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Halloran PF, Madill-Thomsen KS, Böhmig G, Bromberg J, Budde K, Barner M, Mackova M, Chang J, Einecke G, Eskandary F, Gupta G, Myślak M, Viklicky O, Akalin E, Alhamad T, Anand S, Arnol M, Baliga R, Banasik M, Bingaman A, Blosser C, Brennan D, Chamienia A, Chow K, Ciszek M, de Freitas D, Dęborska-Materkowska D, Debska-Ślizień A, Djamali A, Domański L, Durlik M, Fatica R, Francis I, Fryc J, Gill J, Gill J, Glyda M, Gourishankar S, Grenda R, Gryczman M, Hruba P, Hughes P, Jittirat A, Jurekovic Z, Kamal L, Kamel M, Kant S, Kasiske B, Kojc N, Konopa J, Lan J, Mannon R, Matas A, Mazurkiewicz J, Miglinas M, Mueller T, Narins S, Naumnik B, Patel A, Perkowska-Ptasińska A, Picton M, Piecha G, Poggio E, Bloudíčkova SR, Samaniego-Picota M, Schachtner T, Shin S, Shojai S, Sikosana M, Slatinská J, Smykal-Jankowiak K, Solanki A, Haler ŽV, Vucur K, Weir MR, Wiecek A, Włodarczyk Z, Yang H, Zaky Z. Subthreshold rejection activity in many kidney transplants currently classified as having no rejection. Am J Transplant 2024:S1600-6135(24)00461-1. [PMID: 39117038 DOI: 10.1016/j.ajt.2024.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/19/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
Most kidney transplant patients who undergo biopsies are classified as having no rejection based on consensus thresholds. However, we hypothesized that because these patients have normal adaptive immune systems, T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR) may exist as subthreshold activity in some transplants currently classified as no rejection. To examine this question, we studied genome-wide microarray results from 5086 kidney transplant biopsies (4170 patients). An updated archetypal analysis designated 56% of biopsies as no rejection. Subthreshold molecular TCMR and/or ABMR activity molecular activity was detectable as elevated classifier scores in many biopsies classified as no rejection, with ABMR activity in many TCMR biopsies and TCMR activity in many ABMR biopsies. In biopsies classified as no rejection histologically and molecularly, molecular TCMR classifier scores correlated with increases in histologic TCMR features and molecular injury, lower eGFR, and higher risk of graft loss, and molecular ABMR activity correlated with increased glomerulitis and donor-specific antibody. No rejection biopsies with high subthreshold TCMR or ABMR activity had a higher probability of having TCMR or ABMR respectively diagnosed in a future biopsy. We conclude that many kidney transplant recipients have unrecognized subthreshold TCMR or ABMR activity, with significant implications for future problems.
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada; University of Alberta, Edmonton, AB, Canada.
