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Pollock NR, Farias TDJ, Kichula KM, Sauter J, Scholz S, Nii-Trebi NI, Khor SS, Tokunaga K, Voorter CE, Groeneweg M, Augusto DG, Arrieta-Bolaños E, Mayor NP, Edinur HA, ElGhazali G, Issler HC, Petzl-Erler ML, Oksenberg JR, Marin WM, Hollenbach JA, Gendzekhadze K, Cita R, Stelet V, Rajalingam R, Koskela S, Clancy J, Chatzistamatiou T, Houwaart T, Kulski J, Guethlein LA, Parham P, Schmidt AH, Dilthey A, Norman PJ. The 18th International HLA & Immunogenetics workshop project report: Creating fully representative MHC reference haplotypes. HLA 2024; 103:e15568. [PMID: 38923286 PMCID: PMC11210686 DOI: 10.1111/tan.15568] [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: 02/05/2024] [Revised: 04/25/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Abstract
A fundamental endeavor of the International Histocompatibility and Immunogenetics Workshop (IHIW) was assembling a collection of DNA samples homozygous through the MHC genomic region. This collection proved invaluable for assay development in the histocompatibility and immunogenetics field, for generating the human reference genome, and furthered our understanding of MHC diversity. Defined by their HLA-A, -B, -C and -DRB1 alleles, the combined frequency of the haplotypes from these individuals is ~20% in Europe. Thus, a significant proportion of MHC haplotypes, both common and rare throughout the world, and including many associated with disease, are not yet represented. In this workshop component, we are collecting the next generation of MHC -homozygous samples, to expand, diversify and modernize this critical community resource that has been foundational to the field. We asked laboratories worldwide to identify samples homozygous through all HLA class I and/or HLA class II genes, or through whole-genome SNP genotyping or sequencing, to have extensive homozygosity tracts within the MHC region. The focus is non-Europeans or those having HLA haplotypes less common in Europeans. Through this effort, we have obtained samples from 537 individuals representing 294 distinct haplotypes, as determined by their HLA class I and II alleles, and an additional 50 haplotypes distinct in HLA class I or II alleles. Although we have expanded the diversity, many populations remain underrepresented, particularly from Africa, and we encourage further participation. The data will serve as a resource for investigators seeking to characterize variation across the MHC genomic region for disease and population studies.
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Affiliation(s)
- Nicholas R. Pollock
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Ticiana D. J. Farias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jürgen Sauter
- DKMS Group, Tübingen, Germany; DKMS Life Science Lab, Dresden, Germany
| | - Stephan Scholz
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 00233, Ghana
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine Hospital, Tokyo, Japan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Christina E. Voorter
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - Mathijs Groeneweg
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - Danillo G. Augusto
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
| | - Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, Royal Free Campus, London, UK
| | - Hisham Atan Edinur
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Gehad ElGhazali
- Immunology laboratory, Sheikh Khalifa Medical City- Purelab, Purehealth, Abu Dhabi and College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hellen C. Issler
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Jorge R. Oksenberg
- 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
| | - 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, San Francisco, CA, 94158, USA
| | - Ketevan Gendzekhadze
- HLA Laboratory, Department of Hematology and HCT, City of Hope National Medical Center, Duarte, CA
| | - Rafael Cita
- Transplant Immunology Laboratory, Pio XII Foundation, Barretos, Brazil
| | - Vinícius Stelet
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Satu Koskela
- Finnish Red Cross Blood Service; Biobank, 01730 Vantaa, Finland
| | - Jonna Clancy
- Finnish Red Cross Blood Service; Biobank, 01730 Vantaa, Finland
| | - Theofanis Chatzistamatiou
- Histocompatibility & Immunogenetics Laboratory, Hellenic Cord Blood Bank, Biomedical Research Foundation, Academy of Athens,11528 Athens, Greece
| | - Torsten Houwaart
- Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 00233, Ghana
| | - Jerzy Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Lisbeth A. Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, USA
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, USA
| | | | - Alexander Dilthey
- Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 00233, Ghana
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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2
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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, Norman PJ, You X, Kichula KM, Dong L, Chen N, He Y, Chen C, Zhang W, Zhu F. High-resolution KIR and HLA genotyping in three Chinese ethnic minorities reveals distinct origins. HLA 2024; 103:e15482. [PMID: 38625090 PMCID: PMC11027949 DOI: 10.1111/tan.15482] [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: 09/22/2023] [Revised: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
Polymorphism of killer-cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands impacts the effector activity of cytotoxic NK cell and T cell subsets. Therefore, understanding the extent and implications of KIR and HLA class I genetic polymorphism across various populations is important for immunological and medical research. In this study, we conducted a high-resolution investigation of KIR and HLA class I diversity in three distinct Chinese ethnic minority populations. We studied the She, Yugur, and Tajik, and compared them with the Zhejiang Han population (Zhe), which represents the majority Southern Han ethnicity. Our findings revealed that the Tajik population exhibited the most diverse KIR copy number, allele, and haplotype diversity among the four populations. This diversity aligns with their proposed ancestral origin, closely resembling that of Iranian populations, with a relatively higher presence of KIR-B genes, alleles, and haplotypes compared with the other Chinese populations. The Yugur population displayed KIR distributions similar to those of the Tibetans and Southeast Asians, whereas the She population resembled the Zhe and other East Asians, as confirmed by genetic distance analysis of KIR. Additionally, we identified 12.9% of individuals across the three minority populations as having KIR haplotypes characterized by specific gene block insertions or deletions. Genetic analysis based on HLA alleles yielded consistent results, even though there were extensive variations in HLA alleles. The observed variations in KIR interactions, such as higher numbers of 2DL1-C2 interactions in Tajik and Yugur populations and of 2DL3-C1 interactions in the She population, are likely shaped by demographic and evolutionary mechanisms specific to their local environments. Overall, our findings offer valuable insights into the distribution of KIR and HLA diversity among three distinct Chinese ethnic minority populations, which can inform future clinical and population studies.
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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
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Xuan You
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Lina Dong
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Nanying Chen
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Yizhen He
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
| | - Chen Chen
- 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
| | - 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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4
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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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Zhou Q, Ghezelji M, Hari A, Ford MKB, Holley C, Mirabello L, Chanock S, Sahinalp SC, Numanagić I. Geny: A Genotyping Tool for Allelic Decomposition of Killer Cell Immunoglobulin-Like Receptor Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582413. [PMID: 38529502 PMCID: PMC10962708 DOI: 10.1101/2024.02.27.582413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Accurate genotyping of Killer cell Immunoglobulin-like Receptor (KIR) genes plays a pivotal role in enhancing our understanding of innate immune responses, disease correlations, and the advancement of personalized medicine. However, due to the high variability of the KIR region and high level of sequence similarity among different KIR genes, the currently available genotyping methods are unable to accurately infer copy numbers, genotypes and haplotypes of individual KIR genes from next-generation sequencing data. Here we introduce Geny, a new computational tool for precise genotyping of KIR genes. Geny utilizes available KIR haplotype databases and proposes a novel combination of expectation-maximization filtering schemes and integer linear programming-based combinatorial optimization models to resolve ambiguous reads, provide accurate copy number estimation and estimate the haplotype of each copy for the genes within the KIR region. We evaluated Geny on a large set of simulated short-read datasets covering the known validated KIR region assemblies and a set of Illumina short-read samples sequenced from 25 validated samples from the Human Pangenome Reference Consortium collection and showed that it outperforms the existing genotyping tools in terms of accuracy, precision and recall. We envision Geny becoming a valuable resource for understanding immune system response and consequently advancing the field of patient-centric medicine.
