1
|
Wright PA, van de Pasch LAL, Dignan FL, Kichula KM, Pollock NR, Norman PJ, Marchan E, Hill L, Vandelbosch S, Fullwood C, Sheldon S, Hampson L, Tholouli E, Poulton KV. Donor KIR2DL1 Allelic Polymorphism Influences Posthematopoietic Progenitor Cell Transplantation Outcomes in the T Cell Depleted and Reduced Intensity Conditioning Setting. Transplant Cell Ther 2024; 30:488.e1-488.e15. [PMID: 38369017 PMCID: PMC11056303 DOI: 10.1016/j.jtct.2024.02.014] [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: 11/21/2023] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
The majority of established KIR clinical assessment algorithms used for donor selection for hematopoietic progenitor cell transplantation (HPCT) evaluate gene content (presence/absence) of the KIR gene complex. In comparison, relatively little is known about the impact of KIR allelic polymorphism. By analyzing donors of T cell depleted (TcD) reduced intensity conditioning (RIC) HPCT, this study investigated the influence on post-transplant outcome of 2 polymorphic residues of the inhibitory KIR2DL1. The aim of this study was to expand upon existing research into the influence of KIR2DL1 allelic polymorphism upon post-transplant outcome. The effects of allele groups upon transplant outcomes were investigated within a patient cohort using a defined treatment protocol of RIC with TcD. Using phylogenetic data, KIR2DL1 allelic polymorphism was categorized into groups on the basis of variation within codons 114 and 245 (positive or negative for the following groups: KIR2DL1*002/001g, KIR2DL1*003, KIR2DL1*004g) and the identification of null alleles. The influence of these KIR2DL1 allele groups in hematopoietic progenitor cell transplantation (HPCT) donors was assessed in the post-transplant data of 86 acute myelogenous leukemia patients receiving RIC TcD HPCT at a single center. KIR2DL1 allele groups in the donor significantly impacted upon 5-year post-transplant outcomes in RIC TcD HPCT. Donor KIR2DL1*003 presented the greatest influence upon post-transplant outcomes, with KIR2DL1*003 positive donors severely reducing 5-year post-transplant overall survival (OS) compared to those receiving a transplant from a KIR2DL1*003 negative donor (KIR2DL1*003 pos versus neg: 27.0% versus 60.0%, P = .008, pc = 0.024) and disease-free survival (DFS) (KIR2DL1*003 pos versus neg: 23.5% versus 60.0%, P = .004, pc = 0.012), and increasing 5-year relapse incidence (KIR2DL1*003 pos versus neg: 63.9% versus 27.2%, P = .009, pc = 0.027). KIR2DL1*003 homozygous and KIR2DL1*003 heterozygous grafts did not present significantly different post-transplant outcomes. Donors possessing the KIR2DL1*002/001 allele group were found to significantly improve post-transplant outcomes, with donors positive for the KIR2DL1*004 allele group presenting a trend towards improvement. KIR2DL1*002/001 allele group (KIR2DL1*002/001g) positive donors improved 5-year OS (KIR2DL1*002/001g pos versus neg: 56.4% versus 27.2%, P = .009, pc = 0.024) and DFS (KIR2DL1*002/001g pos versus neg: 53.8% versus 25.5%, P = .018, pc = 0.036). KIR2DL1*004 allele group (KIR2DL1*004g) positive donors trended towards improving 5-year OS (KIR2DL1*004g pos versus neg: 53.3% versus 35.5%, P = .097, pc = 0.097) and DFS (KIR2DL1*004g pos versus neg: 50.0% versus 33.9%, P = .121, pc = 0.121), and reducing relapse incidence (KIR2DL1*004g pos versus neg: 33.1% versus 54.0%, P = .079, pc = 0.152). The presented findings suggest donor selection algorithms for TcD RIC HPCT should consider avoiding KIR2DL1*003 positive donors, where possible, and contributes to the mounting evidence that KIR assessment in donor selection algorithms should reflect the conditioning regime protocol used.
