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Cohen GS, Gareau AJ, Kallarakal MA, Farooq T, Bettinotti MP, Sullivan HC, Madbouly A, Krummey SM. HLA Genotype Imputation Results in Largely Accurate Epitope Mismatch Risk Categorization Across Racial Groups. Transplant Direct 2024; 10:e1639. [PMID: 38911277 PMCID: PMC11191912 DOI: 10.1097/txd.0000000000001639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/09/2024] [Indexed: 06/25/2024] Open
Abstract
Background Biomarkers that predict posttransplant alloimmunity could lead to improved long-term graft survival. Evaluation of the number of mismatched epitopes between donor and recipient HLA proteins, termed molecular mismatch analysis, has emerged as an approach to classify transplant recipients as having high, intermediate, or low risk of graft rejection. When high-resolution genotypes are unavailable, molecular mismatch analysis requires algorithmic assignment, or imputation, of a high-resolution genotyping. Although imputation introduces inaccuracies in molecular mismatch analyses, it is unclear whether these inaccuracies would impact the clinical risk assessment for graft rejection. Methods Using renal transplant patients and donors from our center, we constructed cohorts of surrogate donor-recipient pairs with high-resolution and low-resolution HLA genotyping that were racially concordant or discordant. We systemically assessed the impact of imputation on molecular mismatch analysis for cohorts of 180-200 donor-recipient pairs for each of 4 major racial groups. We also evaluated the effect of imputation for a racially diverse validation cohort of 35 real-world renal transplant pairs. Results In the surrogate donor-recipient cohorts, imputation preserved the molecular mismatch risk category for 90.5%-99.6% of racially concordant donor-recipient pairs and 92.5%-100% of racially discordant pairs. In the validation cohort, which comprised 72% racially discordant pairs, we found that imputation preserved the molecular mismatch risk category for 97.1% of pairs. Conclusions Overall, these data demonstrate that imputation preserves the molecular mismatch risk assessment in the vast majority of cases and provides evidence supporting imputation in the performance of molecular mismatch analysis for clinical assessment.
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Affiliation(s)
- Gregory S. Cohen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alison J. Gareau
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Johns Hopkins Immunogenetics Laboratory, Baltimore, MD
| | | | - Tayyiaba Farooq
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Maria P. Bettinotti
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Johns Hopkins Immunogenetics Laboratory, Baltimore, MD
| | - H. Cliff Sullivan
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Abeer Madbouly
- National Marrow Donor Program/Be The Match, Minneapolis, MN
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN
| | - Scott M. Krummey
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Johns Hopkins Immunogenetics Laboratory, Baltimore, MD
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Johnson AC, Zhang J, Karadkhele G, Gragert L, Hertzberg V, Larsen CP. Belatacept with time-limited tacrolimus coimmunosuppression modifies the 3-year risk of eplet mismatch in kidney transplantation. Am J Transplant 2024; 24:260-270. [PMID: 37778459 PMCID: PMC10842047 DOI: 10.1016/j.ajt.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Solid organ transplant donor-recipient eplet mismatch has been correlated with donor-specific antibody (DSA) formation, antibody-mediated rejection, and overall rejection rates. However, studies have been predominantly in patients on tacrolimus-based immunosuppression regimens and have not fully explored differences in ethnically and racially diverse populations. Evidence indicates that patients on belatacept have lower rates of DSA formation, suggesting mediation of the immunogenicity of mismatched human leukocyte antigen polymorphisms. We performed a retrospective, single-center analysis of class II eplet disparity in a cohort of kidney transplant recipients treated using belatacept with tacrolimus induction (Bela/TacTL) or tacrolimus regimens between 2016 and 2019. Bela/TacTL (n = 294) and tacrolimus (n = 294) cohorts were propensity score-matched with standardized difference <0.15. Single-molecule eplet risk level was associated with immune event rates for both groups. In Cox regression analysis stratified by eplet risk level, Bela/TacTL immunosuppression was associated with a decreased rate of DSA (hazard ratio [HR] = 0.4), antibody-mediated rejection (HR = 0.2), and rejection (HR = 0.45). In the low-risk group, cumulative graft failure was lower for patients on Bela/TacTL (P < .02). Analysis of eplet mismatch burden may be a useful adjunct in identifying high-risk populations with increased immunosuppression requirements and should encourage the design of allocation rules to incentivize lower-risk pairings without negatively impacting equity in access.
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Affiliation(s)
- Aileen C Johnson
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Joan Zhang
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Geeta Karadkhele
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Loren Gragert
- Department of Pathology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Vicki Hertzberg
- Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Christian P Larsen
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA.
