Publications

Debora L. Gisch, Michelle Brennan, Blue B. Lake, Jeannine Basta, Mark Keller, Ricardo Melo Ferreira, Shreeram Akilesh, Reetika Ghag, Charles Lu, Ying-Hua Cheng, Kimberly S. Collins, Samir V. Parikh, Brad H. Rovin, Lynn Robbins, Kimberly Y. Conklin, Dinh Diep, Bo Zhang, Amanda Knoten, Daria Barwinska, Mahla Asghari, Angela R. Sabo, Michael J. Ferkowicz, Timothy A Sutton, Katherine J Kelly, Ian H. De Boer, Sylvia E. Rosas, Krzysztof Kiryluk, Jeffrey B. Hodgin, Fadhl Alakwaa, Nichole Jefferson, Joseph P. Gaut, Nils Gehlenborg, Carrie L. Phillips, Tarek M. El-Achkar, Pierre C. Dagher, Takashi Hato, Kun Zhang, Jonathan Himmelfarb, Matthias Kretzler, Shamim Mollah, Kidney Precision Medicine Project (KPMP), Sanjay Jain, Michael Rauchman, Michael T. Eadon
Nature Communications
(
15(1):433
)
,
January 10, 2024
DOI:
10.1038/s41467-023-44467-6
|
PMID:
38199997
|
PMCID:
PMC10781985
Summary

Goal: Thisstudy sought to define regions of gene activation or repression that controlhuman kidney cells in states of health, injury, and repair to understand themolecular pathogenesis of kidney disease.

Results: Thestudy measures dual single nucleus RNA expression and chromatin accessibility,DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histonemodifications to decipher the chromatin landscape and gene regulation of thekidney in reference and adaptive injury states. We establish aspatially-anchored epigenomic atlas to define the kidney's active, silent, andregulatory accessible chromatin regions across the genome. Using this atlas, wenote distinct control of adaptive injury in different epithelial cell types. Aproximal tubule cell transcription factor network of ELF3, KLF6, and KLF10regulates the transition between health and injury, while in thick ascendinglimb cells this transition is regulated by NR2F1. Further, combinedperturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximaltubular cell subtypes, one of which manifested a repair trajectory afterknockout.

Implications forPatients: Cell injury states have been shown to correlatewith CKD progression. This study attempts to understand how cells transitionfrom health to injury and what genes control that transition. Thiscorresponding atlas will serve as a foundation to facilitate targetedcell-specific therapeutics by reprogramming gene regulatory networks.

Victoria-Castro, Angela M.; Corona-Villalobos, Celia P.; Xu, Alan Y.; Onul, Ingrid; Huynh, Courtney; Chen, Sarah W.; Ugwuowo, Ugochukwu; Sarkisova, Natalya; Dighe, Ashveena L.; Blank, Kristina N.; Blanc, Victoria M.; Rose, Michael P.; Himmelfarb, Jonathan; de Boer, Ian H.; Tuttle, Katherine R.; Roberts, Glenda V.; for the Kidney Precision Medicine Project
CJASN
(
)
,
October 23, 2023
DOI:
DOI: 10.2215/CJN.0000000000000334
|
PMID:
37871973
|
PMCID:
Summary

Goal:Scientists led by Angela Victoria-Castro and Celia Pamela Corona-Villabolos wanted to understand how people feel about kidney biopsies in the Kidney Precision Medicine Project. They aimed to learn about the emotions and physical experiences of participants during and after the biopsy, as well as the reasons why they decided to be part of the project.

Results:The study found that kidney biopsies can be emotionally challenging, causing anxiety for participants. People shared feelings of discomfort during and after the biopsy. Clear communication and informed consent were highlighted as crucial for participants to feel more at ease. The study also uncovered different reasons motivating people to join the project, providing valuable insights for improving the process.

Implications for Patients:For patients, this research shows that scientists care about their experiences. By understanding the emotional and physical impact of kidney biopsies, doctors can make the process more comfortable. The findings emphasize the importance of clear communication and ensuring patients have all the information they need before joining such studies, with the ultimate goal of improving the overall experience for patients in medical studies and making healthcare more patient-centered.

Tarek M. El-Achkar, Michael T. Eadon, Matthias Kretzler, Jonathan Himmelfarb, Kidney Precision Medicine Project
American Journal of Kidney Diseases
(
)
,
October 13, 2023
DOI:
https://doi.org/10.1053/j.ajkd.2023.08.015
|
PMID:
|
PMCID:
Summary

Chronic kidney disease (CKD) and acute kidney injury (AKI) are heterogeneous syndromes defined clinically by serial measures of kidney function. Each condition possesses strong histopathologic associations including glomerular obsolescence or acute tubular necrosis, respectively. Despite such characterization, there remains wide variation in patient outcomes and treatment responses. Precision medicine efforts, as exemplified by the Kidney Precision Medicine Project (KPMP), have begun to establish evolving, spatially-anchored, cellular and molecular atlases of the cell types, states and niches of the kidney in health and disease. The KPMP atlas provides molecular context for CKD and AKI disease drivers, and will help define subtypes of disease that are not readily apparent from canonical functional or histopathologic characterization, but instead appreciable through advanced clinical phenotyping, pathomic, transcriptomic, proteomic, epigenomic, and metabolomic interrogation of kidney biopsy samples. This perspective outlines the structure of the KPMP, its approach to the integration of these diverse datasets, and its major outputs relevant to future patient care.

Steven Menez, Steven G Coca, Dennis G Moledina, Yumeng Wen, Lili Chan Heather Thiessen-Philbrook, Wassim Obeid , Brian T Garibaldi , Evren U Azeloglu , Ugochukwu Ugwuowo , C John Sperati , Lois J Arend , Avi Z Rosenberg , Madhurima Kaushal , Sanjay Jain , F Perry Wilson , Chirag R Parikh ; TRIKIC Consortium
American Journal of Kidney Diseases
(
82(3)
)
,
September 1, 2023
DOI:
10.1053/j.ajkd.2023.03.010
|
PMID:
37263570
|
PMCID:
PMC10229201
Summary

Patients hospitalized with COVID-19 are at increased risk for long-term adverse health outcomes, but not all patients suffer long-term kidney dysfunction. Identification of patients with COVID-19 who are at high risk for adverse kidney events may have important implications in terms of nephrology follow-up and patient counseling. In this study, we found that the plasma biomarkers soluble tumor necrosis factor receptor 1 (sTNFR1) and sTNFR2 measured in hospitalized patients with COVID-19 were associated with a greater risk of adverse kidney outcomes. Along with clinical variables previously shown to predict adverse kidney events in patients with COVID-19, both sTNFR1 and sTNFR2 are also strong predictors of adverse kidney outcomes.