Collapse
Affiliation(s)
- Paul A Wright
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK; Histocompatibility & Immunogenetics Laboratory, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, Merseyside, UK.
| | | | - Fiona L Dignan
- Clinical Haematology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Katherine M Kichula
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Denver, Colorado
| | - Nicholas R Pollock
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Denver, Colorado
| | - Paul J Norman
- Department of Biomedical Informatics and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Denver, Colorado
| | - Earl Marchan
- Clinical Haematology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Lesley Hill
- Clinical Haematology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | | | - Catherine Fullwood
- Division of Population Health, Health Services Research & Primary Care, University of Manchester, Manchester, Greater Manchester, UK
| | - Stephen Sheldon
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Lynne Hampson
- Division of Cancer Sciences, University of Manchester, Manchester, Greater Manchester, UK
| | - Eleni Tholouli
- Clinical Haematology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Kay V Poulton
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK; Faculty of Biology, Medicine & Health, University of Manchester, Manchester, Greater Manchester, UK
| |
Collapse
|
2
|
Wright PW, Li H, Rahman MA, Anderson EM, Karwan M, Carrell J, Anderson SK. The KIR2DL1 intermediate upstream element participates in gene activation. Immunogenetics 2023; 75:495-506. [PMID: 37801092 PMCID: PMC10651540 DOI: 10.1007/s00251-023-01321-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/24/2023] [Indexed: 10/07/2023]
Abstract
The human KIR genes encode a family of class I MHC receptors that are expressed on subsets of NK cells. The expression of KIR proteins is controlled by a stochastic process, and competition between sense and antisense promoter elements has been suggested to program the variegated expression of these genes. Previous studies have demonstrated distinct roles of distal, intermediate, and proximal sense promoter/enhancer elements in gene activation and expression. Conversely, proximal and intronic antisense promoter transcripts have been associated with gene silencing at different stages of NK cell development. In the current study, we examine the effect of intermediate promoter deletion on KIR2DL1 expression in the YTS cell line. Homozygous deletion of the KIR2DL1 intermediate element did not affect proximal promoter activity but resulted in increased detection of upstream transcripts. No significant changes in alternative mRNA splicing or expression levels of KIR2DL1 protein were observed. However, intermediate element deletion was associated with a reduced frequency of gene activation by 5-azacytidine. Taken together, these results indicate that the intermediate element is not an enhancer required for KIR expression; however, it is required for the efficient activation of the gene.
Collapse
Affiliation(s)
- Paul W Wright
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Md Ahasanur Rahman
- Cancer Innovation Laboratory, Center for Cancer Research, NCI, Frederick, MD, 21702, USA
| | - Erik M Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, NCI, Frederick, MD, 21702, USA
| | - Megan Karwan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
- Cancer Innovation Laboratory, Center for Cancer Research, NCI, Frederick, MD, 21702, USA
| | - Jeffrey Carrell
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
- Cancer Innovation Laboratory, Center for Cancer Research, NCI, Frederick, MD, 21702, USA
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
- Cancer Innovation Laboratory, Center for Cancer Research, NCI, Frederick, MD, 21702, USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Vollmers S, Lobermeyer A, Niehrs A, Fittje P, Indenbirken D, Nakel J, Virdi S, Brias S, Trenkner T, Sauer G, Peine S, Behrens GM, Lehmann C, Meurer A, Pauli R, Postel N, Roider J, Scholten S, Spinner CD, Stephan C, Wolf E, Wyen C, Richert L, Norman PJ, Sauter J, Schmidt AH, Hoelzemer A, Altfeld M, Körner C. Host KIR/HLA-C Genotypes Determine HIV-Mediated Changes of the NK Cell Repertoire and Are Associated With Vpu Sequence Variations Impacting Downmodulation of HLA-C. Front Immunol 2022; 13:922252. [PMID: 35911762 PMCID: PMC9334850 DOI: 10.3389/fimmu.2022.922252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/13/2022] [Indexed: 12/29/2022] Open
Abstract
NK cells play a pivotal role in viral immunity, utilizing a large array of activating and inhibitory receptors to identify and eliminate virus-infected cells. Killer-cell immunoglobulin-like receptors (KIRs) represent a highly polymorphic receptor family, regulating NK cell activity and determining the ability to recognize target cells. Human leukocyte antigen (HLA) class I molecules serve as the primary ligand for KIRs. Herein, HLA-C stands out as being the dominant ligand for the majority of KIRs. Accumulating evidence indicated that interactions between HLA-C and its inhibitory KIR2DL receptors (KIR2DL1/L2/L3) can drive HIV-1-mediated immune evasion and thus may contribute to the intrinsic control of HIV-1 infection. Of particular interest in this context is the recent observation that HIV-1 is able to adapt