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Zhen Z, Dong Z, Gao L, Wang Q, Chen X, Na J, Yuan Y. Novel mutation in XPNPEP3 in a patient with heart failure without nephronophthisis-like nephropathy (NPHPL1): case report and literature review. BMC Pediatr 2024; 24:632. [PMID: 39363162 PMCID: PMC11451151 DOI: 10.1186/s12887-024-05124-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024] Open
Abstract
BACKGROUND X-PROLYL AMINOPEPTIDASE 3: (XPNPEP3) mutations are known to cause nephronophthisis-like nephropathy-1 (NPHPL1), a rare autosomal-recessive kidney disease characterized by progressive kidney failure and cystic kidney disease in childhood. The full phenotypic spectrum associated with mutations in XPNPEP3 is not fully elucidated. CASE PRESENTATION: A 13-year-old Chinese female patient with intellectual disability presented with a 2-year history of convulsions and fatigue, with a recent episode of swelling, breathlessness, and nocturnal dyspnea lasting 10 days. The patient was diagnosed with heart failure and kidney failure. Whole exome sequencing revealed a homozygous c.970-2 A > G mutation in XPNPEP3 associated with severe cardiac dysfunction and neurological symptoms, including epilepsy and intellectual disability. Notably, kidney ultrasound did not reveal the typical changes of NPHPL1, and kidney failure was hypothesized to be secondary to cardiac dysfunction rather than primary kidney pathology. CONCLUSIONS: This case suggests the possible association of additional phenotypic features associated with XPNPEP3 mutations, emphasizing the need for further investigation into the heterogeneous clinical presentations associated with XPNPEP3 mutations. The findings highlight the importance of considering alternative phenotypes in patients with genetic mutations traditionally associated with specific diseases. Segregation and functional analyses are necessary to determine causality between the c.970-2 A > G XPNPEP3 mutation and disease.
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Affiliation(s)
- Zhen Zhen
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Ziyan Dong
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Lu Gao
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Qin Wang
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Xi Chen
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Jia Na
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Yue Yuan
- Department of Cardiology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China.
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2
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Beyrent E, Wei DT, Beacham GM, Park S, Zheng J, Paszek MJ, Hollopeter G. Dimerization activates the Inversin complex in C. elegans. Mol Biol Cell 2024; 35:ar127. [PMID: 39110529 DOI: 10.1091/mbc.e24-05-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024] Open
Abstract
Genetic, colocalization, and biochemical studies suggest that the ankyrin repeat-containing proteins Inversin (INVS) and ANKS6 function with the NEK8 kinase to control tissue patterning and maintain organ physiology. It is unknown whether these three proteins assemble into a static "Inversin complex" or one that adopts multiple bioactive forms. Through the characterization of hyperactive alleles in C. elegans, we discovered that the Inversin complex is activated by dimerization. Genome engineering of an RFP tag onto the nematode homologues of INVS (MLT-4) and NEK8 (NEKL-2) induced a gain-of-function, cyst-like phenotype that was suppressed by monomerization of the fluorescent tag. Stimulated dimerization of MLT-4 or NEKL-2 using optogenetics was sufficient to recapitulate the phenotype of a constitutively active Inversin complex. Further, dimerization of NEKL-2 bypassed a lethal MLT-4 mutant, demonstrating that the dimeric form is required for function. We propose that dynamic switching between at least two functionally distinct states - an active dimer and an inactive monomer - gates the output of the Inversin complex.
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Affiliation(s)
- Erika Beyrent
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
- Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY 14853
| | - Derek T Wei
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
- Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY 14853
| | - Gwendolyn M Beacham
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
- Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY 14853
| | - Sangwoo Park
- Field of Biophysics, Cornell University, Ithaca, NY 14853
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Jian Zheng
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Matthew J Paszek
- Field of Biophysics, Cornell University, Ithaca, NY 14853
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Gunther Hollopeter
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
- Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, NY 14853
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Gabriel GC, Ganapathiraju M, Lo CW. The Role of Cilia and the Complex Genetics of Congenital Heart Disease. Annu Rev Genomics Hum Genet 2024; 25:309-327. [PMID: 38724024 DOI: 10.1146/annurev-genom-121222-105345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Congenital heart disease (CHD) can affect up to 1% of live births, and despite abundant evidence of a genetic etiology, the genetic landscape of CHD is still not well understood. A large-scale mouse chemical mutagenesis screen for mutations causing CHD yielded a preponderance of cilia-related genes, pointing to a central role for cilia in CHD pathogenesis. The genes uncovered by the screen included genes that regulate ciliogenesis and cilia-transduced cell signaling as well as many that mediate endocytic trafficking, a cell process critical for both ciliogenesis and cell signaling. The clinical relevance of these findings is supported by whole-exome sequencing analysis of CHD patients that showed enrichment for pathogenic variants in ciliome genes. Surprisingly, among the ciliome CHD genes recovered were many that encoded direct protein-protein interactors. Assembly of the CHD genes into a protein-protein interaction network yielded a tight interactome that suggested this protein-protein interaction may have functional importance and that its disruption could contribute to the pathogenesis of CHD. In light of these and other findings, we propose that an interactome enriched for ciliome genes may provide the genomic context for the complex genetics of CHD and its often-observed incomplete penetrance and variable expressivity.
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Affiliation(s)
- George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; ,
| | - Madhavi Ganapathiraju
- Carnegie Mellon University in Qatar, Doha, Qatar
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA;
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; ,
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4
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Wolf MTF, Bonsib SM, Larsen CP, Hildebrandt F. Nephronophthisis: a pathological and genetic perspective. Pediatr Nephrol 2024; 39:1977-2000. [PMID: 37930417 DOI: 10.1007/s00467-023-06174-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 11/07/2023]
Abstract
Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease and is one of the most frequent genetic causes for kidney failure (KF) in children and adolescents. Over 20 genes cause NPHP and over 90 genes contribute to renal ciliopathies often involving multiple organs. About 15-20% of NPHP patients have additional extrarenal symptoms affecting other organs than the kidneys. The involvement of additional organ systems in syndromic forms of NPHP is explained by shared expression of most NPHP gene products in centrosomes and primary cilia, a sensory organelle present in most mammalian cells. This finding resulted in the classification of NPHP as a ciliopathy. If extrarenal symptoms are present in addition to NPHP, these disorders are defined as NPHP-related ciliopathies (NPHP-RC) and can involve the retina (e.g., with Senior-Løken syndrome), CNS (central nervous system) (e.g., with Joubert syndrome), liver (e.g., Boichis and Arima syndromes), or bone (e.g., Mainzer-Saldino and Sensenbrenner syndromes). This review focuses on the pathological findings and the recent genetic advances in NPHP and NPHP-RC. Different mechanisms and signaling pathways are involved in NPHP ranging from planar cell polarity, sonic hedgehog signaling (Shh), DNA damage response pathway, Hippo, mTOR, and cAMP signaling. A number of therapeutic interventions appear to be promising, ranging from vasopressin receptor 2 antagonists such as tolvaptan, cyclin-dependent kinase inhibitors such as roscovitine, Hh agonists such as purmorphamine, and mTOR inhibitors such as rapamycin.
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Affiliation(s)
- Matthias T F Wolf
- Division of Pediatric Nephrology, University of Texas, Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
- Division of Pediatric Nephrology, C.S. Mott Children's Hospital, University of Michigan, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109, USA.
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5
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Beyrent E, Wei DT, Beacham GM, Park S, Zheng J, Paszek MJ, Hollopeter G. Dimerization activates the Inversin complex in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594761. [PMID: 38798613 PMCID: PMC11118560 DOI: 10.1101/2024.05.17.594761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Genetic, colocalization, and biochemical studies suggest that the ankyrin repeat-containing proteins Inversin (INVS) and ANKS6 function with the NEK8 kinase to control tissue patterning and maintain organ physiology. It is unknown whether these three proteins assemble into a static "Inversin complex" or one that adopts multiple bioactive forms. Through characterization of hyperactive alleles in C. elegans , we discovered that the Inversin complex is activated by dimerization. Genome engineering of an RFP tag onto the nematode homologs of INVS (MLT-4) and NEK8 (NEKL-2) induced a gain-of-function, cyst-like phenotype that was suppressed by monomerization of the fluorescent tag. Stimulated dimerization of MLT-4 or NEKL-2 using optogenetics was sufficient to recapitulate the phenotype of a constitutively active Inversin complex. Further, dimerization of NEKL-2 bypassed a lethal MLT-4 mutant, demonstrating that the dimeric form is required for function. We propose that dynamic switching between at least two functionally distinct states-an active dimer and an inactive monomer-gates the output of the Inversin complex.
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6
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Troutman AD, Srinivasan S, Metzger CE, Fallen PB, Chen N, O'Neill KD, Allen MR, Biruete A, Moe SM, Avin KG. Musculoskeletal Health Worsened from Carnitine Supplementation and Not Impacted by a Novel Individualized Treadmill Training Protocol. Am J Nephrol 2024; 55:369-379. [PMID: 38377965 PMCID: PMC11147712 DOI: 10.1159/000537827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
INTRODUCTION Chronic kidney disease (CKD) negatively affects musculoskeletal health, leading to reduced mobility, and quality of life. In healthy populations, carnitine supplementation and aerobic exercise have been reported to improve musculoskeletal health. However, there are inconclusive results regarding their effectiveness and safety in CKD. We hypothesized that carnitine supplementation and individualized treadmill exercise would improve musculoskeletal health in CKD. METHODS We used a spontaneously progressive CKD rat model (Cy/+ rat) (n = 11-12/gr): (1) Cy/+ (CKD-Ctrl), (2) CKD-carnitine (CKD-Carn), and (3) CKD-treadmill (CKD-TM). Carnitine (250 mg/kg) was injected daily for 10 weeks. Rats in the treadmill group ran 4 days/week on a 5° incline for 10 weeks progressing from 30 min/day for week one to 40 min/day for week two to 50 min/day for the remaining 8 weeks. At 32 weeks of age, we assessed overall cardiopulmonary fitness, muscle function, bone histology and architecture, and kidney function. Data were analyzed by one-way ANOVA with Tukey's multiple comparisons tests. RESULTS Moderate to severe CKD was confirmed by biochemistries for blood urea nitrogen (mean 43 ± 5 mg/dL CKD-Ctrl), phosphorus (mean 8 ± 1 mg/dL CKD-Ctrl), parathyroid hormone (PTH; mean 625 ± 185 pg/mL CKD-Ctrl), and serum creatinine (mean 1.1 ± 0.2 mg/mL CKD-Ctrl). Carnitine worsened phosphorous (mean 11 ± 3 mg/dL CKD-Carn; p < 0.0001), PTH (mean 1,738 ± 1,233 pg/mL CKD-Carn; p < 0.0001), creatinine (mean 1 ± 0.3 mg/dL CKD-Carn; p < 0.0001), cortical bone thickness (mean 0.5 ± 0.1 mm CKD-Ctrl, 0.4 ± 0.1 mm CKD-Carn; p < 0.05). Treadmill running significantly improves maximal aerobic capacity when compared to CKD-Ctrl (mean 14 ± 2 min CKD-TM, 10 ± 2 min CKD-Ctrl; p < 0.01). CONCLUSION Carnitine supplementation worsened CKD progression, mineral metabolism biochemistries, and cortical porosity and did not have an impact on physical function. Individualized treadmill running improved maximal aerobic capacity but did not have an impact on CKD progression or bone properties. Future studies should seek to better understand carnitine doses in conditions of compromised renal function to prevent toxicity which may result from elevated carnitine levels and to optimize exercise prescriptions for musculoskeletal health.
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Affiliation(s)
- Ashley D Troutman
- Department of Physical Therapy, School of Health and Human Sciences, Indiana University, Indianapolis, Indiana, USA
| | - Shruthi Srinivasan
- Division of Nephrology and Hypertension, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Corinne E Metzger
- Department of Anatomy, Physiology and Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Paul B Fallen
- Department of Anatomy, Physiology and Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Neal Chen
- Division of Nephrology and Hypertension, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kalisha D O'Neill
- Division of Nephrology and Hypertension, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Matthew R Allen
- Department of Anatomy, Physiology and Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Roudebush Veterans Affairs Medical Center, Indianapolis, Indiana, USA
| | - Annabel Biruete
- Division of Nephrology and Hypertension, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Nutrition Science, Purdue University, West Lafayette, Indiana, USA
| | - Sharon M Moe
- Division of Nephrology and Hypertension, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Anatomy, Physiology and Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Keith G Avin
- Department of Physical Therapy, School of Health and Human Sciences, Indiana University, Indianapolis, Indiana, USA
- Division of Nephrology and Hypertension, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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7
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Kofotolios I, Bonios MJ, Adamopoulos M, Mourouzis I, Filippatos G, Boletis JN, Marinaki S, Mavroidis M. The Han:SPRD Rat: A Preclinical Model of Polycystic Kidney Disease. Biomedicines 2024; 12:362. [PMID: 38397964 PMCID: PMC10887417 DOI: 10.3390/biomedicines12020362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) stands as the most prevalent hereditary renal disorder in humans, ultimately culminating in end-stage kidney disease. Animal models carrying mutations associated with polycystic kidney disease have played an important role in the advancement of ADPKD research. The Han:SPRD rat model, carrying an R823W mutation in the Anks6 gene, is characterized by cyst formation and kidney enlargement. The mutated protein, named Samcystin, is localized in cilia of tubular epithelial cells and seems to be involved in cystogenesis. The homozygous Anks6 mutation leads to end-stage renal disease and death, making it a critical factor in kidney development and function. This review explores the utility of the Han:SPRD rat model, highlighting its phenotypic similarity to human ADPKD. Specifically, we discuss its role in preclinical trials and its importance for investigating the pathogenesis of the disease and developing new therapeutic approaches.