Kumar Sharma, Guanshi Zhang, Jens Hansen, Petter Bjornstad, Hak Joo Lee, Rajasree Menon, Leila Hejazi, Jian-Jun Liu, Anthony Franzone, Helen C. Looker, Byeong Yeob Choi, Roman Fernandez, Manjeri A. Venkatachalam, Luxcia Kugathasan, Vikas S. Sridhar, Loki Natarajan, Jing Zhang, Varun Sharma, Brian Kwan, Sushrut Waikar, Jonathan Himmelfarb, Katherine Tuttle, Bryan Kestenbaum, Tobias Fuhrer, Harold Feldman, Ian H. de Boer, Fabio C. Tucci, John Sedor, Hiddo Lambers Heerspink, Jennifer Schaub, Edgar Otto, Jeffrey B. Hodgin, Matthias Kretzler, Christopher Anderton, Theodore Alexandrov, David Cherney, Su Chi Lim, Robert G. Nelson, Jonathan Gelfond, Ravi Iyengar, and the Kidney Precision Medicine Project
JCI
(
133(2)
)
,
August 24, 2023
DOI:
10.1172/JCI170341
|
PMID:
37616058
|
PMCID:
PMC10575723
Summary
Lauren Bernard, Ashley R. Wang, Steven Menez, Joel M. Henderson, Ashveena Dighe, Glenda V. Roberts, Christine Stutzke, Katherine R. Tuttle, R. Tyler Miller
Kidney Medicine
(
)
,
August 5, 2023
DOI:
doi.org/10.1016/j.xkme.2023.100707
|
PMID:
|
PMCID:
Summary

The utility of kidney biopsy is debated among clinicians, and patients’ perspectives are even less explored. To address these gaps, we synthesized perspectives from clinicians and patient participants of the Kidney Precision Medicine Project (KPMP). Both before and after biopsy, clinicians were surveyed on how the procedure affected their clinical management, diagnosis, and prognosis. After biopsy, participants shared how the procedure affected their diagnosis, medication, and lifestyle changes. Clinicians and patients shared an appreciation for the biopsy’s impact on medical management but diverged in their takeaways on diagnosis and prognosis. These findings highlight the need for greater collaboration between patients and clinicians, particularly as they navigate shared decision-making when considering kidney biopsy

Ferkowicz, Michael J.; Verma, Ashish; Barwinska, Daria; Ferreira, Ricardo Melo; Henderson, Joel M.; Kirkpatrick, Mary; Silva, Paolo S.; Steenkamp, Devin W.; Phillips, Carrie L.; Waikar, Sushrut S.; Sutton, Timothy A.; for the Kidney Precision Medicine Project
CJASN
(
10.2215/CJN.0000000000000276
)
,
August 3, 2023
DOI:
DOI: 10.2215/CJN.0000000000000276
|
PMID:
|
PMCID:
Summary
Blue B. Lake, Rajasree Menon, Seth Winfree, Qiwen Hu, Ricardo Melo Ferreira, Kian Kalhor, Daria Barwinska, Edgar A. Otto, Michael Ferkowicz, Dinh Diep, Nongluk Plongthongkum, Amanda Knoten, Sarah Urata, Laura H. Mariani, Abhijit S. Naik, Sean Eddy, Bo Zhang, Yan Wu, Diane Salamon, James C. Williams, Xin Wang, Karol S. Balderrama, Paul J. Hoover, Evan Murray, Jamie L. Marshall, Teia Noel, Anitha Vijayan, Austin Hartman, Fei Chen, Sushrut S. Waikar, Sylvia E. Rosas, Francis P. Wilson, Paul M. Palevsky, Krzysztof Kiryluk, John R. Sedor, Robert D. Toto, Chirag R. Parikh, Eric H. Kim, Rahul Satija, Anna Greka, Evan Z. Macosko, Peter V. Kharchenko, Joseph P. Gaut, Jeffrey B. Hodgin, KPMP Consortium, Michael T. Eadon, Pierre C. Dagher, Tarek M. El-Achkar, Kun Zhang, Matthias Kretzler & Sanjay Jain
Nature
(
619:585-594
)
,
July 19, 2023
DOI:
doi.org/10.1038/s41586-023-05769-3
|
PMID:
|
PMCID:
Summary
Victor Hugo Canela, William S. Bowen, Ricardo Melo Ferreira, Farooq Syed, James E. Lingeman, Angela R. Sabo, Daria Barwinska, Seth Winfree, Blue B. Lake, Ying-Hua Cheng, Joseph P. Gaut, Michael Ferkowicz, Kaice A. LaFavers, Kun Zhang, Fredric L. Coe, Elaine Worcester, the Kidney Precision Medicine Project, Sanjay Jain, Michael T. Eadon, James C. Williams Jr. & Tarek M. El-Achkar
Nature Communications
(
14(4140)
)
,
July 19, 2023
DOI:
doi.org/10.1038/s41467-023-38975-8
|
PMID:
|
PMCID:
Summary

Kidney stone disease causes significant morbidity and increases health care utilization. In this work, we decipher the cellular and molecular niche of the human renal papilla in patients with calcium oxalate (CaOx) stone disease and healthy subjects. In addition to identifying cell types important in papillary physiology, we characterize collecting duct cell subtypes and an undifferentiated epithelial cell type that was more prevalent in stone patients. Despite the focal nature of mineral deposition in nephrolithiasis, we uncover a global injury signature characterized by immune activation, oxidative stress and extracellular matrix remodeling. We also identify the association of MMP7 and MMP9 expression with stone disease and mineral deposition, respectively. MMP7 and MMP9 are significantly increased in the urine of patients with CaOx stone disease, and their levels correlate with disease activity. Our results define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human papilla and identify associated urinary biomarkers.

Bhatraju PK, Stanaway IB, Palmer MR, Menon R, Schaub JA, Menez S, Srivastava A, Wilson FP, Kiryluk K, Palevsky PM, Naik AS, Sakr SS, Jarvik GP, Parikh CR, Ware LB, Ikizler TA, Siew ED, Chinchilli VM, Coca SG, Garg AX, Go AS, Kaufman JS, Kimmel PL, Himmelfarb J, Wurfel MM.
Kidney360
(
4(7)
)
,
July 1, 2023
DOI:
10.34067/KID.0000000000000175
|
PMID:
37273234
|
PMCID:
PMC10371295
Summary

Key points: Two genetic variants in the DISP1-TLR5 gene locus were associated with risk of AKI. DISP1 and TLR5 were differentially regulated in kidney biopsy tissue from patients with AKI compared with no AKI.

