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Fingerson S, Maiers M, Bolon YT, Devine SM, Spellman SR. Expanding donor options: haploidentical transplant recipients are also highly likely to have a 7/8-matched unrelated donor. Blood Adv 2024; 8:758-765. [PMID: 38127270 PMCID: PMC10847856 DOI: 10.1182/bloodadvances.2023011814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
ABSTRACT The use of haploidentical related donor (HRD) hematopoietic cell transplants (HCTs) in the United States grew by more than fourfold in the last decade, driven mainly by use of posttransplant cyclophosphamide (PTCy)-based graft-versus-host-disease prophylaxis. However, not all patients have a suitable HRD available. In this study, we explored the existence of unrelated donors (URDs) on the National Marrow Donor Program (NMDP) registry at the 8/8- or 7/8-match level for patients receiving HRD HCT in the United States and reporting to the Center for International Blood and Marrow Transplant Research between 2013 and 2020. The data consist of 9696 HRD HCT recipients. The NMDP search prognosis score and a search simulation were used to estimate counts of URD matches on the registry. NMDP search prognosis varied by patient ancestry, with 27.5% non-Hispanic White having a good score compared with 4.6% of African American HRD HCT recipients. Overall, 34% of recipients had ≥1 8/8-matched URDs and 84% had ≥1 7/8 URDs. Recipients of older HRDs (≥35 years) had a likelihood of between 20%- 65% of having ≥5 existing 7/8-matched URDs who were aged ≤35 years. Donor-selection practices varied among the 10 highest-volume HRD centers: 6 had >20% chance of an existing 8/8-matched URD for their HRD recipients, whereas 4 centers had low likelihood of identifying an 8/8-matched URD. In conclusion, although most US patients undergoing HRD HCT do not have an existing 8/8 URD, the majority have an existing 7/8-matched URD. Studies comparing outcomes in patients receiving either HRD or 7/8-matched URD HCT and PTCy-based graft-versus-host disease prophylaxis may be warranted.
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Affiliation(s)
- Stephanie Fingerson
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Martin Maiers
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Steven M. Devine
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
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2
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Crivello P, Arrieta-Bolaños E, He M, Wang T, Fingerson S, Gadalla SM, Paczesny S, Marsh SG, Lee SJ, Spellman SR, Bolon YT, Fleischhauer K. Impact of the HLA Immunopeptidome on Survival of Leukemia Patients After Unrelated Donor Transplantation. J Clin Oncol 2023; 41:2416-2427. [PMID: 36669145 PMCID: PMC10150892 DOI: 10.1200/jco.22.01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/10/2022] [Accepted: 11/15/2022] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Immunopeptidome divergence between mismatched HLA-DP is a determinant of T-cell alloreactivity and clinical tolerability after fully HLA-A, -B, -C, -DRB1, -DQB1 matched unrelated donor hematopoietic cell transplantation (UD-HCT). Here, we tested this concept in HLA-A, -B, and -C disparities after single class I HLA-mismatched UD-HCT. PATIENTS AND METHODS We studied 2,391 single class I HLA-mismatched and 14,426 fully HLA-matched UD-HCT performed between 2008 and 2018 for acute leukemia or myelodysplastic syndromes. Hierarchical clustering of experimentally determined peptide-binding motifs (PBM) was used as a proxy for immunopeptidome divergence of HLA-A, -B, or -C disparities, allowing us to classify 1,629/2,391 (68.1%) of the HLA-mismatched UD-HCT as PBM-matched or PBM-mismatched. Risks associated with PBM-matching status were assessed by Cox proportional hazards models, with overall survival (OS) as the primary end point. RESULTS Relative to full matches, bidirectional or unidirectional PBM mismatches in graft-versus-host (GVH) direction (PBM-GVH mismatches, 60.7%) were associated with significantly lower OS (hazard ratio [HR], 1.48; P < .0001), while unidirectional PBM mismatches in host-versus-graft direction or PBM matches (PBM-GVH matches, 39.3%) were not (HR, 1.13; P = .1017). PBM-GVH mismatches also had significantly lower OS than PBM-GVH matches in direct comparison (HR, 1.32; P = .0036). The hazards for transplant-related mortality and acute and chronic graft-versus-host disease but not relapse increased stepwise from full HLA matches to single PBM-GVH matches, and single PBM-GVH mismatches. A webtool for PBM-matching of single class I HLA-mismatched donor-recipient pairs was developed. CONCLUSION PBM-GVH mismatches inform mortality risks after single class I HLA-mismatched UD-HCT, suggesting that prospective consideration of directional PBM-matching status might improve outcome. These findings highlight immunopeptidome divergence between mismatched HLA as a driver of clinical tolerability in UD-HCT.