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Affiliation(s)
- Ioannis Kofotolios
- Clinic of Nephrology and Renal Tranplantation, Laiko Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece (M.M.)
| | - Michael J. Bonios
- Heart Failure and Transplant Unit, Onassis Cardiac Surgery Center, 17674 Athens, Greece;
| | - Markos Adamopoulos
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece (M.M.)
| | - Iordanis Mourouzis
- Department of Pharmacology, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Gerasimos Filippatos
- Department of Cardiology, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - John N. Boletis
- Clinic of Nephrology and Renal Tranplantation, Laiko Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Smaragdi Marinaki
- Clinic of Nephrology and Renal Tranplantation, Laiko Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Manolis Mavroidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece (M.M.)
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8
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Biruete A, Chen NX, Metzger CE, Srinivasan S, O'Neill K, Fallen PB, Fonseca A, Wilson HE, de Loor H, Evenepoel P, Swanson KS, Allen MR, Moe SM. The Dietary Fiber Inulin Slows Progression of Chronic Kidney Disease-Mineral Bone Disorder (CKD-MBD) in a Rat Model of CKD. JBMR Plus 2023; 7:e10837. [PMID: 38130753 PMCID: PMC10731114 DOI: 10.1002/jbm4.10837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 12/23/2023] Open
Abstract
Chronic kidney disease (CKD)-mineral bone disorder (CKD-MBD) leads to fractures and cardiovascular disease. Observational studies suggest beneficial effects of dietary fiber on both bone and cardiovascular outcomes, but the effect of fiber on CKD-MBD is unknown. To determine the effect of fiber on CKD-MBD, we fed the Cy/+ rat with progressive CKD a casein-based diet of 0.7% phosphate with 10% inulin (fermentable fiber) or cellulose (non-fermentable fiber) from 22 weeks to either 30 or 32 weeks of age (~30% and ~15% of normal kidney function; CKD 4 and 5). We assessed CKD-MBD end points of biochemistry, bone quantity and quality, cardiovascular health, and cecal microbiota and serum gut-derived uremic toxins. Results were analyzed by two-way analysis of variance (ANOVA) to evaluate the main effects of CKD stage and inulin, and their interaction. The results showed that in CKD animals, inulin did not alter kidney function but reduced the increase from stage 4 to 5 in serum levels of phosphate and parathyroid hormone, but not fibroblast growth factor-23 (FGF23). Bone turnover and cortical bone parameters were similarly improved but mechanical properties were not altered. Inulin slowed progression of aorta and cardiac calcification, left ventricular mass index, and fibrosis. To understand the mechanism, we assessed intestinal microbiota and found changes in alpha and beta diversity and significant changes in several taxa with inulin, together with a reduction in circulating gut derived uremic toxins such as indoxyl sulfate and short-chain fatty acids. In conclusion, the addition of the fermentable fiber inulin to the diet of CKD rats led to a slowed progression of CKD-MBD without affecting kidney function, likely mediated by changes in the gut microbiota composition and lowered gut-derived uremic toxins. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC. on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Annabel Biruete
- Department of Nutrition SciencePurdue UniversityWest LafayetteINUSA
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisINUSA
| | - Neal X. Chen
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisINUSA
| | - Corinne E. Metzger
- Department of Anatomy, Cell Biology, and PhysiologyIndiana University School of MedicineIndianapolisINUSA
| | - Shruthi Srinivasan
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisINUSA
| | - Kalisha O'Neill
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisINUSA
| | - Paul B. Fallen
- Department of Anatomy, Cell Biology, and PhysiologyIndiana University School of MedicineIndianapolisINUSA
| | - Austin Fonseca
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisINUSA
| | - Hannah E. Wilson
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisINUSA
| | - Henriette de Loor
- KU Leuven Department of Microbiology and ImmunologyNephrology and Renal Transplantation Research Group, KU LeuvenLeuvenBelgium
| | - Pieter Evenepoel
- KU Leuven Department of Microbiology and ImmunologyNephrology and Renal Transplantation Research Group, KU LeuvenLeuvenBelgium
- Department of Nephrology and Renal TransplantationUniversity Hospitals LeuvenLeuvenBelgium
| | - Kelly S. Swanson
- Department of Animal SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Matthew R. Allen
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisINUSA
- Department of Anatomy, Cell Biology, and PhysiologyIndiana University School of MedicineIndianapolisINUSA
| | - Sharon M. Moe
- Department of Medicine, Division of NephrologyIndiana University School of MedicineIndianapolisINUSA
- Department of Anatomy, Cell Biology, and PhysiologyIndiana University School of MedicineIndianapolisINUSA
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Liu K, Chen R, Wang X, Gong Y, Shi J, Gu B, Zhou Y, Cai W. Biallelic ANKS6 null variants cause notable extrarenal phenotypes in a nephronophthisis patient and lead to hepatobiliary abnormalities by YAP1 deficiency. Clin Genet 2023; 104:625-636. [PMID: 37525964 DOI: 10.1111/cge.14412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
The ankyrin repeat and sterile alpha motif domain containing 6 (ANKS6) gene, encoding an inversin compartment protein of the primary cilium, was recently reported as a pathogenic gene of nephronophthisis (MIM PS256100). Extrarenal manifestations are frequently observed in this disease, however, potential genotype-phenotype correlations and the underlying mechanisms remain poorly understood. Here we described an infant with kidney failure, hepatobiliary abnormalities, and heart disease, in whom whole exome sequencing identified compound heterozygous variants in ANKS6, including a novel nonsense variant p.Trp458* and a recurrent splicing variant c.2394+1G > A. mRNA expression studies showed that the splicing variant caused aberrant mRNA splicing with exon 13 skipping and the biallelic variants were predicted to cause loss of ANKS6 function. We systematically characterized the clinical and genetic spectra of the disease and revealed that biallelic null variants in ANKS6 cause more severe kidney disease and more extrarenal manifestations, thus establishing a clear genotype-phenotype correlation for the disease. Further evaluations showed that ANKS6 deficiency reduced YAP1 expression in the patient's bile duct epithelium and ANKS6 promotes YAP1 transcriptional activity in a dose-dependent manner, indicating that loss of ANKS6 function causes hepatobiliary abnormalities through YAP1 deficiency during biliary morphogenesis and development, which may offer new therapeutic targets.
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Affiliation(s)
- Keqiang Liu
- Department of Pediatric Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Ru Chen
- Department of Pediatric Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoying Wang
- Department of Pathology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiming Gong
- Department of Pediatric Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Shi
- Department of Pediatric Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Beilin Gu
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Ying Zhou
- Department of Pediatric Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Cai
- Department of Pediatric Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
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10
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Claus LR, Chen C, Stallworth J, Turner JL, Slaats GG, Hawks AL, Mabillard H, Senum SR, Srikanth S, Flanagan-Steet H, Louie RJ, Silver J, Lerner-Ellis J, Morel C, Mighton C, Sleutels F, van Slegtenhorst M, van Ham T, Brooks AS, Dorresteijn EM, Barakat TS, Dahan K, Demoulin N, Goffin EJ, Olinger E, Larsen M, Hertz JM, Lilien MR, Obeidová L, Seeman T, Stone HK, Kerecuk L, Gurgu M, Yousef Yengej FA, Ammerlaan CME, Rookmaaker MB, Hanna C, Rogers RC, Duran K, Peters E, Sayer JA, van Haaften G, Harris PC, Ling K, Mason JM, van Eerde AM, Steet R. Certain heterozygous variants in the kinase domain of the serine/threonine kinase NEK8 can cause an autosomal dominant form of polycystic kidney disease. Kidney Int 2023; 104:995-1007. [PMID: 37598857 PMCID: PMC10592035 DOI: 10.1016/j.kint.2023.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/22/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) resulting from pathogenic variants in PKD1 and PKD2 is the most common form of PKD, but other genetic causes tied to primary cilia function have been identified. Biallelic pathogenic variants in the serine/threonine kinase NEK8 cause a syndromic ciliopathy with extra-kidney manifestations. Here we identify NEK8 as a disease gene for ADPKD in 12 families. Clinical evaluation was combined with functional studies using fibroblasts and tubuloids from affected individuals. Nek8 knockout mouse kidney epithelial (IMCD3) cells transfected with wild type or variant NEK8 were further used to study ciliogenesis, ciliary trafficking, kinase function, and DNA damage responses. Twenty-one affected monoallelic individuals uniformly exhibited cystic kidney disease (mostly neonatal) without consistent extra-kidney manifestations. Recurrent de novo mutations of the NEK8 missense variant p.Arg45Trp, including mosaicism, were seen in ten families. Missense variants elsewhere within the kinase domain (p.Ile150Met and p.Lys157Gln) were also identified. Functional studies demonstrated normal localization of the NEK8 protein to the proximal cilium and no consistent cilia formation defects in patient-derived cells. NEK8-wild type protein and all variant forms of the protein expressed in Nek8 knockout IMCD3 cells were localized to cilia and supported ciliogenesis. However, Nek8 knockout IMCD3 cells expressing NEK8-p.Arg45Trp and NEK8-p.Lys157Gln showed significantly decreased polycystin-2 but normal ANKS6 localization in cilia. Moreover, p.Arg45Trp NEK8 exhibited reduced kinase activity in vitro. In patient derived tubuloids and IMCD3 cells expressing NEK8-p.Arg45Trp, DNA damage signaling was increased compared to healthy passage-matched controls. Thus, we propose a dominant-negative effect for specific heterozygous missense variants in the NEK8 kinase domain as a new cause of PKD.
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Affiliation(s)
- Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Joshua L Turner
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Gisela G Slaats
- Department of Nephrology and Hypertension, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandra L Hawks
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Holly Mabillard
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Sujata Srikanth
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Raymond J Louie
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Josh Silver
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Chantal Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Frank Sleutels
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tjakko van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eiske M Dorresteijn
- Department of Pediatric Nephrology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Karin Dahan
- Institute Pathology and Genetic, Center of Human Genetics, Charleroi, Belgium
| | - Nathalie Demoulin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Jean Goffin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Olinger
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Martin Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marc R Lilien
- Department of Pediatric Nephrology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Lena Obeidová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tomas Seeman
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pediatrics, University Hospital Ostrava, Ostrava, Czech Republic; Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Hillarey K Stone
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Larissa Kerecuk
- Birmingham Women's and Children's National Health Services (NHS) Foundation Trust, National Institute for Health Care and Research (NIHR) Clinical Research Network (CRN) West Midlands, Birmingham, UK
| | - Mihai Gurgu
- Fundeni Clinical Institute, Bucharest, Romania
| | - Fjodor A Yousef Yengej
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Carola M E Ammerlaan
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Christian Hanna
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA; Division of Pediatric Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - R Curtis Rogers
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Karen Duran
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Edith Peters
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - John A Sayer
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK; National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Newcastle, UK
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter C Harris
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA.
| | - Jennifer M Mason
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA.
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Richard Steet
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA.
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11
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Rothé B, Ikawa Y, Zhang Z, Katoh TA, Kajikawa E, Minegishi K, Xiaorei S, Fortier S, Dal Peraro M, Hamada H, Constam DB. Bicc1 ribonucleoprotein complexes specifying organ laterality are licensed by ANKS6-induced structural remodeling of associated ANKS3. PLoS Biol 2023; 21:e3002302. [PMID: 37733651 PMCID: PMC10513324 DOI: 10.1371/journal.pbio.3002302] [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: 01/24/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023] Open
Abstract
Organ laterality of vertebrates is specified by accelerated asymmetric decay of Dand5 mRNA mediated by Bicaudal-C1 (Bicc1) on the left side, but whether binding of this or any other mRNA to Bicc1 can be regulated is unknown. Here, we found that a CRISPR-engineered truncation in ankyrin and sterile alpha motif (SAM)-containing 3 (ANKS3) leads to symmetric mRNA decay mediated by the Bicc1-interacting Dand5 3' UTR. AlphaFold structure predictions of protein complexes and their biochemical validation by in vitro reconstitution reveal a novel interaction of the C-terminal coiled coil domain of ANKS3 with Bicc1 that inhibits binding of target mRNAs, depending on the conformation of ANKS3 and its regulation by ANKS6. The dual regulation of RNA binding by mutually opposing structured protein domains in this multivalent protein network emerges as a novel mechanism linking associated laterality defects and possibly other ciliopathies to perturbed dynamics in Bicc1 ribonucleoparticle (RNP) formation.
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Affiliation(s)
- Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Lausanne, Switzerland
| | - Yayoi Ikawa
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Zhidian Zhang
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV IBI, Lausanne, Switzerland
| | - Takanobu A. Katoh
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Eriko Kajikawa
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Katsura Minegishi
- Department of Molecular Therapy, National Institutes of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Sai Xiaorei
- Department of Molecular Therapy, National Institutes of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Simon Fortier
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV IBI, Lausanne, Switzerland
| | - Hiroshi Hamada
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Daniel B. Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Lausanne, Switzerland
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12
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Leggatt GP, Seaby EG, Veighey K, Gast C, Gilbert RD, Ennis S. A Role for Genetic Modifiers in Tubulointerstitial Kidney Diseases. Genes (Basel) 2023; 14:1582. [PMID: 37628633 PMCID: PMC10454709 DOI: 10.3390/genes14081582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
With the increased availability of genomic sequencing technologies, the molecular bases for kidney diseases such as nephronophthisis and mitochondrially inherited and autosomal-dominant tubulointerstitial kidney diseases (ADTKD) has become increasingly apparent. These tubulointerstitial kidney diseases (TKD) are monogenic diseases of the tubulointerstitium and result in interstitial fibrosis and tubular atrophy (IF/TA). However, monogenic inheritance alone does not adequately explain the highly variable onset of kidney failure and extra-renal manifestations. Phenotypes vary considerably between individuals harbouring the same pathogenic variant in the same putative monogenic gene, even within families sharing common environmental factors. While the extreme end of the disease spectrum may have dramatic syndromic manifestations typically diagnosed in childhood, many patients present a more subtle phenotype with little to differentiate them from many other common forms of non-proteinuric chronic kidney disease (CKD). This review summarises the expanding repertoire of genes underpinning TKD and their known phenotypic manifestations. Furthermore, we collate the growing evidence for a role of modifier genes and discuss the extent to which these data bridge the historical gap between apparently rare monogenic TKD and polygenic non-proteinuric CKD (excluding polycystic kidney disease).
