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Zhao E, Bomback M, Khan A, Murthy SK, Solowiejczyk D, Vora NL, Gilmore KL, Giordano JL, Wapner RJ, Sanna-Cherchi S, Lyford A, Jelin AC, Gharavi AG, Hays T. The expanded spectrum of human disease associated with GREB1L likely includes complex congenital heart disease. Prenat Diagn 2024; 44:343-351. [PMID: 38285371 PMCID: PMC11040453 DOI: 10.1002/pd.6527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
OBJECTIVE GREB1L has been linked prenatally to Potter's sequence, as well as less severe anomalies of the kidney, uterus, inner ear, and heart. The full phenotypic spectrum is unknown. The purpose of this study was to characterize known and novel pre- and postnatal phenotypes associated with GREB1L. METHODS We solicited cases from the Fetal Sequencing Consortium, screened a population-based genomic database, and conducted a comprehensive literature search to identify disease cases associated with GREB1L. We present a detailed phenotypic spectrum and molecular changes. RESULTS One hundred twenty-seven individuals with 51 unique pathogenic or likely pathogenic GREB1L variants were identified. 24 (47%) variants were associated with isolated kidney anomalies, 19 (37%) with anomalies of multiple systems, including one case of hypoplastic left heart syndrome, five (10%) with isolated sensorineural hearing loss, two (4%) with isolated uterine agenesis; and one (2%) with isolated tetralogy of Fallot. CONCLUSION GREB1L may cause complex congenital heart disease (CHD) in humans. Clinicians should consider GREB1L testing in the setting of CHD, and cardiac screening in the setting of GREB1L variants.
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Affiliation(s)
- Emily Zhao
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miles Bomback
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sarath Krishna Murthy
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - David Solowiejczyk
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelly L. Gilmore
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Jessica L. Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Alex Lyford
- Department of Mathematics and Statistics, Middlebury College, Middlebury, Vermont, USA
| | - Angie C. Jelin
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ali G. Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Thomas Hays
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
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Kirschen GW, Blakemore K, Al-Kouatly HB, Fridkis G, Baschat A, Gearhart J, Jelin AC. The genetic etiologies of bilateral renal agenesis. Prenat Diagn 2024; 44:205-221. [PMID: 38180355 DOI: 10.1002/pd.6516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
OBJECTIVE The goal of this study was to review and analyze the medical literature for cases of prenatal and/or postnatally diagnosed bilateral renal agenesis (BRA) and create a comprehensive summary of the genetic etiologies known to be associated with this condition. METHODS A literature search was conducted as a scoping review employing Online Mendeliain Inheritance in Man, PubMed, and Cochrane to identify cases of BRA with known underlying genetic (chromosomal vs. single gene) etiologies and those described in syndromes without any known genetic etiology. The cases were further categorized as isolated versus non-isolated, describing additional findings reported prenatally, postnatally, and postmortem. Inheritance pattern was also documented when appropriate in addition to the reported timing of diagnosis and sex. RESULTS We identified six cytogenetic abnormalities and 21 genes responsible for 20 single gene disorders associated with BRA. Five genes have been reported to associate with BRA without other renal anomalies; sixteen others associate with both BRA as well as unilateral renal agenesis. Six clinically recognized syndromes/associations were identified with an unknown underlying genetic etiology. Genetic etiologies of BRA are often phenotypically expressed as other urogenital anomalies as well as complex multi-system syndromes. CONCLUSION Multiple genetic etiologies of BRA have been described, including cytogenetic abnormalities and monogenic syndromes. The current era of the utilization of exome and genome-wide sequencing is likely to significantly expand our understanding of the underlying genetic architecture of BRA.
