Browsing by Author "Alpers, Charles E."

Now showing 1 - 4 of 4
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    A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project
    (American Physiological Society, 2021) El-Achkar, Tarek M.; Eadon, Michael T.; Menon, Rajasree; Lake, Blue B.; Sigdel, Tara K.; Alexandrov, Theodore; Parikh, Samir; Zhang, Guanshi; Dobi, Dejan; Dunn, Kenneth W.; Otto, Edgar A.; Anderton, Christopher R.; Carson, Jonas M.; Luo, Jinghui; Park, Chris; Hamidi, Habib; Zhou, Jian; Hoover, Paul; Schroeder, Andrew; Joanes, Marianinha; Azeloglu, Evren U.; Sealfon, Rachel; Winfree, Seth; Steck, Becky; He, Yongqun; D’Agati, Vivette; Iyengar, Ravi; Troyanskaya, Olga G.; Barisoni, Laura; Gaut, Joseph; Zhang, Kun; Laszik, Zoltan; Rovin, Brad H.; Dagher, Pierre C.; Sharma, Kumar; Sarwal, Minnie M.; Hodgin, Jeffrey B.; Alpers, Charles E.; Kretzler, Matthias; Jain, Sanjay; Medicine, School of Medicine
    Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. We describe a “follow the tissue” pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.
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    Molecular mechanisms and therapeutic targets for diabetic kidney disease
    (Elsevier, 2022) Tuttle, Katherine R.; Agarwal, Rajiv; Alpers, Charles E.; Bakris, George L.; Brosius, Frank C.; Kolkhof, Peter; Uribarri, Jaime; Medicine, School of Medicine
    Diabetic kidney disease has a high global disease burden and substantially increases the risk of kidney failure and cardiovascular events. Despite treatment, there is substantial residual risk of disease progression with existing therapies. Therefore, there is an urgent need to better understand the molecular mechanisms driving diabetic kidney disease to help identify new therapies that slow progression and reduce associated risks. Diabetic kidney disease is initiated by diabetes-related disturbances in glucose metabolism, which then trigger other metabolic, hemodynamic, inflammatory, and fibrotic processes that contribute to disease progression. This review summarizes existing evidence on the molecular drivers of diabetic kidney disease onset and progression, focusing on inflammatory and fibrotic mediators—factors that are largely unaddressed as primary treatment targets and for which there is increasing evidence supporting key roles in the pathophysiology of diabetic kidney disease. Results from recent clinical trials highlight promising new drug therapies, as well as a role for dietary strategies, in treating diabetic kidney disease
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    Molecular Signatures of Diabetic Kidney Disease Hiding in a Patient with Hypertension-Related Kidney Disease: A Clinical Pathologic Molecular Correlation
    (Wolters Kluwer, 2022) Patel, Jiten; Torrealba, Jose R.; Poggio, Emilio D.; Bebiak, Jack; Alpers, Charles E.; Grewenow, Stephanie M.; Toto, Robert D.; Eadon, Michael T.; Kidney Precision Medicine Project; Medicine, School of Medicine
    The Kidney Precision Medicine Project (KPMP) seeks to establish a molecular atlas of the kidney in health and disease and improve our understanding of the molecular drivers of CKD and AKI. Herein, we describe the case of a 66-year-old woman with CKD who underwent a protocol KPMP kidney biopsy. Her clinical history included well-controlled diabetes mellitus, hypertension, and proteinuria. The patient’s histopathology was consistent with modest hypertension-related kidney injury, without overt diabetic kidney disease. Transcriptomic signatures of the glomerulus, interstitium, and tubular subsegments were obtained from laser microdissected tissue. The molecular signatures that were uncovered revealed evidence of early diabetic kidney disease adaptation and ongoing active tubular injury with enriched pathways related to mesangial cell hypertrophy, glycosaminoglycan biosynthesis, and apoptosis. Molecular evidence of diabetic kidney disease was found across the nephron. Novel molecular assays can supplement and enrich the histopathologic diagnosis obtained from a kidney biopsy.
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    Rationale and design of the Kidney Precision Medicine Project
    (Elsevier, 2021) de Boer, Ian H.; Alpers, Charles E.; Azeloglu, Evren U.; Balis, Ulysses G. J.; Barasch, Jonathan M.; Barisoni, Laura; Blank, Kristina N.; Bomback, Andrew S.; Brown, Keith; Dagher, Pierre C.; Dighe, Ashveena L.; Eadon, Michael T.; El-Achkar, Tarek M.; Gaut, Joseph P.; Hacohen, Nir; He, Yongqun; Hodgin, Jeffrey B.; Jain, Sanjay; Kellum, John A.; Kiryluk, Krzysztof; Knight, Richard; Laszik, Zoltan G.; Lienczewski, Chrysta; Mariani, Laura H.; McClelland, Robyn L.; Menez, Steven; Moledina, Dennis G.; Mooney, Sean D.; O'Toole, John F.; Palevsky, Paul M.; Parikh, Chirag R.; Poggio, Emilio D.; Rosas, Sylvia E.; Rosengart, Matthew R.; Sarwal, Minnie M.; Schaub, Jennifer A.; Sedor, John R.; Sharma, Kumar; Steck, Becky; Toto, Robert D.; Troyanskaya, Olga G.; Tuttle, Katherine R.; Vazquez, Miguel A.; Waikar, Sushrut S.; Williams, Kayleen; Wilson, Francis Perry; Zhang, Kun; Iyengar, Ravi; Kretzler, Matthias; Himmelfarb, Jonathan; Kidney Precision Medicine Project; Medicine, School of Medicine
    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-donor kidney biopsies) will also be evaluated. Traditional and digital pathology will be combined with transcriptomic, proteomic, and metabolomic 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 10 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.