51
|
Development of data-driven models for the flow cytometric crossmatch. Hum Immunol 2019; 80:983-989. [PMID: 31530432 DOI: 10.1016/j.humimm.2019.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/13/2019] [Accepted: 09/05/2019] [Indexed: 01/08/2023]
Abstract
HLA laboratories use virtual crossmatching (VXM) to predict recipient and donor compatibility using HLA antibody data and donor HLA type. Increasingly, transplant centers are utilizing VXM as the final compatibility determination prior to transplant. However, the VXM interpretation is based on HLA experience of individual transplant centers. This study developed data-driven algorithms that predicted flow cytometric crossmatch (FCXM) outcomes using HLA antibody mean fluorescent intensity (MFI) data and donor HLA typing without the need for human interpretation.Two algorithms were evaluated; an MFI Optimal-Threshold model and a Least-Squares-Fitting model. The Optimal-Threshold model correctly determined between 81.5% and 85.5% of T or B-cell responses. A class I antibody MFI threshold of 4670 was optimal for predicting T-cell response while an antibody MFI threshold of 6180 was optimal for predicting B-cell responses. HLA class I antibodies had a 1.47-fold greater influence on FCXM outcomes than class II antibodies. HLA-B antibodies influenced T and B-cell responses more than HLA-A or -C (-B > -A > -C). The Least-Squares-Fitting model increased accuracy to 94.1% and 88.8% for T and B-cell responses, respectively. The algorithms described here provide enhanced FCXM prediction and novel insights into the influence of specific HLA antibodies on the crossmatch outcome.
Collapse
|
52
|
Fürst D, Neuchel C, Tsamadou C, Schrezenmeier H, Mytilineos J. HLA Matching in Unrelated Stem Cell Transplantation up to Date. Transfus Med Hemother 2019; 46:326-336. [PMID: 31832058 DOI: 10.1159/000502263] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/13/2019] [Indexed: 12/27/2022] Open
Abstract
Unrelated hematopoietic stem cell transplantation (HSCT) has evolved from an experimental protocol to a potentially curative first-line treatment in certain disease instances. Factors enabling this transformation were the optimization of treatment protocols and supportive care as well as the availability of a large number of donors worldwide along with the higher quality and reliability of HLA typing. The main criterion for donor selection is HLA compatibility. In this review we discuss the current clinical evidence of HLA matching in unrelated HSCT. In this context, we address methodical aspects of transplantation immunobiology research and discuss the impact of locus and resolution of HLA differences. Furthermore, we address special constellations such as unidirectional mismatches or the presence of nonexpressed alleles as well as HLA alloimmunization and describe the perspective for HLA typing and matching strategies in the future, given the implementation of novel complete or near-complete gene typing approaches using next-generation sequencing short read technology, which are now entering the standard of clinical care.
Collapse
Affiliation(s)
- Daniel Fürst
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christine Neuchel
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Chrysanthi Tsamadou
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Joannis Mytilineos
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| |
Collapse
|
53
|
Selection of unrelated donors and cord blood units for hematopoietic cell transplantation: guidelines from the NMDP/CIBMTR. Blood 2019; 134:924-934. [PMID: 31292117 PMCID: PMC6753623 DOI: 10.1182/blood.2019001212] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/24/2019] [Indexed: 01/01/2023] Open
Abstract
Allogeneic hematopoietic cell transplantation involves consideration of both donor and recipient characteristics to guide the selection of a suitable graft. Sufficient high-resolution donor-recipient HLA match is of primary importance in transplantation with adult unrelated donors, using conventional graft-versus-host disease prophylaxis. In cord blood transplantation, optimal unit selection requires consideration of unit quality, cell dose and HLA-match. In this summary, the National Marrow Donor Program (NMDP) and the Center for International Blood and Marrow Transplant Research, jointly with the NMDP Histocompatibility Advisory Group, provide evidence-based guidelines for optimal selection of unrelated donors and cord blood units.
Collapse
|
54
|
Carey BS, Poulton KV, Poles A. Factors affecting HLA expression: A review. Int J Immunogenet 2019; 46:307-320. [PMID: 31183978 DOI: 10.1111/iji.12443] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022]
Abstract
The detection and semiquantitative measurement of circulating human leucocyte antigen (HLA)-specific antibodies is essential for the management of patients before and after transplantation. In addition, the pretransplant cross-match to assess the reactivity of recipient HLA antibody against donor lymphocytes has long been the gold standard to prevent hyperacute rejection. Whilst both of these tests assume that recipient HLA-specific antibody is the only variable in the assessment of transplant risk, this is not the case. Transplant immunologists recognize that some HLA antigens are expressed at levels a magnitude lower than others (e.g., HLA-C, HLA-DQ), but within loci, and between different cell types there are many factors that influence HLA expression in both resting and activated cells. HLA is not usually expressed without the specific promoter proteins NLRC5, for HLA class I, and CIITA, for class II. The quantity of HLA protein production is then affected by factors including promoter region polymorphisms, alternative exon splice sites, methylation and microRNA-directed degradation. Different loci are influenced by multiple combinations of these control mechanisms making prediction of HLA regulation difficult, but an ability to measure the cellular expression of each HLA antigen, in conjunction with knowledge of circulating HLA-specific antibody, would lead to a more informed algorithm to assess transplant risk.
Collapse
Affiliation(s)
- B Sean Carey
- Histocompatibility and Immunogenetics, Combined Laboratory, University Hospitals Plymouth, Plymouth, UK
| | | | - Anthony Poles
- Histocompatibility and Immunogenetics, Combined Laboratory, University Hospitals Plymouth, Plymouth, UK
| |
Collapse
|
55
|
Balgansuren G, Regen L, Sprague M, Shelton N, Petersdorf E, Hansen JA. Identification of the rs9277534 HLA-DP expression marker by next generation sequencing for the selection of unrelated donors for hematopoietic cell transplantation. Hum Immunol 2019; 80:828-833. [PMID: 31176504 DOI: 10.1016/j.humimm.2019.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/10/2019] [Accepted: 05/23/2019] [Indexed: 11/18/2022]
Abstract
Mismatching of an unrelated donor against a high-expression HLA-DPB1 recipient allele is associated with a high risk of graft-versus-host disease and mortality. The Seattle Cancer Care Alliance (SCCA) and Fred Hutchinson Cancer Research Center transplant program employs an algorithm to match for HLA-A, B, C, DRB1, DQB1 and DPB1 alleles (12/12) and to avoid, whenever possible, donor mismatching against a recipient high-expression HLA-DPB1 allele. HLA-DPB1 expression is associated with the rs9277534 A/G polymorphism located in the 3'UTR of the HLA-DPB1 gene. Next generation sequencing of HLA-DPB1 using the Illumina TruSight HLA V2 Sequencing Panel and Conexio Assign software analyses provides information on rs9277534 variants without the need for any additional SNP testing. Here we present the molecular location of rs9277534 in NGS data and discuss the challenges to resolve HLA-DPB1 ambiguities.
Collapse
Affiliation(s)
- Gansuvd Balgansuren
- Clinical Immunogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA, USA; University of Washington, Seattle, WA, USA.
| | - Lois Regen
- Clinical Immunogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Maggie Sprague
- Clinical Immunogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Nakita Shelton
- Clinical Immunogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Effie Petersdorf
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA; University of Washington, Seattle, WA, USA
| | - John A Hansen
- Clinical Immunogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA; University of Washington, Seattle, WA, USA
| |
Collapse
|
56
|
Integrate CRISPR/Cas9 for protein expression of HLA-B*38:68Q via precise gene editing. Sci Rep 2019; 9:8067. [PMID: 31147565 PMCID: PMC6542842 DOI: 10.1038/s41598-019-44336-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/14/2019] [Indexed: 11/16/2022] Open
Abstract
The determination of null- or low-expressed HLA alleles is clinically relevant in both hematopoietic stem cell transplantation and solid organ transplantation. We studied the expression level of a questionable (Q) HLA-B*38:68Q allele, which carries a 9-nucleotide (nt) deletion at codon 230–232 in exon 4 of HLA-B*38:01:01:01 using CRISPR/Cas9 gene editing technology. CRISPR/Cas9 gene editing of HLA-B*38:01:01:01 homozygous EBV B cell line resulted in one HLA-B*38:68Q/B*38:01:01:01 heterozygous and one HLA-B*38:68Q homozygous clone. Flow cytometric analysis of monoclonal anti-Bw4 antibody showed the protein expression of HLA-B*38:01:01:01 in homozygous cells was 2.2 fold higher than HLA-B*38:68Q/B*38:01:01:01 heterozygous cells, and the expression of HLA-B*38:68Q/B*38:01:01:01 heterozygous cells was over 2.0 fold higher than HLA-B*38:68Q homozygous cells. The HLA-B*38:68Q expression was further confirmed using anti-B38 polyclonal antibody. Similarly, the expression of the HLA-B*38:01:01:01 homozygous cells was 1.5 fold higher than that of HLA-B*38:68Q/B*38:01:01:01 heterozygous cells, and the HLA-B*38:68Q/B*38:01:01:01 heterozygous cells was over 1.6 fold higher than that of HLA-B*38:68Q homozygous cells. The treatment of HLA-B*38:68Q homozygous cells with IFN-γ significantly increased its expression. In conclusion, we demonstrate that HLA-B*38:68Q is a low-expressing HLA allele. The CRISPR/Cas9 technology is a useful tool to induce precise gene editing in HLA genes to enable the characterization of HLA gene variants on expression and function.