to host HLA-C genotypes through Vpu-mediated downmodulation of HLA-C. However, our understanding of the complex interplay between KIR/HLA immunogenetics, NK cell-mediated immune pressure and HIV-1 immune escape is still limited. Therefore, we investigated the impact of specific KIR/HLA-C combinations on the NK cell receptor repertoire and HIV-1 Vpu protein sequence variations of 122 viremic, untreated HIV-1+ individuals. Compared to 60 HIV-1- controls, HIV-1 infection was associated with significant changes within the NK cell receptor repertoire, including reduced percentages of NK cells expressing NKG2A, CD8, and KIR2DS4. In contrast, the NKG2C+ and KIR3DL2+ NK cell sub-populations from HIV-1+ individuals was enlarged compared to HIV-1- controls. Stratification along KIR/HLA-C genotypes revealed a genotype-dependent expansion of KIR2DL1+ NK cells that was ultimately associated with increased binding affinities between KIR2DL1 and HLA-C allotypes. Lastly, our data hinted to a preferential selection of Vpu sequence variants that were associated with HLA-C downmodulation in individuals with high KIR2DL/HLA-C binding affinities. Altogether, our study provides evidence that HIV-1-associated changes in the KIR repertoire of NK cells are to some extent predetermined by host KIR2DL/HLA-C genotypes. Furthermore, analysis of Vpu sequence polymorphisms indicates that differential KIR2DL/HLA-C binding affinities may serve as an additional mechanism how host genetics impact immune evasion by HIV-1.
Collapse
Affiliation(s)
| | | | | | - Pia Fittje
- Leibniz Institute of Virology, Hamburg, Germany
| | | | | | | | - Sebastien Brias
- Leibniz Institute of Virology, Hamburg, Germany
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Gabriel Sauer
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Sven Peine
- Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georg M.N. Behrens
- Department for Rheumatology and Clinical Immunology, Hannover Medical School, Hannover, Germany
| | - Clara Lehmann
- Department I for Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Anja Meurer
- Center for Internal Medicine and Infectiology, Munich, Germany
| | - Ramona Pauli
- Medizinisches Versorgungszentrum (MVZ) am Isartor, Munich, Germany
| | - Nils Postel
- Prinzmed, Practice for Infectious Diseases, Munich, Germany
| | - Julia Roider
- Department of Internal Medicine IV, Department of Infectious Diseases, Ludwig-Maximilians University Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | | | - Christoph D. Spinner
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Technical University of Munich, School of Medicine, University Hospital rechts der Isar, Department of Internal Medicine II, Munich, Germany
| | - Christoph Stephan
- Infectious Diseases Unit, Goethe-University Hospital Frankfurt, Frankfurt, Germany
| | | | - Christoph Wyen
- Department I for Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, Cologne, Germany
- Praxis am Ebertplatz, Cologne, Germany
| | - Laura Richert
- University of Bordeaux, Inserm U1219 Bordeaux Population Health, Inria Sistm, Bordeaux, France
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States
| | | | | | - Angelique Hoelzemer
- Leibniz Institute of Virology, Hamburg, Germany
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marcus Altfeld
- Leibniz Institute of Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Christian Körner
- Leibniz Institute of Virology, Hamburg, Germany
- *Correspondence: Christian Körner,
| |
Collapse
|
5
|
Wu CY, Zhang B, Kim H, Anderson SK, Miller JS, Cichocki F. Ascorbic Acid Promotes KIR Demethylation during Early NK Cell Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:1513-1523. [PMID: 32759296 PMCID: PMC7484163 DOI: 10.4049/jimmunol.2000212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/12/2020] [Indexed: 12/28/2022]
Abstract
Variegated expression of killer Ig-like receptors (KIR) in human NK cells is a stochastic process exclusive to subsets of mature NK cells and CD8+ T cells. Allele-specific KIR expression is maintained by DNA methylation within the proximal promoter regions. Because KIR genes are densely methylated in NK cell progenitors, there is an implied stage of human NK cell development in which DNA demethylation takes place to allow for active transcription. When and how this process occurs is unknown. In this study, we show that KIR proximal promoters are densely methylated in less mature CD56bright NK cells and are progressively demethylated in CD56dim NK cells as they mature and acquire KIR. We hypothesized that ten-eleven translocation (TET) enzymes, which oxidize 5mC on DNA could mediate KIR promoter demethylation. The catalytic efficiency of TET enzymes is known to be enhanced by ascorbic acid. We found that the addition of ascorbic acid to ex vivo culture of sorted CD56bright NK cells increased the frequency of KIR expression in a dose-dependent manner and facilitated demethylation of proximal promoters. A marked enrichment of the transcription factor Runx3 as well as TET2 and TET3 was observed within proximal KIR promoters in CD56bright NK cells cultured with ascorbic acid. Additionally, overexpression of TET3 and Runx3 promoted KIR expression in CD56bright NK cells and NK-92 cells. Our results show that KIR promoter demethylation can be induced in CD56bright, and this process is facilitated by ascorbic acid.
