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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.
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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
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Tao S, You X, Wang J, Zhang W, He J, Zhu F. Determination for KIR genotype and allele copy number via real-time quantitative PCR method. Immunogenetics 2024; 76:137-143. [PMID: 38206349 DOI: 10.1007/s00251-023-01331-7] [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: 08/04/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
Killer cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) play crucial roles in regulating NK cell activity. Here, we report a real-time quantitative PCR (qPCR) to genotype all KIR genes and their copy numbers simultaneously. With 18 pairs of locus-specific primers, we identified KIR genes by Ct values and determined KIR copy number using the 2-∆Ct method. Haplotypes were assigned based on KIR gene copy numbers. The real-time qPCR results were consistent with the NGS method, except for one sample with KIR2DL5 discrepancy. qPCR is a multiplex method that can identify KIR copy number, which helps obtain a relatively accurate haplotype structure, facilitating increased KIR research in laboratories where NGS or other high-resolution methods are not available.
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Affiliation(s)
- Sudan Tao
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Xuan You
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Jielin Wang
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Wei Zhang
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Ji He
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Faming Zhu
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China.
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Barela Hudgell MA, Momtaz F, Jafri A, Alekseyev MA, Smith LC. Local Genomic Instability of the SpTransformer Gene Family in the Purple Sea Urchin Inferred from BAC Insert Deletions. Genes (Basel) 2024; 15:222. [PMID: 38397211 PMCID: PMC10887614 DOI: 10.3390/genes15020222] [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: 01/09/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The SpTransformer (SpTrf) gene family in the purple sea urchin, Strongylocentrotus purpuratus, encodes immune response proteins. The genes are clustered, surrounded by short tandem repeats, and some are present in genomic segmental duplications. The genes share regions of sequence and include repeats in the coding exon. This complex structure is consistent with putative local genomic instability. Instability of the SpTrf gene cluster was tested by 10 days of growth of Escherichia coli harboring bacterial artificial chromosome (BAC) clones of sea urchin genomic DNA with inserts containing SpTrf genes. After the growth period, the BAC DNA inserts were analyzed for size and SpTrf gene content. Clones with multiple SpTrf genes showed a variety of deletions, including loss of one, most, or all genes from the cluster. Alternatively, a BAC insert with a single SpTrf gene was stable. BAC insert instability is consistent with variations in the gene family composition among sea urchins, the types of SpTrf genes in the family, and a reduction in the gene copy number in single coelomocytes. Based on the sequence variability among SpTrf genes within and among sea urchins, local genomic instability of the family may be important for driving sequence diversity in this gene family that would be of benefit to sea urchins in their arms race with marine microbes.
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Affiliation(s)
- Megan A. Barela Hudgell
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Farhana Momtaz
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Abiha Jafri
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Max A. Alekseyev
- Department of Mathematics and the Computational Biology Institute, George Washington University, Washington, DC 20052, USA;
| | - L. Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
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4
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Tian W, Li LX, Cheng W, Jin HK, Zhang SS. Leukocyte immunoglobulin-like receptor A3 gene deletion in five Chinese populations and protective association with nasopharyngeal carcinoma. Int J Immunogenet 2024; 51:32-38. [PMID: 38015196 DOI: 10.1111/iji.12647] [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: 08/09/2023] [Revised: 10/17/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Among the thirteen leukocyte Ig-like receptor (LILR) loci located at 19q13.4, LILRA3 is unique in that it encodes a soluble protein lacking the transmembrane and cytoplasmic domains, and a 6.7 kb deletion spanning the first seven exons has been detected in some human individuals. Presently, there is a lack of data about the distribution of LILRA3 gene deletion in more diverse ethnic groups. Also, no previous studies have investigated the correlation between copy number variation (CNV) of LILRA3 and nasopharyngeal carcinoma (NPC). In this study, five populations from China mainland: two Southern Han populations, Hunan (N = 1478) and Guandong (N = 107); one Southeastern Han population, Fujian (N = 439); and two Northern populations, Inner Mongolia Han (N = 104) and Mongol population from Inner Mongolia (N = 158) were investigated for CNV of LILRA3 using polymerase chain reaction-sequence-specific priming (PCR-SSP) method. LILRA3 variants were also examined in a cohort of NPC cases (N = 1142) in Hunan Han population. The five Chinese populations demonstrated northward increase in frequency of the deleted form of LILRA3 gene (LILRA3*Del) (all corrected p values < 0.05). Inter-population comparison also uncovered significant differentiation in the distribution of CNV of LILRA3 among modern human populations. LILRA3*Del was found to confer significantly reduced risk to NPC in Hunan Han population (at allelic level: OR = 0.79, 95% CI = 0.71-0.89, p < 0.0001; at genotype level: OR = 0.63, 95% CI = 0.51-0.79, p < 0.0001). No interaction was found between LILRA3 variants and HLA-A*02:07, HLA-A*11:01, HLA-B*13 and HLA-B*46:01 alleles in susceptibility to NPC. Our study constitutes the first demonstration of LILRA3 gene as a locus linked to NPC susceptibility in a southern Chinese population. Future independent studies in other populations are warranted to confirm the findings reported in this study.
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Affiliation(s)
- Wei Tian
- Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, China
- Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, China
| | - Li Xin Li
- Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, China
| | - Wen Cheng
- Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, China
| | - He Kun Jin
- Department of Radiotherapy, Hunan Cancer Hospital (the affiliated Cancer Hospital of XiangYa School of Medicine of Central South University), Changsha, China
| | - Sha Shuang Zhang
- Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, China
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Zhang Q, Locke AF, Alvarez AC, Cabarong ML, Liv LC, Alfaro BGP, Gjertson DW, Reed EF. Advancing precision in histocompatibility and immunogenetics: a comprehensive review of the UCLA exchange program. Front Genet 2024; 15:1352764. [PMID: 38362203 PMCID: PMC10867271 DOI: 10.3389/fgene.2024.1352764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Precise typing of human leukocyte antigens (HLA) is crucial for clinical hematopoietic stem cell and solid organ transplantations, transfusion medicine, HLA-related disease association, and drug hypersensitivity analysis. The UCLA Cell Exchange program has played a vital role in providing educational and proficiency testing surveys to HLA laboratories worldwide for the past 5 decades. This article highlights the significant contribution of the UCLA Cell and DNA Exchange Programs in advancing HLA antibody testing, genotyping, crossmatches, and, more recently, virtual crossmatches. Additionally, we discuss future directions of the UCLA Cell Exchange program to support histocompatibility testing to adapt to the fast-evolving field of immunotherapy, tolerance and xenotransplantation.
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Affiliation(s)
- Qiuheng Zhang
- UCLA Immunogenetics Center, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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Baek IC, Choi EJ, Kim HJ, Choi H, Shin HS, Lim DG, Kim TG. Association of KIR Genes with Middle East Respiratory Syndrome Coronavirus Infection in South Koreans. J Clin Med 2024; 13:258. [PMID: 38202265 PMCID: PMC10779705 DOI: 10.3390/jcm13010258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Middle East respiratory syndrome (MERS) is a lower respiratory tract disease caused by a beta coronavirus (CoV) called MERS-CoV, characterized by a high mortality rate. We aimed to evaluate the association between genetic variation in killer cell immunoglobulin-like receptors (KIRs) and the risk of MERS in South Koreans. METHODS KIR genes were genotyped by multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP). A case-control study was performed to identify the odds ratios (OR) of KIR genes for MERS and the association of KIR genes and their ligands, human leukocyte antigens (HLA) genes. RESULTS KIR2DS4D and KIR3DP1F showed higher frequencies in the group of all patients infected with MERS-CoV than in the control group (p = 0.023, OR = 2.4; p = 0.039, OR = 2.7). KIR2DL1, KIR2DP1, and KIR3DP1D were significantly associated with moderate/mild (Mo/Mi) cases. KIR2DL2, KIR2DS1, and KIR3DP1F were affected in severe cases. When we investigated the association between KIR genes and their ligands in MERS patient and control groups, KIR3DL1+/Bw4(80I)+, KIR3DL1+/Bw6+, KIR3DL1+/Bw6-, KIR2DS1+/C2+, and KIR3DS+/Bw4(80I)+ were associated with MERS. KIR3DL1+/Bw6- was found in Mo/Mi cases. KIR2DS1+/C2+ and KIR2DS2+/C1+ were found in severe cases. CONCLUSION Further investigations are needed to prove the various immune responses of MERS-CoV-infected cells according to variations in the KIR gene and ligand gene. A treatment strategy based on current research on the KIR gene and MERS-CoV will suggest potential treatment targets.
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Affiliation(s)
- In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (I.-C.B.); (E.-J.C.); (H.-J.K.); (H.C.)
| | - Eun-Jeong Choi
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (I.-C.B.); (E.-J.C.); (H.-J.K.); (H.C.)
| | - Hyoung-Jae Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (I.-C.B.); (E.-J.C.); (H.-J.K.); (H.C.)
| | - Haeyoun Choi
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (I.-C.B.); (E.-J.C.); (H.-J.K.); (H.C.)
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Infectious Diseases, College of Medicine, Eulji University, Daejeon 34824, Republic of Korea;
| | - Dong-Gyun Lim
- Translational Research Center, Research Institute of Public Health, National Medical Center, Seoul 04564, Republic of Korea
| | - Tai-Gyu Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (I.-C.B.); (E.-J.C.); (H.-J.K.); (H.C.)
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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Choi EJ, Baek IC, Park S, Kim HJ, Kim TG. Development of cost-effective and fast KIR genotyping by multiplex PCR-SSP. HLA 2024; 103:e15191. [PMID: 37688498 DOI: 10.1111/tan.15191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 09/11/2023]
Abstract
Killer-cell immunoglobulin-like receptors (KIR) control natural killer (NK) cell functions by recognizing HLA molecules and modulating the activity of NK cells. The KIR gene cluster contains polymorphic and highly homologous genes. Diversity of the KIR region is achieved through differences in gene content, allelic polymorphism, and gene copy number, which result in unrelated individuals having different KIR genotypes and individualized immune responses that are relevant to multiple aspects of human health and disease. Therefore, KIR genotyping is increasingly used in epidemiological studies. Here, we developed multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP) to compensate for the shortcomings of the conventional PCR-SSP method, which is most commonly used for KIR analysis. Multiplex PCR-SSP method involves six multiplex reactions that detect 16 KIR genes and distinguish variant types of some KIR genes by adding two reactions. The assay was evaluated in a blind survey using a panel of 40 reference DNA standards from the UCLA KIR Exchange Program. The results are 100% concordant with the genotype determined using Luminex-based reverse sequence-specific oligonucleotide typing systems. Additionally, we investigated the currently known 16 KIR genes and their common variants in 120 unrelated Korean individuals. The results were consistent with the KIR genotype previously reported by Hwang et al. This multiplex PCR-SSP is an efficient method for analyzing KIR genotypes in both small- and large-scale studies with minimal labor, reagents, and DNA. Furthermore, by providing a better definition of KIR polymorphisms it can contribute to developments in immunogenetics.
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Affiliation(s)
- Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - In-Cheol Baek
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Silvia Park
- Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee-Je Kim
- Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tai-Gyu Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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8
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Al Hadra B, Lukanov T, Mihaylova A, Naumova E. High-resolution characterization of KIR genes polymorphism in healthy subjects from the Bulgarian population-A pilot study. HLA 2024; 103:e15341. [PMID: 38180282 DOI: 10.1111/tan.15341] [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: 08/11/2023] [Revised: 12/14/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024]
Abstract
Although killer-cell immunoglobulin-like receptor (KIR) gene content has been widely studied in health and disease, with the advancement of next-generation sequencing (NGS) technology the high-resolution characterization of this complex gene region has become achievable. KIR allele-level diversity has lately been described across human populations. The present study aimed to analyze for the first time the allele-level polymorphism of nine KIR genes in 155 healthy, unrelated individuals from the Bulgarian population by applying NGS. The highest degree of polymorphism was detected for the KIR3DL3 gene with 40 observed alleles at five-digit resolution in total, 22 of which were common. On the other hand, the KIR3DS1 gene was found to have the lowest degree of polymorphism among the studied KIR genes with one common allele: KIR3DS1*01301 (31.6%). To better understand KIR allelic associations and patterns in Bulgarians, we have estimated the pairwise linkage disequilibrium (LD) for the 10 KIR loci, where KIR2DL3*00501 allele was found in strong LD with KIR2DL1*00101 (D' = 1.00, R2 = 0.742). This is the first study investigating KIR polymorphism at the allele level in a population from the South-East European region. Considering the effect of the populationally shaped KIR allelic polymorphism on NK cell function, this data could lead to a better understanding of the genetic heterogeneity of this region and can be carried into clinical practice by improvement of the strategies taken for NK-mediated diseases.
