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      A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients

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      Nature Communications
      Nature Publishing Group UK
      Renal replacement therapy, Epidemiology, Pathology

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          Abstract

          In kidney transplantation, day-zero biopsies are used to assess organ quality and discriminate between donor-inherited lesions and those acquired post-transplantation. However, many centers do not perform such biopsies since they are invasive, costly and may delay the transplant procedure. We aim to generate a non-invasive virtual biopsy system using routinely collected donor parameters. Using 14,032 day-zero kidney biopsies from 17 international centers, we develop a virtual biopsy system. 11 basic donor parameters are used to predict four Banff kidney lesions: arteriosclerosis, arteriolar hyalinosis, interstitial fibrosis and tubular atrophy, and the percentage of renal sclerotic glomeruli. Six machine learning models are aggregated into an ensemble model. The virtual biopsy system shows good performance in the internal and external validation sets. We confirm the generalizability of the system in various scenarios. This system could assist physicians in assessing organ quality, optimizing allograft allocation together with discriminating between donor derived and acquired lesions post-transplantation.

          Abstract

          Despite being recommended, day-zero biopsies are often not performed, due to the cost and time. Here, the authors show that machine learning and donor’s basic parameters can predict the biopsy, offering a reliable virtual estimation of the day-zero biopsy findings.

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            Index for rating diagnostic tests

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              No free lunch theorems for optimization

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                Author and article information

                Contributors
                alexandre.loupy@inserm.fr
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                16 January 2024
                16 January 2024
                2024
                : 15
                : 554
                Affiliations
                [1 ]Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, ( https://ror.org/05f82e368) F-75015 Paris, France
                [2 ]GRID grid.413328.f, ISNI 0000 0001 2300 6614, Kidney Transplant Department, , Saint-Louis Hospital, Assistance Publique – Hôpitaux de Paris, ; Paris, France
                [3 ]OneLegacy, Los Angeles, CA USA
                [4 ]GRID grid.19006.3e, ISNI 0000 0000 9632 6718, David Geffen School of Medicine at UCLA, ; Los Angeles, CA USA
                [5 ]GRID grid.66875.3a, ISNI 0000 0004 0459 167X, Division of Nephrology and Hypertension, , Mayo Clinic Transplant Center, ; Rochester, MN USA
                [6 ]Department of Surgery, Mayo Clinic, ( https://ror.org/02qp3tb03) Rochester, MN USA
                [7 ]Department of Microbiology, Immunology and Transplantation, KU Leuven, ( https://ror.org/05f950310) Leuven, Belgium
                [8 ]Organ Transplant Center, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, ( https://ror.org/0064kty71) Guangdong, China
                [9 ]Néphrologie-Immunologie Clinique, Hôpital Bretonneau, CHU Tours, Tours, France
                [10 ]GRID grid.15781.3a, ISNI 0000 0001 0723 035X, Department of Nephrology and Organ Transplantation, , Paul Sabatier University, INSERM, ; Toulouse, France
                [11 ]Department of Nephrology-Dialysis-Transplantation, Centre hospitalier universitaire de Liège, ( https://ror.org/044s61914) Liège, Belgium
                [12 ]Department of Pathology and Cell Biology, Columbia University Medical Center, ( https://ror.org/01esghr10) New York, NY USA
                [13 ]Division of Nephrology, Department of Medicine, University of British Columbia, ( https://ror.org/03rmrcq20) Vancouver, BC Canada
                [14 ]GRID grid.410458.c, ISNI 0000 0000 9635 9413, Kidney Transplant Department, , Hospital Clínic i Provincial de Barcelona, ; Barcelona, Spain
                [15 ]GRID grid.412116.1, ISNI 0000 0004 1799 3934, Department of Nephrology, , AP-HP Hôpital Henri Mondor, ; Créteil, Île de France France
                [16 ]Nephrology Department, Hospital Vall d’Hebrón, Autonomous University of Barcelona, ( https://ror.org/052g8jq94) Barcelona, Spain
                [17 ]GRID grid.50550.35, ISNI 0000 0001 2175 4109, Department of Pathology, Necker-Enfants Malades Hospital, , Assistance Publique - Hôpitaux de Paris, ; Paris, France
                [18 ]Faculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of Alberta, ( https://ror.org/0160cpw27) Edmonton, AB Canada
                [19 ]Department of nephrology, arterial hypertension, dialysis and transplantation, University Hospital Centre Zagreb, ( https://ror.org/00r9vb833) Zagreb, Croatia
                [20 ]Institute of Pathology, RWTH Aachen University Hospital, ( https://ror.org/04xfq0f34) Aachen, Germany
                [21 ]Department of Laboratory Medicine and Pathology, Mayo Clinic, ( https://ror.org/02qp3tb03) Rochester, MN USA
                [22 ]GRID grid.1010.0, ISNI 0000 0004 1936 7304, Department of Renal and Transplantation, , University of Adelaide, Royal Adelaide Hospital Campus, ; Adelaide, SA Australia
                [23 ]GRID grid.50550.35, ISNI 0000 0001 2175 4109, Department of Kidney Transplantation, Necker-Enfants Malades Hospital, , Assistance Publique - Hôpitaux de Paris, ; Paris, France
                [24 ]GRID grid.25879.31, ISNI 0000 0004 1936 8972, Renal-Electrolyte and Hypertension Division, Perelman School of Medicine, , University of Pennsylvania, ; Philadephia, PA USA
                Author information
                http://orcid.org/0000-0002-8495-9782
                http://orcid.org/0000-0002-0686-5457
                http://orcid.org/0000-0002-2969-9121
                http://orcid.org/0000-0002-7222-3356
                http://orcid.org/0000-0001-9921-4284
                http://orcid.org/0000-0001-9072-9871
                http://orcid.org/0000-0003-0342-8179
                Article
                44595
                10.1038/s41467-023-44595-z
                10791605
                38228634
                da75d252-f5c6-4b72-abec-014de2fe5e4a
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 26 June 2023
                : 21 December 2023
                Funding
                Funded by: French government managed by the National Research Agency (ANR) with the grant agreement ANR-17-RHUS-0010 and European Union’s Horizon 2020 research and innovation program EU-TRAIN with the grant agreement no. 754995 provided financial support. The funders of this study had no role in the study design, data collection, analysis, or interpretation of the manuscript.
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                © Springer Nature Limited 2024

                Uncategorized
                renal replacement therapy,epidemiology,pathology
                Uncategorized
                renal replacement therapy, epidemiology, pathology

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