Collapse
Affiliation(s)
- Cheng-Ying Wu
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455; and
| | - Bin Zhang
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455; and
| | - Hansol Kim
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455; and
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jeffrey S Miller
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455; and
| | - Frank Cichocki
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455; and
| |
Collapse
|
6
|
Bruijnesteijn J, de Groot NG, Bontrop RE. The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates. Front Immunol 2020; 11:582804. [PMID: 33013938 PMCID: PMC7516082 DOI: 10.3389/fimmu.2020.582804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/18/2020] [Indexed: 12/26/2022] Open
Abstract
The activity and function of natural killer (NK) cells are modulated through the interactions of multiple receptor families, of which some recognize MHC class I molecules. The high level of MHC class I polymorphism requires their ligands either to interact with conserved epitopes, as is utilized by the NKG2A receptor family, or to co-evolve with the MHC class I allelic variation, which task is taken up by the killer cell immunoglobulin-like receptor (KIR) family. Multiple molecular mechanisms are responsible for the diversification of the KIR gene system, and include abundant chromosomal recombination, high mutation rates, alternative splicing, and variegated expression. The combination of these genetic mechanisms generates a compound array of diversity as is reflected by the contraction and expansion of KIR haplotypes, frequent birth of fusion genes, allelic polymorphism, structurally distinct isoforms, and variegated expression, which is in contrast to the mainly allelic nature of MHC class I polymorphism in humans. A comparison of the thoroughly studied human and macaque KIR gene repertoires demonstrates a similar evolutionarily conserved toolbox, through which selective forces drove and maintained the diversified nature of the KIR gene cluster. This hypothesis is further supported by the comparative genetics of KIR haplotypes and genes in other primate species. The complex nature of the KIR gene system has an impact upon the education, activity, and function of NK cells in coherence with an individual’s MHC class I repertoire and pathogenic encounters. Although selection operates on an individual, the continuous diversification of the KIR gene system in primates might protect populations against evolving pathogens.
Collapse
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
| |
Collapse
|
7
|
Vargas LDB, Dourado RM, Amorim LM, Ho B, Calonga-Solís V, Issler HC, Marin WM, Beltrame MH, Petzl-Erler ML, Hollenbach JA, Augusto DG. Single Nucleotide Polymorphism in KIR2DL1 Is Associated With HLA-C Expression in Global Populations. Front Immunol 2020; 11:1881. [PMID: 32983108 PMCID: PMC7478174 DOI: 10.3389/fimmu.2020.01881] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Regulation of NK cell activity is mediated through killer-cell immunoglobulin-like receptors (KIR) ability to recognize human leukocyte antigen (HLA) class I molecules as ligands. Interaction of KIR and HLA is implicated in viral infections, autoimmunity, and reproduction and there is growing evidence of the coevolution of these two independently segregating gene families. By leveraging KIR and HLA-C data from 1000 Genomes consortium we observed that the KIR2DL1 variant rs2304224 * T is associated with lower expression of HLA-C in individuals carrying the ligand HLA-C2 (p = 0.0059). Using flow cytometry, we demonstrated that this variant is also associated with higher expression of KIR2DL1 on the NK cell surface (p = 0.0002). Next, we applied next generation sequencing to analyze KIR2DL1 sequence variation in 109 Euro and 75 Japanese descendants. Analyzing the extended haplotype homozygosity, we show signals of positive selection for rs4806553 * G and rs687000 * G, which are in linkage disequilibrium with rs2304224 * T. Our results suggest that lower expression of HLA-C2 ligands might be compensated for higher expression of the receptor KIR2DL1 and bring new insights into the coevolution of KIR and HLA.
