MD, Zhu Y, Janssen WJ, Vivian JP, Trowsdale J, Getahun A, Rossjohn J, Cambier J, Loh L, Norman PJ. Polymorphic KIR3DL3 expression modulates tissue-resident and innate-like T cells. Sci Immunol 2023; 8:eade5343. [PMID: 37390222 PMCID: PMC10360443 DOI: 10.1126/sciimmunol.ade5343] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Most human killer cell immunoglobulin-like receptors (KIR) are expressed by natural killer (NK) cells and recognize HLA class I molecules as ligands. KIR3DL3 is a conserved but polymorphic inhibitory KIR recognizing a B7 family ligand, HHLA2, and is implicated for immune checkpoint targeting. The expression profile and biological function of KIR3DL3 have been somewhat elusive, so we searched extensively for KIR3DL3 transcripts, revealing highly enriched expression in γδ and CD8+ T cells rather than NK cells. These KIR3DL3-expressing cells are rare in the blood and thymus but more common in the lungs and digestive tract. High-resolution flow cytometry and single-cell transcriptomics showed that peripheral blood KIR3DL3+ T cells have an activated transitional memory phenotype and are hypofunctional. The T cell receptor (TCR) usage is biased toward genes from early rearranged TCR-α variable segments or Vδ1 chains. In addition, we show that TCR-mediated stimulation can be inhibited through KIR3DL3 ligation. Whereas we detected no impact of KIR3DL3 polymorphism on ligand binding, variants in the proximal promoter and at residue 86 can reduce expression. Together, we demonstrate that KIR3DL3 is up-regulated alongside unconventional T cell stimulation and that individuals may vary in their ability to express KIR3DL3. These results have implications for the personalized targeting of KIR3DL3/HHLA2 checkpoint inhibition.
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Affiliation(s)
- William H. Palmer
- Department of Biomedical Informatics, University of
Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology & Microbiology, University of
Colorado School of Medicine, Aurora, CO, USA
| | - Laura Ann Leaton
- Department of Biomedical Informatics, University of
Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology & Microbiology, University of
Colorado School of Medicine, Aurora, CO, USA
| | - Ana Campos Codo
- Department of Biomedical Informatics, University of
Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology & Microbiology, University of
Colorado School of Medicine, Aurora, CO, USA
| | - Bergren Crute
- Department of Immunology & Microbiology, University of
Colorado School of Medicine, Aurora, CO, USA
| | - James Roest
- Infection and Immunity Program and Department of
Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash
University, Clayton, Victoria, Australia
| | - Shiying Zhu
- Infection and Immunity Program and Department of
Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash
University, Clayton, Victoria, Australia
| | - Jan Petersen
- Infection and Immunity Program and Department of
Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash
University, Clayton, Victoria, Australia
| | - Richard P. Tobin
- Department of Surgery, Division of Surgical Oncology,
University of Colorado School of Medicine, Aurora, CO, USA
| | - Patrick S. Hume
- Department of Medicine, National Jewish Health, Denver, CO,
USA
| | - Matthew Stone
- Department of Surgery, Division of Surgical Oncology,
University of Colorado School of Medicine, Aurora, CO, USA
| | - Adrie van Bokhoven
- Department of Pathology, University of Colorado School of
Medicine, Aurora, CO, USA
| | - Mark E. Gerich
- Division of Gastroenterology and Hepatology, University of
Colorado School of Medicine, Aurora, CO, USA
| | - Martin D. McCarter
- Department of Surgery, Division of Surgical Oncology,
University of Colorado School of Medicine, Aurora, CO, USA
| | - Yuwen Zhu
- Department of Surgery, Division of Surgical Oncology,
University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Julian P. Vivian
- Infection and Immunity Program and Department of
Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash
University, Clayton, Victoria, Australia
| | | | - Andrew Getahun
- Department of Immunology & Microbiology, University of
Colorado School of Medicine, Aurora, CO, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of
Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash
University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University,
School of Medicine, Heath Park, Cardiff, UK
| | - John Cambier
- Department of Immunology & Microbiology, University of
Colorado School of Medicine, Aurora, CO, USA
| | - Liyen Loh
- Department of Immunology & Microbiology, University of
Colorado School of Medicine, Aurora, CO, USA
- Department of Microbiology and Immunology, University of
Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville,
Australia
| | - Paul J. Norman
- Department of Biomedical Informatics, University of
Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology & Microbiology, University of
Colorado School of Medicine, Aurora, CO, USA
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6
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Bruijnesteijn J. HLA/MHC and KIR characterization in humans and non-human primates using Oxford Nanopore Technologies and Pacific Biosciences sequencing platforms. HLA 2023; 101:205-221. [PMID: 36583332 DOI: 10.1111/tan.14957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The gene products of the HLA/MHC and KIR multigene families are important modulators of the immune system and are associated with health and disease. Characterization of the genes encoding these receptors has been integrated into different biomedical applications, including transplantation and reproduction biology, immune therapies and in fundamental research into disease susceptibility or resistance. Conventional short-read sequencing strategies have shown their value in high throughput typing, but are insufficient to uncover the entire complexity of the highly polymorphic HLA/MHC and KIR gene systems. The implementation of single-molecule and real-time sequencing platforms, offered by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), revolutionized the fields of genomics and transcriptomics. Using fundamentally distinct principles, these platforms generate long-read data that can unwire the plasticity of the HLA/MHC and KIR genes, including high-resolution characterization of genes, alleles, phased haplotypes, transcription levels and epigenetics modification patterns. These insights might have profound clinical relevance, such as improved matching of donors and patients in clinical transplantation, but could also lift disease association studies to a higher level. Even more, a comprehensive characterization may refine animal models in preclinical studies. In this review, the different HLA/MHC and KIR characterization approaches using PacBio and ONT platforms are described and discussed.
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Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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7
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Ren X, Peng M, Xing P, Wei Y, Galbo PM, Corrigan D, Wang H, Su Y, Dong X, Sun Q, Li Y, Zhang X, Edelmann W, Zheng D, Zang X. Blockade of the immunosuppressive KIR2DL5/PVR pathway elicits potent human NK cell-mediated antitumor immunity. J Clin Invest 2022; 132:e163620. [PMID: 36377656 PMCID: PMC9663162 DOI: 10.1172/jci163620] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/23/2022] [Indexed: 09/29/2023] Open
Abstract
Cancer immunotherapy targeting the TIGIT/PVR pathway is currently facing challenges. KIR2DL5, a member of the human killer cell, immunoglobulin-like receptor (KIR) family, has recently been identified as another binding partner for PVR. The biology and therapeutic potential of the KIR2DL5/PVR pathway are largely unknown. Here we report that KIR2DL5 was predominantly expressed on human NK cells with mature phenotype and cytolytic function and that it bound to PVR without competition with the other 3 known PVR receptors. The interaction between KIR2DL5 on NK cells and PVR on target cells induced inhibitory synapse formation, whereas new monoclonal antibodies blocking the KIR2DL5-PVR interaction robustly augmented the NK cytotoxicity against PVR+ human tumors. Mechanistically, both intracellular ITIM and ITSM of KIR2DL5 underwent tyrosine phosphorylation after engagement, which was essential for KIR2DL5-mediated NK suppression by recruiting SHP-1 and/or SHP-2. Subsequently, ITIM/SHP-1/SHP-2 and ITSM/SHP-1 downregulated the downstream Vav1/ERK1/2/p90RSK/NF-κB signaling. KIR2DL5+ immune cells infiltrated in various types of PVR+ human cancers. Markedly, the KIR2DL5 blockade reduced tumor growth and improved overall survival across multiple NK cell-based humanized tumor models. Thus, our results revealed functional mechanisms of KIR2DL5-mediated NK cell immune evasion, demonstrated blockade of the KIR2DL5/PVR axis as a therapy for human cancers, and provided an underlying mechanism for the clinical failure of anti-TIGIT therapies.
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Affiliation(s)
- Xiaoxin Ren
- Department of Microbiology and Immunology and
| | - Mou Peng
- Department of Microbiology and Immunology and
| | - Peng Xing
- Department of Microbiology and Immunology and
| | - Yao Wei
- Department of Microbiology and Immunology and
| | - Phillip M. Galbo
- Department of Microbiology and Immunology and
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Hao Wang
- Department of Microbiology and Immunology and
| | - Yingzhen Su
- Department of Microbiology and Immunology and
| | | | - Qizhe Sun
- Department of Microbiology and Immunology and
| | - Yixian Li
- Department of Microbiology and Immunology and
- Division of Pediatric Hematology/Oncology/Transplant and Cellular Therapy, Children’s Hospital at Montefiore, Bronx, New York, USA
| | | | | | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- Departments of Neurology and Neuroscience
| | - Xingxing Zang
- Department of Microbiology and Immunology and
- Department of Oncology
- Department of Medicine, and
- Department of Urology, Albert Einstein College of Medicine, Bronx, New York, USA
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8
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Pollock NR, Harrison GF, Norman PJ. Immunogenomics of Killer Cell Immunoglobulin-Like Receptor (KIR) and HLA Class I: Coevolution and Consequences for Human Health. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:1763-1775. [PMID: 35561968 PMCID: PMC10038757 DOI: 10.1016/j.jaip.2022.04.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022]
Abstract
Interactions of killer cell immunoglobin-like receptors (KIR) with human leukocyte antigens (HLA) class I regulate effector functions of key cytotoxic cells of innate and adaptive immunity. The extreme diversity of this interaction is genetically determined, having evolved in the ever-changing environment of pathogen exposure. Diversity of KIR and HLA genes is further facilitated by their independent segregation on separate chromosomes. That fetal implantation relies on many of the same types of immune cells as infection control places certain constraints on the evolution of KIR interactions with HLA. Consequently, specific inherited combinations of receptors and ligands may predispose to specific immune-mediated diseases, including autoimmunity. Combinatorial diversity of KIR and HLA class I can also differentiate success rates of immunotherapy directed to these diseases. Progress toward both etiopathology and predicting response to therapy is being achieved through detailed characterization of the extent and consequences of the combinatorial diversity of KIR and HLA. Achieving these goals is more tractable with the development of integrated analyses of molecular evolution, function, and pathology that will establish guidelines for understanding and managing risks. Here, we present what is known about the coevolution of KIR with HLA class I and the impact of their complexity on immune function and homeostasis.
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Affiliation(s)
- Nicholas R Pollock
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo.
