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Tanaka S, Ninomiya T, Fujisaki K, Yoshida H, Nagata M, Masutani K, Tokumoto M, Mitsuiki K, Hirakata H, Fujimi S, Kiyohara Y, Kitazono T, Tsuruya K. The Fukuoka Kidney disease Registry (FKR) Study: design and methods. Clin Exp Nephrol 2016; 21:465-473. [PMID: 27339444 DOI: 10.1007/s10157-016-1294-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Chronic kidney disease (CKD) is an established independent risk factor for progression to end-stage renal disease (ESRD) and incidence of cardiovascular disease (CVD). The onset and progression of CKD are associated with both genetic predisposition and various lifestyle-related factors, but little is known about the influence of genetic-environmental interactions on the incidence of ESRD or CVD in patients with CKD. METHODS The Fukuoka Kidney disease Registry (FKR) Study is designed as one of the largest prospective, multicenter, observational cohort studies in non-dialysis dependent CKD patients. The FKR Study aims to enroll approximately 5000 individuals at multiple clinical centers and follow them for up to at least 5 years. At baseline, subjects enrolled in the FKR Study will fill out extensive lifestyle-related questionnaires. Further, their health status and treatments will be monitored annually through a research network of nephrology centers. Blood and urine samples, including DNA/RNA, will be collected at the time of enrolment and every 5-years follow-up. CONCLUSIONS The FKR Study will provide many insights into the onset and progression of CKD, which will suggest hypothesis-driven interventional clinical trials aimed at reducing the burden of CKD. The features of the FKR Study may also facilitate innovative research to identify and validate novel risk factors, including genetic susceptibility and biomarkers, using biomaterials by high-throughput omics technologies.
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Affiliation(s)
- Shigeru Tanaka
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Internal Medicine, Fukuoka Dental College, Fukuoka, Japan
| | - Toshiharu Ninomiya
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Division of Research Management, Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kiichiro Fujisaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hisako Yoshida
- Department of Integrated Therapy for Chronic Kidney Disease, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masaharu Nagata
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kosuke Masutani
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masanori Tokumoto
- Department of Internal Medicine, Fukuoka Dental College, Fukuoka, Japan
| | - Koji Mitsuiki
- Division of Nephrology and Dialysis Center, Japanese Red Cross Fukuoka Hospital, Fukuoka, Japan
| | - Hideki Hirakata
- Division of Nephrology and Dialysis Center, Japanese Red Cross Fukuoka Hospital, Fukuoka, Japan
| | | | - Yutaka Kiyohara
- Department of Environmental Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takanari Kitazono
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuhiko Tsuruya
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan. .,Department of Integrated Therapy for Chronic Kidney Disease, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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Rosenberg AZ, Palmer M, Merlino L, Troost JP, Gasim A, Bagnasco S, Avila-Casado C, Johnstone D, Hodgin JB, Conway C, Gillespie BW, Nast CC, Barisoni L, Hewitt SM. The Application of Digital Pathology to Improve Accuracy in Glomerular Enumeration in Renal Biopsies. PLoS One 2016; 11:e0156441. [PMID: 27310011 PMCID: PMC4911144 DOI: 10.1371/journal.pone.0156441] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 05/14/2016] [Indexed: 12/02/2022] Open
Abstract
Background In renal biopsy reporting, quantitative measurements, such as glomerular number and percentage of globally sclerotic glomeruli, is central to diagnostic accuracy and prognosis. The aim of this study is to determine the number of glomeruli and percent globally sclerotic in renal biopsies by means of registration of serial tissue sections and manual enumeration, compared to the numbers in pathology reports from routine light microscopic assessment. Design We reviewed 277 biopsies from the Nephrotic Syndrome Study Network (NEPTUNE) digital pathology repository, enumerating 9,379 glomeruli by means of whole slide imaging. Glomerular number and the percentage of globally sclerotic glomeruli are values routinely recorded in the official renal biopsy pathology report from the 25 participating centers. Two general trends in reporting were noted: total number per biopsy or average number per level/section. Both of these approaches were assessed for their accuracy in comparison to the analogous numbers of annotated glomeruli on WSI. Results The number of glomeruli annotated was consistently higher than those reported (p<0.001); this difference was proportional to the number of glomeruli. In contrast, percent globally sclerotic were similar when calculated on total glomeruli, but greater in FSGS when calculated on average number of glomeruli (p<0.01). The difference in percent globally sclerotic between annotated and those recorded in pathology reports was significant when global sclerosis is greater than 40%. Conclusions Although glass slides were not available for direct comparison to whole slide image annotation, this study indicates that routine manual light microscopy assessment of number of glomeruli is inaccurate, and the magnitude of this error is proportional to the total number of glomeruli.
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MESH Headings
- Biopsy
- Glomerulonephritis, IGA/diagnostic imaging
- Glomerulonephritis, IGA/pathology
- Glomerulonephritis, IGA/surgery
- Glomerulonephritis, Membranous/diagnostic imaging
- Glomerulonephritis, Membranous/pathology
- Glomerulonephritis, Membranous/surgery
- Glomerulosclerosis, Focal Segmental/diagnostic imaging
- Glomerulosclerosis, Focal Segmental/pathology
- Glomerulosclerosis, Focal Segmental/surgery
- Humans
- Kidney Glomerulus/diagnostic imaging
- Kidney Glomerulus/pathology
- Kidney Glomerulus/surgery
- Microscopy/methods
- Nephrotic Syndrome/diagnostic imaging
- Nephrotic Syndrome/pathology
- Nephrotic Syndrome/surgery
- Signal Processing, Computer-Assisted
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Affiliation(s)
- Avi Z. Rosenberg
- Department of Pathology, Children’s National Medical Center, Washington, DC, United States of America
- National Institute of Digestive Diseases and Kidney, National Institutes of Health, Bethesda, MD, United States of America
| | - Matthew Palmer
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Lino Merlino
- Department of Pathology, University of Miami, Miami, FL, United States of America
| | - Jonathan P. Troost
- Department of Pediatrics, Division of Pediatric Nephrology, University of Michigan, Ann Arbor, MI, United States of America
| | - Adil Gasim
- Department of Pathology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Serena Bagnasco
- Department of Pathology, The Johns Hopkins School of Medicine, Baltimore, MD, United States of America
| | | | - Duncan Johnstone
- Department of Medicine, Section of Nephrology, Hypertension and Kidney Transplantation Temple University, Philadelphia, PA, United States of America
| | - Jeffrey B. Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - Catherine Conway
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Brenda W. Gillespie
- Biostatistics Department, School of Public Health, University of Michigan, Ann Arbor, MI, United States of America
| | - Cynthia C. Nast
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Laura Barisoni
- Department of Pathology, University of Miami, Miami, FL, United States of America
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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Gillies CE, Otto EA, Vega-Warner V, Robertson CC, Sanna-Cherchi S, Gharavi A, Crawford B, Bhimma R, Winkler C, Kang HM, Sampson MG. tarSVM: Improving the accuracy of variant calls derived from microfluidic PCR-based targeted next generation sequencing using a support vector machine. BMC Bioinformatics 2016; 17:233. [PMID: 27287006 PMCID: PMC4902911 DOI: 10.1186/s12859-016-1108-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/02/2016] [Indexed: 12/30/2022] Open
Abstract
Background Targeted sequencing of discrete gene sets is a cost effective strategy to screen subjects for monogenic forms of disease. One method to achieve this pairs microfluidic PCR with next generation sequencing. The PCR step of this pipeline creates challenges in accurate variant calling. This includes that most reads targeting a specific exon are duplicates that have been amplified from the PCR step. To reduce false positive variant calls from these experiments, previous studies have used threshold-based filtering of alternative allele depth ratio and manual inspection of the alignments. However even after manual inspection and filtering, many variants fail to be validated via Sanger sequencing. To improve the accuracy of variant calling from these experiments, we are challenged to design a variant filtering strategy that sufficiently models microfluidic PCR-specific issues. Results We developed an open source variant filtering pipeline, targeted sequencing support vector machine (“tarSVM”), that uses a Support Vector Machine (SVM) and a new score the normalized allele dosage test to identify high quality variants from microfluidic PCR data. tarSVM maximizes training knowledge by selecting variants that are likely true and likely false variants by incorporating knowledge from the 1000 Genomes and the Exome Aggregation Consortium projects. tarSVM improves on previous approaches by synthesizing variant features from the Genome Analysis Toolkit and allele dosage information. We compared the accuracy of tarSVM versus existing variant quality filtering strategies on two cohorts (n = 474 and n = 1152), and validated our method on a third cohort (n = 75). In the first cohort, our method achieved 84.5 % accuracy of predicting whether or not a variant would be validated with Sanger sequencing versus 78.8 % for the second most accurate method. In the second cohort, our method had an accuracy of 73.3 %, versus 61.5 % for the second best method. Finally, our method had a false discovery rate of 5 % for the validation cohort. Conclusions tarSVM increases the accuracy of variant calling when using microfluidic PCR based targeted sequencing approaches. This results in higher confidence downstream analyses, and ultimately reduces the costs Sanger validation. Our approach is less labor intensive than existing approaches, and is available as an open source pipeline for read trimming, aligning, variant calling, and variant quality filtering on GitHub at https://github.com/christopher-gillies/TargetSpecificGATKSequencingPipeline. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1108-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher E Gillies
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Edgar A Otto
- Department of Internal Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Virginia Vega-Warner
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Catherine C Robertson
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Ali Gharavi
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Brendan Crawford
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Rajendra Bhimma
- Department of Paediatrics and Child Health, University of KwaZulu Natal, Durban, South Africa
| | - Cheryl Winkler
- NCI, Frederick National Lab for Cancer Research, Molecular Genetics Epidemiology Section, Frederick, MD, USA
| | | | | | - Hyun Min Kang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Matthew G Sampson
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, USA. .,, 3560B MSRB2, 1150 West Medical Center Drive, Ann Arbor, MI, 48109, USA.
