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Siji A, Karthik KN, Pardeshi VC, Hari PS, Vasudevan A. Targeted gene panel for genetic testing of south Indian children with steroid resistant nephrotic syndrome. BMC MEDICAL GENETICS 2018; 19:200. [PMID: 30458709 PMCID: PMC6245897 DOI: 10.1186/s12881-018-0714-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 11/07/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Steroid resistant nephrotic syndrome (SRNS) is a genetically heterogeneous disease with significant phenotypic variability. More than 53 podocyte-expressed genes are implicated in SRNS which complicates the routine use of genetic screening in the clinic. Next generation sequencing technology (NGS) allows rapid screening of multiple genes in large number of patients in a cost-effective manner. METHODS We developed a targeted panel of 17 genes to determine relative frequency of mutations in south Indian ethnicity and feasibility of using the assay in a clinical setting. Twenty-five children with SRNS and 3 healthy individuals were screened. RESULTS In this study, novel variants including 1 pathogenic variant (2 patients) and 3 likely pathogenic variants (3 patients) were identified. In addition, 2 novel variants of unknown significance (VUS) in 2 patients (8% of total patients) were also identified. CONCLUSIONS The results show that genetic screening in SRNS using NGS is feasible in a clinical setting. However the panel needs to be screened in a larger cohort of children with SRNS in order to assess the utility of the customised targeted panel in Indian children with SRNS. Determining the prevalence of variants in Indian population and improvising the bioinformatics-based filtering strategy for a more accurate differentiation of pathogenic variants from those that are benign among the VUS will help in improving medical and genetic counselling in SRNS.
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Affiliation(s)
- Annes Siji
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | - K N Karthik
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | | | - P S Hari
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | - Anil Vasudevan
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India. .,Department of Pediatric Nephrology, St. John's Medical College Hospital, Bangalore, India.
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3
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Mariani LH, Bomback AS, Canetta PA, Flessner MF, Helmuth M, Hladunewich MA, Hogan JJ, Kiryluk K, Nachman PH, Nast CC, Rheault MN, Rizk DV, Trachtman H, Wenderfer SE, Bowers C, Hill-Callahan P, Marasa M, Poulton CJ, Revell A, Vento S, Barisoni L, Cattran D, D'Agati V, Jennette JC, Klein JB, Laurin LP, Twombley K, Falk RJ, Gharavi AG, Gillespie BW, Gipson DS, Greenbaum LA, Holzman LB, Kretzler M, Robinson B, Smoyer WE, Guay-Woodford LM. CureGN Study Rationale, Design, and Methods: Establishing a Large Prospective Observational Study of Glomerular Disease. Am J Kidney Dis 2018; 73:218-229. [PMID: 30420158 PMCID: PMC6348011 DOI: 10.1053/j.ajkd.2018.07.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023]
Abstract
RATIONALE & OBJECTIVES Glomerular diseases, including minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, and immunoglobulin A (IgA) nephropathy, share clinical presentations, yet result from multiple biological mechanisms. Challenges to identifying underlying mechanisms, biomarkers, and new therapies include the rarity of each diagnosis and slow progression, often requiring decades to measure the effectiveness of interventions to prevent end-stage kidney disease (ESKD) or death. STUDY DESIGN Multicenter prospective cohort study. SETTING & PARTICIPANTS Cure Glomerulonephropathy (CureGN) will enroll 2,400 children and adults with minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, or IgA nephropathy (including IgA vasculitis) and a first diagnostic kidney biopsy within 5 years. Patients with ESKD and those with secondary causes of glomerular disease are excluded. EXPOSURES Clinical data, including medical history, medications, family history, and patient-reported outcomes, are obtained, along with a digital archive of kidney biopsy images and blood and urine specimens at study visits aligned with clinical care 1 to 4 times per year. OUTCOMES Patients are followed up for changes in estimated glomerular filtration rate, disease activity, ESKD, and death and for nonrenal complications of disease and treatment, including infection, malignancy, cardiovascular, and thromboembolic events. ANALYTICAL APPROACH The study design supports multiple longitudinal analyses leveraging the diverse data domains of CureGN and its ancillary program. At 2,400 patients and an average of 2 years' initial follow-up, CureGN has 80% power to detect an HR of 1.4 to 1.9 for proteinuria remission and a mean difference of 2.1 to 3.0mL/min/1.73m2 in estimated glomerular filtration rate per year. LIMITATIONS Current follow-up can only detect large differences in ESKD and death outcomes. CONCLUSIONS Study infrastructure will support a broad range of scientific approaches to identify mechanistically distinct subgroups, identify accurate biomarkers of disease activity and progression, delineate disease-specific treatment targets, and inform future therapeutic trials. CureGN is expected to be among the largest prospective studies of children and adults with glomerular disease, with a broad goal to lessen disease burden and improve outcomes.