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9
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Grewal RK, Das J. Spatially resolved in silico modeling of NKG2D signaling kinetics suggests a key role of NKG2D and Vav1 Co-clustering in generating natural killer cell activation. PLoS Comput Biol 2022; 18:e1010114. [PMID: 35584138 PMCID: PMC9154193 DOI: 10.1371/journal.pcbi.1010114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/31/2022] [Accepted: 04/18/2022] [Indexed: 11/18/2022] Open
Abstract
Natural Killer (NK) cells provide key resistance against viral infections and tumors. A diverse set of activating and inhibitory NK cell receptors (NKRs) interact with cognate ligands presented by target host cells, where integration of dueling signals initiated by the ligand-NKR interactions determines NK cell activation or tolerance. Imaging experiments over decades have shown micron and sub-micron scale spatial clustering of activating and inhibitory NKRs. The mechanistic roles of these clusters in affecting downstream signaling and activation are often unclear. To this end, we developed a predictive in silico framework by combining spatially resolved mechanistic agent based modeling, published TIRF imaging data, and parameter estimation to determine mechanisms by which formation and spatial movements of activating NKG2D microclusters affect early time NKG2D signaling kinetics in a human cell line NKL. We show co-clustering of NKG2D and the guanosine nucleotide exchange factor Vav1 in NKG2D microclusters plays a dominant role over ligand (ULBP3) rebinding in increasing production of phospho-Vav1(pVav1), an activation marker of early NKG2D signaling. The in silico model successfully predicts several scenarios of inhibition of NKG2D signaling and time course of NKG2D spatial clustering over a short (~3 min) interval. Modeling shows the presence of a spatial positive feedback relating formation and centripetal movements of NKG2D microclusters, and pVav1 production offers flexibility towards suppression of activating signals by inhibitory KIR ligands organized in inhomogeneous spatial patterns (e.g., a ring). Our in silico framework marks a major improvement in developing spatiotemporal signaling models with quantitatively estimated model parameters using imaging data. Natural Killer cells are lymphocytes of our innate immunity and provide important resistance against viral infections and tumors. NK cells scan the local environment with diverse activating and inhibitory NK cell receptors (NKRs) and remain tolerized or lyse target cells expressing cognate ligands to NKRs. NKRs have been found to form micron sized clusters (or microclusters) as they interact with cognate ligands, and mechanisms regarding how the formation and movements of these microclusters influence NK cell signaling and activation, specifically related to activating NKRs, are often unclear. To this end, we develop a predictive spatially resolved early-time NK cell signaling model to study the interplay between membrane-proximal biochemical signaling events and the kinetics of microclusters of activating NKG2D and inhibitory KIR2DL2 receptors. We used published TIRF imaging data to validate our in silico models and estimate model parameters. Predictions from multiple in silico models are tested against a variety of data obtained from published imaging experiments and immunoassays. Our analysis suggests co-clustering of NKG2D and the guanosine nucleotide exchange factor Vav1 in the microclusters plays a major role in enhancing downstream activating signals. The developed framework can be extended to describe spatiotemporal signaling for other activating NKRs including CD16.
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Affiliation(s)
- Rajdeep Kaur Grewal
- Battelle Center for Mathematical Medicine, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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10
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Ritari J, Hyvärinen K, Partanen J, Koskela S. KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population. PeerJ 2022; 10:e12692. [PMID: 35036093 PMCID: PMC8744484 DOI: 10.7717/peerj.12692] [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: 08/26/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. Through regulation of natural killer (NK) cell activity KIRs participate in tumour surveillance and clearing viral infections. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Inferring KIR gene content from genetic variant data is therefore desirable for immunogenetic analysis, particularly in the context of growing biobank genome data collections that rely on genotyping by microarray. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 807 Finnish biobank samples genotyped for 5900 KIR-region SNPs and analysed for KIR gene content with targeted sequencing. Cross-validation results demonstrate a high mean overall accuracy of 98.5% (95% CI [97.0-99.2]%) which compares favourably with previous methods including short-read sequencing based approaches.
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Affiliation(s)
- Jarmo Ritari
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | | | - Satu Koskela
- Finnish Red Cross Blood Service, Helsinki, Finland
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11
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Relevance of Polymorphic KIR and HLA Class I Genes in NK-Cell-Based Immunotherapies for Adult Leukemic Patients. Cancers (Basel) 2021; 13:cancers13153767. [PMID: 34359667 PMCID: PMC8345033 DOI: 10.3390/cancers13153767] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Immunotherapies are promising approaches to curing different acute leukemias. Natural killer (NK) cells are lymphocytes that are efficient in the elimination of leukemic cells. NK-cell-based immunotherapies are particularly attractive, but the landscape of the heterogeneity of NK cells must be deciphered. This review provides an overview of the polymorphic KIR and HLA class I genes that modulate the NK cell repertoire and how these markers can improve the outcomes of patients with acute leukemia. A better knowledge of these genetic markers that are linked to NK cell subsets that are efficient against hematological diseases will optimize hematopoietic stem-cell donor selection and NK immunotherapy design. Abstract Since the mid-1990s, the biology and functions of natural killer (NK) cells have been deeply investigated in healthy individuals and in people with diseases. These effector cells play a particularly crucial role after allogeneic hematopoietic stem-cell transplantation (HSCT) through their graft-versus-leukemia (GvL) effect, which is mainly mediated through polymorphic killer-cell immunoglobulin-like receptors (KIRs) and their cognates, HLA class I ligands. In this review, we present how KIRs and HLA class I ligands modulate the structural formation and the functional education of NK cells. In particular, we decipher the current knowledge about the extent of KIR and HLA class I gene polymorphisms, as well as their expression, interaction, and functional impact on the KIR+ NK cell repertoire in a physiological context and in a leukemic context. In addition, we present the impact of NK cell alloreactivity on the outcomes of HSCT in adult patients with acute leukemia, as well as a description of genetic models of KIRs and NK cell reconstitution, with a focus on emergent T-cell-repleted haplo-identical HSCT using cyclosphosphamide post-grafting (haplo-PTCy). Then, we document how the immunogenetics of KIR/HLA and the immunobiology of NK cells could improve the relapse incidence after haplo-PTCy. Ultimately, we review the emerging NK-cell-based immunotherapies for leukemic patients in addition to HSCT.
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12
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Migdal M, Ruan DF, Forrest WF, Horowitz A, Hammer C. MiDAS-Meaningful Immunogenetic Data at Scale. PLoS Comput Biol 2021; 17:e1009131. [PMID: 34228721 PMCID: PMC8284797 DOI: 10.1371/journal.pcbi.1009131] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 07/16/2021] [Accepted: 05/30/2021] [Indexed: 12/15/2022] Open
Abstract
Human immunogenetic variation in the form of HLA and KIR types has been shown to be strongly associated with a multitude of immune-related phenotypes. However, association studies involving immunogenetic loci most commonly involve simple analyses of classical HLA allelic diversity, resulting in limitations regarding the interpretability and reproducibility of results. We here present MiDAS, a comprehensive R package for immunogenetic data transformation and statistical analysis. MiDAS recodes input data in the form of HLA alleles and KIR types into biologically meaningful variables, allowing HLA amino acid fine mapping, analyses of HLA evolutionary divergence as well as experimentally validated HLA-KIR interactions. Further, MiDAS enables comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS thus closes the gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to immune and disease biology. It is freely available under a MIT license.
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Affiliation(s)
- Maciej Migdal
- Roche Global IT Solution Centre (RGITSC), Warsaw, Poland
| | - Dan Fu Ruan
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - William F. Forrest
- Department of OMNI Bioinformatics, Genentech, South San Francisco, California, United States of America
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christian Hammer
- Department of Cancer Immunology, Genentech, South San Francisco, California, United States of America
- Department of Human Genetics, Genentech, South San Francisco, California, United States of America
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13
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Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C. Nat Commun 2021; 12:2173. [PMID: 33846289 PMCID: PMC8041999 DOI: 10.1038/s41467-021-22359-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/12/2021] [Indexed: 01/07/2023] Open
Abstract
The closely related inhibitory killer-cell immunoglobulin-like receptors (KIR), KIR2DL2 and KIR2DL3, regulate the activation of natural killer cells (NK) by interacting with the human leukocyte antigen-C1 (HLA-C1) group of molecules. KIR2DL2, KIR2DL3 and HLA-C1 are highly polymorphic, with this variation being associated with differences in the onset and progression of some human diseases. However, the molecular bases underlying these associations remain unresolved. Here, we determined the crystal structures of KIR2DL2 and KIR2DL3 in complex with HLA-C*07:02 presenting a self-epitope. KIR2DL2 differed from KIR2DL3 in docking modality over HLA-C*07:02 that correlates with variabilty of recognition of HLA-C1 allotypes. Mutagenesis assays indicated differences in the mechanism of HLA-C1 allotype recognition by KIR2DL2 and KIR2DL3. Similarly, HLA-C1 allotypes differed markedly in their capacity to inhibit activation of primary NK cells. These functional differences derive, in part, from KIR2DS2 suggesting KIR2DL2 and KIR2DL3 binding geometries combine with other factors to distinguish HLA-C1 functional recognition.
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14
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Chen J, Madireddi S, Nagarkar D, Migdal M, Vander Heiden J, Chang D, Mukhyala K, Selvaraj S, Kadel EE, Brauer MJ, Mariathasan S, Hunkapiller J, Jhunjhunwala S, Albert ML, Hammer C. In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales. Brief Bioinform 2020; 22:5906908. [PMID: 32940337 PMCID: PMC8138874 DOI: 10.1093/bib/bbaa223] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Immunogenetic variation in humans is important in research, clinical diagnosis and increasingly a target for therapeutic intervention. Two highly polymorphic loci play critical roles, namely the human leukocyte antigen (HLA) system, which is the human version of the major histocompatibility complex (MHC), and the Killer-cell immunoglobulin-like receptors (KIR) that are relevant for responses of natural killer (NK) and some subsets of T cells. Their accurate classification has typically required the use of dedicated biological specimens and a combination of in vitro and in silico efforts. Increased availability of next generation sequencing data has led to the development of ancillary computational solutions. Here, we report an evaluation of recently published algorithms to computationally infer complex immunogenetic variation in the form of HLA alleles and KIR haplotypes from whole-genome or whole-exome sequencing data. For both HLA allele and KIR gene typing, we identified tools that yielded >97% overall accuracy for four-digit HLA types, and >99% overall accuracy for KIR gene presence, suggesting the readiness of in silico solutions for use in clinical and high-throughput research settings.
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Affiliation(s)
- Jieming Chen
- Department of Bioinformatics and Computational Biology
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15
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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: 17] [Impact Index Per Article: 4.3] [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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16
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Hanson AL, Vukcevic D, Leslie S, Harris J, Lê Cao KA, Kenna TJ, Brown MA. Epistatic interactions between killer immunoglobulin-like receptors and human leukocyte antigen ligands are associated with ankylosing spondylitis. PLoS Genet 2020; 16:e1008906. [PMID: 32804949 PMCID: PMC7451988 DOI: 10.1371/journal.pgen.1008906] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 08/27/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
The killer immunoglobulin-like receptors (KIRs), found predominantly on the surface of natural killer (NK) cells and some T-cells, are a collection of highly polymorphic activating and inhibitory receptors with variable specificity for class I human leukocyte antigen (HLA) ligands. Fifteen KIR genes are inherited in haplotypes of diverse gene content across the human population, and the repertoire of independently inherited KIR and HLA alleles is known to alter risk for immune-mediated and infectious disease by shifting the threshold of lymphocyte activation. We have conducted the largest disease-association study of KIR-HLA epistasis to date, enabled by the imputation of KIR gene and HLA allele dosages from genotype data for 12,214 healthy controls and 8,107 individuals with the HLA-B*27-associated immune-mediated arthritis, ankylosing spondylitis (AS). We identified epistatic interactions between KIR genes and their ligands (at both HLA subtype and allele resolution) that increase risk of disease, replicating analyses in a semi-independent cohort of 3,497 cases and 14,844 controls. We further confirmed that the strong AS-association with a pathogenic variant in the endoplasmic reticulum aminopeptidase gene ERAP1, known to alter the HLA-B*27 presented peptidome, is not modified by carriage of the canonical HLA-B receptor KIR3DL1/S1. Overall, our data suggests that AS risk is modified by the complement of KIRs and HLA ligands inherited, beyond the influence of HLA-B*27 alone, which collectively alter the proinflammatory capacity of KIR-expressing lymphocytes to contribute to disease immunopathogenesis. Cells of the immune system utilise various cell-surface receptors to differentiate between healthy and infected or malignant cells, enabling targeted inflammatory responses while minimising damage to self-tissue. In instances where the immune system fails to correctly differentiate healthy from diseased tissue, or inflammatory activity is poorly regulated, autoimmune or autoinflammatory conditions can develop. Here we have investigated a possible role for a class of immune-cell activating and inhibitory receptors in the pathogenesis of ankylosing spondylitis (AS), a common but poorly understood inflammatory arthritis in which the immune system causes severe damage to the joints of the pelvis and spine. Using genetic information from 12,214 healthy controls and 8,107 individuals with AS we were able to identify combinations of independently inherited immune cell receptors and their ligands that increase or decrease an individual’s risk of disease. This research provides new insight into the nature of co-inherited genetic factors that may collectively alter the proinflammatory capacity of immune cells, contributing to the immunopathogenesis of immune-mediated diseases.