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204
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Morphometry Predicts Early GFR Change in Primary Proteinuric Glomerulopathies: A Longitudinal Cohort Study Using Generalized Estimating Equations. PLoS One 2016; 11:e0157148. [PMID: 27285824 PMCID: PMC4902229 DOI: 10.1371/journal.pone.0157148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/25/2016] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Most predictive models of kidney disease progression have not incorporated structural data. If structural variables have been used in models, they have generally been only semi-quantitative. METHODS We examined the predictive utility of quantitative structural parameters measured on the digital images of baseline kidney biopsies from the NEPTUNE study of primary proteinuric glomerulopathies. These variables were included in longitudinal statistical models predicting the change in estimated glomerular filtration rate (eGFR) over up to 55 months of follow-up. RESULTS The participants were fifty-six pediatric and adult subjects from the NEPTUNE longitudinal cohort study who had measurements made on their digital biopsy images; 25% were African-American, 70% were male and 39% were children; 25 had focal segmental glomerular sclerosis, 19 had minimal change disease, and 12 had membranous nephropathy. We considered four different sets of candidate predictors, each including four quantitative structural variables (for example, mean glomerular tuft area, cortical density of patent glomeruli and two of the principal components from the correlation matrix of six fractional cortical areas-interstitium, atrophic tubule, intact tubule, blood vessel, sclerotic glomerulus, and patent glomerulus) along with 13 potentially confounding demographic and clinical variables (such as race, age, diagnosis, and baseline eGFR, quantitative proteinuria and BMI). We used longitudinal linear models based on these 17 variables to predict the change in eGFR over up to 55 months. All 4 models had a leave-one-out cross-validated R2 of about 62%. CONCLUSIONS Several combinations of quantitative structural variables were significantly and strongly associated with changes in eGFR. The structural variables were generally stronger than any of the confounding variables, other than baseline eGFR. Our findings suggest that quantitative assessment of diagnostic renal biopsies may play a role in estimating the baseline risk of succeeding loss of renal function in future clinical studies, and possibly in clinical practice.
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205
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The partnership of patient advocacy groups and clinical investigators in the rare diseases clinical research network. Orphanet J Rare Dis 2016; 11:66. [PMID: 27194034 PMCID: PMC4870759 DOI: 10.1186/s13023-016-0445-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Among the unique features of the Rare Diseases Clinical Research Network (RDCRN) Program is the requirement for each Consortium to include patient advocacy groups (PAGs) as research partners. This development has transformed the work of the RDCRN and is a model for collaborative research. This article outlines the roles patients and PAGs play in the RDCRN and reports on the PAGs' impact on the Network's success. METHODS Principal Investigators from the 17 RDCRN Consortia and 28 representatives from 76 PAGs affiliated with these Consortia were contacted by email to provide feedback via an online RDCRN survey. Impact was measured in the key areas of 1) Research logistics; 2) Outreach and communication; and 3) Funding and in-kind support. Rating choices were: 1-very negative, 2-somewhat negative, 3-no impact, 4-somewhat positive, and 5-very positive. RESULTS Twenty-seven of the PAGs (96 %) disseminate information about the RDCRN within the patient community. The Consortium Principal Investigators also reported high levels of PAG involvement. Sixteen (94 %) Consortium Principal Investigators and 25 PAGs (89 %) reported PAGs participation in protocol review, study design, Consortium conference calls, attending Consortium meetings, or helping with patient recruitment. CONCLUSIONS PAGs are actively involved in shaping Consortia's research agendas, help ensure the feasibility and success of research protocols by assisting with study design and patient recruitment, and support training programs. This extensive PAG-Investigator partnership in the RDCRN has had a strongly positive impact on the success of the Network.
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206
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Lee JE, Lee YH, Kim SY, Kim YG, Moon JY, Jeong KH, Lee TW, Ihm CG, Kim S, Kim KH, Kim DK, Kim YS, Kim CD, Park CW, Lee DY, Lee SH. Systematic biomarker discovery and coordinative validation for different primary nephrotic syndromes using gas chromatography-mass spectrometry. J Chromatogr A 2016; 1453:105-15. [PMID: 27247212 DOI: 10.1016/j.chroma.2016.05.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/04/2016] [Accepted: 05/15/2016] [Indexed: 11/24/2022]
Abstract
The goal of this study is to identify systematic biomarker panel for primary nephrotic syndromes from urine samples by applying a non-target metabolite profiling, and to validate their utility in independent sampling and analysis by multiplex statistical approaches. Nephrotic syndrome (NS) is a nonspecific kidney disorder, which is mostly represented by minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), and membranous glomerulonephritis (MGN). Since urine metabolites may mirror disease-specific functional perturbations in kidney injury, we examined urine samples for distinctive metabolic changes to identify biomarkers for clinical applications. We developed unbiased multi-component covarianced models from a discovery set with 48 samples (12 healthy controls, 12 MCD, 12 FSGS, and 12 MGN). To extensively validate their diagnostic potential, new batch from 54 patients with primary NS were independently examined a year after. In the independent validation set, the model including citric acid, pyruvic acid, fructose, ethanolamine, and cysteine effectively discriminated each NS using receiver operating characteristic (ROC) analysis except MCD-MGN comparison; nonetheless an additional metabolite multi-composite greatly improved the discrimination power between MCD and MGN. Finally, we proposed the re-constructed metabolic network distinctively dysregulated by the different NSs that may deepen comprehensive understanding of the disease mechanistic, and help the enhanced identification of NS and therapeutic plans for future.