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Affiliation(s)
- Bushra Al Hadra
- Clinic of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
- Department of Clinical Immunology, Medical University, Sofia, Bulgaria
| | - Tsvetelin Lukanov
- Clinic of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
- Department of Clinical Immunology, Medical University, Sofia, Bulgaria
| | - Anastasiya Mihaylova
- Clinic of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
| | - Elissaveta Naumova
- Clinic of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
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Farias TD, Brugiapaglia S, Croci S, Magistroni P, Curcio C, Zguro K, Fallerini C, Fava F, Pettini F, Kichula KM, Pollock NR, Font-Porterias N, Palmer WH, Marin WM, Baldassarri M, Bruttini M, Hollenbach JA, Hendricks AE, Meloni I, Novelli F, Renieri A, Furini S, Norman PJ, Amoroso A. HLA-DPB1*13:01 associates with enhanced, and KIR2DS4*001 with diminished protection from developing severe COVID-19. HLA 2024; 103:e15251. [PMID: 37850268 PMCID: PMC10873037 DOI: 10.1111/tan.15251] [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: 01/04/2023] [Revised: 08/22/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023]
Abstract
Extreme polymorphism of HLA and killer-cell immunoglobulin-like receptors (KIR) differentiates immune responses across individuals. Additional to T cell receptor interactions, subsets of HLA class I act as ligands for inhibitory and activating KIR, allowing natural killer (NK) cells to detect and kill infected cells. We investigated the impact of HLA and KIR polymorphism on the severity of COVID-19. High resolution HLA class I and II and KIR genotypes were determined from 403 non-hospitalized and 1575 hospitalized SARS-CoV-2 infected patients from Italy collected in 2020. We observed that possession of the activating KIR2DS4*001 allotype is associated with severe disease, requiring hospitalization (OR = 1.48, 95% CI 1.20-1.85, pc = 0.017), and this effect is greater in individuals homozygous for KIR2DS4*001 (OR = 3.74, 95% CI 1.75-9.29, pc = 0.003). We also observed the HLA class II allotype, HLA-DPB1*13:01 protects SARS-CoV-2 infected patients from severe disease (OR = 0.49, 95% CI 0.33-0.74, pc = 0.019). These association analyses were replicated using logistic regression with sex and age as covariates. Autoantibodies against IFN-α associated with COVID-19 severity were detected in 26% of 156 hospitalized patients tested. HLA-C*08:02 was more frequent in patients with IFN-α autoantibodies than those without, and KIR3DL1*01502 was only present in patients lacking IFN-α antibodies. These findings suggest that KIR and HLA polymorphism is integral in determining the clinical outcome following SARS-CoV-2 infection, by influencing the course both of innate and adaptive immunity.
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Affiliation(s)
- Ticiana D.J. Farias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Silvia Brugiapaglia
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Susanna Croci
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Paola Magistroni
- Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Claudia Curcio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Kristina Zguro
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
| | - Francesco Pettini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, 53100, Italy
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Nicholas R. Pollock
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Neus Font-Porterias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - William H. Palmer
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Wesley M. Marin
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
| | - Jill A. Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Audrey E. Hendricks
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Mathematical and Statistical Sciences, and Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Ilaria Meloni
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Francesco Novelli
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
- Molecular Biotechnology Center, University of Turin, Turin, 10126, Italy
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, 53100, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Antonio Amoroso
- Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
- Department of Medical Sciences, University of Turin, Turin, 10126, Italy
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10
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de Groot NG, Heijmans CM, van der Wiel MK, Bruijnesteijn J, Bontrop RE. The KIR repertoire of a West African chimpanzee population is characterized by limited gene, allele, and haplotype variation. Front Immunol 2023; 14:1308316. [PMID: 38149259 PMCID: PMC10750417 DOI: 10.3389/fimmu.2023.1308316] [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: 10/06/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction The killer cell immunoglobulin-like receptors (KIR) play a pivotal role in modulating the NK cell responses, for instance, through interaction with major histocompatibility complex (MHC) class I molecules. Both gene systems map to different chromosomes but co-evolved during evolution. The human KIR gene family is characterized by abundant allelic polymorphism and copy number variation. In contrast, our knowledge of the KIR repertoire in chimpanzees is limited to 39 reported alleles, with no available population data. Only three genomic KIR region configurations have been mapped, and seventeen additional ones were deduced by genotyping. Methods Previously, we documented that the chimpanzee MHC class I repertoire has been skewed due to an ancient selective sweep. To understand the depth of the sweep, we set out to determine the full-length KIR transcriptome - in our MHC characterized pedigreed West African chimpanzee cohort - using SMRT sequencing (PacBio). In addition, the genomic organization of 14 KIR haplotypes was characterized by applying a Cas9-mediated enrichment approach in concert with long-read sequencing by Oxford Nanopore Technologies. Results In the cohort, we discovered 35 undescribed and 15 already recorded Patr-KIR alleles, and a novel hybrid KIR gene. Some KIR transcripts are subject to evolutionary conserved alternative splicing events. A detailed insight on the KIR region dynamics (location and order of genes) was obtained, however, only five new KIR region configurations were detected. The population data allowed to investigate the distribution of the MHC-C1 and C2-epitope specificity of the inhibitory lineage III KIR repertoire, and appears to be skewed towards C2. Discussion Although the KIR region is known to evolve fast, as observed in other primate species, our overall conclusion is that the genomic architecture and repertoire in West African chimpanzees exhibit only limited to moderate levels of variation. Hence, the ancient selective sweep that affected the chimpanzee MHC class I region may also have impacted the KIR system.
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Affiliation(s)
- Natasja G. de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Corrine M.C. Heijmans
- 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
| | - Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E. Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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11
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Redondo-García S, Barritt C, Papagregoriou C, Yeboah M, Frendeus B, Cragg MS, Roghanian A. Human leukocyte immunoglobulin-like receptors in health and disease. Front Immunol 2023; 14:1282874. [PMID: 38022598 PMCID: PMC10679719 DOI: 10.3389/fimmu.2023.1282874] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023] Open
Abstract
Human leukocyte immunoglobulin (Ig)-like receptors (LILR) are a family of 11 innate immunomodulatory receptors, primarily expressed on lymphoid and myeloid cells. LILRs are either activating (LILRA) or inhibitory (LILRB) depending on their associated signalling domains (D). With the exception of the soluble LILRA3, LILRAs mediate immune activation, while LILRB1-5 primarily inhibit immune responses and mediate tolerance. Abnormal expression and function of LILRs is associated with a range of pathologies, including immune insufficiency (infection and malignancy) and overt immune responses (autoimmunity and alloresponses), suggesting LILRs may be excellent candidates for targeted immunotherapies. This review will discuss the biology and clinical relevance of this extensive family of immune receptors and will summarise the recent developments in targeting LILRs in disease settings, such as cancer, with an update on the clinical trials investigating the therapeutic targeting of these receptors.
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Affiliation(s)
- Silvia Redondo-García
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Christopher Barritt
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
- Lister Department of General Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
- School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, United Kingdom
| | - Charys Papagregoriou
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Muchaala Yeboah
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Björn Frendeus
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
- BioInvent International AB, Lund, Sweden
| | - Mark S. Cragg
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Ali Roghanian
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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12
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Ameen R, Titus R, Geo JA, Al Shemmari S, Geraghty DE, Pyo CW, Askar M. KIR genotype and haplotype repertoire in Kuwaiti healthy donors, hematopoietic cell transplant recipients and healthy family members. HLA 2023; 102:179-191. [PMID: 36960942 DOI: 10.1111/tan.15029] [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: 10/06/2022] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/25/2023]
Abstract
The gene complex located on chromosome 19q13.4 encodes the Killer-cell Immunoglobulin-like Receptors (KIRs), which exhibit remarkable polymorphism in both gene content and sequences. Further, the repertoire of KIR genes varies within and between populations, creating a diverse pool of KIR genotypes. This study was carried out to characterize KIR genotypes and haplotypes among 379 Arab Kuwaiti individuals including 60 subjects from 20 trio families, 49 hematopoietic cell transplantation (HCT) recipients and 270 healthy Kuwaiti volunteer HCT donors. KIR Genotyping was performed by a combination of reverse sequence specific oligonucleotide probes (rSSO) and/or Real Time PCR. The frequencies of KIR genes in 270 healthy Kuwaiti volunteer donors were compared to previously reported frequencies in other populations. In addition, we compared the differences in KIR repertoire of patients and healthy donors to investigate the reproducibility of previously reported significant differences between patients with hematological malignancies and healthy donors. The observed frequencies in our cohort volunteer HCT donors was comparable to those reported in neighboring Arab populations. The activating genes KIR2DS1, KIR2DS5 and KIR3DS1 and the inhibitory gene KIR2DL5 were significantly more frequent in patients compared to healthy donors, however, none of the previously reported differences were reproducible in our Kuwaiti cohort. This report is the first description of KIR gene carrier frequency and haplotype characterization in a fairly large cohort of the Kuwaiti population, which may have implications in KIR based HCT donor selection strategies.
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Affiliation(s)
- Reem Ameen
- Department of Medical Laboratory Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Roshni Titus
- Department of Medical Laboratory Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Jeethu Anu Geo
- Department of Medical Laboratory Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Salem Al Shemmari
- Department of Medicine, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Medhat Askar
- College of Medicine, Qatar University, Doha, Qatar
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13
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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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14
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Gowdavally S, Tsamadou C, Platzbecker U, Sala E, Valerius T, Klein S, Kröger N, Wulf G, Einsele H, Thurner L, Schaefer-Eckart K, Freitag S, Casper J, Dürholt M, Kaufmann M, Hertenstein B, Ringhoffer M, Schmeller S, Neuchel C, Rode I, Amann EM, Richter A, Schrezenmeier H, Mytilineos J, Fuerst D. KIR2DS4 and its variant KIR1D in KIR-AA genotype donors showed differential survival impact in patients with lymphoid disease after HLA-matched unrelated hematopoietic stem cell transplantation. Transplant Cell Ther 2023:S2666-6367(23)01236-8. [PMID: 37150297 DOI: 10.1016/j.jtct.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/07/2023] [Indexed: 05/09/2023]
Abstract
Previous studies illustrated associations between presence of activating killer cell immunoglobulin-like receptor (KIR) genes and lower susceptibility to hematologic malignancies in humans. In addition, favorable hematopoietic stem cell transplantation (HSCT) outcomes were reported in patients, who received transplants from donors with KIR genotypes dominant for activating KIR receptors. However, the association of activating KIR genes on an allelic level with disease and their impact on HSCT outcome has been only scarcely investigated. To this end, we genotyped a large transplantation cohort for KIR two Ig domains and short cytoplasmic tail 4 (KIR2DS4) polymorphisms and investigated their association with disease. We next investigated the impact of KIR-AA genotype donor KIR2DS4 polymorphisms (AA/KIR2DS4 versus (vs.) AA/KIR1D), on clinical outcome of HSCT in patient subgroups (myeloid vs. lymphoid). Among 2810 transplant pairs, 68.8% (n=1934) were 10/10 human leukocyte antigen (HLA) matched and 31.2% (n=876) were 9/10 HLA-matched. The distribution of KIR one Ig domain (KIR1D) in patients vs. donors was equal (P value = 0.205). Multivariate analysis in 10/10 HLA-matched patients with lymphoid disease showed improved HSCT outcome (overall survival (OS): hazard ratio (HR) 0.62, P=0.002; disease free survival (DFS): HR 0.70, P=0.011; graft-versus-host disease free and relapse-free survival (GRFS): HR 0.67, P=0.002; non-relapse mortality (NRM): HR 0.55, P<0.001) when they received grafts from AA/KIR1D donors. This effect was not seen in either 9/10 HLA-matched patients with lymphoid disease or patients with myeloid disease. Our study indicates that the presence of KIR1D alleles is not associated with disease in patients and interestingly, using grafts from AA/KIR1D donors translated into a beneficial survival outcome in 10/10 HLA-matched patients with lymphoid disease.