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Affiliation(s)
- Gregory W Kirschen
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Karin Blakemore
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Jefferson Health, Philadelphia, New York, USA
| | - Gila Fridkis
- Physician Affiliate Group of New York, P.C. (PAGNY), Department of Pediatrics, Metropolitan Hospital Center, New York, New York, USA
| | - Ahmet Baschat
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - John Gearhart
- Department of Urology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Angie C Jelin
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
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Verbitsky M, Krishnamurthy S, Krithivasan P, Hughes D, Khan A, Marasà M, Vena N, Khosla P, Zhang J, Lim TY, Glessner JT, Weng C, Shang N, Shen Y, Hripcsak G, Hakonarson H, Ionita-Laza I, Levy B, Kenny EE, Loos RJ, Kiryluk K, Sanna-Cherchi S, Crosslin DR, Furth S, Warady BA, Igo RP, Iyengar SK, Wong CS, Parsa A, Feldman HI, Gharavi AG. Genomic Disorders in CKD across the Lifespan. J Am Soc Nephrol 2023; 34:607-618. [PMID: 36302597 PMCID: PMC10103259 DOI: 10.1681/asn.2022060725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
SIGNIFICANCE STATEMENT Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis. BACKGROUND Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility. METHODS We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II ( n =248), Chronic Renal Insufficiency Cohort (CRIC) study ( n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort. RESULTS We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk. CONCLUSION Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Natalie Vena
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Pavan Khosla
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Joseph T. Glessner
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology and Columbia Genome Center, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David R. Crosslin
- Division of Biomedical Informatics and Genomics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Susan Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Afshin Parsa
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Medicine, Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Kolvenbach CM, Dworschak GC, Rieke JM, Woolf AS, Reutter H, Odermatt B, Hilger AC. Modelling human lower urinary tract malformations in zebrafish. Mol Cell Pediatr 2023; 10:2. [PMID: 36977792 PMCID: PMC10050536 DOI: 10.1186/s40348-023-00156-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Advances in molecular biology are improving our understanding of the genetic causes underlying human congenital lower urinary tract (i.e., bladder and urethral) malformations. This has recently led to the identification of the first disease-causing variants in the gene BNC2 for isolated lower urinary tract anatomical obstruction (LUTO), and of WNT3 and SLC20A1 as genes implicated in the pathogenesis of the group of conditions called bladder-exstrophy-epispadias complex (BEEC). Implicating candidate genes from human genetic data requires evidence of their influence on lower urinary tract development and evidence of the found genetic variants' pathogenicity. The zebrafish (Danio rerio) has many advantages for use as a vertebrate model organism for the lower urinary tract. Rapid reproduction with numerous offspring, comparable anatomical kidney and lower urinary tract homology, and easy genetic manipulability by Morpholino®-based knockdown or CRISPR/Cas editing are among its advantages. In addition, established marker staining for well-known molecules involved in urinary tract development using whole-mount in situ hybridization (WISH) and the usage of transgenic lines expressing fluorescent protein under a tissue-specific promoter allow easy visualization of phenotypic abnormalities of genetically modified zebrafish. Assays to examine the functionality of the excretory organs can also be modeled in vivo with the zebrafish. The approach of using these multiple techniques in zebrafish not only enables rapid and efficient investigation of candidate genes for lower urinary tract malformations derived from human data, but also cautiously allows transferability of causality from a non-mammalian vertebrate to humans.
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Affiliation(s)
- Caroline M Kolvenbach
- Institute of Anatomy, Medical Faculty, University of Bonn, Bonn, Germany.
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Gabriel C Dworschak
- Institute of Anatomy, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Department of Neuropediatrics, University Hospital Bonn, Bonn, Germany
| | - Johanna M Rieke
- Department of Pediatrics, Children's Hospital Medical Center, University Hospital Bonn, Bonn, Germany
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Heiko Reutter
- Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Benjamin Odermatt
- Institute of Anatomy, Medical Faculty, University of Bonn, Bonn, Germany
| | - Alina C Hilger
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
- Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, Erlangen, Germany
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5
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Allred ET, Perens EA, Coufal NG, Sanford Kobayashi E, Kingsmore SF, Dimmock DP. Genomic sequencing has a high diagnostic yield in children with congenital anomalies of the heart and urinary system. Front Pediatr 2023; 11:1157630. [PMID: 36999085 PMCID: PMC10043482 DOI: 10.3389/fped.2023.1157630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/24/2023] [Indexed: 04/01/2023] Open
Abstract
Background Congenital heart defects (CHD) and congenital anomalies of the kidney and urinary tract (CAKUT) account for significant morbidity and mortality in childhood. Dozens of monogenic causes of anomalies in each organ system have been identified. However, even though 30% of CHD patients also have a CAKUT and both organs arise from the lateral mesoderm, there is sparse overlap of the genes implicated in the congenital anomalies for these organ systems. We sought to determine whether patients with both CAKUT and CHD have a monogenic etiology, with the long-term goal of guiding future diagnostic work up and improving outcomes. Methods Retrospective review of electronic medical records (EMR), identifying patients admitted to Rady Children's Hospital between January 2015 and July 2020 with both CAKUT and CHD who underwent either whole exome sequencing (WES) or whole genome sequencing (WGS). Data collected included demographics, presenting phenotype, genetic results, and mother's pregnancy history. WGS data was reanalyzed with a specific focus on the CAKUT and CHD phenotype. Genetic results were reviewed to identify causative, candidate, and novel genes for the CAKUT and CHD phenotype. Associated additional structural malformations were identified and categorized. Results Thirty-two patients were identified. Eight patients had causative variants for the CAKUT/CHD phenotype, three patients had candidate variants, and three patients had potential novel variants. Five patients had variants in genes not associated with the CAKUT/CHD phenotype, and 13 patients had no variant identified. Of these, eight patients were identified as having possible alternative causes for their CHD/CAKUT phenotype. Eighty-eight percent of all CAKUT/CHD patients had at least one additional organ system with a structural malformation. Conclusions Overall, our study demonstrated a high rate of monogenic etiologies in hospitalized patients with both CHD and CAKUT, with a diagnostic rate of 44%. Thus, physicians should have a high suspicion for genetic disease in this population. Together, these data provide valuable information on how to approach acutely ill patients with CAKUT and CHD, including guiding diagnostic work up for associated phenotypes, as well as novel insights into the genetics of CAKUT and CHD overlap syndromes in hospitalized children.
