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1. Results from part A of the multi-center, double-blind, randomized, placebo-controlled NefIgArd trial, which evaluated targeted-release formulation of budesonide for the treatment of primary immunoglobulin A nephropathy

Author

Jonathan Barratt, Richard Lafayette, Jens Kristensen, Andrew Stone, Daniel Cattran, Jürgen Floege, Vladimir Tesar, Hernán Trimarchi, Hong Zhang, Necmi Eren, Alexander Paliege, Brad H. Rovin, Guillermo Fragale, Alejandra Karl, Patricia Losisolo, Ivan Gonzalez Hoyos, Mauro Guillermo Lampo, Matias Monkowski, Jorge De La Fuente, Magdalena Alvarez, Daniela Stoppa, Carlos Chiurchiu, Pablo Antonio Novoa, Marcelo Orias, Maria Belen Barron, Ana Giotto, Mariano Arriola, Evelin Cassini, Rafael Maldonado, Maria Paula Dionisi, Jessica Ryan, Nigel Toussaint, Grant Luxton, Chen Au Peh, Vicki Levidiotis, Ross Francis, Richard Phoon, Elena Fedosiuk, Dmitry Toropilov, Ruslan Yakubtsevich, Elena Mikhailova, Christophe Bovy, Nathalie Demoulin, Jean-Michel Hougardy, Bart Maes, Marijn Speeckaert, Louis-Philippe Laurin, Sean Barbour, Melanie Masse, Michelle Hladunewich, Heather Reich, Serge Cournoyer, Karthik Tennankore, Jicheng Lv, Zhangsuo Liu, Caili Wang, Shaomei Li, Qun Luo, Zhaohui Ni, Tiekun Yan, Ping Fu, Hong Cheng, Bicheng Liu, Wanhong Lu, Jianqin Wang, Qinkai Chen, DeGuang Wang, Zuying Xiong, Menghua Chen, Yan Xu, Jiali Wei, Pearl Pai, Lianhua Chen, Jitka Rehorova, Dita Maixnerova, Roman Safranek, Ivan Rychlik, Miroslav Hruby, Satu Makela, Kati Vaaraniemi, Fernanda Ortiz, Eric Alamartine, Maite Daroux, Claire Cartery, Francois Vrtovsnik, Jean-Emmanuel Serre, Eleni Stamellou, Volker Vielhauer, Christian Hugo, Klemens Budde, Britta Otte, Martin Nitschke, Evangelia Ntounousi, Ioannis Boletis, Aikaterini Papagianni, Dimitrios Goumenos, Konstantinos Stylianou, Synodi Zermpala, Ciro Esposito, Mario Gennaro Cozzolino, Sara Maria Viganò, Loreto Gesualdo, Michal Nowicki, Tomasz Stompor, Ilona Kurnatowska, Sung Gyun Kim, Yong-Lim Kim, Ki-Ryang Na, Dong Ki Kim, Su-Hyun Kim, Luis Quintana Porras, Eva Rodriguez Garcia, Irene Agraz Pamplona, Alfons Segarra, Marian Goicoechea, Bengt Fellstrom, Sigrid Lundberg, Peter Hemmingsson, Gregor Guron, Anna Sandell, Cheng-Hsu Chen, Bulent Tokgoz, Soner Duman, Mehmet Riza Altiparmak, Metin Ergul, Peter Maxwell, Patrick Mark, Kieran McCafferty, Arif Khwaja, Chee Kay Cheung, Matthew Hall, Albert Power, Durga Kanigicherla, Richard Baker, Jim Moriarty, Amr Mohamed, Joseph Aiello, Pietro Canetta, Isabelle Ayoub, Derrick Robinson, Surabhi Thakar, Amy Mottl, Isaac Sachmechi, Bernard Fischbach, Harmeet Singh, Jeffrey Mulhern, Fahmeedah Kamal, Douglas Linfert, Dana Rizk, Shikha Wadhwani, Menaka Sarav, Kirk Campbell, Gaia Coppock, Randy