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Affiliation(s)
- Sowmya Gowdavally
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, Ulm, and University Hospital Ulm, Germany; Institute of Transfusion Medicine, University of Ulm, Germany
| | - Chrysanthi Tsamadou
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, Ulm, and University Hospital Ulm, Germany; Institute of Transfusion Medicine, University of Ulm, Germany
| | - Uwe Platzbecker
- Department of Hematology/Oncology, University of Leipzig, Germany
| | - Elisa Sala
- Department of Internal Medicine III, University of Ulm, Germany
| | - Thomas Valerius
- Section for Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian Albrechts University, Kiel, Germany
| | - Stefan Klein
- Universitätsmedizin Mannheim, Med. Klinik III, Mannheim, Germany
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Hospital Hamburg Eppendorf, Germany
| | - Gerald Wulf
- Hematology and Medical Oncology, University Medicine Goettingen
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Germany
| | - Lorenz Thurner
- Department Internal Medicine I, Universitätsklinikum des Saarlandes, Homburg, Germany
| | | | - Sebastian Freitag
- Department of Medicine III, Hematology/Oncology/Palliative Care, Rostock University Medical Center, Rostock,Germany
| | - Jochen Casper
- Department of Oncology and Hematology, Klinikum Oldenburg, University Clinic, Oldenburg, Germany
| | | | - Martin Kaufmann
- 2nd Department of Internal Medicine, Oncology and Hematology, Robert Bosch Hospital Stuttgart, Germany
| | | | - Mark Ringhoffer
- Medizinische Klinik III, Städtisches Klinikum Karlsruhe, Germany
| | - Sandra Schmeller
- DRST - German Registry for Stem Cell Transplantation, Ulm, Germany
| | - Christine Neuchel
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, Ulm, and University Hospital Ulm, Germany; Institute of Transfusion Medicine, University of Ulm, Germany
| | - Immanuel Rode
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, Ulm, and University Hospital Ulm, Germany; Institute of Transfusion Medicine, University of Ulm, Germany
| | - Elisa Maria Amann
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, Ulm, and University Hospital Ulm, Germany; Institute of Transfusion Medicine, University of Ulm, Germany
| | - Anita Richter
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, Ulm, and University Hospital Ulm, Germany; Institute of Transfusion Medicine, University of Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, Ulm, and University Hospital Ulm, Germany; Institute of Transfusion Medicine, University of Ulm, Germany
| | - Joannis Mytilineos
- DRST - German Registry for Stem Cell Transplantation, Ulm, Germany; ZKRD - Zentrales Knochenmarkspender-Register für Deutschland, German National Bone Marrow Donor Registry, Germany
| | - Daniel Fuerst
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg - Hessen, Ulm, and University Hospital Ulm, Germany; Institute of Transfusion Medicine, University of Ulm, Germany.
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15
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Roshan Zamir M, Ariafar A, Ghaderi A, Amirzargar A. The impact of killer cell immunoglobulin-like receptor (KIR) genes and human leukocyte antigen (HLA) class I ligands on predisposition or protection against prostate cancer. Immunobiology 2023; 228:152319. [PMID: 36599262 DOI: 10.1016/j.imbio.2022.152319] [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: 08/20/2022] [Revised: 12/02/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022]
Abstract
Natural killer (NK) cell development largely depends on killer cell immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I ligands. In the current study, we investigated the role of KIR genes, HLA ligands, and KIR-HLA combinations in vulnerability or protection against prostate cancer (PC). To analyze the frequency of 16 KIR genes and 5 HLA ligands, polymerase chain reaction with sequence-specific primers (PCR-SSP) was conducted in 150 PC patients and 200 healthy controls (CNs). KIR2DL5 (p = 0.0346, OR = 0.606, CI = 0.3916-0.9336), KIR2DS5 (p = 0.0227, OR = 0.587, CI = 0.3793-0.9139), HLA-B Bw4Thr80 (p = 0.0401, OR = 0.3552, CI = 0.1466-0.9059), HLA Bw4 (p = 0.0190, OR = 0.4744, CI = 0.2656-0.8521), and T4 gene cluster (including KIR2DS5-2DL5-3DS1-2DS1 genes) (p = 0.0194, OR = 0.5575, CI = 0.3449-0.8938) had a lower frequency in the PC patients compared to the control group. Moreover, a lower frequency of the genotypes contacting activating KIR (aKIR) > inhibitory KIR (iKIR) (p = 0.0298, OR = 0.5291, CI = 0.3056-0.9174) and iKIR + HLA < aKIR + HLA (p = 0.0183, OR = 0.2197, CI = 0.0672-0.7001) in PC patients compared to the CNs implies a protective role for aKIR genes. In the case of KIR-HLA interactions, we detected a significant association between KIR3DS1+ + HLA-A Bw4+ (p = 0.0113, OR = 0.5093, CI = 0.3124-0.8416) and KIR3DL1- + HLA-A Bw4+ (p = 0.0306, OR = 0.1153, CI = 0.0106-0.6537) combinations and resistance to prostate cancer. In contrast, the presence of KIR3DL1 in the absence of HLA-A Bw4 (p = 0.0040, OR = 2.00, CI = 1.264-3.111), HLA Bw4 (p = 0.0296, OR = 2.066, CI = 1.094-3.906), and HLA-Bw4Thr80 (p = 0.0071, OR = 2.505, CI = 1.319-4.703) genes probably predisposes to prostate cancer. Carrying the CxT4 genotype in PC patients was positively associated with lower tumor grades (Gleason score ≤ 6) (p = 0.0331, OR = 3.290, and CI = 1.181-8.395). Altogether, our data suggest a protective role for aKIRs, HLA-B Bw4Thr80, and HLA Bw4 ligands as well as a predisposing role for certain KIR-HLA combinations in prostate cancer. The findings of this study offer new insight into the population's risk assessment for prostate cancer in men. Additionally, predicting immunotherapy response based on KIR-HLA combinations aids in implementing the most effective therapeutic approach in the early stages of the disease.
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Affiliation(s)
- Mina Roshan Zamir
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ali Ariafar
- Urology-Oncology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Urology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Aliakbar Amirzargar
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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16
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Gunavathy N, Asirvatham A, Chitra A, Jayalakshmi M. Association of Killer Cell Immunoglobulin-Like Receptors and Their HLA-Ligands with Type 1 Diabetes Among South Indian Population. Immunol Invest 2023; 52:270-285. [PMID: 36705596 DOI: 10.1080/08820139.2023.2165940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Type 1 diabetes (T1D) is a multifactorial autoimmune disease, involving strong genetic components with familial predisposition. Killer cell immunoglobulin-like receptors (KIRs) found on the surface of NK cells have ligands of human leukocyte antigen (HLA) class I that are associated with T1D. The present study evaluates the influence of KIR genes and their HLA-ligands in the aetiology of T1D among the South Indian population. METHODS A total of 125 T1D patients, along with their parents (n = 126) and siblings (n = 52) were recruited. PCR-based genotyping was performed for KIR genes and HLA class I ligands. The gene frequencies were compared between patients and siblings/parents. Linkage-disequilibrium (LD) analysis was performed to assess the genetic association between KIR gene pairs. RESULTS The results show significant differences in HLA-ligands of KIR genes between patients and parents. The HLA-C1C1 homozygosity was found to be a predisposing risk factor, and HLA-C1C2 heterozygosity was protective towards T1D along with either the activating KIR2DS2 or inhibitory KIRs 2DL1, 2DL2, 2DL3. However, the frequency of inhibitory KIR3DL1 significantly increased in the presence of HLA-B Bw4 Ile80 in parents when compared to patients showing a protective effect on T1D. Two pairs of KIR genes, 2DS4-3DL1 and 2DS1-2DL5, showed strong LD in patients, siblings and parents. CONCLUSION The KIR-HLA ligand combinations have a significant effect on T1D aetiology among the South Indian population. This study defines a pattern for family-based association studies with genotypic information about KIR genes and their HLA-ligands, providing the first evidence towards T1D among the South Indian population.
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Affiliation(s)
- Nagarajan Gunavathy
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Arthur Asirvatham
- Department of Diabetology, Government Rajaji Hospital, Madurai, India
| | - Ayyappan Chitra
- Institute of Child Health and Research Centre, Government Rajaji Hospital, Madurai, India
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17
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Alomar S, Alkhuriji A, Alkhulaifi FM, Mansour L, Al-Jurayyan A, Aldossari GS, Albalawi AE, Alanazi AD. Relationship between KIR genotypes and HLA-ligands with SARS-CoV-2 infection in the Saudi population. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2023; 35:102416. [PMID: 36338940 PMCID: PMC9622466 DOI: 10.1016/j.jksus.2022.102416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 10/09/2022] [Accepted: 10/26/2022] [Indexed: 05/28/2023]
Abstract
Aim To ascertain whether killer cell immunoglobulin-like receptors (KIR) genes polymorphisms and HLA-I ligands are associated with COVID-19 in Saudi Arabia. Methods Eighty-seven COVID-19 patients who tested positive for SARS-CoV-2 and one hundred and fourteen healthy controls were enrolled in this study for genotyping of the 16 KIR genes, HLA-C1 and -C2 allotypes and HLA-G 14-bp indels polymorphisms using the sequence specific primer polymerase chain reaction (SSP-PCR) method. KIR genotype frequency differences and combination KIR-HLA-C ligand were tested for significance. Results Framework genes KIR2DL4, KIR3DL2, KIR3DL3, and KIR3DP2 were present in all individuals. The frequencies of KIR2DL2 and KIR2D4 were higher in COVID-19 positive patients than in healthy individuals. The frequencies of the combination KIR2DL2-HLA-C2 was also significantly higher in patients affected by COVID-19 compared with healthy controls. Conclusion It was found that the inhibitory KIR2DL2 gene in isolation or combined with its HLA-C2 ligand could be associated with susceptibility to COVID-19 in the Saudi population.
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Affiliation(s)
- Suliman Alomar
- Doping Research Chair, Department of Zoology, College of Science, King Saud University, PO. Box: 2455, Riyadh 11451, Saudi Arabia
- Zoology Department, College of Sciences, King Saud University, Post Office Box 2455, Riyadh 11451, Saudi Arabia
| | - Afrah Alkhuriji
- Zoology Department, College of Sciences, King Saud University, Post Office Box 2455, Riyadh 11451, Saudi Arabia
| | - Fadwa M Alkhulaifi
- Biology Department, College of Science, Imam Abdulrahman bin Faisal University, Saudi Arabia
| | - Lamjed Mansour
- Zoology Department, College of Sciences, King Saud University, Post Office Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah Al-Jurayyan
- Immunology and HLA Section, Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ghadeer S Aldossari
- Serology, Immunology and HLA, Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Aishah Eid Albalawi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 47912, Saudi Arabia
| | - Abdullah D Alanazi
- Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University, P.O. Box 1040, Ad-Dawadimi 11911, Saudi Arabia
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18
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Monos DS, Rajalingam R. The Major Histocompatibility Complex. Clin Immunol 2023. [DOI: 10.1016/b978-0-7020-8165-1.00005-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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19
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Distinct frequency patterns of LILRB3 and LILRA6 allelic variants in Europeans. Immunogenetics 2022; 75:263-267. [DOI: 10.1007/s00251-022-01286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022]
Abstract
Abstract
The leukocyte immunoglobulin–like receptor (LILR)B3 and LILRA6 genes encode homologous myeloid inhibitory and activating orphan receptors, respectively. Both genes exhibit a strikingly high level of polymorphism at the amino acid level and LILRA6 (but not LILRB3) displays copy number variation (CNV). Although multiple alleles have been reported for both genes, limited data is available on frequencies of these alleles among humans. We have sequenced LILRB3/A6 exons encoding signal peptides and ectodomains in 91 healthy blood donors of European descent who carry one or two copies of LILRA6 per diploid genome. Analysis of haplotypes among individuals with two LILRA6 copies, representing the majority in this cohort (N = 86), shows that common LILRB3 and LILRA6 alleles encode some distinct amino acid sequences in homologous regions of the receptors, which could potentially impact their respective functions differentially. Comparison of sequences in individuals with one vs. two copies of LILRA6 supports non-allelic homologous recombination between LILRB3 and LILRA6 as a mechanism for generating LILRA6 CNV and LILRB3 diversity. These data characterize LILRB3/LILRA6 genetic variation in more detail than previously described and underscore the need to determine their ligands.
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20
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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: 16] [Impact Index Per Article: 8.0] [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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21
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Bernard NF, Alsulami K, Pavey E, Dupuy FP. NK Cells in Protection from HIV Infection. Viruses 2022; 14:v14061143. [PMID: 35746615 PMCID: PMC9231282 DOI: 10.3390/v14061143] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/05/2023] Open
Abstract
Some people, known as HIV-exposed seronegative (HESN) individuals, remain uninfected despite high levels of exposure to HIV. Understanding the mechanisms underlying their apparent resistance to HIV infection may inform strategies designed to protect against HIV infection. Natural Killer (NK) cells are innate immune cells whose activation state depends on the integration of activating and inhibitory signals arising from cell surface receptors interacting with their ligands on neighboring cells. Inhibitory NK cell receptors use a subset of major histocompatibility (MHC) class I antigens as ligands. This interaction educates NK cells, priming them to respond to cells with reduced MHC class I antigen expression levels as occurs on HIV-infected cells. NK cells can interact with both autologous HIV-infected cells and allogeneic cells bearing MHC antigens seen as non self by educated NK cells. NK cells are rapidly activated upon interacting with HIV-infected or allogenic cells to elicit anti-viral activity that blocks HIV spread to new target cells, suppresses HIV replication, and kills HIV-infected cells before HIV reservoirs can be seeded and infection can be established. In this manuscript, we will review the epidemiological and functional evidence for a role for NK cells in protection from HIV infection.