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Affiliation(s)
- Gary P. Leggatt
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Eleanor G. Seaby
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| | - Kristin Veighey
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Christine Gast
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
| | - Rodney D. Gilbert
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Department of Paediatric Nephrology, Southampton Children’s Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Sarah Ennis
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
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13
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Wang H, Zaiser F, Eckert P, Ruf J, Kayser N, Veenstra AC, Müller M, Haas R, Walz G, Yakulov TA. Inversin (NPHP2) and Vangl2 are required for normal zebrafish cloaca formation. Biochem Biophys Res Commun 2023; 673:9-15. [PMID: 37352572 DOI: 10.1016/j.bbrc.2023.06.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 05/31/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
Nephronophthisis (NPH), an autosomal recessive ciliopathy, results from mutations in more than 20 different genes (NPHPs). These gene products form protein complexes that regulate trafficking within the cilium, a microtubular structure that plays a crucial role in developmental processes. Several NPHPs, including NPHP2/Inversin, have been linked to extraciliary functions. In addition to defining a specific segment of primary cilia (Inversin compartment), NPHP2 participates in planar cell polarity (PCP) signaling along with Dishevelled and Vangl family members. We used the mutant zebrafish line invssa36157, containing a stop codon at amino acid 314, to characterize tissue-specific functions of zebrafish Nphp2. The invssa36157 line exhibits mild ciliopathy phenotypes and increased glomerular and cloaca cyst formation. These mutants showed enhanced susceptibility to the simultaneous depletion of the nphp1/nphp2/nphp8 module, known to be involved in the cytoskeletal organization of epithelial cells. Notably, simultaneous depletion of zebrafish nphp1 and vangl2 led to a pronounced increase in cloaca malformations in the invssa36157 mutant embryos. Time-lapse imaging showed that the pronephric cells correctly migrated towards the ectodermal cells in these embryos, but failed to form the cloaca opening. Despite these abnormal developments, cellular fate does not seem to be affected in nphp1 and vangl2 MO-depleted invssa36157 mutants, as shown by in situ hybridizations for markers of pronephros and ectodermal cell development. However, significantly reduced apoptotic activity was observed in this double knockdown model, signifying the role of apoptosis in cloacal morphogenesis. Our findings underscore the critical interplay of nphp1, nphp2/Inversin, and vangl2 in orchestrating normal cloaca formation in zebrafish, shedding light on the complex molecular mechanisms underlying ciliopathy-associated phenotypes.
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Affiliation(s)
- Hui Wang
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Friedemann Zaiser
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Priska Eckert
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Johannes Ruf
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Nicolas Kayser
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Anna C Veenstra
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Merle Müller
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Rebecca Haas
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Gerd Walz
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Albertstrasse 19, 79104, Freiburg, Germany
| | - Toma A Yakulov
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany.
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14
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Rothé B, Fortier S, Gagnieux C, Schmuziger C, Constam DB. Antagonistic interactions among structured domains in the multivalent Bicc1-ANKS3-ANKS6 protein network govern phase transitioning of target mRNAs. iScience 2023; 26:106855. [PMID: 37275520 PMCID: PMC10232731 DOI: 10.1016/j.isci.2023.106855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
The growing number of diseases linked to aberrant phase transitioning of ribonucleoproteins highlights the need to uncover how the interplay between multivalent protein and RNA interactions is regulated. Cytoplasmic granules of the RNA binding protein Bicaudal-C (Bicc1) are regulated by the ciliopathy proteins ankyrin (ANK) and sterile alpha motif (SAM) domain-containing ANKS3 and ANKS6, but whether and how target mRNAs are affected is unknown. Here, we show that head-to-tail polymers of Bicc1 nucleated by its SAM domain are interconnected by K homology (KH) domains in a protein meshwork that mediates liquid-to-gel transitioning of client transcripts. Moreover, while the dispersion of these granules by ANKS3 concomitantly released bound mRNAs, co-recruitment of ANKS6 by ANKS3 reinstated Bicc1 condensation and ribonucleoparticle assembly. RNA-independent Bicc1 polymerization and its dual regulation by ANKS3 and ANKS6 represent a new mechanism to couple the reversible immobilization of client mRNAs to controlled protein phase transitioning between distinct metastable states.
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Affiliation(s)
- Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Simon Fortier
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Céline Gagnieux
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Céline Schmuziger
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Daniel B. Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
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15
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Koslow M, Zhu P, McCabe C, Xu X, Lin X. Kidney transcriptome and cystic kidney disease genes in zebrafish. Front Physiol 2023; 14:1184025. [PMID: 37256068 PMCID: PMC10226271 DOI: 10.3389/fphys.2023.1184025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/20/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction: Polycystic kidney disease (PKD) is a condition where fluid filled cysts form on the kidney which leads to overall renal failure. Zebrafish has been recently adapted to study polycystic kidney disease, because of its powerful embryology and genetics. However, there are concerns on the conservation of this lower vertebrate in modeling polycystic kidney disease. Methods: Here, we aim to assess the molecular conservation of zebrafish by searching homologues polycystic kidney disease genes and carrying transcriptome studies in this animal. Results and Discussion: We found that out of 82 human cystic kidney disease genes, 81 have corresponding zebrafish homologs. While 75 of the genes have a single homologue, only 6 of these genes have two homologs. Comparison of the expression level of the transcripts enabled us to identify one homolog over the other homolog with >70% predominance, which would be prioritized for future experimental studies. Prompted by sexual dimorphism in human and rodent kidneys, we studied transcriptome between different sexes and noted significant differences in male vs. female zebrafish, indicating that sex dimorphism also occurs in zebrafish. Comparison between zebrafish and mouse identified 10% shared genes and 38% shared signaling pathways. String analysis revealed a cluster of genes differentially expressed in male vs. female zebrafish kidneys. In summary, this report demonstrated remarkable molecular conservation, supporting zebrafish as a useful animal model for cystic kidney disease.
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Affiliation(s)
- Matthew Koslow
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Ping Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Chantal McCabe
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
| | - Xueying Lin
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
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16
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Joseph BB, Naslavsky N, Binti S, Conquest S, Robison L, Bai G, Homer RO, Grant BD, Caplan S, Fay DS. Conserved NIMA kinases regulate multiple steps of endocytic trafficking. PLoS Genet 2023; 19:e1010741. [PMID: 37099601 PMCID: PMC10166553 DOI: 10.1371/journal.pgen.1010741] [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: 12/22/2022] [Revised: 05/08/2023] [Accepted: 04/11/2023] [Indexed: 04/27/2023] Open
Abstract
Human NIMA-related kinases have primarily been studied for their roles in cell cycle progression (NEK1/2/6/7/9), checkpoint-DNA-damage control (NEK1/2/4/5/10/11), and ciliogenesis (NEK1/4/8). We previously showed that Caenorhabditis elegans NEKL-2 (NEK8/9 homolog) and NEKL-3 (NEK6/7 homolog) regulate apical clathrin-mediated endocytosis (CME) in the worm epidermis and are essential for molting. Here we show that NEKL-2 and NEKL-3 also have distinct roles in controlling endosome function and morphology. Specifically, loss of NEKL-2 led to enlarged early endosomes with long tubular extensions but showed minimal effects on other compartments. In contrast, NEKL-3 depletion caused pronounced defects in early, late, and recycling endosomes. Consistently, NEKL-2 was strongly localized to early endosomes, whereas NEKL-3 was localized to multiple endosomal compartments. Loss of NEKLs also led to variable defects in the recycling of two resident cargoes of the trans-Golgi network (TGN), MIG-14/Wntless and TGN-38/TGN38, which were missorted to lysosomes after NEKL depletion. In addition, defects were observed in the uptake of clathrin-dependent (SMA-6/Type I BMP receptor) and independent cargoes (DAF-4/Type II BMP receptor) from the basolateral surface of epidermal cells after NEKL-2 or NEKL-3 depletion. Complementary studies in human cell lines further showed that siRNA knockdown of the NEKL-3 orthologs NEK6 and NEK7 led to missorting of the mannose 6-phosphate receptor from endosomes. Moreover, in multiple human cell types, depletion of NEK6 or NEK7 disrupted both early and recycling endosomal compartments, including the presence of excess tubulation within recycling endosomes, a defect also observed after NEKL-3 depletion in worms. Thus, NIMA family kinases carry out multiple functions during endocytosis in both worms and humans, consistent with our previous observation that human NEKL-3 orthologs can rescue molting and trafficking defects in C. elegans nekl-3 mutants. Our findings suggest that trafficking defects could underlie some of the proposed roles for NEK kinases in human disease.
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Affiliation(s)
- Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Naava Naslavsky
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Shaonil Binti
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Sylvia Conquest
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Lexi Robison
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Ge Bai
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Rafael O. Homer
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Barth D. Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Steve Caplan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
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17
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Grand K, Stoltz M, Rizzo L, Röck R, Kaminski MM, Salinas G, Getwan M, Naert T, Pichler R, Lienkamp SS. HNF1B Alters an Evolutionarily Conserved Nephrogenic Program of Target Genes. J Am Soc Nephrol 2023; 34:412-432. [PMID: 36522156 PMCID: PMC10103355 DOI: 10.1681/asn.2022010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
SIGNIFICANCE STATEMENT Mutations in hepatocyte nuclear factor-1 β ( HNF1B ) are the most common monogenic causes of congenital renal malformations. HNF1B is necessary to directly reprogram fibroblasts to induced renal tubule epithelial cells (iRECs) and, as we demonstrate, can induce ectopic pronephric tissue in Xenopus ectodermal organoids. Using these two systems, we analyzed the effect of HNF1B mutations found in patients with cystic dysplastic kidney disease. We found cross-species conserved targets of HNF1B, identified transcripts that are differentially regulated by the patient-specific mutant protein, and functionally validated novel HNF1B targets in vivo . These results highlight evolutionarily conserved transcriptional mechanisms and provide insights into the genetic circuitry of nephrogenesis. BACKGROUND Hepatocyte nuclear factor-1 β (HNF1B) is an essential transcription factor during embryogenesis. Mutations in HNF1B are the most common monogenic causes of congenital cystic dysplastic renal malformations. The direct functional consequences of mutations in HNF1B on its transcriptional activity are unknown. METHODS Direct reprogramming of mouse fibroblasts to induced renal tubular epithelial cells was conducted both with wild-type HNF1B and with patient mutations. HNF1B was expressed in Xenopus ectodermal explants. Transcriptomic analysis by bulk RNA-Seq identified conserved targets with differentially regulated expression by the wild-type or R295C mutant. CRISPR/Cas9 genome editing in Xenopus embryos evaluated transcriptional targets in vivo . RESULTS HNF1B is essential for reprogramming mouse fibroblasts to induced renal tubular epithelial cells and induces development of ectopic renal organoids from pluripotent Xenopus cells. The mutation R295C retains reprogramming and inductive capacity but alters the expression of specific sets of downstream target genes instead of diminishing overall transcriptional activity of HNF1B. Surprisingly, targets associated with polycystic kidney disease were less affected than genes affected in congenital renal anomalies. Cross-species-conserved transcriptional targets were dysregulated in hnf1b CRISPR-depleted Xenopus embryos, confirming their dependence on hnf1b . CONCLUSIONS HNF1B activates an evolutionarily conserved program of target genes that disease-causing mutations selectively disrupt. These findings provide insights into the renal transcriptional network that controls nephrogenesis.
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Affiliation(s)
- Kelli Grand
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Martine Stoltz
- The University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ludovica Rizzo
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Ruth Röck
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Michael M. Kaminski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | | | - Maike Getwan
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Thomas Naert
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Roman Pichler
- The University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Soeren S. Lienkamp
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
- The University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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18
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Biruete A, Chen NX, Metzger CE, Srinivasan S, O’Neill K, Fallen PB, Fonseca A, Wilson HE, de Loor H, Evenepoel P, Swanson KS, Allen MR, Moe SM. The Dietary Fermentable Fiber Inulin Alters the Intestinal Microbiome and Improves Chronic Kidney Disease Mineral-Bone Disorder in a Rat Model of CKD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526093. [PMID: 36778372 PMCID: PMC9915522 DOI: 10.1101/2023.01.29.526093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background Dietary fiber is important for a healthy diet, but intake is low in CKD patients and the impact this has on the manifestations of CKD-Mineral Bone Disorder (MBD) is unknown. Methods The Cy/+ rat with progressive CKD was fed a casein-based diet of 0.7% phosphate with 10% inulin (fermentable fiber) or cellulose (non-fermentable fiber) from 22 weeks to either 30 or 32 weeks of age (~30 and ~15 % of normal kidney function). We assessed CKD-MBD, cecal microbiota, and serum gut-derived uremic toxins. Two-way ANOVA was used to evaluate the effect of age and inulin diet, and their interaction. Results In CKD animals, dietary inulin led to changes in microbiota alpha and beta diversity at 30 and 32 weeks, with higher relative abundance of several taxa, including Bifidobacterium and Bacteroides , and lower Lactobacillus . Inulin reduced serum levels of gut-derived uremic toxins, phosphate, and parathyroid hormone, but not fibroblast growth factor-23. Dietary inulin decreased aorta and cardiac calcification and reduced left ventricular mass index and cardiac fibrosis. Bone turnover and cortical bone parameters were improved with inulin; however, bone mechanical properties were not altered. Conclusions The addition of the fermentable fiber inulin to the diet of CKD rats led to changes in the gut microbiota composition, lowered gut-derived uremic toxins, and improved most parameters of CKD-MBD. Future studies should assess this fiber as an additive therapy to other pharmacologic and diet interventions in CKD. Significance Statement Dietary fiber has well established beneficial health effects. However, the impact of fermentable dietary fiber on the intestinal microbiome and CKD-MBD is poorly understood. We used an animal model of progressive CKD and demonstrated that the addition of 10% of the fermentable fiber inulin to the diet altered the intestinal microbiota and lowered circulating gut-derived uremic toxins, phosphorus, and parathyroid hormone. These changes were associated with improved cortical bone parameters, lower vascular calcification, and reduced cardiac hypertrophy, fibrosis and calcification. Taken together, dietary fermentable fiber may be a novel additive intervention to traditional therapies of CKD-MBD.