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Zhou Y, Song L, Li H. Full resolution HLA and KIR genes annotation for human genome assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576452. [PMID: 38328160 PMCID: PMC10849470 DOI: 10.1101/2024.01.20.576452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The HLA (Human Leukocyte Antigen) genes and the KIR (Killer cell Immunoglobulin-like Receptor) genes are critical to immune responses and are associated with many immune-related diseases. Located in highly polymorphic regions, they are hard to be studied with traditional short-read alignment-based methods. Although modern long-read assemblers can often assemble these genes, using existing tools to annotate HLA and KIR genes in these assemblies remains a non-trivial task. Here, we describe Immuannot, a new computation tool to annotate the gene structures of HLA and KIR genes and to type the allele of each gene. Applying Immuannot to 56 regional and 212 whole-genome assemblies from previous studies, we annotated 9,931 HLA and KIR genes and found that almost half of these genes, 4,068, had novel sequences compared to the current Immuno Polymorphism Database (IPD). These novel gene sequences were represented by 2,664 distinct alleles, some of which contained non-synonymous variations resulting in 92 novel protein sequences. We demonstrated the complex haplotype structures at the two loci and reported the linkage between HLA/KIR haplotypes and gene alleles. We anticipate that Immuannot will speed up the discovery of new HLA/KIR alleles and enable the association of HLA/KIR haplotype structures with clinical outcomes in the future.
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Affiliation(s)
- Ying Zhou
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Li Song
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, 03755, USA
| | - Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
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7
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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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8
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Montero-Martin G, Kichula KM, Misra MK, Vargas LB, Marin WM, Hollenbach JA, Fernández-Viña MA, Elfishawi S, Norman PJ. Exceptional diversity of KIR and HLA class I in Egypt. HLA 2024; 103:e15177. [PMID: 37528739 PMCID: PMC11068459 DOI: 10.1111/tan.15177] [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: 02/16/2023] [Revised: 05/25/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Genetically determined variation of killer cell immunoglobulin like receptors (KIR) and their HLA class I ligands affects multiple aspects of human health. Their extreme diversity is generated through complex interplay of natural selection for pathogen resistance and reproductive health, combined with demographic structure and dispersal. Despite significant importance to multiple health conditions of differential effect across populations, the nature and extent of immunogenetic diversity is under-studied for many geographic regions. Here, we describe the first high-resolution analysis of KIR and HLA class I combinatorial diversity in Northern Africa. Analysis of 125 healthy unrelated individuals from Cairo in Egypt yielded 186 KIR alleles arranged in 146 distinct centromeric and 79 distinct telomeric haplotypes. The most frequent haplotypes observed were KIR-A, encoding two inhibitory receptors specific for HLA-C, two that are specific for HLA-A and -B, and no activating receptors. Together with 141 alleles of HLA class I, 75 of which encode a KIR ligand, we identified a mean of six distinct interacting pairs of inhibitory KIR and HLA allotypes per individual. We additionally characterize 16 KIR alleles newly identified in the study population. Our findings place Egyptians as one of the most highly diverse populations worldwide, with important implications for transplant matching and studies of immune-mediated diseases.
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Affiliation(s)
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Maneesh K. Misra
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of Chicago Medicine, Chicago, IL, USA
| | - Luciana B. Vargas
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Wesley M. Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jill A. Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | | | - Sally Elfishawi
- BMT lab unit, Clinical Pathology Dept., National Cancer Institute, Cairo University, Cairo, Egypt
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
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9
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Philippon C, Tao S, Clement D, Haroun-Izquierdo A, Kichula KM, Netskar H, Brandt L, Oei VS, Kanaya M, Lanuza PM, Schaffer M, Goodridge JP, Horowitz A, Zhu F, Hammer Q, Sohlberg E, Majhi RK, Kveberg L, Önfelt B, Norman PJ, Malmberg KJ. Allelic variation of KIR and HLA tunes the cytolytic payload and determines functional hierarchy of NK cell repertoires. Blood Adv 2023; 7:4492-4504. [PMID: 37327114 PMCID: PMC10440473 DOI: 10.1182/bloodadvances.2023009827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/18/2023] [Accepted: 06/04/2023] [Indexed: 06/18/2023] Open
Abstract
The functionality of natural killer (NK) cells is tuned during education and is associated with remodeling of the lysosomal compartment. We hypothesized that genetic variation in killer cell immunoglobulin-like receptor (KIR) and HLA, which is known to influence the functional strength of NK cells, fine-tunes the payload of effector molecules stored in secretory lysosomes. To address this possibility, we performed a high-resolution analysis of KIR and HLA class I genes in 365 blood donors and linked genotypes to granzyme B loading and functional phenotypes. We found that granzyme B levels varied across individuals but were stable over time in each individual and genetically determined by allelic variation in HLA class I genes. A broad mapping of surface receptors and lysosomal effector molecules revealed that DNAM-1 and granzyme B levels served as robust metric of the functional state in NK cells. Variation in granzyme B levels at rest was tightly linked to the lytic hit and downstream killing of major histocompatibility complex-deficient target cells. Together, these data provide insights into how variation in genetically hardwired receptor pairs tunes the releasable granzyme B pool in NK cells, resulting in predictable hierarchies in global NK cell function.
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Affiliation(s)
- Camille Philippon
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Sudan Tao
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Dennis Clement
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Alvaro Haroun-Izquierdo
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Katherine M. Kichula
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Herman Netskar
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Ludwig Brandt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincent Sheng Oei
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Minoru Kanaya
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Pilar Maria Lanuza
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marie Schaffer
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Amir Horowitz
- Department of Oncological Sciences, The Marc and Jennifer Lipshultz Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Faming Zhu
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Quirin Hammer
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ebba Sohlberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rakesh Kumar Majhi
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Lise Kveberg
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Björn Önfelt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Paul J. Norman
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Karl-Johan Malmberg
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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10
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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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11
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Zhang Y, Yan AW, Boelen L, Hadcocks L, Salam A, Gispert DP, Spanos L, Bitria LM, Nemat-Gorgani N, Traherne JA, Roberts C, Koftori D, Taylor GP, Forton D, Norman PJ, Marsh SG, Busch R, Macallan DC, Asquith B. KIR-HLA interactions extend human CD8+ T cell lifespan in vivo. J Clin Invest 2023; 133:e169496. [PMID: 37071474 PMCID: PMC10266773 DOI: 10.1172/jci169496] [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: 02/06/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUNDThere is increasing evidence, in transgenic mice and in vitro, that inhibitory killer cell immunoglobulin-like receptors (iKIRs) can modulate T cell responses. Furthermore, we have previously shown that iKIRs are an important determinant of T cell-mediated control of chronic viral infection and that these results are consistent with an increase in the CD8+ T cell lifespan due to iKIR-ligand interactions. Here, we tested this prediction and investigated whether iKIRs affect T cell lifespan in humans in vivo.METHODSWe used stable isotope labeling with deuterated water to quantify memory CD8+ T cell survival in healthy individuals and patients with chronic viral infections.RESULTSWe showed that an individual's iKIR-ligand genotype was a significant determinant of CD8+ T cell lifespan: in individuals with 2 iKIR-ligand gene pairs, memory CD8+ T cells survived, on average, for 125 days; in individuals with 4 iKIR-ligand gene pairs, the memory CD8+ T cell lifespan doubled to 250 days. Additionally, we showed that this survival advantage was independent of iKIR expression by the T cell of interest and, further, that the iKIR-ligand genotype altered the CD8+ and CD4+ T cell immune aging phenotype.CONCLUSIONSTogether, these data reveal an unexpectedly large effect of iKIR genotype on T cell survival.FUNDINGWellcome Trust; Medical Research Council; EU Horizon 2020; EU FP7; Leukemia and Lymphoma Research; National Institute of Health Research (NIHR) Imperial Biomedical Research Centre; Imperial College Research Fellowship; National Institutes of Health; Jefferiss Trust.