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Affiliation(s)
- Nicole F. Bernard
- Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, QC H4A3J1, Canada; (K.A.); (E.P.); (F.P.D.)
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Division of Clinical Immunology, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-(514)-934-1934 (ext. 44584)
| | - Khlood Alsulami
- Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, QC H4A3J1, Canada; (K.A.); (E.P.); (F.P.D.)
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Erik Pavey
- Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, QC H4A3J1, Canada; (K.A.); (E.P.); (F.P.D.)
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Franck P. Dupuy
- Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, QC H4A3J1, Canada; (K.A.); (E.P.); (F.P.D.)
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
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22
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NurWaliyuddin HZA, Norazmi MN, Zafarina Z. Allelic Polymorphisms of Killer Immunoglobulin-Like Receptor Genes in Malay and Orang Asli Populations of Peninsular Malaysia. Hum Immunol 2022; 83:564-573. [PMID: 35483989 DOI: 10.1016/j.humimm.2022.04.005] [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: 10/04/2021] [Revised: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/04/2022]
Abstract
Next-generation DNA sequencing (NGS) technology advancements provide new insight into the level of variation in killer immunoglobulin-like receptor (KIR) genes. High resolution allele genotyping of seven KIR genes was conducted among 94 unrelated Malay and Orang Asli (OA) individuals of Peninsular Malaysia. A manual bioinformatics analysis is performed and optimised by Sanger sequencing method. The Malays expressed a total of 22 alleles, as compared to only 15 alleles in the OA population. In total, 12 centromeric and 9 telomeric allelic haplotypes were identified in the Malays, whereas 8 centromeric and 5 telomeric allelic haplotypes were identified in the OA. The KIR2DL1, KIR2DL3, and KIR2DS4 genes exhibited a high degree of variation and balanced distribution in the Malay and OA populations. On the other hand, KIR2DL4, KIR3DL1, KIR3DL2 and KIR3DL3 genes exhibited a high degree of conservation, with less number of alleles identified and the dominance of a single allele at high frequency. High-resolution KIR allele genotyping has revealed unique sequence variations and allelic haplotypes between individuals and populations. The distributions of KIR alleles and haplotypes are useful for genetic population studies and serve as a baseline for future transplantation matching and disease association research.
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Affiliation(s)
- Hanis Z A NurWaliyuddin
- Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Mohd Nor Norazmi
- Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Zainuddin Zafarina
- Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia; Analytical Biochemistry Research Centre (ABrC), Inkubator Inovasi Universiti (I(2)U), SAINS@usm, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia.
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23
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Falco M, Meazza R, Alicata C, Canevali P, Muntasell A, Bottino C, Moretta L, Pende D, Lopez-Botet M. Epitope characterization of a monoclonal antibody that selectively recognizes KIR2DL1 allotypes. HLA 2022; 100:107-118. [PMID: 35411634 PMCID: PMC9544867 DOI: 10.1111/tan.14630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
Killer immunoglobulin‐like receptor (KIR) genes code for a family of inhibitory and activating receptors, finely tuning NK cell function. Numerous studies reported the relevance of KIR allelic polymorphism on KIR expression, ligand affinity, and strength in signal transduction. Although KIR variability, including gene copy number and allelic polymorphism, in combination with HLA class I polymorphism, impacts both KIR expression and NK cell education, only a precise phenotypic analysis can define the size of the different KIRpos NK cell subsets. In this context, reagents recognizing a limited number of KIRs is essential. In this study, we have characterized the specificity of an anti‐KIR mAb termed HP‐DM1. Testing its binding to HEK‐293T cells transfected with plasmids coding for different KIRs, we demonstrated that HP‐DM1 mAb exclusively reacts with KIR2DL1. Using site‐directed mutagenesis, we identified the four amino acids relevant for HP‐DM1 recognition: M44, S67, R68, and T70. HP‐DM1 mAb binds to a conformational epitope including M44, the residue crucial for HLA‐C K80 recognition by KIR2DL1. Based on the HP‐DM1 epitope characterization, we could extend its reactivity to all KIR2DL1 allotypes identified except for KIR2DL1*022 and, most likely, KIR2DL1*020, predicting that it does not recognize any other KIR with the only exception of KIR2DS1*013. Moreover, by identifying the residues relevant for HP‐DM1 binding, continuously updating of its reactivity will be facilitated.
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Affiliation(s)
| | | | | | | | - Aura Muntasell
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Cristina Bottino
- IRCCS Istituto Giannina Gaslini, Genoa, Italy.,DIMES, University of Genoa, Genoa, Italy
| | | | - Daniela Pende
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Miguel Lopez-Botet
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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24
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Bruijnesteijn J, de Groot N, de Vos-Rouweler AJM, de Groot NG, Bontrop RE. Comparative genetics of KIR haplotype diversity in humans and rhesus macaques: the balancing act. Immunogenetics 2022; 74:313-326. [PMID: 35291021 DOI: 10.1007/s00251-022-01259-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/01/2022] [Indexed: 12/25/2022]
Abstract
The role of natural killer (NK) cells is tightly modulated by interactions of killer cell immunoglobulin-like receptors (KIR) with their ligands of the MHC class I family. Several characteristics of the KIR gene products are conserved in primate evolution, like the receptor structures and the variegated expression pattern. At the genomic level, however, the clusters encoding the KIR family display species-specific diversity, reflected by differential gene expansions and haplotype architecture. The human KIR cluster is extensively studied in large cohorts from various populations, which revealed two KIR haplotype groups, A and B, that represent more inhibitory and more activating functional profiles, respectively. So far, genomic KIR analyses in large outbred populations of non-human primate species are lacking. In this study, we roughly quadrupled the number of rhesus macaques studied for their KIR transcriptome (n = 298). Using segregation analysis, we defined 112 unique KIR region configurations, half of which display a more inhibitory profile, whereas the other half has a more activating potential. The frequencies and functional potential of these profiles might mirror the human KIR haplotype groups. However, whereas the human group A and B KIR haplotypes are confined to largely fixed organizations, the haplotypes in macaques feature highly variable gene content. Moreover, KIR homozygosity was hardly encountered in this panel of macaques. This study exhibits highly diverse haplotype architectures in humans and macaques, which nevertheless might have an equivalent effect on the modulation of NK cell activity.
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Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands.
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands
- Theoretical Biology and Bioinformatics Group, Utrecht University, 3527, Utrecht, the Netherlands
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25
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Downing J, D'Orsogna L. High-resolution human KIR genotyping. Immunogenetics 2022; 74:369-379. [PMID: 35050404 PMCID: PMC9262774 DOI: 10.1007/s00251-021-01247-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022]
Abstract
Killer immunoglobulin-like receptors (KIR) regulate the function of natural killer cells through interactions with various ligands on the surface of cells, thereby determining whether natural killer (NK) cells are to be activated or inhibited from killing the cell being interrogated. The genes encoding these proteins display extensive variation through variable gene content, copy number and allele polymorphism. The combination of KIR genes and their ligands is implicated in various clinical settings including haematopoietic stem cell and solid organ transplant and infectious disease progression. The determination of KIR genes has been used as a factor in the selection of optimal stem cell donors with haplotype variations in recipient and donor giving differential clinical outcomes. Methods to determine KIR genes have primarily involved ascertaining the presence or absence of genes in an individual. With the more recent introduction of massively parallel clonal next-generation sequencing and single molecule very long read length third-generation sequencing, high-resolution determination of KIR alleles has become feasible. Determining the extent and functional impact of allele variation has the potential to lead to further optimisation of clinical outcomes as well as a deeper understanding of the functional properties of the receptors and their interactions with ligands. This review summarizes recently published high-resolution KIR genotyping methods and considers the various advantages and disadvantages of the approaches taken. In addition the application of allele level genotyping in the setting of transplantation and infectious disease control is discussed.
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Affiliation(s)
- Jonathan Downing
- Department of Clinical Immunology, PathWest, Perth, WA, Australia. .,School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.
| | - Lloyd D'Orsogna
- Department of Clinical Immunology, PathWest, Perth, WA, Australia.,School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
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26
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Killer-cell immunoglobulin-like receptor genotype and haplotype combinations in children treated for acute lymphoblastic leukemia. Cent Eur J Immunol 2021; 46:210-216. [PMID: 34764789 PMCID: PMC8568030 DOI: 10.5114/ceji.2021.108178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/28/2020] [Indexed: 11/17/2022] Open
Abstract
Introduction Acute lymphoblastic leukemia (ALL) is the most common malignancy diagnosed in children. The factors predisposing to ALL remain mostly unknown. Natural killer (NK) cells are a component of innate immunity. Their role is to eliminate cells that were infected with viruses or underwent a neoplastic transformation. The activity of NK cells is regulated by their activating and inhibitory receptors, inter alia killer-cell immunoglobulin-like receptors (KIRs). The available data about a link between the incidence of ALL and KIR genotype are highly inconclusive, and further research is needed to explain whether such a relationship truly exists. The aim of this study was to analyze KIR genotype and haplotype combinations in children treated for ALL. Material and methods The study included 49 children diagnosed with ALL at 1.2-19.8 years of age. The control group was composed of 43 healthy subjects aged between 1.2 and 21.9 years. DNA was isolated using QIAamp DNA Mini kits. KIR genotypes were identified by a polymerase chain reaction (PCR) with sequence-specific primers (SSPs). The analysis also included KIR haplotype combinations: AA, AB and BB. Results Patients with ALL and controls did not differ significantly in the frequencies of individual KIR genes and haplotypes. However, the overall frequency of all 6 activating KIR genes in patients with ALL was significantly higher than in the controls (24.5% vs. 4.7%, p = 0.019). Conclusions The findings presented here imply that individual KIR genes do not play a significant role in the pathogenesis of ALL. Nevertheless, a higher number of activating KIR genes may constitute a risk factor for this malignancy.
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27
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Storm L, Bruijnesteijn J, de Groot NG, Bontrop RE. The Genomic Organization of the LILR Region Remained Largely Conserved Throughout Primate Evolution: Implications for Health And Disease. Front Immunol 2021; 12:716289. [PMID: 34737739 PMCID: PMC8562567 DOI: 10.3389/fimmu.2021.716289] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
The genes of the leukocyte immunoglobulin-like receptor (LILR) family map to the leukocyte receptor complex (LRC) on chromosome 19, and consist of both activating and inhibiting entities. These receptors are often involved in regulating immune responses, and are considered to play a role in health and disease. The human LILR region and evolutionary equivalents in some rodent and bird species have been thoroughly characterized. In non-human primates, the LILR region is annotated, but a thorough comparison between humans and non-human primates has not yet been documented. Therefore, it was decided to undertake a comprehensive comparison of the human and non-human primate LILR region at the genomic level. During primate evolution the organization of the LILR region remained largely conserved. One major exception, however, is provided by the common marmoset, a New World monkey species, which seems to feature a substantial contraction of the number of LILR genes in both the centromeric and the telomeric region. Furthermore, genomic analysis revealed that the killer-cell immunoglobulin-like receptor gene KIR3DX1, which maps in the LILR region, features one copy in humans and great ape species. A second copy, which might have been introduced by a duplication event, was observed in the lesser apes, and in Old and New World monkey species. The highly conserved gene organization allowed us to standardize the LILR gene nomenclature for non-human primate species, and implies that most of the receptors encoded by these genes likely fulfill highly preserved functions.