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Park K, Leroux MR. Composition, organization and mechanisms of the transition zone, a gate for the cilium. EMBO Rep 2022; 23:e55420. [PMID: 36408840 PMCID: PMC9724682 DOI: 10.15252/embr.202255420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The cilium evolved to provide the ancestral eukaryote with the ability to move and sense its environment. Acquiring these functions required the compartmentalization of a dynein-based motility apparatus and signaling proteins within a discrete subcellular organelle contiguous with the cytosol. Here, we explore the potential molecular mechanisms for how the proximal-most region of the cilium, termed transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins and helps to ensure ciliary autonomy and homeostasis. These include a unique complement and spatial organization of proteins that span from the microtubule-based axoneme to the ciliary membrane; a protein picket fence; a specialized lipid microdomain; differential membrane curvature and thickness; and lastly, a size-selective molecular sieve. In addition, the TZ must be permissive for, and functionally integrates with, ciliary trafficking systems (including intraflagellar transport) that cross the barrier and make the ciliary compartment dynamic. The quest to understand the TZ continues and promises to not only illuminate essential aspects of human cell signaling, physiology, and development, but also to unravel how TZ dysfunction contributes to ciliopathies that affect multiple organ systems, including eyes, kidney, and brain.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
- Present address:
Terry Fox LaboratoryBC CancerVancouverBCCanada
- Present address:
Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Michel R Leroux
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
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20
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Boettcher S, Simons M. Model organisms for functional validation in genetic renal disease. MED GENET-BERLIN 2022; 34:287-296. [PMID: 38836086 PMCID: PMC11006349 DOI: 10.1515/medgen-2022-2162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Functional validation is key for establishing new disease genes in human genetics. Over the years, model organisms have been utilized in a very effective manner to prove causality of genes or genetic variants for a wide variety of diseases. Also in hereditary renal disease, model organisms are very helpful for functional validation of candidate genes and variants identified by next-generation sequencing strategies and for obtaining insights into the pathophysiology. Due to high genetic conservation as well as high anatomical and physiological similarities with the human kidney, almost all genetic kidney diseases can be studied in the mouse. However, mouse work is time consuming and expensive, so there is a need for alternative models. In this review, we will provide an overview of model organisms used in renal research, focusing on mouse, zebrafish, frog, and fruit flies.
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Affiliation(s)
- Susanne Boettcher
- Sektion Nephrogenetik, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Matias Simons
- Sektion Nephrogenetik, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
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21
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Volkova YL, Pickel C, Jucht AE, Wenger RH, Scholz CC. The Asparagine Hydroxylase FIH: A Unique Oxygen Sensor. Antioxid Redox Signal 2022; 37:913-935. [PMID: 35166119 DOI: 10.1089/ars.2022.0003] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Limited oxygen availability (hypoxia) commonly occurs in a range of physiological and pathophysiological conditions, including embryonic development, physical exercise, inflammation, and ischemia. It is thus vital for cells and tissues to monitor their local oxygen availability to be able to adjust in case the oxygen supply is decreased. The cellular oxygen sensor factor inhibiting hypoxia-inducible factor (FIH) is the only known asparagine hydroxylase with hypoxia sensitivity. FIH uniquely combines oxygen and peroxide sensitivity, serving as an oxygen and oxidant sensor. Recent Advances: FIH was first discovered in the hypoxia-inducible factor (HIF) pathway as a modulator of HIF transactivation activity. Several other FIH substrates have now been identified outside the HIF pathway. Moreover, FIH enzymatic activity is highly promiscuous and not limited to asparagine hydroxylation. This includes the FIH-mediated catalysis of an oxygen-dependent stable (likely covalent) bond formation between FIH and selected substrate proteins (called oxomers [oxygen-dependent stable protein oligomers]). Critical Issues: The (patho-)physiological function of FIH is only beginning to be understood and appears to be complex. Selective pharmacologic inhibition of FIH over other oxygen sensors is possible, opening new avenues for therapeutic targeting of hypoxia-associated diseases, increasing the interest in its (patho-)physiological relevance. Future Directions: The contribution of FIH enzymatic activity to disease development and progression should be analyzed in more detail, including the assessment of underlying molecular mechanisms and relevant FIH substrate proteins. Also, the molecular mechanism(s) involved in the physiological functions of FIH remain(s) to be determined. Furthermore, the therapeutic potential of recently developed FIH-selective pharmacologic inhibitors will need detailed assessment. Antioxid. Redox Signal. 37, 913-935.
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Affiliation(s)
- Yulia L Volkova
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Christina Pickel
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Roland H Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Carsten C Scholz
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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22
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Zhu H, Zhao ZH, Zhu SY, Xiong F, He LH, Zhang Y, Wang J. Renal-hepatic-pancreatic dysplasia-1 with a novel NPHP3 genotype: a case report and review of the literature. BMC Pediatr 2022; 22:603. [PMID: 36253741 PMCID: PMC9578240 DOI: 10.1186/s12887-022-03659-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Renal-hepatic-pancreatic dysplasia type 1 (RHPD1) is a rare sporadic and autosomal recessive disorder with unknown incidence. RHPD1 is caused by biallelic pathogenic variants in NPHP3, which encode nephrocystin, an important component of the ciliary protein complex. CASE PRESENTATION In this case report, we describe a male newborn who was confirmed by ultrasound to have renal enlargement with multiple cysts, pancreatic enlargement with cysts, and increased liver echogenicity, leading to the clinical diagnosis of RHPD. In addition, a compound heterozygous pathogenic variant, namely, NPHP3 c.1761G > A (p. W587*) and the c.69delC (p. Gly24Ala24*11) variant, was detected by WES. The patient was clinically and genetically diagnosed with RHPD1. At 34 h of life, the infant died of respiratory insufficiency. CONCLUSION This is the first published case of RHPD1 in China. This study broadens the known range of RHPD1 due to NPHP3 pathogenic variants.
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Affiliation(s)
- Hui Zhu
- Department of Pediatrics, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Zhi-Hui Zhao
- Department of Neonatology, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Shu-Yao Zhu
- Department of Pediatrics, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Fu Xiong
- Department of Pediatrics, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Li-Hong He
- Ultrasonic Department, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Yong Zhang
- Department of Neonatology, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China.
| | - Jin Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
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23
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Biruete A, Metzger CE, Chen NX, Swallow EA, Vrabec C, Clinkenbeard EL, Stacy AJ, Srinivasan S, O'Neill K, Avin KG, Allen MR, Moe SM. Effects of ferric citrate and intravenous iron sucrose on markers of mineral, bone, and iron homeostasis in a rat model of CKD-MBD. Nephrol Dial Transplant 2022; 37:1857-1867. [PMID: 35482713 PMCID: PMC9494145 DOI: 10.1093/ndt/gfac162] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Anemia and chronic kidney disease-mineral and bone disorder (CKD-MBD) are common and begin early in CKD. Limited studies have concurrently compared the effects of ferric citrate (FC) versus intravenous (IV) iron on CKD-MBD and iron homeostasis in moderate CKD. METHODS We tested the effects of 10 weeks of 2% FC versus IV iron sucrose in rats with moderate CKD (Cy/+ male rat) and untreated normal (NL) littermates. Outcomes included a comprehensive assessment of CKD-MBD, iron homeostasis and oxidative stress. RESULTS CKD rats had azotemia, elevated phosphorus, parathyroid hormone and fibroblast growth factor-23 (FGF23). Compared with untreated CKD rats, treatment with FC led to lower plasma phosphorus, intact FGF23 and a trend (P = 0.07) toward lower C-terminal FGF23. FC and IV iron equally reduced aorta and heart calcifications to levels similar to NL animals. Compared with NL animals, CKD animals had higher bone turnover, lower trabecular volume and no difference in mineralization; these were unaffected by either iron treatment. Rats treated with IV iron had cortical and bone mechanical properties similar to NL animals. FC increased the transferrin saturation rate compared with untreated CKD and NL rats. Neither iron treatment increased oxidative stress above that of untreated CKD. CONCLUSIONS Oral FC improved phosphorus homeostasis, some iron-related parameters and the production and cleavage of FGF23. The intermittent effect of low-dose IV iron sucrose on cardiovascular calcification and bone should be further explored in moderate-advanced CKD.
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Affiliation(s)
- Annabel Biruete
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Nutrition and Dietetics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Corinne E Metzger
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Neal X Chen
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Elizabeth A Swallow
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Curtis Vrabec
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- College of Osteopathic Medicine, Marian University, Indianapolis, IN, USA
| | - Erica L Clinkenbeard
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alexander J Stacy
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shruthi Srinivasan
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kalisha O'Neill
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Keith G Avin
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Physical Therapy, Indiana University School of Health and Human Sciences, Indiana University, Indianapolis, IN, USA
| | - Matthew R Allen
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Roudebush Veterans Affairs Medical Center, Indianapolis, IN, IN, USA
| | - Sharon M Moe
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Roudebush Veterans Affairs Medical Center, Indianapolis, IN, IN, USA
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24
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Li ZD, Abuduxikuer K, Wang L, Hao CZ, Zhang J, Wang MX, Li LT, Qiu YL, Xie XB, Lu Y, Wang JS. Defining pathogenicity of NOTCH2 variants for diagnosis of Alagille syndrome type 2 using a large cohort of patients. Liver Int 2022; 42:1836-1848. [PMID: 35567760 DOI: 10.1111/liv.15292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/09/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Alagille syndrome (ALGS) type 2 caused by mutations in NOTCH2 has genotypic and phenotypic heterogeneity. Diagnosis in some atypical patients with isolated hepatic presentation could be missed. METHODS Using 2087 patients with paediatric liver manifestations, NOTCH2 allele frequencies, in-silico prediction, protein domains and clinical features were analysed to define the pathogenicity of NOTCH2 variants for diagnosis of ALGS type 2. RESULTS Among 2087 patients with paediatric liver manifestations, significantly more NOTCH2 variants were absent in gnomAD in patients with elevated γ-glutamyltransferase (GGT) (p = .041). Significantly more NOTCH2 variants which were absent in gnomAD were located in protein functional domains (p = .038). When missense variants were absent in gnomAD and predicted to be pathogenic by at least three out of seven in-silico tools, they were found to be significantly associated with liver manifestations with elevated GGT (p = .003). Comparing this to patients with likely benign (LB) variants, the patients with likely-pathogenic (LP) variants have significantly more liver manifestations with elevated GGT (p = .0001). Significantly more patients with LP variants had extra-hepatic phenotypes of ALGS compared with those patients with LB variants (p = .0004). CONCLUSION When NOTCH2 variants are absent in gnomAD, null variants and missense variants which were predicted to be pathogenic by at least three in-silico tools could be considered pathogenic in patients with high GGT chronic liver diseases.
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Affiliation(s)
- Zhong-Die Li
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Kuerbanjiang Abuduxikuer
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Li Wang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Chen-Zhi Hao
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Jing Zhang
- Department of Pediatrics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Meng-Xuan Wang
- Department of Pediatrics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Li-Ting Li
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Yi-Ling Qiu
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Xin-Bao Xie
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Yi Lu
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Jian-She Wang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defect, Shanghai, China
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25
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Kayser N, Zaiser F, Veenstra AC, Wang H, Göcmen B, Eckert P, Franz H, Köttgen A, Walz G, Yakulov TA. Clock genes rescue nphp mutations in zebrafish. Hum Mol Genet 2022; 31:4143-4158. [PMID: 35861640 PMCID: PMC9759334 DOI: 10.1093/hmg/ddac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 01/21/2023] Open
Abstract
The zebrafish pronephros model, using morpholino oligonucleotides (MO) to deplete target genes, has been extensively used to characterize human ciliopathy phenotypes. Recently, discrepancies between MO and genetically defined mutants have questioned this approach. We analyzed zebrafish with mutations in the nphp1-4-8 module to determine the validity of MO-based results. While MO-mediated depletion resulted in glomerular cyst and cloaca malformation, these ciliopathy-typical manifestations were observed at a much lower frequency in zebrafish embryos with defined nphp mutations. All nphp1-4-8 mutant zebrafish were viable and displayed decreased manifestations in the next (F2) generation, lacking maternal RNA contribution. While genetic compensation was further supported by the observation that nphp4-deficient mutants became partially refractory to MO-based nphp4 depletion, zebrafish embryos, lacking one nphp gene, became more sensitive to MO-based depletion of additional nphp genes. Transcriptome analysis of nphp8 mutant embryos revealed an upregulation of the circadian clock genes cry1a and cry5. MO-mediated depletion of cry1a and cry5 caused ciliopathy phenotypes in wild-type embryos, while cry1a and cry5 depletion in maternal zygotic nphp8 mutant embryos increased the frequency of glomerular cysts compared to controls. Importantly, cry1a and cry5 rescued the nephropathy-related phenotypes in nphp1, nphp4 or nphp8-depleted zebrafish embryos. Our results reveal that nphp mutant zebrafish resemble the MO-based phenotypes, albeit at a much lower frequency. Rapid adaption through upregulation of circadian clock genes seems to ameliorate the loss of nphp genes, contributing to phenotypic differences.