Sara Denicolò,Viji Nair, Johannes Leierer, Michael Rudnicki, Matthias Kretzler, Gert Mayer, Wenjun Ju, Paul Perco
Biomolecules
(
13(1): 89
)
,
December 31, 2022
DOI:
10.3390/biom13010089
|
PMID:
36671474
|
PMCID:
PMC9855364
Summary
Jiahao Liu, Viji Nair, Yi-yang Zhao, Dong-yuan Chang, Felix Eichinger, Emily C. Tanner, Damian Fermin, Keith A. Bellovich, Susan Steigerwalt, Zeenat Bhat, Jennifer J. Hawkins, Lalita Subramanian, Sylvia E. Rosas, John R. Sedor, Miguel A. Vasquez, Sushrut S. Waikar, Markus Bitzer, Subramaniam Pennathur, Frank Brosius, Min Chen, Matthias Kretzler, Wenjun Ju, for the Kidney Precision Medicine Project and Michigan Translational Core C-PROBE Investigator Group
Diabetes
(
71(12):2664-2676
)
,
December 1, 2022
DOI:
10.2337/db22-0169
|
PMID:
36331122
|
PMCID:
PMC9750948
Summary
Samir Parikh, Sethu Madhavan, John Shapiro, Richard Knight, Avi Rosenberg, Chirag Parikh, Brad Rovin, Steven Menez
Clinical Journal of the American Society of Nephrology
(
)
,
November 7, 2022
DOI:
|
PMID:
36344211
|
PMCID:
Summary

Goal: To explore a case of acute kidney injury (AKI) in a pregnant woman, presumed to be related to NSAID use, who underwent kidney biopsy, pairing standard pathological investigation with newer, molecular methods to interrogate the kidney tissue.

Results: the standard pathological results showed evidence of acute tubular injury, without significant scarring in other parts of the kidney. However, the molecular investigation, looking at protein signatures in the kidney tissue, showed evidence of inflammation and scarring in the kidney that was not clearly evident on pathology.

Implications for patients: This case of AKI highlights how the molecular evaluation of kidney tissue performed by investigators in the KPMP adds significant, additional information beyond standard investigation done currently in clinical practice. These new methods add further precision to the diagnosis of AKI and hold promise for future clinical use.

Brendon Lutnick, David Manthey, Jan U. Becker, Brandon Ginley, Katharina Moos, Jonathan E. Zuckerman, Luis Rodrigues, Alexander J. Gallan, Laura Barisoni, Charles E. Alpers, Xiaoxin X. Wang, Komuraiah Myakala, Bryce A. Jones. Moshe Levi, Jeffrey B. Kopp, Teruhiko Yoshida, Seung Seok Han, Sanjay Jain, Avi Z. Rosenberg, Kuang Yu. Jen, Pinaki Sarder, the Kidney Precision Medicine Project
Communications Medicine
(
)
,
August 19, 2022
DOI:
https://doi.org/10.1038/s43856-022-00138-z
|
PMID:
|
PMCID:
Summary

Goal: Artificial intelligence (AI) is the ability of a computer to conduct complex tasks that humans are capable of performing. AI is useful in the field of pathology, which involves analyzing images of the microscopic structure of different tissues. However, AI can be difficult to setup and apply to the task. One specific task, segmentation, involves picking specific structures out of tissue images and is a prime candidate for automation with AI.

Results: In our study, we have created a tool for pathology image segmentation which runs in the cloud (is accessible over the web). We demonstrate the tool by using it to segment various structures from kidney tissue.

Implication for Patients: Our experiments show that the tool is easy to use, accurate, and can estimate the presence of one type of scarring as reliably as human experts. Doctors will be able to use our tool to consult patient diagnosis over the web with other colleagues, and offer objective diagnosis with the help of AI.

 

Jens Hansen, Rachel Sealfon, Rajasree Menon, Michael T. Eadon, Blue B. Lake, Becky Steck, Dejan Dobi, Samir Parikh, Tara K. Sigdel, Guanshi Zhang, Dusan Velickovic, Daria Barwinska, Theodore Alexandrov, Priyanka Rashmi, Edgar A. Otto, Michael P. Rose, Christopher R. Anderton, John P. Shapiro, Annapurna Pamreddy, Seth Winfree, Yongqun He, Ian H. de Boer, Jeffrey B. Hodgin, Laura Barisoni, Abhijit S. Naik, Kumar Sharma, Minnie M. Sarwal, Kun Zhang, Jonathan Himmelfarb, Brad Rovin, Tarek M. El-Achkar, Zoltan Laszik, John Cijiang He, Pierre C. Dagher, M. Todd Valerius, Sanjay Jain, Lisa Satlin, Olga G. Troyanskaya, Matthias Kretzler, Ravi Iyengar, Evren U. Azeloglu, for the Kidney Precision Medicine Project
Science Advances
(
Vol 8, Issue 23
)
,
June 10, 2022
DOI:
10.1126/sciadv.abn4965
|
PMID:
35675394
|
PMCID:
PMC9176741
Summary

Kidney Precision Medicine Project (KPMP) is building a spatially-specified human tissue atlas at the single-cell resolution with molecular details of the kidney in health and disease. Here, we describe the construction of an integrated reference tissue map of cells, pathways and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 55 subjects. We use single-cell and -nucleus transcriptomics, subsegmental laser microdissection bulk transcriptomics and proteomics, near-single-cell proteomics, 3-D nondestructive and CODEX imaging, and spatial metabolomics data to hierarchically identify genes, pathways and cells. Integrated data from these different technologies coherently describe cell types/subtypes within different nephron segments and interstitium. These spatial profiles identify cell-level functional organization of the kidney tissue as indicative of their physiological functions and map different cell subtypes to genes, proteins, metabolites and pathways. Comparison of transcellular sodium reabsorption along the nephron to levels of mRNAs encoding the different sodium transporter genes indicate that mRNA levels are largely congruent with physiological activity.This reference atlas provides an initial framework for molecular classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.

Jiten Patel, Jose R. Torrealba, Emilio D. Poggio, Jack Bebiak, Charles E. Alpers, Stephanie M. Grewenow, Robert D. Toto and Michael T. Eadon; for the Kidney Precision Medicine Project
Clinical Journal of the American Society of Neprhology
(
17 (4) 594-601
)
,
April 17, 2022
DOI:
https://doi.org/10.2215/CJN.10350721
|
PMID:
34911732
|
PMCID:
PMC8993486
Summary

Goal: The goal of this study was to link the KPMP's molecular data to established clinical and pathologic assessments, providing a complete and individualized interpretation of a subject's kidney biopsy specimen.

Result: Despite a lack of overt pathologic evidence of diabetic kidney disease, early molecular features of diabetes were found within the kidney, consistent with the subject's clinical diagnosis.

 Implication for patients: This is the first published example of the KPMP integrating molecular information into the clinical and pathologic evaluation of an individual patient's kidney disease.