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Affiliation(s)
- Erika T. Allred
- Department of Pediatrics, University of California, San Diego, CA, United States
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
- Correspondence: Erika T. Allred
| | - Elliot A. Perens
- Department of Pediatrics, University of California, San Diego, CA, United States
| | - Nicole G. Coufal
- Department of Pediatrics, University of California, San Diego, CA, United States
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - Erica Sanford Kobayashi
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
- Department of Pediatrics, Children's Hospital of Orange County, Orange, CA, United States
| | | | - David P. Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
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6
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Wu S, Wang X, Dai S, Zhang G, Zhou J, Shen Y. A novel missense mutation in GREB1L identified in a three-generation family with renal hypodysplasia/aplasia-3. Orphanet J Rare Dis 2022; 17:413. [PMID: 36371238 PMCID: PMC9652819 DOI: 10.1186/s13023-022-02553-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/11/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Renal hypodysplasia/aplasia-3 (RHDA3), as the most severe end of the spectrum of congenital anomalies of the kidney and urinary tract, is mainly caused by mutations in GREB1L. However, the mutations in GREB1L identified to date only explain a limited proportion of RHDA3 cases, and the mechanism of GREB1L mutations causing RHDA3 is unclear. RESULTS According to whole-exome sequencing, a three-generation family suffering from RHDA3 was investigated with a novel missense mutation in GREB1L, c.4507C>T. All three-generation patients suffered from unilateral absent kidney. This missense mutation resulted in sharp downregulation of mRNA and protein expression, which might lead to RHDA3. Mechanistically, through RNA-sequencing, it was found that the mRNA levels of PAX2 and PTH1R, which are key molecules involved in the development of the kidney, were significantly downregulated by knocking out GREB1L in vitro. CONCLUSIONS This novel missense mutation in GREB1L can be helpful in the genetic diagnosis of RHDA3, and the discovery of the potential mechanism that GREB1L mutations involved in RHDA3 pathogenesis can promote the adoption of optimal treatment measures and the development of personalized medicine directly targeting these effects.
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Affiliation(s)
- Sixian Wu
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xiang Wang
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Siyu Dai
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Guohui Zhang
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Jiaojiao Zhou
- grid.412901.f0000 0004 1770 1022Division of Ultrasound, West China Hospital of Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Ying Shen
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
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7
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Missense Variants in GFRA1 and NPNT Are Associated with Congenital Anomalies of the Kidney and Urinary Tract. Genes (Basel) 2022; 13:genes13101687. [PMID: 36292572 PMCID: PMC9601797 DOI: 10.3390/genes13101687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
The use of next-generation sequencing (NGS) has helped in identifying many genes that cause congenital anomalies of the kidney and urinary tract (CAKUT). Bilateral renal agenesis (BRA) is the most severe presentation of CAKUT, and its association with autosomal recessively inherited genes is expanding. Highly consanguineous populations can impact the detection of recessively inherited genes. Here, we report two families harboring homozygous missense variants in recently described genes, NPNT and GFRA1. Two consanguineous families with neonatal death due to CAKUT were investigated. Fetal ultrasound of probands identified BRA in the first family and severe renal cystic dysplasia in the second family. Exome sequencing coupled with homozygosity mapping was performed, and Sanger sequencing was used to confirm segregation of alleles in both families. In the first family with BRA, we identified a homozygous missense variant in GFRA1: c.362A>G; p.(Tyr121Cys), which is predicted to damage the protein structure. In the second family with renal cystic dysplasia, we identified a homozygous missense variant in NPNT: c.56C>G; p.(Ala19Gly), which is predicted to disrupt the signal peptide site. We report two Saudi Arabian consanguineous families with CAKUT phenotypes that included renal agenesis caused by missense variants in GFRA1 and NPNT, confirming the role of these two genes in human kidney development.