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Affiliation(s)
| | | | | | | | - Burulca Göcmen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79106, Germany
| | - Priska Eckert
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Henriette Franz
- Department of Biomedicine, University of Basel, Pestalozzistr. 20, Basel CH-4056, Switzerland
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79106, Germany
| | - Gerd Walz
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Albertstrasse 19, Freiburg 79104, Germany
| | - Toma A Yakulov
- To whom correspondence should be addressed. Tel: +49 76127063036;
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26
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Van De Weghe JC, Gomez A, Doherty D. The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies. Annu Rev Genomics Hum Genet 2022; 23:301-329. [PMID: 35655331 DOI: 10.1146/annurev-genom-121321-093528] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Joubert syndrome (JS), Meckel syndrome (MKS), and nephronophthisis (NPH) ciliopathy spectrum could be the poster child for advances and challenges in Mendelian human genetics over the past half century. Progress in understanding these conditions illustrates many core concepts of human genetics. The JS phenotype alone is caused by pathogenic variants in more than 40 genes; remarkably, all of the associated proteins function in and around the primary cilium. Primary cilia are near-ubiquitous, microtubule-based organelles that play crucial roles in development and homeostasis. Protruding from the cell, these cellular antennae sense diverse signals and mediate Hedgehog and other critical signaling pathways. Ciliary dysfunction causes many human conditions termed ciliopathies, which range from multiple congenital malformations to adult-onset single-organ failure. Research on the genetics of the JS-MKS-NPH spectrum has spurred extensive functional work exploring the broadly important role of primary cilia in health and disease. This functional work promises to illuminate the mechanisms underlying JS-MKS-NPH in humans, identify therapeutic targets across genetic causes, and generate future precision treatments. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Arianna Gomez
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA;
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA;
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27
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König JC, Karsay R, Gerß J, Schlingmann KP, Dahmer-Heath M, Telgmann AK, Kollmann S, Ariceta G, Gillion V, Bockenhauer D, Bertholet-Thomas A, Mastrangelo A, Boyer O, Lilien M, Decramer S, Schanstra J, Pohl M, Schild R, Weber S, Hoefele J, Drube J, Cetiner M, Hansen M, Thumfart J, Tönshoff B, Habbig S, Liebau MC, Bald M, Bergmann C, Pennekamp P, Konrad M. Refining Kidney Survival in 383 Genetically Characterized Patients With Nephronophthisis. Kidney Int Rep 2022; 7:2016-2028. [PMID: 36090483 PMCID: PMC9459005 DOI: 10.1016/j.ekir.2022.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction Nephronophthisis (NPH) comprises a group of rare disorders accounting for up to 10% of end-stage kidney disease (ESKD) in children. Prediction of kidney prognosis poses a major challenge. We assessed differences in kidney survival, impact of variant type, and the association of clinical characteristics with declining kidney function. Methods Data was obtained from 3 independent sources, namely the network for early onset cystic kidney diseases clinical registry (n = 105), an online survey sent out to the European Reference Network for Rare Kidney Diseases (n = 60), and a literature search (n = 218). Results A total of 383 individuals were available for analysis: 116 NPHP1, 101 NPHP3, 81 NPHP4 and 85 NPHP11/TMEM67 patients. Kidney survival differed between the 4 cohorts with a highly variable median age at onset of ESKD as follows: NPHP3, 4.0 years (interquartile range 0.3–12.0); NPHP1, 13.5 years (interquartile range 10.5–16.5); NPHP4, 16.0 years (interquartile range 11.0–25.0); and NPHP11/TMEM67, 19.0 years (interquartile range 8.7–28.0). Kidney survival was significantly associated with the underlying variant type for NPHP1, NPHP3, and NPHP4. Multivariate analysis for the NPHP1 cohort revealed growth retardation (hazard ratio 3.5) and angiotensin-converting enzyme inhibitor (ACEI) treatment (hazard ratio 2.8) as 2 independent factors associated with an earlier onset of ESKD, whereas arterial hypertension was linked to an accelerated glomerular filtration rate (GFR) decline. Conclusion The presented data will enable clinicians to better estimate kidney prognosis of distinct patients with NPH and thereby allow personalized counseling.
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Nardozi D, Palumbo S, Khan AUM, Sticht C, Bieback K, Sadeghi S, Kluth MA, Keese M, Gretz N. Potential Therapeutic Effects of Long-Term Stem Cell Administration: Impact on the Gene Profile and Kidney Function of PKD/Mhm (Cy/+) Rats. J Clin Med 2022; 11:jcm11092601. [PMID: 35566725 PMCID: PMC9102853 DOI: 10.3390/jcm11092601] [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: 04/11/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Cystic kidney disease (CKD) is a heterogeneous group of genetic disorders and one of the most common causes of end-stage renal disease. Here, we investigate the potential effects of long-term human stem cell treatment on kidney function and the gene expression profile of PKD/Mhm (Cy/+) rats. Human adipose-derived stromal cells (ASC) and human skin-derived ABCB5+ stromal cells (2 × 106) were infused intravenously or intraperitoneally monthly, over 6 months. Additionally, ASC and ABCB5+-derived conditioned media were administrated intraperitoneally. The gene expression profile results showed a significant reprogramming of metabolism-related pathways along with downregulation of the cAMP, NF-kB and apoptosis pathways. During the experimental period, we measured the principal renal parameters as well as renal function using an innovative non-invasive transcutaneous device. All together, these analyses show a moderate amelioration of renal function in the ABCB5+ and ASC-treated groups. Additionally, ABCB5+ and ASC-derived conditioned media treatments lead to milder but still promising improvements. Even though further analyses have to be performed, the preliminary results obtained in this study can lay the foundations for a novel therapeutic approach with the application of cell-based therapy in CKD.
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Affiliation(s)
- Daniela Nardozi
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer, 68167 Mannheim, Germany; (D.N.); (S.P.); (A.u.M.K.); (C.S.)
- Vascular Surgery, University Hospital Mannheim, 68167 Mannheim, Germany;
| | - Stefania Palumbo
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer, 68167 Mannheim, Germany; (D.N.); (S.P.); (A.u.M.K.); (C.S.)
| | - Arif ul Maula Khan
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer, 68167 Mannheim, Germany; (D.N.); (S.P.); (A.u.M.K.); (C.S.)
| | - Carsten Sticht
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer, 68167 Mannheim, Germany; (D.N.); (S.P.); (A.u.M.K.); (C.S.)
| | - Karen Bieback
- Institute of Transfusion Medicine and Immunology, Mannheim Institute of Innate Immunoscience, German Red Cross Blood Service Baden-Württemberg—Hessen, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany;
| | - Samar Sadeghi
- RHEACELL GmbH & Co.KG/TICEBA GmbH, 69120 Heidelberg, Germany; (S.S.); (M.A.K.)
| | - Mark Andreas Kluth
- RHEACELL GmbH & Co.KG/TICEBA GmbH, 69120 Heidelberg, Germany; (S.S.); (M.A.K.)
| | - Michael Keese
- Vascular Surgery, University Hospital Mannheim, 68167 Mannheim, Germany;
| | - Norbert Gretz
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer, 68167 Mannheim, Germany; (D.N.); (S.P.); (A.u.M.K.); (C.S.)
- Correspondence:
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Yasunaga T, Wiegel J, Bergen MD, Helmstädter M, Epting D, Paolini A, Çiçek Ö, Radziwill G, Engel C, Brox T, Ronneberger O, Walentek P, Ulbrich MH, Walz G. Microridge-like structures anchor motile cilia. Nat Commun 2022; 13:2056. [PMID: 35440631 PMCID: PMC9018822 DOI: 10.1038/s41467-022-29741-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 03/30/2022] [Indexed: 01/11/2023] Open
Abstract
Several tissues contain cells with multiple motile cilia that generate a fluid or particle flow to support development and organ functions; defective motility causes human disease. Developmental cues orient motile cilia, but how cilia are locked into their final position to maintain a directional flow is not understood. Here we find that the actin cytoskeleton is highly dynamic during early development of multiciliated cells (MCCs). While apical actin bundles become increasingly more static, subapical actin filaments are nucleated from the distal tip of ciliary rootlets. Anchorage of these subapical actin filaments requires the presence of microridge-like structures formed during MCC development, and the activity of Nonmuscle Myosin II. Optogenetic manipulation of Ezrin, a core component of the microridge actin-anchoring complex, or inhibition of Myosin Light Chain Kinase interfere with rootlet anchorage and orientation. These observations identify microridge-like structures as an essential component of basal body rootlet anchoring in MCCs.
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Affiliation(s)
- Takayuki Yasunaga
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Johannes Wiegel
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Max D Bergen
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Martin Helmstädter
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Daniel Epting
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Andrea Paolini
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Özgün Çiçek
- Pattern Recognition and Image Processing, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 52, 79110, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Gerald Radziwill
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Christina Engel
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Thomas Brox
- Pattern Recognition and Image Processing, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 52, 79110, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Olaf Ronneberger
- Pattern Recognition and Image Processing, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 52, 79110, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Peter Walentek
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Maximilian H Ulbrich
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Gerd Walz
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany.
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany.
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Djenoune L, Berg K, Brueckner M, Yuan S. A change of heart: new roles for cilia in cardiac development and disease. Nat Rev Cardiol 2022; 19:211-227. [PMID: 34862511 PMCID: PMC10161238 DOI: 10.1038/s41569-021-00635-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 12/27/2022]
Abstract
Although cardiac abnormalities have been observed in a growing class of human disorders caused by defective primary cilia, the function of cilia in the heart remains an underexplored area. The primary function of cilia in the heart was long thought to be restricted to left-right axis patterning during embryogenesis. However, new findings have revealed broad roles for cilia in congenital heart disease, valvulogenesis, myocardial fibrosis and regeneration, and mechanosensation. In this Review, we describe advances in our understanding of the mechanisms by which cilia function contributes to cardiac left-right axis development and discuss the latest findings that highlight a broader role for cilia in cardiac development. Specifically, we examine the growing line of evidence connecting cilia function to the pathogenesis of congenital heart disease. Furthermore, we also highlight research from the past 10 years demonstrating the role of cilia function in common cardiac valve disorders, including mitral valve prolapse and aortic valve disease, and describe findings that implicate cardiac cilia in mechanosensation potentially linking haemodynamic and contractile forces with genetic regulation of cardiac development and function. Finally, given the presence of cilia on cardiac fibroblasts, we also explore the potential role of cilia in fibrotic growth and summarize the evidence implicating cardiac cilia in heart regeneration.
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Affiliation(s)
- Lydia Djenoune
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kathryn Berg
- Department of Paediatrics, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Martina Brueckner
- Department of Paediatrics, Yale University School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Shiaulou Yuan
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Airik M, McCourt B, Ozturk TT, Huynh AB, Zhang X, Tometich JT, Topaloglu R, Ozen H, Orhan D, Nejak-Bowen K, Monga SP, Hand TW, Ozaltin F, Airik R. Mitigation of portal fibrosis and cholestatic liver disease in ANKS6-deficient livers by macrophage depletion. FASEB J 2022; 36:e22157. [PMID: 35032404 PMCID: PMC8852242 DOI: 10.1096/fj.202101387r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/19/2021] [Accepted: 12/27/2021] [Indexed: 02/03/2023]
Abstract
Congenital hepatic fibrosis (CHF) is a developmental liver disease that is caused by mutations in genes that encode ciliary proteins and is characterized by bile duct dysplasia and portal fibrosis. Recent work has demonstrated that mutations in ANKS6 can cause CHF due to its role in bile duct development. Here, we report a novel ANKS6 mutation, which was identified in an infant presenting with neonatal jaundice due to underlying biliary abnormalities and liver fibrosis. Molecular analysis revealed that ANKS6 liver pathology is associated with the infiltration of inflammatory macrophages to the periportal fibrotic tissue and ductal epithelium. To further investigate the role of macrophages in CHF pathophysiology, we generated a novel liver-specific Anks6 knockout mouse model. The mutant mice develop biliary abnormalities and rapidly progressing periportal fibrosis reminiscent of human CHF. The development of portal fibrosis in Anks6 KO mice coincided with the accumulation of inflammatory monocytes and macrophages in the mutant liver. Gene expression and flow cytometric analysis demonstrated the preponderance of M1- over M2-like macrophages at the onset of fibrosis. A critical role for macrophages in promoting peribiliary fibrosis was demonstrated by depleting the macrophages with clodronate liposomes which effectively reduced inflammatory gene expression and fibrosis, and ameliorated tissue histology and biliary function in Anks6 KO livers. Together, this study demonstrates that macrophages play an important role in the initiation of liver fibrosis in ANKS6-deficient livers and their therapeutic elimination may provide an avenue to mitigate CHF in patients.
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Affiliation(s)
- Merlin Airik
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Blake McCourt
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tugba Tastemel Ozturk
- Division of Pediatric Nephrology, Department of Pediatrics, Hacettepe University, Ankara, Turkey
| | - Amy B Huynh
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaoyi Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Justin T Tometich
- R.K. Mellon Institute for Pediatric Research, Department of Pediatrics, Division of Infectious Disease, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, 15224
| | - Rezan Topaloglu
- Division of Pediatric Nephrology, Department of Pediatrics, Hacettepe University, Ankara, Turkey
| | - Hasan Ozen
- Division of Gastroenterology, Department of Pediatrics, Hacettepe University, Ankara, Turkey
| | - Diclehan Orhan
- Pediatric Pathology Unit, Department of Pediatrics, Hacettepe University, Ankara, Turkey
| | - Kari Nejak-Bowen
- Department of Pathology and Pittsburgh Liver Research Center, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Satdarshan P Monga
- Department of Pathology and Pittsburgh Liver Research Center, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Timothy W Hand
- R.K. Mellon Institute for Pediatric Research, Department of Pediatrics, Division of Infectious Disease, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, 15224
| | - Fatih Ozaltin
- Division of Pediatric Nephrology, Department of Pediatrics, Hacettepe University, Ankara, Turkey,Nephrogenetics Laboratory, Division of Pediatric Nephrology, Department of Pediatrics, Hacettepe University, Ankara, Turkey
| | - Rannar Airik
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Corresponding Author: Name: Rannar Airik, PhD, Address: UPMC Children’s Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA, , Tel.: +1 (412) 692-6229, Fax.: +1 (412) 692-7816
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OUP accepted manuscript. Hum Mol Genet 2022; 31:2295-2306. [DOI: 10.1093/hmg/ddac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
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Afsar B, Afsar RE, Demiray A, Altay S, Korkmaz H, Yildiz A, Covic A, Ortiz A, Kanbay M. OUP accepted manuscript. Clin Kidney J 2022; 15:1275-1283. [PMID: 35756735 PMCID: PMC9217633 DOI: 10.1093/ckj/sfac029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 11/15/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent hereditary kidney disease. Recent evidence suggests that the pathogenesis of ADPKD is a complex web of abnormal cellular processes including altered cell signaling, disordered cell metabolism, impaired autophagy, increased apoptosis, mitochondrial dysfunction and chronic inflammation. Sodium–glucose cotransporter (SGLT) inhibitors (SGLTi) reduce body weight, blood pressure and blood glucose levels, have kidney and cardiovascular protective activity, and have been reported to decrease inflammation, increase autophagy and improve mitochondrial dysfunction. We now review results from preclinical studies on SGLTi for ADPKD identified through a systematic search of the MEDLINE, Cochrane Library, Embase and PubMed databases. Potential underlying mechanisms for the conflicting results reported as well as implications for clinical translation are discussed, as ADPKD patients were excluded from clinical trials exploring kidney protection by SGLT2 inhibitors (SGLT2i). However, they were not excluded from cardiovascular safety trials or trials for cardiovascular conditions. A post-hoc analysis of the kidney function trajectories and safety of SGLT2i in ADPKD patients enrolled in such trials may provide additional information. In conclusion, SGLT2i are cardio- and nephroprotective in diverse clinical situations. Currently, it is unclear whether ADPKD patients may benefit from SGLT2i in terms of kidney function preservation, and their safety in this population remains unexplored. We propose a roadmap to address this unmet clinical need.