Christine P. Limonte, Erkka Valo, Viktor Drel, Loki Natarajan, Manjula Darshi, Carol Forsblom, Clark M. Henderson, Andrew N. Hoofnagle, Wenjun Ju, Matthias Kretzler, Daniel Montemayor, Viji Nair, Robert G. Nelson, John F. O’Toole, Robert D. Toto, Sylvia E. Rosas, John Ruzinski, Niina Sandholm, Insa M. Schmidt, Tomas Vaisar, Sushrut S. Waikar, Jing Zhang, Peter Rossing, Tarunveer S. Ahluwalia, Per-Henrik Groop, Subramaniam Pennathur, Janet K. Snell-Bergeon, Tina Costacou, Trevor J. Orchard, Kumar Sharma, Ian H. de Boer
Diabetes Care
(
)
,
April 2, 2022
DOI:
https://doi.org/10.2337/dc21-2204
|
PMID:
35377940
|
PMCID:
PMC9210873
Summary
Rajasree Menon, Edgar A. Otto, Celine C. Berthier, Viji Nair, Evan A. Farkash, Jeffrey B. Hodgin, Yingbao Yang, Jinghui Luo, Kenneth J. Woodside, Haniyeh Zamani, Silas P. Norman, Roger C. Wiggins, Matthias Kretzler, and Abhijit S. Naik
Kidney International
(
VOLUME 101, ISSUE 4, P779-792
)
,
April 1, 2022
DOI:
https://doi.org/10.1016/j.kint.2021.11.031
|
PMID:
34952098
|
PMCID:
PMC9067613
Summary

Rajasree Menon, Andrew S. Bomback, Blue B. Lake, Christy Stutzke, Stephanie M. Grewenow, Steven Menez, Vivette D. D’Agati, Sanjay Jain, for the Kidney Precision Medicine Project
Kidney International
(
)
,
March 8, 2022
DOI:
https:// doi.org/10.1016/j.kint.2022.03.011
|
PMID:
35339536
|
PMCID:
Summary

Goal:  To definemolecular and cellular features in a biopsy from an AKI patient using singlenucleus / cell RNA sequencing methods in conjunction with detailed histopathologicalanalysis and clinical course in order to gain mechanistic insights intocellular diversity, injury states, and clinical outcome.

Results: The molecular studies reveal remarkable cellularheterogeneity  and presence of alteredcell states reflecting cellular injury and repair in a  number of proximal and distal nephron celltypes, blood vessels, fibroblasts and immune cell.  Correlates of the injured and regeneratingcells were identified by histopathology including features of regeneration, tubularinjury and remodeling in this patient. By leveraging the KPPMP+HuBMAP master kidney atlas, the molecularanalysis further permitted identification of genes and pathways associated withadaptive / maladaptive repair. Signatures associated with NSAID use were detected in altered tubuleseven after discontinuation of these medicines.

Implication for Patients: The molecular and pathologicalanalysis enables assessment of injury and repair processes and etiology of AKIat the time of the biopsy.  Identificationof pathways that may be predictive of recovery or worsening kidney function canbe useful in assessing prognosis.  Asmore of these datasets are obtained, we may be able to have a knowledge base torelate these pathways with clinical outcomes and potentially use therapeuticdrugs to inhibit those related to worsening kidney function.

Catherine R. Butler, Paul S. Appelbaum, Heather Ascani, Mark Aulisio, Catherine E. Campbell, Ian H. de Boer, Ashveena L. Dighe, Daniel E. Hall, Jonathan Himmelfarb, Richard Knight, Karla Mehl, Raghavan Murugan,Sylvia E. Rosas, John R. Sedor, John F. O’Toole, Katherine R. Tuttle, Sushrut S. Waikar, and Michael Freeman, for the Kidney Precision Medicine Project
American Journal of Kidney Diseases
(
)
,
December 3, 2021
DOI:
https://doi.org/10.1053/j.ajkd.2021.10.006
|
PMID:
34871700
|
PMCID:
PMC9166631
Summary

Goal: Participation in the Kidney Precision Medicine Project(KPMP) means undergoing kidney biopsy and while the KPMP safety protocols are intended to minimize risk of this procedure, participants nonetheless accept some personal risk.

Results: Design and implementation of the KPMP has involved substantial ethical deliberation, and in this article, we use this experience as an example to understand the ethical foundation and implications of research that involves risk to participants.

Implication for Patients: Specifically, efforts to respect diverse participant values, support participants’ opportunity to act altruistically, and enhancing benefits to participants’ community are critical features of the KPMP research paradigm needed to respect and support participant in research that involves some personal risk.

 

Andreas Bueckle, Kilian Buehling, Patrick C. Shih, Katy Börner
PLoS ONE
(
PLoS ONE 16(10): e0258103.
)
,
October 27, 2021
DOI:
https://doi.org/10.1371/journal.pone.0258103
|
PMID:
34705835
|
PMCID:
PMC8550408
Summary

Goal: In our paper (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0258103), we tested three implementations of a tissue registration user interface (one on a 2D screen, two in virtual reality or VR) with regards to accuracy, completion time, and satisfaction with 42 human subjects.

Results: We found that while the VR implementations allow user to be significantly faster, more satisfied, and more accurate with regards to rotation, there was no difference regarding position accuracy, once again showing the viability of 2D interfaces for registering human tissue block inside 3D reference organs.

Implications for patients: Our incremental research and development towards accurate, quick, and satisfying 2D tissue registration enables the continued improvement of the user interfaces for building a Human Reference Atlas (https://hubmapconsortium.github.io/ccf/) in HuBMAP (https://commonfund.nih.gov/hubmap) with the goal of mapping the human body at single-cell level.

Veličković D, Bečejac T, Mamedov S, Sharma K, Ambalavanan N, Alexandrov T, Anderton CR
Analytic Chemistry
(
93(40):13421-13425
)
,
October 12, 2021
DOI:
10.1021/acs.analchem.1c02347
|
PMID:
34581565
|
PMCID:
Summary
Amodu, A., Porteny, T., Schmidt, I.M., Ladin, K., & Waikar, S.S.
(
3(6)
)
,
September 22, 2021
DOI:
10.1016/j.xkme.2021.06.014
|
PMID:
34939011
|
PMCID:
PMC8664729
Summary

Rationale & Objective: Although kidney biopsy is a useful tool, nephrologists’ approach toward biopsies is inconsistent for reasons incompletely understood, including lack of established clinical guidelines. We examined contemporary clinical decision-making patterns among nephrologists to perform native kidney biopsy. Study Design: Qualitative study using semistructured interviews. Results: Twenty nephrologists were interviewed: 16 (80%) were from academic centers, 3 (15%) performed their own biopsies, and 7 (35%) had been in practice for less than 10 years. The median time of practice was 14 years. We found substantial variability among the nephrologists in their attitude toward using kidney biopsy, which reflected individual differences in weighing the risks and benefits of the procedure for an individual patient. Five overarching themes were identified: operator comfort with biopsy and availability of interventional radiologist, exposure to biopsy during training and years of experience, concerns about the invasiveness of biopsy and inflicting harm, perception of evidence base and limited treatment options, and patient characteristics and preference. Conclusions: Multiple factors influence nephrologists’ decision to pursue kidney biopsy, with substantial variability among nephrologists that can have meaningful clinical implications. This suggests the need to establish consensus guidelines to make biopsy practice more standardized.