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Affiliation(s)
- Laura H Mariani
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI; Arbor Research Collaborative for Health, Ann Arbor, MI.
| | - Andrew S Bomback
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Pietro A Canetta
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Michael F Flessner
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | | | - Michelle A Hladunewich
- Division of Nephrology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Jonathan J Hogan
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Patrick H Nachman
- Division of Renal Diseases and Hypertension, Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Cynthia C Nast
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Michelle N Rheault
- Division of Nephrology, Department of Pediatrics, University of Minnesota Masonic Children's Hospital, Minneapolis, MN
| | - Dana V Rizk
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Howard Trachtman
- Division of Nephrology, Department of Pediatrics, New York University Langone Medical Center, New York, NY
| | - Scott E Wenderfer
- Renal Section, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Corinna Bowers
- Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Maddalena Marasa
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Caroline J Poulton
- Division of Nephrology and Hypertension, Kidney Center, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Adelaide Revell
- Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Suzanne Vento
- Division of Nephrology, Department of Pediatrics, New York University Langone Medical Center, New York, NY
| | | | - Dan Cattran
- Division of Nephrology, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Vivette D'Agati
- Department of Pathology, Columbia University Medical Center, New York, NY
| | - J Charles Jennette
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
| | - Jon B Klein
- Department of Medicine, The University of Louisville School of Medicine, and Robley Rex VA Medical Center, Louisville, KY
| | | | - Katherine Twombley
- Pediatric Nephrology, Medical University of South Carolina, Charleston, SC
| | - Ronald J Falk
- Division of Nephrology and Hypertension, Kidney Center, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Brenda W Gillespie
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Debbie S Gipson
- Division of Nephrology, Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | | | - Lawrence B Holzman
- Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Matthias Kretzler
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Bruce Robinson
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI; Arbor Research Collaborative for Health, Ann Arbor, MI
| | - William E Smoyer
- Center for Clinical and Translational Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Lisa M Guay-Woodford
- Center for Translational Science, Children's National Health System, Washington, DC
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Asharam K, Bhimma R, David VA, Coovadia HM, Qulu WP, Naicker T, Gillies CE, Vega-Warner V, Johnson RC, Limou S, Kopp JB, Sampson M, Nelson GW, Winkler CA. NPHS2 V260E Is a Frequent Cause of Steroid-Resistant Nephrotic Syndrome in Black South African Children. Kidney Int Rep 2018; 3:1354-1362. [PMID: 30450462 PMCID: PMC6224675 DOI: 10.1016/j.ekir.2018.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/12/2018] [Accepted: 07/23/2018] [Indexed: 11/23/2022] Open
Abstract
Introduction In South Africa (SA), steroid-resistant nephrotic syndrome (SRNS) is more frequent in black than in Indian children. Methods Seeking a genetic basis for this disparity, we enrolled 33 Indian and 31 black children with steroid-sensitive nephrotic syndrome (SSNS) and SRNS from KwaZulu-Natal, SA; SRNS children underwent kidney biopsy. We sequenced NPHS2 and genotyped APOL1 in 15 SSNS and 64 SRNS unrelated patients and 104 controls and replicated results in 18 black patients with steroid-resistant focal segmental glomerulosclerosis (SR-FSGS). Known FSGS genes (n = 21) were sequenced in a subset of patients. Results Homozygosity for NPHS2 V260E was found in 8 of 30 black children with SRNS (27%); all 260E/E carriers had SR-FSGS. Combining