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Affiliation(s)
- Jung-Eun Lee
- The Dept. of Bio and Fermentation Convergence Technology, BK21 PLUS project, Kookmin University, Seoul, Republic of Korea; Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Yu Ho Lee
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Se-Yun Kim
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Yang Gyun Kim
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Ju-Young Moon
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Kyung-Hwan Jeong
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Tae Won Lee
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Chun-Gyoo Ihm
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Sooah Kim
- The Dept. of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Kyoung Heon Kim
- The Dept. of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Dong Ki Kim
- Division of Nephrology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yon Su Kim
- Division of Nephrology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chan-Duck Kim
- Division of Nephrology, Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Cheol Whee Park
- Division of Nephrology, Department of Internal Medicine, College of Medicine, The St. Mary's Hospital of Catholic University of Korea, Seoul, Republic of Korea
| | - Do Yup Lee
- The Dept. of Bio and Fermentation Convergence Technology, BK21 PLUS project, Kookmin University, Seoul, Republic of Korea.
| | - Sang-Ho Lee
- Division of Nephrology, Department of Internal Medicine, College of medicine, Kyung Hee University, Seoul, Republic of Korea.
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Sánchez BN, Wu M, Song PXK, Wang W. Study design in high-dimensional classification analysis. Biostatistics 2016; 17:722-36. [PMID: 27154835 DOI: 10.1093/biostatistics/kxw018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/03/2016] [Indexed: 12/31/2022] Open
Abstract
Advances in high throughput technology have accelerated the use of hundreds to millions of biomarkers to construct classifiers that partition patients into different clinical conditions. Prior to classifier development in actual studies, a critical need is to determine the sample size required to reach a specified classification precision. We develop a systematic approach for sample size determination in high-dimensional (large [Formula: see text] small [Formula: see text]) classification analysis. Our method utilizes the probability of correct classification (PCC) as the optimization objective function and incorporates the higher criticism thresholding procedure for classifier development. Further, we derive the theoretical bound of maximal PCC gain from feature augmentation (e.g. when molecular and clinical predictors are combined in classifier development). Our methods are motivated and illustrated by a study using proteomics markers to classify post-kidney transplantation patients into stable and rejecting classes.
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Affiliation(s)
- Brisa N Sánchez
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Meihua Wu
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Peter X K Song
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wen Wang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
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Guan Y, Martini S, Mariani LH. Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. Semin Nephrol 2016. [PMID: 26215861 DOI: 10.1016/j.semnephrol.2015.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In the past decade, population genetics has gained tremendous success in identifying genetic variations that are statistically relevant to renal diseases and kidney function. However, it is challenging to interpret the functional relevance of the genetic variations found by population genetics studies. In this review, we discuss studies that integrate multiple levels of data, especially transcriptome profiles and phenotype data, to assign functional roles of genetic variations involved in kidney function. Furthermore, we introduce state-of-the-art machine learning algorithms, Bayesian networks, support vector machines, and Gaussian process regression, which have been applied successfully to integrating genetic, regulatory, and clinical information to predict clinical outcomes. These methods are likely to be deployed successfully in the nephrology field in the near future.
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Affiliation(s)
- Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI; Department of Internal Medicine, University of Michigan, Ann Arbor, MI; Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI
| | - Sebastian Martini
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI; Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Laura H Mariani
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
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Sampson MG, Pollak MR. Opportunities and Challenges of Genotyping Patients With Nephrotic Syndrome in the Genomic Era. Semin Nephrol 2016. [PMID: 26215859 DOI: 10.1016/j.semnephrol.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Both targeted and genome-wide linkage and association studies have identified a number of genes and genetic variants associated with nephrotic syndrome (NS). Genotype-phenotype studies of patients with these variants have identified correlations of clear clinical significance. Combined with improved genomic technologies, this has resulted in increasing, and justifiable, enthusiasm for incorporating our patients' genomic information into our clinical management decisions. Here, we summarize our understanding of NS-associated genetic factors, namely rare causal mutations or common risk alleles in apolipoprotein L1. We discuss the complexities inherent in trying to ascribe risk or causality to these variants, particularly as we seek to extend genetic testing to a broader group of patients, including many with sporadic disease. Overall, the thoughtful application and interpretation of these genetic tests will maximize the benefits to our patients with NS in the form of more precise clinical care.
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Affiliation(s)
- Matthew G Sampson
- Department of Pediatrics, Division of Nephrology, University of Michigan School of Medicine, Ann Arbor, MI.
| | - Martin R Pollak
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
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211
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Selewski DT, Herreshoff EG, Gipson DS. Optimizing Enrollment of Patients into Nephrology Research Studies. Clin J Am Soc Nephrol 2016; 11:512-7. [PMID: 26185262 PMCID: PMC4791824 DOI: 10.2215/cjn.00500115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Advances in medical care and biomedical research depend on the participation of human subjects. Poor patient enrollment in research has limited past clinical and translational research endeavors in nephrology. Simultaneously, patients and their caregivers are seeking better diagnostic, monitoring, and therapeutic approaches to improve or restore kidney and overall health. This manuscript will discuss a framework and strategies to optimize patient enrollment within nephrology research and provide examples of success from existing nephrology research programs.
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Affiliation(s)
- David T Selewski
- Division of Nephrology, Department of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Emily G Herreshoff
- Division of Nephrology, Department of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Debbie S Gipson
- Division of Nephrology, Department of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
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Hurdles to the introduction of new therapies for immune-mediated kidney diseases. Nat Rev Nephrol 2016; 12:205-16. [PMID: 26804020 DOI: 10.1038/nrneph.2015.206] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Innovative immunotherapies continue to markedly benefit many disciplines in clinical medicine but disappointingly, these benefits have not translated to the treatment of kidney diseases despite encouraging findings from preclinical models of kidney dysfunction. This lack of progress in nephrology might relate to the unique biology of the kidney. More likely, this lack of progress relates to conceptual hurdles in the application of newer therapies to renal disease. In this Review we discuss seven hurdles that must be addressed in order to appropriately assess and introduce immunologic therapies for immune-mediated kidney disease: the use of appropriate criteria to define disease categories; issues relating to the heterogeneity of kidney diseases and how this heterogeneity affects approaches to treatment; issues related to the rarity of most kidney diseases; the paucity of good animal models of human kidney disease; issues relating to trial design; problems with current approaches to the identification and use of appropriate and feasible study end points; and a lack of adequate biomarkers of intrarenal inflammation and parenchymal injury. We suggest that overcoming these hurdles, in addition to searching for better therapeutic targets, will be necessary to progress the treatment of immune-mediated kidney disease into a new age of drug therapy.
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213
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Chanchlani R, Parekh RS. Ethnic Differences in Childhood Nephrotic Syndrome. Front Pediatr 2016; 4:39. [PMID: 27148508 PMCID: PMC4835686 DOI: 10.3389/fped.2016.00039] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/04/2016] [Indexed: 01/10/2023] Open
Abstract
Nephrotic syndrome is a common glomerular disease in children with significant variability in both incidence and steroid responsiveness among various ethnic groups. The average incidence of nephrotic syndrome is 2-16.9 per 100,000 children worldwide. Understanding the variability by ethnicity may point to potential factors leading to nephrotic syndrome, which remains elusive, and may highlight factors accounting for differences in medication response. The emerging role of genetic factors associated with steroid responsive and steroid-resistant forms of nephrotic syndrome within an ethnic group can provide insight into potential biological mechanisms leading to disease. For example, among African-Americans, the risk variants in APOL1 are associated with a more than 10-fold increase in risk of focal segmental glomerulosclerosis and high-risk carriers have a twofold greater risk of progression to end-stage renal disease. Ongoing collaborative studies should consider capturing data on self-reported ethnicity to understand differences in incidence and outcomes. In the future, the availability of whole-genome data will provide an excellent opportunity for new clinical and translational research in childhood nephrotic syndrome and lead to a better understanding of the disease.