Francesca Solagna, Caterina Tezze, Maja T Lindenmeyer, Shun Lu, Guochao Wu, Shuya Liu, Yu Zhao, Robert Mitchell, Charlotte Meyer, Saleh Omairi, Temel Kilic, Andrea Paolini, Olli Ritvos, Arja Pasternack, Antonios Matsakas, Dominik Kylies, Julian Schulze Zur Wiesch, Jan-Eric Turner, Nicola Wanner, Viji Nair, Felix Eichinger, Rajasree Menon, Ina V Martin, Barbara M Klinkhammer, Elion Hoxha, Clemens D Cohen, Pierre-Louis Tharaux, Peter Boor, Tammo Ostendorf, Matthias Kretzler, Marco Sandri, Oliver Kretz, Victor G Puelles, Ketan Patel, Tobias B Huber.
J Clin Invest
(
131(11)
)
,
June 1, 2021
DOI:
10.1172/JCI135821
|
PMID:
34060483
|
PMCID:
PMC8159690
Summary
Insa M.Schmidt, Mia R.Colona, Bryan R.Kestenbaum, Leonidas G.Alexopoulos, RagnarPalsson, AnandSrivastava, JingLiu, Isaac E.Stillman, Helmut G.Rennke, Vishal S.Vaidya, Haojia Wu, Benjamin D.Humphreys, Sushrut S.Waikar, Kidney Precision Medicine Project (KPMP)
Kidney International
(
S0085-2538(21)00505-6
)
,
May 26, 2021
DOI:
https://doi.org/10.1016/j.kint.2021.04.037
|
PMID:
34051265
|
PMCID:
PMC8384690
Summary

Goal: Kidney fibrosis can result in structural damage and impairment of kidney function but non-invasive biomarkers (e.g., proteins measured in a patient’s blood or urine) to assess kidney fibrosis are currently not available.

Results: In this study, we identified SMOC2, PEDF, and CDH11 as promising new biomarker proteins that may be used to estimate the degree of fibrosis in patients with kidney disease and identify patients at high risk of kidney disease progression.

Implication for Patients: These biomarkers may be used as markers of response to treatment, for example facilitating the investigation of new therapies that are under development for the treatment of kidney fibrosis

Yi Zheng, Clarissa A Cassol, Saemi Jung, Divya Veerapaneni, Vipul C Chitalia, Kevin Y M Ren, Shubha S Bellur, Peter Boor, Laura M Barisoni, Sushrut S Waikar, Margrit Betke, Vijaya B Kolachalama
The American Journal of Pathology
(
May-2021
)
,
May 21, 2021
DOI:
https://doi.org/10.1016/j.ajpath.2021.05.005
|
PMID:
34033750
|
PMCID:
PMC8453248
Summary

Goal: To develop a widely applicable way to stratify kidney disease severity. Chronic kidney damage is assessed by scoring the amount of interstitial fibrosis and tubular atrophy (IFTA) in a renal biopsy sample.

Results: A novel Artificial Intelligence (AI) tool was developed to predict the grade of IFTA, a known structural correlate of progressive and chronic kidney disease.

Implication for Patients: Having a computer model that can mimic an expert pathologist's workflow and assess disease grade can further the potential to increase efficiency in clinical practices. AI models that can automatically score the extent of chronic damage in the kidney can serve as a second opinion tool in clinical practices.

Steven Menez, Wenjun Ju, Rajasree Menon, Dennis G. Moledina, Heather Thiessen Philbrook, Eric McArthur, Yaqi Jia, Wassim Obeid, Sherry G. Mansour, Jay L. Koyner, Michael G. Shlipak, Steven G. Coca, Amit X. Garg, Andrew S. Bomback, John A. Kellum, Matthias Kretzler, Chirag R. Parikh
Journal of Clinical Investigation
(
6(11):e147464
)
,
May 11, 2021
DOI:
https://doi.org/10.1172/jci.insight.147464
|
PMID:
33974569
|
PMCID:
PMC8262289
Summary
Katherine R Tuttle, Jack Bebiak, Keith Brown, Catherine Campbell, Ashveena Dighe, Lynda Hyashi, Nichole Jefferson, Glenda V Roberts, Christy Stutzke, Richard Knight, Kidney Precision Medicine Project
Kidney International
(
VOLUME 99, ISSUE 3, P511-514
)
,
March 1, 2021
DOI:
https://doi.org/10.1016/j.kint.2020.10.036
|
PMID:
33637195
|
PMCID:
Summary

Goal: To guide scientific inquiry toward clinically meaningful benefit, patients are equal partners for priority setting, study design and conduct, and dissemination of findings.

Results: Patient partners in the Community Engagement Committee led the development of the informed consent process, the ethics statement, the return-of-results plan, a “patient primer” for scientists, and community advisory boards at the recruitment sites.

Implication for Patients: Patients’ viewpoints and priorities have been central in directing the KPMP to produce research that brings clinically meaningful benefit to them.

Ian H. de Boer, MD, MS, Charles E. Alpers, MD, Tarek M. El-Achkar, MD, Evren Azeloglu, PhD, Ulysses G. J. Balis, MD, PhD, Jonathan M. Barasch, MD, PhD, Laura Barisoni, MD, Kristina Blank, MPH, Andrew S. Bomback, MD, Keith Brown, Pierre C. Dagher, MD, Ashveena L. Dighe, MS, MPH, Michael T. Eadon, MD, Joseph P. Gaut, MD, PhD, Nir Hacohen, PhD, Yongqun He, PhD, Jeffrey B. Hodgin, MD, PhD, Sanjay Jain, MD, PhD, John A. Kellum, MD, Krzysztof Kiryluk, MD, MS, Richard Knight, and Zoltan G. Laszik, MD, PhD, Chrysta Lienczewski, Laura H. Mariani, MD, Robyn L. Mcclelland, PhD, Steven Menez, MD, Dennis Moledina, MD, PhD, Sean D. Mooney, PhD, John O’Toole, MD, Paul M. Palevsky, MD, Chirag R. Parikh, MD, PhD, Emilio Poggio, MD, Sylvia Rosas, MD, Matthew R. Rosengart, MD, MPH, Minnie Sarwal, MD, PhD, Jennifer A. Schaub, MD, John R. Sedor, MD, Kumar Sharma, MD, Becky Steck, Robert Toto, MD, Olga Troyanskaya, PhD, Katherine Tuttle, MD, Miguel Vazquez, MD, Sushrut S. Waikar, MD, Kayleen Williams, MPH, Francis Perry Wilson, MD, Kun Zhang, PhD, Srinivas Ravi Iyengar, PhD, Matthias Kretzler, MD, Jonathan Himmelfarb, and For the Kidney Precision Medicine Project
Kidney International
(
VOLUME 99, ISSUE 3, P498-510
)
,
March 1, 2021
DOI:
https://doi.org/10.1016/j.kint.2020.08.039
|
PMID:
33637194
|
PMCID:
PMC8330551
Summary

Goal: Describe the objectives and study design of the Kidney Precision Medicine Project, and the rationale for kidney precision medicine.