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Affiliation(s)
- Aimee L. Hanson
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
| | | | - Damjan Vukcevic
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
- Data Science, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Stephen Leslie
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
- Data Science, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- School of Biosciences, University of Melbourne, Parkville, Victoria Australia
| | - Jessica Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
| | - Tony J. Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Matthew A. Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- * E-mail:
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17
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Goodson-Gregg FJ, Krepel SA, Anderson SK. Tuning of human NK cells by endogenous HLA-C expression. Immunogenetics 2020; 72:205-215. [PMID: 32219494 PMCID: PMC7182622 DOI: 10.1007/s00251-020-01161-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/11/2020] [Indexed: 12/14/2022]
Abstract
NK cells are primarily responsible for detecting malignant or pathogen-infected cells, and their function is influenced both by stress-associated activating signals and opposing inhibitory signals from receptors that recognize self MHC. The receptors that produce this inhibitory signal shift from the NKG2A:HLA-E system to that of KIR:HLA as the NK cells mature. This maturation is associated with an increase in lytic activity, as well as an increase in HLA-C protein levels controlled by the NK-specific HLA-C promoter, NK-Pro. We propose that modulation of the translatability of HLA-C transcripts in NK cells constitutes an evolutionary mechanism to control cis inhibitory signaling by HLA-C, which fine tunes NK cell activity. Furthermore, the high degree of variability in KIR receptor affinity for HLA alleles, as well as the variable expression levels of both KIR and HLA, suggest an evolutionary requirement for the tuning of NK lytic activity. Various data have demonstrated that mature NK cells may gain or lose lytic activity when placed in different environments. This indicates that NK cell activity may be more a function of constant tuning by inhibitory signals, rather than a static, irreversible "license to kill" granted to mature NK cells. Inhibitory signaling controls the filling of the cytolytic granule reservoir, which becomes depleted if there are insufficient inhibitory signals, leading to a hyporesponsive NK cell. We propose a novel model for the tuning of human NK cell activity via cis interactions in the context of recent findings on the mechanism of NK education.
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Affiliation(s)
- Frederick J Goodson-Gregg
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Stacey A Krepel
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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18
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Presence of donor-encoded centromeric KIR B content increases the risk of infectious mortality in recipients of myeloablative, T-cell deplete, HLA-matched HCT to treat AML. Bone Marrow Transplant 2020; 55:1975-1984. [PMID: 32203258 DOI: 10.1038/s41409-020-0858-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 02/06/2023]
Abstract
The reported influence of donor Killer-cell Immunoglobulin-like Receptor (KIR) genes on the outcomes of haematopoietic cell transplantation (HCT) are contradictory, in part due to diversity of disease, donor sources, era and conditioning regimens within and between different studies. Here, we describe the results of a retrospective clinical analysis establishing the effect of donor KIR motifs on the outcomes of 119 HLA-matched, unrelated donor HCT for adult acute myeloid leukaemia (AML) using myeloablative conditioning (MAC) in a predominantly T-cell deplete (TCD) cohort. We observed that HCT involving donors with at least one KIR B haplotype were more likely to result in non-relapse mortality (NRM) than HCT involving donors with two KIR A haplotypes (p = 0.019). Upon separation of KIR haplotypes into their centromeric (Cen) and telomeric (Tel) motif structures, we demonstrated that the Cen-B motif was largely responsible for this effect (p = 0.001). When the cause of NRM was investigated further, infection was the dominant cause of death (p = 0.006). No evidence correlating donor KIR B haplotype with relapse risk was observed. The results from this analysis confirm previous findings in the unrelated, TCD, MAC transplant setting and imply a protective role for donor-encoded Cen-A motifs against infection in allogeneic HCT recipients.
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19
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Kennedy PR, Barthen C, Williamson DJ, Pitkeathly WTE, Hazime KS, Cumming J, Stacey KB, Hilton HG, Carrington M, Parham P, Davis DM. Genetic diversity affects the nanoscale membrane organization and signaling of natural killer cell receptors. Sci Signal 2019; 12:eaaw9252. [PMID: 31848320 PMCID: PMC6944503 DOI: 10.1126/scisignal.aaw9252] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic diversity in human natural killer (NK) cell receptors is linked to resistance and susceptibility to many diseases. Here, we tested the effect of this diversity on the nanoscale organization of killer cell immunoglobulin-like receptors (KIRs). Using superresolution microscopy, we found that inhibitory KIRs encoded by different genes and alleles were organized differently at the surface of primary human NK cells. KIRs that were found at low abundance assembled into smaller clusters than those formed by KIRs that were more highly abundant, and at low abundance, there was a greater proportion of KIRs in clusters. Upon receptor triggering, a structured interface called the immune synapse assembles, which facilitates signal integration and controls NK cell responses. Here, triggering of low-abundance receptors resulted in less phosphorylation of the downstream phosphatase SHP-1 but more phosphorylation of the adaptor protein Crk than did triggering of high-abundance receptors. In cells with greater KIR abundance, SHP-1 dephosphorylated Crk, which potentiated NK cell spreading during activation. Thus, genetic variation modulates both the abundance and nanoscale organization of inhibitory KIRs. That is, as well as the number of receptors at the cell surface varying with genotype, the way in which these receptors are organized in the membrane also varies. Essentially, a change in the average surface abundance of a protein at the cell surface is a coarse descriptor entwined with changes in local nanoscale clustering. Together, our data indicate that genetic diversity in inhibitory KIRs affects membrane-proximal signaling and, unexpectedly, the formation of activating immune synapses.
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Affiliation(s)
- Philippa R Kennedy
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
| | - Charlotte Barthen
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
| | - David J Williamson
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
| | - William T E Pitkeathly
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
| | - Khodor S Hazime
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
| | - Joshua Cumming
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
| | - Kevin B Stacey
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
| | - Hugo G Hilton
- Department of Structural Biology, Stanford University School of Medicine, D159, Sherman Fairchild Science Building, 299 Campus Drive West, Stanford, CA 94305, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Building 560, Room 21-89, Frederick, MD 21702, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, D159, Sherman Fairchild Science Building, 299 Campus Drive West, Stanford, CA 94305, USA
| | - Daniel M Davis
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK.
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20
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The Evolutionary Arms Race between Virus and NK Cells: Diversity Enables Population-Level Virus Control. Viruses 2019; 11:v11100959. [PMID: 31627371 PMCID: PMC6832630 DOI: 10.3390/v11100959] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022] Open
Abstract
Viruses and natural killer (NK) cells have a long co-evolutionary history, evidenced by patterns of specific NK gene frequencies in those susceptible or resistant to infections. The killer immunoglobulin-like receptors (KIR) and their human leukocyte antigen (HLA) ligands together form the most polymorphic receptor-ligand partnership in the human genome and govern the process of NK cell education. The KIR and HLA genes segregate independently, thus creating an array of reactive potentials within and between the NK cell repertoires of individuals. In this review, we discuss the interplay between NK cell education and adaptation with virus infection, with a special focus on three viruses for which the NK cell response is often studied: human immunodeficiency virus (HIV), hepatitis C virus (HCV) and human cytomegalovirus (HCMV). Through this lens, we highlight the complex co-evolution of viruses and NK cells, and their impact on viral control.
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21
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Pende D, Falco M, Vitale M, Cantoni C, Vitale C, Munari E, Bertaina A, Moretta F, Del Zotto G, Pietra G, Mingari MC, Locatelli F, Moretta L. Killer Ig-Like Receptors (KIRs): Their Role in NK Cell Modulation and Developments Leading to Their Clinical Exploitation. Front Immunol 2019; 10:1179. [PMID: 31231370 PMCID: PMC6558367 DOI: 10.3389/fimmu.2019.01179] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/09/2019] [Indexed: 12/19/2022] Open
Abstract
Natural killer (NK) cells contribute to the first line of defense against viruses and to the control of tumor growth and metastasis spread. The discovery of HLA class I specific inhibitory receptors, primarily of killer Ig-like receptors (KIRs), and of activating receptors has been fundamental to unravel NK cell function and the molecular mechanisms of tumor cell killing. Stemmed from the seminal discoveries in early '90s, in which Alessandro Moretta was the major actor, an extraordinary amount of research on KIR specificity, genetics, polymorphism, and repertoire has followed. These basic notions on NK cells and their receptors have been successfully translated to clinical applications, primarily to the haploidentical hematopoietic stem cell transplantation to cure otherwise fatal leukemia in patients with no HLA compatible donors. The finding that NK cells may express the PD-1 inhibitory checkpoint, particularly in cancer patients, may allow understanding how anti-PD-1 therapy could function also in case of HLA class Ineg tumors, usually susceptible to NK-mediated killing. This, together with the synergy of therapeutic anti-checkpoint monoclonal antibodies, including those directed against NKG2A or KIRs, emerging in recent or ongoing studies, opened new solid perspectives in cancer therapy.
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Affiliation(s)
- Daniela Pende
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Michela Falco
- Laboratory of Clinical and Experimental Immunology, Integrated Department of Services and Laboratories, IRCCS Istituto G. Gaslini, Genoa, Italy
| | - Massimo Vitale
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Claudia Cantoni
- Laboratory of Clinical and Experimental Immunology, Integrated Department of Services and Laboratories, IRCCS Istituto G. Gaslini, Genoa, Italy
- Department of Experimental Medicine (DIMES), Center of Excellence for Biomedical Research, Università di Genova, Genoa, Italy
| | - Chiara Vitale
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Experimental Medicine (DIMES), Università di Genova, Genoa, Italy
| | - Enrico Munari
- Department of Pathology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Italy
| | - Alice Bertaina
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics Stanford School of Medicine, Stanford, CA, United States
| | - Francesca Moretta
- Department of Laboratory Medicine, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Italy
| | - Genny Del Zotto
- Core Facilities, Integrated Department of Services and Laboratories, IRCCS Istituto G. Gaslini, Genoa, Italy
| | - Gabriella Pietra
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Experimental Medicine (DIMES), Università di Genova, Genoa, Italy
| | - Maria Cristina Mingari
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Experimental Medicine (DIMES), Center of Excellence for Biomedical Research, Università di Genova, Genoa, Italy
| | - Franco Locatelli
- Department of Oncohematology and Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Lorenzo Moretta
- Laboratory of Tumor Immunology, Department of Immunology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
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22
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The IRE1 endoplasmic reticulum stress sensor activates natural killer cell immunity in part by regulating c-Myc. Nat Immunol 2019; 20:865-878. [PMID: 31086333 PMCID: PMC6588410 DOI: 10.1038/s41590-019-0388-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 03/29/2019] [Indexed: 01/04/2023]
Abstract
Natural killer (NK) cells are critical mediators of host immunity to pathogens. Here, we demonstrate that the endoplasmic reticulum stress sensor inositol-requiring enzyme 1 (IRE1α) and its substrate transcription factor X-box-binding protein 1 (XBP1) drive NK cell responses against viral infection and tumors in vivo. IRE1α-XBP1 were essential for expansion of activated mouse and human NK cells and are situated downstream of the mammalian target of rapamycin signaling pathway. Transcriptome and chromatin immunoprecipitation analysis revealed c-Myc as a new and direct downstream target of XBP1 for regulation of NK cell proliferation. Genetic ablation or pharmaceutical blockade of IRE1α downregulated c-Myc, and NK cells with c-Myc haploinsufficency phenocopied IRE1α-XBP1 deficiency. c-Myc overexpression largely rescued the proliferation defect in IRE1α-/- NK cells. Like c-Myc, IRE1α-XBP1 also promotes oxidative phosphorylation in NK cells. Overall, our study identifies a IRE1α-XBP1-cMyc axis in NK cell immunity, providing insight into host protection against infection and cancer.