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Lhotte R, Letort V, Usureau C, Jorge-Cordeiro D, Siemowski J, Gabet L, Cournede PH, Taupin JL. Improving HLA typing imputation accuracy and eplet identification with local next-generation sequencing training data. HLA 2024; 103:e15222. [PMID: 38589051 DOI: 10.1111/tan.15222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/26/2023] [Accepted: 08/26/2023] [Indexed: 04/10/2024]
Abstract
Assessing donor/recipient HLA compatibility at the eplet level requires second field DNA typings but these are not always available. These can be estimated from lower-resolution data either manually or with computational tools currently relying, at best, on data containing typing ambiguities. We gathered NGS typing data from 61,393 individuals in 17 French laboratories, for loci A, B, and C (100% of typings), DRB1 and DQB1 (95.5%), DQA1 (39.6%), DRB3/4/5, DPB1, and DPA1 (10.5%). We developed HaploSFHI, a modified iterative maximum likelihood algorithm, to impute second field HLA typings from low- or intermediate-resolution ones. Compared with the reference tools HaploStats, HLA-EMMA, and HLA-Upgrade, HaploSFHI provided more accurate predictions across all loci on two French test sets and four European-independent test sets. Only HaploSFHI could impute DQA1, and solely HaploSFHI and HaploStats provided DRB3/4/5 imputations. The improved performance of HaploSFHI was due to our local and nonambiguous data. We provided explanations for the most common imputation errors and pinpointed the variability of a low number of low-resolution haplotypes. We thus provided guidance to select individuals for whom sequencing would optimize incompatibility assessment and cost-effectiveness of HLA typing, considering not only well-imputed second field typing(s) but also well-imputed eplets.
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Affiliation(s)
- Romain Lhotte
- Immunology and Histocompatibility Laboratory, Saint-Louis Hospital, Paris, France
- MICS-Research laboratory in Mathematics and Computer Science at CentraleSupélec, Gif-Sur-Yvette, France
- INSERM U976 Eq. 3 HIPI IRSL Saint-Louis Hospital, Université de Paris-Cité, Paris, France
| | - Véronique Letort
- MICS-Research laboratory in Mathematics and Computer Science at CentraleSupélec, Gif-Sur-Yvette, France
| | - Cédric Usureau
- Immunology and Histocompatibility Laboratory, Saint-Louis Hospital, Paris, France
| | | | - Jérémy Siemowski
- Immunology and Histocompatibility Laboratory, Saint-Louis Hospital, Paris, France
| | - Lionel Gabet
- MICS-Research laboratory in Mathematics and Computer Science at CentraleSupélec, Gif-Sur-Yvette, France
| | - Paul-Henry Cournede
- MICS-Research laboratory in Mathematics and Computer Science at CentraleSupélec, Gif-Sur-Yvette, France
| | - Jean-Luc Taupin
- Immunology and Histocompatibility Laboratory, Saint-Louis Hospital, Paris, France
- INSERM U976 Eq. 3 HIPI IRSL Saint-Louis Hospital, Université de Paris-Cité, Paris, France
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4
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Lemieux W, Fleischer D, Yang AY, Niemann M, Oualkacha K, Klement W, Richard L, Polychronakos C, Liwski R, Claas F, Gebel HM, Keown PA, Lewin A, Sapir-Pichhadze R. Dissecting the impact of molecular T-cell HLA mismatches in kidney transplant failure: A retrospective cohort study. Front Immunol 2022; 13:1067075. [PMID: 36505483 PMCID: PMC9730505 DOI: 10.3389/fimmu.2022.1067075] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Kidney transplantation is the optimal treatment in end-stage kidney disease, but de-novo donor specific antibody development continues to negatively impact patients undergoing kidney transplantation. One of the recent advances in solid organ transplantation has been the definition of molecular mismatching between donors and recipients' Human Leukocyte Antigens (HLA). While not fully integrated in standard clinical care, cumulative molecular mismatch at the level of eplets (EMM) as well as the PIRCHE-II score have shown promise in predicting transplant outcomes. In this manuscript, we sought to study whether certain T-cell molecular mismatches (TcEMM) were highly predictive of death-censored graft failure (DCGF). Methods We studied a retrospective cohort of kidney donor:recipient pairs from the Scientific Registry of Transplant Recipients (2000-2015). Allele level HLA-A, B, C, DRB1 and DQB1 types were imputed from serologic types using the NMDP algorithm. TcEMMs were then estimated using the PIRCHE-II algorithm. Multivariable Accelerated Failure Time (AFT) models assessed the association between each TcEMM and DCGF. To discriminate between TcEMMs most predictive of DCGF, we fit multivariable Lasso penalized regression models. We identified co-expressed TcEMMs using weighted correlation network analysis (WGCNA). Finally, we conducted sensitivity analyses to address PIRCHE and IMGT/HLA version updates. Results A total of 118,309 donor:recipient pairs meeting the eligibility criteria were studied. When applying the PIRCHE-II algorithm, we identified 1,935 distinct TcEMMs at the population level. A total of 218 of the observed TcEMM were independently associated with DCGF by AFT models. The Lasso penalized regression model with post selection inference identified a smaller subset of 86 TcEMMs (56 and 30 TcEMM derived from HLA Class I and II, respectively) to be highly predictive of DCGF. Of the observed TcEMM, 38.14% appeared as profiles of highly co-expressed TcEMMs. In addition, sensitivity analyses identified that the selected TcEMM were congruent across IMGT/HLA versions. Conclusion In this study, we identified subsets of TcEMMs highly predictive of DCGF and profiles of co-expressed mismatches. Experimental verification of these TcEMMs determining immune responses and how they may interact with EMM as predictors of transplant outcomes would justify their consideration in organ allocation schemes and for modifying immunosuppression regimens.