Results: 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.

Implication for Patients: All data from the Kidney Precision Medicine Project will be made readily available for broad use by scientists, clinicians, and patients.

Daria Barwinska, Tarek M El-Achkar, Ricardo Melo Ferreira, Farooq Syed, Ying-Hua Cheng, Seth Winfree, Michael J Ferkowicz, Takashi Hato, Kimberly S Collins, Kenneth W Dunn, Katherine J Kelly, Timothy A Sutton, Brad H Rovin, Samir V Parikh, Carrie L Phillips, Pierre C Dagher, Michael T Eadon, Kidney Precision Medicine Project
Science Advances
(
Vol. 7, no. 7, eabd3359
)
,
February 10, 2021
DOI:
10.1126/sciadv.abd3359
|
PMID:
33568476
|
PMCID:
PMC7875540
Summary
Michael T Eadon, Sam Lampe, Mirza M Baig, Kimberly S Collins, Ricardo Melo Ferreira, Henry Mang, Ying-Hua Cheng, Daria Barwinska, Tarek M El-Achkar, Tae-Hwi Schwantes-An, Seth Winfree, Constance J Temm, Michael J Ferkowicz, Kenneth W Dunn, Katherine J Kelly, Timothy A Sutton, Sharon M Moe, Ranjani N Moorthi, Carrie L Phillips, Pierre C Dagher, Kidney Precision Medicine Project
Nephrol Dial Transplant
(
)
,
February 4, 2021
DOI:
10.1093/ndt/gfaa331
|
PMID:
33537765
|
PMCID:
PMC8826640
Summary

Goal: Idiopathic nodular mesangial sclerosis, also called idiopathic nodular glomerulosclerosis (ING), is a rare clinical entity with an unclear pathogenesis.

Results: The hallmark of this disease is the presence of nodular mesangial sclerosis on histology without clinical evidence of diabetes kidney disease (DKD) or other predisposing diagnoses.  

Implication for Patients: Despite similar clinical and histopathologic characteristics in ING and DKD, the uncovered transcriptomic signature suggests that ING has distinct molecular features from nodular DKD.

Puthumana, J., thiessen-Philbrook, H., Xu, L., Coca, S.G., Garg, A.X., Himmelfarb, J., Bhatraju, P.K., Ikizler, T.A., Siew, E.D., Ware, L.B., Liu, K.D., Go, A.S., Kaufman, J.S., Kimmel, P.L., Chinchilli, V.M., Cantley, L.G., Parikh, C.R.
The Journal of Clinical Investigation
(
131(3)
)
,
February 1, 2021
DOI:
doi.org/10.1172/jci139927
|
PMID:
33290282
|
PMCID:
PMC7843225
Summary

INTRODUCTIONAcute kidney injury and chronic kidney disease (CKD) are common in hospitalized patients. To inform clinical decision making, more accurate information regarding risk of long-term progression to kidney failure is required.METHODSWe enrolled 1538 hospitalized patients in a multicenter, prospective cohort study. Monocyte chemoattractant protein 1 (MCP-1/CCL2), uromodulin (UMOD), and YKL-40 (CHI3L1) were measured in urine samples collected during outpatient follow-up at 3 months. We followed patients for a median of 4.3 years and assessed the relationship between biomarker levels and changes in estimated glomerular filtration rate (eGFR) over time and the development of a composite kidney outcome (CKD incidence, CKD progression, or end-stage renal disease). We paired these clinical studies with investigations in mouse models of renal atrophy and renal repair to further understand the molecular basis of these markers in kidney disease progression.RESULTSHigher MCP-1 and YKL-40 levels were associated with greater eGFR decline and increased incidence of the composite renal outcome, whereas higher UMOD levels were associated with smaller eGFR declines and decreased incidence of the composite kidney outcome. A multimarker score increased prognostic accuracy and reclassification compared with traditional clinical variables alone. The mouse model of renal atrophy showed greater Ccl2 and Chi3l1 mRNA expression in infiltrating macrophages and neutrophils, respectively, and evidence of progressive renal fibrosis compared with the repair model. The repair model showed greater Umod expression in the loop of Henle and correspondingly less fibrosis.CONCLUSIONSBiomarker levels at 3 months after hospitalization identify patients at risk for kidney disease progression.

Tarek M El-Achkar, Michael T Eadon, Rajasree Menon, Blue B Lake, Tara K Sigdel, Theodore Alexandrov, Samir Parikh, Guanshi Zhang, Dejan Dobi, Kenneth W Dunn, Edgar A Otto, Christopher R Anderton, Jonas M Carson, Jinghui Luo, Chris Park, Habib Hamidi, Jian Zhou, Paul Hoover, Andrew Schroeder, Marianinha Joanes, Evren U Azeloglu, Rachel Sealfon, Seth Winfree, Becky Steck, Yongqun He, Vivette D'Agati, Ravi Iyengar, Olga G Troyanskaya, Laura Barisoni, Joseph Gaut, Kun Zhang, Zoltan Laszik, Brad H Rovin, Pierre C Dagher, Kumar Sharma, Minnie M Sarwal, Jeffrey B Hodgin, Charles E Alpers, Matthias Kretzler, Sanjay Jain
Physiological Genomics
(
2021/01/11 Vol. 53, No. 1
)
,
January 11, 2021
DOI:
https://doi.org/10.1152/physiolgenomics.00104.2020
|
PMID:
33197228
|
PMCID:
PMC7847045
Summary
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, Kidney Precision Medicine Project
Nature: Laboratory Investigations
(
06 January 2021
)
,
January 6, 2021
DOI:
https://doi.org/10.1038/s41374-020-00518-w
|
PMID:
33408350
|
PMCID:
PMC8363780
Summary
Katherine R Tuttle, Richard Knight, Paul S Appelbaum, Tanima Arora, Shweta Bansal, Jack Bebiak, Keith Brown, Catherine Campbell, Leslie Cooperman, Celia P Corona-Villalobos, Ashveena Dighe, Ian H de Boer, Daniel E Hall, Nichole Jefferson, Stacey Jolly, Asra Kermani, Simon C Lee, Karla Mehl, Raghavan Murugan, Glenda V Roberts, Sylvia E Rosas, Jonathan Himmelfarb, R Tyler Miller, Kidney Precision Medicine Project
CJASN
(
November 2020, CJN.10270620
)
,
November 1, 2020
DOI:
https://doi.org/10.2215/CJN.10270620
|
PMID:
33257411
|
PMCID:
PMC8092068
Summary

Goal: Describe patient and community engagement and the value they bring to the KPMP.

Results: The Community Engagement Committee guides KPMP research priorities from perspectives of patients and clinicians, and assures that the science is developed and conducted in a manner relevant to study participants and the clinical community.