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Affiliation(s)
- Lisanne Storm
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - 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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28
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Piekarska K, Radwan P, Tarnowska A, Wiśniewski A, Radwan M, Wilczyński JR, Malinowski A, Nowak I. ERAP, KIR, and HLA-C Profile in Recurrent Implantation Failure. Front Immunol 2021; 12:755624. [PMID: 34745129 PMCID: PMC8569704 DOI: 10.3389/fimmu.2021.755624] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/04/2021] [Indexed: 01/29/2023] Open
Abstract
The mother's uterine immune system is dominated by uterine natural killer (NK) cells during the first trimester of pregnancy. These cells express killer cell immunoglobulin-like receptors (KIRs) of inhibitory or activating function. Invading extravillous trophoblast cells express HLA-C molecules, and both maternal and paternal HLA-C allotypes are presented to KIRs. Endoplasmic reticulum aminopeptidase 1 (ERAP1) and 2 (ERAP2) shape the HLA class I immunopeptidome. The ERAPs remove N-terminal residues from antigenic precursor peptides and generate optimal-length peptides to fit into the HLA class I groove. The inability to form the correct HLA class I complexes with the appropriate peptides may result in a lack of immune response by NK cells. The aim of this study was to investigate the role of ERAP1 and ERAP2 polymorphisms in the context of KIR and HLA-C genes in recurrent implantation failure (RIF). In addition, for the first time, we showed the results of ERAP1 and ERAP2 secretion into the peripheral blood of patients and fertile women. We tested a total of 881 women. Four hundred ninety-six females were patients who, together with their partners, participated in in vitro fertilization (IVF). A group of 385 fertile women constituted the control group. Women positive for KIR genes in the Tel AA region and HLA-C2C2 were more prevalent in the RIF group than in fertile women (p/pcorr. = 0.004/0.012, OR = 2.321). Of the ERAP polymorphisms studied, two of them (rs26653 and rs26618) appear to affect RIF susceptibility in HLA-C2-positive patients. Moreover, fertile women who gave birth in the past secreted significantly more ERAP1 than IVF women and control pregnant women (p < 0.0001 and p = 0.0005, respectively). In the case of ERAP2, the opposite result was observed; i.e., fertile women secreted far less ERAP2 than IVF patients (p = 0.0098). Patients who became pregnant after in vitro fertilization embryo transfer (IVF-ET) released far less ERAP2 than patients who miscarried (p = 0.0032). Receiver operating characteristic (ROC) analyses indicate a value of about 2.9 ng/ml of ERAP2 as a point of differentiation between patients who miscarried and those who gave birth to a healthy child. Our study indicates that both ERAP1 and ERAP2 may be involved in processes related to reproduction.
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Affiliation(s)
- Karolina Piekarska
- Laboratory of Immunogenetics and Tissue Immunology, Department of Clinical Immunology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Paweł Radwan
- Department of Reproductive Medicine, Gameta Hospital, Rzgów, Poland
| | - Agnieszka Tarnowska
- Laboratory of Immunogenetics and Tissue Immunology, Department of Clinical Immunology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Wiśniewski
- Laboratory of Immunogenetics and Tissue Immunology, Department of Clinical Immunology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Michał Radwan
- Department of Reproductive Medicine, Gameta Hospital, Rzgów, Poland
- Faculty of Health Sciences, The Mazovian State University in Płock, Płock, Poland
| | - Jacek R. Wilczyński
- Department of Surgical and Oncological Gynecology, Medical University of Łódź, Łódź, Poland
| | - Andrzej Malinowski
- Department of Surgical, Endoscopic and Oncologic Gynecology, Polish Mothers’ Memorial Hospital—Research Institute, Łódź, Poland
- Medical Centre Gynemed, Łódź, Poland
| | - Izabela Nowak
- Laboratory of Immunogenetics and Tissue Immunology, Department of Clinical Immunology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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Vargas LDB, Beltrame MH, Ho B, Marin WM, Dandekar R, Montero-Martín G, Fernández-Viña MA, Hurtado AM, Hill KR, Tsuneto LT, Hutz MH, Salzano FM, Petzl-Erler ML, Hollenbach JA, Augusto DG. Remarkably low KIR and HLA diversity in Amerindians reveals signatures of strong purifying selection shaping the centromeric KIR region. Mol Biol Evol 2021; 39:6388041. [PMID: 34633459 PMCID: PMC8763117 DOI: 10.1093/molbev/msab298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The killer-cell immunoglobulin-like receptors (KIR) recognize human leukocyte antigen (HLA) molecules to regulate the cytotoxic and inflammatory responses of natural killer cells. KIR genes are encoded by a rapidly evolving gene family on chromosome 19 and present an unusual variation of presence and absence of genes and high allelic diversity. Although many studies have associated KIR polymorphism with susceptibility to several diseases over the last decades, the high-resolution allele-level haplotypes have only recently started to be described in populations. Here, we use a highly innovative custom next-generation sequencing method that provides a state-of-art characterization of KIR and HLA diversity in 706 individuals from eight unique South American populations: five Amerindian populations from Brazil (three Guarani and two Kaingang); one Amerindian population from Paraguay (Aché); and two urban populations from Southern Brazil (European and Japanese descendants from Curitiba). For the first time, we describe complete high-resolution KIR haplotypes in South American populations, exploring copy number, linkage disequilibrium, and KIR-HLA interactions. We show that all Amerindians analyzed to date exhibit the lowest numbers of KIR-HLA interactions among all described worldwide populations, and that 83-97% of their KIR-HLA interactions rely on a few HLA-C molecules. Using multiple approaches, we found signatures of strong purifying selection on the KIR centromeric region, which codes for the strongest NK cell educator receptors, possibly driven by the limited HLA diversity in these populations. Our study expands the current knowledge of KIR genetic diversity in populations to understand KIR-HLA coevolution and its impact on human health and survival.
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Affiliation(s)
- Luciana de Brito Vargas
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Marcia H Beltrame
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Brenda Ho
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Wesley M Marin
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ravi Dandekar
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Gonzalo Montero-Martín
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | | | - A Magdalena Hurtado
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
| | - Kim R Hill
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
| | - Luiza T Tsuneto
- Departamento de Análises Clínicas, Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil
| | - Mara H Hutz
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158, USA
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil.,Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
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Behairy OG, El-Shimi OS, Shalan NH, Baghdady SM. Association of the killer immunoglobulin-like receptor genes KIR2DS1 and KIR2DS4 with pediatric autoimmune hepatitis type I in Egypt. EGYPTIAN LIVER JOURNAL 2021. [DOI: 10.1186/s43066-021-00145-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Killer cell immunoglobulin-like receptors (KIR) are considered to be the key receptors that control the development and function of human natural killer cells which play complex mechanisms in autoimmune diseases. We aimed in this study to assess possible associations between killer cell immunoglobulin-like receptors (KIR2DS1 and 2DS4) genes and susceptibility to autoimmune hepatitis type I in Egyptian children.
Results
In the case-control study conducted on eighty children diagnosed as autoimmune hepatitis (AIH) type I and eighty apparently healthy age and sex-matched control, we found that KIR2DS1, -2DS4, KIR2DS4-full length allele, and homozygous KIR2DS4-full/full variant were significantly associated with AIH-I, while the KIR1D allele and homozygous KIR2DS4-del/del variant were significantly observed in controls (P < 0.05 each). Absence of KIR2DS4 gene was significant among ANA positive AIH-I patients, patients on steroid therapy alone, and patients showing complete disease remission (P < 0.05 each). Higher activity and fibrosis indices were found significantly in patients lacking one or both studied genes.
Conclusions
Children carrying KIR2DS1, -2DS4 genes, KIR2DS4-full length allele, and homozygous KIR2DS4-full/full variant could be more susceptible to develop autoimmune hepatitis type I.
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Donor Killer Immunoglobulin Receptor Gene Content and Ligand Matching and Outcomes of Pediatric Patients with Juvenile Myelomonocytic Leukemia Following Unrelated Donor Transplantation. Transplant Cell Ther 2021; 27:926.e1-926.e10. [PMID: 34407489 DOI: 10.1016/j.jtct.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/21/2022]
Abstract
Natural killer (NK) cell determinants predict relapse-free survival after allogeneic hematopoietic cell transplantation (HCT) for acute myelogenous leukemia, and previous studies have shown a beneficial graft-versus-leukemia effect in patients with juvenile myelomonocytic leukemia (JMML). However, whether NK cell determinants predict protection against relapse for JMML patients undergoing HCT is unknown. Therefore, we investigated NK cell-related donor and recipient immunogenetics as determinants of HCT outcomes in patients with JMML. Patients with JMML (age 0 to <19 years) who underwent a first allogeneic HCT from an unrelated donor between 2000 and 2017 and had available donor samples from the Center for International Blood and Marrow Transplant Research Repository were included. Donor killer immunoglobulin receptor (KIR) typing was performed on pre-HCT samples. The primary endpoint was disease-free survival (DFS); secondary endpoints included relapse, grade II-IV acute graft versus-host-disease (aGVHD), chronic GVHD (cGVHD), GVHD-free relapse-free survival, transplantation-related mortality, and overall survival (OS). Donor KIR models tested included KIR genotype (AA versus Bx), B content (0-1 versus ≥2), centromeric and telomeric region score (AA versus AB versus BB), B content score (best, better, or neutral), composite score (2 versus 3 versus 4), activating KIR content, and the presence of KIR2DS4. Ligand-ligand and KIR-ligand mismatch effects on outcomes were analyzed in HLA-mismatched donors (≤7/8; n = 74) only. Univariate analyses were performed for primary and secondary outcomes of interest, with a P value <.05 considered significant. One hundred sixty-five patients (113 males), with a median follow-up of 85 months (range, 6 to 216 months) met the study criteria. Of these, 111 underwent an unrelated donor HCT and 54 underwent a UCB HCT. Almost all (n = 161; 98%) received a myeloablative conditioning regimen. After exclusion of recipients of reduced-intensity/nonmyeloablative conditioning regimens and ex vivo T cell-depleted grafts (n = 8), there were 42 AA donors and 115 Bx donors, respectively. Three-year DFS, OS, relapse, and GRFS for the entire cohort were 58% (95% confidence interval [CI], 50% to 66%), 67% (95% CI, 59% to 74%), 26% (95% CI, 19% to 33%), and 27% (95% CI, 19% to 35%), respectively. The cumulative incidence of grade II-IV aGVHD at 100 days was 36% (95% CI, 27% to 44%), and that of cGVHD at 1 year was 23% (95% CI, 17% to 30%). There were no differences between AA donors and Bx donors for any recipient survival outcomes. The risk of grade II-IV aGVHD was lower in patients with donors with a B content score of ≥2 (hazard ratio [HR], 0.46; 95% CI, 0.26 to 0.83; P = .01), an activating KIR content score of >3 (HR, 0.52; 95% CI, 0.29 to 0.95; P = .032), centromeric A/B score (HR, 0.57; 95% CI, 033 to 0.98; P = .041), and telomeric A/B score (HR, 0.58; 95% CI, 0.34 to 1.00; P = .048). To our knowledge, this is the first study analyzing the association of NK cell determinants and outcomes in JMML HCT recipients. This study identifies potential benefits of donor KIR-B genotypes in reducing aGVHD. Our findings warrant further study of the role of NK cells in enhancing the graft-versus-leukemia effect via recognition of JMML blasts.
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Marin WM, Dandekar R, Augusto DG, Yusufali T, Heyn B, Hofmann J, Lange V, Sauter J, Norman PJ, Hollenbach JA. High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING. PLoS Comput Biol 2021; 17:e1008904. [PMID: 34339413 PMCID: PMC8360517 DOI: 10.1371/journal.pcbi.1008904] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/12/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
The killer-cell immunoglobulin-like receptor (KIR) complex on chromosome 19 encodes receptors that modulate the activity of natural killer cells, and variation in these genes has been linked to infectious and autoimmune disease, as well as having bearing on pregnancy and transplant outcomes. The medical relevance and high variability of KIR genes makes short-read sequencing an attractive technology for interrogating the region, providing a high-throughput, high-fidelity sequencing method that is cost-effective. However, because this gene complex is characterized by extensive nucleotide polymorphism, structural variation including gene fusions and deletions, and a high level of homology between genes, its interrogation at high resolution has been thwarted by bioinformatic challenges, with most studies limited to examining presence or absence of specific genes. Here, we present the PING (Pushing Immunogenetics to the Next Generation) pipeline, which incorporates empirical data, novel alignment strategies and a custom alignment processing workflow to enable high-throughput KIR sequence analysis from short-read data. PING provides KIR gene copy number classification functionality for all KIR genes through use of a comprehensive alignment reference. The gene copy number determined per individual enables an innovative genotype determination workflow using genotype-matched references. Together, these methods address the challenges imposed by the structural complexity and overall homology of the KIR complex. To determine copy number and genotype determination accuracy, we applied PING to European and African validation cohorts and a synthetic dataset. PING demonstrated exceptional copy number determination performance across all datasets and robust genotype determination performance. Finally, an investigation into discordant genotypes for the synthetic dataset provides insight into misaligned reads, advancing our understanding in interpretation of short-read sequencing data in complex genomic regions. PING promises to support a new era of studies of KIR polymorphism, delivering high-resolution KIR genotypes that are highly accurate, enabling high-quality, high-throughput KIR genotyping for disease and population studies.