Collapse
|
57
|
Aguiar VRC, César J, Delaneau O, Dermitzakis ET, Meyer D. Expression estimation and eQTL mapping for HLA genes with a personalized pipeline. PLoS Genet 2019; 15:e1008091. [PMID: 31009447 PMCID: PMC6497317 DOI: 10.1371/journal.pgen.1008091] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 05/02/2019] [Accepted: 03/13/2019] [Indexed: 01/07/2023] Open
Abstract
The HLA (Human Leukocyte Antigens) genes are well-documented targets of balancing selection, and variation at these loci is associated with many disease phenotypes. Variation in expression levels also influences disease susceptibility and resistance, but little information exists about the regulation and population-level patterns of expression. This results from the difficulty in mapping short reads originated from these highly polymorphic loci, and in accounting for the existence of several paralogues. We developed a computational pipeline to accurately estimate expression for HLA genes based on RNA-seq, improving both locus-level and allele-level estimates. First, reads are aligned to all known HLA sequences in order to infer HLA genotypes, then quantification of expression is carried out using a personalized index. We use simulations to show that expression estimates obtained in this way are not biased due to divergence from the reference genome. We applied our pipeline to the GEUVADIS dataset, and compared the quantifications to those obtained with reference transcriptome. Although the personalized pipeline recovers more reads, we found that using the reference transcriptome produces estimates similar to the personalized pipeline (r ≥ 0.87) with the exception of HLA-DQA1. We describe the impact of the HLA-personalized approach on downstream analyses for nine classical HLA loci (HLA-A, HLA-C, HLA-B, HLA-DRA, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). Although the influence of the HLA-personalized approach is modest for eQTL mapping, the p-values and the causality of the eQTLs obtained are better than when the reference transcriptome is used. We investigate how the eQTLs we identified explain variation in expression among lineages of HLA alleles. Finally, we discuss possible causes underlying differences between expression estimates obtained using RNA-seq, antibody-based approaches and qPCR. The level at which a gene is expressed can have important influence on the phenotype of an organism, including its predisposition to develop diseases. One way to estimate gene expression is by quantifying the abundance of RNA. RNA-seq has become the method of choice to provide such estimates at the genomewide scale. However, the application of RNA-seq to HLA genes —key players in the immune adaptive response— has remained a rarely explored approach. This is due to the problem of mapping bias, which causes deficient read alignment at genes which are very polymorphic and different from the reference genome. This has motivated approaches that replace the single reference genome with personalized sequences, comprised of the individual’s specific HLA genotype. Here we explore the use of computational frameworks to obtain reliable expression levels for HLA genes from RNA-seq datasets. We present a pipeline in which the quantification of HLA expression is carried out using methods which account for HLA diversity, avoiding the biases of standard approaches. We then evaluate the impact of this form of quantifying HLA expression on downstream analyses. The pipeline also allows us to integrate information on eQTLs with expression levels at the HLA allele-level, which can help disentangle different contributions to disease phenotypes and help understand the regulatory architecture at the HLA region.
Collapse
Affiliation(s)
- Vitor R. C. Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (VRCA); (DM)
| | - Jônatas César
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Olivier Delaneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (VRCA); (DM)
| |
Collapse
|
58
|
Hurley CK, Ng J. Continue to focus clinical decision-making on the antigen recognition domain for the present. Hum Immunol 2019; 80:79-84. [DOI: 10.1016/j.humimm.2018.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/10/2018] [Accepted: 04/15/2018] [Indexed: 02/04/2023]
|
59
|
Shieh M, Chitnis N, Clark P, Johnson FB, Kamoun M, Monos D. Computational assessment of miRNA binding to low and high expression HLA-DPB1 allelic sequences. Hum Immunol 2019; 80:53-61. [DOI: 10.1016/j.humimm.2018.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/27/2018] [Accepted: 09/12/2018] [Indexed: 12/31/2022]
|
60
|
Petersdorf EW, O'hUigin C. The MHC in the era of next-generation sequencing: Implications for bridging structure with function. Hum Immunol 2019; 80:67-78. [PMID: 30321633 PMCID: PMC6542361 DOI: 10.1016/j.humimm.2018.10.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/24/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022]
Abstract
The MHC continues to have the most disease-associations compared to other regions of the human genome, even in the genome-wide association study (GWAS) and single nucleotide polymorphism (SNP) era. Analysis of non-coding variation and their impact on the level of expression of HLA allotypes has shed new light on the potential mechanisms underlying HLA disease associations and alloreactivity in transplantation. Next-generation sequencing (NGS) technology has the capability of delineating the phase of variants in the HLA antigen-recognition site (ARS) with non-coding regulatory polymorphisms. These relationships are critical for understanding the qualitative and quantitative implications of HLA gene diversity. This article summarizes current understanding of non-coding region variation of HLA loci, the consequences of regulatory variation on HLA expression, the role for evolution in shaping lineage-specific expression, and the impact of HLA expression on disease susceptibility and transplantation outcomes. A role for phased sequencing methods for the MHC, and perspectives for future directions in basic and applied immunogenetic studies of the MHC are presented.
Collapse
Affiliation(s)
- Effie W Petersdorf
- University of Washington, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, D4-115, Seattle, WA 98109, United States.
| | - Colm O'hUigin
- Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Microbiome and Genetics Core, Building 37, Room 4140B, Bethesda, MD 20852, United States.
| |
Collapse
|
61
|
|
62
|
Allen ES, Yang B, Garrett J, Ball ED, Maiers M, Morris GP. Improved accuracy of clinical HLA genotyping by next-generation DNA sequencing affects unrelated donor search results for hematopoietic stem cell transplantation. Hum Immunol 2018; 79:848-854. [DOI: 10.1016/j.humimm.2018.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/10/2018] [Accepted: 10/10/2018] [Indexed: 11/24/2022]
|
63
|
Fleischhauer K, Hsu KC, Shaw BE. Prevention of relapse after allogeneic hematopoietic cell transplantation by donor and cell source selection. Bone Marrow Transplant 2018; 53:1498-1507. [PMID: 29795435 PMCID: PMC7286200 DOI: 10.1038/s41409-018-0218-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/16/2018] [Accepted: 03/24/2018] [Indexed: 01/27/2023]
Abstract
Allogeneic hematopoietic cell transplantation (HCT) is the most established form of cancer immunotherapy and has been successfully applied for the treatment and cure of otherwise lethal neoplastic blood disorders. Cancer immune surveillance is mediated to a large extent by alloreactive T and natural killer (NK) cells recognizing genetic differences between patient and donor. Profound insights into the biology of these effector cells has been obtained over recent years and used for the development of innovative strategies for intelligent donor selection, aiming for improved graft-versus-leukemia effect without unmanageable graft-versus-host disease. The cellular composition of the stem cell source plays a major role in modulating these effects. This review summarizes the current state-of the-art of donor selection according to HLA, NK alloreactivity and stem cell source.
Collapse
Affiliation(s)
- Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany.
- German Cancer Consortium, Heidelberg, Germany.
| | - Katharine C Hsu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology Program, Sloan Kettering Institute, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Bronwen E Shaw
- Center for International Blood and Marrow Transplant Research (CIBMTR), Froedtert & the Medical College of Wisconsin, Milwaukee, WI, USA.
| |
Collapse
|
64
|
Meurer T, Arrieta-Bolaños E, Metzing M, Langer MM, van Balen P, Falkenburg JHF, Beelen DW, Horn PA, Fleischhauer K, Crivello P. Dissecting Genetic Control of HLA-DPB1 Expression and Its Relation to Structural Mismatch Models in Hematopoietic Stem Cell Transplantation. Front Immunol 2018; 9:2236. [PMID: 30344521 PMCID: PMC6183238 DOI: 10.3389/fimmu.2018.02236] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/10/2018] [Indexed: 11/22/2022] Open
Abstract
HLA expression levels have been suggested to be genetically controlled by single nucleotide polymorphisms (SNP) in the untranslated regions (UTR), and expression variants have been associated with the outcome of chronic viral infection and hematopoietic stem cell transplantation (HSCT). In particular, the 3′UTR rs9277534-G/A SNP in HLA-DPB1 has been associated with graft-versus-host-disease after HSCT (Expression model); however its relevance in different immune cells and its mode of action have not been systematically addressed. In addition, there is a strong though not complete overlap between the rs9277534-G/A SNP and structural HLA-DPB1 T cell epitope (TCE) groups which have also been associated with HSCT outcome (TCE Structural model). Here we confirm and extend previous findings of significantly higher HLA-DPB1 expression in B cell lines, unstimulated primary B cells, and monocytes homozygous for rs9277534-G compared to those homozygous for rs9277534-A. However, these differences were abrogated by interferon-γ stimulation or differentiation into dendritic cells. We identify at least seven 3′UTR rs9277534-G/A haplotypes differing by a total of 37 SNP, also characterized by linkage to length variants of a short tandem repeat (STR) in intron 2 and TCE group assignment. 3′UTR mapping did not show any significant differences in post-transcriptional regulation assessed by luciferase assays between two representative rs9277534-G/A haplotypes for any of eight overlapping fragments. Moreover, no evidence for alternative splicing associated with the intron 2 STR was obtained by RT-PCR. In an exemplary cohort of 379 HLA-DPB1 mismatched donor-recipient pairs, risk prediction by the Expression model and the Structural TCE model was 36.7% concordant, with the majority of discordances due to non-applicability of the Expression model. HLA-DPB1 from different TCE groups expressed in the absence of the 3′UTR at similar levels by transfected HeLa cells elicited significantly different mean alloreactive CD4+ T-cell responses, as assessed by CD137 upregulation assays in 178 independent cultures. Taken together, our data provide new insights into the cell type-specific and mechanistic basis of the association between the rs9277534-G/A SNP and HLA-DPB1 expression, and show that, despite partial overlap between both models in HSCT risk-prediction, differential alloreactivity determined by the TCE structural model occurs independently from HLA-DPB1 differential expression.