Implications for Patients: Patients have guided the KPMP to produce research aligned with their priorities, and set new benchmarks for patient leadership in precision medicine research.

Rajasree Menon, Edgar A Otto, Rachel Sealfon, Viji Nair, Aaron K Wong, Chandra L Theesfeld, Xi Chen, Yuan Wang, Avinash S Boppana, Jinghui Luo, Yingbao Yang, Peter M Kasson, Jennifer A Schaub, Celine C Berthier, Sean Eddy, Chrysta C Lienczewski, Bradley Godfrey, Susan L Dagenais, Ryann Sohaney, John Hartman, Damian Fermin, Lalita Subramanian, Helen C Looker, Jennifer L Harder, Laura H Mariani, Jeffrey B Hodgin, Jonathan Z Sexton, Christiane E Wobus, Abhijit S Naik, Robert G Nelson, Olga G Troyanskaya, Matthias Kretzler
Kidney International
(
2020 Oct 07
)
,
October 7, 2020
DOI:
https://doi.org/10.1016/j.kint.2020.09.015
|
PMID:
32511461
|
PMCID:
PMC7241118
Summary
Emilio D Poggio, Robyn L McClelland, Kristina N Blank, Spencer Hansen, Shweta Bansal, Andrew S Bomback, Pietro A Canetta, Pascale Khairallah, Krzysztof Kiryluk, Stewart H Lecker, Gearoid M McMahon, Paul M Palevsky, Samir Parikh, Sylvia E Rosas, Katherine Tuttle, Miguel A Vazquez, Anitha Vijayan, Brad H Rovin, Kidney Precision Medicine Project
CJASN
(
October 2020, CJN.04710420
)
,
October 1, 2020
DOI:
https://doi.org/10.2215/CJN.04710420
|
PMID:
33060160
|
PMCID:
PMC7646247
Summary
Tara K. Sigdel, Paul D Piehowski, Sudeshna Roy, Juliane Liberto, Joshua R Hansen, Adam C Swensen, Rui Zhao, Ying Zhu, Priyanka Rashmi, Andrew Schroeder, Izabella Damm, Swastika Sur, Jinghui Luo, Yingbao Yang, Wei-Jun Qian, Minnie M Sarwal, Kidney Precision Medicine Project (KPMP) Consortium
Frontiers in Medicine
(
17 Sept 2020
)
,
September 17, 2020
DOI:
https://doi.org/10.3389/fmed.2020.00499
|
PMID:
33072769
|
PMCID:
PMC7533534
Summary

Goal: The goal was to study Proximal Tubular and Glomerular proteins using laser capture microdissection followed by mass spectrometry.

Results: We established near single-cell proteomics protocol kidney tissue and identified more than 2,500 human proteins of which 25 proteins) were specific to proximal tubules  and 67 were specific to glomerulus  (Glom; n = 67 proteins) regions.

Implication for Patients: This near-single-cell proteomics workflow can be extended to other kidney micro-compartments which ultimately will help understand changes in the proteomic landscape of normal kidneys as well as different etiologies of acute and chronic kidney disease.

Edison Ong, Lucy L Wang, Jennifer Schaub, John F O'Toole, Becky Steck, Avi Z Rosenberg, Frederick Dowd, Jens Hansen, Laura Barisoni, Sanjay Jain, Ian H de Boer, M Todd Valerius, Sushrut S Waikar, Christopher Park, Dana C Crawford, Theodore Alexandrov, Christopher R Anderton, Christian Stoeckert, Chunhua Weng, Alexander D Diehl, Christopher J Mungall, Melissa Haendel, Peter N Robinson, Jonathan Himmelfarb, Ravi Iyengar, Matthias Kretzler, Sean Mooney, Yongqun He, Kidney Precision Medicine Project
Nature Reviews Nephrology
(
16 September 2020
)
,
September 16, 2020
DOI:
10.1038/s41581-020-00335-w
|
PMID:
32939051
|
PMCID:
PMC8012202
Summary

Goal: To model the kidney disease using ontology.

Results: The development of two new community-based ontologies — the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation —supports the creation of the Kidney Tissue Atlas, which aims to provide a comprehensive molecular, cellular and anatomical map of the kidney, leading to more advanced kidney disease modeling and analysis.

Implication for Patients: The usage of ontology supports the standard data integration and analysis of kidney precision medicine.

Jessica K. Lukowski, Annapurna Pamreddy, Dusan Velickovic, Guanshi Zhang, Ljiljana Pasa-Tolic, Theodore Alexandrov, Kumar Sharma, Christopher R. Anderton, and the Kidney Precision Medicine Project
J. Am. Soc. Mass Spectrom
(
September 8, 2020
)
,
September 8, 2020
DOI:
https://doi.org/10.1021/jasms.0c00256
|
PMID:
32897710
|
PMCID:
PMC8162764
Summary

Goal: We sought to understand the optimal storage conditions for spatial lipidomic analysis of human kidney tissue sections, as it is common practice to share tissue among the consortium and between tissue interrogation sites.

Results: Overall, we found that molecular degradation of the tissue sections was unavoidable over time, regardless of storage conditions, but storing tissue sections in an inert gas at low temperatures can curtail molecular degradation within tissue sections.

Implications for Patients: By storing kidney tissue sections under these optimal conditions we can maximize the molecular readout from the kidney biopsies.

Keith D. Brown, Catherine Campbell, Glenda V. Roberts
Nat Rev Nephr
(
2020 Aug 08
)
,
August 8, 2020
DOI:
10.1038/s41581-020-0319-0
|
PMID:
32760017
|
PMCID:
PMC7404073
Summary

Interviews with three individuals who have been affected by kidney failure for their views on the importance of understanding the drivers of kidney disease, and what they hope might be achieved with this information.

Daria Barwinska, Michael J Ferkowicz, Ying-Hua Cheng, Seth Winfree, Kenneth W Dunn, Katherine J Kelly, Timothy A Sutton, Brad H Rovin, Samir V Parikh, Carrie L Phillips, Pierre C Dagher, Tarek M El-Achkar, Michael T Eadon, Kidney Precision Medicine Project
JoVE
(
June 9, 2020
)
,
June 9, 2020
DOI:
10.3791/61371
|
PMID:
32597856
|
PMCID:
PMC8136155
Summary
Rajasree Menon, Edgar A Otto, Paul Hoover, Sean Eddy, Laura Mariani, Bradley Godfrey, Celine C Berthier, Felix Eichinger, Lalita Subramanian, Jennifer Harder, Wenjun Ju, Viji Nair, Maria Larkina, Abhijit S Naik, Jinghui Luo, Sanjay Jain, Rachel Sealfon, Olga Troyanskaya, Nir Hacohen, Jeffrey B Hodgin, Matthias Kretzler, Kidney Precision Medicine Project Kpmp, Nephrotic Syndrome Study Network (NEPTUNE)
JCI Insight
(
2020 Mar 26;5(6):e133267
)
,
March 26, 2020
DOI:
10.1172/jci.insight.133267
|
PMID:
32107344
|
PMCID:
PMC7213795
Summary
Dušan Veličković, Guanshi Zhang, Dejan Bezbradica, Arunima Bhattacharjee, Ljiljana Paša-Tolić, Kumar Sharma, Theodore Alexandrov, Christopher R. Anderton, and KPMP Consortium
J Am Soc Mass Spec
(
2020 Feb 06;31(3):508-516
)
,
February 6, 2020
DOI:
10.1021/jasms.9b00074
|
PMID:
32126772
|
PMCID:
PMC7293970
Summary

Goal: The goal of this research was to develop a reliable and robust optimization strategy for our spatial metabolomics assay’s sample preparation steps that could be utilized universally for different tissue types.