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Affiliation(s)
- Wesley M. Marin
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Ravi Dandekar
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Danillo G. Augusto
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Tasneem Yusufali
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | | | | | | | | | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jill A. Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
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Sun H, Martin TG, Marra J, Kong D, Keats J, Macé S, Chiron M, Wolf JL, Venstrom JM, Rajalingam R. Individualized genetic makeup that controls natural killer cell function influences the efficacy of isatuximab immunotherapy in patients with multiple myeloma. J Immunother Cancer 2021; 9:jitc-2021-002958. [PMID: 34272304 PMCID: PMC8287616 DOI: 10.1136/jitc-2021-002958] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Phase IIb clinical trial with isatuximab (Isa)-lenalidomide (Len)-dexamethasone (Dex) showed an improved progression-free survival (PFS) in patients with relapsed or refractory multiple myeloma (RRMM), but the efficacy varied by patient. Antibody-dependent cell-mediated cytotoxicity (ADCC) by natural killer (NK) cells plays a crucial role in arbitrating antitumor activities of therapeutic-antibodies. We tested if patient-specific genetic makeup known to set NK cell functional threshold influence response to Isa-Len-Dex therapy. METHODS We characterized 57 patients with RRMM receiving Isa-Len-Dex for polymorphisms of killer-cell immunoglobulin-like receptors (KIR), human leukocyte antigen (HLA) class I, and FCGR3A loci. In vitro ADCC assay, coincubating primary NK cells expressing specific KIR repertoire with multiple myeloma cell lines (MM cells) expressing selected HLA class I ligands, was used to confirm the identified genetic correlatives of clinical response. RESULTS Patients with KIR3DL2+ and its cognate-ligand HLA-A3/11+ had superior PFS than patients missing this combination (HR=0.43; p=0.02), while patients carrying KIR2DL1+ and HLA-C2C2+ compared with to patients missing this pair showed short PFS (HR=3.54; p=0.05). Patients with KIR3DL2+ and HLA-A3/11+ plus high-affinity FCGR3A-158V allele showed the most prolonged PFS (HR=0.35; p=0.007). Consistent with these clinical data, mechanistic experiments demonstrated that NK cells expressing KIR3DL2 trigger greater ADCC when MM cells express HLA-A3/11. Inversely, NK cells expressing KIR2DL1 do not kill if MM cells express the HLA-C2C2 ligand. NK cells expressing high-affinity FCGR3A-158VV-induced greater ADCC compared with those with low-affinity FCGR3A-158FF. CONCLUSIONS Our results suggest that KIR3DL2+ and HLA-A3/11+ with FCGR3A-158V markers lead to enhanced Isa-dependent NK-mediated cytolysis against MM cells and results in improved PFS in patients with RRMM treated by Isa-Len-Dex. Moreover, the presence of KIR2DL1+ and HLA-C2C2+ identifies patients who may have a lower response to Isa-Len-Dex therapy linked to a reduced NK-mediated ADCC. These biomarkers could potentially identify, via precision medicine, patients more likely to respond to Isa-Len-Dex immunotherapy. TRIAL REGISTRATION NUMBER NCT01749969.
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Affiliation(s)
- Haibo Sun
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, California, USA
| | - Thomas G Martin
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - John Marra
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Denice Kong
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, California, USA
| | - Jonathon Keats
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Sandrine Macé
- Translational and Experimental Medicine, Sanofi Research & Development, Vitry-sur-Seine, France
| | - Marielle Chiron
- Translational and Experimental Medicine, Sanofi Research & Development, Vitry-sur-Seine, France
| | - Jeffrey L Wolf
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey M Venstrom
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, California, USA
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Shen C, Ge Z, Dong C, Wang C, Shao J, Cai W, Huang P, Fan H, Li J, Zhang Y, Yue M. Genetic Variants in KIR/HLA-C Genes Are Associated With the Susceptibility to HCV Infection in a High-Risk Chinese Population. Front Immunol 2021; 12:632353. [PMID: 34220799 PMCID: PMC8253047 DOI: 10.3389/fimmu.2021.632353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/31/2021] [Indexed: 12/24/2022] Open
Abstract
Background KIR/HLA-C signaling pathway influences the innate immune response which is the first defense to hepatitis C virus (HCV) infection. The aim of this study was to determine the association between the genetic polymorphisms of KIR/HLA-C genes and the outcomes of HCV infection in a high-risk Chinese population. Methods In this case-control study, four single nucleotide polymorphisms (SNPs) of KIR/HLA-C genes (KIR2DS4/KIR2DS1/KIR2DL1 rs35440472, HLA-C rs2308557, HLA-C rs1130838, and HLA-C rs2524094) were genotyped by TaqMan assay among drug users and hemodialysis (HD) patients including 1,378 uninfected control cases, 307 subjects with spontaneous viral clearance, and 217 patients with persistent HCV infection. Bioinformatics analysis was used to functionally annotate the SNPs. Results After logistic regression analysis, the rs35440472-A and rs1130838-A alleles were found to be associated with a significantly elevated risk of HCV infection (OR = 1.562, 95% CI: 1.229–1.987, P < 0.001; OR = 2.134, 95% CI: 1.180–3.858, P = 0.012, respectively), which remained significant after Bonferroni correction (0.05/4). The combined effect of their risk alleles and risk genotypes (rs35440472-AA and rs1130838-AA) were linked to the increased risk of HCV infection in a locus-dosage manner (all Ptrend < 0.001). Based on the SNPinfo web server, rs35440472 was predicted to be a transcription factor binding site (TFBS) while rs1130838 was predicted to have a splicing (ESE or ESS) function. Conclusion KIR2DS4/KIR2DS1/KIR2DL1 rs35440472-A and HLA-C rs1130838-A variants are associated with increased susceptibility to HCV infection in a high-risk Chinese population.
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Affiliation(s)
- Chao Shen
- Department of Epidemiology and Biostatistics, Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhijun Ge
- Department of Critical Care Medicine, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China
| | - Chen Dong
- Department of Epidemiology and Statistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Chunhui Wang
- Institute of Epidemiology and Microbiology, Eastern Theater Command Centers for Disease Control and Prevention, Nanjing, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jianguo Shao
- Department of Digestive Medicine, Third Affiliated Hospital of Nantong University, Nantong, China
| | - Weihua Cai
- Department of General Surgery, Third Affiliated Hospital of Nantong University, Nantong, China
| | - Peng Huang
- Department of Epidemiology and Biostatistics, Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Haozhi Fan
- Department of Information, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Infectious Diseases, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yun Zhang
- Institute of Epidemiology and Microbiology, Eastern Theater Command Centers for Disease Control and Prevention, Nanjing, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ming Yue
- Department of Infectious Diseases, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Abstract
In all human cells, human leukocyte antigen (HLA) class I glycoproteins assemble with a peptide and take it to the cell surface for surveillance by lymphocytes. These include natural killer (NK) cells and γδ T cells of innate immunity and αβ T cells of adaptive immunity. In healthy cells, the presented peptides derive from human proteins, to which lymphocytes are tolerant. In pathogen-infected cells, HLA class I expression is perturbed. Reduced HLA class I expression is detected by KIR and CD94:NKG2A receptors of NK cells. Almost any change in peptide presentation can be detected by αβ CD8+ T cells. In responding to extracellular pathogens, HLA class II glycoproteins, expressed by specialized antigen-presenting cells, present peptides to αβ CD4+ T cells. In comparison to the families of major histocompatibility complex (MHC) class I, MHC class II and αβ T cell receptors, the antigenic specificity of the γδ T cell receptors is incompletely understood.
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Affiliation(s)
- Zakia Djaoud
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA; ,
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA; ,
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Bolarín JM, Pérez-Cárceles M, Luna A, Minguela A, Muro M, Legaz I. Killer cell immunoglobulin-like receptors (KIR) genes can be an adequate tool in forensic anthropological studies: evaluation in a wide Caucasian Spanish population. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.1930156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- J. M. Bolarín
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - M.D. Pérez-Cárceles
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - A. Luna
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - A. Minguela
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - M. Muro
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - I. Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
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Muriuki BM, Forconi CS, Oluoch PO, Bailey JA, Ghansah A, Moormann AM, Ong'echa JM. Association of killer cell immunoglobulin-like receptors with endemic Burkitt lymphoma in Kenyan children. Sci Rep 2021; 11:11343. [PMID: 34059753 PMCID: PMC8166913 DOI: 10.1038/s41598-021-90596-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/09/2021] [Indexed: 02/04/2023] Open
Abstract
Endemic Burkitt lymphoma (eBL) is an aggressive pediatric B cell lymphoma, common in Equatorial Africa. Co-infections with Epstein-Barr virus (EBV) and Plasmodium falciparum, coupled with c-myc translocation are involved in eBL etiology. Infection-induced immune evasion mechanisms to avoid T cell cytotoxicity may increase the role of Natural killer (NK) cells in anti-tumor immunosurveillance. Killer immunoglobulin-like receptor (KIR) genes on NK cells exhibit genotypic and allelic variations and are associated with susceptibility to diseases and malignancies. However, their role in eBL pathogenesis remains undefined. This retrospective study genotyped sixteen KIR genes and compared their frequencies in eBL patients (n = 104) and healthy geographically-matched children (n = 104) using sequence-specific primers polymerase chain reaction (SSP-PCR) technique. The relationship between KIR polymorphisms with EBV loads and eBL pathogenesis was investigated. Possession of ≥ 4 activating KIRs predisposed individuals to eBL (OR = 3.340; 95% CI 1.530-7.825; p = 0.004). High EBV levels were observed in Bx haplogroup (p = 0.016) and AB genotypes (p = 0.042) relative to AA haplogroup and AA genotype respectively, in eBL patients but not in healthy controls. Our results suggest that KIR-mediated NK cell stimulation could mute EBV control, contributing to eBL pathogenesis.
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Affiliation(s)
- Beatrice M Muriuki
- West African Center for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Catherine S Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Peter O Oluoch
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - John M Ong'echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya.
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38
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Deng Z, Zhen J, Harrison GF, Zhang G, Chen R, Sun G, Yu Q, Nemat-Gorgani N, Guethlein LA, He L, Tang M, Gao X, Cai S, Palmer WH, Shortt JA, Gignoux CR, Carrington M, Zou H, Parham P, Hong W, Norman PJ. Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians. Mol Biol Evol 2021; 38:2582-2596. [PMID: 33616658 PMCID: PMC8136484 DOI: 10.1093/molbev/msab053] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human natural killer (NK) cells are essential for controlling infection, cancer, and fetal development. NK cell functions are modulated by interactions between polymorphic inhibitory killer cell immunoglobulin-like receptors (KIR) and polymorphic HLA-A, -B, and -C ligands expressed on tissue cells. All HLA-C alleles encode a KIR ligand and contribute to reproduction and immunity. In contrast, only some HLA-A and -B alleles encode KIR ligands and they focus on immunity. By high-resolution analysis of KIR and HLA-A, -B, and -C genes, we show that the Chinese Southern Han (CHS) are significantly enriched for interactions between inhibitory KIR and HLA-A and -B. This enrichment has had substantial input through population admixture with neighboring populations, who contributed HLA class I haplotypes expressing the KIR ligands B*46:01 and B*58:01, which subsequently rose to high frequency by natural selection. Consequently, over 80% of Southern Han HLA haplotypes encode more than one KIR ligand. Complementing the high number of KIR ligands, the CHS KIR locus combines a high frequency of genes expressing potent inhibitory KIR, with a low frequency of those expressing activating KIR. The Southern Han centromeric KIR region encodes strong, conserved, inhibitory HLA-C-specific receptors, and the telomeric region provides a high number and diversity of inhibitory HLA-A and -B-specific receptors. In all these characteristics, the CHS represent other East Asians, whose NK cell repertoires are thus enhanced in quantity, diversity, and effector strength, likely augmenting resistance to endemic viral infections.