Collapse
Affiliation(s)
- Thuja Meurer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | | | - Maximilian Metzing
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Mona-May Langer
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Dietrich W Beelen
- Department of Bone Marrow Transplantation, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany.,Deusches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| | - Pietro Crivello
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| |
Collapse
|
65
|
Kelly A, Trowsdale J. Genetics of antigen processing and presentation. Immunogenetics 2018; 71:161-170. [PMID: 30215098 PMCID: PMC6394470 DOI: 10.1007/s00251-018-1082-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/24/2018] [Indexed: 12/31/2022]
Abstract
Immune response to disease requires coordinated expression of an army of molecules. The highly polymorphic MHC class I and class II molecules are key to control of specificity of antigen presentation. Processing of the antigen, to peptides or other moieties, requires other sets of molecules. For classical class I, this includes TAP peptide transporters, proteasome components and Tapasin, genes which are encoded within the MHC. Similarly, HLA-DO and -DM, which influence presentation by HLA class II molecules, are encoded in the MHC region. Analysis of MHC mutants, including point mutations and large deletions, has been central to understanding the roles of these genes. Mouse genetics has also played a major role. Many other genes have been identified including those controlling expression of HLA class I and class II at the transcriptional level. Another genetic approach that has provided insight has been the analysis of microorganisms, including viruses and bacteria that escape immune recognition by blocking these antigen processing and presentation pathways. Here, we provide a brief history of the genetic approaches, both traditional and modern, that have been used in the quest to understand antigen processing and presentation.
Collapse
Affiliation(s)
- Adrian Kelly
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK
| | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK.
| |
Collapse
|
66
|
Habets THPM, Hepkema BG, Kouprie N, Schnijderberg MCA, van Smaalen TC, Bungener LB, Christiaans MHL, Bos GMJ, Vanderlocht J. The prevalence of antibodies against the HLA-DRB3 protein in kidney transplantation and the correlation with HLA expression. PLoS One 2018; 13:e0203381. [PMID: 30192820 PMCID: PMC6128541 DOI: 10.1371/journal.pone.0203381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 08/20/2018] [Indexed: 11/29/2022] Open
Abstract
Human leukocyte antigen (HLA)-DRB3 is a functional HLA class II gene, which has a limited allele diversity in the human population. Furthermore, the HLA-DRB3 gene is only present in a subset of individuals. Therefore, in organ transplantation, this HLA molecule is frequently mismatched between patient and graft donor and thus antibodies against this mismatched HLA molecule can develop. In this study, we aimed to evaluate the prevalence and reactivity of these antibodies and aimed to identify factors that underlie antibody formation against HLA-DRB3. We showed in our patient cohort that HLA-DRB3 antibodies are identified in about 7% of all patients that were screened with solid phase assays. In these assays, we observed multiple antibody reactivity patterns indicating that HLA-DRB3 harbours multiple epitopes. In those cases, where we succeeded at tracing back the induction of these antibodies to the molecular HLA typing of the immunogenic event, we noticed a different frequency of HLA-DRB1 allele groups in the donors as compared to a control group. To a certain extent this distribution (e.g. HLA-DRB1*11 individuals) could be linked to an altered expression level. However, it also appears that different HLA-DRB3 alleles (e.g. HLA-DRB3*01 group) vary in their immunogenicity without having an expression difference. In conclusion, our study provides information on the immunogenicity and reactivity patterns of antibodies against HLA-DRB3 in kidney transplantation, and it points towards the possibility of HLA expression as a factor underlying antibody formation.
Collapse
Affiliation(s)
- Thomas H. P. M. Habets
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center +, Maastricht, The Netherlands
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center +, Maastricht, The Netherlands
| | - Bouke G. Hepkema
- Transplantation Immunology, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Niels Kouprie
- Transplantation Immunology, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Melanie C. A. Schnijderberg
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center +, Maastricht, The Netherlands
| | - Tim C. van Smaalen
- Department of Surgery, Maastricht University Medical Center +, Maastricht, The Netherlands
| | - Laura B. Bungener
- Transplantation Immunology, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten H. L. Christiaans
- Department of Internal Medicine, Division of Nephrology, Maastricht University Medical Center +, Maastricht, The Netherlands
| | - Gerard M. J. Bos
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center +, Maastricht, The Netherlands
- CiMaas BV, Maastricht, The Netherlands
| | - Joris Vanderlocht
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center +, Maastricht, The Netherlands
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center +, Maastricht, The Netherlands
- Central Diagnostic Laboratory, Maastricht University Medical Center +, Maastricht, The Netherlands
- * E-mail:
| |
Collapse
|
67
|
Petersdorf EW. In celebration of Ruggero Ceppellini: HLA in transplantation. HLA 2018; 89:71-76. [PMID: 28102037 DOI: 10.1111/tan.12955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/19/2016] [Indexed: 12/17/2022]
Abstract
The availability of hematopoietic cell transplantation as curative therapy for blood disorders has been dramatically improved through a better understanding of the human leukocyte antigen (HLA) barrier. Although a fully compatible unrelated donor is preferable, transplantation from donors with a limited degree of HLA mismatching is associated with acceptable outcomes in many cases. Research on the limits of HLA mismatching, and the features that define permissible HLA mismatches will continue to enable transplantation to be more broadly available to patients in need.
Collapse
Affiliation(s)
- E W Petersdorf
- Fred Hutchinson Cancer Research Center, Division of Clinical Research, Seattle, Washington
| |
Collapse
|
68
|
Tie R, Zhang T, Yang B, Fu H, Han B, Yu J, Tan Y, Huang H. Clinical implications of HLA locus mismatching in unrelated donor hematopoietic cell transplantation: a meta-analysis. Oncotarget 2018; 8:27645-27660. [PMID: 28206973 PMCID: PMC5432365 DOI: 10.18632/oncotarget.15291] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 01/26/2017] [Indexed: 01/10/2023] Open
Abstract
It remains controversial that the impacts of individual HLA locus mismatches on clinical outcomes of patients receiving unrelated-donor hematopoietic cell transplantation (HCT), as compared to HLA allele matched controls. We conducted a meta-analysis to address these issues. Four databases (PubMed, Embase, Web of Science and the Cochrane Library) were searched to select eligible studies. All donor-recipient pairs were high-resolution typing for HLA-A, -B, -C, -DRB1, DQB1 and DPB1 loci. Multivariate-adjusted hazard ratios (HRs) were extracted and pooled using a random-effects model. A total of 36 studies were included, with 100,072 patients receiving HCT. Surprisingly, we found that HLA-DQB1 locus mismatches had no significantly increased risk of multiple outcomes including acute and chronic graft-versus-host disease (GVHD), overall mortality and disease relapse (HR, 1.07; P = .153; HR, 1.07; P = .271; HR, 1.09; P = .230; HR, 1.07; P = .142 and HR, 1.02; P = .806, respectively). Mismatched HLA-DPB1 was significantly associated with a reduced risk of disease relapse (HR, 0.74; P < .001) but not with increased risks of transplant-related mortality (TRM) and overall mortality (HR, 1.09; P = .591; I2 = 74.2% and HR, 1.03; P = .460, respectively). In conclusion, HLA-DQB1 locus mismatches is a permissive mismatching. HLA-DPB1 locus mismatches significantly protect against leukemia relapse. Refining effects of individual HLA locus mismatches contributes to predicting prognosis of patients receiving unrelated donor HCT.
Collapse
Affiliation(s)
- Ruxiu Tie
- Bone Marrow Transplantation Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Tiansong Zhang
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital, Shanghai, China
| | - Bo Yang
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Huarui Fu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Biqing Han
- Bone Marrow Transplantation Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jian Yu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yamin Tan
- Bone Marrow Transplantation Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
69
|
Bertaina A, Andreani M. Major Histocompatibility Complex and Hematopoietic Stem Cell Transplantation: Beyond the Classical HLA Polymorphism. Int J Mol Sci 2018; 19:E621. [PMID: 29470425 PMCID: PMC5855843 DOI: 10.3390/ijms19020621] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/11/2018] [Accepted: 02/20/2018] [Indexed: 01/11/2023] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) represents a curative treatment for many patients with hematological malignant or non-malignant disorders. Evaluation of potential donors for HSCT includes a rigorous assessment of the human leukocyte antigens (HLA) match status of family members, and the identification of suitable unrelated donors. Genes encoding transplantation antigens are placed both within and outside the major histocompatibility complex (MHC). The human MHC is located on the short arm of chromosome 6 and contains a series of genes encoding two distinct types of highly polymorphic cell surface glycoproteins. Donors for HSCT are routinely selected based on the level of matching for HLA-A, -B, -C, -DRB1, and -DQB1 loci. However, disease relapse, graft-versus-host-disease, and infection remain significant risk factors of morbidity and mortality. In the same breath, in high-risk patients, graft-versus-leukemia effects inherent in HLA mismatching play a substantial immunological role to limit the recurrence of post-transplant disease. The definition of a suitable donor is ever changing, shaped not only by current typing technology, but also by the specific transplant procedure. Indeed, a more complete understanding of permissible HLA mismatches and the role of Killer Immunoglobulin-like receptors' genes increases the availability of HLA-haploidentical and unrelated donors.