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8
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Wopperer FJ, Knaup KX, Stanzick KJ, Schneider K, Jobst-Schwan T, Ekici AB, Uebe S, Wenzel A, Schliep S, Schürfeld C, Seitz R, Bernhardt W, Gödel M, Wiesener A, Popp B, Stark KJ, Gröne HJ, Friedrich B, Weiß M, Basic-Jukic N, Schiffer M, Schröppel B, Huettel B, Beck BB, Sayer JA, Ziegler C, Büttner-Herold M, Amann K, Heid IM, Reis A, Pasutto F, Wiesener MS. Diverse molecular causes of unsolved autosomal dominant tubulointerstitial kidney diseases. Kidney Int 2022; 102:405-420. [DOI: 10.1016/j.kint.2022.04.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Accepted: 04/08/2022] [Indexed: 12/11/2022]
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9
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Khan K, Ahram DF, Liu YP, Westland R, Sampogna RV, Katsanis N, Davis EE, Sanna-Cherchi S. Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations. Kidney Int 2022; 101:473-484. [PMID: 34780871 PMCID: PMC8934530 DOI: 10.1016/j.kint.2021.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development.
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Affiliation(s)
- Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address)
| | - Dina F. Ahram
- Division of Nephrology, Columbia University, New York, USA
| | - Yangfan P. Liu
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, USA.,Department of Pediatric Nephrology, Amsterdam UMC- Emma Children’s Hospital, Amsterdam, NL
| | | | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA (current address); Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
| | - Erica E. Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address).,Department of Pediatrics and Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,To whom correspondence should be addressed: ADDRESS CORRESPONDENCE TO: Simone Sanna-Cherchi, MD, Division of Nephrology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA; Phone: 212-851-4925; Fax: 212-851-5461; . Erica E. Davis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7662; Fax: 312-503-7343; , Nicholas Katsanis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7339; Fax: 312-503-7343;
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA.
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10
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Pontecorvi P, Megiorni F, Camero S, Ceccarelli S, Bernardini L, Capalbo A, Anastasiadou E, Gerini G, Messina E, Perniola G, Benedetti Panici P, Grammatico P, Pizzuti A, Marchese C. Altered Expression of Candidate Genes in Mayer-Rokitansky-Küster-Hauser Syndrome May Influence Vaginal Keratinocytes Biology: A Focus on Protein Kinase X. BIOLOGY 2021; 10:biology10060450. [PMID: 34063745 PMCID: PMC8223793 DOI: 10.3390/biology10060450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a rare and complex disease defined by congenital aplasia of the vagina and uterus in 46,XX women, often associated with kidney and urinary tract anomalies. The aetiopathogenesis of MRKH syndrome is still largely unknown. Herein, we investigated the role of selected candidate genes in the aetiopathogenesis of MRKH syndrome, with a focus on PRKX, which encodes for protein kinase X. Through RT-qPCR analyses performed on vaginal dimple samples from patients, and principal component analysis (PCA), we highlighted a phenotype-related expression pattern of PRKX, MUC1, HOXC8 and GREB1L in MRKH patients. By using an in vitro approach, we proved that PRKX ectopic overexpression in a cell model of vaginal keratinocytes promotes cell motility through epithelial-to-mesenchymal transition (EMT) activation, a fundamental process in urogenital tract morphogenesis. Moreover, our findings showed that PRKX upregulation in vaginal keratinocytes is able to affect transcriptional levels of HOX genes, implicated in urinary and genital tract development. Our study identified the dysregulation of PRKX expression as a possible molecular cause for MRKH syndrome. Moreover, we propose the specific role of PRKX in vaginal keratinocyte biology as one of the possible mechanisms underlying this complex disease.
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Affiliation(s)
- Paola Pontecorvi
- Department of Experimental Medicine, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (P.P.); (F.M.); (S.C.); (E.A.); (G.G.); (E.M.); (A.P.)
| | - Francesca Megiorni
- Department of Experimental Medicine, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (P.P.); (F.M.); (S.C.); (E.A.); (G.G.); (E.M.); (A.P.)
| | - Simona Camero
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (S.C.); (G.P.); (P.B.P.)
| | - Simona Ceccarelli
- Department of Experimental Medicine, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (P.P.); (F.M.); (S.C.); (E.A.); (G.G.); (E.M.); (A.P.)
| | - Laura Bernardini
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Foundation-Viale Cappuccini, 1, 71013 San Giovanni Rotondo (FG), Italy; (L.B.); (A.C.)
| | - Anna Capalbo
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Foundation-Viale Cappuccini, 1, 71013 San Giovanni Rotondo (FG), Italy; (L.B.); (A.C.)
| | - Eleni Anastasiadou
- Department of Experimental Medicine, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (P.P.); (F.M.); (S.C.); (E.A.); (G.G.); (E.M.); (A.P.)
| | - Giulia Gerini
- Department of Experimental Medicine, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (P.P.); (F.M.); (S.C.); (E.A.); (G.G.); (E.M.); (A.P.)
| | - Elena Messina
- Department of Experimental Medicine, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (P.P.); (F.M.); (S.C.); (E.A.); (G.G.); (E.M.); (A.P.)
| | - Giorgia Perniola
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (S.C.); (G.P.); (P.B.P.)
| | - Pierluigi Benedetti Panici
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (S.C.); (G.P.); (P.B.P.)
| | - Paola Grammatico
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University of Rome-San Camillo-Forlanini Hospital, Circonvallazione Gianicolense, 87, 00152 Rome, Italy;
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (P.P.); (F.M.); (S.C.); (E.A.); (G.G.); (E.M.); (A.P.)