Luciano, John Sedor, Rupali Avasare, Wai Lang Lau, Zermpala, Synodi, Esposito, Ciro, Cozzolino, Mario Gennaro, Viganò, Sara Maria, Gesualdo, Loreto, Nowicki, Michal, Stompor, Tomasz, Kurnatowska, Ilona, Kim, Sung Gyun, Kim, Yong-Lim, Na, Ki-Ryang, Kim, Dong Ki, Kim, Su-Hyun, Porras, Luis Quintana, Garcia, Eva Rodriguez, Pamplona, Irene Agraz, Segarra, Alfons, Goicoechea, Marian, Fellstrom, Bengt, Lundberg, Sigrid, Hemmingsson, Peter, Guron, Gregor, Sandell, Anna, Chen, Cheng-Hsu, Tokgoz, Bulent, Duman, Soner, Altiparmak, Mehmet Riza, Ergul, Metin, Maxwell, Peter, Mark, Patrick, Fragale, Guillermo, McCafferty, Kieran, Khwaja, Arif, Cheung, Chee Kay, Hall, Matthew, Power, Albert, Kanigicherla, Durga, Baker, Richard, Moriarty, Jim, Mohamed, Amr, Aiello, Joseph, Karl, Alejandra, Canetta, Pietro, Ayoub, Isabelle, Robinson, Derrick, Thakar, Surabhi, Mottl, Amy, Sachmechi, Isaac, Fischbach, Bernard, Singh, Harmeet, Mulhern, Jeffrey, Kamal, Fahmeedah, Losisolo, Patricia, Linfert, Douglas, Rizk, Dana, Wadhwani, Shikha, Sarav, Menaka, Campbell, Kirk, Coppock, Gaia, Luciano, Randy, Sedor, John, Avasare, Rupali, Lau, Wai Lang, Trimarchi, Hernán, Hoyos, Ivan Gonzalez, Lampo, Mauro Guillermo, Monkowski, Matias, De La Fuente, Jorge, Alvarez, Magdalena, Stoppa, Daniela, Chiurchiu, Carlos, Novoa, Pablo Antonio, Orias, Marcelo, Barron, Maria Belen, Giotto, Ana, Arriola, Mariano, Cassini, Evelin, Maldonado, Rafael, Dionisi, Maria Paula, Ryan, Jessica, Toussaint, Nigel, Luxton, Grant, Peh, Chen Au, Levidiotis, Vicki, Francis, Ross, Phoon, Richard, Fedosiuk, Elena, Toropilov, Dmitry, Yakubtsevich, Ruslan, Mikhailova, Elena, Bovy, Christophe, Demoulin, Nathalie, Hougardy, Jean-Michel, Maes, Bart, Speeckaert, Marijn, Laurin, Louis-Philippe, Barbour, Sean, Masse, Melanie, Hladunewich, Michelle, Reich, Heather, Cournoyer, Serge, Tennankore, Karthik, Lv, Jicheng, Liu, Zhangsuo, Wang, Caili, Li, Shaomei, Luo, Qun, Ni, Zhaohui, Yan, Tiekun, Fu, Ping, Cheng, Hong, Liu, Bicheng, Lu, Wanhong, Wang, Jianqin, Chen, Qinkai, Wang, DeGuang, Xiong, Zuying, Chen, Menghua, Xu, Yan, Wei, Jiali, Pai, Pearl, Chen, Lianhua, Rehorova, Jitka, Maixnerova, Dita, Safranek, Roman, Rychlik, Ivan, Hruby, Miroslav, Makela, Satu, Vaaraniemi, Kati, Ortiz, Fernanda, Alamartine, Eric, Daroux, Maite, Cartery, Claire, Vrtovsnik, Francois, Serre, Jean-Emmanuel, Stamellou, Eleni, Vielhauer, Volker, Hugo, Christian, Budde, Klemens, Otte, Britta, Nitschke, Martin, Ntounousi, Evangelia, Boletis, Ioannis, Papagianni, Aikaterini, Goumenos, Dimitrios, Stylianou, Konstantinos, UCL - SSS/IREC/NEFR - Pôle de Néphrologie, and UCL - (SLuc) Service de néphrologie

Subjects
gut-associated lymphoid tissue, glucocorticoids, Nephrology, glomerular disease, IgA nephropathy
Abstract