Collapse
Affiliation(s)
- Alice Bertaina
- Department of Pediatric Hematology and Oncology, IRCCS, Ospedale Bambino Gesu', 00165 Rome, Italy.
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, 00133 Rome, Italy.
| |
Collapse
|
70
|
Geneugelijk K, Spierings E. Matching donor and recipient based on predicted indirectly recognizable human leucocyte antigen epitopes. Int J Immunogenet 2018; 45:41-53. [PMID: 29464898 DOI: 10.1111/iji.12359] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/21/2017] [Accepted: 02/01/2018] [Indexed: 12/27/2022]
Abstract
The predicted indirectly recognizable human leucocyte antigen (HLA) epitopes (PIRCHE) algorithm is a novel in silico algorithm to determine donor-recipient compatibility. The PIRCHE algorithm determines donor-recipient compatibility by counting the number of mismatched HLA-derived epitopes that are involved in indirect T-cell alloimmune responses; these epitopes are designated as PIRCHE. Over the last few years, the PIRCHE algorithm has been investigated in both hematopoietic stem cell transplantation and solid organ transplantation. This review describes the theory of the algorithm, its application in transplantation, and highlights the future perspectives on the clinical application of the PIRCHE algorithm.
Collapse
Affiliation(s)
- K Geneugelijk
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - E Spierings
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| |
Collapse
|
71
|
Development of an Unrelated Donor Selection Score Predictive of Survival after HCT: Donor Age Matters Most. Biol Blood Marrow Transplant 2018; 24:1049-1056. [PMID: 29454040 DOI: 10.1016/j.bbmt.2018.02.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/08/2018] [Indexed: 12/23/2022]
Abstract
Donor factors, in addition to HLA matching status, have been associated with recipient survival in unrelated donor (URD) hematopoietic cell transplantation (HCT); however, there is no hierarchical algorithm that weights the characteristics of individual donors against each other in a quantitative manner to facilitate donor selection. The goal of this study was to develop and validate a donor selection score that prioritizes donor characteristics associated with better survival in 8/8 HLA-matched URDs. Two separate patient/donor cohorts, the first receiving HCT between 1999 and 2011 (n = 5952, c1), and the second between 2012 and 2014 (n = 4510, c2) were included in the analysis. Both cohorts were randomly spilt, 2:1, into training and testing sets. Despite studying over 10,000 URD transplants, we were unable to validate a donor selection score. The only donor characteristic associated with better survival was younger age, with 2-year survival being 3% better when a donor 10 years younger is selected. These results support previous studies suggesting prioritization of a younger 8/8 HLA-matched donor. This large dataset also shows that none of the other donor clinical factors tested were reproducibly associated with survival, and hence flexibility in selecting URDs based on other characteristics is justified. These data support a simplified URD selection process and have significant implications for URD registries.
Collapse
|
72
|
Ramsuran V, Naranbhai V, Horowitz A, Qi Y, Martin MP, Yuki Y, Gao X, Walker-Sperling V, Del Prete GQ, Schneider DK, Lifson JD, Fellay J, Deeks SG, Martin JN, Goedert JJ, Wolinsky SM, Michael NL, Kirk GD, Buchbinder S, Haas D, Ndung'u T, Goulder P, Parham P, Walker BD, Carlson JM, Carrington M. Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells. Science 2018; 359:86-90. [PMID: 29302013 PMCID: PMC5933048 DOI: 10.1126/science.aam8825] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 10/16/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022]
Abstract
The highly polymorphic human leukocyte antigen (HLA) locus encodes cell surface proteins that are critical for immunity. HLA-A expression levels vary in an allele-dependent manner, diversifying allele-specific effects beyond peptide-binding preference. Analysis of 9763 HIV-infected individuals from 21 cohorts shows that higher HLA-A levels confer poorer control of HIV. Elevated HLA-A expression provides enhanced levels of an HLA-A–derived signal peptide that specifically binds and determines expression levels of HLA-E, the ligand for the inhibitory NKG2A natural killer (NK) cell receptor. HLA-B haplotypes that favor NKG2A-mediated NK cell licensing (i.e., education) exacerbate the deleterious effect of high HLA-A on HIV control, consistent with NKG2A-mediated inhibition impairing NK cell clearance of HIV-infected targets. Therapeutic blockade of HLA-E:NKG2A interaction may yield benefit in HIV disease.
Collapse
Affiliation(s)
- Veron Ramsuran
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.,KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Vivek Naranbhai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Maureen P Martin
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yuko Yuki
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Victoria Walker-Sperling
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Douglas K Schneider
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Steven G Deeks
- Department of Medicine University of California, San Francisco, CA 94143, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143, USA
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Susan Buchbinder
- Department of Medicine University of California, San Francisco, CA 94143, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143, USA.,San Francisco Department of Public Health, HIV Research Section, San Francisco, CA 94102, USA
| | - David Haas
- Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.,African Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Philip Goulder
- African Health Research Institute, Durban, South Africa.,Department of Paediatrics, University of Oxford, Oxford, UK
| | - Peter Parham
- Departments of Structural Biology and Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.,African Health Research Institute, Durban, South Africa.,Institute for Medical and Engineering Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA. .,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| |
Collapse
|
73
|
Dendrou CA, Petersen J, Rossjohn J, Fugger L. HLA variation and disease. Nat Rev Immunol 2018; 18:325-339. [PMID: 29292391 DOI: 10.1038/nri.2017.143] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fifty years since the first description of an association between HLA and human disease, HLA molecules have proven to be central to physiology, protective immunity and deleterious, disease-causing autoimmune reactivity. Technological advances have enabled pivotal progress in the determination of the molecular mechanisms that underpin the association between HLA genetics and functional outcome. Here, we review our current understanding of HLA molecules as the fundamental platform for immune surveillance and responsiveness in health and disease. We evaluate the scope for personalized antigen-specific disease prevention, whereby harnessing HLA-ligand interactions for clinical benefit is becoming a realistic prospect.
Collapse
Affiliation(s)
- Calliope A Dendrou
- Nuffield Department of Medicine, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jan Petersen
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Lars Fugger
- Danish National Research Foundation Centre PERSIMUNE, Rigshospitalet, University of Copenhagen, Copenhagen DK-2100, Denmark.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| |
Collapse
|
74
|
Petersdorf EW, Anasetti C. Unrelated Donor Hematopoietic Cell Transplantation. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
75
|
Pan N, Lu S, Wang W, Miao F, Sun H, Wu S, Nan D, Qiu J, Xu J, Zhang J. Quantification of classical HLA class I mRNA by allele-specific, real-time polymerase chain reaction for most Han individuals. HLA 2017; 91:112-123. [PMID: 29178661 DOI: 10.1111/tan.13186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 12/29/2022]
Abstract
Recent studies have shown that expression levels of different alleles at the same HLA class I locus can vary dramatically, which might have a broad influence on human disease. However, precise quantification of the relative expression level of each HLA allele is challenging, because distinguishing different alleles on the same locus is difficult. Here, we developed a series of allele-specific, real-time polymerase chain reaction assays for quantifying HLA class I allele mRNA in most Han individuals. The alleles of almost all heterozygous genotypes with a frequency higher than 0.5% in our population (78 alleles on HLA-A locus, 124 alleles on HLA-B locus, and 74 alleles on HLA-C locus) were specifically amplified. The specificity of the amplification was strictly validated by setting the corresponding negative control for each allele of each genotype. The amplification efficiency of each reaction was determined, and the slopes of the reactions were compared. This study provides a tool for detecting the comprehensive expression profile of HLA class I alleles and will be useful not only for the investigation of the molecular mechanism underlying HLA allele expression regulation but also for exploration of immunological mechanisms involving HLA expression in the fields of tumour immune evasion, viral infection, auto-immune disorders, and graft vs host disease after haematopoietic stem cell transplantation.
Collapse
Affiliation(s)
- N Pan
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - S Lu
- Center of Liver Transplantation, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - W Wang
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - F Miao
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - H Sun
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - S Wu
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China.,Stem Cells and Regenerative Medicine Key Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - D Nan
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - J Qiu
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China.,The Second Affiliated Hospital of Southeast University, Nanjing, China
| | - J Xu
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China.,Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
| | - J Zhang
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| |
Collapse
|
76
|
Koparde V, Abdul Razzaq B, Suntum T, Sabo R, Scalora A, Serrano M, Jameson-Lee M, Hall C, Kobulnicky D, Sheth N, Feltz J, Contaifer D, Wijesinghe D, Reed J, Roberts C, Qayyum R, Buck G, Neale M, Toor A. Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation. PLoS One 2017; 12:e0187771. [PMID: 29194460 PMCID: PMC5711034 DOI: 10.1371/journal.pone.0187771] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/25/2017] [Indexed: 12/01/2022] Open
Abstract
Quantitative relationship between the magnitude of variation in minor histocompatibility antigens (mHA) and graft versus host disease (GVHD) pathophysiology in stem cell transplant (SCT) donor-recipient pairs (DRP) is not established. In order to elucidate this relationship, whole exome sequencing (WES) was performed on 27 HLA matched related (MRD), & 50 unrelated donors (URD), to identify nonsynonymous single nucleotide polymorphisms (SNPs). An average 2,463 SNPs were identified in MRD, and 4,287 in URD DRP (p<0.01); resulting peptide antigens that may be presented on HLA class I molecules in each DRP were derived in silico (NetMHCpan ver2.0) and the tissue expression of proteins these were derived from determined (GTex). MRD DRP had an average 3,670 HLA-binding-alloreactive peptides, putative mHA (pmHA) with an IC50 of <500 nM, and URD, had 5,386 (p<0.01). To simulate an alloreactive donor cytotoxic T cell response, the array of pmHA in each patient was considered as an operator matrix modifying a hypothetical cytotoxic T cell clonal vector matrix; each responding T cell clone’s proliferation was determined by the logistic equation of growth, accounting for HLA binding affinity and tissue expression of each alloreactive peptide. The resulting simulated organ-specific alloreactive T cell clonal growth revealed marked variability, with the T cell count differences spanning orders of magnitude between different DRP. Despite an estimated, uniform set of constants used in the model for all DRP, and a heterogeneously treated group of patients, higher total and organ-specific T cell counts were associated with cumulative incidence of moderate to severe GVHD in recipients. In conclusion, exome wide sequence differences and the variable alloreactive peptide binding to HLA in each DRP yields a large range of possible alloreactive donor T cell responses. Our findings also help understand the apparent randomness observed in the development of alloimmune responses.
