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Buerger F, Merz LM, Saida K, Yu S, Salmanullah D, Lemberg K, Mertens ND, Mansour B, Kolvenbach CM, Yousef K, Braun A, Franken GAC, Endlich N, Schneider R, Shril S, Hildebrandt F. Quantitative phenotyping of Nphs1 knockout mice as a prerequisite for gene replacement studies. Am J Physiol Renal Physiol 2024. [PMID: 38482553 DOI: 10.1152/ajprenal.00412.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024] Open
Abstract
Steroid-resistant nephrotic (SRNS) syndrome is the second most frequent cause of chronic kidney disease before the age of 25 years. Nephrin, encoded by NPHS1, localizes to the slit diaphragm of glomerular podocytes and is the predominant structural component of the glomerular filtration barrier. Biallelic variants in NPHS1 can cause congenital nephrotic syndrome of the Finnish type (CNS-1) for which, to date, no causative therapy is available. Recently, adeno-associated virus (AAV) vectors targeting the glomerular podocyte have been assessed as a means for gene replacement therapy. We here established quantitative and reproducible phenotyping of a published, conditional Nphs1 knockout mouse model (Nphs1tm1.1Pgarg/J and Nphs2-Cre+) in preparation of a gene replacement study employing AAV vectors. Nphs1 knockout mice (Nphs1fl/fl Nphs2-Cre+) exhibited: i) A median survival rate of 18 days (range from 9-43 days; males 16.5 days, females 20 days); ii) Average foot process (FP) density of 1.0 FP/µm compared to 2.0 FP/µm in controls, and mean filtration slit density was 2.64 µm/µm2 compared to 4.36 µm/µm2 in controls; iii) A high number of proximal tubular microcysts; iv) Development of proteinuria within the first week of life as evidenced by urine albumin/creatinine ratios; v) Significantly reduced levels of serum albumin, and elevated BUN and creatinine levels. For none of these phenotypes in Nphs1 knockout mice, significant differences between sexes were observed. We quantitatively characterized 5 different phenotypic features of CNS in Nphs1fl/fl Nphs2-Cre+ mice. Our results will facilitate future gene replacement therapy projects by allowing for sensitive detection of, even subtle molecular, effects.
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Affiliation(s)
- Florian Buerger
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, MA, United States
| | - Lea M Merz
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, United States
| | - Ken Saida
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, MA, United States
| | - Seyoung Yu
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, MA, United States
| | - Daanya Salmanullah
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, MA, United States
| | - Katharina Lemberg
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Nils D Mertens
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, MA, United States
| | - Bshara Mansour
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, MA, United States
| | | | - Kirollos Yousef
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, MA, United States
| | - Alina Braun
- Pediatrics, Boston Children's Hospital, Boston, MA, United States
| | - Gijs A C Franken
- Pediatrics, Boston Children's Hospital, Boston, MA, United States
| | | | - Ronen Schneider
- Pediatrics, Nephrology, Boston Children's Hospital, Boston, MA, United States
| | - Shrilee Shril
- Nephrology, Boston Children's Hospital, Boston, MA, United States
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Pantel D, Mertens ND, Schneider R, Hölzel S, Kari JA, Desoky SE, Shalaby MA, Lim TY, Sanna-Cherchi S, Shril S, Hildebrandt F. Copy number variation analysis in 138 families with steroid-resistant nephrotic syndrome identifies causal homozygous deletions in PLCE1 and NPHS2 in two families. Pediatr Nephrol 2024; 39:455-461. [PMID: 37670083 PMCID: PMC10979458 DOI: 10.1007/s00467-023-06134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/06/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
BACKGROUND Steroid-resistant nephrotic syndrome (SRNS) is the second most common cause of kidney failure in children and adults under the age of 20 years. Previously, we were able to detect by exome sequencing (ES) a known monogenic cause of SRNS in 25-30% of affected families. However, ES falls short of detecting copy number variants (CNV). Therefore, we hypothesized that causal CNVs could be detected in a large SRNS cohort. METHODS We performed genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on a cohort of 138 SRNS families, in whom we previously did not identify a genetic cause through ES. We evaluated ES and CNV data for variants in 60 known SRNS genes and in 13 genes in which variants are known to cause a phenocopy of SRNS. We applied previously published, predefined criteria for CNV evaluation. RESULTS We detected a novel CNV in two genes in 2 out of 138 families (1.5%). The 9,673 bp homozygous deletion in PLCE1 and the 6,790 bp homozygous deletion in NPHS2 were confirmed across the breakpoints by PCR and Sanger sequencing. CONCLUSIONS We confirmed that CNV analysis can identify the genetic cause in SRNS families that remained unsolved after ES. Though the rate of detected CNVs is minor, CNV analysis can be used when there are no other genetic causes identified. Causative CNVs are less common in SRNS than in other monogenic kidney diseases, such as congenital anomalies of the kidneys and urinary tract, where the detection rate was 5.3%. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Dalia Pantel
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Nils D Mertens
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Ronen Schneider
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Selina Hölzel
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Jameela A Kari
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohamed A Shalaby
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA.
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Kolvenbach CM, Zheng B, Merz LM, Mertens ND, Mansour B, Wang C, Seltzsam S, Schneider S, Schierbaum L, Pantel D, Chen J, van der Ven AT, Bello JO, Shril S, Hildebrandt F. A homozygous truncating ETV4 variant in a Nigerian family with congenital anomalies of the kidney and urinary tract. Am J Med Genet A 2023; 191:1355-1359. [PMID: 36694287 PMCID: PMC10081948 DOI: 10.1002/ajmg.a.63127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/03/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most prevalent cause of chronic kidney disease that manifests in children. To date ~23 different monogenic causes have been implicated in isolated forms of human CAKUT, but the vast majority remains elusive. In a previous study, we identified a homozygous missense variant in E26 transformation-specific (ETS) Variant Transcription Factor 4 (ETV4) causing CAKUT via dysregulation of the transcriptional function of ETV4, and a resulting abrogation of GDNF/RET/ETV4 signaling pathway. This CAKUT family remains the only family with an ETV4 variant reported so far. Here, we describe one additional CAKUT family with a homozygous truncating variant in ETV4 (p.(Lys6*)) that was identified by exome sequencing. The variant was found in an individual with isolated CAKUT displaying posterior urethral valves and renal dysplasia. The newly identified stop variant conceptually truncates the ETS_PEA3_N and ETS domains that regulate DNA-binding transcription factor activity. The variant has never been reported homozygously in the gnomAD database. To our knowledge, we here report the first CAKUT family with a truncating variant in ETV4, potentially causing the isolated CAKUT phenotype observed in the affected individual.
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Affiliation(s)
- Caroline M Kolvenbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Institute of Anatomy, Medical Faculty, University of Bonn, Bonn, Germany
| | - Bixia Zheng
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Lea M Merz
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatrics, University Hospital Leipzig, Leipzig, Germany
| | - Nils D Mertens
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bshara Mansour
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Chunyan Wang
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Steve Seltzsam
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sophia Schneider
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Schierbaum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Dalia Pantel
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Jing Chen
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Amelie T van der Ven
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jibril O Bello
- Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Nigeria.,Department of Surgery, College of Medicine, Nursing & Health Sciences, Fiji National University, Suva, Fiji
| | - Shirlee Shril
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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