Kidney international 103(2), 391-402 (2022). doi:10.1016/j.kint.2022.09.017, Published by Elsevier, New York, NY

Published
2022
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2. Development and external validation of a diagnostic model for biopsy-proven acute interstitial nephritis using electronic health record data

Author

Dennis G Moledina, Michael T Eadon, Frida Calderon, Yu Yamamoto, Melissa Shaw, Mark A Perazella, Michael Simonov, Randy Luciano, Tae-Hwi Schwantes-An, Gilbert Moeckel, Michael Kashgarian, Michael Kuperman, Wassim Obeid, Lloyd G Cantley, Chirag R Parikh, and F Perry Wilson

Subjects
Transplantation, Nephrology, Tumor Necrosis Factor-alpha, Creatinine, Biopsy, Interleukin-9, food and beverages, Humans, Electronic Health Records, Nephritis, Interstitial, Original Article, Biomarkers
Abstract

Background Patients with acute interstitial nephritis (AIN) can present without typical clinical features, leading to a delay in diagnosis and treatment. We therefore developed and validated a diagnostic model to identify patients at risk of AIN using variables from the electronic health record. Methods In patients who underwent a kidney biopsy at Yale University between 2013 and 2018, we tested the association of >150 variables with AIN, including demographics, comorbidities, vital signs and laboratory tests (training set 70%). We used least absolute shrinkage and selection operator methodology to select prebiopsy features associated with AIN. We performed area under the receiver operating characteristics curve (AUC) analysis with internal (held-out test set 30%) and external validation (Biopsy Biobank Cohort of Indiana). We tested the change in model performance after the addition of urine biomarkers in the Yale AIN study. Results We included 393 patients (AIN 22%) in the training set, 158 patients (AIN 27%) in the test set, 1118 patients (AIN 11%) in the validation set and 265 patients (AIN 11%) in the Yale AIN study. Variables in the selected model included serum creatinine {adjusted odds ratio [aOR] 2.31 [95% confidence interval (CI) 1.42–3.76]}, blood urea nitrogen:creatinine ratio [aOR 0.40 (95% CI 0.20–0.78)] and urine dipstick specific gravity [aOR 0.95 (95% CI 0.91–0.99)] and protein [aOR 0.39 (95% CI 0.23–0.68)]. This model showed an AUC of 0.73 (95% CI 0.64–0.81) in the test set, which was similar to the AUC in the external validation cohort [0.74 (95% CI 0.69–0.79)]. The AUC improved to 0.84 (95% CI 0.76–0.91) upon the addition of urine interleukin-9 and tumor necrosis factor-α. Conclusions We developed and validated a statistical model that showed a modest AUC for AIN diagnosis, which improved upon the addition of urine biomarkers. Future studies could evaluate this model and biomarkers to identify unrecognized cases of AIN.