Collapse
Affiliation(s)
- Vishal Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Badar Abdul Razzaq
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Tara Suntum
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Roy Sabo
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Allison Scalora
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Myrna Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Max Jameson-Lee
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Charles Hall
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - David Kobulnicky
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Nihar Sheth
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Juliana Feltz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Daniel Contaifer
- School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Dayanjan Wijesinghe
- School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Catherine Roberts
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Rehan Qayyum
- Section of Hospital Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Gregory Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael Neale
- Departments of Psychiatry and Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Amir Toor
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
| |
Collapse
|
77
|
Petersdorf EW. Which factors influence the development of GVHD in HLA-matched or mismatched transplants? Best Pract Res Clin Haematol 2017; 30:333-335. [PMID: 29156205 PMCID: PMC5967625 DOI: 10.1016/j.beha.2017.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The sheer diversity of HLA alleles makes the probability of finding matched unrelated donors for patients requiring hematopoietic cell transplantation (HCT) a complex situation. New evidence suggests that mismatching at certain HLA loci may provide a greater benefit in terms of graft-versus-leukemia effect than other mismatches when HLA-matched donors are not available. This review summarizes the current understanding of HLA matching requirements for unrelated donor HCT.
Collapse
Affiliation(s)
- Effie W Petersdorf
- University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA; Fred Hutchinson Cancer Research Center, Division of Clinical Research, 1100 Fairview Ave North, Seattle, WA 98109, USA.
| |
Collapse
|
78
|
Kulkarni S, Ramsuran V, Rucevic M, Singh S, Lied A, Kulkarni V, O'hUigin C, Le Gall S, Carrington M. Posttranscriptional Regulation of HLA-A Protein Expression by Alternative Polyadenylation Signals Involving the RNA-Binding Protein Syncrip. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:3892-3899. [PMID: 29055006 PMCID: PMC5812486 DOI: 10.4049/jimmunol.1700697] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/25/2017] [Indexed: 01/15/2023]
Abstract
Genomic variation in the untranslated region (UTR) has been shown to influence HLA class I expression level and associate with disease outcomes. Sequencing of the 3'UTR of common HLA-A alleles indicated the presence of two polyadenylation signals (PAS). The proximal PAS is conserved, whereas the distal PAS is disrupted within certain alleles by sequence variants. Using 3'RACE, we confirmed expression of two distinct forms of the HLA-A 3'UTR based on use of either the proximal or the distal PAS, which differ in length by 100 bp. Specific HLA-A alleles varied in the usage of the proximal versus distal PAS, with some alleles using only the proximal PAS, and others using both the proximal and distal PAS to differing degrees. We show that the short and the long 3'UTR produced similar mRNA expression levels. However, the long 3'UTR conferred lower luciferase activity as compared with the short form, indicating translation inhibition of the long 3'UTR. RNA affinity pull-down followed by mass spectrometry analysis as well as RNA coimmunoprecipitation indicated differential binding of Syncrip to the long versus short 3'UTR. Depletion of Syncrip by small interfering RNA increased surface expression of an HLA-A allotype that uses primarily the long 3'UTR, whereas an allotype expressing only the short form was unaffected. Furthermore, specific blocking of the proximal 3'UTR reduced surface expression without decreasing mRNA expression. These data demonstrate HLA-A allele-specific variation in PAS usage, which modulates their cell surface expression posttranscriptionally.
Collapse
Affiliation(s)
- Smita Kulkarni
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139;
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Veron Ramsuran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
- Centre for the AIDS Programme of Research in South Africa, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; and
| | | | - Sukhvinder Singh
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Alexandra Lied
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Viraj Kulkarni
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Colm O'hUigin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| |
Collapse
|
79
|
Identification of novel polymorphisms and two distinct haplotype structures in dog leukocyte antigen class I genes: DLA-88, DLA-12 and DLA-64. Immunogenetics 2017; 70:237-255. [DOI: 10.1007/s00251-017-1031-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/19/2017] [Indexed: 12/14/2022]
|
80
|
Shared peptide binding of HLA Class I and II alleles associate with cutaneous nevirapine hypersensitivity and identify novel risk alleles. Sci Rep 2017; 7:8653. [PMID: 28819312 PMCID: PMC5561238 DOI: 10.1038/s41598-017-08876-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/05/2017] [Indexed: 11/08/2022] Open
Abstract
Genes of the human leukocyte antigen (HLA) system encode cell-surface proteins involved in regulation of immune responses, and the way drugs interact with the HLA peptide binding groove is important in the immunopathogenesis of T-cell mediated drug hypersensitivity syndromes. Nevirapine (NVP), is an HIV-1 antiretroviral with treatment-limiting hypersensitivity reactions (HSRs) associated with multiple class I and II HLA alleles. Here we utilize a novel analytical approach to explore these multi-allelic associations by systematically examining HLA molecules for similarities in peptide binding specificities and binding pocket structure. We demonstrate that primary predisposition to cutaneous NVP HSR, seen across ancestral groups, can be attributed to a cluster of HLA-C alleles sharing a common binding groove F pocket with HLA-C*04:01. An independent association with a group of class II alleles which share the HLA-DRB1-P4 pocket is also observed. In contrast, NVP HSR protection is afforded by a cluster of HLA-B alleles defined by a characteristic peptide binding groove B pocket. The results suggest drug-specific interactions within the antigen binding cleft can be shared across HLA molecules with similar binding pockets. We thereby provide an explanation for multiple HLA associations with cutaneous NVP HSR and advance insight into its pathogenic mechanisms.
Collapse
|
81
|
What compatibility in 2017 for the haematopoietic stem cell transplantation? Transfus Clin Biol 2017; 24:124-130. [PMID: 28709842 DOI: 10.1016/j.tracli.2017.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 12/25/2022]
Abstract
The diversification of potential donors to perform stem cell allografts now enables to propose a compatible graft cell source adapted to the different clinical situations. Transplants with a geno-identical sibling donor, otherwise with the most HLA-compatible unrelated donor, remain the first-line solutions. Alternative transplants allow to graft patients having no donors in international registries, owing to the rarity of their HLA typing. They are carried out with fairly incompatible grafts and are therefore limited by the existence in the recipient of preformed anti-HLA antibodies which predispose to their rejection. The simple prevention of acute Graft-versus-host disease in haplo-identical transplants, as well as the availability of donors, explain why they have very often replaced placental stem cell transplants. These latter remain useful for pediatric patients or in the absence of family donors.
Collapse
|
82
|
Kaur G, Gras S, Mobbs JI, Vivian JP, Cortes A, Barber T, Kuttikkatte SB, Jensen LT, Attfield KE, Dendrou CA, Carrington M, McVean G, Purcell AW, Rossjohn J, Fugger L. Structural and regulatory diversity shape HLA-C protein expression levels. Nat Commun 2017; 8:15924. [PMID: 28649982 PMCID: PMC5490200 DOI: 10.1038/ncomms15924] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 05/12/2017] [Indexed: 12/14/2022] Open
Abstract
Expression of HLA-C varies widely across individuals in an allele-specific manner. This variation in expression can influence efficacy of the immune response, as shown for infectious and autoimmune diseases. MicroRNA binding partially influences differential HLA-C expression, but the additional contributing factors have remained undetermined. Here we use functional and structural analyses to demonstrate that HLA-C expression is modulated not just at the RNA level, but also at the protein level. Specifically, we show that variation in exons 2 and 3, which encode the α1/α2 domains, drives differential expression of HLA-C allomorphs at the cell surface by influencing the structure of the peptide-binding cleft and the diversity of peptides bound by the HLA-C molecules. Together with a phylogenetic analysis, these results highlight the diversity and long-term balancing selection of regulatory factors that modulate HLA-C expression.