Collapse
Affiliation(s)
- Luciana de Brito Vargas
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Renata M Dourado
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Leonardo M Amorim
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Brenda Ho
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Verónica Calonga-Solís
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Hellen C Issler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Wesley M Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Marcia H Beltrame
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| |
Collapse
|
8
|
Bruijnesteijn J, van der Wiel MKH, de Groot N, Otting N, de Vos-Rouweler AJM, Lardy NM, de Groot NG, Bontrop RE. Extensive Alternative Splicing of KIR Transcripts. Front Immunol 2018; 9:2846. [PMID: 30564240 PMCID: PMC6288254 DOI: 10.3389/fimmu.2018.02846] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
The killer-cell Ig-like receptors (KIR) form a multigene entity involved in modulating immune responses through interactions with MHC class I molecules. The complexity of the KIR cluster is reflected by, for instance, abundant levels of allelic polymorphism, gene copy number variation, and stochastic expression profiles. The current transcriptome study involving human and macaque families demonstrates that KIR family members are also subjected to differential levels of alternative splicing, and this seems to be gene dependent. Alternative splicing may result in the partial or complete skipping of exons, or the partial inclusion of introns, as documented at the transcription level. This post-transcriptional process can generate multiple isoforms from a single KIR gene, which diversifies the characteristics of the encoded proteins. For example, alternative splicing could modify ligand interactions, cellular localization, signaling properties, and the number of extracellular domains of the receptor. In humans, we observed abundant splicing for KIR2DL4, and to a lesser extent in the lineage III KIR genes. All experimentally documented splice events are substantiated by in silico splicing strength predictions. To a similar extent, alternative splicing is observed in rhesus macaques, a species that shares a close evolutionary relationship with humans. Splicing profiles of Mamu-KIR1D and Mamu-KIR2DL04 displayed a great diversity, whereas Mamu-KIR3DL20 (lineage V) is consistently spliced to generate a homolog of human KIR2DL5 (lineage I). The latter case represents an example of convergent evolution. Although just a single KIR splice event is shared between humans and macaques, the splicing mechanisms are similar, and the predicted consequences are comparable. In conclusion, alternative splicing adds an additional layer of complexity to the KIR gene system in primates, and results in a wide structural and functional variety of KIR receptors and its isoforms, which may play a role in health and disease.
Collapse
Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marit K H van der Wiel
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Nanine de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Nel Otting
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | | | - Neubury M Lardy
- Department of Immunogenetics, Sanquin, Amsterdam, 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
| |
Collapse
|
9
|
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.
Collapse
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
| | | |
Collapse
|
10
|
Li H, Wright PW, McCullen M, Anderson SK. Characterization of KIR intermediate promoters reveals four promoter types associated with distinct expression patterns of KIR subtypes. Genes Immun 2016; 17:66-74. [PMID: 26656451 PMCID: PMC4724278 DOI: 10.1038/gene.2015.56] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/27/2015] [Accepted: 11/11/2015] [Indexed: 01/30/2023]
Abstract
The human killer cell immunoglobulin-like receptor (KIR) genes contain multiple promoters that control the process of gene activation and variegated expression of KIR on natural killer (NK) and T cells. Specific subfamilies of KIR genes have differences in the timing and tissue specificity of expression: however, previous studies of the proximal KIR promoters have not shown significant differences in activity between differentially expressed KIR gene subsets. The recent identification of an intermediate KIR promoter (ProI) associated with KIR2DL1 expression suggested a central role for this element in KIR expression. The current study identifies ProI elements in all of the KIR genes, revealing four classes of ProI that correspond with four distinct expression phenotypes of KIR subgroups: KIR2DL2/S2/L3 that are expressed early in reconstituting NK after transplant; KIR2DL4 that is expressed by CD56-bright NK in a non-variegated manner; KIR3DL3 that is not expressed by circulating NK cells; and the remaining KIR that are expressed by subsets of CD56-dim NK. The four classes of ProI are structurally diverse and display distinct functional properties. Altogether, these results indicate that KIR ProI elements contribute to the tissue/cell-type specificity of KIR transcription and cooperate with the probabilistic proximal promoter to control KIR expression.