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Affiliation(s)
- Zhihui Deng
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Jianxin Zhen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
- Central Laboratory, Shenzhen Baoan Women’s and Children’s Hospital, Shenzhen, Guangdong, P. R. China
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Guobin Zhang
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Rui Chen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Ge Sun
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Qiong Yu
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Liumei He
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Mingzhong Tang
- Clinical Laboratory, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, P. R. China
| | - Xiaojiang Gao
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Siqi Cai
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - William H Palmer
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jonathan A Shortt
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD21702, and Ragon Institute of MGH, Cambridge, MA, USA
| | - Hongyan Zou
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenxu Hong
- Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
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39
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CD8 + T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph. Nat Commun 2021; 12:2931. [PMID: 34006841 PMCID: PMC8132304 DOI: 10.1038/s41467-021-23212-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/19/2021] [Indexed: 02/03/2023] Open
Abstract
Indigenous people worldwide are at high risk of developing severe influenza disease. HLA-A*24:02 allele, highly prevalent in Indigenous populations, is associated with influenza-induced mortality, although the basis for this association is unclear. Here, we define CD8+ T-cell immune landscapes against influenza A (IAV) and B (IBV) viruses in HLA-A*24:02-expressing Indigenous and non-Indigenous individuals, human tissues, influenza-infected patients and HLA-A*24:02-transgenic mice. We identify immunodominant protective CD8+ T-cell epitopes, one towards IAV and six towards IBV, with A24/PB2550-558-specific CD8+ T cells being cross-reactive between IAV and IBV. Memory CD8+ T cells towards these specificities are present in blood (CD27+CD45RA- phenotype) and tissues (CD103+CD69+ phenotype) of healthy individuals, and effector CD27-CD45RA-PD-1+CD38+CD8+ T cells in IAV/IBV patients. Our data show influenza-specific CD8+ T-cell responses in Indigenous Australians, and advocate for T-cell-mediated vaccines that target and boost the breadth of IAV/IBV-specific CD8+ T cells to protect high-risk HLA-A*24:02-expressing Indigenous and non-Indigenous populations from severe influenza disease.
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40
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Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, Bos KI, Forrest S, Hernández-Zaragoza DI, Sauter J, Solloch U, Schmidt AH, Schuenemann VJ, Reiter E, Kairies MS, Weiß R, Arnold S, Wahl J, Hollenbach JA, Kohlbacher O, Herbig A, Norman PJ, Krause J. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol 2021; 38:4059-4076. [PMID: 34002224 PMCID: PMC8476174 DOI: 10.1093/molbev/msab147] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggests that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.
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Affiliation(s)
- Alexander Immel
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - András Szolek
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Rodrigo Barquera
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Madeline K Robinson
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - William H Palmer
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Maria A Spyrou
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Stephen Forrest
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Diana I Hernández-Zaragoza
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | | | | | | | - Verena J Schuenemann
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ella Reiter
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Madita S Kairies
- Institute for Archaeological Sciences, WG Palaeoanthropology, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Rainer Weiß
- State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Susanne Arnold
- State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Joachim Wahl
- Institute for Archaeological Sciences, WG Palaeoanthropology, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Jill A Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, USA
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.,Quantitative Biology Center, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.,Translational Bioinformatics, University Hospital Tübingen, Sand 14, 72076 Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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41
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Amorim LM, Augusto DG, Nemat-Gorgani N, Montero-Martin G, Marin WM, Shams H, Dandekar R, Caillier S, Parham P, Fernández-Viña MA, Oksenberg JR, Norman PJ, Hollenbach JA. High-Resolution Characterization of KIR Genes in a Large North American Cohort Reveals Novel Details of Structural and Sequence Diversity. Front Immunol 2021; 12:674778. [PMID: 34025673 PMCID: PMC8137979 DOI: 10.3389/fimmu.2021.674778] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
The KIR (killer-cell immunoglobulin-like receptor) region is characterized by structural variation and high sequence similarity among genes, imposing technical difficulties for analysis. We undertook the most comprehensive study to date of KIR genetic diversity in a large population sample, applying next-generation sequencing in 2,130 United States European-descendant individuals. Data were analyzed using our custom bioinformatics pipeline specifically designed to address technical obstacles in determining KIR genotypes. Precise gene copy number determination allowed us to identify a set of uncommon gene-content KIR haplotypes accounting for 5.2% of structural variation. In this cohort, KIR2DL4 is the framework gene that most varies in copy number (6.5% of all individuals). We identified phased high-resolution alleles in large multi-locus insertions and also likely founder haplotypes from which they were deleted. Additionally, we observed 250 alleles at 5-digit resolution, of which 90 have frequencies ≥1%. We found sequence patterns that were consistent with the presence of novel alleles in 398 (18.7%) individuals and contextualized multiple orphan dbSNPs within the KIR complex. We also identified a novel KIR2DL1 variant, Pro151Arg, and demonstrated by molecular dynamics that this substitution is predicted to affect interaction with HLA-C. No previous studies have fully explored the full range of structural and sequence variation of KIR as we present here. We demonstrate that pairing high-throughput sequencing with state-of-art computational tools in a large cohort permits exploration of all aspects of KIR variation including determination of population-level haplotype diversity, improving understanding of the KIR system, and providing an important reference for future studies.
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Affiliation(s)
- Leonardo M. Amorim
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danillo G. Augusto
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | - Gonzalo Montero-Martin
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Wesley M. Marin
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Hengameh Shams
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Ravi Dandekar
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Stacy Caillier
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Peter Parham
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | | | - Jorge R. Oksenberg
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, CA, United States
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42
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Tao S, He Y, Kichula KM, Wang J, He J, Norman PJ, Zhu F. High-Resolution Analysis Identifies High Frequency of KIR-A Haplotypes and Inhibitory Interactions of KIR With HLA Class I in Zhejiang Han. Front Immunol 2021; 12:640334. [PMID: 33995358 PMCID: PMC8121542 DOI: 10.3389/fimmu.2021.640334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/07/2021] [Indexed: 12/24/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIR) interact with human leukocyte antigen (HLA) class I molecules, modulating critical NK cell functions in the maintenance of human health. Characterizing the distribution and characteristics of KIR and HLA allotype diversity across defined human populations is thus essential for understanding the multiple associations with disease, and for directing therapies. In this study of 176 Zhejiang Han individuals from Southeastern China, we describe diversity of the highly polymorphic KIR and HLA class I genes at high resolution. KIR-A haplotypes, which carry four inhibitory receptors specific for HLA-A, B or C, are known to associate with protection from infection and some cancers. We show the Chinese Southern Han from Zhejiang are characterized by a high frequency of KIR-A haplotypes and a high frequency of C1 KIR ligands. Accordingly, interactions of inhibitory KIR2DL3 with C1+HLA are more frequent in Zhejiang Han than populations outside East Asia. Zhejiang Han exhibit greater diversity of inhibitory than activating KIR, with three-domain inhibitory KIR exhibiting the greatest degree of polymorphism. As distinguished by gene copy number and allele content, 54 centromeric and 37 telomeric haplotypes were observed. We observed 6% of the population to have KIR haplotypes containing large-scale duplications or deletions that include complete genes. A unique truncated haplotype containing only KIR2DL4 in the telomeric region was also identified. An additional feature is the high frequency of HLA-B*46:01, which may have arisen due to selection pressure from infectious disease. This study will provide further insight into the role of KIR and HLA polymorphism in disease susceptibility of Zhejiang Chinese.
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Affiliation(s)
- Sudan Tao
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Yanmin He
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jielin Wang
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Ji He
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Faming Zhu
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
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43
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Coexistence of inhibitory and activating killer-cell immunoglobulin-like receptors to the same cognate HLA-C2 and Bw4 ligands confer breast cancer risk. Sci Rep 2021; 11:7932. [PMID: 33846431 PMCID: PMC8041876 DOI: 10.1038/s41598-021-86964-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
Human leukocyte antigen (HLA) class I-specific killer-cell immunoglobulin-like receptors (KIR) regulate natural killer (NK) cell function in eliminating malignancy. Breast cancer (BC) patients exhibit reduced NK-cytotoxicity in peripheral blood. To test the hypothesis that certain KIR-HLA combinations impairing NK-cytotoxicity predispose to BC risk, we analyzed KIR and HLA polymorphisms in 162 women with BC and 278 controls. KIR-Bx genotypes increased significantly in BC than controls (83.3% vs. 71.9%, OR 1.95), and the increase was more pronounced in advanced-cancer (OR 5.3). No difference was observed with inhibitory KIR (iKIR) and HLA-ligand combinations. The activating KIR (aKIR) and HLA-ligand combinations, 2DS1 + C2 (OR 2.98) and 3DS1 + Bw4 (OR 2.6), were significantly increased in advanced-BC. All patients with advanced-cancer carrying 2DS1 + C2 or 3DS1 + Bw4 also have their iKIR counterparts 2DL1 and 3DL1, respectively. Contrarily, the 2DL1 + C2 and 3DL1 + Bw4 pairs without their aKIR counterparts are significantly higher in controls. These data suggest that NK cells expressing iKIR to the cognate HLA-ligands in the absence of putative aKIR counterpart are instrumental in antitumor response. These data provide a new framework for improving the utility of genetic risk scores for individualized surveillance.
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44
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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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45
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Foltz JA, Hess BT, Bachanova V, Bartlett NL, Berrien-Elliott MM, McClain E, Becker-Hapak M, Foster M, Schappe T, Kahl B, Mehta-Shah N, Cashen AF, Marin ND, McDaniels K, Moreno C, Mosior M, Gao F, Griffith OL, Griffith M, Wagner JA, Epperla N, Rock AD, Lee J, Petti AA, Soon-Shiong P, Fehniger TA. Phase I Trial of N-803, an IL15 Receptor Agonist, with Rituximab in Patients with Indolent Non-Hodgkin Lymphoma. Clin Cancer Res 2021; 27:3339-3350. [PMID: 33832946 DOI: 10.1158/1078-0432.ccr-20-4575] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/25/2021] [Accepted: 04/02/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE N-803 is an IL15 receptor superagonist complex, designed to optimize in vivo persistence and trans-presentation, thereby activating and expanding natural killer (NK) cells and CD8+ T cells. Monoclonal antibodies (mAbs) direct Fc receptor-bearing immune cells, including NK cells, to recognize and eliminate cancer targets. The ability of IL15R agonists to enhance tumor-targeting mAbs in patients has not been reported previously. PATIENTS AND METHODS Relapsed/refractory patients with indolent non-Hodgkin lymphoma were treated with rituximab and intravenous or subcutaneous N-803 on an open-label, dose-escalation phase I study using a 3+3 design (NCT02384954). Primary endpoint was maximum tolerated dose. Immune correlates were performed using multidimensional analysis via mass cytometry and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) which simultaneously measures protein and single-cell RNA expression. RESULTS This immunotherapy combination was safe and well tolerated and resulted in durable clinical responses including in rituximab-refractory patients. Subcutaneous N-803 plus rituximab induced sustained proliferation, expansion, and activation of peripheral blood NK cells and CD8 T cells, with increased NK cell and T cells present 8 weeks following last N-803 treatment. CITE-seq revealed a therapy-altered NK cell molecular program, including enhancement of AP-1 transcription factor. Furthermore, the monocyte transcriptional program was remodeled with enhanced MHC expression and antigen-presentation genes. CONCLUSIONS N-803 combines with mAbs to enhance tumor targeting in patients, and warrants further investigation in combination with immunotherapies.
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Affiliation(s)
| | - Brian T Hess
- Medical University of South Carolina, Charleston, South Carolina
| | | | | | | | - Ethan McClain
- Washington University School of Medicine, St. Louis, Missouri
| | | | - Mark Foster
- Washington University School of Medicine, St. Louis, Missouri
| | - Timothy Schappe
- Washington University School of Medicine, St. Louis, Missouri
| | - Brad Kahl
- Washington University School of Medicine, St. Louis, Missouri
| | - Neha Mehta-Shah
- Washington University School of Medicine, St. Louis, Missouri
| | - Amanda F Cashen
- Washington University School of Medicine, St. Louis, Missouri
| | - Nancy D Marin
- Washington University School of Medicine, St. Louis, Missouri
| | | | - Chaz Moreno
- Washington University School of Medicine, St. Louis, Missouri
| | - Matthew Mosior
- Washington University School of Medicine, St. Louis, Missouri
| | - Feng Gao
- Washington University School of Medicine, St. Louis, Missouri
| | - Obi L Griffith
- Washington University School of Medicine, St. Louis, Missouri
| | | | - Julia A Wagner
- Washington University School of Medicine, St. Louis, Missouri
| | | | | | - John Lee
- ImmunityBio, Culver City, California
| | - Allegra A Petti
- Washington University School of Medicine, St. Louis, Missouri
| | | | - Todd A Fehniger
- Washington University School of Medicine, St. Louis, Missouri.