Results: Through development of a novel experimental design coupled with mathematical modeling, we can optimize sample preparation for spatial metabolomics (via matrix-assisted laser desorption/ionization mass spectrometry imaging) with minimal time and tissue utilization.

Implication for Patients: This approach will ensure that we will obtain the highest quality spatial metabolomics data from the invaluable KPMP tissue biopsies.

Beatriz Desanti De Oliveira, Katherine Xu, Tian H. Shen, Miriam Callahan, Krzysztof Kiryluk, Vivette D. D’Agati, Nicholas P. Tatonetti, Jonathan Barasch & Prasad Devarajan
Nat Rev Nephrol
(
2019 Oct;15(10):599-612
)
,
October 1, 2019
DOI:
10.1038/s41581-019-0184-x
|
PMID:
31439924
|
PMCID:
PMC7303545
Summary
Blue B Lake, Song Chen, Masato Hoshi, Nongluk Plongthongkum, Diane Salamon, Amanda Knoten, Anitha Vijayan, Ramakrishna Venkatesh, Eric H Kim, Derek Gao, Joseph Gaut, Kun Zhang, Sanjay Jain
Nat Commun
(
2019 Jun 27;10(1):2832
)
,
June 27, 2019
DOI:
10.1038/s41467-019-10861-2
|
PMID:
31249312
|
PMCID:
PMC6597610
Summary

Goal: To profile the diverse molecular cell type composition of human kidneys, we developed a reproducible method for isolating and sequencing RNA transcripts within single kidney nuclei.

Results: This enabled gene expression profiling of cell types spanning the major functional units of the kidney with minimal processing artifacts.

Implication for Patients: Using this approach, our analysis portrays remarkable cellular and molecular heterogeneity and insights into kidney organization, function and disease.

Paul L. Kimmel, Nichole Jefferson, Jenna M. Norton and Robert A. Star
Clin J Am Soc Nephrol
(
2019 May 7;14(5):768-770
)
,
May 7, 2019
DOI:
10.2215/CJN.14591218
|
PMID:
30917992
|
PMCID:
PMC6500937
Summary

Goal: To reflect on two NIDDK consortia and the benefits of community-engaged research to nephrology.

Results: Putting patients first and meaningfully involving them in nephrology research as full partners may increase research relevance and efficiency, with particular benefits for studies addressing underserved or minority populations.  

Implication for Patients: Inclusion of the patient and community perspective across the spectrum of nephrology research may benefit patients, investigators, and the nephrology field as a whole.

Brad P. Dieter, Radica Z Alicic, Katherine R. Tuttle
Am J Physiol Renal Physiol
(
2018 Dec 1;315(6):F1519-F1525
)
,
December 1, 2018
DOI:
10.1152/ajprenal.00211.2018
|
PMID:
30110568
|
PMCID:
PMC6337002
Summary

Goal: A review article covering the effects of GLP-1 receptor agonists on the diabetic kidney from clinical trial data to basic science and preclinical studies.

Results: These data set the stage for understanding mechanistic underpinnings, inclusive of tissue interrogation akin to KPMP, for kidney protection by GLP-1 receptor agonists.

Implication for Patients: Linking kidney disease mechanisms to therapeutic interventions helps to identify individuals who may benefit from a specific therapy.

Krzysztof Kiryluk, Andrew S Bomback, Yim-Ling Cheng, Katherine Xu, Pablo G Camara, Raul Rabadan, Peter A Sims, Jonathan Barasch
Semin Nephrol
(
2018 Jan;38(1):40-51
)
,
January 1, 2018
DOI:
10.1016/j.semnephrol.2017.09.006
|
PMID:
29291761
|
PMCID:
PMC5753434
Summary
Samir Parikh, Sethu Madhavan, John Shapiro, Richard Knight, Avi Z Rosenberg, Chirag R Parikh, Brad Rovin, Steven Menez, for the Kidney Precision Medicine Project
CJASN
(
18(3):p 402-410
)
,
DOI:
DOI: 10.2215/CJN.09260822
|
PMID:
|
PMCID:
Summary
Rajasree Menon, Edgar A Otto, Laura Barisoni, Ricardo Melo Ferreira, Christine P Limonte, Bradley Godfrey, Felix Eichinger, Viji Nair, Abhijit S Naik, Lalita Subramanian, Vivette D'Agati, Joel M Henderson, Leal Herlitz, Krzysztof Kiryluk, Dennis G Moledina, Gilbert W Moeckel, Paul M Palevsky, Chirag R Parikh, Parmjeet Randhawa, Sylvia E Rosas, Avi Z Rosenberg, Isaac Stillman, Robert Toto, Jose Torrealba, Miguel A Vazquez, Sushrut S Waikar, Charles E Alpers, Robert G Nelson, Michael T Eadon, Matthias Kretzler, Jeffrey B Hodgin; Kidney Precision Medicine Project (KPMP); Nephrotic Syndrome Study Network (NEPTUNE)
medRxiv
(
)
DOI:
10.1101/2023.06.14.23291150
|
PMID:
37398386
|
PMCID:
PMC10312894
Summary
Katy Börner, Ellen M. Quardokus, Bruce W. Herr II, Leonard E. Cross, Elizabeth G. Record, Yingnan Ju, Andreas D. Bueckle, James P. Sluka, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Nathan H. Patterson, Mark A. Musen, Griffin M. Weber
arXiv
(
2007.14474.
)
DOI:
https://doi.org/10.48550/arXiv.2007.14474
|
PMID:
|
PMCID:
Summary
Andrew W. Schroeder, Swastika Sur, Priyanka Rashmi, Izabella Damm, Arya Zarinsefat, Matthias Kretzler, Jeff Hodgin, George Hartoularos, Tara Sigdel, Jimmie Chun Ye, Minnie M. Sarwal, for the Kidney Precision Medicine Project
BioRxiv 973925 [Preprint]
(
2020 Mar 04
)
DOI:
10.1101/2020.03.02.973925
|
PMID:
|
PMCID:
Summary

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