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Affiliation(s)
- Yan Zhang
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Ada W.C. Yan
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lies Boelen
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Linda Hadcocks
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Arafa Salam
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | | | - Loiza Spanos
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
- School of Life and Health Sciences, University of Roehampton, London, United Kingdom
| | - Laura Mora Bitria
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Neda Nemat-Gorgani
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - James A. Traherne
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Chrissy Roberts
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Danai Koftori
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Graham P. Taylor
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- National Centre for Human Retrovirology, St Mary’s Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Daniel Forton
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
- Department of Gastroenterology and Hepatology, St George’s University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Paul J. Norman
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Biomedical Informatics and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Steven G.E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
- UCL Cancer Institute, UCL, London, United Kingdom
| | - Robert Busch
- School of Life and Health Sciences, University of Roehampton, London, United Kingdom
| | - Derek C. Macallan
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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12
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Song L, Bai G, Liu XS, Li B, Li H. Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data. Genome Res 2023; 33:923-931. [PMID: 37169596 PMCID: PMC10519407 DOI: 10.1101/gr.277585.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Killer cell immunoglobulin like receptor (KIR) genes and human leukocyte antigen (HLA) genes play important roles in innate and adaptive immunity. They are highly polymorphic and cannot be genotyped with standard variant calling pipelines. Compared with HLA genes, many KIR genes are similar to each other in sequences and may be absent in the chromosomes. Therefore, although many tools have been developed to genotype HLA genes using common sequencing data, none of them work for KIR genes. Even specialized KIR genotypers could not resolve all the KIR genes. Here we describe T1K, a novel computational method for the efficient and accurate inference of KIR or HLA alleles from RNA-seq, whole-genome sequencing, or whole-exome sequencing data. T1K jointly considers alleles across all genotyped genes, so it can reliably identify present genes and distinguish homologous genes, including the challenging KIR2DL5A/KIR2DL5B genes. This model also benefits HLA genotyping, where T1K achieves high accuracy in benchmarks. Moreover, T1K can call novel single-nucleotide variants and process single-cell data. Applying T1K to tumor single-cell RNA-seq data, we found that KIR2DL4 expression was enriched in tumor-specific CD8+ T cells. T1K may open the opportunity for HLA and KIR genotyping across various sequencing applications.
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Affiliation(s)
- Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gali Bai
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
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13
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Bruijnesteijn J. HLA/MHC and KIR characterization in humans and non-human primates using Oxford Nanopore Technologies and Pacific Biosciences sequencing platforms. HLA 2023; 101:205-221. [PMID: 36583332 DOI: 10.1111/tan.14957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The gene products of the HLA/MHC and KIR multigene families are important modulators of the immune system and are associated with health and disease. Characterization of the genes encoding these receptors has been integrated into different biomedical applications, including transplantation and reproduction biology, immune therapies and in fundamental research into disease susceptibility or resistance. Conventional short-read sequencing strategies have shown their value in high throughput typing, but are insufficient to uncover the entire complexity of the highly polymorphic HLA/MHC and KIR gene systems. The implementation of single-molecule and real-time sequencing platforms, offered by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), revolutionized the fields of genomics and transcriptomics. Using fundamentally distinct principles, these platforms generate long-read data that can unwire the plasticity of the HLA/MHC and KIR genes, including high-resolution characterization of genes, alleles, phased haplotypes, transcription levels and epigenetics modification patterns. These insights might have profound clinical relevance, such as improved matching of donors and patients in clinical transplantation, but could also lift disease association studies to a higher level. Even more, a comprehensive characterization may refine animal models in preclinical studies. In this review, the different HLA/MHC and KIR characterization approaches using PacBio and ONT platforms are described and discussed.
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Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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14
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Gao GF, Liu D, Zhan X, Li B. Analysis of KIR gene variants in The Cancer Genome Atlas and UK Biobank using KIRCLE. BMC Biol 2022; 20:191. [PMID: 36002830 PMCID: PMC9400285 DOI: 10.1186/s12915-022-01392-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 08/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natural killer (NK) cells represent a critical component of the innate immune system's response against cancer and viral infections, among other diseases. To distinguish healthy host cells from infected or tumor cells, killer immunoglobulin receptors (KIR) on NK cells bind and recognize Human Leukocyte Antigen (HLA) complexes on their target cells. However, NK cells exhibit great diversity in their mechanism of activation, and the outcomes of their activation are not yet understood fully. Just like the HLAs they bind, KIR receptors exhibit high allelic diversity in the human population. Here we provide a method to identify KIR allele variants from whole exome sequencing data and uncover novel associations between these variants and various molecular and clinical correlates. RESULTS In order to better understand KIRs, we have developed KIRCLE, a novel method for genotyping individual KIR genes from whole exome sequencing data, and used it to analyze approximately sixty-thousand patient samples in The Cancer Genome Atlas (TCGA) and UK Biobank. We were able to assess population frequencies for different KIR alleles and demonstrate that, similar to HLA alleles, individuals' KIR alleles correlate strongly with their ethnicities. In addition, we observed associations between different KIR alleles and HLA alleles, including HLA-B*53 with KIR3DL2*013 (Fisher's exact FDR = 7.64e-51). Finally, we showcased statistically significant associations between KIR alleles and various clinical correlates, including peptic ulcer disease (Fisher's exact FDR = 0.0429) and age of onset of atopy (Mann-Whitney U FDR = 0.0751). CONCLUSIONS We show that KIRCLE is able to infer KIR variants accurately and consistently, and we demonstrate its utility using data from approximately sixty-thousand individuals from TCGA and UK Biobank to discover novel molecular and clinical correlations with KIR germline variants. Peptic ulcer disease and atopy are just two diseases in which NK cells may play a role beyond their "classical" realm of anti-tumor and anti-viral responses. This tool may be used both as a benchmark for future KIR-variant-inference algorithms, and to better understand the immunogenomics of and disease processes involving KIRs.
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Affiliation(s)
- Galen F Gao
- School of Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dajiang Liu
- Institute for Personalized Medicine, College of Medicine, Pennsylvania State University, Hershey, PA, 17033, USA
| | - Xiaowei Zhan
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Bo Li
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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15
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Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity. Nat Commun 2022; 13:4073. [PMID: 35835762 PMCID: PMC9283523 DOI: 10.1038/s41467-022-31626-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/24/2022] [Indexed: 12/13/2022] Open
Abstract
Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans (n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY, MC1R and UVSSA. Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms. Natural Killer cells are key mediators of anti-tumour immunosurveillance and anti-viral immunity. Here, the authors map regulatory genetic variation in primary Natural Killer cells, providing new insights into their role in human health and disease.
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16
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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: 12] [Impact Index Per Article: 6.0] [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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17
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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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18
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Sakaue S, Hosomichi K, Hirata J, Nakaoka H, Yamazaki K, Yawata M, Yawata N, Naito T, Umeno J, Kawaguchi T, Matsui T, Motoya S, Suzuki Y, Inoko H, Tajima A, Morisaki T, Matsuda K, Kamatani Y, Yamamoto K, Inoue I, Okada Y. Decoding the diversity of killer immunoglobulin-like receptors by deep sequencing and a high-resolution imputation method. CELL GENOMICS 2022; 2:100101. [PMID: 36777335 PMCID: PMC9903714 DOI: 10.1016/j.xgen.2022.100101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/07/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
Abstract
The killer cell immunoglobulin-like receptor (KIR) recognizes human leukocyte antigen (HLA) class I molecules and modulates the function of natural killer cells. Despite its role in immunity, the complex genomic structure has limited a deep understanding of the KIR genomic landscape. Here we conduct deep sequencing of 16 KIR genes in 1,173 individuals. We devise a bioinformatics pipeline incorporating copy number estimation and insertion or deletion (indel) calling for high-resolution KIR genotyping. We define 118 alleles in 13 genes and demonstrate a linkage disequilibrium structure within and across KIR centromeric and telomeric regions. We construct a KIR imputation reference panel (nreference = 689, imputation accuracy = 99.7%), apply it to biobank genotype (ntotal = 169,907), and perform phenome-wide association studies of 85 traits. We observe a dearth of genome-wide significant associations, even in immune traits implicated previously to be associated with KIR (the smallest p = 1.5 × 10-4). Our pipeline presents a broadly applicable framework to evaluate innate immunity in large-scale datasets.