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Affiliation(s)
- Rahul Chanchlani
- Division of Pediatric Nephrology, Hospital for Sick Children, Toronto, ON, Canada; Child Health Evaluative Sciences, Research Institute, Hospital for Sick Children, Toronto, ON, Canada; Division of Pediatric Nephrology, McMaster Children's Hospital, Hamilton, ON, Canada
| | - Rulan S Parekh
- Division of Pediatric Nephrology, Hospital for Sick Children, Toronto, ON, Canada; Child Health Evaluative Sciences, Research Institute, Hospital for Sick Children, Toronto, ON, Canada; Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON, Canada
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214
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Hjorten R, Anwar Z, Reidy KJ. Long-term Outcomes of Childhood Onset Nephrotic Syndrome. Front Pediatr 2016; 4:53. [PMID: 27252935 PMCID: PMC4879783 DOI: 10.3389/fped.2016.00053] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 05/06/2016] [Indexed: 12/13/2022] Open
Abstract
There are limited studies on long-term outcomes of childhood onset nephrotic syndrome (NS). A majority of children with NS have steroid-sensitive nephrotic syndrome (SSNS). Steroid-resistant nephrotic syndrome (SRNS) is associated with a high risk of developing end-stage renal disease. Biomarkers and analysis of genetic mutations may provide new information for prognosis in SRNS. Frequently relapsing and steroid-dependent NS is associated with long-term complications, including dyslipidemia, cataracts, osteoporosis and fractures, obesity, impaired growth, and infertility. Long-term complications of SSNS are likely to be under-recognized. There remain many gaps in our knowledge of long-term outcomes of childhood NS, and further study is indicated.
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Affiliation(s)
- Rebecca Hjorten
- Pediatrics Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine , Bronx, NY , USA
| | - Zohra Anwar
- Pediatrics Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine , Bronx, NY , USA
| | - Kimberly Jean Reidy
- Pediatrics Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine , Bronx, NY , USA
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215
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Gipson DS, Troost JP, Lafayette RA, Hladunewich MA, Trachtman H, Gadegbeku CA, Sedor JR, Holzman LB, Moxey-Mims MM, Perumal K, Kaskel FJ, Nelson PJ, Tuttle KR, Bagnasco SM, Hogan MC, Dell KM, Appel GB, Lieske JC, Ilori TO, Sethna CB, Fervenza FC, Hogan SL, Nachman PH, Rosenberg AZ, Greenbaum LA, Meyers KEC, Hewitt SM, Choi MJ, Kopp JB, Zhdanova O, Hodgin JB, Johnstone DB, Adler SG, Avila-Casado C, Neu AM, Hingorani SR, Lemley KV, Nast CC, Brady TM, Barisoni-Thomas L, Fornoni A, Jennette JC, Cattran DC, Palmer MB, Gibson KL, Reich HN, Mokrzycki MH, Sambandam KK, Zilleruelo GE, Licht C, Sampson MG, Song P, Mariani LH, Kretzler M. Complete Remission in the Nephrotic Syndrome Study Network. Clin J Am Soc Nephrol 2015; 11:81-9. [PMID: 26656320 DOI: 10.2215/cjn.02560315] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 09/24/2015] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES This analysis from the Nephrotic Syndrome Study Network (NEPTUNE) assessed the phenotypic and pathology characteristics of proteinuric patients undergoing kidney biopsy and defined the frequency and factors associated with complete proteinuria remission (CRever). DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We enrolled adults and children with proteinuria ≥0.5 g/d at the time of first clinically indicated renal biopsy at 21 sites in North America from April 2010 to June 2014 into a prospective cohort study. NEPTUNE central pathologists assigned participants to minimal-change disease (MCD), FSGS, membranous nephropathy, or other glomerulopathy cohorts. Outcome measures for this analysis were (1) CRever with urine protein-to-creatinine ratio (UPC) <0.3 g/g with preserved native kidney function and (2) ESRD. Continuous variables are reported as median and interquartile range (IQR; 25th, 75th percentile). Cox proportional hazards modeling was used to assess factors associated with CRever. RESULTS We enrolled 441 patients: 116 (27%) had MCD, 142 (32%) had FSGS, 66 (15%) had membranous nephropathy, and 117 (27%) had other glomerulopathy. The baseline UPC was 4.1 g/g (IQR, 1.9, 7.7) and the eGFR was 81 ml/min per 1.73 m(2) (IQR, 50, 105). Median duration of observation was 19 months (IQR, 11, 30). CRever occurred in 46% of patients, and 4.6% progressed to ESRD. Multivariate analysis demonstrated that higher prebiopsy proteinuria (hazard ratio, 0.3; 95% confidence interval, 0.2 to 0.5) and pathology diagnosis (FSGS versus MCD; hazard ratio, 0.2; 95% confidence interval, 0.1 to 0.5) were inversely associated with CRever. The effect of immunosuppressive therapy on remission varied by pathology diagnosis. CONCLUSIONS In NEPTUNE, the high frequency of other pathology in proteinuric patients affirms the value of the diagnostic kidney biopsy. Clinical factors, including level of proteinuria before biopsy, pathology diagnosis, and immunosuppression, are associated with complete remission.
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Affiliation(s)
- Debbie S Gipson
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material.
| | - Jonathan P Troost
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Richard A Lafayette
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Michelle A Hladunewich
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Howard Trachtman
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Crystal A Gadegbeku
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - John R Sedor
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Lawrence B Holzman
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Marva M Moxey-Mims
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Kalyani Perumal
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Frederick J Kaskel
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Peter J Nelson
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Katherine R Tuttle
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Serena M Bagnasco
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Marie C Hogan
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Katherine M Dell
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Gerald B Appel
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - John C Lieske
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Titilayo O Ilori
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Christine B Sethna
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Fernando C Fervenza
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Susan L Hogan
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Patrick H Nachman
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Avi Z Rosenberg
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Larry A Greenbaum
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Kevin E C Meyers
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Stephen M Hewitt
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Michael J Choi
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Jeffrey B Kopp
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Olga Zhdanova
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Jeffrey B Hodgin
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Duncan B Johnstone
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Sharon G Adler
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Carmen Avila-Casado
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Alicia M Neu
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Sangeeta R Hingorani
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Kevin V Lemley
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Cynthia C Nast
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Tammy M Brady
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Laura Barisoni-Thomas
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Alessia Fornoni
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - J Charles Jennette
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Daniel C Cattran
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Matthew B Palmer
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Keisha L Gibson
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Heather N Reich
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Michele H Mokrzycki
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Kamalanathan K Sambandam
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Gaston E Zilleruelo
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Christoph Licht
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Matthew G Sampson
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Peter Song
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Laura H Mariani
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
| | - Matthias Kretzler
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
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216
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Mariani LH, Kretzler M. Pro: 'The usefulness of biomarkers in glomerular diseases'. The problem: moving from syndrome to mechanism--individual patient variability in disease presentation, course and response to therapy. Nephrol Dial Transplant 2015; 30:892-8. [PMID: 25994659 DOI: 10.1093/ndt/gfv108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The diagnosis and treatment decisions in glomerular disease are principally based on renal pathology and nonspecific clinical laboratory measurements such as serum creatinine and urine protein. Using these classification approaches, patients have marked variability in rate of progression and response to therapy, exposing a significant number of patients to toxicity without benefit. Additionally, clinical trials are at risk of not being able to detect an efficacious therapy in relevant subgroups as patients with shared clinical-pathologic diagnoses have heterogeneous underlying pathobiology. To change this treatment paradigm, biomarkers that reflect the molecular mechanisms underlying the clinical-pathologic diagnoses are needed. Recent progress to identify such biomarkers has been aided by advances in molecular profiling, large-scale data generation and multi-scalar data integration, including prospectively collected clinical data. This article reviews the evolving success stories in glomerular disease biomarkers across the genotype-phenotype continuum and highlights opportunities to transition to precision medicine in glomerular disease.