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23
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Le Luduec JB, Boudreau JE, Freiberg JC, Hsu KC. Novel Approach to Cell Surface Discrimination Between KIR2DL1 Subtypes and KIR2DS1 Identifies Hierarchies in NK Repertoire, Education, and Tolerance. Front Immunol 2019; 10:734. [PMID: 31024561 PMCID: PMC6460669 DOI: 10.3389/fimmu.2019.00734] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/19/2019] [Indexed: 12/26/2022] Open
Abstract
Cumulative activating and inhibitory receptor signaling controls the functional output of individual natural killer (NK) cells. Investigation of how competing signals impact response, however, has been hampered by the lack of available antibodies capable of distinguishing inhibitory and activating receptors with highly homologous ectodomains. Utilizing a novel combination of monoclonal antibodies with specificity for discrete inhibitory KIR2DL1 and activating KIR2DS1 allotypes found among 230 healthy donors, we investigated allele-specific receptor expression and function driven by KIR2DL1 and KIR2DS1 alleles. We found that co-expression of the HLA-C2 ligand diminishes KIR2DL1, but not KIR2DS1, cell surface staining, but does not impact the respective frequencies of KIR2DL1- and KIR2DS1-expressing cells within the NK repertoire. We can distinguish by flow cytometry NK cell populations expressing the most common KIR2DL1-C245 allotypes from those expressing the most common KIR2DL1-R245 allotypes, and we show that the informative differential binding anti-KIR2DL1/S1 clone 1127B is determined by amino acid residue T154. Although both KIR2DL1-C245 and KIR2DL1-R245 subtypes can be co-expressed in the same cell, NK cells preferentially express one or the other. Cells expressing KIR2DL1-C245 exhibited a lower KIR2DL1 cell surface density and lower missing-self reactivity in comparison to cells expressing KIR2DL1-R245. We found no difference, however, in sensitivity to inhibition or cell surface stability between the two KIR2DL1 isoforms, and both demonstrated similar expansion among NKG2C+ KIR2DL1+ NK cells in HCMV-seropositive healthy individuals. In addition to cell surface density of KIR2DL1, copy number of cognate HLA-C2 hierarchically impacted the effector capacity of both KIR2DL1+ cells and the tolerization of KIR2DS1+ NK cells. HLA-C2 tolerization of KIR2DS1+ NK cells could be overridden, however, by education via co-expressed self-specific inhibitory receptors, such as the heterodimer CD94/NKG2A. Our results demonstrate that effector function of NK cells expressing KIR2DL1 or KIR2DS1 is highly influenced by genetic variability and is calibrated by co-expression of additional NK receptors and cognate HLA-C2 ligands. These findings define the molecular conditions under which NK cells are activated or inhibited, potentially informing selection of donors for adoptive NK therapies.
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Affiliation(s)
- Jean-Benoît Le Luduec
- Immunology Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, United States
| | - Jeanette E. Boudreau
- Immunology Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, United States
| | - Julian C. Freiberg
- Immunology Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, United States
| | - Katharine C. Hsu
- Immunology Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, United States
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medical College, New York, NY, United States
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24
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Goodridge JP, Jacobs B, Saetersmoen ML, Clement D, Hammer Q, Clancy T, Skarpen E, Brech A, Landskron J, Grimm C, Pfefferle A, Meza-Zepeda L, Lorenz S, Wiiger MT, Louch WE, Ask EH, Liu LL, Oei VYS, Kjällquist U, Linnarsson S, Patel S, Taskén K, Stenmark H, Malmberg KJ. Remodeling of secretory lysosomes during education tunes functional potential in NK cells. Nat Commun 2019; 10:514. [PMID: 30705279 PMCID: PMC6355880 DOI: 10.1038/s41467-019-08384-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/04/2019] [Indexed: 01/13/2023] Open
Abstract
Inhibitory signaling during natural killer (NK) cell education translates into increased responsiveness to activation; however, the intracellular mechanism for functional tuning by inhibitory receptors remains unclear. Secretory lysosomes are part of the acidic lysosomal compartment that mediates intracellular signalling in several cell types. Here we show that educated NK cells expressing self-MHC specific inhibitory killer cell immunoglobulin-like receptors (KIR) accumulate granzyme B in dense-core secretory lysosomes that converge close to the centrosome. This discrete morphological phenotype is independent of transcriptional programs that regulate effector function, metabolism and lysosomal biogenesis. Meanwhile, interference of signaling from acidic Ca2+ stores in primary NK cells reduces target-specific Ca2+-flux, degranulation and cytokine production. Furthermore, inhibition of PI(3,5)P2 synthesis, or genetic silencing of the PI(3,5)P2-regulated lysosomal Ca2+-channel TRPML1, leads to increased granzyme B and enhanced functional potential, thereby mimicking the educated state. These results indicate an intrinsic role for lysosomal remodeling in NK cell education.
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Affiliation(s)
- Jodie P Goodridge
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Benedikt Jacobs
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Michelle L Saetersmoen
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Dennis Clement
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14186, Stockholm, Sweden
| | - Trevor Clancy
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Ellen Skarpen
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Andreas Brech
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Johannes Landskron
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318, Oslo, Norway
| | - Christian Grimm
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Munich (LMU), Munich, 80336, Germany
| | - Aline Pfefferle
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14186, Stockholm, Sweden
| | - Leonardo Meza-Zepeda
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, 0310, Norway.,Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, 0310, Norway
| | - Susanne Lorenz
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, 0310, Norway
| | - Merete Thune Wiiger
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - William E Louch
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424, Oslo, Norway
| | - Eivind Heggernes Ask
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Lisa L Liu
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14186, Stockholm, Sweden
| | - Vincent Yi Sheng Oei
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Una Kjällquist
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Sandip Patel
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Kjetil Taskén
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318, Oslo, Norway
| | - Harald Stenmark
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway
| | - Karl-Johan Malmberg
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway. .,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310, Oslo, Norway. .,Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14186, Stockholm, Sweden.
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25
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Le Luduec JB, Kudva A, Boudreau JE, Hsu KC. Novel multiplex PCR-SSP method for centromeric KIR allele discrimination. Sci Rep 2018; 8:14853. [PMID: 30291273 PMCID: PMC6173694 DOI: 10.1038/s41598-018-33135-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/12/2018] [Indexed: 12/03/2022] Open
Abstract
Allelic diversity of the KIR2DL receptors drive differential expression and ligand-binding affinities that impact natural killer cell function and patient outcomes for diverse cancers. We have developed a global intermediate resolution amplification-refractory mutation system (ARMS) PCR-SSP method for distinguishing functionally relevant subgroups of the KIR2DL receptors, as defined by phylogenetic study of the protein sequences. Use of the ARMS design makes the method reliable and usable as a kit, with all reactions utilizing the same conditions. Six reactions define six subgroups of KIR2DL1; four reactions define three subgroups of KIR2DL2; and five reactions define four subgroups of KIR2DL3. Using KIR allele data from a cohort of 426 European-Americans, we identified the most common KIR2DL subtypes and developed the high-throughput PCR-based methodology, which was validated on a separate cohort of 260 healthy donors. Linkage disequilibrium analysis between the different KIR2DL alleles revealed that seven allelic combinations represent more than 95% of the observed population genotypes for KIR2DL1/L2/L3. In summary, our findings enable rapid typing of the most common KIR2DL receptor subtypes, allowing more accurate prediction of co-inheritance and providing a useful tool for the discrimination of observed differences in surface expression and effector function among NK cells exhibiting disparate KIR2DL allotypes.
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Affiliation(s)
- Jean-Benoît Le Luduec
- Immunology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Anupa Kudva
- Immunology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeanette E Boudreau
- Immunology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA.,Departments of Pathology and Microbiology & Immunology, Dalhousie University, Halifax, Canada
| | - Katharine C Hsu
- Immunology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA. .,Department of Medicine, Weill Cornell Medical College, New York, NY, USA. .,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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26
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Heatley SL, Mullighan CG, Doherty K, Danner S, O'Connor GM, Hahn U, Szer J, Schwarer A, Bradstock K, Sullivan LC, Bardy PG, Brooks AG. Activating KIR Haplotype Influences Clinical Outcome Following HLA-Matched Sibling Hematopoietic Stem Cell Transplantation. HLA 2018; 92:74-82. [PMID: 29943500 DOI: 10.1111/tan.13327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/03/2018] [Accepted: 06/22/2018] [Indexed: 01/30/2023]
Abstract
Natural killer cells are thought to influence the outcome of hematopoietic stem cell transplant (HSCT), impacting on relapse, overall survival, graft versus host disease and the control of infection, in part through the complex interplay between the large and genetically diverse killer immunoglobulin-like receptor (KIR) family and their ligands. This study examined the relationship between KIR gene content and clinical outcomes including the control of opportunistic infections such as cytomegalovirus in the setting of human leucocyte antigen (HLA)-matched sibling HSCT in an Australian cohort. The presence of the KIR B haplotype which contain more activating receptors in the donor, in particular centromeric B haplotype genes (Cen-B), was associated with improved overall survival of patients with acute myeloid leukemia (AML) undergoing sibling HSCT and receiving myeloablative conditioning. Donor Cen-B haplotype was also associated with reduced acute graft versus host disease grades II-IV whereas donor telomeric-B haplotype was associated with decreased incidence of CMV reactivation. In contrast, we were not able to demonstrate a reduced rate of relapse when the donor had KIR Cen-B, however relapse with a donor Cen-A haplotype was a competing risk factor to poor overall survival. Here we show that the presence of donor activating KIR led to improved outcome for the patient, potentially through reduced relapse rates and decreased incidence of acute GvHD translating to improved overall survival. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- S L Heatley
- University of Melbourne, Melbourne, Vic, Australia
- Australian Red Cross Blood Service, Adelaide, SA, Australia
| | - C G Mullighan
- St Jude Children's Research Hospital, Memphis, TN, USA
| | - K Doherty
- Australian Red Cross Blood Service, Adelaide, SA, Australia
| | - S Danner
- Australian Red Cross Blood Service, Adelaide, SA, Australia
- Royal Adelaide and Queen Elizabeth Hospitals, SA Pathology, Adelaide, SA, Australia
| | - G M O'Connor
- University of Melbourne, Melbourne, Vic, Australia
| | - U Hahn
- Royal Adelaide and Queen Elizabeth Hospitals, SA Pathology, Adelaide, SA, Australia
| | - J Szer
- University of Melbourne, Melbourne, Vic, Australia
- Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - A Schwarer
- Alfred Hospital, Melbourne, Vic, Australia
| | | | - L C Sullivan
- University of Melbourne, Melbourne, Vic, Australia
| | - P G Bardy
- Australian Red Cross Blood Service, Adelaide, SA, Australia
- Royal Adelaide and Queen Elizabeth Hospitals, SA Pathology, Adelaide, SA, Australia
| | - A G Brooks
- University of Melbourne, Melbourne, Vic, Australia
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27
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Locatelli F, Pende D, Falco M, Della Chiesa M, Moretta A, Moretta L. NK Cells Mediate a Crucial Graft-versus-Leukemia Effect in Haploidentical-HSCT to Cure High-Risk Acute Leukemia. Trends Immunol 2018; 39:577-590. [PMID: 29793748 DOI: 10.1016/j.it.2018.04.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
Abstract
Natural killer (NK) cells are involved in innate defenses against viruses and tumors. Their function is finely tuned by activating and inhibitory receptors. Among the latter, killer immunoglobulin-like receptors and CD94/NKG2A recognize human leukocyte antigen (HLA) Class I molecules, allowing NK cells to discriminate between normal and aberrant cells, as well as to recognize allogeneic cells, because of their ability to sense HLA polymorphisms. This latter phenomenon plays a key role in HLA-haploidentical hematopoietic stem cell transplantation (haplo-HSCT) for high-risk acute leukemia patients transplanted from an NK-alloreactive donor. Different haplo-HSCT settings have been developed, either T depleted or T replete - the latter requiring graft-versus-host disease prophylaxis. A novel graft manipulation, based on depletion of αβ T cells and B cells, allows infusion of fully mature, including alloreactive, NK cells. The excellent patient clinical outcome underscores the importance of these innate cells in cancer therapy.