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Foundation-Viale Cappuccini, 1, 71013 San Giovanni Rotondo (FG), Italy; (L.B.); (A.C.)
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome—Viale Regina Elena 324, 00161 Rome, Italy; (P.P.); (F.M.); (S.C.); (E.A.); (G.G.); (E.M.); (A.P.)
- Correspondence: ; Tel.: +39-06-4997-2872
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11
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Zhou XY, Zheng HY, Han L, Wang Y, Zhang L, Shu XM, Zhang ML, Liu GN, Ding LS. Copy Number Variations Analysis Identifies QPRT as a Candidate Gene Associated With Susceptibility for Solitary Functioning Kidney. Front Genet 2021; 12:575830. [PMID: 34079576 PMCID: PMC8165445 DOI: 10.3389/fgene.2021.575830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/06/2021] [Indexed: 01/03/2023] Open
Abstract
Background The lack of understanding of molecular pathologies of the solitary functioning kidney makes improving and strengthening the continuity of care between pediatric and adult nephrological patients difficult. Copy number variations (CNVs) account for a molecular cause of solitary functioning kidney, but characterization of the pathogenic genes remains challenging. Methods In our prospective cohort study, 99 fetuses clinically diagnosed with a solitary functioning kidney were enrolled and evaluated using chromosomal microarray analysis (CMA). The genetic drivers for the pathogenic CNVs were analyzed. We characterized QPRT localization in fetal kidneys using immunohistochemistry and its expression in adult kidneys using quantitative RT-PCR. Further, QPRT was knocked down using siRNA in human embryonic kidney (HEK293T) cells, and the cell cycle and proliferation were tested. Results Besides one Triple X syndrome and one Down syndrome, we identified a total of 45 CNVs out of 34 subjects. Among the 14 pathogenic CNVs, CNV 16p11.2 reached the highest number of records with the phenotype of kidney anomalies in the Decipher database. Among the 26 genes within the 16p11.2 region, as a key enzyme for nicotinamide adenine dinucleotide (NAD+) biosynthesis, QPRT was distinctly localized in renal tubules but was barely observed in renal interstitial and glomeruli in fetal kidneys. The loss of QPRT prevented cells’ efficient transition into S phase, affected cell-cycle progression, and abrogated proliferation of human embryonic kidney cells. Conclusion Our data suggest that QPRT is a candidate gene associated with susceptibility for solitary functioning kidney. The CNVs discovered in our study exhibit great potential for future applications in genetic counseling and pregnancy management.
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Affiliation(s)
- Xiao Y Zhou
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Hao Y Zheng
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Li Han
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yan Wang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Li Zhang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Xiao M Shu
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Mu L Zhang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Guan N Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Lian S Ding
- Department of Neurosurgery, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
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12
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Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, Marasà M, Kim H, Lim TY, Weng PL, Sánchez-Rodríguez E, Mitrotti A, Ahram DF, Zanoni F, Fasel DA, Westland R, Sampson MG, Zhang JY, Bodria M, Kil BH, Shril S, Gesualdo L, Torri F, Scolari F, Izzi C, van Wijk JA, Saraga M, Santoro D, Conti G, Barton DE, Dobson MG, Puri P, Furth SL, Warady BA, Pisani I, Fiaccadori E, Allegri L, Degl'Innocenti ML, Piaggio G, Alam S, Gigante M, Zaza G, Esposito P, Lin F, Simões-e-Silva AC, Brodkiewicz A, Drozdz D, Zachwieja K, Miklaszewska M, Szczepanska M, Adamczyk P, Tkaczyk M, Tomczyk D, Sikora P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Lozanovski VJ, Gucev Z, Ionita-Laza I, Stanaway IB, Crosslin DR, Wong CS, Hildebrandt F, Barasch J, Kenny EE, Loos RJ, Levy B, Ghiggeri GM, Hakonarson H, Latos-Bieleńska A, Materna-Kiryluk A, Darlow JM, Tasic V, Willer C, Kiryluk K, Sanna-Cherchi S, Mendelsohn CL, Gharavi AG. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. J Am Soc Nephrol 2021; 32:805-820. [PMID: 33597122 PMCID: PMC8017540 DOI: 10.1681/asn.2020050681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Vesicoureteral reflux (VUR) is a common, familial genitourinary disorder, and a major cause of pediatric urinary tract infection (UTI) and kidney failure. The genetic basis of VUR is not well understood. METHODS A diagnostic analysis sought rare, pathogenic copy number variant (CNV) disorders among 1737 patients with VUR. A GWAS was performed in 1395 patients and 5366 controls, of European ancestry. RESULTS Altogether, 3% of VUR patients harbored an undiagnosed rare CNV disorder, such as the 1q21.1, 16p11.2, 22q11.21, and triple X syndromes ((OR, 3.12; 95% CI, 2.10 to 4.54; P=6.35×10-8) The GWAS identified three study-wide significant and five suggestive loci with large effects (ORs, 1.41-6.9), containing canonical developmental genes expressed in the developing urinary tract (WDPCP, OTX1, BMP5, VANGL1, and WNT5A). In particular, 3.3% of VUR patients were homozygous for an intronic variant in WDPCP (rs13013890; OR, 3.65; 95% CI, 2.39 to 5.56; P=1.86×10-9). This locus was associated with multiple genitourinary phenotypes in the UK Biobank and eMERGE studies. Analysis of Wnt5a mutant mice confirmed the role of Wnt5a signaling in bladder and ureteric morphogenesis. CONCLUSIONS These data demonstrate the genetic heterogeneity of VUR. Altogether, 6% of patients with VUR harbored a rare CNV or a common variant genotype conferring an OR >3. Identification of these genetic risk factors has multiple implications for clinical care and for analysis of outcomes in VUR.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Sarah E. Graham
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Hyunwoo Kim
- Department of Urology, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Patricia L. Weng
- Department of Pediatric Nephrology, University of California, Los Angeles Medical Center and University of California, Los Angeles Medical Center-Santa Monica, Los Angeles, California
| | | | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Dina F. Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David A. Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Matthew G. Sampson
- Division of Nephrology, Boston Children’s Hospital, Boston, Massachusetts
| | - Jun Y. Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Torri
- Department of Pediatric Surgery, Spedali Civili Children’s Hospital of Brescia, Brescia, Italy
| | - Francesco Scolari
- Chair and Division of Nephrology, University and Spedali Civili Hospital, Brescia, Italy
| | - Claudia Izzi
- Division of Nephrology and Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - David E. Barton
- University College Dublin School of Medicine, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Mark G. Dobson
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Pediatric Surgery, Beacon Hospital, University College Dublin, Dublin, Ireland
| | - Susan L. Furth
- Division of Nephrology, Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Division of Nephrology, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Children’s Mercy Kansas City, Kansas City, Missouri
| | - Isabella Pisani
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Landino Allegri
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Maria Ludovica Degl'Innocenti
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Gianluigi Zaza
- Renal and Dialysis Unit, Department of Medicine, School of Medicine, University of Verona, Verona, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, Nephrology, Dialysis and Transplantation Clinics, Genoa University and IRCCS Policlinico San Martino, Genova, Italy
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, New York
| | - Ana Cristina Simões-e-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotheraphy and Management of Acute Poisoning, Pomeranian Medical University, Szczecin, Poland
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Poland
| | | | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Vladimir J. Lozanovski
- University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Zoran Gucev
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | | | - Ian B. Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - David R. Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Urology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - John M. Darlow
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Cristen Willer
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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13
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Wang A, Ji B, Wu F, Zhao X. Clinical Exome Sequencing Identifies a Novel Mutation of the GREB1L Gene in a Chinese Family with Renal Agenesis. Genet Test Mol Biomarkers 2020; 24:520-526. [PMID: 32598191 DOI: 10.1089/gtmb.2020.0036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Renal agenesis (RA) is one of the most severe congenital anomalies of the kidney and urinary tract; it is known to be highly genetically heterogeneous. The purpose of this study was to explore the clinical significance of genetic diagnostics in a Chinese RA family. Methods: Five members of an RA family and 100 healthy people were recruited. Clinical exome sequencing was conducted to explore the underlying genetic cause in the affected family. Results: Exome sequencing identified a novel missense mutation (c.2333T>A, p.Val778Asp) in the GREB1L gene. This GREB1L variant was not detected in controls and was predicted to be highly damaging to the physiological function of the GREB1L protein. Conclusion: We identified a novel c.2333T>A variant in the GREB1L gene that extends the mutational spectrum associated with renal agenesis.