Collapse
Affiliation(s)
- Gurman Kaur
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Stephanie Gras
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Jesse I. Mobbs
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Julian P. Vivian
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Adrian Cortes
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Barber
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Subita Balaram Kuttikkatte
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Lise Torp Jensen
- Department of Clinical Medicine, Aarhus University Hospital, 8200N Aarhus, Denmark
| | - Kathrine E. Attfield
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Calliope A. Dendrou
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
| | - Anthony W. Purcell
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Lars Fugger
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Department of Clinical Medicine, Aarhus University Hospital, 8200N Aarhus, Denmark
| |
Collapse
|
83
|
Maniangou B, Legrand N, Alizadeh M, Guyet U, Willem C, David G, Charpentier E, Walencik A, Retière C, Gagne K. Killer Immunoglobulin-Like Receptor Allele Determination Using Next-Generation Sequencing Technology. Front Immunol 2017; 8:547. [PMID: 28579987 PMCID: PMC5437120 DOI: 10.3389/fimmu.2017.00547] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/24/2017] [Indexed: 02/05/2023] Open
Abstract
The impact of natural killer (NK) cell alloreactivity on hematopoietic stem cell transplantation (HSCT) outcome is still debated due to the complexity of graft parameters, HLA class I environment, the nature of killer cell immunoglobulin-like receptor (KIR)/KIR ligand genetic combinations studied, and KIR+ NK cell repertoire size. KIR genes are known to be polymorphic in terms of gene content, copy number variation, and number of alleles. These allelic polymorphisms may impact both the phenotype and function of KIR+ NK cells. We, therefore, speculate that polymorphisms may alter donor KIR+ NK cell phenotype/function thus modulating post-HSCT KIR+ NK cell alloreactivity. To investigate KIR allele polymorphisms of all KIR genes, we developed a next-generation sequencing (NGS) technology on a MiSeq platform. To ensure the reliability and specificity of our method, genomic DNA from well-characterized cell lines were used; high-resolution KIR typing results obtained were then compared to those previously reported. Two different bioinformatic pipelines were used allowing the attribution of sequencing reads to specific KIR genes and the assignment of KIR alleles for each KIR gene. Our results demonstrated successful long-range KIR gene amplifications of all reference samples using intergenic KIR primers. The alignment of reads to the human genome reference (hg19) using BiRD pipeline or visualization of data using Profiler software demonstrated that all KIR genes were completely sequenced with a sufficient read depth (mean 317× for all loci) and a high percentage of mapping (mean 93% for all loci). Comparison of high-resolution KIR typing obtained to those published data using exome capture resulted in a reported concordance rate of 95% for centromeric and telomeric KIR genes. Overall, our results suggest that NGS can be used to investigate the broad KIR allelic polymorphism. Hence, these data improve our knowledge, not only on KIR+ NK cell alloreactivity in HSCT but also on the role of KIR+ NK cell populations in control of viral infections and diseases.
Collapse
Affiliation(s)
- Bercelin Maniangou
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Nolwenn Legrand
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Mehdi Alizadeh
- Laboratoire de Recherche et Développement, EFS Rennes, Rennes, France
| | - Ulysse Guyet
- L'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Catherine Willem
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Gaëlle David
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | | | | | - Christelle Retière
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Katia Gagne
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France.,Laboratoire d'Histocompatibilité, EFS Nantes, Nantes, France.,LabeX Transplantex, Université de Strasbourg, Strasbourg, France
| |
Collapse
|
84
|
Petersdorf EW. Role of major histocompatibility complex variation in graft-versus-host disease after hematopoietic cell transplantation. F1000Res 2017; 6:617. [PMID: 28529723 PMCID: PMC5419254 DOI: 10.12688/f1000research.10990.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 01/01/2023] Open
Abstract
Graft-versus-host disease (GVHD) remains a significant potentially life-threatening complication of allogeneic hematopoietic cell transplantation (HCT). Since the discovery of the human leukocyte antigen (HLA) system over 50 years ago, significant advances have clarified the nature of HLA variation between transplant recipients and donors as a chief etiology of GVHD. New information on coding and non-coding gene variation and GVHD risk provides clinicians with options to consider selected mismatched donors when matched donors are not available. These advances have increased the availability of unrelated donors for patients in need of a transplant and have lowered the overall morbidity and mortality of HCT.
Collapse
|
85
|
Bogunia-Kubik K, Łacina P. From genetic single candidate gene studies to complex genomics of GvHD. Br J Haematol 2017; 178:661-675. [DOI: 10.1111/bjh.14704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
- Laboratory of Tissue Immunology; Medical Centre; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
| |
Collapse
|
86
|
Ramsuran V, Hernández-Sanchez PG, O'hUigin C, Sharma G, Spence N, Augusto DG, Gao X, García-Sepúlveda CA, Kaur G, Mehra NK, Carrington M. Sequence and Phylogenetic Analysis of the Untranslated Promoter Regions for HLA Class I Genes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 198:2320-2329. [PMID: 28148735 PMCID: PMC5340644 DOI: 10.4049/jimmunol.1601679] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/02/2017] [Indexed: 01/09/2023]
Abstract
Polymorphisms located within the MHC have been linked to many disease outcomes by mechanisms not yet fully understood in most cases. Variants located within untranslated regions of HLA genes are involved in allele-specific expression and may therefore underlie some of these disease associations. We determined sequences extending nearly 2 kb upstream of the transcription start site for 68 alleles from 57 major lineages of classical HLA class I genes. The nucleotide diversity within this promoter segment roughly follows that seen within the coding regions, with HLA-B showing the highest (∼1.9%), followed by HLA-A (∼1.8%), and HLA-C showing the lowest diversity (∼0.9%). Despite its greater diversity, HLA-B mRNA expression levels determined in 178 European Americans do not vary in an allele- or lineage-specific manner, unlike the differential expression levels of HLA-A or HLA-C reported previously. Close proximity of promoter sequences in phylogenetic trees is roughly reflected by similarity of expression pattern for most HLA-A and -C loci. Although promoter sequence divergence might impact promoter activity, we observed no clear link between the phylogenetic structures as represented by pairwise nucleotide differences in the promoter regions with estimated differences in mRNA expression levels for the classical class I loci. Further, no pair of class I loci showed coordinated expression levels, suggesting that distinct mechanisms across loci determine their expression level under nonstimulated conditions. These data serve as a foundation for more in-depth analysis of the functional consequences of promoter region variation within the classical HLA class I loci.
Collapse
Affiliation(s)
- Veron Ramsuran
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Pedro G Hernández-Sanchez
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina de la Universidad Autónoma de San Luis Potosi, 78210 San Luis Potosi, Mexico
| | - Colm O'hUigin
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Gaurav Sharma
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi 110029, India
- Laboratory Oncology, Dr. B.R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi 110029, India; and
| | - Niamh Spence
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
- Laboratory Oncology, Dr. B.R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi 110029, India; and
| | - Danillo G Augusto
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, CEP 81531-980, Brazil
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Christian A García-Sepúlveda
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina de la Universidad Autónoma de San Luis Potosi, 78210 San Luis Potosi, Mexico
| | - Gurvinder Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Narinder K Mehra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702;
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| |
Collapse
|
87
|
Caillat-Zucman S. New insights into the understanding of MHC associations with immune-mediated disorders. HLA 2016; 89:3-13. [DOI: 10.1111/tan.12947] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- S. Caillat-Zucman
- Laboratoire d'Immunologie et Histocompatibilité; Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Diderot; Paris France
| |
Collapse
|
88
|
Pharmacokinetics, Pharmacodynamics and Pharmacogenomics of Immunosuppressants in Allogeneic Haematopoietic Cell Transplantation: Part I. Clin Pharmacokinet 2016; 55:525-50. [PMID: 26563168 DOI: 10.1007/s40262-015-0339-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although immunosuppressive treatments and target concentration intervention (TCI) have significantly contributed to the success of allogeneic haematopoietic cell transplantation (alloHCT), there is currently no consensus on the best immunosuppressive strategies. Compared with solid organ transplantation, alloHCT is unique because of the potential for bidirectional reactions (i.e. host-versus-graft and graft-versus-host). Postgraft immunosuppression typically includes a calcineurin inhibitor (cyclosporine or tacrolimus) and a short course of methotrexate after high-dose myeloablative conditioning, or a calcineurin inhibitor and mycophenolate mofetil after reduced-intensity conditioning. There are evolving roles for the antithymyocyte globulins (ATGs) and sirolimus as postgraft immunosuppression. A review of the pharmacokinetics and TCI of the main postgraft immunosuppressants is presented in this two-part review. All immunosuppressants are characterized by large intra- and interindividual pharmacokinetic variability and by narrow therapeutic indices. It is essential to understand immunosuppressants' pharmacokinetic properties and how to use them for individualized treatment incorporating TCI to improve outcomes. TCI, which is mandatory for the calcineurin inhibitors and sirolimus, has become an integral part of postgraft immunosuppression. TCI is usually based on trough concentration monitoring, but other approaches include measurement of the area under the concentration-time curve (AUC) over the dosing interval or limited sampling schedules with maximum a posteriori Bayesian personalization approaches. Interpretation of pharmacodynamic results is hindered by the prevalence of studies enrolling only a small number of patients, variability in the allogeneic graft source and variability in postgraft immunosuppression. Given the curative potential of alloHCT, the pharmacodynamics of these immunosuppressants deserves to be explored in depth. Development of sophisticated systems pharmacology models and improved TCI tools are needed to accurately evaluate patients' exposure to drugs in general and to immunosuppressants in particular. Sequential studies, first without and then with TCI, should be conducted to validate the clinical benefit of TCI in homogenous populations; randomized trials are not feasible, because there are higher-priority research questions in alloHCT. In Part I of this article, we review the alloHCT process to facilitate optimal design of pharmacokinetic and pharmacodynamics studies. We also review the pharmacokinetics and TCI of calcineurin inhibitors and methotrexate.