Published
2021

3. Rationale and design of the Kidney Precision Medicine Project

Author

Ian H. de Boer, Charles E. Alpers, Evren U. Azeloglu, Ulysses G.J. Balis, Jonathan M. Barasch, Laura Barisoni, Kristina N. Blank, Andrew S. Bomback, Keith Brown, Pierre C. Dagher, Ashveena L. Dighe, Michael T. Eadon, Tarek M. El-Achkar, Joseph P. Gaut, Nir Hacohen, Yongqun He, Jeffrey B. Hodgin, Sanjay Jain, John A. Kellum, Krzysztof Kiryluk, Richard Knight, Zoltan G. Laszik, Chrysta Lienczewski, Laura H. Mariani, Robyn L. McClelland, Steven Menez, Dennis G. Moledina, Sean D. Mooney, John F. O’Toole, Paul M. Palevsky, Chirag R. Parikh, Emilio D. Poggio, Sylvia E. Rosas, Matthew R. Rosengart, Minnie M. Sarwal, Jennifer A. Schaub, John R. Sedor, Kumar Sharma, Becky Steck, Robert D. Toto, Olga G. Troyanskaya, Katherine R. Tuttle, Miguel A. Vazquez, Sushrut S. Waikar, Kayleen Williams, Francis Perry Wilson, Kun Zhang, Ravi Iyengar, Matthias Kretzler, Jonathan Himmelfarb, Stewart Lecker, Isaac Stillman, Sushrut Waikar, Gearoid Mcmahon, Astrid Weins, Samuel Short, Paul Hoover, Mark Aulisio, Leslie Cooperman, Leal Herlitz, John O’Toole, Emilio Poggio, John Sedor, Stacey Jolly, Paul Appelbaum, Olivia Balderes, Jonathan Barasch, Andrew Bomback, Pietro A. Canetta, Vivette D. d’Agati, Satoru Kudose, Karla Mehl, Jai Radhakrishnan, Chenhua Weng, Theodore Alexandrov, Tarek Ashkar, Daria Barwinska, Pierre Dagher, Kenneth Dunn, Michael Eadon, Michael Ferkowicz, Katherine Kelly, Timothy Sutton, Seth Winfree, Chirag Parikh, Avi Rosenberg, Pam Villalobos, Rubab Malik, Derek Fine, Mohammed Atta, Jose Manuel Monroy Trujillo, Alison Slack, Sylvia Rosas, Mark Williams, Evren Azeloglu, Cijang (John) He, Jens Hansen, Samir Parikh, Brad Rovin, Chris Anderton, Ljiljana Pasa-Tolic, Dusan Velickovic, Jessica Lukowski, George (Holt) Oliver, Joseph Ardayfio, Jack Bebiak, Taneisha Campbell, Catherine Campbell, Lynda Hayashi, Nichole Jefferson, Robert Koewler, Glenda Roberts, John Saul, Anna Shpigel, Edith Christine Stutzke, Lorenda Wright, Leslie Miegs, Roy Pinkeney, Rachel Sealfon, Olga Troyanskaya, Katherine Tuttle, Dejan Dobi, Yury Goltsev, Blue Lake, Maria Joanes, Zoltan Laszik, Andrew Schroeder, Minnie Sarwal, Tara Sigdel, Ulysses Balis, Victoria Blanc, Oliver He, Jeffrey Hodgin, Laura Mariani, Rajasree Menon, Edgar Otto, Jennifer Schaub, Sean Eddy, Michele Elder, Daniel Hall, John Kellum, Mary Kruth, Raghav Murugan, Paul Palevsky, Parmjeet Randhawa, Matthew Rosengart, Sunny Sims-Lucas, Mary Stefanick, Stacy Stull, Mitchell Tublin, Charles Alpers, Ian de Boer, Ashveena Dighe, Robyn Mcclelland, Sean Mooney, Stuart Shankland, Kristina Blank, Jonas Carson, Frederick Dowd, Zach Drager, Christopher Park, Guanshi Zhang, Shweta Bansal, Manjeri Venkatachalam, Asra Kermani, Simon Lee, Christopher Lu, Tyler Miller, Orson Moe, Harold Park, Kamalanathan Sambandam, Francisco Sanchez, Jose Torrealba, Toto Robert, Miguel Vazquez, Nancy Wang, Joe Gaut, Anitha Vijayan, Randy Luciano, Dennis Moledina, Ugwuowo Ugochukwu, and Sandy Alfano

Subjects
0301 basic medicine, Adult, Proteomics, medicine.medical_specialty, 030232 urology & nephrology, Subgroup analysis, Disease, urologic and male genital diseases, Kidney, Article, 03 medical and health sciences, 0302 clinical medicine, Diabetes mellitus, medicine, Humans, Prospective Studies, Precision Medicine, Renal Insufficiency, Chronic, Intensive care medicine, Prospective cohort study, business.industry, urogenital system, Acute kidney injury, Acute Kidney Injury, Precision medicine, medicine.disease, female genital diseases and pregnancy complications, 030104 developmental biology, medicine.anatomical_structure, Nephrology, business, Kidney disease
Abstract