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Affiliation(s)
- Ancong Wang
- Department of Reproductive Medicine, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
- Department of Obstetrics and Gynecology, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
| | - Baoju Ji
- Department of Clinical Laboratory, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
| | - Fengxia Wu
- Department of Anatomy, School of Basic Medical Sciences, Shandong University, Jinan, Shandong Province, P.R. China
| | - Xiangyu Zhao
- Department of Clinical Laboratory, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
- Department of Medical Genetics, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
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14
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Little MH, Quinlan C. Advances in our understanding of genetic kidney disease using kidney organoids. Pediatr Nephrol 2020; 35:915-926. [PMID: 31065797 DOI: 10.1007/s00467-019-04259-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/27/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
A significant proportion of kidney disease presenting in childhood is likely genetic in origin with a growing number of genes implicated in its development. However, many children may have changes in previously undescribed or unrecognised genes. The recent development of methods for generating human kidney organoids from human pluripotent stem cells has the potential to substantially change the rate of diagnosis and the development of new treatments for some forms of genetic kidney disease. In this review, we discuss how accurately a kidney organoid models the human kidney, identifying the strengths and weaknesses of these potentially patient-derived models of renal disease.
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Affiliation(s)
- Melissa H Little
- Murdoch Children's Research Institute, Flemington Rd., Parkville, VIC, Australia. .,Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC, Australia. .,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia.
| | - Catherine Quinlan
- Murdoch Children's Research Institute, Flemington Rd., Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia.,Department of Nephrology, Royal Children's Hospital, Flemington Rd., Parkville, VIC, Australia
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15
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Jacquinet A, Boujemla B, Fasquelle C, Thiry J, Josse C, Lumaka A, Brischoux-Boucher E, Dubourg C, David V, Pasquier L, Lehman A, Morcel K, Guerrier D, Bours V. GREB1L variants in familial and sporadic hereditary urogenital adysplasia and Mayer-Rokitansky-Kuster-Hauser syndrome. Clin Genet 2020; 98:126-137. [PMID: 32378186 DOI: 10.1111/cge.13769] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022]
Abstract
Congenital uterine anomalies (CUA) may have major impacts on the health and social well-being of affected individuals. Their expressivity is variable, with the most severe end of the spectrum being the absence of any fully or unilaterally developed uterus (aplastic uterus), which is a major feature in Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH). So far, etiologies of CUA remain largely unknown. As reports of familial occurrences argue for strong genetic contributors in some cases, we performed whole exome sequencing in nine multiplex families with recurrence of uterine and kidney malformations, a condition called hereditary urogenital adysplasia. Heterozygous likely causative variants in the gene GREB1L were identified in four of these families, confirming GREB1L as an important gene for proper uterine and kidney development. The apparent mode of inheritance was autosomal dominant with incomplete penetrance. The four families included fetuses with uterovaginal aplasia and bilateral renal agenesis, highlighting the importance to investigate GREB1L in such phenotypes. Subsequent sequencing of the gene in a cohort of 68 individuals with MRKH syndrome or uterine malformation (mostly sporadic cases) identified six additional variants of unknown significance. We therefore conclude that heterozygous GREB1L variants contribute to MRKH syndrome and this probably requires additional genetic or environmental factors for full penetrance.
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Affiliation(s)
- Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.,Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Bouchra Boujemla
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Corinne Fasquelle
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium
| | - Jerôme Thiry
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Claire Josse
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium.,Medical Oncology, Centre Hospitalier Universitaire CHU Liege, Liège, Belgium
| | - Aimé Lumaka
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Christèle Dubourg
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France.,Department of Molecular Genetics and Genomics, Université de Rennes, CHU Rennes, Rennes, France
| | - Véronique David
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France.,Department of Molecular Genetics and Genomics, Université de Rennes, CHU Rennes, Rennes, France
| | - Laurent Pasquier
- Department of Medical Genetics, CLAD Ouest, Université de Rennes, CHU Rennes, Rennes, France
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, BC Children's Hospital and BC Women's Hospital, Vancouver, British Columbia, Canada
| | - Karine Morcel
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France
| | - Daniel Guerrier
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France
| | - Vincent Bours
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.,Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
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16
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Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. Cell 2020; 177:446-462.e16. [PMID: 30951671 DOI: 10.1016/j.cell.2019.03.024] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/29/2018] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
Abstract
Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.
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17
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Talati AN, Webster CM, Vora NL. Prenatal genetic considerations of congenital anomalies of the kidney and urinary tract (CAKUT). Prenat Diagn 2019; 39:679-692. [PMID: 31343747 DOI: 10.1002/pd.5536] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 12/20/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) constitute 20% of all congenital malformations occurring in one in 500 live births. Worldwide, CAKUT are responsible for 40% to 50% of pediatric and 7% of adult end-stage renal disease. Pathogenic variants in genes causing CAKUT include monogenic diseases such as polycystic kidney disease and ciliopathies, as well as syndromes that include isolated kidney disease in conjunction with other abnormalities. Prenatal diagnosis most often occurs using ultrasonography; however, further genetic diagnosis may be made using a variety of testing strategies. Family history and pathologic examination can also provide information to improve the ability to make a prenatal diagnosis of CAKUT. Here, we provide a comprehensive overview of genetic considerations in the prenatal diagnosis of CAKUT disorders. Specifically, we discuss monogenic causes of CAKUT, associated ultrasound characteristics, and considerations for genetic diagnosis, antenatal care, and postnatal care.