Collapse
Affiliation(s)
- H Li
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Lab, Frederick, MD, USA
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - P W Wright
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Lab, Frederick, MD, USA
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - M McCullen
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - S K Anderson
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Lab, Frederick, MD, USA
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| |
Collapse
|
11
|
Dunphy SE, Guinan KJ, Chorcora CN, Jayaraman J, Traherne JA, Trowsdale J, Pende D, Middleton D, Gardiner CM. 2DL1, 2DL2 and 2DL3 all contribute to KIR phenotype variability on human NK cells. Genes Immun 2015; 16:301-10. [PMID: 25950617 DOI: 10.1038/gene.2015.15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/06/2015] [Accepted: 03/31/2015] [Indexed: 01/16/2023]
Abstract
Natural killer (NK) cells are lymphocytes that function as part of the innate immune system. Their activity is controlled by a range of inhibitory and activating receptors, including the important killer-cell immunoglobulin-like receptors (KIR). The KIR are a multi-gene family of receptors that interact with the human leukocyte antigen (HLA) class I family of molecules and are characterised by extensive allelic polymorphism. Their expression on the cell surface of NK cells is highly variable, but the factors responsible for this variability are not yet clearly understood. In the current study, we investigated KIR expression in a healthy human cohort that we had previously characterised in depth at a genetic level, with KIR allele typing and HLA class I ligand genotypes available for all donors (n=198). Allelic polymorphism significantly affected the phenotypic expression of all KIR analysed, whereas HLA ligand background influenced the expression levels of 2DL1 and 2DL3. In particular, we found that although 2DL2 may influence 2DL1 expression, this appears to be owing to variation in 2DL1 copy number. Finally, the inhibitory receptor LILRB1 had higher expression levels in individuals with B/B KIR genotypes, suggesting a possible relationship between KIR and non-KIR receptors, which serves to balance NK cell activation potential.
Collapse
Affiliation(s)
- S E Dunphy
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin 2, Ireland
| | - K J Guinan
- Current address: BioAtlantis Ltd., Kerry Technology Park, Tralee, Co. Kerry, Ireland
| | - C Ní Chorcora
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin 2, Ireland
| | - J Jayaraman
- Cambridge Institute for Medical Research, University of Cambridge; Division of Immunology, Cambridge, UK
| | - J A Traherne
- 1] Cambridge Institute for Medical Research, University of Cambridge; Division of Immunology, Cambridge, UK [2] Department of Pathology, University of Cambridge, Cambridge, UK
| | - J Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - D Pende
- Immunology Laboratory, IRCCS AOU San Martino-IST, Largo Rosanna Benzi 10, Genova, Italy
| | - D Middleton
- Transplant Immunology Laboratory, Royal Liverpool University Hospital, Liverpool, UK
| | - C M Gardiner
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin 2, Ireland
| |
Collapse
|
12
|
Anderson SK. Probabilistic bidirectional promoter switches: noncoding RNA takes control. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e191. [PMID: 25181276 PMCID: PMC4222648 DOI: 10.1038/mtna.2014.42] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/29/2014] [Indexed: 12/29/2022]
Abstract
The discovery of probabilistic promoter switches in genes that code for class I major histocompatibility complex receptors in mouse and human provides a useful paradigm to explain programmed cell fate decisions. These switches have preset probabilities of transcribing in either the sense or antisense direction, and the characteristics of individual switches are programmed by the relative affinity of competing transcription factor-binding sites. The noncoding RNAs produced from these switches can either activate or suppress gene transcription, based on their location relative to the promoter responsible for gene expression in mature cells. The switches are active in a developmental phase that precedes gene expression by mature cells, thus temporally separating the stochastic events that determine gene activation from the protein expression phase. This allows the probabilistic generation of variegated gene expression in the absence of selection and ensures that mature cells have stable expression of the genes. Programmed probabilistic switches may control cell fate decisions in many developmental systems, and therefore, it is important to investigate noncoding RNAs expressed by progenitor cells to determine if they are expressed in a stochastic manner at the single cell level. This review provides a summary of current knowledge regarding murine and human switches, followed by speculation on the possible involvement of probabilistic switches in other systems of programmed differentiation.
Collapse
Affiliation(s)
- Stephen K Anderson
- Basic Science Program, Leidos Biomedical Research Inc; Lab of Experimental Immunology, Frederick National Lab, Frederick, Maryland, USA
- The Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| |
Collapse
|