Collapse
|
89
|
Bettens F, Buhler S, Tiercy JM. Allorecognition of HLA-C Mismatches by CD8 + T Cells in Hematopoietic Stem Cell Transplantation Is a Complex Interplay between Mismatched Peptide-Binding Region Residues, HLA-C Expression, and HLA-DPB1 Disparities. Front Immunol 2016; 7:584. [PMID: 28018351 PMCID: PMC5151176 DOI: 10.3389/fimmu.2016.00584] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
HLA-C locus mismatches (MMs) are the most frequent class I disparities in unrelated hematopoietic stem cell transplantation (HSCT) and have a detrimental impact on clinical outcome. Recently, a few retrospective clinical studies have reported some variability in the immunogenicity of HLA-C incompatibilities. To get better insight into presumably permissive HLA-C MMs, we have developed a one-way in vitro mixed lymphocyte reaction (MLR) assay allowing to quantify activated CD56-CD137+CD8+ lymphocytes in HLA-C incompatible combinations. T cell-mediated alloresponses were correlated with genetic markers such as HLA-C mRNA expression and the number of amino acid (aa) MMs in the α1/α2 domains (peptide-binding region). Because of the high rate of HLA-DPB1 incompatibilities in HLA-A-, B-, C-, DRB1-, and DQB1-matched unrelated HSCT patient/donor pairs, the impact of HLA-DPB1 mismatching, a potential bystander of CD4+ T cell activation, was also considered. Heterogeneous alloresponses were measured in 63 HLA-C-mismatched pairs with a positive assay in 52% of the combinations (2.3-18.6% activated CTLs), representing 24 different HLA-A~B~DRB1~DQB1 haplotypes. There was no correlation between measured alloresponses and mRNA expression of the mismatched HLA-C alleles. The HLA-C*03:03/03:04 MM did not induce any positive alloresponse in five MLRs. We also identified HLA-C*02:02 and HLA-C*06:02 as mismatched alleles with lower immunogenicity, and HLA-C*14:02 as a more immunogenic MM. A difference of at least 10 aa residues known to impact peptide/T cell receptor (TCR) binding and a bystander HLA-DPB1 incompatibility had a significant impact on CTL alloreactivity (p = 0.021). The same HLA-C MM, when recognized by two different responders with the same HLA haplotypes, was recognized differently, emphasizing the role of the T-cell repertoire of responding cells. In conclusion, mismatched HLA-C alleles differing by 10 or more aas in the peptide/TCR-binding region, when occurring together with HLA-DPB1 incompatibilities, should be considered as high-risk MMs in unrelated HSCT.
Collapse
Affiliation(s)
- Florence Bettens
- National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, University Hospitals Geneva , Geneva , Switzerland
| | - Stéphane Buhler
- National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, University Hospitals Geneva , Geneva , Switzerland
| | - Jean-Marie Tiercy
- National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, University Hospitals Geneva , Geneva , Switzerland
| |
Collapse
|
90
|
Dellgren C, Ekwelum VAC, Ormhøj M, Pallesen N, Knudsen J, Nehlin JO, Barington T. Low Constitutive Cell Surface Expression of HLA-B Is Caused by a Posttranslational Mechanism Involving Glu180 and Arg239. THE JOURNAL OF IMMUNOLOGY 2016; 197:4807-4816. [PMID: 27821669 DOI: 10.4049/jimmunol.1502546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 10/11/2016] [Indexed: 12/18/2022]
Abstract
HLA class I cell surface expression is crucial for normal immune responses, and variability in HLA expression may influence the course of infections. We have previously shown that classical HLA class I expression on many human cell types is biased with greatly reduced expression of HLA-B compared with HLA-A in the absence of inflammatory signals. In the search for the mechanisms responsible for this discrepancy, we have recently reported that the regulation is mainly posttranslational and that the C-terminal part of the α2 domain and the α3 domain contain the molecular determinants that explain most of the variability of expression between common HLA-A and -B allomorphs. In this study, we present a fine mapping of the structural determinants that allow such variability by exchanging key amino acids located within the C-terminal part of the α2 domain and the α3 domain of HLA-A2 and -B8, including Glu/Asp at position 177, Gln/Glu at position 180, Gly/Arg at position 239, and Pro/Ser at position 280. We found that the HLA-A2 and -B8 expression profiles could be interconverted to a large extent by mutual exchange of Gln/Glu at position 180 or by Gly/Arg at position 239. The presence of Gln180 and Gly239, as in HLA-A2, led to higher cell surface expression levels when compared with the presence of Glu180 and Arg239, as in HLA-B8. This indicates that the amino acids at positions 180 and 239 determine the level of cell surface expression of common HLA-A and -B allomorphs, probably by affecting HLA processing in the Ag presentation pathway.
Collapse
Affiliation(s)
- Christoffer Dellgren
- Department of Clinical Immunology, Odense University Hospital, 5000 Odense, Denmark
| | - Vanessa A C Ekwelum
- Department of Clinical Immunology, Odense University Hospital, 5000 Odense, Denmark
| | - Maria Ormhøj
- Department of Clinical Immunology, Odense University Hospital, 5000 Odense, Denmark
| | - Nicole Pallesen
- Department of Clinical Immunology, Odense University Hospital, 5000 Odense, Denmark
| | - Julie Knudsen
- Department of Clinical Immunology, Odense University Hospital, 5000 Odense, Denmark
| | - Jan O Nehlin
- Department of Clinical Immunology, Odense University Hospital, 5000 Odense, Denmark
| | - Torben Barington
- Department of Clinical Immunology, Odense University Hospital, 5000 Odense, Denmark
| |
Collapse
|
91
|
Polymorphisme des gènes HLA et KIR et l’impact sur le devenir de la greffe et le choix du donneur non apparenté de cellules souche hématopoïétiques : recommandations de la Société francophone de greffe de moelle et de thérapie cellulaire (SFGM-TC). Bull Cancer 2016; 103:S243-S247. [DOI: 10.1016/j.bulcan.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/01/2016] [Indexed: 02/02/2023]
|
92
|
Yin Y, Lan JH, Nguyen D, Valenzuela N, Takemura P, Bolon YT, Springer B, Saito K, Zheng Y, Hague T, Pasztor A, Horvath G, Rigo K, Reed EF, Zhang Q. Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples. PLoS One 2016; 11:e0165810. [PMID: 27798706 PMCID: PMC5087893 DOI: 10.1371/journal.pone.0165810] [Citation(s) in RCA: 34] [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: 05/17/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022] Open
Abstract
Background Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA. Methods Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3’ UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing. Results Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%). Conclusion Long-range, unambiguous HLA genotyping is achievable on clinical buccal swab-extracted DNA. Importantly, full-length gene sequencing and the ability to curate full sequence data will permit future interrogation of the impact of introns, expanded exons, and other gene regulatory sequences on clinical outcomes in transplantation.
Collapse
Affiliation(s)
- Yuxin Yin
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - James H. Lan
- University of British Columbia Clinician Investigator Program, Vancouver, BC, Canada
| | - David Nguyen
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - Nicole Valenzuela
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - Ping Takemura
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - Yung-Tsi Bolon
- National Marrow Donor Program, Minneapolis, MN, United States of America
| | - Brianna Springer
- National Marrow Donor Program, Minneapolis, MN, United States of America
| | - Katsuyuki Saito
- One Lambda, Thermo Fisher Scientific, Canoga Park, CA, United States of America
| | - Ying Zheng
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | | | | | | | | | - Elaine F. Reed
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - Qiuheng Zhang
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
- * E-mail:
| |
Collapse
|
93
|
Grubic Z, Stingl Jankovic K, Maskalan M, Serventi-Seiwerth R, Mikulic M, Nemet D, Burek Kamenaric M, Labar B, Zunec R. The effect of HLA allele and haplotype polymorphisms on donor matching in hematopoietic stem cell transplantation - Croatian experience. Hum Immunol 2016; 77:1120-1127. [PMID: 27756586 DOI: 10.1016/j.humimm.2016.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 11/29/2022]
Abstract
The knowledge of HLA characteristics of a patient's population helps to predict the probability of finding a MUD. The study included 170 transplanted patients for whom a search for a MUD in BMDW was performed and a sample of 4000 volunteer unrelated donors from the Croatian Bone Marrow Donor Registry (CBMDR). Patients and their MUDs were typed for HLA-A, -B, -C, -DRB1, and -DQB1 loci using PCR-SSO and PCR-SSP methods while donors were typed for HLA-A, -B, -C, and -DRB1 loci using the PCR-SSO method. A comparison of allele frequencies at tested HLA loci between patients and donors from CBMDR did not reveal significant differences. The majority of patients (117, 68.8%) had a 10/10 MUD, 45 (26.5%) patients had a 9/10 MUD and eight (4.7%) patients had an 8/10 MUD. The highest number of mismatches (MM) was present at HLA-DRB1 (19; 31.1%). The presence of DRB1*11 and DRB1*04 allelic groups among patients caused allelic MMs at HLA-DRB1 in most cases. The presence of an infrequent HLA-B∼C haplotype resulted in the HLA-C MM at antigen level in the majority of cases. The present study clarified HLA factors that cause difficulties in searching for a 10/10 MUD for Croatian patients.