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Affiliation(s)
- Pietro Crivello
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium, partner site Essen/Düsseldorf (DKTK), Heidelberg, Germany
| | - Meilun He
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Tao Wang
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI
- Department of Medicine, Medical College of Wisconsin, CIBMTR (Center for International Blood and Marrow Transplant Research), Milwaukee, WI
| | - Stephanie Fingerson
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, NIH-NCI Clinical Genetics Branch, Rockville, MD
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Steven G.E. Marsh
- Anthony Nolan Research Institute and University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Stephanie J. Lee
- Department of Medicine, Medical College of Wisconsin, CIBMTR (Center for International Blood and Marrow Transplant Research), Milwaukee, WI
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Stephen R. Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Yung-Tsi Bolon
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium, partner site Essen/Düsseldorf (DKTK), Heidelberg, Germany
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Fingerson S, Bolon YT, Maiers M, Devine SM, Spellman S. An Exploration of Unrelated Donor Existence for Patients Who Received Haploidentical Hematopoietic Cell Transplants. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00366-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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4
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Fuchs EJ, McCurdy SR, Solomon SR, Wang T, Herr MR, Modi D, Grunwald MR, Nishihori T, Kuxhausen M, Fingerson S, McKallor C, Bashey A, Kasamon YL, Bolon YT, Saad A, McGuirk J, Paczesny S, Gadalla SM, Marsh SGE, Shaw BE, Spellman SR, Lee SJ, Petersdorf EW. HLA informs risk predictions after haploidentical stem cell transplantation with posttransplantation cyclophosphamide. Blood 2022; 139:1452-1468. [PMID: 34724567 PMCID: PMC8914182 DOI: 10.1182/blood.2021013443] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/18/2021] [Indexed: 11/20/2022] Open
Abstract
Hematopoietic cell transplantation from HLA-haploidentical related donors is increasingly used to treat hematologic cancers; however, characteristics of the optimal haploidentical donor have not been established. We studied the role of donor HLA mismatching in graft-versus-host disease (GVHD), disease recurrence, and survival after haploidentical donor transplantation with posttransplantation cyclophosphamide (PTCy) for 1434 acute leukemia or myelodysplastic syndrome patients reported to the Center for International Blood and Marrow Transplant Research. The impact of mismatching in the graft-versus-host vector for HLA-A, -B, -C, -DRB1, and -DQB1 alleles, the HLA-B leader, and HLA-DPB1 T-cell epitope (TCE) were studied using multivariable regression methods. Outcome was associated with HLA (mis)matches at individual loci rather than the total number of HLA mismatches. HLA-DRB1 mismatches were associated with lower risk of disease recurrence. HLA-DRB1 mismatching with HLA-DQB1 matching correlated with improved disease-free survival. HLA-B leader matching and HLA-DPB1 TCE-nonpermissive mismatching were each associated with improved overall survival. HLA-C matching lowered chronic GVHD risk, and the level of HLA-C expression correlated with transplant-related mortality. Matching status at the HLA-B leader and HLA-DRB1, -DQB1, and -DPB1 predicted disease-free survival, as did patient and donor cytomegalovirus serostatus, patient age, and comorbidity index. A web-based tool was developed to facilitate selection of the best haploidentical-related donor by calculating disease-free survival based on these characteristics. In conclusion, HLA factors influence the success of haploidentical transplantation with PTCy. HLA-DRB1 and -DPB1 mismatching and HLA-C, -B leader, and -DQB1 matching are favorable. Consideration of HLA factors may help to optimize the selection of haploidentical related donors.