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Affiliation(s)
- Franco Locatelli
- IRCCS Ospedale Pediatrico Bambino Gesù, Dipartimento di Oncoematologia e Terapia Cellulare e Genica, Roma, Italy; Università degli Studi di Pavia, Dipartimento di Scienze Pediatriche, Pavia, Italy
| | - Daniela Pende
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Michela Falco
- IRCCS Istituto Giannina Gaslini, Dipartimento dei Laboratori di Ricerca, Genova, Italy
| | - Mariella Della Chiesa
- Università degli Studi di Genova, Dipartimento di Medicina Sperimentale, Genova, Italy; Centro di Eccellenza per la Ricerca Biomedica, Università degli Studi di Genova, Genova, Italy
| | - Alessandro Moretta
- Università degli Studi di Genova, Dipartimento di Medicina Sperimentale, Genova, Italy; Centro di Eccellenza per la Ricerca Biomedica, Università degli Studi di Genova, Genova, Italy
| | - Lorenzo Moretta
- IRCCS Ospedale Pediatrico Bambino Gesù, Area di Ricerca Immunologica, Roma, Italy.
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28
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Niu C, Li M, Zhu S, Chen Y, Zhou L, Xu D, Li W, Cui J, Liu Y, Chen J. Decitabine Inhibits Gamma Delta T Cell Cytotoxicity by Promoting KIR2DL2/3 Expression. Front Immunol 2018; 9:617. [PMID: 29632540 PMCID: PMC5879086 DOI: 10.3389/fimmu.2018.00617] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/12/2018] [Indexed: 12/25/2022] Open
Abstract
Gamma delta (γδ) T cells, which possess potent cytotoxicity against a wide range of cancer cells, have become a potential avenue for adoptive immunotherapy. Decitabine (DAC) has been reported to enhance the immunogenicity of tumor cells, thereby reinstating endogenous immune recognition and tumor lysis. However, DAC has also been demonstrated to have direct effects on immune cells. In this study, we report that DAC inhibits γδ T cell proliferation. In addition, DAC increases the number of KIR2DL2/3-positive γδ T cells, which are less cytotoxic than the KIR2DL2/3-negative γδ T cells. We found that DAC upregulated KIR2DL2/3 expression in KIR2DL2/3-negative γδ T cells by inhibiting KIR2DL2/3 promoter methylation, which enhances the binding of KIR2DL2/3 promoter to Sp-1 and activates KIR2DL2/3 gene expression. Our data demonstrated that DAC can inhibit the function of human γδ T cells at both cellular and molecular levels, which confirms and extrapolates the results of previous studies showing that DAC can negatively regulate the function of NK cells and αβ T cells of the immune system.
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Affiliation(s)
- Chao Niu
- Department of Translational Medicine, The First Hospital of Jilin University, Changchun, China.,Department of Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Min Li
- Department of Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Shan Zhu
- Department of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Yongchong Chen
- Department of Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Lei Zhou
- Department of Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Dongsheng Xu
- Department of Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Wei Li
- Department of Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Jiuwei Cui
- Department of Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Yongjun Liu
- Department of Translational Medicine, The First Hospital of Jilin University, Changchun, China.,Sanofi Research and Development, Cambridge, MA, United States
| | - Jingtao Chen
- Department of Translational Medicine, The First Hospital of Jilin University, Changchun, China
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29
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Boudreau JE, Hsu KC. Natural killer cell education in human health and disease. Curr Opin Immunol 2018; 50:102-111. [PMID: 29413815 DOI: 10.1016/j.coi.2017.11.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/18/2017] [Indexed: 02/06/2023]
Abstract
Natural killer (NK) cells maintain immune homeostasis by detecting and eliminating damaged cells. Simultaneous activating and inhibitory input are integrated by NK cells, with the net signal prompting cytotoxicity and cytokine production, or inhibition. Chief among the inhibitory ligands for NK cells are 'self' human leukocyte antigen (HLA) molecules, which are sensed by killer immunoglobulin-like receptors (KIR). Through a process called 'education', the functional capabilities of each NK cell are counterbalanced by their sensitivity for inhibition by co-inherited 'self' HLA. HLA and their ligands, the killer immunoglobulin-like receptors (KIR), are encoded by polymorphic, polygenic gene loci that segregate independently, therefore, NK education and function differ even between related individuals. In this review, we describe how variation in NK education, reactivity and sensitivity for inhibition impacts reproductive success, infection, cancer, inflammatory and autoimmune diseases.
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Affiliation(s)
- Jeanette E Boudreau
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada; Department of Pathology, Dalhousie University, Halifax, Canada
| | - Katharine C Hsu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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30
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Boudreau JE, Hsu KC. Natural Killer Cell Education and the Response to Infection and Cancer Therapy: Stay Tuned. Trends Immunol 2018; 39:222-239. [PMID: 29397297 DOI: 10.1016/j.it.2017.12.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/23/2017] [Accepted: 12/01/2017] [Indexed: 12/29/2022]
Abstract
The functional capacities of natural killer (NK) cells differ within and between individuals, reflecting considerable genetic variation. 'Licensing/arming', 'disarming', and 'tuning' are models that have been proposed to explain how interactions between MHC class I molecules and their cognate inhibitory receptors - Ly49 in mice and KIR in humans - 'educate' NK cells for variable reactivity and sensitivity to inhibition. In this review we discuss recent progress toward understanding the genetic, epigenetic, and molecular features that titrate NK effector function and inhibition, and the impact of variable NK cell education on human health and disease.
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Affiliation(s)
- Jeanette E Boudreau
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada; Department of Pathology, Dalhousie University, Halifax, Canada.
| | - Katharine C Hsu
- Immunology Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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31
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Gentle NL, Loubser S, Paximadis M, Puren A, Tiemessen CT. Killer-cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) class I genetic diversity in four South African populations. Hum Immunol 2017; 78:503-509. [PMID: 28571758 DOI: 10.1016/j.humimm.2017.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 11/29/2022]
Abstract
Killer-cell Immunoglobulin-like Receptor (KIR) and Human Leukocyte Antigen (HLA) genotypes vary considerably between individuals and populations due to KIR/HLA allelic variation and variable haplotype configurations of KIR. HLA mediate natural killer cell activity by serving as KIR ligands. KIR/HLA polymorphisms associate with both disease susceptibility and severity. We determined the frequencies of KIR, KIR genotypes and KIR-HLA combinations in 364 healthy individuals from four South African populations. Study participants included black African (n=167), Caucasian (n=97), Mixed ancestry (n=50) and Indian (n=50) individuals. We identified 48 KIR genotypes that included two genotypes not previously reported. Based on KIR gene content, Indian individuals represented the most distinct group, showing the highest frequencies of KIR2DL2, KIR2DL5, KIR2DS1, KIR2DS2, KIR2DS3 and KIR3DS1, the lowest frequencies of KIR2DL3, KIR2DS4 and KIR3DL1; and a KIR2DL4-negative individual. KIR2DS1 and KIR3DS1 were infrequent in black African populations. HLA-C2 was more common in black African individuals, while HLA-C1 predominated in the other populations. Indian individuals were more likely to possess KIR2DL2 paired with HLA-C1, while Caucasian individuals exhibited the highest frequencies of KIR2DL3 paired with HLA-C1. This report provides comprehensive reference data for further study of the roles of KIR/HLA in non-communicable and infectious diseases in South African populations.
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Affiliation(s)
- Nikki L Gentle
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Adrian Puren
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2000, South Africa.
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32
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Sim MJW, Malaker SA, Khan A, Stowell JM, Shabanowitz J, Peterson ME, Rajagopalan S, Hunt DF, Altmann DM, Long EO, Boyton RJ. Canonical and Cross-reactive Binding of NK Cell Inhibitory Receptors to HLA-C Allotypes Is Dictated by Peptides Bound to HLA-C. Front Immunol 2017; 8:193. [PMID: 28352266 PMCID: PMC5348643 DOI: 10.3389/fimmu.2017.00193] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human natural killer (NK) cell activity is regulated by a family of killer cell immunoglobulin-like receptors (KIRs) that bind human leukocyte antigen (HLA) class I. Combinations of KIR and HLA genotypes are associated with disease, including susceptibility to viral infection and disorders of pregnancy. KIR2DL1 binds HLA-C alleles of group C2 (Lys80). KIR2DL2 and KIR2DL3 bind HLA-C alleles of group C1 (Asn80). However, this model cannot explain HLA-C allelic effects in disease or the impact of HLA-bound peptides. The goal of this study was to determine the extent to which the endogenous HLA-C peptide repertoire can influence the specific binding of inhibitory KIR to HLA-C allotypes. RESULTS The impact of HLA-C bound peptide on inhibitory KIR binding was investigated taking advantage of the fact that HLA-C*05:01 (HLA-C group 2, C2) and HLA-C*08:02 (HLA-C group 1, C1) have identical sequences apart from the key KIR specificity determining epitope at residues 77 and 80. Endogenous peptides were eluted from HLA-C*05:01 and used to test the peptide dependence of KIR2DL1 and KIR2DL2/3 binding to HLA-C*05:01 and HLA-C*08:02 and subsequent impact on NK cell function. Specific binding of KIR2DL1 to the C2 allotype occurred with the majority of peptides tested. In contrast, KIR2DL2/3 binding to the C1 allotype occurred with only a subset of peptides. Cross-reactive binding of KIR2DL2/3 with the C2 allotype was restricted to even fewer peptides. Unexpectedly, two peptides promoted binding of the C2 allotype-specific KIR2DL1 to the C1 allotype. We showed that presentation of endogenous peptides or HIV Gag peptides by HLA-C can promote KIR cross-reactive binding. CONCLUSION KIR2DL2/3 binding to C1 is more peptide selective than that of KIR2DL1 binding to C2, providing an explanation for KIR2DL3-C1 interactions appearing weaker than KIR2DL1-C2. In addition, cross-reactive binding of KIR is characterized by even higher peptide selectivity. We demonstrate a hierarchy of functional peptide selectivity of KIR-HLA-C interactions with relevance to NK cell biology and human disease associations. This selective peptide sequence-driven binding of KIR provides a potential mechanism for pathogen as well as self-peptide to modulate NK cell activation through altering levels of inhibition.