Chronic kidney disease (CKD) and acute kidney injury (AKI) are common, heterogeneous, and morbid diseases. Mechanistic characterization of CKD and AKI in patients may facilitate a precision medicine approach to prevention, diagnosis, and treatment. The Kidney Precision Medicine Project aims to ethically and safely obtain kidney biopsies from participants with CKD or AKI, create a reference kidney atlas, and characterize disease subgroups to stratify patients based on molecular features of disease, clinical characteristics, and associated outcomes. An additional aim is to identify critical cells, pathways, and targets for novel therapies and preventive strategies. This project is a multicenter prospective cohort study of adults with CKD or AKI who undergo a protocol kidney biopsy for research purposes. This investigation focuses on kidney diseases that are most prevalent and therefore substantially burden the public health, including CKD attributed to diabetes or hypertension and AKI attributed to ischemic and toxic injuries. Reference kidney tissues (for example, living kidney donor biopsies) will also be evaluated. Traditional and digital pathology will be combined with transcriptomic, proteomic, and metabolomics analysis of the kidney tissue as well as deep clinical phenotyping for supervised and unsupervised subgroup analysis and systems biology analysis. Participants will be followed prospectively for ten years to ascertain clinical outcomes. Cell types, locations, and functions will be characterized in health and disease in an open, searchable, online kidney tissue atlas. All data from the Kidney Precision Medicine Project will be made readily available for broad use by scientists, clinicians, and patients.

Published
2021

5. Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline

Author

Michael J. Ferkowicz, Seth Winfree, Angela R. Sabo, Malgorzata M. Kamocka, Suraj Khochare, Daria Barwinska, Michael T. Eadon, Ying-Hua Cheng, Carrie L. Phillips, Timothy A. Sutton, Katherine J. Kelly, Pierre C. Dagher, Tarek M. El-Achkar, Kenneth W. Dunn, Richard Knight, Stewart Lecker, Isaac Stillman, Gearoid Mcmahon, Sus Waikar, Astrid Weins, Nir Hacohen, Paul Hoover, Mark Aulisio, Leslie Cooperman, Leal Herlitz, John O'toole, Emilio Poggio, John Sedor, Paul Appelbaum, Jonathan Barasch, Andrew Bomback, Vivette D'agati, Krzysztof Kiryluk, Karla Mehl, Ning (Sunny) Shang, Chenhua Weng, Laura Barisoni, Theodore Alexandrov, Tarek Ashkar, Pierre Dagher, Kenneth Dunn, Michael Eadon, Michael Ferkowicz, Katherine Kelly, Timothy Sutton, Steven Menez, Chirag Parikh, Avi Rosenberg, Pam Villalobos, Alison Slack, Sylvia Rosas, Mark Williams, Evren Azeloglu, Cijang (John) He, Ravi Iyengar, Samir Parikh, Chris Anderton, Ljiljana Pasa-Tolic, Dusan Velickovic, George (Holt) Oliver, Joseph Ardayfio, Jack Bebiak, Keith Brown, Taneisha Campbell, Catherine Campbell, Lynda Hayashi, Nichole Jefferson, Robert Koewler, Glenda Roberts, John Saul, Anna Shpigel, Edith Christine Stutzke, Lorenda Wright, Leslie Miegs, Roy Pinkeney, Rachel Sealfon, Olga Troyanskaya, Katherine Tuttle, Yury Goltsev, Blue Lake, Kun Zhang, Dejan Dobi, Maria Joanes, Zoltan Laszik, Garry Nolan, Andrew Schroeder, Ulysses Balis, Oliver He, Jeffrey Hodgin, Matthias Kretzler, Laura Mariani, Rajasree Menon, Edgar Otto, Jennifer Schaub, Becky Steck, Michele Elder, Daniel Hall, John Kellum, Mary Kruth, Raghav Murugan, Paul Palevsky, Parmjeet Randhawa, Matthew Rosengart, Sunny Sims-Lucas, Mary Stefanick, Stacy Stull, Mitchell Tublin, Charles Alpers, Ian De Boer, Malia Fullerton, Jonathan Himmelfarb, Robyn Mcclelland, Sean Mooney, Stuart Shankland, Kayleen Williams, Kristina Blank, Ashveena Dighe, Jonas Carson, Frederick Dowd, Zach Drager, Kumar Sharma, Guanshi Zhang, Asra Kermani, Simon Lee, Christopher Lu, Tyler Miller, Orson Moe, Harold Park, Kamalanathan Sambandam, Francisco Sanchez, Jose Torrealba, Toto Robert, Miguel Vazquez, Nancy Wang, Joe Gaut, Sanjay Jain, Anitha Vijayan, Randy Luciano, Dennis Moledina, Ugwuowo Ugochukwu, and Francis Perry Wilson