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Affiliation(s)
- Laura H Mariani
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, MI, USA Arbor Research Collaborative for Health, Ann Arbor, MI, USA
| | - Matthias Kretzler
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, MI, USA Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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217
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Reich HN, Sabelnykova VY, Boutros PC. Matching Kidneys and Urines: Establishing Noninvasive Surrogates of Intrarenal Events in Primary Glomerulonephritis. Semin Nephrol 2015. [PMID: 26215863 DOI: 10.1016/j.semnephrol.2015.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Kidney biopsy is the gold standard procedure for providing diagnostic and prognostic information for patients with glomerular-based diseases, however, the utility of this procedure for assessing longitudinal disease activity is limited. The intense search for noninvasive biomarkers of kidney disease activity and injury is driven in large part by the inherent risks of the kidney biopsy procedure and limited information derived from the morphologic description of biopsy findings. Furthermore, gaps in our understanding of the core intrarenal molecular processes underlying the development and progression of glomerular-based diseases has limited the development of effective targeted therapy. In this review, we discuss the potential utility of molecular analysis of the urine to provide a dynamic window into intrarenal molecular and morphologic responses. We focus on molecular analysis of the urine to identify noninvasive surrogate markers of kidney responses, with the goal of using these biomarkers as more sensitive indicators of progression and tissue-level responses to therapeutic interventions in patients with primary glomerulonephritis.
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Affiliation(s)
- Heather N Reich
- The Toronto Glomerulonephritis Registry, University Health Network, Gabor Zellerman Chair in Nephrology Research at the University of Toronto Department of Medicine, Toronto, Ontario, Canada.
| | - Veronica Y Sabelnykova
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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218
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Sampson MG, Robertson CC, Martini S, Mariani LH, Lemley KV, Gillies CE, Otto EA, Kopp JB, Randolph A, Vega-Warner V, Eichinger F, Nair V, Gipson DS, Cattran DC, Johnstone DB, O'Toole JF, Bagnasco SM, Song PX, Barisoni L, Troost JP, Kretzler M, Sedor JR. Integrative Genomics Identifies Novel Associations with APOL1 Risk Genotypes in Black NEPTUNE Subjects. J Am Soc Nephrol 2015; 27:814-23. [PMID: 26150607 DOI: 10.1681/asn.2014111131] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/31/2015] [Indexed: 01/13/2023] Open
Abstract
APOL1 variants have been associated with renal phenotypes in blacks. To refine clinical outcomes and discover mechanisms of APOL1-associated kidney injury, we analyzed clinical and genomic datasets derived from 90 black subjects in the Nephrotic Syndrome Study Network (NEPTUNE), stratified by APOL1 risk genotype. Ninety subjects with proteinuria ≥0.5 g/d were enrolled at first biopsy for primary nephrotic syndrome and followed. Clinical outcomes were determined, and renal histomorphometry and sequencing of Mendelian nephrotic syndrome genes were performed. APOL1 variants were genotyped, and glomerular and tubulointerstitial transcriptomes from protocol renal biopsy cores were analyzed for differential and correlative gene expression. Analyses were performed under the recessive model (high-risk genotype defined by two risk alleles). APOL1 high-risk genotype was significantly associated with a 17 ml/min per 1.73 m(2) lower eGFR and a 69% reduction in the probability of complete remission at any time, independent of histologic diagnosis. Neither APOL1 risk group was enriched for Mendelian mutations. On renal biopsy, high-risk genotype was associated with increased fractional interstitial area, interstitial fibrosis, and tubular atrophy. Risk genotype was not associated with intrarenal APOL1 mRNA expression levels. Differential expression analysis demonstrated an increased steady-state level of five genes associated with the high-risk genotype (CXCL9, CXCL11, and UBD in glomerulus; SNOR14B and MUC13 in tubulointerstitium). APOL1 tubulointerstitial coexpression analysis showed coexpression of APOL1 mRNA levels with a group of intrarenal transcripts that together were associated with increased interstitial fibrosis and tubular atrophy. These data indicate the high-risk APOL1 genotype confers renal risk across histopathologic diagnoses.
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Affiliation(s)
- Matthew G Sampson
- Division of Nephrology, Department of Pediatrics and Communicable Diseases,
| | | | - Sebastian Martini
- Division of Nephrology, Departments of Internal Medicine and Computational Medicine and Bioinformatics, and
| | - Laura H Mariani
- Division of Nephrology, Departments of Internal Medicine and Computational Medicine and Bioinformatics, and
| | - Kevin V Lemley
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Los Angeles, University of Southern California School of Medicine, Los Angeles, California
| | | | - Edgar A Otto
- Division of Nephrology, Department of Pediatrics and Communicable Diseases
| | - Jeffrey B Kopp
- Kidney Diseases Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Anne Randolph
- Division of Nephrology, Departments of Internal Medicine and Computational Medicine and Bioinformatics, and
| | | | - Felix Eichinger
- Division of Nephrology, Departments of Internal Medicine and Computational Medicine and Bioinformatics, and
| | - Viji Nair
- Division of Nephrology, Departments of Internal Medicine and Computational Medicine and Bioinformatics, and
| | - Debbie S Gipson
- Division of Nephrology, Department of Pediatrics and Communicable Diseases
| | - Daniel C Cattran
- Department of Nephrology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Duncan B Johnstone
- Division of Nephrology, Department of Internal Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - John F O'Toole
- Division of Nephrology, Department of Internal Medicine and
| | - Serena M Bagnasco
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Peter X Song
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan; and
| | - Laura Barisoni
- Department of Pathology, University of Miami, Miller School of Medicine, Miami, Florida
| | - Jonathan P Troost
- Division of Nephrology, Department of Pediatrics and Communicable Diseases
| | - Matthias Kretzler
- Division of Nephrology, Departments of Internal Medicine and Computational Medicine and Bioinformatics, and Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - John R Sedor
- Division of Nephrology, Department of Internal Medicine and Department of Physiology and Biophysics, Case Western Reserve University and Rammelkamp Center for Education and Research, MetroHealth System, Cleveland, Ohio
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219
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Cianciolo RE, Mohr FC, Aresu L, Brown CA, James C, Jansen JH, Spangler WL, van der Lugt JJ, Kass PH, Brovida C, Cowgill LD, Heiene R, Polzin DJ, Syme H, Vaden SL, van Dongen AM, Lees GE. World Small Animal Veterinary Association Renal Pathology Initiative: Classification of Glomerular Diseases in Dogs. Vet Pathol 2015; 53:113-35. [PMID: 25957358 DOI: 10.1177/0300985815579996] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Evaluation of canine renal biopsy tissue has generally relied on light microscopic (LM) evaluation of hematoxylin and eosin-stained sections ranging in thickness from 3 to 5 µm. Advanced modalities, such as transmission electron microscopy (TEM) and immunofluorescence (IF), have been used sporadically or retrospectively. Diagnostic algorithms of glomerular diseases have been extrapolated from the World Health Organization classification scheme for human glomerular disease. With the recent establishment of 2 veterinary nephropathology services that evaluate 3-µm sections with a panel of histochemical stains and routinely perform TEM and IF, a standardized objective species-specific approach for the diagnosis of canine glomerular disease was needed. Eight veterinary pathologists evaluated 114 parameters (lesions) in renal biopsy specimens from 89 dogs. Hierarchical cluster analysis of the data revealed 2 large categories of glomerular disease based on the presence or absence of immune complex deposition: The immune complex-mediated glomerulonephritis (ICGN) category included cases with histologic lesions of membranoproliferative or membranous patterns. The second category included control dogs and dogs with non-ICGN (glomerular amyloidosis or focal segmental glomerulosclerosis). Cluster analysis performed on only the LM parameters led to misdiagnosis of 22 of the 89 cases-that is, ICGN cases moved to the non-ICGN branch of the dendrogram or vice versa, thereby emphasizing the importance of advanced diagnostic modalities in the evaluation of canine glomerular disease. Salient LM, TEM, and IF features for each pattern of disease were identified, and a preliminary investigation of related clinicopathologic data was performed.