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Affiliation(s)
- Malcolm J. W. Sim
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, USA
- Lung Immunology Group, Department of Medicine, Imperial College London, London, UK
| | - Stacy A. Malaker
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Ayesha Khan
- Lung Immunology Group, Department of Medicine, Imperial College London, London, UK
| | - Janet M. Stowell
- Lung Immunology Group, Department of Medicine, Imperial College London, London, UK
| | | | - Mary E. Peterson
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, USA
| | - Sumati Rajagopalan
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, USA
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Daniel M. Altmann
- Lung Immunology Group, Department of Medicine, Imperial College London, London, UK
| | - Eric O. Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, USA
| | - Rosemary J. Boyton
- Lung Immunology Group, Department of Medicine, Imperial College London, London, UK
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Béziat V, Hilton HG, Norman PJ, Traherne JA. Deciphering the killer-cell immunoglobulin-like receptor system at super-resolution for natural killer and T-cell biology. Immunology 2016; 150:248-264. [PMID: 27779741 PMCID: PMC5290243 DOI: 10.1111/imm.12684] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
Killer-cell immunoglobulin-like receptors (KIRs) are components of two fundamental biological systems essential for human health and survival. First, they contribute to host immune responses, both innate and adaptive, through their expression by natural killer cells and T cells. Second, KIR play a key role in regulating placentation, and hence reproductive success. Analogous to the diversity of their human leucocyte antigen class I ligands, KIR are extremely polymorphic. In this review, we describe recent developments, fuelled by methodological advances, that are helping to decipher the KIR system in terms of haplotypes, polymorphisms, expression patterns and their ligand interactions. These developments are delivering deeper insight into the relevance of KIR in immune system function, evolution and disease.
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Affiliation(s)
- Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Paul J Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Stanford, CA, USA
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Shaffer BC, Hsu KC. How important is NK alloreactivity and KIR in allogeneic transplantation? Best Pract Res Clin Haematol 2016; 29:351-358. [PMID: 27890259 DOI: 10.1016/j.beha.2016.10.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Relapse of acute myelogenous leukemia (AML) after allogeneic hematopoietic cell transplantation (allo HCT) is a major cause of death in transplant recipients. Efforts to control relapse by promoting donor T-cell alloreactivity, such as withdrawal of immune suppression or donor lymphocyte infusions, are limited by the propensity to induce graft versus host disease (GVHD) and by inadequate efficacy. Therefore, options for AML patients who have relapsed AML after allo HCT are few and outcomes are poor. Similar to T-cells, natural killer (NK) cells have potent anti-leukemia effector capacity, and yet unlike T-cells, NK cells do not mediate GVHD. Furthermore, their function does not require matching of human leukocyte antigens (HLA) between donor and recipient. Maximizing donor NK alloreactivity thus holds the exciting possibility to induce the graft versus leukemia (GVL) effect without engendering GVHD. Among the array of activating and inhibitory NK cell surface receptors, the killer Ig-like receptors (KIR) play a central role in modulating NK effector function. Here we will review how KIR mediates donor alloreactivity, discuss the role of KIR gene and allele typing to optimize allo HCT donor selection, and discuss how KIR may aid adoptive NK and other cell therapies.
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Affiliation(s)
- Brian C Shaffer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Katharine C Hsu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Immunology Program, Sloan Kettering Institute, New York, NY, United States; Department of Medicine, Weill Cornell Medical College, New York, NY, United States.
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35
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Stephens C, Moreno-Casares A, López-Nevot MÁ, García-Cortés M, Medina-Cáliz I, Hallal H, Soriano G, Roman E, Ruiz-Cabello F, Romero-Gomez M, Lucena MI, Andrade RJ. Killer Immunoglobulin-Like Receptor Profiles Are not Associated with Risk of Amoxicillin-Clavulanate-Induced Liver Injury in Spanish Patients. Front Pharmacol 2016; 7:280. [PMID: 27616993 PMCID: PMC4999432 DOI: 10.3389/fphar.2016.00280] [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: 07/15/2016] [Accepted: 08/15/2016] [Indexed: 12/03/2022] Open
Abstract
Natural killer cells are an integral part of the immune system and represent a large proportion of the lymphocyte population in the liver. The activity of these cells is regulated by various cell surface receptors, such as killer Ig-like receptors (KIR) that bind to human leukocyte antigen (HLA) class I ligands on the target cell. The composition of KIR receptors has been suggested to influence the development of specific diseases, in particularly autoimmune diseases, cancer and reproductive diseases. The role played in idiosyncratic drug-induced liver injury (DILI) is currently unknown. In this study, we examined KIR gene profiles and HLA class I polymorphisms in amoxicillin-clavulanate (AC) DILI patients in search for potential risk associations. One hundred and two AC DILI patients and 226 controls were genotyped for the presence or absence of 16 KIR loci, including the two pseudogenes 2DP1 and 3DP1. No significant differences were found in the distribution of individual KIRs between patients and controls, which were comparable to previously reported KIR data from ethnically similar cohorts. The 21.6 and 21.2% of the patients and controls, respectively, were homozygous haplotype A carriers, while 78.4 and 78.8%, respectively, contained at least one B haplotype (Bx). The genotypes translated into 27 (AC DILI) and 46 (controls) different gene profiles, with 19 being present in both groups. The most frequent Bx gene profile containing KIRs 2DS2, 2DL2, 2DL3, 2DP1, 2DL1, 3DL1, 2DS4, 3DL2, 3DL3, 2DL4, and 3PD1 was present in 16% of the DILI patients and 14% of the controls. The distribution of HLA class I epitopes did not differ significantly between AC DILI patients and controls. The most frequent receptor-ligand combinations in the DILI patients were 2DL3 + epitope C1 (67%) and 3DL1 + Bw4 motif (67%), while 2DL1 + epitope C2 (69%) and 3DL1 + Bw4 motif (69%) predominated in the controls. This is to our knowledge the first analysis of KIR receptor-HLA ligand associations in DILI, although our findings do not support evidence of these genetic variations playing a major role in AC DILI development.
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Affiliation(s)
- Camilla Stephens
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd Málaga, Spain
| | - Antonia Moreno-Casares
- Unidad de Gestión Clínica de Laboratorio, Departamento de Bioquímica y Biología Molecular III/Inmunología, Instituto de Investigación Biosanitario de Granada, Complejo Hospitalario de Granada, Universidad de Granada Granada, Spain
| | - Miguel-Ángel López-Nevot
- Unidad de Gestión Clínica de Laboratorio, Departamento de Bioquímica y Biología Molecular III/Inmunología, Instituto de Investigación Biosanitario de Granada, Complejo Hospitalario de Granada, Universidad de Granada Granada, Spain
| | - Miren García-Cortés
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd Málaga, Spain
| | - Inmaculada Medina-Cáliz
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd Málaga, Spain
| | - Hacibe Hallal
- Servicio de Aparato Digestivo, Hospital Morales Meseguer Murcia, Spain
| | - German Soriano
- Servicio de Gastroenterología, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, CIBERehd Barcelona, Spain
| | - Eva Roman
- Servicio de Gastroenterología, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, CIBERehdBarcelona, Spain; Escola Universitària d'Infermeria-Sant Pau, Universitat Autònoma de BarcelonaBarcelona, Spain
| | | | - Manuel Romero-Gomez
- Unidad de Gestión Clínica de Aparato Digestivo Intercentros, Hospitales Universitarios Virgen Macarena-Virgen del Rocio, CIBERehd Seville, Spain
| | - M Isabel Lucena
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd Málaga, Spain
| | - Raúl J Andrade
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd Málaga, Spain
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36
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Bari R, Schell S, Tuggle M, Leung W. An Improved Method With High Specificity for KIR2DL1 Functional Allele Typing. Lab Med 2016. [PMID: 26199260 DOI: 10.1309/lmmn1k6sbrjcgd9j] [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] [Indexed: 02/07/2023] Open
Abstract
As new killer-cell immunoglobulin-like receptor (KIR) alleles are discovered, a challenge in KIR typing is maintaining sensitivity and specificity. A single nucleotide polymorphism assay can be used to type functional KIR2DL1 alleles. We improved recently on the earlier method by using a higher-specificity assay. The major modifications include the development of sequence-specific primers to selectively amplify the transmembrane domain of all known KIR2DL1 alleles via polymerase chain reaction with sequence-specific primers (PCR-SSP), and using the PCR products as the template for a revised KIR2DL1 functional allele-typing assay. This modified method allows high-throughput typing with high specificity.
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Affiliation(s)
- Rafijul Bari
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sarah Schell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - MaCal Tuggle
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wing Leung
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
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37
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AlHossiny M, Luo L, Frazier WR, Steiner N, Gusev Y, Kallakury B, Glasgow E, Creswell K, Madhavan S, Kumar R, Upadhyay G. Ly6E/K Signaling to TGFβ Promotes Breast Cancer Progression, Immune Escape, and Drug Resistance. Cancer Res 2016; 76:3376-86. [PMID: 27197181 DOI: 10.1158/0008-5472.can-15-2654] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 03/29/2016] [Indexed: 12/11/2022]
Abstract
Stem cell antigen Sca-1 is implicated in murine cancer stem cell biology and breast cancer models, but the role of its human homologs Ly6K and Ly6E in breast cancer are not established. Here we report increased expression of Ly6K/E in human breast cancer specimens correlates with poor overall survival, with an additional specific role for Ly6E in poor therapeutic outcomes. Increased expression of Ly6K/E also correlated with increased expression of the immune checkpoint molecules PDL1 and CTLA4, increased tumor-infiltrating T regulatory cells, and decreased natural killer (NK) cell activation. Mechanistically, Ly6K/E was required for TGFβ signaling and proliferation in breast cancer cells, where they contributed to phosphorylation of Smad1/5 and Smad2/3. Furthermore, Ly6K/E promoted cytokine-induced PDL1 expression and activation and binding of NK cells to cancer cells. Finally, we found that Ly6K/E promoted drug resistance and facilitated immune escape in this setting. Overall, our results establish a pivotal role for a Ly6K/E signaling axis involving TGFβ in breast cancer pathophysiology and drug response, and highlight this signaling axis as a compelling realm for therapeutic invention. Cancer Res; 76(11); 3376-86. ©2016 AACR.