Collapse
Affiliation(s)
- Zorana Grubic
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia.
| | - Katarina Stingl Jankovic
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marija Maskalan
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ranka Serventi-Seiwerth
- Department of Haematology, Internal Clinic, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Mirta Mikulic
- Croatian Bone Marrow Donor Registry, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Damir Nemet
- Department of Haematology, Internal Clinic, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marija Burek Kamenaric
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Boris Labar
- Department of Haematology, Internal Clinic, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Renata Zunec
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| |
Collapse
|
94
|
Little AM, Green A, Harvey J, Hemmatpour S, Latham K, Marsh SGE, Poulton K, Sage D. BSHI Guideline: HLA matching and donor selection for haematopoietic progenitor cell transplantation. Int J Immunogenet 2016; 43:263-86. [DOI: 10.1111/iji.12282] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/06/2016] [Accepted: 06/06/2016] [Indexed: 12/29/2022]
Affiliation(s)
- A-M. Little
- Histocompatibility and Immunogenetics Laboratory; Gartnavel General Hospital; Glasgow UK
- Institute of Infection, Immunity and Inflammation; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
| | - A. Green
- Histocompatibility and Immunogenetics Laboratory; NHS Blood and Transplant; Filton UK
| | - J. Harvey
- Histocompatibility and Immunogenetics Laboratory; NHS Blood and Transplant; Filton UK
| | - S. Hemmatpour
- Histocompatibility and Immunogenetics Laboratory; NHS Blood and Transplant; London Tooting UK
| | - K. Latham
- Anthony Nolan Research Institute; Royal Free Hospital; London UK
| | - S. G. E. Marsh
- Anthony Nolan Research Institute; Royal Free Hospital; London UK
- Cancer Institute; University College London; London UK
| | - K. Poulton
- Transplantation Laboratory; Manchester Royal Infirmary; Manchester UK
- British Society for Histocompatibility & Immunogenetics
| | - D. Sage
- Histocompatibility and Immunogenetics Laboratory; NHS Blood and Transplant; London Tooting UK
| |
Collapse
|
95
|
Petersdorf EW. Mismatched unrelated donor transplantation. Semin Hematol 2016; 53:230-236. [PMID: 27788760 DOI: 10.1053/j.seminhematol.2016.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/20/2016] [Indexed: 11/11/2022]
Abstract
There are now more than 25 million volunteer donors registered worldwide for patients in need of a life-saving hematopoietic cell transplant to cure blood disorders. Although a human leukocyte antigen (HLA)-matched donor remains the preferred stem cell source for transplantation, the use of a donor with limited HLA mismatching may be considered. Significant advances in clinical and basic research have been instrumental in furthering the understanding of donor-recipient HLA mismatches that are better tolerated than other mismatches. An increased appreciation of the role of regulatory region variation that affects the level of HLA expression provides new approaches for the selection of HLA-mismatched donors.
Collapse
Affiliation(s)
- Effie W Petersdorf
- Department of Medicine, University of Washington; Seattle Cancer Care Alliance; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA.
| |
Collapse
|
96
|
Tiercy JM. How to select the best available related or unrelated donor of hematopoietic stem cells? Haematologica 2016; 101:680-7. [PMID: 27252513 DOI: 10.3324/haematol.2015.141119] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/09/2016] [Indexed: 11/09/2022] Open
Abstract
Recognition of HLA incompatibilities by the immune system represents a major barrier to allogeneic hematopoietic stem cell transplantation. HLA genotypically identical sibling donors are, therefore, the gold standard for transplantation purposes, but only 30% patients have such a donor. For the remaining 70% patients alternative sources of stem cells are a matched unrelated adult volunteer donor, a haploidentical donor or a cord blood unit. The definition of 'HLA matching' depends on the level of resolution and on which loci are tested. The development of HLA molecular typing technologies and the availability of more than 27 million donors in the international database has greatly facilitated unrelated donor searches. The gold standard is high resolution typing at the HLA-A, -B, -C, -DRB1, and -DQB1 loci (10/10 match). Single disparities for HLA-A, -B, - C, or -DRB1 are associated with increased risk of post-transplant complications, but less so in patients with advanced disease, and in those undergoing T-cell-depleted allografting. HLA-DQB1 mismatches seem to be better tolerated and some HLA-C, -DRB1 and -DPB1 disparities are potentially less immunogenic. HLA typing by next-generation sequencing methods is likely to change matching algorithms by providing full sequence information on all HLA loci in a single step. In most European populations a 10/10 matched donor can be found for at least 50% of patients and an additional 20-30% patients may have a 9/10 matched donor. Genetic factors that help in identifying donors with less immunogenic mismatches are discussed. Haploidentical donors are increasingly used as an alternative source of stem cells for those patients lacking a matched unrelated donor.
Collapse
Affiliation(s)
- Jean-Marie Tiercy
- National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, University Hospitals Geneva, Switzerland
| |
Collapse
|
97
|
Wang J, Yao FZ, Ji X, Zhu XM, Su PC. Identification of a novel HLA-C allele, HLA-C*07:477 in a Drung Chinese individual. HLA 2016; 87:468-9. [PMID: 27168457 DOI: 10.1111/tan.12814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 11/30/2022]
Abstract
HLA-C*07:477 has one nonsynonymous nucleotide change from HLA-C*07:02:01:01 in codon 176, exon 3 (AAG>GAG).
Collapse
Affiliation(s)
- J Wang
- Clinical Transfusion Research Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, Chengdu, PR China
| | - F Z Yao
- Transfusion Medicine Research Department, Yunnan Kunming Blood Center, Kunming, PR China
| | - X Ji
- Clinical Transfusion Research Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, Chengdu, PR China
| | - X M Zhu
- Transfusion Medicine Research Department, Yunnan Kunming Blood Center, Kunming, PR China
| | - P C Su
- Transfusion Medicine Research Department, Yunnan Kunming Blood Center, Kunming, PR China
| |
Collapse
|
98
|
Apps R, Del Prete GQ, Chatterjee P, Lara A, Brumme ZL, Brockman MA, Neil S, Pickering S, Schneider DK, Piechocka-Trocha A, Walker BD, Thomas R, Shaw GM, Hahn BH, Keele BF, Lifson JD, Carrington M. HIV-1 Vpu Mediates HLA-C Downregulation. Cell Host Microbe 2016; 19:686-95. [PMID: 27173934 PMCID: PMC4904791 DOI: 10.1016/j.chom.2016.04.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/08/2016] [Accepted: 04/05/2016] [Indexed: 12/31/2022]
Abstract
Many pathogens evade cytotoxic T lymphocytes (CTLs) by downregulating HLA molecules on infected cells, but the loss of HLA can trigger NK cell-mediated lysis. HIV-1 is thought to subvert CTLs while preserving NK cell inhibition by Nef-mediated downregulation of HLA-A and -B but not HLA-C molecules. We find that HLA-C is downregulated by most primary HIV-1 clones, including transmitted founder viruses, in contrast to the laboratory-adapted NL4-3 virus. HLA-C reduction is mediated by viral Vpu and reduces the ability of HLA-C restricted CTLs to suppress viral replication in CD4+ cells in vitro. HLA-A/B are unaffected by Vpu, and primary HIV-1 clones vary in their ability to downregulate HLA-C, possibly in response to whether CTLs or NK cells dominate immune pressure through HLA-C. HIV-2 also suppresses HLA-C expression through distinct mechanisms, underscoring the immune pressure HLA-C exerts on HIV. This viral immune evasion casts new light on the roles of CTLs and NK cells in immune responses against HIV.
Collapse
Affiliation(s)
- Richard Apps
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Pramita Chatterjee
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Abigail Lara
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V67 1Y6, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V67 1Y6, Canada
| | - Stuart Neil
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Suzanne Pickering
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Douglas K Schneider
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139-3583, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139-3583, USA
| | - Rasmi Thomas
- Host Genetics Section, US Military HIV Research Program, Silver Spring, MD 20910, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104-6076, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104-6076, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139-3583, USA.
| |
Collapse
|
99
|
Shepherd BL, Dauya E, Ferrand R, Rowland-Jones S, Yindom LM. Isolation of full-length HLA-C*18:02 allele in an individual from Sub-Saharan Africa. HLA 2016; 87:471-2. [PMID: 27098306 DOI: 10.1111/tan.12804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 11/27/2022]
Abstract
The full-length sequence of HLA-C*18:02 differs from that of HLA-C*18:01 by a single nucleotide polymorphism.
Collapse
Affiliation(s)
- B L Shepherd
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - E Dauya
- Department of Infectious Disease, Biomedical Research and Training Institute, Harare, Zimbabwe
| | - R Ferrand
- Department of Infectious Disease, Biomedical Research and Training Institute, Harare, Zimbabwe.,Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - S Rowland-Jones
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - L-M Yindom
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
100
|
René C, Lozano C, Eliaou JF. Expression of classical HLA class I molecules: regulation and clinical impacts: Julia Bodmer Award Review 2015. HLA 2016; 87:338-49. [PMID: 27060357 DOI: 10.1111/tan.12787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022]
Abstract
Human leukocyte antigen (HLA) class I genes are ubiquitously expressed, but in a tissue specific-manner. Their expression is primarily regulated at the transcriptional level and can be modulated both positively and negatively by different stimuli. Advances in sequencing technologies led to the identification of new regulatory variants located in the untranslated regions (UTRs), which could influence the expression. After a brief description of the mechanisms underlying the transcriptional regulation of HLA class I genes expression, we will review how the expression levels of HLA class I genes could affect biological and pathological processes. Then, we will discuss on the differential expression of HLA class I genes according to the locus, allele and UTR polymorphisms and its clinical impact. This interesting field of study led to a new dimension of HLA typing, going beyond a qualitative aspect.
Collapse
Affiliation(s)
- C René
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France.,Faculté de Médecine, University of Montpellier, Montpellier, France.,INSERM U1183, Institute for Regenerative Medicine and Biotherapy (IRMB), CHU Montpellier, Montpellier, France
| | - C Lozano
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France
| | - J-F Eliaou
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France.,Faculté de Médecine, University of Montpellier, Montpellier, France.,INSERM U1194, IRCM, University of Montpellier, Montpellier, France
| |
Collapse
|