| | | | | | | | - Klemens Budde
- Charite-Medical University of Berlin, Berlin, Germany
| | | | - Martina Mackova
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
| | - Jessica Chang
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
| | | | | | - Gaurav Gupta
- Virginia Commonwealth University, Richmond, VA, USA
| | | | - Ondrej Viklicky
- Institute for Experimental and Clinical Medicine, Prague, Czech Republic
| | | | - Tarek Alhamad
- Washington University at St. Louis, St. Louis, MO, USA
| | - Sanjiv Anand
- Intermountain Transplant Services, Murray, UT, USA
| | - Miha Arnol
- University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Adam Bingaman
- Methodist Transplant and Specialty Hospital, San Antonio, TX, USA
| | | | - Daniel Brennan
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Kevin Chow
- The Royal Melbourne Hospital, Parkville, Australia
| | | | | | | | | | | | | | | | | | - Iman Francis
- Henry Ford Transplant Institute, Detroit, MI, USA
| | - Justyna Fryc
- Medical University in Bialystok, Białystok, Poland
| | - John Gill
- St. Paul's Hospital, Vancouver, BC, Canada
| | | | | | | | - Ryszard Grenda
- The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Petra Hruba
- The Children's Memorial Health Institute, Warsaw, Poland
| | - Peter Hughes
- The Royal Melbourne Hospital, Parkville, Australia
| | | | | | - Layla Kamal
- Virginia Commonwealth University, Richmond, VA, USA
| | | | - Sam Kant
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Nika Kojc
- University of Ljubljana, Ljubljana, Slovenia
| | | | - James Lan
- St. Paul's Hospital, Vancouver, BC, Canada
| | - Roslyn Mannon
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Marius Miglinas
- Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | | | - Seth Narins
- PinnacleHealth Transplant Associates, Harrisburg, PA, USA
| | | | - Anita Patel
- Henry Ford Transplant Institute, Detroit, MI, USA
| | | | | | | | | | | | | | | | - Sung Shin
- University of Ulsan College of Medicine/Assan Medical Center, Seoul, South Korea
| | | | | | | | | | - Ashish Solanki
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | | | | - Harold Yang
- PinnacleHealth Transplant Associates, Harrisburg, PA, USA
| | - Ziad Zaky
- Cleveland Clinic Foundation, Cleveland, OH, USA
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Schapranow MP, Bayat M, Rasheed A, Naik M, Graf V, Schmidt D, Budde K, Cardinal H, Sapir-Pichhadze R, Fenninger F, Sherwood K, Keown P, Günther OP, Pandl KD, Leiser F, Thiebes S, Sunyaev A, Niemann M, Schimanski A, Klein T. NephroCAGE-German-Canadian Consortium on AI for Improved Kidney Transplantation Outcome: Protocol for an Algorithm Development and Validation Study. JMIR Res Protoc 2023; 12:e48892. [PMID: 38133915 PMCID: PMC10770792 DOI: 10.2196/48892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Recent advances in hardware and software enabled the use of artificial intelligence (AI) algorithms for analysis of complex data in a wide range of daily-life use cases. We aim to explore the benefits of applying AI to a specific use case in transplant nephrology: risk prediction for severe posttransplant events. For the first time, we combine multinational real-world transplant data, which require specific legal and technical protection measures. OBJECTIVE The German-Canadian NephroCAGE consortium aims to develop and evaluate specific processes, software tools, and methods to (1) combine transplant data of more than 8000 cases over the past decades from leading transplant centers in Germany and Canada, (2) implement specific measures to protect sensitive transplant data, and (3) use multinational data as a foundation for developing high-quality prognostic AI models. METHODS To protect sensitive transplant data addressing the first and second objectives, we aim to implement a decentralized NephroCAGE federated learning infrastructure upon a private blockchain. Our NephroCAGE federated learning infrastructure enables a switch of paradigms: instead of pooling sensitive data into a central database for analysis, it enables the transfer of clinical prediction models (CPMs) to clinical sites for local data analyses. Thus, sensitive transplant data reside protected in their original sites while the comparable small algorithms are exchanged instead. For our third objective, we will compare the performance of selected AI algorithms, for example, random forest and extreme gradient boosting, as foundation for CPMs to predict severe short- and long-term posttransplant risks, for example, graft failure or mortality. The CPMs will be trained on donor and recipient data from retrospective cohorts of kidney transplant patients. RESULTS We have received initial funding for NephroCAGE in February 2021. All clinical partners have applied for and received ethics approval as of 2022. The process of exploration of clinical transplant database for variable extraction has started at all the centers in 2022. In total, 8120 patient records have been retrieved as of August 2023. The development and validation of CPMs is ongoing as of 2023. CONCLUSIONS For the first time, we will (1) combine kidney transplant data from nephrology centers in Germany and Canada, (2) implement federated learning as a foundation to use such real-world transplant data as a basis for the training of CPMs in a privacy-preserving way, and (3) develop a learning software system to investigate population specifics, for example, to understand population heterogeneity, treatment specificities, and individual impact on selected posttransplant outcomes. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/48892.