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Affiliation(s)
- Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Corresponding author
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirofumi Nakaoka
- Human Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Public Health, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Makoto Yawata
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, and National University Health System, Singapore 119228, Singapore
- NUSMed Immunology Translational Research Programme, and Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore 117609, Singapore
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Nobuyo Yawata
- Department of Ocular Pathology and Imaging Science, Kyushu University, 812-8582, Japan
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Takaaki Kawaguchi
- Division of Gastroenterology, Department of Medicine, Tokyo Yamate Medical Center, Tokyo 169-0073, Japan
| | - Toshiyuki Matsui
- Department of Gastroenterology, Fukuoka University Chikushi Hospital, Fukuoka 818-0067, Japan
| | - Satoshi Motoya
- Department of Gastroenterology, Sapporo-Kosei General Hospital, Sapporo 060-0033, Japan
| | - Yasuo Suzuki
- Department of Internal Medicine, Faculty of Medicine, Toho University, Chiba 274-8510, Japan
| | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Takayuki Morisaki
- Division of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita 565-0871, Japan
- Corresponding author
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19
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Walwyn-Brown K, Pugh J, Cocker AT, Beyzaie N, Singer BB, Olive D, Guethlein LA, Parham P, Djaoud Z. Phosphoantigen-stimulated γδ T cells suppress natural killer cell-responses to missing-self. Cancer Immunol Res 2022; 10:558-570. [PMID: 35263761 DOI: 10.1158/2326-6066.cir-21-0696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/14/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022]
Abstract
γδ T cells stimulated by phosphoantigens (pAg) are potent effectors that secrete Th1 cytokines and kill tumor cells. Consequently, they are considered candidates for use in cancer immunotherapy. However, they have proven only moderately effective in several clinical trials. We studied the consequences of pAg-stimulated γδ T-cell interactions with Natural Killer (NK) cells and CD8+ T cells, major innate and adaptive effectors, respectively. We found that pAg-stimulated γδ T cells suppressed NK-cell responses to "missing-self" but had no effect on antigen-specific CD8+ T-cell responses. Extensive analysis of the secreted cytokines showed that pAg-stimulated γδ T cells had a pro-inflammatory profile. CMV-pp65-specific CD8+ T cells primed with pAg-stimulated γδ T cells showed little effect on responses to pp65-loaded target cells. By contrast, NK cells primed similarly with γδ T cells had impaired capacity to degranulate and produce IFNγ in response to HLA class I-deficient targets. This effect depended on BTN3A1 and required direct contact between NK cells and γδ T cells. γδ T cell-priming of NK cells also led to a downregulation of NKG2D and NKp44 on NK cells. Every NK-cell subset was affected by γδ T cell-mediated immunosuppression, but the strongest effect was on KIR+NKG2A- NK cells. We therefore report a previously unknown function for γδ T cells, as brakes of NK-cell responses to "missing-self". This provides a new perspective for optimizing the use of γδ T cells in cancer immunotherapy and for assessing their role in immune responses to pAg-producing pathogens.
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Affiliation(s)
| | | | | | | | | | - Daniel Olive
- Aix Marseille Univ, CNRS, Inserm, Institut Paoli-Calmettes, CRCM,, Marseille, France
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20
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Harrison GF, Leaton LA, Harrison EA, Kichula KM, Viken MK, Shortt J, Gignoux CR, Lie BA, Vukcevic D, Leslie S, Norman PJ. Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1. PLoS Comput Biol 2022; 18:e1009059. [PMID: 35192601 PMCID: PMC8896733 DOI: 10.1371/journal.pcbi.1009059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 03/04/2022] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Highly polymorphic interaction of KIR3DL1 and KIR3DS1 with HLA class I ligands modulates the effector functions of natural killer (NK) cells and some T cells. This genetically determined diversity affects severity of infections, immune-mediated diseases, and some cancers, and impacts the course of immunotherapies, including transplantation. KIR3DL1 is an inhibitory receptor, and KIR3DS1 is an activating receptor encoded by the KIR3DL1/S1 gene that has more than 200 diverse and divergent alleles. Determination of KIR3DL1/S1 genotypes for medical application is hampered by complex sequence and structural variation, requiring targeted approaches to generate and analyze high-resolution allele data. To overcome these obstacles, we developed and optimized a model for imputing KIR3DL1/S1 alleles at high-resolution from whole-genome SNP data. We designed the model to represent a substantial component of human genetic diversity. Our Global imputation model is effective at genotyping KIR3DL1/S1 alleles with an accuracy ranging from 88% in Africans to 97% in East Asians, with mean specificity of 99% and sensitivity of 95% for alleles >1% frequency. We used the established algorithm of the HIBAG program, in a modification named Pulling Out Natural killer cell Genomics (PONG). Because HIBAG was designed to impute HLA alleles also from whole-genome SNP data, PONG allows combinatorial diversity of KIR3DL1/S1 with HLA-A and -B to be analyzed using complementary techniques on a single data source. The use of PONG thus negates the need for targeted sequencing data in very large-scale association studies where such methods might not be tractable.
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Affiliation(s)
- Genelle F. Harrison
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Laura Ann Leaton
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Erica A. Harrison
- Independent Researcher, Broomfield, Colorado, United States of America
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Marte K. Viken
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Jonathan Shortt
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Christopher R. Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Benedicte A. Lie
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Damjan Vukcevic
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia
| | - Stephen Leslie
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
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21
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Concurrent use of two independent methods prevents erroneous HLA typing of deceased organ donors – An important strategy for patient safety and accurate virtual crossmatching for broader sharing. Hum Immunol 2022; 83:458-466. [DOI: 10.1016/j.humimm.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 11/21/2022]
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22
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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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23
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Ritari J, Hyvärinen K, Partanen J, Koskela S. KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population. PeerJ 2022; 10:e12692. [PMID: 35036093 PMCID: PMC8744484 DOI: 10.7717/peerj.12692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. Through regulation of natural killer (NK) cell activity KIRs participate in tumour surveillance and clearing viral infections. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Inferring KIR gene content from genetic variant data is therefore desirable for immunogenetic analysis, particularly in the context of growing biobank genome data collections that rely on genotyping by microarray. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 807 Finnish biobank samples genotyped for 5900 KIR-region SNPs and analysed for KIR gene content with targeted sequencing. Cross-validation results demonstrate a high mean overall accuracy of 98.5% (95% CI [97.0-99.2]%) which compares favourably with previous methods including short-read sequencing based approaches.