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46
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Tao S, Kichula KM, Harrison GF, Farias TDJ, Palmer WH, Leaton LA, Hajar CGN, Zefarina Z, Edinur HA, Zhu F, Norman PJ. The combinatorial diversity of KIR and HLA class I allotypes in Peninsular Malaysia. Immunology 2021; 162:389-404. [PMID: 33283280 PMCID: PMC7968402 DOI: 10.1111/imm.13289] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/16/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIRs) interact with polymorphic human leucocyte antigen (HLA) class I molecules, modulating natural killer (NK) cell functions and affecting both the susceptibility and outcome of immune-mediated diseases. The KIR locus is highly diverse in gene content, copy number and allelic polymorphism within individuals and across geographical populations. To analyse currently under-represented Asian and Pacific populations, we investigated the combinatorial diversity of KIR and HLA class I in 92 unrelated Malay and 75 Malaysian Chinese individuals from the Malay Peninsula. We identified substantial allelic and structural diversity of the KIR locus in both populations and characterized novel variations at each analysis level. The Malay population is more diverse than Malay Chinese, likely representing a unique history including admixture with immigrating populations spanning several thousand years. Characterizing the Malay population are KIR haplotypes with large structural variants present in 10% individuals, and KIR and HLA alleles previously identified in Austronesian populations. Despite the differences in ancestries, the proportion of HLA allotypes that serve as KIR ligands is similar in each population. The exception is a significantly reduced frequency of interactions of KIR2DL1 with C2+ HLA-C in the Malaysian Chinese group, caused by the low frequency of C2+ HLA. One likely implication is a greater protection from preeclampsia, a pregnancy disorder associated with KIR2DL1, which shows higher incidence in the Malay than in the Malaysian Chinese. This first complete, high-resolution, characterization of combinatorial diversity of KIR and HLA in Malaysians will form a valuable reference for future clinical and population studies.
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Affiliation(s)
- Sudan Tao
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
- Blood Center of Zhejiang ProvinceKey Laboratory of Blood Safety Research of Zhejiang ProvinceHangzhouZhejiangChina
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Genelle F. Harrison
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Ticiana Della Justina Farias
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - William H. Palmer
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Laura Ann Leaton
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | | | - Zulkafli Zefarina
- School of Medical SciencesUniversiti Sains Malaysia, Health CampusKelantanMalaysia
| | - Hisham Atan Edinur
- School of Health SciencesUniversiti Sains Malaysia, Health CampusKelantanMalaysia
| | - Faming Zhu
- Blood Center of Zhejiang ProvinceKey Laboratory of Blood Safety Research of Zhejiang ProvinceHangzhouZhejiangChina
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
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47
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Sugawara S, Manickam C, Reeves K. TRIGGERED: could refocused cell signaling be key to natural killer cell-based HIV immunotherapeutics? AIDS 2021; 35:165-176. [PMID: 33116071 PMCID: PMC7775286 DOI: 10.1097/qad.0000000000002743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Natural killer (NK) cells are one of the critical innate immune effector cells that directly kill tumors and virus-infected cells, and modulate other immune cells including dendritic cells, CD4+ and CD8+ T cells. Signals from activating and inhibitory surface receptors orchestrate the regulatory and cytotoxic functions of NK cells. Although a number of surface receptors are involved, multiple signaling molecules are shared so that NK cell responses are synergistically regulated. Many pathogens and tumors evade NK cell responses by targeting NK cell signaling. Particularly in HIV/simian immunodeficiency virus (SIV) infection, the NK cell repertoire is diminished by changes in subsets of NK cells, expression of activating and inhibitory receptors, and intracellular signaling molecules. However, in-depth studies on intracellular signaling in NK cells in HIV/SIV infections remain limited. Checkpoint blockade and chimeric antigen receptor (CAR)-NK cells have demonstrated enhanced NK cell activities against tumors and viral infections. In addition, targeting intracellular signaling molecules by small molecules could also improve NK cell responses towards HIV/SIV infection in vivo. Therefore, further understanding of NK cell signaling including identification of key signaling molecules is crucial to maximize the efficacy of NK cell-based treatments. Herein, we review the current state of the literature and outline potential future avenues where optimized NK cells could be utilized in HIV-1 cure strategies and other immunotherapeutics in PLWH.
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Affiliation(s)
- Sho Sugawara
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Cordelia Manickam
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA
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48
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Hirayasu K, Sun J, Hasegawa G, Hashikawa Y, Hosomichi K, Tajima A, Tokunaga K, Ohashi J, Hanayama R. Characterization of LILRB3 and LILRA6 allelic variants in the Japanese population. J Hum Genet 2021; 66:739-748. [PMID: 33526815 DOI: 10.1038/s10038-021-00906-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/09/2022]
Abstract
Leukocyte immunoglobulin (Ig)-like receptors (LILRs) are encoded by members of a human multigene family, comprising 11 protein-coding genes and two pseudogenes. Among the LILRs, LILRB3 and LILRA6 show the highest homology with each other, along with high allelic and copy number variations. Therefore, it has been difficult to discriminate between them, both genetically and functionally, precluding disease association studies of LILRB3 and LILRA6. In this study, we carefully performed variant screening of LILRB3 and LILRA6 by cDNA cloning from Japanese individuals and identified four allelic lineages showing significantly high non-synonymous-to-synonymous ratios in pairwise comparisons. Furthermore, the extracellular domains of the LILRB3*JP6 and LILRA6*JP1 alleles were identical at the DNA level, suggesting that gene conversion-like events diversified LILRB3 and LILRA6. To determine the four allelic lineages from genomic DNA, we established a lineage typing method that accurately estimated the four allelic lineages in addition to specific common alleles from genomic DNA. Analysis of LILRA6 copy number variation revealed one, two, and three copies of LILRA6 in the Japanese-in-Tokyo (JPT) population. Flow cytometric analysis showed that an anti-LILRB3 antibody did not recognize the second most common lineage in the Japanese population, indicating significant amino acid differences across the allelic lineages. Taken together, our findings indicate that our lineage typing is useful for classifying the lineage-specific functions of LILRB3 and LILRA6, serving as the basis for disease association studies.
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Affiliation(s)
- Kouyuki Hirayasu
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan. .,Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan.
| | - Jinwen Sun
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Gen Hasegawa
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Yuko Hashikawa
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan
| | - Kazuyoshi Hosomichi
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Atsushi Tajima
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rikinari Hanayama
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan.,WPI Nano Life Science Institute (NanoLSI), Kanazawa University, Kakuma, Kanazawa, Ishikawa, Japan
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49
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Schetelig J, Baldauf H, Koster L, Kuxhausen M, Heidenreich F, de Wreede LC, Spellman S, van Gelder M, Bruno B, Onida F, Lange V, Massalski C, Potter V, Ljungman P, Schaap N, Hayden P, Lee SJ, Kröger N, Hsu K, Schmidt AH, Yakoub-Agha I, Robin M. Haplotype Motif-Based Models for KIR-Genotype Informed Selection of Hematopoietic Cell Donors Fail to Predict Outcome of Patients With Myelodysplastic Syndromes or Secondary Acute Myeloid Leukemia. Front Immunol 2021; 11:584520. [PMID: 33542712 PMCID: PMC7851088 DOI: 10.3389/fimmu.2020.584520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
Results from registry studies suggest that harnessing Natural Killer (NK) cell reactivity mediated through Killer cell Immunoglobulin-like Receptors (KIR) could reduce the risk of relapse after allogeneic Hematopoietic Cell Transplantation (HCT). Several competing models have been developed to classify donors as KIR-advantageous or disadvantageous. Basically, these models differ by grouping donors based on distinct KIR–KIR–ligand combinations or by haplotype motif assignment. This study aimed to validate different models for unrelated donor selection for patients with Myelodysplatic Syndromes (MDS) or secondary Acute Myeloid Leukemia (sAML). In a joint retrospective study of the European Society for Blood and Marrow Transplantation (EBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) registry data from 1704 patients with secondary AML or MDS were analysed. The cohort consisted mainly of older patients (median age 61 years) with high risk disease who had received chemotherapy-based reduced intensity conditioning and anti-thymocyte globulin prior to allogeneic HCT from well-matched unrelated stem cell donors. The impact of the predictors on Overall Survival (OS) and relapse incidence was tested in Cox regression models adjusted for patient age, a modified disease risk index, performance status, donor age, HLA-match, sex-match, CMV-match, conditioning intensity, type of T-cell depletion and graft type. KIR genes were typed using high-resolution amplicon-based next generation sequencing. In univariable and multivariable analyses none of the models predicted OS and the risk of relapse consistently. Our results do not support the hypothesis that optimizing NK-mediated alloreactivity is possible by KIR-genotype informed selection of HLA-matched unrelated donors. However, in the context of allogeneic transplantation, NK-cell biology is complex and only partly understood. KIR-genes are highly diverse and current assignment of haplotype motifs based on the presence or absence of selected KIR genes is over-simplistic. As a consequence, further research is highly warranted and should integrate cutting edge knowledge on KIR genetics, and NK-cell biology into future studies focused on homogeneous groups of patients and treatment modalities.
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Affiliation(s)
- Johannes Schetelig
- Medizinische Klinik und Poliklinik I, University Hospital Dresden, Dresden, Germany.,DKMS Clinical Trials Unit, Dresden, Germany
| | | | | | - Michelle Kuxhausen
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Falk Heidenreich
- Medizinische Klinik und Poliklinik I, University Hospital Dresden, Dresden, Germany.,DKMS Clinical Trials Unit, Dresden, Germany
| | - Liesbeth C de Wreede
- DKMS Clinical Trials Unit, Dresden, Germany.,Leiden University Medical Center, Department of Biomedical Data Sciences, Leiden, Netherlands
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Michel van Gelder
- Maastricht University Medical Center, Department of Internal Medicine, Maastricht, Netherlands
| | - Benedetto Bruno
- A.O.U. Citta della Salute e della Scienza di Torino, Turin, Italy
| | - Francesco Onida
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | | | | | | | - Per Ljungman
- Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | | | | | - Stephanie J Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | | | - Kathy Hsu
- Memorial Sloan Kettering Cancer Center, New York & Scientific Director, CIBMTR Immunobiology Working Committee, New York City, NY, United States
| | - Alexander H Schmidt
- DKMS Clinical Trials Unit, Dresden, Germany.,DKMS Life Science Lab, Dresden, Germany
| | | | - Marie Robin
- Hopital Saint-Louis, APHP, Université de Paris, Paris, France
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50
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Legaz I, Bolarín JM, Navarro E, Campillo JA, Moya R, Pérez-Cárceles MD, Luna A, Osuna E, Miras M, Muro M, Minguela A, Alvarez López R. KIR2DL2/S2 and KIR2DS5 in alcoholic cirrhotic patients undergoing liver transplantation. Arch Med Sci 2021; 17:764-774. [PMID: 34025847 PMCID: PMC8130473 DOI: 10.5114/aoms.2019.84410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/23/2019] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION The molecular mechanisms underlying alcoholic liver fibrosis and cirrhosis are not completely understood. Hepatic fibrosis involves the interplay of diverse cells and factors, including hepatic stellate cells (HSCs), Kupffer, NK cells, and T-lymphocyte subsets. Killer-cell immunoglobulin-like receptors (KIR) are membrane receptors involved in mediation between NK and activated HSCs, regulating NK cell function through their interaction with HLA-I molecules. The aim of this study was to analyse the genetic association between KIR genes and the susceptibility to or protection from alcoholic cirrhosis (AC) in a cohort of male AC patients undergoing liver transplantation (LT) with and without concomitant viral infections. MATERIAL AND METHODS KIR genotyping was performed in nuclear DNA extracted from 281 AC patients and compared with 319 male controls. RESULTS Significant differences between total AC patients and healthy controls were only found in the case of KIR2DL2 and KIR2DS5. KIR2DL2 was significantly underrepresented in non-viral AC patients (52.6% vs. 63.3%; p = 0.015), while patients heterozygous for KIR2DL2 were also underrepresented in the non-viral AC group compared with controls (p = 0.034). KIR2DS5 was overrepresented in this group compared with healthy controls (p = 0.002). All these observations were only evident in AC patients older than 54 years old. CONCLUSIONS Our data suggest a contrary effect of KIR2DL2 and KIR2DS5 in AC patients older than 54 years, in whom the presence of KIR2DL2 appears to be protective against AC, whereas the presence of KIR2DS5 seems to promote the fibrotic process, particularly in patients with no associated viral infection.
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Affiliation(s)
- Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
- Research Institute on Ageing, University of Murcia, Murcia, Spain
| | - Jose Miguel Bolarín
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - Elena Navarro
- Digestive Medicine Service, Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - Jose Antonio Campillo
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - Rosa Moya
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - María Dolores Pérez-Cárceles
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
- Research Institute on Ageing, University of Murcia, Murcia, Spain
| | - Aurelio Luna
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - Eduardo Osuna
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
- Research Institute on Ageing, University of Murcia, Murcia, Spain
| | - Manuel Miras
- Digestive Medicine Service, Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - Manuel Muro
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - Alfredo Minguela
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - Rocio Alvarez López
- Immunology Service, Instituto Murciano de Investigación Biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
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