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Affiliation(s)
- R E Cianciolo
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - F C Mohr
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - L Aresu
- Facoltà di Medicina Veterinaria, Dipartimento di Biomedicina comparata e Alimentazione, Università di Padova, Legnaro, Italy
| | - C A Brown
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - C James
- IDEXX Laboratories, Ltd., Wetherby, United Kingdom
| | - J H Jansen
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | | | - J J van der Lugt
- IDEXX Europe, BV, Hoofddorp, The Netherlands Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - P H Kass
- Department of Population Health and Production, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - C Brovida
- ANUBI Ospedale per Animali da Compagnia, Moncalieri, Italy
| | - L D Cowgill
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - R Heiene
- Blue Star Animal Hospital, Gothenburg, Sweden PetVett Dyresykehus, Oslo, Norway Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - D J Polzin
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA
| | - H Syme
- Department of Clinical Sciences, Royal Veterinary College, Hatfield, UK
| | - S L Vaden
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - A M van Dongen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - G E Lees
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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220
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Nast CC, Lemley KV, Hodgin JB, Bagnasco S, Avila-Casado C, Hewitt SM, Barisoni L. Morphology in the Digital Age: Integrating High-Resolution Description of Structural Alterations With Phenotypes and Genotypes. Semin Nephrol 2015; 35:266-78. [PMID: 26215864 PMCID: PMC4764351 DOI: 10.1016/j.semnephrol.2015.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conventional light microscopy has been used to characterize and classify renal diseases, evaluate histopathology in studies and trials, and educate renal pathologists and nephrologists. The advent of digital pathology, in which a glass slide can be scanned to create whole slide images (WSIs) for viewing and manipulating on a computer monitor, provides real and potential advantages compared with conventional light microscopy. Software tools such as annotation, morphometry, and image analysis can be applied to WSIs for studies or educational purposes, and the digital images are available globally to clinicians, pathologists, and investigators. New ways of assessing renal pathology with observational data collection may allow better morphologic correlations and integration with molecular and genetic signatures, refinements of classification schema, and understanding of disease pathogenesis. In multicenter studies, WSIs, which require additional quality assurance steps, provide efficiency by reducing slide shipping and consensus conference costs, and they allow slide viewing anytime and anywhere. Although validation studies for the routine diagnostic use of digital pathology still are needed, this is a powerful tool currently available for translational research, clinical trials, and education in renal pathology.
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Affiliation(s)
- Cynthia C. Nast
- Dept of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Kevin V. Lemley
- Division of Nephrology, Children’s Hospital Los Angeles, Los Angeles, CA
| | | | - Serena Bagnasco
- Department of Pathology, Johns Hopkins University Medical Center, Baltimore, MD
| | | | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda MD
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221
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Grahammer F, Benzing T, Huber TB. New insights into mechanisms of glomerular injury and repair from the 10th International Podocyte Conference 2014. Kidney Int 2015; 87:885-93. [DOI: 10.1038/ki.2015.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 01/17/2023]
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222
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Glassock RJ. Con: Kidney biopsy: an irreplaceable tool for patient management in nephrology. Nephrol Dial Transplant 2015; 30:528-31. [DOI: 10.1093/ndt/gfv044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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223
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Malaga-Dieguez L, Bouhassira D, Gipson D, Trachtman H. Novel therapies for FSGS: preclinical and clinical studies. Adv Chronic Kidney Dis 2015; 22:e1-6. [PMID: 25704355 DOI: 10.1053/j.ackd.2014.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a rare but important cause of end-stage kidney disease in children and adults. Current therapy, consisting of corticosteroids and calcineurin inhibitors, fails to achieve a sustained remission in most patients. Therefore, there is a pressing need to develop new treatments for this glomerulopathy. Traditional approaches have focused on agents that modulate the immune system. In this review, we summarize preclinical and clinical data with newer agents that may ameliorate FSGS. We focus on drugs that inhibit immune injury or inflammation, such as abatacept, rituximab, adalimumab, and stem cells. The potential of agents that block the glomerular action of circulating permeability factors such as soluble urokinase receptor is reviewed. Finally, because fibrosis represents the final common pathway of glomerular damage in FSGS, the experience with a wide range of antifibrotic agents is presented. Despite extensive research on the podocyte dysfunction in the pathogenesis of FSGS, there are few agents that directly target podocyte structure or viability. We conclude that FSGS is a heterogeneous disorder and that intensified translational research is vital to improve our understanding of distinct subtypes that have a defined prognosis and predictable response to targeted therapeutic interventions.
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Sampson MG, Hodgin JB, Kretzler M. Defining nephrotic syndrome from an integrative genomics perspective. Pediatr Nephrol 2015; 30:51-63; quiz 59. [PMID: 24890338 PMCID: PMC4241380 DOI: 10.1007/s00467-014-2857-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/06/2014] [Accepted: 05/14/2014] [Indexed: 12/15/2022]
Abstract
Nephrotic syndrome (NS) is a clinical condition with a high degree of morbidity and mortality, caused by failure of the glomerular filtration barrier, resulting in massive proteinuria. Our current diagnostic, prognostic and therapeutic decisions in NS are largely based upon clinical or histological patterns such as "focal segmental glomerulosclerosis" or "steroid sensitive". Yet these descriptive classifications lack the precision to explain the physiologic origins and clinical heterogeneity observed in this syndrome. A more precise definition of NS is required to identify mechanisms of disease and capture various clinical trajectories. An integrative genomics approach to NS applies bioinformatics and computational methods to comprehensive experimental, molecular and clinical data for holistic disease definition. A unique aspect is analysis of data together to discover NS-associated molecules, pathways, and networks. Integrating multidimensional datasets from the outset highlights how molecular lesions impact the entire individual. Data sets integrated range from genetic variation to gene expression, to histologic changes, to progression of chronic kidney disease (CKD). This review will introduce the tenets of integrative genomics and suggest how it can increase our understanding of NS from molecular and pathophysiological perspectives. A diverse group of genome-scale experiments are presented that have sought to define molecular signatures of NS. Finally, the Nephrotic Syndrome Study Network (NEPTUNE) will be introduced as an international, prospective cohort study of patients with NS that utilizes an integrated systems genomics approach from the outset. A major NEPTUNE goal is to achieve comprehensive disease definition from a genomics perspective and identify shared molecular drivers of disease.