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Affiliation(s)
- Midrar AlHossiny
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Linlin Luo
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University Medical Center, Washington, DC
| | - William R Frazier
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Noriko Steiner
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Yuriy Gusev
- Department of Oncology, Georgetown University Medical Center, Washington, DC. Innovation Center for Biomedical Informatics (ICBI), Georgetown University Medical Center, Washington, DC
| | - Bhaskar Kallakury
- Department of Pathology, Georgetown University Medical Center, Washington, DC
| | - Eric Glasgow
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Karen Creswell
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Subha Madhavan
- Department of Oncology, Georgetown University Medical Center, Washington, DC. Innovation Center for Biomedical Informatics (ICBI), Georgetown University Medical Center, Washington, DC
| | - Rakesh Kumar
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC
| | - Geeta Upadhyay
- Department of Oncology, Georgetown University Medical Center, Washington, DC. Innovation Center for Biomedical Informatics (ICBI), Georgetown University Medical Center, Washington, DC.
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Bari R, Thapa R, Bao J, Li Y, Zheng J, Leung W. KIR2DL2/2DL3-E(35) alleles are functionally stronger than -Q(35) alleles. Sci Rep 2016; 6:23689. [PMID: 27030405 PMCID: PMC4814820 DOI: 10.1038/srep23689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/09/2016] [Indexed: 11/26/2022] Open
Abstract
KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E35) are functionally stronger than those with glutamine at the same position (Q35). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E35 could kill more target cells lacking their ligands than NK cells with the weaker -Q35 alleles, indicating better licensing of KIR2DL2/L3+ NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation.
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Affiliation(s)
- Rafijul Bari
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rajoo Thapa
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ju Bao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ying Li
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jie Zheng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wing Leung
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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The effects of killer cell immunoglobulin-like receptor (KIR) genes on susceptibility to HIV-1 infection in the Polish population. Immunogenetics 2016; 68:327-37. [PMID: 26888639 PMCID: PMC4842214 DOI: 10.1007/s00251-016-0906-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/01/2016] [Indexed: 01/06/2023]
Abstract
Killer cell immunoglobulin-like receptors (KIR) are the most polymorphic receptors of natural killer (NK) cells. Their activity diversifies the functions of NK cells in the antiviral immune response, so the presence of certain KIR may affect transmission of HIV-1. The aim of the study was to evaluate the influence of KIR genes on the susceptibility to HIV-1 infection in the Polish population depending on the route of exposure. We determined the frequencies of activating (2DS1, 2DS2, 2DS3, 2DS4f, 2DS4del, 2DS5, 3DS1) and inhibitory (2DL1, 2DL2, 2DL3, 2DL5, 3DL1) KIRs in HIV-1-positive patients (n = 459), individuals exposed to HIV-1 but uninfected (EU, n = 118) and in uninfected, healthy blood donors (BD, n = 98). Analysis was performed using stepwise logistic regression. Apart from KIRs, CCR5-∆32, and CCR2-64I, alleles were also analyzed, as we knew or suspected that these features could affect susceptibility to HIV infection. The regression confirmed the protective effect of CCR5-∆32 (OR = 0.25, p = 0.006) and CCR2-64I (OR = 0.59, p = 0.032) against HIV infection. Among KIR genes, 2DL3 was found to be a protective factor (OR = 0.30, p = 0.015). A similar effect was seen for 3DS1 but only in intravenous drug users (IDUs) (OR = 0.30, p = 0.019), not in sexually exposed people. 2DL5 was found to be a factor facilitating HIV infection (OR = 2.13, p = 0.013). A similar effect was observed for 2DL2 but only in females (OR = 2.15, p = 0.040), and 2DS1 in IDUs (OR = 3.03, p = 0.022). Our results suggest a beneficial role of KIR3DS1 and 2DL3 supporting resistance to HIV infection and a harmful effect of 2DS1, 2DL5, and 2DL2 genes promoting HIV acquisition.
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NK Cell and CD4+FoxP3+ Regulatory T Cell Based Therapies for Hematopoietic Stem Cell Engraftment. Stem Cells Int 2016; 2016:9025835. [PMID: 26880996 PMCID: PMC4736409 DOI: 10.1155/2016/9025835] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 10/22/2015] [Indexed: 11/18/2022] Open
Abstract
Allogeneic hematopoietic cell transplantation (HCT) is a powerful therapy to treat multiple hematological diseases. The intensive conditioning regimens used to allow for donor hematopoietic stem cell (HSC) engraftment are often associated with severe toxicity, delayed immune reconstitution, life-threatening infections, and thus higher relapse rates. Additionally, due to the high incidence of graft versus host disease (GvHD), HCT protocols have evolved to prevent such disease that has a detrimental impact on antitumor and antiviral responses. Here, we analyzed the role of host T and natural killer (NK) cells in the rejection of donor HSC engraftment as well as the impact of donor regulatory T cells (Treg) and NK cells on HSC engraftment. We review some of the current strategies that utilize NK or Treg to improve allogeneic HCT therapy in order to accomplish better HSC engraftment and immune reconstitution and achieve a lower incidence of cancer relapse, opportunistic infections, and GvHD.
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Hölzemer A, Thobakgale CF, Jimenez Cruz CA, Garcia-Beltran WF, Carlson JM, van Teijlingen NH, Mann JK, Jaggernath M, Kang SG, Körner C, Chung AW, Schafer JL, Evans DT, Alter G, Walker BD, Goulder PJ, Carrington M, Hartmann P, Pertel T, Zhou R, Ndung’u T, Altfeld M. Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South Africa. PLoS Med 2015; 12:e1001900; discussion e1001900. [PMID: 26575988 PMCID: PMC4648589 DOI: 10.1371/journal.pmed.1001900] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/07/2015] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Viruses can evade immune surveillance, but the underlying mechanisms are insufficiently understood. Here, we sought to understand the mechanisms by which natural killer (NK) cells recognize HIV-1-infected cells and how this virus can evade NK-cell-mediated immune pressure. METHODS AND FINDINGS Two sequence mutations in p24 Gag associated with the presence of specific KIR/HLA combined genotypes were identified in HIV-1 clade C viruses from a large cohort of infected, untreated individuals in South Africa (n = 392), suggesting viral escape from KIR+ NK cells through sequence variations within HLA class I-presented epitopes. One sequence polymorphism at position 303 of p24 Gag (TGag303V), selected for in infected individuals with both KIR2DL3 and HLA-C*03:04, enabled significantly better binding of the inhibitory KIR2DL3 receptor to HLA-C*03:04-expressing cells presenting this variant epitope compared to the wild-type epitope (wild-type mean 18.01 ± 10.45 standard deviation [SD] and variant mean 44.67 ± 14.42 SD, p = 0.002). Furthermore, activation of primary KIR2DL3+ NK cells from healthy donors in response to HLA-C*03:04+ target cells presenting the variant epitope was significantly reduced in comparison to cells presenting the wild-type sequence (wild-type mean 0.78 ± 0.07 standard error of the mean [SEM] and variant mean 0.63 ± 0.07 SEM, p = 0.012). Structural modeling and surface plasmon resonance of KIR/peptide/HLA interactions in the context of the different viral sequence variants studied supported these results. Future studies will be needed to assess processing and antigen presentation of the investigated HIV-1 epitope in natural infection, and the consequences for viral control. CONCLUSIONS These data provide novel insights into how viruses can evade NK cell immunity through the selection of mutations in HLA-presented epitopes that enhance binding to inhibitory NK cell receptors. Better understanding of the mechanisms by which HIV-1 evades NK-cell-mediated immune pressure and the functional validation of a structural modeling approach will facilitate the development of novel targeted immune interventions to harness the antiviral activities of NK cells.
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Affiliation(s)
- Angelique Hölzemer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Heinrich-Pette-Institut, Leibniz Institute for Experimental Virology, Hamburg, Germany
- First Department of Internal Medicine, University Medical Center Hamburg—Eppendorf, Hamburg, Germany
| | - Christina F. Thobakgale
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Camilo A. Jimenez Cruz
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York, United States of America
| | | | | | | | - Jaclyn K. Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Manjeetha Jaggernath
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Seung-gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York, United States of America
| | - Christian Körner
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Heinrich-Pette-Institut, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Amy W. Chung
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jamie L. Schafer
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Microbiology, New England Primate Research Center, Southborough, Massachusetts, United States of America
| | - David T. Evans
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Microbiology, New England Primate Research Center, Southborough, Massachusetts, United States of America
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Philip J. Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Pia Hartmann
- First Department of Internal Medicine, Division of Infectious Diseases, University of Cologne, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Thomas Pertel
- Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York, United States of America
| | - Thumbi Ndung’u
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Marcus Altfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Heinrich-Pette-Institut, Leibniz Institute for Experimental Virology, Hamburg, Germany
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Hilton HG, Guethlein LA, Goyos A, Nemat-Gorgani N, Bushnell DA, Norman PJ, Parham P. Polymorphic HLA-C Receptors Balance the Functional Characteristics of KIR Haplotypes. THE JOURNAL OF IMMUNOLOGY 2015; 195:3160-70. [PMID: 26311903 DOI: 10.4049/jimmunol.1501358] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/22/2015] [Indexed: 01/04/2023]
Abstract
The human killer cell Ig-like receptor (KIR) locus comprises two groups of KIR haplotypes, termed A and B. These are present in all human populations but with different relative frequencies, suggesting they have different functional properties that underlie their balancing selection. We studied the genomic organization and functional properties of the alleles of the inhibitory and activating HLA-C receptors encoded by KIR haplotypes. Because every HLA-C allotype functions as a ligand for KIR, the interactions between KIR and HLA-C dominate the HLA class I-mediated regulation of human NK cells. The C2 epitope is recognized by inhibitory KIR2DL1 and activating KIR2DS1, whereas the C1 epitope is recognized by inhibitory KIR2DL2 and KIR2DL3. This study shows that the KIR2DL1, KIR2DS1, and KIR2DL2/3 alleles form distinctive phylogenetic clades that associate with specific KIR haplotypes. KIR A haplotypes are characterized by KIR2DL1 alleles that encode strong inhibitory C2 receptors and KIR2DL3 alleles encoding weak inhibitory C1 receptors. In striking contrast, KIR B haplotypes are characterized by KIR2DL1 alleles that encode weak inhibitory C2 receptors and KIR2DL2 alleles encoding strong inhibitory C1 receptors. The wide-ranging properties of KIR allotypes arise from substitutions throughout the KIR molecule. Such substitutions can influence cell surface expression, as well as the avidity and specificity for HLA-C ligands. Consistent with the crucial role of inhibitory HLA-C receptors in self-recognition, as well as NK cell education and response, most KIR haplotypes have both a functional C1 and C2 receptor, despite the considerable variation that occurs in ligand recognition and surface expression.