Subjects
0301 basic medicine, Computer science, Confocal, Cytological Techniques, Context (language use), Kidney, Article, Pathology and Forensic Medicine, law.invention, Flow cytometry, 03 medical and health sciences, 0302 clinical medicine, Imaging, Three-Dimensional, Confocal microscopy, law, Microscopy, medicine, Humans, Image analysis, Molecular Biology, Fluorescent Dyes, Microscopy, Confocal, medicine.diagnostic_test, Cell Biology, Autofluorescence, 030104 developmental biology, Microscopy, Fluorescence, Multiphoton, 030220 oncology & carcinogenesis, Cytometry, Software, Biomedical engineering
Abstract

The advent of personalized medicine has driven the development of novel approaches for obtaining detailed cellular and molecular information from clinical tissue samples. Tissue cytometry is a promising new technique that can be used to enumerate and characterize each cell in a tissue and, unlike flow cytometry and other single-cell techniques, does so in the context of the intact tissue, preserving spatial information that is frequently crucial to understanding a cell’s physiology, function, and behavior. However, the wide-scale adoption of tissue cytometry as a research tool has been limited by the fact that published examples utilize specialized techniques that are beyond the capabilities of most laboratories. Here we describe a complete and accessible pipeline, including methods of sample preparation, microscopy, image analysis, and data analysis for large-scale three-dimensional tissue cytometry of human kidney tissues. In this workflow, multiphoton microscopy of unlabeled tissue is first conducted to collect autofluorescence and second-harmonic images. The tissue is then labeled with eight fluorescent probes, and imaged using spectral confocal microscopy. The raw 16-channel images are spectrally deconvolved into 8-channel images, and analyzed using the Volumetric Tissue Exploration and Analysis (VTEA) software developed by our group. We applied this workflow to analyze millimeter-scale tissue samples obtained from human nephrectomies and from renal biopsies from individuals diagnosed with diabetic nephropathy, generating a quantitative census of tens of thousands of cells in each. Such analyses can provide useful insights that can be linked to the biology or pathology of kidney disease. The approach utilizes common laboratory techniques, is compatible with most commercially-available confocal microscope systems and all image and data analysis is conducted using the VTEA image analysis software, which is available as a plug-in for ImageJ. Tissue cytometry is a promising new microscopy technique that can be used to enumerate and characterize each cell in a tissue. Here the authors describe a complete and accessible pipeline, including methods of sample preparation, microscopy, image analysis, and data analysis for large-scale three-dimensional tissue cytometry of human kidney tissues.

Published
2020

6. Rationale and design of the Transformative Research in Diabetic Nephropathy (TRIDENT) Study

Author

Raymond R. Townsend, Paolo Guarnieri, Christos Argyropoulos, Shira Blady, Carine M. Boustany-Kari, Kishor Devalaraja-Narashimha, Lori Morton, Amy K. Mottl, Uptal Patel, Matthew Palmer, Michael J. Ross, Lea Sarov-Blat, Kathryn Steinbugler, Katalin Susztak, Randy Luciano, Michael Ross, Pietro Canetta, Krik Campbell, Jonathan Hogan, Amy Mottl, Oliver Lenz, Harold Szerlip, Shweta Bansal, Chip Brosius, Jeffery Schelling, Salem Almaani, Matthias Kretzler, Tamara Isakova, Rupali Avasare, and Richard Lafayette

Subjects
Adult, Aged, 80 and over, Male, Pathology, medicine.medical_specialty, Adolescent, business.industry, Biopsy, Kidney Glomerulus, Middle Aged, medicine.disease, Diabetic nephropathy, Observational Studies as Topic, Young Adult, Nephrology, Research Design, Glomerulus, Medicine, Humans, Diabetic Nephropathies, Female, Prospective Studies, business, Aged, Glomerular Filtration Rate
Published
2019

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