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Affiliation(s)
- William Lemieux
- Centre for Outcomes Research and Evaluation (CORE), Research Institute of McGill University Health Centre, Montréal, QC, Canada,Medical Affairs & Innovation, Héma-Québec, Montréal, QC, Canada
| | - David Fleischer
- Department of Mathematics and Statistics, McGill University, Montreal, QC, Canada
| | - Archer Yi Yang
- Department of Mathematics and Statistics, McGill University, Montreal, QC, Canada
| | | | - Karim Oualkacha
- Department of Mathematics, Université du Québec à Montreal, Montreal, QC, Canada
| | - William Klement
- Division of Organ Donation and Transplantation, Canadian Blood Services, Ottawa, ON, Canada
| | - Lucie Richard
- Transfusion medicine/Reference Laboratory, Héma-Québec, Montréal, QC, Canada
| | - Constantin Polychronakos
- Department of Pediatrics, The Research Institute of the McGill University Health Centre and the Montreal Children’s Hospital, Montréal, QC, Canada
| | - Robert Liwski
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Frans Claas
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Howard M. Gebel
- Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Paul A. Keown
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Antoine Lewin
- Medical Affairs & Innovation, Héma-Québec, Montréal, QC, Canada,Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Ruth Sapir-Pichhadze
- Centre for Outcomes Research and Evaluation (CORE), Research Institute of McGill University Health Centre, Montréal, QC, Canada,Division of Nephrology and the Multi-Organ Transplant Program, Royal Victoria Hospital, McGill University Health Centre, Montréal, QC, Canada,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada,*Correspondence: Ruth Sapir-Pichhadze,
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Renuncio-García M, González-López E, Carreras E, Villa J, Romón-Alonso I, Roa-Bautista A, Gutiérrez-Larrañaga M, Comins-Boo A, Irure-Ventura J, López-Hoyos M, San Segundo D. Estimation of Antibody-Verified Eplet Mismatch Load, 2-Field HLA Resolution vs Imputation in a Large Cohort of European Donors. Transplant Proc 2022; 54:2414-2418. [DOI: 10.1016/j.transproceed.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/13/2022] [Indexed: 11/05/2022]
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Meneghini M, Perona A, Crespo E, Bemelman F, Reinke P, Viklicky O, Giral M, Palou E, Torija A, Donadeu L, Melilli E, Zuñiga J, Sefrin A, Lachmann N, Hu L, Hruba P, Guillot-Gueguen C, Brouard S, Grinyo J, Bestard O. On the clinical relevance of using complete high-resolution HLA typing for an accurate interpretation of posttransplant immune-mediated graft outcomes. Front Immunol 2022; 13:924825. [PMID: 36248818 PMCID: PMC9559221 DOI: 10.3389/fimmu.2022.924825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
Complete and high-resolution (HR) HLA typing improves the accurate assessment of donor–recipient compatibility and pre-transplant donor-specific antibodies (DSA). However, the value of this information to identify de novo immune-mediated graft events and its impact on outcomes has not been assessed. In 241 donor/recipient kidney transplant pairs, DNA samples were re-evaluated for six-locus (A/B/C/DRB1/DQB1+A1/DPB1) HR HLA typing. De novo anti-HLA antibodies were assessed using solid-phase assays, and dnDSA were classified either (1) as per current clinical practice according to three-locus (A/B/DRB1) low-resolution (LR) typing, estimating donor HLA-C/DQ typing with frequency tables, or (2) according to complete six-locus HR typing. The impact on graft outcomes was compared between groups. According to LR HLA typing, 36 (15%) patients developed dnDSA (LR_dnDSA+). Twenty-nine out of 36 (80%) were confirmed to have dnDSA by HR typing (LR_dnDSA+/HR_dnDSA+), whereas 7 (20%) did not (LR_dnDSA+/HR_dnDSA−). Out of 49 LR_dnDSA specificities, 34 (69%) were confirmed by HR typing whereas 15 (31%) LR specificities were not confirmed. LR_dnDSA+/HR_dnDSA+ patients were at higher risk of ABMR as compared to dnDSA− and LR_dnDSA+/HR_dnDSA− (logRank < 0.001), and higher risk of death-censored graft loss (logRank = 0.001). Both LR_dnDSA+ (HR: 3.51, 95% CI = 1.25–9.85) and LR_dnDSA+/HR_dnDSA+ (HR: 4.09, 95% CI = 1.45–11.54), but not LR_dnDSA+/HR_dnDSA− independently predicted graft loss. The implementation of HR HLA typing improves the characterization of biologically relevant de novo anti-HLA DSA and discriminates patients with poorer graft outcomes.