SR-FSGS patients from the 2 groups, 14 of 42 (33%) were homozygous for V260E. One black control was heterozygous for V260E; no Indian patients or controls were carriers. Haplotype analysis indicated that homozygosity for V260E was not explained by cryptic consanguinity. Children with NPHS2 260E/E developed SRNS at earlier age than noncarriers (34 vs. 78 months, P = 0.01), and none achieved partial or complete remission (0% vs. 47%, P = 0.002). APOL1 variants did not associate with NS. Sequencing FSGS genes identified a CD2AP predicted pathogenic variant in the heterozygous state in 1 Indian case with SR-FSGS. Conclusion NPHS2 260E/E was present in one-third of black FSGS patients, was absent in black controls and Indian patients, and affected patients were unresponsive to therapy. Genotyping V260E in black children from South Africa with NS will identify a substantial group with SR-FSGS, potentially sparing these children biopsy and ineffective steroid treatment.
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Affiliation(s)
| | | | - Victor A. David
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Hoosen M. Coovadia
- University of KwaZulu-Natal, Durban, South Africa
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa
| | | | | | - Christopher E. Gillies
- Department of Pediatrics-Nephrology; University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Virginia Vega-Warner
- Department of Pediatrics-Nephrology; University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Randall C. Johnson
- Advanced Biomedical Computing Center, Frederick National Laboratory, Frederick, Maryland, USA
| | - Sophie Limou
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, USA
| | - Jeffrey B. Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Mathew Sampson
- Department of Pediatrics-Nephrology; University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - George W. Nelson
- Advanced Biomedical Computing Center, Frederick National Laboratory, Frederick, Maryland, USA
| | - Cheryl A. Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, USA
- Correspondence: Cheryl A. Winkler, 8560 Progress Drive, National Cancer Institute, Frederick National Laboratory, Frederick, Maryland 21701, USA.
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Wen Y, Shah S, Campbell KN. Molecular Mechanisms of Proteinuria in Focal Segmental Glomerulosclerosis. Front Med (Lausanne) 2018; 5:98. [PMID: 29713631 PMCID: PMC5912003 DOI: 10.3389/fmed.2018.00098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 03/26/2018] [Indexed: 01/01/2023] Open
Abstract
Focal segmental glomerulosclerosis (FSGS) is the most common primary glomerular disease resulting in end-stage renal disease in the USA and is increasing in prevalence worldwide. It is a diverse clinical entity with idiopathic, genetic, metabolic, infectious, and other causes that culminate in a characteristic histologic pattern of injury. Proteinuria is a hallmark of FSGS as well as other primary and secondary glomerular disorders. The magnitude of proteinuria at disease onset and during treatment has prognostic implications for renal survival as well as associated cardiovascular morbidity and mortality. Significant advances over the last two decades have shed light on the molecular architecture of the glomerular filtration barrier. The podocyte is the target cell for injury in FSGS. A growing list of disease-causing gene mutations encoding proteins that regulate podocyte survival and homeostasis has been identified in FSGS patients. Several pathogenic and regulatory pathways have been uncovered that result in proteinuria in rodent models and human FSGS. The recurrence of proteinuria and FSGS after kidney transplantation is supporting evidence for the role of a circulating permeability factor in disease pathogenesis. These advances reviewed herein have significant implications for disease classification and therapeutic drug development for FSGS.
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Affiliation(s)
- Yumeng Wen
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sapna Shah
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kirk N Campbell
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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