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Affiliation(s)
- Ephraim J Fuchs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD
| | | | - Scott R Solomon
- Northside Hospital Cancer Institute, Blood and Marrow Transplant Program, Atlanta, GA
| | - Tao Wang
- Department of Medicine, Center for International Blood and Marrow Transplant Research (CIBMTR), Medical College of Wisconsin, Milwaukee, WI
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI
| | | | | | - Michael R Grunwald
- Department of Hematologic Oncology and Blood Disorders, Levine Cancer Institute, Atrium Health, Charlotte, NC
| | - Taiga Nishihori
- Department of Blood and Marrow Transplant and Cellular Immunotherapy (BMT CI), Moffitt Cancer Center, Tampa, FL
| | - Michelle Kuxhausen
- CIBMTR, National Marrow Donor Program/Be The Match Foundation, Minneapolis, MN
| | - Stephanie Fingerson
- CIBMTR, National Marrow Donor Program/Be The Match Foundation, Minneapolis, MN
| | - Caroline McKallor
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Asad Bashey
- Northside Hospital Cancer Institute, Blood and Marrow Transplant Program, Atlanta, GA
| | - Yvette L Kasamon
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD
| | - Yung-Tsi Bolon
- CIBMTR, National Marrow Donor Program/Be The Match Foundation, Minneapolis, MN
| | - Ayman Saad
- Division of Hematology, Ohio State University, Columbus, OH
| | - Joseph McGuirk
- Division of Hematologic Malignancies and Cellular Therapeutics, The University of Kansas Cancer Center, Kansas City, KS
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology and Genetics, National Institutes of Health, National Cancer Institute, Clinical Genetics Branch, Rockville, MD
| | - Steven G E Marsh
- Anthony Nolan Research Institute-University College London Cancer Institute, Royal Free Campus, London, United Kingdom; and
| | - Bronwen E Shaw
- Department of Medicine, Center for International Blood and Marrow Transplant Research (CIBMTR), Medical College of Wisconsin, Milwaukee, WI
| | - Stephen R Spellman
- CIBMTR, National Marrow Donor Program/Be The Match Foundation, Minneapolis, MN
| | - Stephanie J Lee
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Medicine, CIBMTR, Medical College of Wisconsin, Milwaukee, WI
| | - Effie W Petersdorf
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
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5
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Sajulga R, Madbouly A, Fingerson S, Gragert L, Bashyal P, Bolon YT, Maiers M. Predicting HLA-DPB1 permissive probabilities through a DPB1 prediction service towards the optimization of HCT donor selection. Hum Immunol 2021; 82:903-911. [PMID: 34362573 DOI: 10.1016/j.humimm.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 12/01/2022]
Abstract
Despite its demonstrated importance in hematopoietic cell transplantation, the HLA-DPB1 locus is only typed in one in five unrelated donors in the United States. Addressing this issue, we developed a DPB1 Prediction Service that leverages seven-locus haplotype frequencies (HLA-A ∼ C ∼ B ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1 ∼ DPB1) to extend the imputation of six-locus HLA typing (HLA-A ∼ C ∼ B ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1) to the HLA-DPB1 locus, including the novel prediction of HLA-DPB1 TCE groups to calculate donor-recipient TCE permissive match probabilities. Simulations of current-day patient searches reveal the service can fill in missing gaps for another four in five donors that appears on lists. To validate its performance, samples of 206,328 registered donors and 5,218 donor-recipient pairs with known high-resolution HLA-DPB1 typing were used for predicted-versus-observed comparisons. These comparisons demonstrated that the predictions were correct for 11.9-19.7% of HLA-DPB1 genotypes, 64.9-70.0% of TCE groups, and 61.0% of permissive match categories. Although HLA-DPB1 match predictions must be confirmed by additional typing, knowledge of TCE match probabilities facilitates rapid and improved identification of best donor options, especially for populations of color. Thus, we developed the TCE Prediction Tool user interface for a pilot program with several transplant centers to preview the accuracy and utility of this prediction framework, which provides valuable upfront optimization of donor selection.