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Affiliation(s)
- Matthieu-P Schapranow
- Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Mozhgan Bayat
- Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Aadil Rasheed
- Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Marcel Naik
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Verena Graf
- Geschäftsbereich IT, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Danilo Schmidt
- Geschäftsbereich IT, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Klemens Budde
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Héloïse Cardinal
- Research Centre, Centre Hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Ruth Sapir-Pichhadze
- Division of Nephrology and Multi-Organ Transplant Program, Department of Medicine and Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Franz Fenninger
- Division of Nephrology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Karen Sherwood
- Division of Nephrology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Paul Keown
- Division of Nephrology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Konstantin D Pandl
- Department of Economics and Management, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Florian Leiser
- Department of Economics and Management, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Scott Thiebes
- Department of Economics and Management, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ali Sunyaev
- Department of Economics and Management, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Ho QY, Phang CY, Liew IT, Lai ML, Tien CSY, Thangaraju S, Chan M, Kee T. Unrepresented human leucocyte antigen alleles in single-antigen bead assays: A single-centre cohort study. Int J Immunogenet 2023; 50:306-315. [PMID: 37776087 DOI: 10.1111/iji.12639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/25/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
Human leucocyte antigen (HLA) alleles may generate antibodies that are undetectable by routine single-antigen beads (SABs) assays if their unique epitopes are unrepresented. We aimed to describe the prevalence and explore the potential impact of unrepresented HLA alleles in standard SAB kits in our cohort. All individuals who had undergone two-field HLA typing (HLA-A/B/C/DRB1/DQA1/-DQB1/-DPA1/-DPB1) from February 2021 to July 2023 were included. Two-field HLA-DRB3/4/5 typing was imputed. Each unrepresented allele was compared with the most similar represented allele in the standard LABScreen, LABScreen ExPlex (One Lambda) and the LIFECODES (Immucor) SAB kits. Differences in eplet expression (HLA Eplet Registry) were identified. Differences in three-dimensional molecular structures were visualized using generated models (SWISS-MODEL). Two-field HLA typing was performed for 116 individuals. Overall, 16.7% of all HLA alleles, found in 36.2% of individuals, were unrepresented by all SAB test kits. Four eplets, found in 12.9% of individuals, were unrepresented in at least 1 SAB kit. Non-Chinese individuals were more likely to have unrepresented HLA alleles and eplets than Chinese individuals. There were differences in HLA allele and eplet representation amongst the different SAB test kits. Use of supplementary SAB test kits may improve HLA allele and eplet representation. Although some HLA alleles were unrepresented, most epitopes were represented in current SAB kits. However, some unrepresented alleles may contain epitopes which may generate undetectable antibodies. Further studies may be needed to investigate the potential clinical impact of these unrepresented alleles and eplets, especially in certain ethnic populations or at-risk individuals.
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Affiliation(s)
- Quan Yao Ho
- Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
- SingHealth Duke-NUS Transplant Centre, Singapore, Singapore
| | - Chew Yen Phang
- Blood Services Group, Health Sciences Authority, Singapore, Singapore
| | - Ian Tatt Liew
- Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
- SingHealth Duke-NUS Transplant Centre, Singapore, Singapore
| | - May Ling Lai
- Blood Services Group, Health Sciences Authority, Singapore, Singapore
| | - Carolyn Shan-Yeu Tien
- Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
- SingHealth Duke-NUS Transplant Centre, Singapore, Singapore
| | - Sobhana Thangaraju
- Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
- SingHealth Duke-NUS Transplant Centre, Singapore, Singapore
| | - Marieta Chan
- Blood Services Group, Health Sciences Authority, Singapore, Singapore
| | - Terence Kee
- Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
- SingHealth Duke-NUS Transplant Centre, Singapore, Singapore
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