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Affiliation(s)
- Matthew G. Sampson
- Division of Nephrology, Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, USA,to whom correspondence should be addressed: Matthew Sampson, Division of Nephrology, University of Michigan School of Medicine, 8220D MSRB III, West Medical Center Drive, Ann Arbor, MI 48109, kidneyomics.org, , Telephone and Fax: 734-647-9361. Matthias Kretzler, Medicine/Nephrology and Computational Medicine and Bioinformatics, University of Michigan, 1560 MSRB II, 1150 W. Medical Center Dr.-SPC5676, Ann Arbor, MI 48109-5676, 734-615-5757, fax: 734-763-0982,
| | - Jeffrey B. Hodgin
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA,to whom correspondence should be addressed: Matthew Sampson, Division of Nephrology, University of Michigan School of Medicine, 8220D MSRB III, West Medical Center Drive, Ann Arbor, MI 48109, kidneyomics.org, , Telephone and Fax: 734-647-9361. Matthias Kretzler, Medicine/Nephrology and Computational Medicine and Bioinformatics, University of Michigan, 1560 MSRB II, 1150 W. Medical Center Dr.-SPC5676, Ann Arbor, MI 48109-5676, 734-615-5757, fax: 734-763-0982,
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225
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Spinale JM, Mariani LH, Kapoor S, Zhang J, Weyant R, Song PX, Wong HN, Troost JP, Gadegbeku CA, Gipson DS, Kretzler M, Nihalani D, Holzman LB. A reassessment of soluble urokinase-type plasminogen activator receptor in glomerular disease. Kidney Int 2014; 87:564-74. [PMID: 25354239 PMCID: PMC4344842 DOI: 10.1038/ki.2014.346] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/05/2014] [Accepted: 08/22/2014] [Indexed: 12/21/2022]
Abstract
It has been suggested that soluble urokinase receptor (suPAR) is a causative circulating factor for and a biomarker of focal and segmental glomerulosclerosis (FSGS). Here we undertook validation of these assumptions in both mouse and human models. Injection of recombinant suPAR in wild-type mice did not induce proteinuria within 24 hours. Moreover, a disease phenotype was not seen in an inducible transgenic mouse model that maintained elevated suPAR concentrations for 6 weeks. Plasma and urine suPAR concentrations were evaluated as clinical biomarkers in 241 patients with glomerular disease from the prospective, longitudinal multi-center observational NEPTUNE cohort. The serum suPAR concentration at baseline inversely correlated with estimated glomerular filtration rate (eGFR) and the urine suPAR/creatinine ratio positively correlated with the urine protein/creatinine ratio. After adjusting for eGFR and urine protein, neither the serum nor urine suPAR level was an independent predictor of FSGS histopathology. A multivariable mixed-effects model of longitudinal data evaluated the association between the change in serum suPAR concentration from baseline with eGFR. After adjusting for baseline suPAR concentration, age, gender, proteinuria and time, the change in suPAR from baseline was associated with eGFR, but this association was not different for patients with FSGS as compared to other diagnoses. Thus, these results do not support a pathological role for suPAR in FSGS.
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Affiliation(s)
- Joann M Spinale
- Division of Nephrology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laura H Mariani
- 1] Arbor Research for Collaborative for Health, Ann Arbor, Michigan, USA [2] Division of Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Shiv Kapoor
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jidong Zhang
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert Weyant
- Arbor Research for Collaborative for Health, Ann Arbor, Michigan, USA
| | - Peter X Song
- Department of Biostatistics, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Hetty N Wong
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jonathan P Troost
- Division of Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Crystal A Gadegbeku
- Nephrology Division, Temple University School of Medicine, Philadelphia, Pennsylvania, USA
| | - Debbie S Gipson
- Division of Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Matthias Kretzler
- Division of Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Deepak Nihalani
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lawrence B Holzman
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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226
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Trachtman H, Benzing T, Sever S, Harris RC, Reiser J. The grand challenge of nephrology. Front Med (Lausanne) 2014; 1:28. [PMID: 25593903 PMCID: PMC4291843 DOI: 10.3389/fmed.2014.00028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 08/22/2014] [Indexed: 11/25/2022] Open
Affiliation(s)
- Howard Trachtman
- Department of Pediatrics, New York University Langone Medical Center , New York, NY , USA
| | - Thomas Benzing
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Systems Biology of Aging Cologne, University of Cologne , Cologne , Germany
| | - Sanja Sever
- Division of Nephrology, Massachusetts General Hospital , Charlestown, MA , USA
| | - Raymond Clement Harris
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University School of Medicine , Nashville, TN , USA
| | - Jochen Reiser
- Department of Medicine, Rush University , Chicago, IL , USA
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227
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The Rare Diseases Clinical Research Network's organization and approach to observational research and health outcomes research. J Gen Intern Med 2014; 29 Suppl 3:S739-44. [PMID: 25029976 PMCID: PMC4124127 DOI: 10.1007/s11606-014-2894-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Established in 2003 by the Office of Rare Diseases Research (ORDR), in collaboration with several National Institutes of Health (NIH) Institutes/Centers, the Rare Diseases Clinical Research Network (RDCRN) consists of multiple clinical consortia conducting research in more than 200 rare diseases. The RDCRN supports longitudinal or natural history, pilot, Phase I, II, and III, case-control, cross-sectional, chart review, physician survey, bio-repository, and RDCRN Contact Registry (CR) studies. To date, there have been 24,684 participants enrolled on 120 studies from 446 sites worldwide. An additional 11,533 individuals participate in the CR. Through a central data management and coordinating center (DMCC), the RDCRN's platform for the conduct of observational research encompasses electronic case report forms, federated databases, and an online CR for epidemiological and survey research. An ORDR-governed data repository (through dbGaP, a database for genotype and phenotype information from the National Library of Medicine) has been created. DMCC coordinates with ORDR to register and upload study data to dbGaP for data sharing with the scientific community. The platform provided by the RDCRN DMCC has supported 128 studies, six of which were successfully conducted through the online CR, with 2,352 individuals accrued and a median enrollment time of just 2 months. The RDCRN has built a powerful suite of web-based tools that provide for integration of federated and online database support that can accommodate a large number of rare diseases on a global scale. RDCRN studies have made important advances in the diagnosis and treatment of rare diseases.
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228
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Abstract
Kidney disease is one of the most prevalent chronic conditions and is a frequent complication of diabetes, cardiovascular disease, and obesity. Recent advances in biomedical research and novel technologies have created opportunities to study kidney disease in a variety of platforms, applied to human populations. The Reviews in this series discuss the kidney in hypertension, diabetes, and monogenic forms of kidney disease, as well as the cellular and molecular mediators of acute kidney injury and fibrosis, IgA nephropathy and idiopathic membranous nephropathy, and kidney transplantation. In this introduction, we briefly review new insights into focal segmental glomerulosclerosis and the role of podocytes in health and disease. Additionally, we discuss how new technologies, therapeutics, and the availability of patient data can help shape the study of kidney disease and ultimately inform policies concerning biomedical research and health care.
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229
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Abstract
At least 10% of adults and nearly all children who receive renal-replacement therapy have an inherited kidney disease. These patients rarely die when their disease progresses and can remain alive for many years because of advances in organ-replacement therapy. However, these disorders substantially decrease their quality of life and have a large effect on health-care systems. Since the kidneys regulate essential homoeostatic processes, inherited kidney disorders have multisystem complications, which add to the usual challenges for rare disorders. In this review, we discuss the nature of rare inherited kidney diseases, the challenges they pose, and opportunities from technological advances, which are well suited to target the kidney. Mechanistic insights from rare disorders are relevant for common disorders such as hypertension, kidney stones, cardiovascular disease, and progression of chronic kidney disease.
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Affiliation(s)
- Olivier Devuyst
- Division of Nephrology, Université catholique de Louvain, Brussels, Belgium; Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
| | - Nine V A M Knoers
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Giuseppe Remuzzi
- IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso and Unit of Nephrology and Dialysis, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Franz Schaefer
- Pediatric Nephrology Division, Center for Pediatric and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
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230
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Abstract
Primary focal segmental glomerulosclerosis (FSGS) accounts for nearly 10 % of patients who require renal replacement therapy. Elevated circulating levels of soluble urokinase receptor (suPAR) have been identified as a biomarker to discriminate primary FSGS from other glomerulopathies. Subsequent reports have questioned the diagnostic utility of this test. In a study in BMC Medicine, Huang et al. demonstrate that urinary soluble urokinase receptor (suPAR) excretion assists in distinguishing primary FSGS from other glomerular diseases, and that high plasma suPAR concentrations are not directly linked to a decline in glomerular filtration rate (GFR). This observation suggests that further investigation of suPAR is warranted in patients with FSGS. It should be interpreted in light of a recent report that B7-1 is expressed in the podocytes of a subset of patients with FSGS, and that blocking this molecule may represent the first successful targeted intervention for this disease. These advances highlight the rapid pace of scientific progress in the field of nephrology. Nephrologists should work together, share resources, and expedite the design of protocols to evaluate these novel biomarkers in a comprehensive and scientifically valid manner.