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Affiliation(s)
- Maria Meneghini
- Kidney Transplant Unit, Nephrology Department. Vall d’Hebron University Hospital, Barcelona, Spain
- Vall d’Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Perona
- Department of Medicine, Barcelona University, Barcelona, Spain
| | - Elena Crespo
- Vall d’Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Frederike Bemelman
- Renal Transplant Unit, Department of Internal Medicine, Amsterdam University Medical Centers, Academic Medical Center - University of Amsterdam, Amsterdam, Netherlands
| | - Petra Reinke
- Berlin Center for Advanced Therapies (BeCAT), Berlin Institute of Health Center for Regenerative Therapies (BCRT) and Department of Nephrology and Intensive Care, Charité Universitätsmedizin Berlin, Berlin Institute of Health, Berlin, Germany
| | - Ondrej Viklicky
- Transplant Laboratory, Institute for Clinical and Experimental Medicine (IKEM), Prague, Czechia
- Department of Nephrology, Institute for Clinical and Experimental Medicine (IKEM), Prague, Czechia
| | - Magali Giral
- Nantes Université, Inserm, Centre Hospitalier Universitaire (CHU) Nantes, Centre de Recherche en Transplantation et Immunologie UMR1064, Institut de Transplantation Urologie-Néphrologie (ITUN), Nantes, France
| | - Eduard Palou
- Histocompatibility Laboratory, Immunology Department. Hospital Clinic, Barcelona, Spain
| | - Alba Torija
- Vall d’Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Donadeu
- Vall d’Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Edoardo Melilli
- Kidney Transplant Unit, Nephrology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Jose Zuñiga
- Kidney Transplant Unit, Nephrology Department. Vall d’Hebron University Hospital, Barcelona, Spain
| | - Anett Sefrin
- Berlin Center for Advanced Therapies (BeCAT), Berlin Institute of Health Center for Regenerative Therapies (BCRT) and Department of Nephrology and Intensive Care, Charité Universitätsmedizin Berlin, Berlin Institute of Health, Berlin, Germany
| | - Nils Lachmann
- HLA- Laboratory, Charité- Universitätsmedizin Berlin, Berlin, Germany
| | - Liu Hu
- Renal Transplant Unit, Department of Internal Medicine, Amsterdam University Medical Centers, Academic Medical Center - University of Amsterdam, Amsterdam, Netherlands
| | - Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine (IKEM), Prague, Czechia
- Department of Nephrology, Institute for Clinical and Experimental Medicine (IKEM), Prague, Czechia
| | - Cécile Guillot-Gueguen
- Nantes Université, Inserm, Centre Hospitalier Universitaire (CHU) Nantes, Centre de Recherche en Transplantation et Immunologie UMR1064, Institut de Transplantation Urologie-Néphrologie (ITUN), Nantes, France
| | - Sophie Brouard
- Nantes Université, Inserm, Centre Hospitalier Universitaire (CHU) Nantes, Centre de Recherche en Transplantation et Immunologie UMR1064, Institut de Transplantation Urologie-Néphrologie (ITUN), Nantes, France
| | - Josep Grinyo
- Department of Medicine, Barcelona University, Barcelona, Spain
| | - Oriol Bestard
- Kidney Transplant Unit, Nephrology Department. Vall d’Hebron University Hospital, Barcelona, Spain
- Vall d’Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- *Correspondence: Oriol Bestard,
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Affiliation(s)
- Allen J Norin
- Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, United States.
| | - Howard M Gebel
- Department of Pathology, Division of Laboratory Medicine, Emory University Hospital, Atlanta, GA, United States
| | - Malek Kamoun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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