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Affiliation(s)
- Baris Afsar
- Department of Medicine, Division of Nephrology, Suleyman Demirel University School of Medicine, Isparta, Turkey
| | - Rengin Elsurer Afsar
- Department of Medicine, Division of Nephrology, Suleyman Demirel University School of Medicine, Isparta, Turkey
| | - Atalay Demiray
- Department of Medicine, Koc University School of Medicine, Istanbul, Turkey
| | - Sevval Altay
- Department of Medicine, Koc University School of Medicine, Istanbul, Turkey
| | - Hakan Korkmaz
- Department of Medicine, Division of Endocrinology, Suleyman Demirel University School of Medicine, Isparta, Turkey
| | - Abdulmecit Yildiz
- Department of Medicine, Division of Nephrology, Uludag University School of Medicine, Bursa, Turkey
| | - Adrian Covic
- Nephrology Clinic, Dialysis and Renal Transplant Center, ‘C.I. PARHON’ University Hospital, and ‘Grigore T. Popa’ University of Medicine, Iasi, Romania
| | - Alberto Ortiz
- Department of Medicine, Universidad Autonoma de Madrid and IIS-Fundacion Jimenez Diaz, Madrid, Spain
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Hoshino Y, Sonoda H, Mikoda N, Ikeda M. Upregulation of NADPH Oxidase 2 Contributes to Renal Fibrosis in pcy Mice: An Experimental Model of Nephronophthisis. Nephron Clin Pract 2021; 146:393-403. [DOI: 10.1159/000520697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 10/29/2021] [Indexed: 11/19/2022] Open
Abstract
<b><i>Background:</i></b> DBA/2FG-<i>pcy</i> (<i>pcy</i>) mice harbor a homozygous <i>Nphp3</i> missense mutation and develop nephronophthisis with renal interstitial fibrosis. Previous studies have shown that aberrant oxygen homeostasis contributes to the renal pathology in <i>pcy</i> mice, but the underlying molecular mechanism remains largely unknown. <b><i>Methods:</i></b> <i>pcy</i> mice and a control strain, DBA/2N (DBA) mice, were used. Renal levels of 62 mRNAs involved in oxygen homeostasis were investigated by real-time PCR, and the resulting data were used for extraction of pathological pathways. On the basis of the genes found to be upregulated and pathway analysis, further studies were performed using immunoblotting, immunohistochemistry, and pharmacological intervention. <b><i>Results:</i></b> In comparison with DBA mice, the levels of 18 mRNAs were altered by >2-fold in <i>pcy</i> mice. Pathway analysis extracted molecular pathways related to oxidative stress, inflammation, and cell adhesion. As the levels of mRNAs relevant to the NADPH oxidase 2 (NOX2) pathway were prominently (4 genes >5-fold) increased in <i>pcy</i> mice, we further analyzed the molecules related to this pathway. A time course study suggested that the pathway was gradually activated in <i>pcy</i> mice from at least 5 weeks of age. Immunohistochemistry study revealed that NOX2 protein was colocalized with a macrophage marker protein in the renal interstitium. Moreover, treatment of <i>pcy</i> mice with apocynin, an inhibitor of the NOX2 pathway, ameliorated the renal fibrosis. <b><i>Conclusion:</i></b> Our findings suggest that the activation of the NOX2 pathway, possibly mediated by macrophage infiltration, plays a pivotal role in progressive renal fibrosis in <i>pcy</i> mice.
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Schwarz H, Popp B, Airik R, Torabi N, Knaup KX, Stoeckert J, Wiech T, Amann K, Reis A, Schiffer M, Wiesener MS, Schueler M. Biallelic ANKS6 mutations cause late onset ciliopathy with chronic kidney disease through YAP dysregulation. Hum Mol Genet 2021; 31:1357-1369. [PMID: 34740236 DOI: 10.1093/hmg/ddab322] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Nephronophthisis-related ciliopathies (NPHP-RC) comprises a group of inherited kidney diseases, caused by mutations in genes encoding proteins localizing to primary cilia. NPHP-RC represent the one of the most frequent monogenic causes of renal failure within the first three decades of life, but its molecular disease mechanisms remains unclear. Here, we identified biallelic ANKS6 mutations in two affected siblings with late onset chronic kidney disease by whole exome sequencing. We employed patient derived fibroblasts generating an in vitro model to study the precise biological impact of distinct human ANKS6 mutations, completed by immunohistochemistry studies on renal biopsy samples. Functional studies using patient derived cells showed an impaired integrity of the ciliary Inversin compartment with reduced cilia length. Further analyses demonstrated that ANKS6 deficiency leads to a dysregulation of Hippo-signaling through nuclear YAP imbalance, and disrupted ciliary localization of YAP. Additionally an altered transcriptional activity of canonical Wnt target genes and altered expression of non-phosphorylated (active) β-catenin and phosphorylated GSK3β were observed. Upon ciliation ANKS6 deficiency revealed a deranged subcellular localization and expression of components of the endocytic recycling compartment. Our results demonstrate that ANKS6 plays a key role in regulating the Hippo pathway and ANKS6 deficiency is linked to dysregulation of signaling pathways. Our study provides molecular clues in understanding pathophysiological mechanisms of NPHP-RC and may offer new therapeutic targets.
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Affiliation(s)
- Hannah Schwarz
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Bernt Popp
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, 04103, Germany.,Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Rannar Airik
- Department of Pediatrics, Division of Nephrology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, 15224, USA
| | - Nasrin Torabi
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Karl X Knaup
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Johanna Stoeckert
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Thorsten Wiech
- Institute of Pathology, Nephropathology Section, University Hospital Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology, University of Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Michael S Wiesener
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Markus Schueler
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
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Gupta S, Ozimek-Kulik JE, Phillips JK. Nephronophthisis-Pathobiology and Molecular Pathogenesis of a Rare Kidney Genetic Disease. Genes (Basel) 2021; 12:genes12111762. [PMID: 34828368 PMCID: PMC8623546 DOI: 10.3390/genes12111762] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The exponential rise in our understanding of the aetiology and pathophysiology of genetic cystic kidney diseases can be attributed to the identification of cystogenic genes over the last three decades. The foundation of this was laid by positional cloning strategies which gradually shifted towards next-generation sequencing (NGS) based screenings. This shift has enabled the discovery of novel cystogenic genes at an accelerated pace unlike ever before and, most notably, the past decade has seen the largest increase in identification of the genes which cause nephronophthisis (NPHP). NPHP is a monogenic autosomal recessive cystic kidney disease caused by mutations in a diverse clade of over 26 identified genes and is the most common genetic cause of renal failure in children. NPHP gene types present with some common pathophysiological features alongside a diverse range of extra-renal phenotypes associated with specific syndromic presentations. This review provides a timely update on our knowledge of this disease, including epidemiology, pathophysiology, anatomical and molecular features. We delve into the diversity of the NPHP causing genes and discuss known molecular mechanisms and biochemical pathways that may have possible points of intersection with polycystic kidney disease (the most studied renal cystic pathology). We delineate the pathologies arising from extra-renal complications and co-morbidities and their impact on quality of life. Finally, we discuss the current diagnostic and therapeutic modalities available for disease management, outlining possible avenues of research to improve the prognosis for NPHP patients.
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Affiliation(s)
- Shabarni Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- Correspondence:
| | - Justyna E. Ozimek-Kulik
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia
- Department of Paediatric Nephrology, Sydney Children’s Hospital Network, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Jacqueline Kathleen Phillips
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
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Naert T, Çiçek Ö, Ogar P, Bürgi M, Shaidani NI, Kaminski MM, Xu Y, Grand K, Vujanovic M, Prata D, Hildebrandt F, Brox T, Ronneberger O, Voigt FF, Helmchen F, Loffing J, Horb ME, Willsey HR, Lienkamp SS. Deep learning is widely applicable to phenotyping embryonic development and disease. Development 2021; 148:273338. [PMID: 34739029 PMCID: PMC8602947 DOI: 10.1242/dev.199664] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Genome editing simplifies the generation of new animal models for congenital disorders. However, the detailed and unbiased phenotypic assessment of altered embryonic development remains a challenge. Here, we explore how deep learning (U-Net) can automate segmentation tasks in various imaging modalities, and we quantify phenotypes of altered renal, neural and craniofacial development in Xenopus embryos in comparison with normal variability. We demonstrate the utility of this approach in embryos with polycystic kidneys (pkd1 and pkd2) and craniofacial dysmorphia (six1). We highlight how in toto light-sheet microscopy facilitates accurate reconstruction of brain and craniofacial structures within X. tropicalis embryos upon dyrk1a and six1 loss of function or treatment with retinoic acid inhibitors. These tools increase the sensitivity and throughput of evaluating developmental malformations caused by chemical or genetic disruption. Furthermore, we provide a library of pre-trained networks and detailed instructions for applying deep learning to the reader's own datasets. We demonstrate the versatility, precision and scalability of deep neural network phenotyping on embryonic disease models. By combining light-sheet microscopy and deep learning, we provide a framework for higher-throughput characterization of embryonic model organisms. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Thomas Naert
- Institute of Anatomy, University of Zurich, Zurich 8057, Switzerland; Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich 8057, Switzerland
| | - Özgün Çiçek
- Department of Computer Science, Albert-Ludwigs-University, Freiburg 79100, Germany
| | - Paulina Ogar
- Institute of Anatomy, University of Zurich, Zurich 8057, Switzerland; Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich 8057, Switzerland
| | - Max Bürgi
- Institute of Anatomy, University of Zurich, Zurich 8057, Switzerland; Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich 8057, Switzerland
| | - Nikko-Ideen Shaidani
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Michael M Kaminski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 10115, Germany.,Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Kelli Grand
- Institute of Anatomy, University of Zurich, Zurich 8057, Switzerland; Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich 8057, Switzerland
| | - Marko Vujanovic
- Institute of Anatomy, University of Zurich, Zurich 8057, Switzerland; Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich 8057, Switzerland
| | - Daniel Prata
- Institute of Anatomy, University of Zurich, Zurich 8057, Switzerland; Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich 8057, Switzerland
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115,USA
| | - Thomas Brox
- Department of Computer Science, Albert-Ludwigs-University, Freiburg 79100, Germany
| | - Olaf Ronneberger
- Department of Computer Science, Albert-Ludwigs-University, Freiburg 79100, Germany.,BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University, Freiburg, Germany.,DeepMind, London WC2H 8AG , UK
| | - Fabian F Voigt
- Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Zurich 8057, Switzerland; Neuroscience Center Zurich, Zurich 8057, Switzerland
| | - Fritjof Helmchen
- Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Zurich 8057, Switzerland; Neuroscience Center Zurich, Zurich 8057, Switzerland
| | - Johannes Loffing
- Institute of Anatomy, University of Zurich, Zurich 8057, Switzerland; Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich 8057, Switzerland
| | - Marko E Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Soeren S Lienkamp
- Institute of Anatomy, University of Zurich, Zurich 8057, Switzerland; Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH), Zurich 8057, Switzerland
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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease. Proc Natl Acad Sci U S A 2021; 118:2106770118. [PMID: 34548398 PMCID: PMC8488674 DOI: 10.1073/pnas.2106770118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic analysis identified ttc30a as a ciliopathy network component, and targeting it replicated skeletal malformations and renal cysts as seen in patients and the amphibian models. A loss of Ttc30a affected cilia by altering posttranslational tubulin modifications. Our findings identify TTC30A/B as a component of ciliary segmentation essential for cartilage differentiation and renal tubulogenesis. These findings may lead to novel therapeutic targets in treating ciliary skeletopathies and cystic kidney disease. Skeletal ciliopathies (e.g., Jeune syndrome, short rib polydactyly syndrome, and Sensenbrenner syndrome) are frequently associated with nephronophthisis-like cystic kidney disease and other organ manifestations. Despite recent progress in genetic mapping of causative loci, a common molecular mechanism of cartilage defects and cystic kidneys has remained elusive. Targeting two ciliary chondrodysplasia loci (ift80 and ift172) by CRISPR/Cas9 mutagenesis, we established models for skeletal ciliopathies in Xenopus tropicalis. Froglets exhibited severe limb deformities, polydactyly, and cystic kidneys, closely matching the phenotype of affected patients. A data mining–based in silico screen found ttc30a to be related to known skeletal ciliopathy genes. CRISPR/Cas9 targeting replicated limb malformations and renal cysts identical to the models of established disease genes. Loss of Ttc30a impaired embryonic renal excretion and ciliogenesis because of altered posttranslational tubulin acetylation, glycylation, and defective axoneme compartmentalization. Ttc30a/b transcripts are enriched in chondrocytes and osteocytes of single-cell RNA-sequenced embryonic mouse limbs. We identify TTC30A/B as an essential node in the network of ciliary chondrodysplasia and nephronophthisis-like disease proteins and suggest that tubulin modifications and cilia segmentation contribute to skeletal and renal ciliopathy manifestations of ciliopathies in a cell type–specific manner. These findings have implications for potential therapeutic strategies.