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Affiliation(s)
- Ray Sajulga
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA.
| | - Abeer Madbouly
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Stephanie Fingerson
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Loren Gragert
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Pradeep Bashyal
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Yung-Tsi Bolon
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Martin Maiers
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA
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6
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Sapir-Pichhadze R, Zhang X, Ferradji A, Madbouly A, Tinckam KJ, Gebel HM, Blum D, Marrari M, Kim SJ, Fingerson S, Bashyal P, Cardinal H, Foster BJ. Epitopes as characterized by antibody-verified eplet mismatches determine risk of kidney transplant loss. Kidney Int 2019; 97:778-785. [PMID: 32059998 DOI: 10.1016/j.kint.2019.10.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/26/2019] [Accepted: 10/17/2019] [Indexed: 01/01/2023]
Abstract
To optimize strategies that mitigate the risk of graft loss associated with HLA incompatibility, we evaluated whether sequence defined HLA targets (eplets) that result in donor-specific antibodies are associated with transplant outcomes. To define this, we fit multivariable Cox proportional hazard models in a cohort of 118 382 United States first kidney transplant recipients to assess risk of death-censored graft failure by increments of ten antibody-verified eplet mismatches. To verify robustness of our findings, we conducted sensitivity analysis in this United States cohort and assessed the role of antibody-verified eplet mismatches as autonomous predictors of transplant glomerulopathy in an independent Canadian cohort. Antibody-verified eplet mismatches were found to be independent predictors of death-censored graft failure with hazard ratios of 1.231 [95% confidence interval 1.195, 1. 268], 1.268 [1.231, 1.305] and 1.411 [1.331, 1.495] for Class I (HLA-A, B, and C), -DRB1 and -DQB1 loci, respectively. To address linkage disequilibrium between HLA-DRB1 and -DQB1, we fit models in a subcohort without HLA-DQB1 eplet mismatches and found hazard ratios for death-censored graft failure of 1.384 [1.293, 1.480] for each additional antibody-verified HLA-DRB1 eplet mismatch. In a subcohort without HLA-DRB1 mismatches, the hazard ratio was 1.384 [1.072, 1.791] for each additional HLA-DQB1 mismatch. In the Canadian cohort, antibody-verified eplet mismatches were independent predictors of transplant glomerulopathy with hazard ratios of 5.511 [1.442, 21.080] for HLA-DRB1 and 3.640 [1.574, 8.416] for -DRB1/3/4/5. Thus, donor-recipient matching for specific HLA eplets appears to be a feasible and clinically justifiable strategy to mitigate risk of graft loss.
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Affiliation(s)
- Ruth Sapir-Pichhadze
- Division of Nephrology, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada; The Multi Organ Transplant Program, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada; Centre for Outcomes Research and Evaluation (CORE), McGill University Health Centre, Montreal, Quebec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada.
| | - Xun Zhang
- Centre for Outcomes Research and Evaluation (CORE), McGill University Health Centre, Montreal, Quebec, Canada
| | - Abdelhakim Ferradji
- Research Institute, McGill University Health Centre, Montreal, Quebec, Canada
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Kathryn J Tinckam
- Division of Nephrology, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; The Kidney Transplant Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Division of Nephrology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Howard M Gebel
- Department of Pathology, Emory University, Atlanta, Georgia, USA
| | - Daniel Blum
- Division of Nephrology, St Michael's Hospital, Toronto, Ontario, Canada
| | - Marilyn Marrari
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - S Joseph Kim
- Division of Nephrology, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; The Kidney Transplant Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Division of Nephrology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Fingerson
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Pradeep Bashyal
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | | | - Bethany J Foster
- Centre for Outcomes Research and Evaluation (CORE), McGill University Health Centre, Montreal, Quebec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada; Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
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Alter I, Gragert L, Fingerson S, Maiers M, Louzoun Y. HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes. PLoS Comput Biol 2017; 13:e1005693. [PMID: 28846675 PMCID: PMC5590998 DOI: 10.1371/journal.pcbi.1005693] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/08/2017] [Accepted: 07/20/2017] [Indexed: 01/03/2023] Open
Abstract