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Affiliation(s)
- Howard Trachtman
- NYU Langone Medical Center, Department of Pediatrics, Division of Nephrology, CTSI, 227 E 30th Street, Room #110, New York, NY, USA.
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231
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Caliskan Y, Kiryluk K. Novel biomarkers in glomerular disease. Adv Chronic Kidney Dis 2014; 21:205-16. [PMID: 24602470 PMCID: PMC3963477 DOI: 10.1053/j.ackd.2013.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/29/2013] [Accepted: 12/31/2013] [Indexed: 12/24/2022]
Abstract
Glomerular diseases are major contributors to the global burden of end-stage kidney disease. The clinical course and outcome of these disorders are extremely variable and difficult to predict. The clinical trajectories range from a benign and spontaneously remitting condition to a symptomatic and rapidly progressive disease. The diagnosis is based entirely on the evaluation of kidney biopsy, but this invasive procedure carries multiple risks and often fails to predict the clinical course or responsiveness to treatment. However, more recent advances in genetics and molecular biology have facilitated elucidation of novel pathogenic mechanisms of these disorders. These discoveries fuel the development of novel biomarkers and offer prospects of noninvasive diagnosis and improved prognostication. Our review focuses on the most promising novel biomarkers that have recently emerged for the major types of glomerular diseases, including immunoglobulin A nephropathy, membranous nephropathy, focal segmental glomerulosclerosis, and membranoproliferative glomerulonephritis.
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MESH Headings
- Biomarkers/blood
- Biomarkers/urine
- Genetic Markers/genetics
- Glomerulonephritis/genetics
- Glomerulonephritis/metabolism
- Glomerulonephritis/pathology
- Glomerulonephritis, IGA/genetics
- Glomerulonephritis, IGA/metabolism
- Glomerulonephritis, IGA/pathology
- Glomerulonephritis, Membranoproliferative/genetics
- Glomerulonephritis, Membranoproliferative/metabolism
- Glomerulonephritis, Membranoproliferative/pathology
- Glomerulonephritis, Membranous/genetics
- Glomerulonephritis, Membranous/metabolism
- Glomerulonephritis, Membranous/pathology
- Glomerulosclerosis, Focal Segmental/genetics
- Glomerulosclerosis, Focal Segmental/metabolism
- Glomerulosclerosis, Focal Segmental/pathology
- Humans
- Kidney/pathology
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Affiliation(s)
- Yasar Caliskan
- Division of Nephrology, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey and Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY; and Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey and Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY; and Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY.
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232
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Witasp A, Ekstrom TJ, Schalling M, Lindholm B, Stenvinkel P, Nordfors L. How can genetics and epigenetics help the nephrologist improve the diagnosis and treatment of chronic kidney disease patients? Nephrol Dial Transplant 2014; 29:972-80. [DOI: 10.1093/ndt/gfu021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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233
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Ju W, Greene CS, Eichinger F, Nair V, Hodgin JB, Bitzer M, Lee YS, Zhu Q, Kehata M, Li M, Jiang S, Rastaldi MP, Cohen CD, Troyanskaya OG, Kretzler M. Defining cell-type specificity at the transcriptional level in human disease. Genome Res 2013; 23:1862-73. [PMID: 23950145 PMCID: PMC3814886 DOI: 10.1101/gr.155697.113] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell-lineage–specific transcripts are essential for differentiated tissue function, implicated in hereditary organ failure, and mediate acquired chronic diseases. However, experimental identification of cell-lineage–specific genes in a genome-scale manner is infeasible for most solid human tissues. We developed the first genome-scale method to identify genes with cell-lineage–specific expression, even in lineages not separable by experimental microdissection. Our machine-learning–based approach leverages high-throughput data from tissue homogenates in a novel iterative statistical framework. We applied this method to chronic kidney disease and identified transcripts specific to podocytes, key cells in the glomerular filter responsible for hereditary and most acquired glomerular kidney disease. In a systematic evaluation of our predictions by immunohistochemistry, our in silico approach was significantly more accurate (65% accuracy in human) than predictions based on direct measurement of in vivo fluorescence-tagged murine podocytes (23%). Our method identified genes implicated as causal in hereditary glomerular disease and involved in molecular pathways of acquired and chronic renal diseases. Furthermore, based on expression analysis of human kidney disease biopsies, we demonstrated that expression of the podocyte genes identified by our approach is significantly related to the degree of renal impairment in patients. Our approach is broadly applicable to define lineage specificity in both cell physiology and human disease contexts. We provide a user-friendly website that enables researchers to apply this method to any cell-lineage or tissue of interest. Identified cell-lineage–specific transcripts are expected to play essential tissue-specific roles in organogenesis and disease and can provide starting points for the development of organ-specific diagnostics and therapies.
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Affiliation(s)
- Wenjun Ju
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
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234
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Abstract
Our understanding of the pathogenesis of most primary glomerular diseases, including IgA nephropathy, membranous nephropathy and focal segmental glomerulosclerosis, is limited. Advances in molecular technology now permit genome-wide, high-throughput characterization of genes and gene products from biological samples. Comprehensive examinations of the genome, transcriptome, proteome and metabolome (collectively known as omics analyses), have been applied to the study of IgA nephropathy, membranous nephropathy and focal segmental glomerulosclerosis in both animal models and human patients. However, most omics studies of primary glomerular diseases, with the exception of large genomic studies, have been limited by inadequate sample sizes and the lack of kidney-specific data sets derived from kidney biopsy samples. Collaborative efforts to develop a standardized approach for prospective recruitment of patients, scheduled monitoring of clinical outcomes, and protocols for sampling of kidney tissues will be instrumental in uncovering the mechanisms that drive these diseases. Integration of molecular data sets with the results of clinical and histopathological studies will ultimately enable these diseases to be characterized in a comprehensive and systematic manner, and is expected to improve the diagnosis and treatment of these diseases.
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235
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Barisoni L, Nast CC, Jennette JC, Hodgin JB, Herzenberg AM, Lemley KV, Conway CM, Kopp JB, Kretzler M, Lienczewski C, Avila-Casado C, Bagnasco S, Sethi S, Tomaszewski J, Gasim AH, Hewitt SM. Digital pathology evaluation in the multicenter Nephrotic Syndrome Study Network (NEPTUNE). Clin J Am Soc Nephrol 2013; 8:1449-59. [PMID: 23393107 DOI: 10.2215/cjn.08370812] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pathology consensus review for clinical trials and disease classification has historically been performed by manual light microscopy with sequential section review by study pathologists, or multi-headed microscope review. Limitations of this approach include high intra- and inter-reader variability, costs, and delays for slide mailing and consensus reviews. To improve this, the Nephrotic Syndrome Study Network (NEPTUNE) is systematically applying digital pathology review in a multicenter study using renal biopsy whole slide imaging (WSI) for observation-based data collection. Study pathology materials are acquired, scanned, uploaded, and stored in a web-based information system that is accessed through a web-browser interface. Quality control includes metadata and image quality review. Initially, digital slides are annotated, with each glomerulus identified, given a unique number, and maintained in all levels until the glomerulus disappears or sections end. The software allows viewing and annotation of multiple slide sections concurrently. Analysis utilizes "descriptors" for patterns of injury, rather than diagnoses, in renal parenchymal compartments. This multidimensional representation via WSI, allows more accurate glomerular counting and identification of all lesions in each glomerulus, with data available in a searchable database. The use of WSI brings about efficiency critical to pathology review in a clinical trial setting, including independent review by multiple pathologists, improved intraobserver and interobserver reproducibility, efficiencies and risk reduction in slide circulation and mailing, centralized management of data integrity and slide images for current or future studies, and web-based consensus meetings. The overall effect is improved incorporation of pathology review in a budget neutral approach.
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Affiliation(s)
- Laura Barisoni
- Department of Pathology, University of Miami, Miller School of Medicine, 1400 NW 12th Avenue, Miami, FL 33136, USA.
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