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Airik M, Schüler M, McCourt B, Weiss AC, Herdman N, Lüdtke TH, Widmeier E, Stolz DB, Nejak-Bowen KN, Yimlamai D, Wu YL, Kispert A, Airik R, Hildebrandt F. Loss of Anks6 leads to YAP deficiency and liver abnormalities. Hum Mol Genet 2021; 29:3064-3080. [PMID: 32886109 PMCID: PMC7733532 DOI: 10.1093/hmg/ddaa197] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 07/03/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022] Open
Abstract
ANKS6 is a ciliary protein that localizes to the proximal compartment of the primary cilium, where it regulates signaling. Mutations in the ANKS6 gene cause multiorgan ciliopathies in humans, which include laterality defects of the visceral organs, renal cysts as part of nephronophthisis and congenital hepatic fibrosis (CHF) in the liver. Although CHF together with liver ductal plate malformations are common features of several human ciliopathy syndromes, including nephronophthisis-related ciliopathies, the mechanism by which mutations in ciliary genes lead to bile duct developmental abnormalities is not understood. Here, we generated a knockout mouse model of Anks6 and show that ANKS6 function is required for bile duct morphogenesis and cholangiocyte differentiation. The loss of Anks6 causes ciliary abnormalities, ductal plate remodeling defects and periportal fibrosis in the liver. Our expression studies and biochemical analyses show that biliary abnormalities in Anks6-deficient livers result from the dysregulation of YAP transcriptional activity in the bile duct-lining epithelial cells. Mechanistically, our studies suggest, that ANKS6 antagonizes Hippo signaling in the liver during bile duct development by binding to Hippo pathway effector proteins YAP1, TAZ and TEAD4 and promoting their transcriptional activity. Together, this study reveals a novel function for ANKS6 in regulating Hippo signaling during organogenesis and provides mechanistic insights into the regulatory network controlling bile duct differentiation and morphogenesis during liver development.
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Affiliation(s)
- Merlin Airik
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Markus Schüler
- Division of Nephrology and Internal Intensive Care Medicine, Charite University, Berlin, Germany.,Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
| | - Blake McCourt
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Nathan Herdman
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Eugen Widmeier
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.,Department of Medicine, Renal Division, Medical Center - University of Freiburg, Freiburg, Germany
| | - Donna B Stolz
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kari N Nejak-Bowen
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dean Yimlamai
- Division of Gastroenterology and Nutrition, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yijen L Wu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Rannar Airik
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Cordido A, Vizoso-Gonzalez M, Garcia-Gonzalez MA. Molecular Pathophysiology of Autosomal Recessive Polycystic Kidney Disease. Int J Mol Sci 2021; 22:6523. [PMID: 34204582 PMCID: PMC8235086 DOI: 10.3390/ijms22126523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is a rare disorder and one of the most severe forms of polycystic kidney disease, leading to end-stage renal disease (ESRD) in childhood. PKHD1 is the gene that is responsible for the vast majority of ARPKD. However, some cases have been related to a new gene that was recently identified (DZIP1L gene), as well as several ciliary genes that can mimic a ARPKD-like phenotypic spectrum. In addition, a number of molecular pathways involved in the ARPKD pathogenesis and progression were elucidated using cellular and animal models. However, the function of the ARPKD proteins and the molecular mechanism of the disease currently remain incompletely understood. Here, we review the clinics, treatment, genetics, and molecular basis of ARPKD, highlighting the most recent findings in the field.
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Affiliation(s)
- Adrian Cordido
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (A.C.); (M.V.-G.)
- Grupo de Medicina Xenómica, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
| | - Marta Vizoso-Gonzalez
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (A.C.); (M.V.-G.)
- Grupo de Medicina Xenómica, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
| | - Miguel A. Garcia-Gonzalez
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (A.C.); (M.V.-G.)
- Grupo de Medicina Xenómica, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
- Fundación Publica Galega de Medicina Xenómica-SERGAS, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
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41
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Hu H, Zhang J, Qiu W, Liang C, Li C, Wei T, Feng Z, Guo Q, Yang K, Liu Z. Comprehensive strategy improves the genetic diagnosis of different polycystic kidney diseases. J Cell Mol Med 2021; 25:6318-6332. [PMID: 34032358 PMCID: PMC8256360 DOI: 10.1111/jcmm.16608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/26/2021] [Indexed: 12/16/2022] Open
Abstract
Polycystic kidney disease (PKD) is known to occur in three main forms, namely autosomal dominant PKD (ADPKD), autosomal recessive PKD (ARPKD) and syndromic PKD (SPKD), based on the clinical manifestations and genetic causes, which are diagnosable from the embryo stage to the later stages of life. Selection of the genetic test for the individuals with diagnostic imaging reports of cystic kidneys without a family history of the disease continues to be a challenge in clinical practice. With the objective of maintaining a limit on the time and medical cost of the procedure, a practical strategy for genotyping and targeted validation to resolve cystogene variations was developed in our clinical laboratory, which combined the techniques of whole-exome sequencing (WES), Long-range PCR (LR-PCR), Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) to work in a stepwise approach. In this context, twenty-six families with renal polycystic disorders were enrolled in the present study. Thirty-two variants involving four ciliary genes (PKD1, PKHD1, TMEM67 and TMEM107) were identified and verified in 23 families (88.5%, 23/26), which expanded the variant spectrum by 16 novel variants. Pathogenic variations in five foetuses of six families diagnosed with PKD were identified using prenatal ultrasound imaging. Constitutional biallelic and digenic variations constituted the pathogenic patterns in these foetuses. The preliminary clinical data highlighted that the WES + LR PCR-based workflow followed in the present study is efficient in detecting divergent variations in PKD. The biallelic and digenic mutations were revealed as the main pathogenic patterns in the foetuses with PKD.
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Affiliation(s)
- Hua‐Ying Hu
- Department of OphthalmologyXiang'an Hospital of Xiamen UniversityFujian Provincial Key Laboratory of Ophthalmology and Visual ScienceSchool of Medicine, Xiamen UniversityFujian Engineering and Research Center of Eye Regenerative MedicineEye Institute of Xiamen UniversityXiamenChina
- Jiaen Genetics LaboratoryBeijing Jiaen HospitalBeijingChina
| | - Jing Zhang
- Prenatal Diagnosis CenterShijiazhuang Obstetrics and Gynecology HospitalHebeiChina
| | - Wei Qiu
- Department of UrologyBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Chao Liang
- Department of Pediatric OrthopedicsShijiazhuang Obstetrics and Gynecology HospitalHebeiChina
| | - Cun‐Xi Li
- Jiaen Genetics LaboratoryBeijing Jiaen HospitalBeijingChina
| | - Tian‐Ying Wei
- Jiaen Genetics LaboratoryBeijing Jiaen HospitalBeijingChina
| | - Zhan‐Ke Feng
- Jiaen Genetics LaboratoryBeijing Jiaen HospitalBeijingChina
| | - Qing Guo
- Prenatal Diagnosis CenterShijiazhuang Obstetrics and Gynecology HospitalHebeiChina
| | - Kai Yang
- Prenatal Diagnosis CenterBeijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijingChina
| | - Zu‐Guo Liu
- Department of OphthalmologyXiang'an Hospital of Xiamen UniversityFujian Provincial Key Laboratory of Ophthalmology and Visual ScienceSchool of Medicine, Xiamen UniversityFujian Engineering and Research Center of Eye Regenerative MedicineEye Institute of Xiamen UniversityXiamenChina
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Stokman MF, Saunier S, Benmerah A. Renal Ciliopathies: Sorting Out Therapeutic Approaches for Nephronophthisis. Front Cell Dev Biol 2021; 9:653138. [PMID: 34055783 PMCID: PMC8155538 DOI: 10.3389/fcell.2021.653138] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in in vitro and/or in vivo models. Despite identification of numerous candidate drugs in rodent models, there has been a lack of clinical trials and there is currently no therapy that halts disease progression in NPH patients. This review covers the most important findings of therapeutic approaches in NPH model systems to date, including hypothesis-driven therapies and untargeted drug screens, approached from the pathophysiology of NPH. Importantly, most animal models used in these studies represent the cystic infantile form of NPH, which is less prevalent than the juvenile form. It appears therefore important to develop new models relevant for juvenile/adult NPH. Alternative non-orthologous animal models and developments in patient-based in vitro model systems are discussed, as well as future directions in personalized therapy for NPH.
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Affiliation(s)
- Marijn F Stokman
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Sophie Saunier
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Alexandre Benmerah
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
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43
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Molecular genetics of renal ciliopathies. Biochem Soc Trans 2021; 49:1205-1220. [PMID: 33960378 DOI: 10.1042/bst20200791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/25/2022]
Abstract
Renal ciliopathies are a heterogenous group of inherited disorders leading to an array of phenotypes that include cystic kidney disease and renal interstitial fibrosis leading to progressive chronic kidney disease and end-stage kidney disease. The renal tubules are lined with epithelial cells that possess primary cilia that project into the lumen and act as sensory and signalling organelles. Mutations in genes encoding ciliary proteins involved in the structure and function of primary cilia cause ciliopathy syndromes and affect many organ systems including the kidney. Recognised disease phenotypes associated with primary ciliopathies that have a strong renal component include autosomal dominant and recessive polycystic kidney disease and their various mimics, including atypical polycystic kidney disease and nephronophthisis. The molecular investigation of inherited renal ciliopathies often allows a precise diagnosis to be reached where renal histology and other investigations have been unhelpful and can help in determining kidney prognosis. With increasing molecular insights, it is now apparent that renal ciliopathies form a continuum of clinical phenotypes with disease entities that have been classically described as dominant or recessive at both extremes of the spectrum. Gene-dosage effects, hypomorphic alleles, modifier genes and digenic inheritance further contribute to the genetic complexity of these disorders. This review will focus on recent molecular genetic advances in the renal ciliopathy field with a focus on cystic kidney disease phenotypes and the genotypes that lead to them. We discuss recent novel insights into underlying disease mechanisms of renal ciliopathies that might be amenable to therapeutic intervention.
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Doornbos C, Roepman R. Moonlighting of mitotic regulators in cilium disassembly. Cell Mol Life Sci 2021; 78:4955-4972. [PMID: 33860332 PMCID: PMC8233288 DOI: 10.1007/s00018-021-03827-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/03/2021] [Accepted: 03/27/2021] [Indexed: 02/07/2023]
Abstract
Correct timing of cellular processes is essential during embryological development and to maintain the balance between healthy proliferation and tumour formation. Assembly and disassembly of the primary cilium, the cell’s sensory signalling organelle, are linked to cell cycle timing in the same manner as spindle pole assembly and chromosome segregation. Mitotic processes, ciliary assembly, and ciliary disassembly depend on the centrioles as microtubule-organizing centres (MTOC) to regulate polymerizing and depolymerizing microtubules. Subsequently, other functional protein modules are gathered to potentiate specific protein–protein interactions. In this review, we show that a significant subset of key mitotic regulator proteins is moonlighting at the cilium, among which PLK1, AURKA, CDC20, and their regulators. Although ciliary assembly defects are linked to a variety of ciliopathies, ciliary disassembly defects are more often linked to brain development and tumour formation. Acquiring a better understanding of the overlap in regulators of ciliary disassembly and mitosis is essential in finding therapeutic targets for the different diseases and types of tumours associated with these regulators.
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Affiliation(s)
- Cenna Doornbos
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. .,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Mandato C, Siano MA, Nazzaro L, Gelzo M, Francalanci P, Rizzo F, D'Agostino Y, Morleo M, Brillante S, Weisz A, Franco B, Vajro P. A ZFYVE19 gene mutation associated with neonatal cholestasis and cilia dysfunction: case report with a novel pathogenic variant. Orphanet J Rare Dis 2021; 16:179. [PMID: 33853651 PMCID: PMC8048179 DOI: 10.1186/s13023-021-01775-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background ZFYVE19 (Zinc Finger FYVE-Type Containing 19) mutations have most recently been associated to a novel type of high gamma-glutamyl transpeptidase (GGT), non-syndromic, neonatal-onset intrahepatic chronic cholestasis possibly associated to cilia dysfunction. Herein, we report a new case with further studies of whole exome sequencing (WES) and immunofluorescence in primary cilia of her cultured fibroblasts which confirm the observation. Results A now 5-year-old girl born to clinically healthy consanguineous Moroccan parents was assessed at 59 days of life due to severe cholestatic jaundice with increased serum bile acids and GGT, and preserved hepatocellular synthetic function. Despite fibrosis/cirrhosis and biliary ducts proliferation on liver biopsy suggested an extrahepatic biliary obstacle, normal intra-operatory cholangiography excluded biliary atresia. Under choleretic treatment, she maintained a clinically stable anicteric cholestasis but developped hyperlipidemia. After exclusion of the main causes of cholestasis by multiple tests, abnormal concentrations of sterols and WES led to a diagnosis of hereditary sitosterolemia (OMIM #618666), likely unrelated to her cholestasis. Further sequencing investigation revealed a homozygous non-sense mutation (p.Arg223Ter) in ZFYVE19 leading to a 222 aa truncated protein and present in both heterozygous parents. Immunofluorescence analysis of primary cilia on cultured skin fibroblasts showed a ciliary phenotype mainly defined by fragmented cilia and centrioles abnormalities. Conclusions Our findings are consistent with and expands the recent evidence linking ZFYVE19 to a novel, likely non-syndromic, high GGT-PFIC phenotype with neonatal onset. Due to the possible role of ZFYVE19 in cilia function and the unprecedented coexistence of a coincidental hereditary sterol disorder in our case, continuous monitoring will be necessary to substantiate type of liver disease progression and/or possible emergence of a multisystemic involvement. What mentioned above confirms that the application of WES in children with undiagnosed cholestasis may lead to the identification of new causative genes, widening the knowledge on the pathophysiology. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01775-8.