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Affiliation(s)
- Hugo G Hilton
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ana Goyos
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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Hilton HG, Norman PJ, Nemat-Gorgani N, Goyos A, Hollenbach JA, Henn BM, Gignoux CR, Guethlein LA, Parham P. Loss and Gain of Natural Killer Cell Receptor Function in an African Hunter-Gatherer Population. PLoS Genet 2015; 11:e1005439. [PMID: 26292085 PMCID: PMC4546388 DOI: 10.1371/journal.pgen.1005439] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/13/2015] [Indexed: 12/12/2022] Open
Abstract
Modulating natural killer cell functions in human immunity and reproduction are diverse interactions between the killer cell immunoglobulin-like receptors (KIR) of Natural Killer (NK) cells and HLA class I ligands on the surface of tissue cells. Dominant interactions are between KIR2DL1 and the C2 epitope of HLA-C and between KIR2DL2/3 and the C1 epitope of HLA-C. KhoeSan hunter-gatherers of Southern Africa represent the earliest population divergence known and are the most genetically diverse indigenous people, qualities reflected in their KIR and HLA genes. Of the ten KhoeSan KIR2DL1 alleles, KIR2DL1*022 and KIR2DL1*026 likely originated in the KhoeSan, and later were transmitted at low frequency to the neighboring Zulus through gene flow. These alleles arose by point mutation from other KhoeSan KIR2DL1 alleles that are more widespread globally. Mutation of KIR2DL1*001 gave rise to KIR2DL1*022, causing loss of C2 recognition and gain of C1 recognition. This makes KIR2DL1*022 a more avid and specific C1 receptor than any KIR2DL2/3 allotype. Mutation of KIR2DL1*012 gave rise to KIR2DL1*026, causing premature termination of translation at the end of the transmembrane domain. This makes KIR2DL1*026 a membrane-associated receptor that lacks both a cytoplasmic tail and signaling function. At higher frequencies than their parental allotypes, the combined effect of the KhoeSan-specific KIR2DL1*022 and KIR2DL1*026 is to reduce the frequency of strong inhibitory C2 receptors and increase the frequency of strong inhibitory C1 receptors. Because interaction of KIR2DL1 with C2 is associated with risk of pregnancy disorder, these functional changes are potentially advantageous. Whereas all other KhoeSan KIR2DL1 alleles are present on a wide diversity of centromeric KIR haplotypes, KIR2DL1*026 is present on a single KIR haplotype and KIR2DL1*022 is present on two very similar haplotypes. The high linkage disequilibrium across their haplotypes is consistent with a recent emergence for these KIR2DL1 alleles that have distinctive functions.
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Affiliation(s)
- Hugo G. Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Paul J. Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Neda Nemat-Gorgani
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ana Goyos
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, California, United States of America
| | - Brenna M. Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Christopher R. Gignoux
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lisbeth A. Guethlein
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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44
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Mulrooney TJ, Zhang AC, Goldgur Y, Boudreau JE, Hsu KC. KIR3DS1-Specific D0 Domain Polymorphisms Disrupt KIR3DL1 Surface Expression and HLA Binding. THE JOURNAL OF IMMUNOLOGY 2015; 195:1242-50. [PMID: 26109640 DOI: 10.4049/jimmunol.1500243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/26/2015] [Indexed: 11/19/2022]
Abstract
KIR3DL1 is a polymorphic inhibitory receptor that modulates NK cell activity through interacting with HLA-A and HLA-B alleles that carry the Bw4 epitope. Amino acid polymorphisms throughout KIR3DL1 impact receptor surface expression and affinity for HLA. KIR3DL1/S1 encodes inhibitory and activating alleles, but despite high homology with KIR3DL1, the activating receptor KIR3DS1 does not bind the same ligand. Allele KIR3DL1*009 resulted from a gene recombination event between the inhibitory receptor allele KIR3DL1*001 and the activating receptor allele KIR3DS1*013. This study analyzed the functional impact of KIR3DS1-specific polymorphisms on KIR3DL1*009 surface expression, binding to HLA, and functional capacity. Flow-cytometric analysis of primary human NK cells as well as transfected HEK293T cells shows that KIR3DL1*009 is expressed at a significantly lower surface density compared with KIR3DL1*001. Using recombinant proteins of KIR3DL1*001, KIR3DL1*009, and KIR3DS1*013 to analyze binding to HLA, we found that although KIR3DL1*009 displayed some evidence of binding to HLA compared with KIR3DS1*013, the binding was minimal compared with KIR3DL1*001 and KIR3DL1*005. Mutagenesis of polymorphic sites revealed that the surface phenotype and reduced binding of KIR3DL1*009 are caused by the combined amino acid polymorphisms at positions 58 and 92 within the D0 extracellular domain. Resulting from these effects, KIR3DL1*009(+) NK cells exhibited significantly less inhibition by HLA-Bw4(+) target cells compared with KIR3DL1*001(+) NK cells. The data from this study contribute novel insight into how KIR3DS1-specific polymorphisms in the extracellular region impact KIR3DL1 surface expression, ligand binding, and inhibitory function.
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Affiliation(s)
| | - Aaron C Zhang
- Immunology Program, Sloan Kettering Institute, New York, NY 10065
| | - Yehuda Goldgur
- Department of Structural Biology, Sloan Kettering Institute, New York, NY 10065
| | | | - Katharine C Hsu
- Immunology Program, Sloan Kettering Institute, New York, NY 10065; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065; and Weill Cornell Medical College, Cornell University, New York, NY 10065
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45
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The production of KIR-Fc fusion proteins and their use in a multiplex HLA class I binding assay. J Immunol Methods 2015; 425:79-87. [PMID: 26096968 DOI: 10.1016/j.jim.2015.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 11/20/2022]
Abstract
Soluble recombinant proteins that comprise the extracellular part of a surface expressed receptor attached to the Fc region of an IgG antibody have facilitated the determination of ligand specificity for an array of immune system receptors. Among such receptors is the family of killer cell immunoglobulin-like receptors (KIR) that recognize HLA class I ligands. These receptors, expressed on natural killer (NK) cells and T cells, play important roles in both immune defense and placental development in early pregnancy. Here we describe a method for the production of two domain KIR-Fc fusion proteins using baculovirus infected insect cells. This method is more scalable than traditional mammalian cell expression systems and produces efficiently folded proteins that carry posttranslational modifications found in native KIR. We also describe a multiplex binding assay using the Luminex platform that determines the avidity and specificity of two domain KIR-Fc for a panel of microbeads, each coated with one of 97 HLA class I allotypes. This assay is simple to perform, and represents a major improvement over the assays used previously, which were limited in the number of KIR and HLA class I combinations that could be assayed at any one time. The results obtained from this assay can be used to predict the response of NK cell and T cells when their KIR recognize HLA class I.
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46
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Foley B, Felices M, Cichocki F, Cooley S, Verneris MR, Miller JS. The biology of NK cells and their receptors affects clinical outcomes after hematopoietic cell transplantation (HCT). Immunol Rev 2015; 258:45-63. [PMID: 24517425 DOI: 10.1111/imr.12157] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural killer (NK) cells were first identified for their capacity to reject bone marrow allografts in lethally irradiated mice without prior sensitization. Subsequently, human NK cells were detected and defined by their non-major histocompatibility complex (MHC)-restricted cytotoxicity toward transformed or virally infected target cells. Karre et al. later proposed 'the missing self hypothesis' to explain the mechanism by which self-tolerant cells could kill targets that had lost self MHC class I. Subsequently, the receptors that recognize MHC class I to mediate tolerance in the host were identified on NK cells. These class I-recognizing receptors contribute to the acquisition of function by a dynamic process known as NK cell education or licensing. In the past, NK cells were assumed to be short lived, but more recently NK cells have been shown to mediate immunologic memory to secondary exposures to cytomegalovirus infection. Because of their ability to lyse tumors with aberrant MHC class I expression and to produce cytokines and chemokines upon activation, NK cells may be primed by many stimuli, including viruses and inflammation, to contribute to a graft-versus-tumor effect. In addition, interactions with other immune cells support the therapeutic potential of NK cells to eradicate tumor and to enhance outcomes after hematopoietic cell transplantation.
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Affiliation(s)
- Bree Foley
- Adult, Oncology and Transplantation, Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN, USA
| | - Martin Felices
- Adult, Oncology and Transplantation, Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN, USA
| | - Frank Cichocki
- Adult, Oncology and Transplantation, Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN, USA
| | - Sarah Cooley
- Adult, Oncology and Transplantation, Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN, USA
| | - Michael R Verneris
- Pediatric Hematology, Oncology and Transplantation, Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey S Miller
- Adult, Oncology and Transplantation, Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN, USA
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47
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Perce-da-Silva DS, Silva LA, Lima-Junior JC, Cardoso-Oliveira J, Ribeiro-Alves M, Santos F, Porto LCMS, Oliveira-Ferreira J, Banic DM. Killer cell immunoglobulin-like receptor (KIR) gene diversity in a population naturally exposed to malaria in Porto Velho, Northern Brazil. ACTA ACUST UNITED AC 2015; 85:190-9. [PMID: 25656387 DOI: 10.1111/tan.12523] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 11/10/2014] [Accepted: 01/13/2015] [Indexed: 11/28/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIR) are expressed mainly in natural killer cells and specifically recognize human leukocyte antigen (HLA) class I molecules. The repertoire of KIR genes and KIR-HLA pairs is known to play a key role in the susceptibilities to and the outcomes of several diseases, including malaria. The aim of this study was to investigate the distribution of KIR genes, KIR genotypes and KIR-HLA pair combinations in a population naturally exposed to malaria from Brazilian Amazon. All 16 KIR genes investigated were present in the studied population. Overall, 46 KIR genotypes were defined. The two most common genotypes in the Porto Velho communities, genotypes 1 and 2, were present at similar frequencies as in the Americas. Principal component analysis based on the frequencies of the KIR genes placed the Porto Velho population closer to the Venezuela Mestizos, USA California hispanic and Brazil Paraná Mixed in terms of KIR gene frequencies. This analysis highlights the multi-ethnic profile of the Porto Velho population. Most of the individuals were found to have at least one inhibitory KIR-HLA pair. Seventy-five KIR-HLA pair combinations were identified. The KIR-2DL2/3_HLA-C1, KIR3DL1_HLA-Bw4 and KIR2DL1_HLA-C2 pairs were the most common. There was no association between KIR genes, KIR genotypes or KIR-HLA pair combinations and malaria susceptibility in the studied population. This is the first report on the distribution of KIR and known HLA ligands in the Porto Velho population. Taken together, these results should provide baseline information that will be relevant to population evolutionary history, malaria and other diseases studies in populations of the Brazilian Amazon.
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Affiliation(s)
- D S Perce-da-Silva
- Laboratory of Simulids and Onchocerciasis "Malaria and Onchocerciasis Research", Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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48
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Zhen JX, Wang DM, Deng ZH. Identification of the novel KIR2DL2*013 allele from a southern Chinese Han individual. ACTA ACUST UNITED AC 2015; 85:148-50. [PMID: 25582216 DOI: 10.1111/tan.12500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 12/08/2014] [Indexed: 11/30/2022]
Abstract
The novel KIR2DL2*013 allele differs from the closest allele KIR2DL2*00302 by two non-synonymous mutations.
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Affiliation(s)
- J-X Zhen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, China
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49
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Zhen JX, Deng ZH. A novel KIR2DL3 allele, KIR2DL3*027, identified in an individual from a southern Chinese Han population. ACTA ACUST UNITED AC 2014; 84:592-4. [PMID: 25352250 DOI: 10.1111/tan.12463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/26/2014] [Accepted: 09/28/2014] [Indexed: 11/26/2022]
Abstract
KIR2DL3*027 differs from the closest allele KIR2DL3*00101 by a nonsynonymous mutation in exon 7.
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Affiliation(s)
- J-X Zhen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, China
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50
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Zhen JX, Wang DM, Deng ZH. A novel KIR2DL3 allele, KIR2DL3*026, found in an individual from a southern Chinese Han population. ACTA ACUST UNITED AC 2014; 84:591-2. [PMID: 25346343 DOI: 10.1111/tan.12459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 08/26/2014] [Accepted: 09/28/2014] [Indexed: 11/28/2022]
Abstract
KIR2DL3*026 differs from the closest allele KIR2DL3*00101 by a nonsynonymous mutation in exon 4.
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Affiliation(s)
- J-X Zhen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, China
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