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Affiliation(s)
- Asha N Talati
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Carolyn M Webster
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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18
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Dai G, Pu Z, Cheng X, Yin J, Chen J, Xu T, Zhang H, Li Z, Chen X, Chen J, Qin Y, Yang S. Whole-Exome Sequencing Reveals Novel Genetic Variation for Dilated Cardiomyopathy in Pediatric Chinese Patients. Pediatr Cardiol 2019; 40:950-957. [PMID: 30993396 DOI: 10.1007/s00246-019-02096-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/22/2019] [Indexed: 12/30/2022]
Abstract
Dilated cardiomyopathy (DCM) is characterized by left or bilateral ventricular dilation and systolic dysfunction without rational conditions, which can lead to progressive heart failure and sudden cardiac death. Most of the pathogenic genes have been reported in adult population by locus mapping in familial cases and animal model studies. However, it still remains challenging to decipher the role of genetics in the etiology of pediatric DCM. We applied whole-exome sequencing (WES) for 30 sporadic pediatric DCM subjects and 100 non-DCM local controls. We identified the pathogenic mutations using bioinformatics tools based on genomic strategies synergistically and confirmed mutations by Sanger sequencing. We identified compound heterozygous nonsense mutations in DSP (c.3799C > T, p.R1267X; c.4444G > T, p.E1482X). In sporadic cases, the two heterozygous mutations in XIRP2 were identified. Then we performed an exome-wide association study with 30 case and 100 control subjects. Interestingly, we could not identify TTN truncating variants in all cases. Collectively, we observed a significant risk signal between carriers of TTN deleterious missense variants and DCM risk (odds ratio 4.0, 95% confidence interval 1.1-22.2, p = 3.12 × 10-2). Our observations expanded the spectrum of mutations and were valuable in the pre- and postnatal screening and genetic diagnosis for DCM.
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Affiliation(s)
- Genyin Dai
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China
| | - Zhening Pu
- Center of Clinical Research, Wuxi People's Hospital of Nanjing Medical University, Wuxi, 214023, China
| | - Xueying Cheng
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China
| | - Jie Yin
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China
| | - Jun Chen
- Department of Echocardiography, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Ting Xu
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China
| | - Han Zhang
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China
| | - Zewei Li
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China
| | - Xuan Chen
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China
| | - Jinlong Chen
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China
| | - Yuming Qin
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China.
| | - Shiwei Yang
- Department of Cardiology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, China.
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Loss-of-function mutations in PTPRJ cause a new form of inherited thrombocytopenia. Blood 2018; 133:1346-1357. [PMID: 30591527 DOI: 10.1182/blood-2018-07-859496] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022] Open
Abstract
Inherited thrombocytopenias (ITs) are a heterogeneous group of disorders characterized by low platelet count that may result in bleeding tendency. Despite progress being made in defining the genetic causes of ITs, nearly 50% of patients with familial thrombocytopenia are affected with forms of unknown origin. Here, through exome sequencing of 2 siblings with autosomal-recessive thrombocytopenia, we identified biallelic loss-of-function variants in PTPRJ . This gene encodes for a receptor-like PTP, PTPRJ (or CD148), which is expressed abundantly in platelets and megakaryocytes. Consistent with the predicted effects of the variants, both probands have an almost complete loss of PTPRJ at the messenger RNA and protein levels. To investigate the pathogenic role of PTPRJ deficiency in hematopoiesis in vivo, we carried out CRISPR/Cas9-mediated ablation of ptprja (the ortholog of human PTPRJ) in zebrafish, which induced a significantly decreased number of CD41+ thrombocytes in vivo. Moreover, megakaryocytes of our patients showed impaired maturation and profound defects in SDF1-driven migration and formation of proplatelets in vitro. Silencing of PTPRJ in a human megakaryocytic cell line reproduced the functional defects observed in patients' megakaryocytes. The disorder caused by PTPRJ mutations presented as a nonsyndromic thrombocytopenia characterized by spontaneous bleeding, small-sized platelets, and impaired platelet responses to the GPVI agonists collagen and convulxin. These platelet functional defects could be attributed to reduced activation of Src family kinases. Taken together, our data identify a new form of IT and highlight a hitherto unknown fundamental role for PTPRJ in platelet biogenesis.
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