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Affiliation(s)
- Claudia Mandato
- Department of Pediatrics, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Maria Anna Siano
- Postgraduate School of Pediatrics Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via Allende, 84081, Baronissi, (SA), Italy
| | - Lucia Nazzaro
- Pediatric Clinic, "SS. Giovanni Di Dio and Ruggi D'Aragona" University of Salerno Hospital, Via San Leonardo, 84131, Salerno, Italy
| | - Monica Gelzo
- Department of Molecular Medicine and Medical Biotechnology, Faculty of Medicine, University of Naples Federico II, Naples, Italy
| | - Paola Francalanci
- Pathology Unit. Department of Laboratories, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
| | - Francesca Rizzo
- Medical Genomics Program, "SS. Giovanni Di Dio and Ruggi D'Aragona" University of Salerno Hospital, Salerno, Italy.,Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno and Genome Research Center for Health (CRGS), Baronissi, (SA), Italy
| | - Ylenia D'Agostino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno and Genome Research Center for Health (CRGS), Baronissi, (SA), Italy
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Simona Brillante
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Alessandro Weisz
- Medical Genomics Program, "SS. Giovanni Di Dio and Ruggi D'Aragona" University of Salerno Hospital, Salerno, Italy.,Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno and Genome Research Center for Health (CRGS), Baronissi, (SA), Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.,Medical Genetics, Department of Medical Translational Science, Faculty of Medicine, University of Naples "Federico II", Naples, Italy
| | - Pietro Vajro
- Postgraduate School of Pediatrics Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via Allende, 84081, Baronissi, (SA), Italy. .,Pediatric Clinic, "SS. Giovanni Di Dio and Ruggi D'Aragona" University of Salerno Hospital, Via San Leonardo, 84131, Salerno, Italy.
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46
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Primary cilia and the DNA damage response: linking a cellular antenna and nuclear signals. Biochem Soc Trans 2021; 49:829-841. [PMID: 33843966 DOI: 10.1042/bst20200751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/17/2022]
Abstract
The maintenance of genome stability involves integrated biochemical activities that detect DNA damage or incomplete replication, delay the cell cycle, and direct DNA repair activities on the affected chromatin. These processes, collectively termed the DNA damage response (DDR), are crucial for cell survival and to avoid disease, particularly cancer. Recent work has highlighted links between the DDR and the primary cilium, an antenna-like, microtubule-based signalling structure that extends from a centriole docked at the cell surface. Ciliary dysfunction gives rise to a range of complex human developmental disorders termed the ciliopathies. Mutations in ciliopathy genes have been shown to impact on several functions that relate to centrosome integrity, DNA damage signalling, responses to problems in DNA replication and the control of gene expression. This review covers recent findings that link cilia and the DDR and explores the various roles played by key genes in these two contexts. It outlines how proteins encoded by ciliary genes impact checkpoint signalling, DNA replication and repair, gene expression and chromatin remodelling. It discusses how these diverse activities may integrate nuclear responses with those that affect a structure of the cell periphery. Additional directions for exploration of the interplay between these pathways are highlighted, with a focus on new ciliary gene candidates that alter genome stability.
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47
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Epting D, Senaratne LDS, Ott E, Holmgren A, Sumathipala D, Larsen SM, Wallmeier J, Bracht D, Frikstad KM, Crowley S, Sikiric A, Barøy T, Käsmann‐Kellner B, Decker E, Decker C, Bachmann N, Patzke S, Phelps IG, Katsanis N, Giles R, Schmidts M, Zucknick M, Lienkamp SS, Omran H, Davis EE, Doherty D, Strømme P, Frengen E, Bergmann C, Misceo D. Loss of CBY1 results in a ciliopathy characterized by features of Joubert syndrome. Hum Mutat 2020; 41:2179-2194. [PMID: 33131181 PMCID: PMC7756669 DOI: 10.1002/humu.24127] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/31/2020] [Accepted: 10/04/2020] [Indexed: 12/17/2022]
Abstract
Ciliopathies are clinically and genetically heterogeneous diseases. We studied three patients from two independent families presenting with features of Joubert syndrome: abnormal breathing pattern during infancy, developmental delay/intellectual disability, cerebellar ataxia, molar tooth sign on magnetic resonance imaging scans, and polydactyly. We identified biallelic loss-of-function (LOF) variants in CBY1, segregating with the clinical features of Joubert syndrome in the families. CBY1 localizes to the distal end of the mother centriole, contributing to the formation and function of cilia. In accordance with the clinical and mutational findings in the affected individuals, we demonstrated that depletion of Cby1 in zebrafish causes ciliopathy-related phenotypes. Levels of CBY1 transcript were found reduced in the patients compared with controls, suggesting degradation of the mutated transcript through nonsense-mediated messenger RNA decay. Accordingly, we could detect CBY1 protein in fibroblasts from controls, but not from patients by immunofluorescence. Furthermore, we observed reduced ability to ciliate, increased ciliary length, and reduced levels of the ciliary proteins AHI1 and ARL13B in patient fibroblasts. Our data show that CBY1 LOF-variants cause a ciliopathy with features of Joubert syndrome.
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Affiliation(s)
- Daniel Epting
- Department of Medicine IV, Faculty of MedicineMedical Center‐University of FreiburgFreiburgGermany
| | | | - Elisabeth Ott
- Department of Medicine IV, Faculty of MedicineMedical Center‐University of FreiburgFreiburgGermany
| | - Asbjørn Holmgren
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
| | - Dulika Sumathipala
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
| | - Selma M. Larsen
- Division of Pediatric and Adolescent MedicineOslo University Hospital, University of OsloOsloNorway
| | - Julia Wallmeier
- Klinik für Kinder‐ und JugendmedizinUniversitätsklinikum MünsterMünsterGermany
| | - Diana Bracht
- Klinik für Kinder‐ und JugendmedizinUniversitätsklinikum MünsterMünsterGermany
| | - Kari‐Anne M. Frikstad
- Department of Radiation Biology, Division of Cancer Medicine, Surgery and Transplantation, Institute for Cancer ResearchOslo University Hospitals–Norwegian Radium HospitalOsloNorway
| | - Suzanne Crowley
- Division of Pediatric and Adolescent MedicineOslo University Hospital, University of OsloOsloNorway
| | - Alma Sikiric
- Department of NeurohabilitationOslo University HospitalOsloNorway
| | - Tuva Barøy
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
| | - Barbara Käsmann‐Kellner
- Section of Pediatric Ophthalmology and Low Vision, Department of OphthalmologyUniversity of SaarlandHomburgGermany
| | - Eva Decker
- Medizinische Genetik MainzLimbach GeneticsMainzGermany
| | | | | | - Sebastian Patzke
- Department of Radiation Biology, Division of Cancer Medicine, Surgery and Transplantation, Institute for Cancer ResearchOslo University Hospitals–Norwegian Radium HospitalOsloNorway
| | - Ian G. Phelps
- Department of Pediatrics, Seattle Children's Research InstituteUniversity of WashingtonSeattleWashingtonUSA
| | - Nicholas Katsanis
- Center for Human Disease ModelingDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Rachel Giles
- Department of Nephrology and HypertensionUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Miriam Schmidts
- International Radboud Institute for Molecular Life SciencesRadboud University NijmegenNijmegenThe Netherlands
| | - Manuela Zucknick
- Oslo Centre for Biostatistics and Epidemiology, Institute for Basic Medical SciencesUniversity of OsloOsloNorway
| | | | - Heymut Omran
- Klinik für Kinder‐ und JugendmedizinUniversitätsklinikum MünsterMünsterGermany
| | - Erica E. Davis
- Center for Human Disease ModelingDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Dan Doherty
- Department of Pediatrics, Seattle Children's Research InstituteUniversity of WashingtonSeattleWashingtonUSA
| | - Petter Strømme
- Division of Pediatric and Adolescent MedicineOslo University Hospital, University of OsloOsloNorway
| | - Eirik Frengen
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
| | - Carsten Bergmann
- Department of Medicine IV, Faculty of MedicineMedical Center‐University of FreiburgFreiburgGermany
- Medizinische Genetik MainzLimbach GeneticsMainzGermany
| | - Doriana Misceo
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
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48
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Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules. Sci Rep 2020; 10:15954. [PMID: 32994509 PMCID: PMC7524721 DOI: 10.1038/s41598-020-72905-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Mutations of cilia-associated molecules cause multiple developmental defects that are collectively termed ciliopathies. However, several ciliary proteins, involved in gating access to the cilium, also assume localizations at other cellular sites including the nucleus, where they participate in DNA damage responses to maintain tissue integrity. Molecular insight into how these molecules execute such diverse functions remains limited. A mass spectrometry screen for ANKS6-interacting proteins suggested an involvement of ANKS6 in RNA processing and/or binding. Comparing the RNA-binding properties of the known RNA-binding protein BICC1 with the three ankyrin-repeat proteins ANKS3, ANKS6 (NPHP16) and INVERSIN (NPHP2) confirmed that certain nephronophthisis (NPH) family members can interact with RNA molecules. We also observed that BICC1 and INVERSIN associate with stress granules in response to translational inhibition. Furthermore, BICC1 recruits ANKS3 and ANKS6 into TIA-1-positive stress granules after exposure to hippuristanol. Our findings uncover a novel function of NPH family members, and provide further evidence that NPH family members together with BICC1 are involved in stress responses to maintain tissue and organ integrity.
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49
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Dahmer-Heath M, Schriever V, Kollmann S, Schleithoff C, Titieni A, Cetiner M, Patzer L, Tönshoff B, Hansen M, Pennekamp P, Gerß J, Konrad M, König J. Systematic evaluation of olfaction in patients with hereditary cystic kidney diseases/renal ciliopathies. J Med Genet 2020; 58:629-636. [PMID: 32917769 DOI: 10.1136/jmedgenet-2020-107192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/01/2020] [Accepted: 07/12/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Hereditary cystic kidney diseases such as nephronophthisis, polycystic kidney disease and Bardet-Biedl syndrome (BBS) are caused by a dysfunction of primary cilia. Cilia are involved in a variety of cellular functions and perceptions, with one of them being the sense of smell. Hyposmia is a typical feature found in patients with BBS. However, reports of olfactory dysfunction in other cystic kidney diseases are sparse. Here we provide a systematic survey on olfaction in a large cohort of patients displaying genetically determined renal ciliopathies. METHODS We performed a match-controlled systematic olfactory evaluation in a group of 75 patients with a defined genetic background using age adapted and validated odour identification tests. RESULTS Test results revealed a significant olfactory deficit in patients carrying TMEM67 variants (n=4), while all other genetic disorders causing nephronophthisis (n=25) or polycystic kidney disease (n=18) were not associated with an impaired sense of smell. Also in patients with BBS, olfactory performance was depending on the underlying molecular defect. While defects in the BBS1 gene (n=9) had no impact on the sense of smell, all other BBS gene disorders (n=19) were associated with significant hyposmia. Noteworthy, there was no correlation of the olfactory deficit with the level of renal impairment. CONCLUSION Hyposmia is a part of the clinical spectrum of BBS and of other renal ciliopathies. Depending on the genetic background, clinicians should be aware of this subtle and so far underappreciated symptom when clinically assessing patients with BBS or TMEM67 gene variants.
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Affiliation(s)
- Mareike Dahmer-Heath
- University Children's Hospital, Department of General Pediatrics, Universitätsklinikum Münster, Münster, Germany
| | - Valentin Schriever
- Abteilung für Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Dresden, Germany
| | - Sabine Kollmann
- University Children's Hospital, Department of General Pediatrics, Universitätsklinikum Münster, Münster, Germany
| | - Carolin Schleithoff
- University Children's Hospital, Department of General Pediatrics, Universitätsklinikum Münster, Münster, Germany
| | - Andrea Titieni
- University Children's Hospital, Department of General Pediatrics, Universitätsklinikum Münster, Münster, Nordrhein-Westfalen, Germany
| | - Metin Cetiner
- Department of Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Ludwig Patzer
- Children's Hospital St. Elisabeth and St. Barbara, Halle (Saale), Germany
| | - Burkhard Tönshoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | | | - Petra Pennekamp
- University Children's Hospital, Department of General Pediatrics, Universitätsklinikum Münster, Münster, Germany
| | - Joachim Gerß
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Martin Konrad
- University Children's Hospital, Department of General Pediatrics, Universitätsklinikum Münster, Münster, Germany
| | - Jens König
- University Children's Hospital, Department of General Pediatrics, Universitätsklinikum Münster, Münster, Germany
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50
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Wilson PC, Love-Gregory L, Corliss M, McNulty S, Heusel JW, Gaut JP. Beyond Panel-Based Testing: Exome Analysis Increases Sensitivity for Diagnosis of Genetic Kidney Disease. KIDNEY360 2020; 1:772-780. [PMID: 35372954 PMCID: PMC8815744 DOI: 10.34067/kid.0001342020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/12/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Next-generation sequencing (NGS) is a useful tool for evaluating patients with suspected genetic kidney disease. Clinical practice relies on the use of targeted gene panels that are ordered based on patient presentation. We compare the diagnostic yield of clinical panel-based testing to exome analysis. METHODS In total, 324 consecutive patients underwent physician-ordered, panel-based NGS testing between December 2014 and October 2018. Gene panels were available for four clinical phenotypes, including atypical hemolytic uremic syndrome (n=224), nephrotic syndrome (n=56), cystic kidney disease (n=26), and Alport syndrome (n=13). Variants were analyzed and clinical reports were signed out by a pathologist or clinical geneticist at the time of testing. Subsequently, all patients underwent retrospective exome analysis to detect additional clinically significant variants in kidney disease genes that were not analyzed as part of the initial clinical gene panel. Resulting variants were classified according to the American College of Medical Genetics and Genomics 2015 guidelines. RESULTS In the initial physician-ordered gene panels, we identified clinically significant pathogenic or likely pathogenic variants in 13% of patients (n=42/324). CFHR3-CFHR1 homozygous deletion was detected in an additional 13 patients with aHUS without a pathogenic or likely pathogenic variant. Diagnostic yield of the initial physician-ordered gene panel was 20% and varied between groups. Retrospective exome analysis identified 18 patients with a previously unknown pathogenic or likely pathogenic variant in a kidney disease gene and eight patients with a high-risk APOL1 genotype. Overall, retrospective exome analysis increased the diagnostic yield of panel-based testing from 20% to 30%. CONCLUSIONS These results highlight the importance of a broad and collaborative approach between the clinical laboratory and their physician clients that employs additional analysis when a targeted panel of kidney disease-causing genes does not return a clinically meaningful result.
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Affiliation(s)
- Parker C. Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Latisha Love-Gregory
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Meagan Corliss
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Samantha McNulty
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Jonathan W. Heusel
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Joseph P. Gaut
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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