A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients
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....
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-01-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-44595-z |
| _version_ | 1797349863560577024 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | Daniel Yoo |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T12:36:32Z |
| format | Article |
| id | doaj.art-764f1576def44d5e8b7b4d5c1a4cde8f |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-08T12:36:32Z |
| publishDate | 2024-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-764f1576def44d5e8b7b4d5c1a4cde8f2024-01-21T12:26:26ZengNature PortfolioNature Communications2041-17232024-01-0115111210.1038/s41467-023-44595-zA Machine Learning-Driven Virtual Biopsy System For Kidney Transplant PatientsDaniel Yoo0Gillian Divard1Marc Raynaud2Aaron Cohen3Tom D. Mone4John Thomas Rosenthal5Andrew J. Bentall6Mark D. Stegall7Maarten Naesens8Huanxi Zhang9Changxi Wang10Juliette Gueguen11Nassim Kamar12Antoine Bouquegneau13Ibrahim Batal14Shana M. Coley15John S. Gill16Federico Oppenheimer17Erika De Sousa-Amorim18Dirk R. J. Kuypers19Antoine Durrbach20Daniel Seron21Marion Rabant22Jean-Paul Duong Van Huyen23Patricia Campbell24Soroush Shojai25Michael Mengel26Oriol Bestard27Nikolina Basic-Jukic28Ivana Jurić29Peter Boor30Lynn D. Cornell31Mariam P. Alexander32P. Toby Coates33Christophe Legendre34Peter P. Reese35Carmen Lefaucheur36Olivier Aubert37Alexandre Loupy38Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationUniversité Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationUniversité Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationOneLegacyOneLegacyDavid Geffen School of Medicine at UCLADivision of Nephrology and Hypertension, Mayo Clinic Transplant CenterDepartment of Surgery, Mayo ClinicDepartment of Microbiology, Immunology and Transplantation, KU LeuvenOrgan Transplant Center, First Affiliated Hospital, Sun Yat-sen University, GuangzhouOrgan Transplant Center, First Affiliated Hospital, Sun Yat-sen University, GuangzhouNéphrologie-Immunologie Clinique, Hôpital Bretonneau, CHU ToursDepartment of Nephrology and Organ Transplantation, Paul Sabatier University, INSERMDepartment of Nephrology-Dialysis-Transplantation, Centre hospitalier universitaire de LiègeDepartment of Pathology and Cell Biology, Columbia University Medical CenterDepartment of Pathology and Cell Biology, Columbia University Medical CenterDivision of Nephrology, Department of Medicine, University of British ColumbiaKidney Transplant Department, Hospital Clínic i Provincial de BarcelonaKidney Transplant Department, Hospital Clínic i Provincial de BarcelonaDepartment of Microbiology, Immunology and Transplantation, KU LeuvenDepartment of Nephrology, AP-HP Hôpital Henri MondorNephrology Department, Hospital Vall d’Hebrón, Autonomous University of BarcelonaDepartment of Pathology, Necker-Enfants Malades Hospital, Assistance Publique - Hôpitaux de ParisUniversité Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationFaculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of AlbertaFaculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of AlbertaFaculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of AlbertaNephrology Department, Hospital Vall d’Hebrón, Autonomous University of BarcelonaDepartment of nephrology, arterial hypertension, dialysis and transplantation, University Hospital Centre ZagrebDepartment of nephrology, arterial hypertension, dialysis and transplantation, University Hospital Centre ZagrebInstitute of Pathology, RWTH Aachen University HospitalDepartment of Laboratory Medicine and Pathology, Mayo ClinicDepartment of Laboratory Medicine and Pathology, Mayo ClinicDepartment of Renal and Transplantation, University of Adelaide, Royal Adelaide Hospital CampusUniversité Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationUniversité Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationUniversité Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationUniversité Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationUniversité Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ RegenerationAbstract 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.https://doi.org/10.1038/s41467-023-44595-z |
| spellingShingle | 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 A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients Nature Communications |
| title | A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients |
| title_full | A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients |
| title_fullStr | A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients |
| title_full_unstemmed | A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients |
| title_short | A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients |
| title_sort | machine learning driven virtual biopsy system for kidney transplant patients |
| url | https://doi.org/10.1038/s41467-023-44595-z |
| work_keys_str_mv | AT danielyoo amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT gilliandivard amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT marcraynaud amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT aaroncohen amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT tomdmone amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT johnthomasrosenthal amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT andrewjbentall amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT markdstegall amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT maartennaesens amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT huanxizhang amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT changxiwang amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT juliettegueguen amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT nassimkamar amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT antoinebouquegneau amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT ibrahimbatal amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT shanamcoley amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT johnsgill amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT federicooppenheimer amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT erikadesousaamorim amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT dirkrjkuypers amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT antoinedurrbach amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT danielseron amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT marionrabant amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT jeanpaulduongvanhuyen amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT patriciacampbell amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT soroushshojai amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT michaelmengel amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT oriolbestard amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT nikolinabasicjukic amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT ivanajuric amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT peterboor amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT lynndcornell amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT mariampalexander amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT ptobycoates amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT christophelegendre amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT peterpreese amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT carmenlefaucheur amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT olivieraubert amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT alexandreloupy amachinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT danielyoo machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT gilliandivard machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT marcraynaud machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT aaroncohen machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT tomdmone machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT johnthomasrosenthal machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT andrewjbentall machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT markdstegall machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT maartennaesens machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT huanxizhang machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT changxiwang machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT juliettegueguen machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT nassimkamar machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT antoinebouquegneau machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT ibrahimbatal machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT shanamcoley machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT johnsgill machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT federicooppenheimer machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT erikadesousaamorim machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT dirkrjkuypers machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT antoinedurrbach machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT danielseron machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT marionrabant machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT jeanpaulduongvanhuyen machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT patriciacampbell machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT soroushshojai machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT michaelmengel machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT oriolbestard machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT nikolinabasicjukic machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT ivanajuric machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT peterboor machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT lynndcornell machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT mariampalexander machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT ptobycoates machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT christophelegendre machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT peterpreese machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT carmenlefaucheur machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT olivieraubert machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients AT alexandreloupy machinelearningdrivenvirtualbiopsysystemforkidneytransplantpatients |