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Affiliation(s)
- Jarmo Ritari
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | | | - Satu Koskela
- Finnish Red Cross Blood Service, Helsinki, Finland
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24
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Croci S, Venneri MA, Mantovani S, Fallerini C, Benetti E, Picchiotti N, Campolo F, Imperatore F, Palmieri M, Daga S, Gabbi C, Montagnani F, Beligni G, Farias TDJ, Carriero ML, Di Sarno L, Alaverdian D, Aslaksen S, Cubellis MV, Spiga O, Baldassarri M, Fava F, Norman PJ, Frullanti E, Isidori AM, Amoroso A, Mari F, Furini S, Mondelli MU, Gen-Covid Multicenter Study, Chiariello M, Renieri A, Meloni I. The polymorphism L412F in TLR3 inhibits autophagy and is a marker of severe COVID-19 in males. Autophagy 2021; 18:1662-1672. [PMID: 34964709 PMCID: PMC9298458 DOI: 10.1080/15548627.2021.1995152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The polymorphism L412F in TLR3 has been associated with several infectious diseases. However, the mechanism underlying this association is still unexplored. Here, we show that the L412F polymorphism in TLR3 is a marker of severity in COVID-19. This association increases in the sub-cohort of males. Impaired macroautophagy/autophagy and reduced TNF/TNFα production was demonstrated in HEK293 cells transfected with TLR3L412F-encoding plasmid and stimulated with specific agonist poly(I:C). A statistically significant reduced survival at 28 days was shown in L412F COVID-19 patients treated with the autophagy-inhibitor hydroxychloroquine (p = 0.038). An increased frequency of autoimmune disorders such as co-morbidity was found in L412F COVID-19 males with specific class II HLA haplotypes prone to autoantigen presentation. Our analyses indicate that L412F polymorphism makes males at risk of severe COVID-19 and provides a rationale for reinterpreting clinical trials considering autophagy pathways. Abbreviations: AP: autophagosome; AUC: area under the curve; BafA1: bafilomycin A1; COVID-19: coronavirus disease-2019; HCQ: hydroxychloroquine; RAP: rapamycin; ROC: receiver operating characteristic; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TLR: toll like receptor; TNF/TNF-α: tumor necrosis factor
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Affiliation(s)
- Susanna Croci
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Mary Anna Venneri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefania Mantovani
- Division of Clinical Immunology and Infectious Diseases, Department of Medicine, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- DIISM-SAILAB, University of Siena, Siena, Italy.,Department of Mathematics, University of Pavia, Pavia, Italy
| | - Federica Campolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesco Imperatore
- Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Core Research Laboratory, Via Fiorentina, Siena, Italy.,Consiglio Nazionale delle Ricerche, Istituto DI Fisiologia Clinica, Siena, Italy
| | - Maria Palmieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Gabbi
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Francesca Montagnani
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Department of Medical Sciences, Infectious and Tropical Diseases Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Giada Beligni
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ticiana D J Farias
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Miriam Lucia Carriero
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Laura Di Sarno
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Diana Alaverdian
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sigrid Aslaksen
- Department of Clinical Science, Universty of Bergen and K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | | | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Elisa Frullanti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Andrea M Isidori
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy.,Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Mario U Mondelli
- Division of Clinical Immunology and Infectious Diseases, Department of Medicine, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | | | - Mario Chiariello
- Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Core Research Laboratory, Via Fiorentina, Siena, Italy.,Consiglio Nazionale delle Ricerche, Istituto DI Fisiologia Clinica, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
| | - Ilaria Meloni
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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25
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Liang H, Lu T, Liu H, Tan L. The Relationships between HLA-A and HLA-B Genes and the Genetic Susceptibility to Breast Cancer in Guangxi. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421100069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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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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27
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Mkorombindo T, Tran-Nguyen TK, Yuan K, Zhang Y, Xue J, Criner GJ, Kim YI, Pilewski JM, Gaggar A, Cho MH, Sciurba FC, Duncan SR. HLA-C and KIR permutations influence chronic obstructive pulmonary disease risk. JCI Insight 2021; 6:e150187. [PMID: 34464355 PMCID: PMC8525585 DOI: 10.1172/jci.insight.150187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/26/2021] [Indexed: 01/04/2023] Open
Abstract
A role for hereditary influences in the susceptibility for chronic obstructive pulmonary disease (COPD) is widely recognized. Cytotoxic lymphocytes are implicated in COPD pathogenesis, and functions of these leukocytes are modulated by interactions between their killer cell Ig-like receptors (KIR) and human leukocyte antigen–Class I (HLA–Class I) molecules on target cells. We hypothesized HLA–Class I and KIR inheritance affect risks for COPD. HLA–Class I alleles and KIR genotypes were defined by candidate gene analyses in multiple cohorts of patients with COPD (total n = 392) and control smokers with normal spirometry (total n = 342). Compared with controls, patients with COPD had overrepresentations of HLA-C*07 and activating KIR2DS1, with underrepresentations of HLA-C*12. Particular HLA-KIR permutations were synergistic; e.g., the presence of HLA-C*07 + KIR2DS1 + HLA-C12null versus HLAC*07null + KIR2DS1null + HLA-C12 was associated with COPD, especially among HLA-C1 allotype homozygotes. Cytotoxicity of COPD lymphocytes was more enhanced by KIR stimulation than those of controls and was correlated with lung function. These data show HLA-C and KIR polymorphisms strongly influence COPD susceptibility and highlight the importance of lymphocyte-mediated cytotoxicity in COPD pathogenesis. Findings here also indicate that HLA-KIR typing could stratify at-risk patients and raise possibilities that HLA-KIR axis modulation may have therapeutic potential.
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Affiliation(s)
- Takudzwa Mkorombindo
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Thi K Tran-Nguyen
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kaiyu Yuan
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jianmin Xue
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Gerard J Criner
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Young-Il Kim
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Division of Preventive Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Joseph M Pilewski
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amit Gaggar
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael H Cho
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Frank C Sciurba
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven R Duncan
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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28
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Aguiar VRC, Augusto DG, Castelli EC, Hollenbach JA, Meyer D, Nunes K, Petzl-Erler ML. An immunogenetic view of COVID-19. Genet Mol Biol 2021; 44:e20210036. [PMID: 34436508 PMCID: PMC8388242 DOI: 10.1590/1678-4685-gmb-2021-0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023] Open
Abstract
Meeting the challenges brought by the COVID-19 pandemic requires an interdisciplinary approach. In this context, integrating knowledge of immune function with an understanding of how genetic variation influences the nature of immunity is a key challenge. Immunogenetics can help explain the heterogeneity of susceptibility and protection to the viral infection and disease progression. Here, we review the knowledge developed so far, discussing fundamental genes for triggering the innate and adaptive immune responses associated with a viral infection, especially with the SARS-CoV-2 mechanisms. We emphasize the role of the HLA and KIR genes, discussing what has been uncovered about their role in COVID-19 and addressing methodological challenges of studying these genes. Finally, we comment on questions that arise when studying admixed populations, highlighting the case of Brazil. We argue that the interplay between immunology and an understanding of genetic associations can provide an important contribution to our knowledge of COVID-19.
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Affiliation(s)
- Vitor R. C. Aguiar
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Danillo G. Augusto
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
- Universidade Federal do Paraná, Departamento de Genética, Curitiba,
PR, Brazil
| | - Erick C. Castelli
- Universidade Estadual Paulista, Faculdade de Medicina de Botucatu,
Departamento de Patologia, Botucatu, SP, Brazil
| | - Jill A. Hollenbach
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
| | - Diogo Meyer
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Kelly Nunes
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
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29
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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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30
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Relevance of Polymorphic KIR and HLA Class I Genes in NK-Cell-Based Immunotherapies for Adult Leukemic Patients. Cancers (Basel) 2021; 13:cancers13153767. [PMID: 34359667 PMCID: PMC8345033 DOI: 10.3390/cancers13153767] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Immunotherapies are promising approaches to curing different acute leukemias. Natural killer (NK) cells are lymphocytes that are efficient in the elimination of leukemic cells. NK-cell-based immunotherapies are particularly attractive, but the landscape of the heterogeneity of NK cells must be deciphered. This review provides an overview of the polymorphic KIR and HLA class I genes that modulate the NK cell repertoire and how these markers can improve the outcomes of patients with acute leukemia. A better knowledge of these genetic markers that are linked to NK cell subsets that are efficient against hematological diseases will optimize hematopoietic stem-cell donor selection and NK immunotherapy design. Abstract Since the mid-1990s, the biology and functions of natural killer (NK) cells have been deeply investigated in healthy individuals and in people with diseases. These effector cells play a particularly crucial role after allogeneic hematopoietic stem-cell transplantation (HSCT) through their graft-versus-leukemia (GvL) effect, which is mainly mediated through polymorphic killer-cell immunoglobulin-like receptors (KIRs) and their cognates, HLA class I ligands. In this review, we present how KIRs and HLA class I ligands modulate the structural formation and the functional education of NK cells. In particular, we decipher the current knowledge about the extent of KIR and HLA class I gene polymorphisms, as well as their expression, interaction, and functional impact on the KIR+ NK cell repertoire in a physiological context and in a leukemic context. In addition, we present the impact of NK cell alloreactivity on the outcomes of HSCT in adult patients with acute leukemia, as well as a description of genetic models of KIRs and NK cell reconstitution, with a focus on emergent T-cell-repleted haplo-identical HSCT using cyclosphosphamide post-grafting (haplo-PTCy). Then, we document how the immunogenetics of KIR/HLA and the immunobiology of NK cells could improve the relapse incidence after haplo-PTCy. Ultimately, we review the emerging NK-cell-based immunotherapies for leukemic patients in addition to HSCT.
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31
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Duygu B, Olieslagers TI, Groeneweg M, Voorter CEM, Wieten L. HLA Class I Molecules as Immune Checkpoints for NK Cell Alloreactivity and Anti-Viral Immunity in Kidney Transplantation. Front Immunol 2021; 12:680480. [PMID: 34295330 PMCID: PMC8290519 DOI: 10.3389/fimmu.2021.680480] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that can kill diseased- or virally-infected cells, mediate antibody dependent cytotoxicity and produce type I immune-associated cytokines upon activation. NK cells also contribute to the allo-immune response upon kidney transplantation either by promoting allograft rejection through lysis of cells of the transplanted organ or by promoting alloreactive T cells. In addition, they protect against viral infections upon transplantation which may be especially relevant in patients receiving high dose immune suppression. NK cell activation is tightly regulated through the integrated balance of signaling via inhibitory- and activating receptors. HLA class I molecules are critical regulators of NK cell activation through the interaction with inhibitory- as well as activating NK cell receptors, hence, HLA molecules act as critical immune checkpoints for NK cells. In the current review, we evaluate how NK cell alloreactivity and anti-viral immunity are regulated by NK cell receptors belonging to the KIR family and interacting with classical HLA class I molecules, or by NKG2A/C and LILRB1/KIR2DL4 engaging non-classical HLA-E or -G. In addition, we provide an overview of the methods to determine genetic variation in these receptors and their HLA ligands.