The major histocompatibility complex (MHC) contains the most polymorphic genetic system in humans, the human leukocyte antigen (HLA) genes of the adaptive immune system. High allelic diversity in HLA is argued to be maintained by balancing selection, such as negative frequency-dependent selection or heterozygote advantage. Selective pressure against immune escape by pathogens can maintain appreciable frequencies of many different HLA alleles. The selection pressures operating on combinations of HLA alleles across loci, or haplotypes, have not been extensively evaluated since the high HLA polymorphism necessitates very large sample sizes, which have not been available until recently. We aimed to evaluate the effect of selection operating at the HLA haplotype level by analyzing HLA A~C~B~DRB1~DQB1 haplotype frequencies derived from over six million individuals genotyped by the National Marrow Donor Program registry. In contrast with alleles, HLA haplotype diversity patterns suggest purifying selection, as certain HLA allele combinations co-occur in high linkage disequilibrium. Linkage disequilibrium is positive (Dij'>0) among frequent haplotypes and negative (Dij'<0) among rare haplotypes. Fitting the haplotype frequency distribution to several population dynamics models, we found that the best fit was obtained when significant positive frequency-dependent selection (FDS) was incorporated. Finally, the Ewens-Watterson test of homozygosity showed excess homozygosity for 5-locus haplotypes within 23 US populations studied, with an average Fnd of 28.43. Haplotype diversity is most consistent with purifying selection for HLA Class I haplotypes (HLA-A, -B, -C), and was not inferred for HLA Class II haplotypes (-DRB1 and—DQB1). We discuss our empirical results in the context of evolutionary theory, exploring potential mechanisms of selection that maintain high linkage disequilibrium in MHC haplotype blocks. The adaptive immune system presents antigens derived from pathogenic and normal self proteins on the cell surface using human leukocyte antigen (HLA) molecules. The HLA loci coding for these molecules are found in major histocompatibility complex (MHC) region, the most polymorphic region in the human genome, with over 15,000 HLA alleles observed so far in the world population. A high frequency of many different HLA alleles is thought be sustained by balancing selection. New HLA alleles may have an advantage over existing frequent alleles since immune escape mutations in pathogens within a population are maintained primarily in epitopes presented on frequent HLA alleles. Host immune function is not determined by single HLA alleles, but by both copies of autosomal HLA genes together (genotypes). Complementarity in function across the two potentially-variant copies of HLA at each locus can result in overdominance and heterozygote advantage at the genotype level. Less explored are selection mechanisms that may be operating across combinations of HLA alleles across loci (haplotypes). Indeed, in addition to high allelic diversity, HLA also has distinctive patterns of haplotype diversity, as certain HLA alleles co-occur in high linkage disequilibrium across five classical HLA loci (HLA-A, -B, -C, -DRB1, -DQB1). We applied multiple population genetic models to a dataset of HLA haplotype frequencies derived from over six million individuals with the goal of determining what type of selection may impact HLA haplotype diversity. We found frequent haplotypes were preferentially maintained in the population across 23 US populations studied. Thus, balancing selection at the allele level and purifying selection at the haplotype level may together affect HLA diversity in human populations.
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Affiliation(s)
- Idan Alter
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Loren Gragert
- National Marrow Donor Program, Minneapolis, Minnesota, United States of America
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Stephanie Fingerson
- National Marrow Donor Program, Minneapolis, Minnesota, United States of America
| | - Martin Maiers
- National Marrow Donor Program, Minneapolis, Minnesota, United States of America
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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8
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Beksac M, Gragert L, Fingerson S, Maiers M, Zhang MJ, Albrecht M, Zhong X, Cozen W, Dispenzieri A, Lonial S, Hari P. HLA polymorphism and risk of multiple myeloma. Leukemia 2016; 30:2260-2264. [PMID: 27461064 DOI: 10.1038/leu.2016.199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Meral Beksac
- Ankara University Department of Hematology, Tissue Typing Laboratories and Donor Registry, Ankara, Turkey
| | - Loren Gragert
- Bioinformatics Research, National Marrow Donor Program / Be The Match, Minneapolis, MN, USA and Tulane Cancer Center, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Stephanie Fingerson
- Bioinformatics Research, National Marrow Donor Program / Be The Match, Minneapolis, MN, USA and Tulane Cancer Center, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program / Be The Match, Minneapolis, MN, USA and Tulane Cancer Center, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Mei-Jie Zhang
- Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Biostatistics, Institute for Health and Society, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mark Albrecht
- Bioinformatics Research, National Marrow Donor Program / Be The Match, Minneapolis, MN, USA and Tulane Cancer Center, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Xiaobo Zhong
- Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wendy Cozen
- Departments of Preventive Medicine and Pathology and Norris Comprehensive Cancer Center, USC Keck School of Medicine, Los Angeles, CA, USA
| | | | - Sagar Lonial
- Department of Hematology and Medical Oncology, Emory University, GA, USA
| | - Parameswaran Hari
- Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
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