Nature Communications (Jan 2024)
A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients
- Daniel Yoo,
- Gillian Divard,
- Marc Raynaud,
- Aaron Cohen,
- Tom D. Mone,
- John Thomas Rosenthal,
- Andrew J. Bentall,
- Mark D. Stegall,
- Maarten Naesens,
- Huanxi Zhang,
- Changxi Wang,
- Juliette Gueguen,
- Nassim Kamar,
- Antoine Bouquegneau,
- Ibrahim Batal,
- Shana M. Coley,
- John S. Gill,
- Federico Oppenheimer,
- Erika De Sousa-Amorim,
- Dirk R. J. Kuypers,
- Antoine Durrbach,
- Daniel Seron,
- Marion Rabant,
- Jean-Paul Duong Van Huyen,
- Patricia Campbell,
- Soroush Shojai,
- Michael Mengel,
- Oriol Bestard,
- Nikolina Basic-Jukic,
- Ivana Jurić,
- Peter Boor,
- Lynn D. Cornell,
- Mariam P. Alexander,
- P. Toby Coates,
- Christophe Legendre,
- Peter P. Reese,
- Carmen Lefaucheur,
- Olivier Aubert,
- Alexandre Loupy
Affiliations
- Daniel Yoo
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- Gillian Divard
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- Marc Raynaud
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- Aaron Cohen
- OneLegacy
- Tom D. Mone
- OneLegacy
- John Thomas Rosenthal
- David Geffen School of Medicine at UCLA
- Andrew J. Bentall
- Division of Nephrology and Hypertension, Mayo Clinic Transplant Center
- Mark D. Stegall
- Department of Surgery, Mayo Clinic
- Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven
- Huanxi Zhang
- Organ Transplant Center, First Affiliated Hospital, Sun Yat-sen University, Guangzhou
- Changxi Wang
- Organ Transplant Center, First Affiliated Hospital, Sun Yat-sen University, Guangzhou
- Juliette Gueguen
- Néphrologie-Immunologie Clinique, Hôpital Bretonneau, CHU Tours
- Nassim Kamar
- Department of Nephrology and Organ Transplantation, Paul Sabatier University, INSERM
- Antoine Bouquegneau
- Department of Nephrology-Dialysis-Transplantation, Centre hospitalier universitaire de Liège
- Ibrahim Batal
- Department of Pathology and Cell Biology, Columbia University Medical Center
- Shana M. Coley
- Department of Pathology and Cell Biology, Columbia University Medical Center
- John S. Gill
- Division of Nephrology, Department of Medicine, University of British Columbia
- Federico Oppenheimer
- Kidney Transplant Department, Hospital Clínic i Provincial de Barcelona
- Erika De Sousa-Amorim
- Kidney Transplant Department, Hospital Clínic i Provincial de Barcelona
- Dirk R. J. Kuypers
- Department of Microbiology, Immunology and Transplantation, KU Leuven
- Antoine Durrbach
- Department of Nephrology, AP-HP Hôpital Henri Mondor
- Daniel Seron
- Nephrology Department, Hospital Vall d’Hebrón, Autonomous University of Barcelona
- Marion Rabant
- Department of Pathology, Necker-Enfants Malades Hospital, Assistance Publique - Hôpitaux de Paris
- Jean-Paul Duong Van Huyen
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- Patricia Campbell
- Faculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of Alberta
- Soroush Shojai
- Faculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of Alberta
- Michael Mengel
- Faculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of Alberta
- Oriol Bestard
- Nephrology Department, Hospital Vall d’Hebrón, Autonomous University of Barcelona
- Nikolina Basic-Jukic
- Department of nephrology, arterial hypertension, dialysis and transplantation, University Hospital Centre Zagreb
- Ivana Jurić
- Department of nephrology, arterial hypertension, dialysis and transplantation, University Hospital Centre Zagreb
- Peter Boor
- Institute of Pathology, RWTH Aachen University Hospital
- Lynn D. Cornell
- Department of Laboratory Medicine and Pathology, Mayo Clinic
- Mariam P. Alexander
- Department of Laboratory Medicine and Pathology, Mayo Clinic
- P. Toby Coates
- Department of Renal and Transplantation, University of Adelaide, Royal Adelaide Hospital Campus
- Christophe Legendre
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- Peter P. Reese
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- Carmen Lefaucheur
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- Olivier Aubert
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- Alexandre Loupy
- Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration
- DOI
- https://doi.org/10.1038/s41467-023-44595-z
- Journal volume & issue
-
Vol. 15,
no. 1
pp. 1 – 12
Abstract
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.