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Affiliation(s)
- Burcu Duygu
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Timo I Olieslagers
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Mathijs Groeneweg
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Christina E M Voorter
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
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32
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Guethlein LA, Beyzaie N, Nemat-Gorgani N, Wang T, Ramesh V, Marin WM, Hollenbach JA, Schetelig J, Spellman SR, Marsh SGE, Cooley S, Weisdorf DJ, Norman PJ, Miller JS, Parham P. Following Transplantation for Acute Myelogenous Leukemia, Donor KIR Cen B02 Better Protects against Relapse than KIR Cen B01. THE JOURNAL OF IMMUNOLOGY 2021; 206:3064-3072. [PMID: 34117109 DOI: 10.4049/jimmunol.2100119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/10/2021] [Indexed: 12/11/2022]
Abstract
In the treatment of acute myelogenous leukemia with allogeneic hematopoietic cell transplantation, we previously demonstrated that there is a greater protection from relapse of leukemia when the hematopoietic cell transplantation donor has either the Cen B/B KIR genotype or a genotype having two or more KIR B gene segments. In those earlier analyses, KIR genotyping could only be assessed at the low resolution of gene presence or absence. To give the analysis greater depth, we developed high-resolution KIR sequence-based typing that defines all the KIR alleles and distinguishes the expressed alleles from those that are not expressed. We now describe and analyze high-resolution KIR genotypes for 890 donors of this human transplant cohort. Cen B01 and Cen B02 are the common CenB haplotypes, with Cen B02 having evolved from Cen B01 by deletion of the KIR2DL5, 2DS3/5, 2DP1, and 2DL1 genes. We observed a consistent trend for Cen B02 to provide stronger protection against relapse than Cen B01 This correlation indicates that protection depends on the donor having inhibitory KIR2DL2 and/or activating KIR2DS2, and is enhanced by the donor lacking inhibitory KIR2DL1, 2DL3, and 3DL1. High-resolution KIR typing has allowed us to compare the strength of the interactions between the recipient's HLA class I and the KIR expressed by the donor-derived NK cells and T cells, but no clinically significant interactions were observed. The trend observed between donor Cen B02 and reduced relapse of leukemia points to the value of studying ever larger transplant cohorts.
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Affiliation(s)
- Lisbeth A Guethlein
- Department of Structural Biology, Stanford University, Stanford, CA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Niassan Beyzaie
- Department of Structural Biology, Stanford University, Stanford, CA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University, Stanford, CA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
| | | | - Wesley M Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | | | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Campus, London, United Kingdom.,University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Sarah Cooley
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN; and
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN; and
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Aurora, CO
| | - Jeffrey S Miller
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN; and
| | - Peter Parham
- Department of Structural Biology, Stanford University, Stanford, CA; .,Department of Microbiology and Immunology, Stanford University, Stanford, CA
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33
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Ahn R, Vukcevic D, Motyer A, Nititham J, Squire DM, Hollenbach JA, Norman PJ, Ellinghaus E, Nair RP, Tsoi LC, Oksenberg J, Foerster J, Lieb W, Weidinger S, Franke A, Elder JT, Jorgenson E, Leslie S, Liao W. Large-Scale Imputation of KIR Copy Number and HLA Alleles in North American and European Psoriasis Case-Control Cohorts Reveals Association of Inhibitory KIR2DL2 With Psoriasis. Front Immunol 2021; 12:684326. [PMID: 34177931 PMCID: PMC8231283 DOI: 10.3389/fimmu.2021.684326] [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: 03/23/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIR) regulate immune responses in NK and CD8+ T cells via interaction with HLA ligands. KIR genes, including KIR2DS1, KIR3DL1, and KIR3DS1 have previously been implicated in psoriasis susceptibility. However, these previous studies were constrained to small sample sizes, in part due to the time and expense required for direct genotyping of KIR genes. Here, we implemented KIR*IMP to impute KIR copy number from single-nucleotide polymorphisms (SNPs) on chromosome 19 in the discovery cohort (n=11,912) from the PAGE consortium, University of California San Francisco, and the University of Dundee, and in a replication cohort (n=66,357) from Kaiser Permanente Northern California. Stratified multivariate logistic regression that accounted for patient ancestry and high-risk HLA alleles revealed that KIR2DL2 copy number was significantly associated with psoriasis in the discovery cohort (p ≤ 0.05). The KIR2DL2 copy number association was replicated in the Kaiser Permanente replication cohort. This is the first reported association of KIR2DL2 copy number with psoriasis and highlights the importance of KIR genetics in the pathogenesis of psoriasis.
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Affiliation(s)
- Richard Ahn
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Damjan Vukcevic
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Allan Motyer
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Joanne Nititham
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - David McG. Squire
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Jill A. Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Division of Personalized Medicine, Department of Immunology and Microbiology, University of Colorado, San Francisco, CA, United States
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Jorge Oksenberg
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - John Foerster
- College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, United Kingdom
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Hospital Schleswig Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - James T. Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Ann Arbor Veterans Affairs Hospital, Dermatology, Ann Arbor, MI, United States
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente, Oakland, CA, United States
| | - Stephen Leslie
- Melbourne Integrative Genomics, The University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
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34
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He M, Zheng ZZ, He QQ, Li DY, Liao KZ, An L, Weng Q, Wang NJ, Wang LP, Sun Q, Wang J, Xiao PL, Du KM, Jiang M. Distribution of killer cell immunoglobulin-like receptor (KIR) genes in a large, multi-centre cohort of Chinese donors. Ann Hum Biol 2021; 48:133-141. [PMID: 34097546 DOI: 10.1080/03014460.2021.1913223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND The killer cell immunoglobulin-like receptor (KIR), which mediates the killing function of NK cells, is an attractive candidate for adoptive cellular therapy. The ethnic distribution for China provides a unique opportunity to investigate KIR gene distribution. AIM The aim of this study was to explore the relationship between population history and the rapidly evolving KIR genetic diversity. SUBJECTS AND METHODS 8050 Chinese donors from 184 hospitals were included to analyse frequency, haplotype, and B-content data of 16 KIR genes, by PCR-SSP for KIR genotyping. RESULTS KIR gene carrier frequencies were found similar to those observed in other studies on Han, but different from Thais, Japanese, Africans, and populations of West Eurasian ancestry. High-frequency KIR genotype profiles found in the present population were consistent with other studies on Han populations but different from those conducted on other cohorts. The majority of our cohort carried group A KIR gene motifs. Additionally, populations with similar geographic locations in China were shown clustered together, while Hainan and Xinjiang provinces were slightly separated from these. CONCLUSION The distribution of KIR genes varies by geographic region, and different ethnic groups may be a confounding factor of KIR diversity.
