Browsing by Author "Waikar, Sushrut S."

Now showing 1 - 4 of 4
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    A Participant-Centered Approach to Understanding Risks and Benefits of Participation in Research Informed by the Kidney Precision Medicine Project
    (Elsevier, 2022) Butler, Catherine R.; Appelbaum, Paul S.; Ascani, Heather; Aulisio, Mark; Campbell, Catherine E.; de Boer, Ian H.; Dighe, Ashveena L.; Hall, Daniel E.; Himmelfarb, Jonathan; Knight, Richard; Mehl, Karla; Murugan, Raghavan; Rosas, Sylvia E.; Sedor, John R.; O'Toole, John F.; Tuttle, Katherine R.; Waikar, Sushrut S.; Freeman, Michael; Kidney Precision Medicine Project; Medicine, School of Medicine
    An understanding of the ethical underpinnings of human subjects research that involves some risk to participants without anticipated direct clinical benefit-such as the kidney biopsy procedure as part of the Kidney Precision Medicine Project (KPMP)-requires a critical examination of the risks as well as the diverse set of countervailing potential benefits to participants. This kind of deliberation has been foundational to the development and conduct of the KPMP. Herein, we use illustrative features of this research paradigm to develop a more comprehensive conceptualization of the types of benefits that may be important to research participants, including respecting pluralistic values, supporting the opportunity to act altruistically, and enhancing benefits to a participant's community. This approach may serve as a model to help researchers, ethicists, and regulators to identify opportunities to better respect and support participants in future research that entails some risk to these participants as well as to improve the quality of research for people with kidney disease.
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    An atlas of healthy and injured cell states and niches in the human kidney
    (Springer Nature, 2023) Lake, Blue B.; Menon, Rajasree; Winfree, Seth; Hu, Qiwen; Ferreira, Ricardo Melo; Kalhor, Kian; Barwinska, Daria; Otto, Edgar A.; Ferkowicz, Michael; Diep, Dinh; Plongthongkum, Nongluk; Knoten, Amanda; Urata, Sarah; Mariani, Laura H.; Naik, Abhijit S.; Eddy, Sean; Zhang, Bo; Wu, Yan; Salamon, Diane; Williams, James C.; Wang, Xin; Balderrama, Karol S.; Hoover, Paul J.; Murray, Evan; Marshall, Jamie L.; Noel, Teia; Vijayan, Anitha; Hartman, Austin; Chen, Fei; Waikar, Sushrut S.; Rosas, Sylvia E.; Wilson, Francis P.; Palevsky, Paul M.; Kiryluk, Krzysztof; Sedor, John R.; Toto, Robert D.; Parikh, Chirag R.; Kim, Eric H.; Satija, Rahul; Greka, Anna; Macosko, Evan Z.; Kharchenko, Peter V.; Gaut, Joseph P.; Hodgin, Jeffrey B.; KPMP Consortium; Eadon, Michael T.; Dagher, Pierre C.; El-Achkar, Tarek M.; Zhang, Kun; Kretzler, Matthias; Jain, Sanjay; Medicine, School of Medicine
    Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.
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    Multi-Scalar Data Integration Links Glomerular Angiopoietin-Tie Signaling Pathway Activation With Progression of Diabetic Kidney Disease
    (American Diabetes Association, 2022) Liu, Jiahao; Nair, Viji; Zhao, Yi-yang; Chang, Dong-yuan; Limonte, Christine; Bansal, Nisha; Fermin, Damian; Eichinger, Felix; Tanner, Emily C.; Bellovich, Keith A.; Steigerwalt, Susan; Bhat, Zeenat; Hawkins, Jennifer J.; Subramanian, Lalita; Rosas, Sylvia E.; Sedor, John R.; Vasquez, Miguel A.; Waikar, Sushrut S.; Bitzer, Markus; Pennathur, Subramaniam; Brosius, Frank C.; De Boer, Ian; Chen, Min; Kretzler, Matthias; Ju, Wenjun; Kidney Precision Medicine Project; Michigan Translational Core C-PROBE Investigator Group; Medicine, School of Medicine
    Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease (ESKD). Prognostic biomarkers reflective of underlying molecular mechanisms are critically needed for effective management of DKD. A three-marker panel was derived from a proteomics analysis of plasma samples by an unbiased machine learning approach from participants (N = 58) in the Clinical Phenotyping and Resource Biobank study. In combination with standard clinical parameters, this panel improved prediction of the composite outcome of ESKD or a 40% decline in glomerular filtration rate. The panel was validated in an independent group (N = 68), who also had kidney transcriptomic profiles. One marker, plasma angiopoietin 2 (ANGPT2), was significantly associated with outcomes in cohorts from the Cardiovascular Health Study (N = 3,183) and the Chinese Cohort Study of Chronic Kidney Disease (N = 210). Glomerular transcriptional angiopoietin/Tie (ANG-TIE) pathway scores, derived from the expression of 154 ANG-TIE signaling mediators, correlated positively with plasma ANGPT2 levels and kidney outcomes. Higher receptor expression in glomeruli and higher ANG-TIE pathway scores in endothelial cells corroborated potential functional effects in the kidney from elevated plasma ANGPT2 levels. Our work suggests that ANGPT2 is a promising prognostic endothelial biomarker with likely functional impact on glomerular pathogenesis in DKD.
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    Plasma proteomics of acute tubular injury
    (Springer Nature, 2024-08-27) Schmidt, Insa M.; Surapaneni, Aditya L.; Zhao, Runqi; Upadhyay, Dhairya; Yeo, Wan-Jin; Schlosser, Pascal; Huynh, Courtney; Srivastava, Anand; Palsson, Ragnar; Kim, Taesoo; Stillman, Isaac E.; Barwinska, Daria; Barasch, Jonathan; Eadon, Michael T.; El-Achkar, Tarek M.; Henderson, Joel; Moledina, Dennis G.; Rosas, Sylvia E.; Claudel, Sophie E.; Verma, Ashish; Wen, Yumeng; Lindenmayer, Maja; Huber, Tobias B.; Parikh, Samir V.; Shapiro, John P.; Rovin, Brad H.; Stanaway, Ian B.; Sathe, Neha A.; Bhatraju, Pavan K.; Coresh, Josef; Kidney Precision Medicine Project; Rhee, Eugene P.; Grams, Morgan E.; Waikar, Sushrut S.; Medicine, School of Medicine
    The kidney tubules constitute two-thirds of the cells of the kidney and account for the majority of the organ’s metabolic energy expenditure. Acute tubular injury (ATI) is observed across various types of kidney diseases and may significantly contribute to progression to kidney failure. Non-invasive biomarkers of ATI may allow for early detection and drug development. Using the SomaScan proteomics platform on 434 patients with biopsy-confirmed kidney disease, we here identify plasma biomarkers associated with ATI severity. We employ regional transcriptomics and proteomics, single-cell RNA sequencing, and pathway analysis to explore biomarker protein and gene expression and enriched biological pathways. Additionally, we examine ATI biomarker associations with acute kidney injury (AKI) in the Kidney Precision Medicine Project (KPMP) (n = 44), the Atherosclerosis Risk in Communities (ARIC) study (n = 4610), and the COVID-19 Host Response and Clinical Outcomes (CHROME) study (n = 268). Our findings indicate 156 plasma proteins significantly linked to ATI with osteopontin, macrophage mannose receptor 1, and tenascin C showing the strongest associations. Pathway analysis highlight immune regulation and organelle stress responses in ATI pathogenesis.