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Affiliation(s)
- Min He
- Hematologic Disease Center, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Xinjiang Uygur Autonomous Region Research Institute of Hematology, Urumqi, China
| | | | - Qing-Qing He
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Dai-Yang Li
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Kuan-Zhen Liao
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Lin An
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Qi Weng
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Ning-Juan Wang
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Li-Ping Wang
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Qin Sun
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Jian Wang
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Pei-Li Xiao
- Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China
| | - Ke-Ming Du
- Xinjiang Uygur Autonomous Region Research Institute of Hematology, Urumqi, China
| | - Ming Jiang
- Hematologic Disease Center, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Xinjiang Uygur Autonomous Region Research Institute of Hematology, Urumqi, China
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35
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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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36
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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: 17] [Impact Index Per Article: 5.7] [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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37
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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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38
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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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39
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Yin Y, Butler C, Zhang Q. Challenges in the application of NGS in the clinical laboratory. Hum Immunol 2021; 82:812-819. [PMID: 33892986 DOI: 10.1016/j.humimm.2021.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS), also known as massively parallel sequencing, has revolutionized genomic research. The current advances in NGS technology make it possible to provide high resolution, high throughput HLA typing in clinical laboratories. The focus of this review is on the recent development and implementation of NGS in clinical laboratories. Here, we examine the critical role of NGS technologies in clinical immunology for HLA genotyping. Two major NGS platforms (Illumina and Ion Torrent) are characterized including NGS library preparation, data analysis, and validation. Challenges of NGS implementation in the clinical laboratory are also discussed, including sequencing error rate, bioinformatics, result interpretation, analytic sensitivity, as well as large data storage. This review aims to promote the broader applications of NGS technology in clinical laboratories and advocate for the novel applications of NGS to drive future research.
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Affiliation(s)
- Yuxin Yin
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Carrie Butler
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Qiuheng Zhang
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA.
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40
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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: 4] [Impact Index Per Article: 1.3] [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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41
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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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42
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Brown NK, Merkens H, Rozemuller EH, Bell D, Bui TM, Kearns J. Reduced PCR-generated errors from a hybrid capture-based NGS assay for HLA typing. Hum Immunol 2021; 82:296-301. [PMID: 33676750 DOI: 10.1016/j.humimm.2021.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/28/2022]
Abstract
Next generation sequencing (NGS) assays are state of the art for HLA genotyping. To sequence on an Illumina sequencer, the DNA of interest must be enriched, fragmented, and bookended with known oligonucleotide sequences, a process known as library construction. Many HLA genotyping assays enrich the target loci by long-range PCR (LR-PCR), prior to fragmentation. This PCR step has been reported to introduce errors in the DNA to be sequenced, including inaccurate replication of repeated sequences, and the in vitro recombination of alleles encoded on separate chromosomes. An alternative library construction method involves fragmentation of genomic DNA, followed by hybrid-capture (HC) enrichment of target HLA loci. This HC-based method involves PCR, but with far fewer cycles. Consequently, the HC method had significantly fewer PCR-induced errors, including more faithful replication of repeated sequences, and the near elimination of recombinant sequences. These improvements likely produce more accurate NGS sequencing data of HLA loci.
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Affiliation(s)
- Nicholas K Brown
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | | | | | - Derrick Bell
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Thanh-Mai Bui
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jane Kearns
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
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43
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Weiss E, Andrade HS, Lara JR, Souza AS, Paz MA, Lima THA, Porto IOP, S B Silva N, Castro CFB, Grotto RMT, Donadi EA, Mendes-Junior CT, Castelli EC. KIR2DL4 genetic diversity in a Brazilian population sample: implications for transcription regulation and protein diversity in samples with different ancestry backgrounds. Immunogenetics 2021; 73:227-241. [PMID: 33595694 DOI: 10.1007/s00251-021-01206-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 11/30/2022]
Abstract
KIR2DL4 is an important immune modulator expressed in natural killer cells; HLA-G is its main ligand. We have characterized the KIR2DL4 genetic diversity by considering the promoter, all exons, and all introns in a highly admixed Brazilian population sample and by using massively parallel sequencing. We introduce a molecular method to amplify and to sequence the complete KIR2DL4 gene. To avoid the mapping bias and genotype errors commonly observed in gene families, we have developed and validated a bioinformatic pipeline designed to minimize these errors and applied it to survey the variability of 220 individuals from the State of São Paulo, southeastern Brazil. We have also compared the KIR2DL4 genetic diversity in the Brazilian cohort with the diversity previously reported by the 1000Genomes consortium. KIR2DL4 presents high linkage disequilibrium throughout the gene, with coding sequences associated with specific promoters. There are few but divergent promoter haplotypes. We have also detected many new KIR2DL4 sequences, all bearing nucleotide exchanges in introns and encoding previously described proteins. Exons 3 and 4, which encode the external domains, are the most variable. The ancestry background influences the KIR2DL4 allele frequencies and must be considered for association studies regarding KIR2DL4.
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Affiliation(s)
- Emiliana Weiss
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Heloisa S Andrade
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Juliana Rodrigues Lara
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Nayane S B Silva
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Camila F Bannwart Castro
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Rejane M T Grotto
- Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,School of Agronomical Sciences, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Eduardo A Donadi
- Department of Medicine, Ribeirão, Preto Medical School, University of São Paulo (USP), Ribeirao Preto, State of Sao Paulo, Brazil
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências E Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil. .,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil. .,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.
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44
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Dilthey AT. State-of-the-art genome inference in the human MHC. Int J Biochem Cell Biol 2021; 131:105882. [PMID: 33189874 DOI: 10.1016/j.biocel.2020.105882] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/20/2022]
Abstract
The Major Histocompatibility Complex (MHC) on the short arm of chromosome 6 is associated with more diseases than any other region of the genome; it encodes the antigen-presenting Human Leukocyte Antigen (HLA) proteins and is one of the key immunogenetic regions of the genome. Accurate genome inference and interpretation of MHC association signals have traditionally been hampered by the region's uniquely complex features, such as high levels of polymorphism; inter-gene sequence homologies; structural variation; and long-range haplotype structures. Recent algorithmic and technological advances have, however, significantly increased the accessibility of genetic variation in the MHC; these developments include (i) accurate SNP-based HLA type imputation; (ii) genome graph approaches for variation-aware genome inference from next-generation sequencing data; (iii) long-read-based diploid de novo assembly of the MHC; (iv) cost-effective targeted MHC sequencing methods. Applied to hundreds of thousands of samples over the last years, these technologies have already enabled significant biological discoveries, for example in the field of autoimmune disease genetics. Remaining challenges concern the development of integrated methods that leverage haplotype-resolved de novo assembly of the MHC for the development of improved MHC genotyping methods for short reads and the construction of improved reference panels for SNP-based imputation. Improved genome inference in the MHC can crucially contribute to an improved genetic and functional understanding of many immune-related phenotypes and diseases.
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Affiliation(s)
- Alexander T Dilthey
- Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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45
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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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46
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Roe D, Kuang R. Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures. Front Immunol 2020; 11:583013. [PMID: 33324401 PMCID: PMC7727328 DOI: 10.3389/fimmu.2020.583013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
The killer-cell immunoglobulin-like receptor (KIR) proteins evolve to fight viruses and mediate the body's reaction to pregnancy. These roles provide selection pressure for variation at both the structural/haplotype and base/allele levels. At the same time, the genes have evolved relatively recently by tandem duplication and therefore exhibit very high sequence similarity over thousands of bases. These variation-homology patterns make it impossible to interpret KIR haplotypes from abundant short-read genome sequencing data at population scale using existing methods. Here, we developed an efficient computational approach for in silico KIR probe interpretation (KPI) to accurately interpret individual's KIR genes and haplotype-pairs from KIR sequencing reads. We designed synthetic 25-base sequence probes by analyzing previously reported haplotype sequences, and we developed a bioinformatics pipeline to interpret the probes in the context of 16 KIR genes and 16 haplotype structures. We demonstrated its accuracy on a synthetic data set as well as a real whole genome sequences from 748 individuals from The Genome of the Netherlands (GoNL). The GoNL predictions were compared with predictions from SNP-based predictions. Our results show 100% accuracy rate for the synthetic tests and a 99.6% family-consistency rate in the GoNL tests. Agreement with the SNP-based calls on KIR genes ranges from 72%-100% with a mean of 92%; most differences occur in genes KIR2DS2, KIR2DL2, KIR2DS3, and KIR2DL5 where KPI predicts presence and the SNP-based interpretation predicts absence. Overall, the evidence suggests that KPI's accuracy is 97% or greater for both KIR gene and haplotype-pair predictions, and the presence/absence genotyping leads to ambiguous haplotype-pair predictions with 16 reference KIR haplotype structures. KPI is free, open, and easily executable as a Nextflow workflow supported by a Docker environment at https://github.com/droeatumn/kpi.
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Affiliation(s)
- David Roe
- Bioinformatics and Computational Biology, University of Minnesota, Rochester, MN, United States
| | - Rui Kuang
- Bioinformatics and Computational Biology, University of Minnesota, Rochester, MN, United States
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
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47
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Ureshino H, Shindo T, Tanaka H, Saji H, Kimura S. HLA Polymorphisms Are Associated with Treatment-Free Remission Following Discontinuation of Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia. Mol Cancer Ther 2020; 20:142-149. [PMID: 33082274 DOI: 10.1158/1535-7163.mct-20-0336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/31/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
Treatment-free remission (TFR) is one of the therapeutic goals for patients with chronic phase chronic myeloid leukemia (CML-CP). Although previous reports indicated that antitumor immunity contributes to TFR, its determinants are still unclear. We previously reported that allelic polymorphisms of killer immunoglobulin-like receptors (KIR) and human leukocyte antigens (HLA) are associated with achievement of deep molecular response (DMR) in patients with CML-CP. Here, we examined the association between TFR and polymorphisms of KIRs and HLAs in patients who discontinued tyrosine kinase inhibitors (TKI). Seventy-six patients were enrolled, and their KIR and HLA polymorphisms and natural killer (NK) cell activation status were investigated as previously described. Overall, 33 patients discontinued TKIs, and 21 of 33 achieved TFR [63.6%; 95% confidence interval (CI), 44.9%-77.5%] at 1 year. Multivariate analysis revealed that male sex (HR, 0.157; 95% CI, 0.031-0.804; P = 0.003) and HLA-A*02:01, *11:01, or *24:02 (HR, 6.386; 95% CI, 1.701-23.980; P = 0.006) were associated with TFR. Patients who achieved DMR and discontinued TKIs exhibited higher NK cell activation status than those who did not. By contrast, there were no significant differences in NK cell activation status between the patients who achieved TFR and those who experienced molecular relapse. These results suggest NK cell activation status contributes to achievement of DMR, whereas T-cell-mediated immunity contributes to TFR in patients with CML-CP.
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Affiliation(s)
- Hiroshi Ureshino
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Saga University, Saga, Japan. .,Department of Drug Discovery and Biomedical Sciences, Saga University, Saga, Japan
| | - Takero Shindo
- Department of Hematology and Oncology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | | | - Shinya Kimura
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Saga University, Saga, Japan.,Department of Drug Discovery and Biomedical Sciences, Saga University, Saga, Japan
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48
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Roe D, Williams J, Ivery K, Brouckaert J, Downey N, Locklear C, Kuang R, Maiers M. Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes. Front Immunol 2020; 11:582927. [PMID: 33162997 PMCID: PMC7581912 DOI: 10.3389/fimmu.2020.582927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/17/2020] [Indexed: 12/04/2022] Open
Abstract
The homology, recombination, variation, and repetitive elements in the natural killer-cell immunoglobulin-like receptor (KIR) region has made full haplotype DNA interpretation impossible in a high-throughput workflow. Here, we present a new approach using long-read sequencing to efficiently capture, sequence, and assemble diploid human KIR haplotypes. Probes were designed to capture KIR fragments efficiently by leveraging the repeating homology of the region. IDT xGen® Lockdown probes were used to capture 2-8 kb of sheared DNA fragments followed by sequencing on a PacBio Sequel. The sequences were error corrected, binned, and then assembled using the Canu assembler. The location of genes and their exon/intron boundaries are included in the workflow. The assembly and annotation was evaluated on 16 individuals (8 African American and 8 Europeans) from whom ground truth was known via long-range sequencing with fosmid library preparation. Using only 18 capture probes, the results show that the assemblies cover 97% of the GenBank reference, are 99.97% concordant, and it takes only 1.8 haplotigs to cover 75% of the reference. We also report the first assembly of diploid KIR haplotypes from long-read WGS. Our targeted hybridization probe capture and sequencing approach is the first of its kind to fully sequence and phase all diploid human KIR haplotypes, and it is efficient enough for population-scale studies and clinical use. The open and free software is available at https://github.com/droeatumn/kass and supported by a environment at https://hub.docker.com/repository/docker/droeatumn/kass.
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Affiliation(s)
- David Roe
- Bioinformatics and Computational Biology, University of Minnesota, Rochester, MN, United States
| | - Jonathan Williams
- DNA Identification Testing Division, Laboratory Corporation of America Holdings, Burlington, NC, United States
| | - Keyton Ivery
- DNA Identification Testing Division, Laboratory Corporation of America Holdings, Burlington, NC, United States
| | - Jenny Brouckaert
- DNA Identification Testing Division, Laboratory Corporation of America Holdings, Burlington, NC, United States
| | - Nick Downey
- Integrated DNA Technologies, Inc., Coralville, IA, United States
| | - Chad Locklear
- Integrated DNA Technologies, Inc., Coralville, IA, United States
| | - Rui Kuang
- Bioinformatics and Computational Biology, University of Minnesota, Rochester, MN, United States
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Martin Maiers
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
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49
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Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, Deikus G, Auckland K, Eichler EE, Marasco WA, Sebra R, Sharp AJ, Smith ML, Bashir A, Watson CT. A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Front Immunol 2020; 11:2136. [PMID: 33072076 PMCID: PMC7539625 DOI: 10.3389/fimmu.2020.02136] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
An incomplete ascertainment of genetic variation within the highly polymorphic immunoglobulin heavy chain locus (IGH) has hindered our ability to define genetic factors that influence antibody-mediated processes. Due to locus complexity, standard high-throughput approaches have failed to accurately and comprehensively capture IGH polymorphism. As a result, the locus has only been fully characterized two times, severely limiting our knowledge of human IGH diversity. Here, we combine targeted long-read sequencing with a novel bioinformatics tool, IGenotyper, to fully characterize IGH variation in a haplotype-specific manner. We apply this approach to eight human samples, including a haploid cell line and two mother-father-child trios, and demonstrate the ability to generate high-quality assemblies (>98% complete and >99% accurate), genotypes, and gene annotations, identifying 2 novel structural variants and 15 novel IGH alleles. We show multiplexing allows for scaling of the approach without impacting data quality, and that our genotype call sets are more accurate than short-read (>35% increase in true positives and >97% decrease in false-positives) and array/imputation-based datasets. This framework establishes a desperately needed foundation for leveraging IG genomic data to study population-level variation in antibody-mediated immunity, critical for bettering our understanding of disease risk, and responses to vaccines and therapeutics.
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Affiliation(s)
- Oscar L Rodriguez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - William S Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matthew Emery
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - James Powell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Maya Strahl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States
| | - Wayne A Marasco
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Icahn Institute of Data Science and Genomic Technology, New York, NY, United States
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States.,Icahn Institute of Data Science and Genomic Technology, New York, NY, United States
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
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50
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Chen J, Madireddi S, Nagarkar D, Migdal M, Vander Heiden J, Chang D, Mukhyala K, Selvaraj S, Kadel EE, Brauer MJ, Mariathasan S, Hunkapiller J, Jhunjhunwala S, Albert ML, Hammer C. In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales. Brief Bioinform 2020; 22:5906908. [PMID: 32940337 PMCID: PMC8138874 DOI: 10.1093/bib/bbaa223] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Immunogenetic variation in humans is important in research, clinical diagnosis and increasingly a target for therapeutic intervention. Two highly polymorphic loci play critical roles, namely the human leukocyte antigen (HLA) system, which is the human version of the major histocompatibility complex (MHC), and the Killer-cell immunoglobulin-like receptors (KIR) that are relevant for responses of natural killer (NK) and some subsets of T cells. Their accurate classification has typically required the use of dedicated biological specimens and a combination of in vitro and in silico efforts. Increased availability of next generation sequencing data has led to the development of ancillary computational solutions. Here, we report an evaluation of recently published algorithms to computationally infer complex immunogenetic variation in the form of HLA alleles and KIR haplotypes from whole-genome or whole-exome sequencing data. For both HLA allele and KIR gene typing, we identified tools that yielded >97% overall accuracy for four-digit HLA types, and >99% overall accuracy for KIR gene presence, suggesting the readiness of in silico solutions for use in clinical and high-throughput research settings.
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Affiliation(s)
- Jieming Chen
- Department of Bioinformatics and Computational Biology
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