1
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Dai R, Wang C, Shen Q, Xu H. The emerging role of clinical genetics in pediatric patients with chronic kidney disease. Pediatr Nephrol 2024; 39:2549-2553. [PMID: 38502225 DOI: 10.1007/s00467-024-06329-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/06/2024] [Accepted: 02/23/2024] [Indexed: 03/21/2024]
Affiliation(s)
- Rufeng Dai
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Chunyan Wang
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
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2
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Li ZL, Wang FM, Wen Y, Ni HF, Zhang XL, Wang B. Renal cell carcinoma in an adult-onset ESRD patient with nephronophthisis harboring NPHP3 deletion: A case report. Heliyon 2024; 10:e28985. [PMID: 38617907 PMCID: PMC11015401 DOI: 10.1016/j.heliyon.2024.e28985] [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: 08/14/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024] Open
Abstract
Background Nephronophthisis (NPHP) is a rare autosomal recessive inherited tubulointerstitial nephropathy, the most prevalent genetic cause of end-stage renal disease (ESRD) in children. Convincing evidence indicated that the overall prevalence of NPHP in adult-onset ESRD is very likely to be an underestimation. Therefore, understanding the genetic background and clinicopathologic features of adult-onset NPHP is warranted. Case presentation we reported one intriguing case with concurrent NPHP3 c.2694-2_2694-1delAG (splicing) variant and c.1082C > G (p.S361C) variant. A 48-year-old male was admitted to our hospital, complained about renal dysfunction for 10 years, and found right renal space-occupying lesion for 1 week. One of the most interesting clinical features is adult-onset ESRD, which differs from previous cases. Another discovery of this study is that the NPHP harboring NPHP3 deletion may be associated with clear cell renal cell carcinoma. Conclusion In conclusion, we report two mutations in the NPHP3 gene that cause NPHP with adult-onset ESRD and renal clear cell carcinoma in a Chinese family, enriching the clinical features of NPHP.
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Affiliation(s)
- Zuo-Lin Li
- Department of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Feng-Mei Wang
- Department of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Yi Wen
- Department of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Hai-Feng Ni
- Department of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Xiao-Liang Zhang
- Department of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Bin Wang
- Department of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
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Gao S, Zhang Q, Ding Y, Wang L, Li Z, Hu F, Yao RE, Yu T, Chang G, Wang X. Molecular and phenotypic characteristics of Bardet-Biedl syndrome in Chinese patients. Orphanet J Rare Dis 2024; 19:149. [PMID: 38584252 PMCID: PMC11000329 DOI: 10.1186/s13023-024-03150-9] [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: 09/08/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Bardet-Biedl syndrome (BBS) is a type of non-motile ciliopathy. To date, 26 genes have been reported to be associated with BBS. However, BBS is genetically heterogeneous, with significant clinical overlap with other ciliopathies, which complicates diagnosis. Disability and mortality rates are high in BBS patients; therefore, it is urgent to improve our understanding of BBS. Thus, our study aimed to describe the genotypic and phenotypic spectra of BBS in China and to elucidate genotype-phenotype correlations. METHODS Twenty Chinese patients diagnosed with BBS were enrolled in this study. We compared the phenotypes of Chinese BBS patients in this study with those from other countries to analyze the phenotypic differences across patients worldwide. In addition, genotype-phenotype correlations were described for our cohort. We also summarized all previously reported cases of BBS in Chinese patients (71 patients) and identified common and specific genetic variants in the Chinese population. RESULTS Twenty-eight variants, of which 10 are novel, in 5 different BBS-associated genes were identified in 20 Chinese BBS patients. By comparing the phenotypes of BBSome-coding genes (BBS2,7,9) with those of chaperonin-coding genes (BBS10,12), we found that patients with mutations in BBS10 and 12 had an earlier age of onset (1.10 Vs. 2.20, p < 0.01) and diagnosis (4.64 Vs. 13.17, p < 0.01), whereas patients with mutations in BBS2, 7, and 9 had a higher body mass index (28.35 Vs. 24.21, p < 0.05) and more vision problems (p < 0.05). Furthermore, in 91 Chinese BBS patients, mutations were predominant in BBS2 (28.89%) and BBS7 (15.56%), and the most frequent variants were in BBS2: c.534 + 1G > T (10/182 alleles) and BBS7: c.1002delT (7/182 alleles), marking a difference from the genotypic spectra of BBS reported abroad. CONCLUSIONS We recruited 20 Chinese patients with BBS for genetic and phenotypic analyses, and identified common clinical manifestations, pathogenic genes, and variants. We also described the phenotypic differences across patients worldwide and among different BBS-associated genes. This study involved the largest cohort of Chinese patients with BBS, and provides new insights into the distinctive clinical features of specific pathogenic variants.
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Affiliation(s)
- Shiyang Gao
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Qianwen Zhang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yu Ding
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Libo Wang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhiying Li
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Feihan Hu
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ru-En Yao
- Department of Genetic Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Tingting Yu
- Department of Genetic Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Guoying Chang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Xiumin Wang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Tong H, Zhao F, Yang Y, Qiu X, Zhu L, Yu Z. Scalp Tumor and Hydroureteronephrosis in Patients with Nephronophthisis and Homozygous NPHP1 Deletion. Clin Pediatr (Phila) 2023; 62:1508-1512. [PMID: 36942623 DOI: 10.1177/00099228231162416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Homozygous deletion of NPHP1 can lead to isolated nephronophthisis (NPHP) and syndromic disorders. However, the phenotype of scalp tumor and hydroureteronephrosis in NPHP patients with homozygous deletion of NPHP1 has not been reported. Clinical data, laboratory results, and genetic testing of 4 NPHP patients were collected. Examination of their eyes, heart, and urinary tract and of their hepatobiliary, skeletal, and central nervous systems was evaluated. Isolated NPHP was observed in 1 case, and syndromic disorders were observed in the other 3 patients. Their syndromic disorders showed NPHP combined with central nervous system defects, eye involvement, scalp tumor, arachnoid cyst, or hydroureteronephrosis. Large homozygous deletions covering the whole NPHP1 gene locus were identified in all 4 patients. We report a novel phenotype of scalp tumor and hydroureteronephrosis in NPHP patients with homozygous deletion of NPHP1, paving an avenue for further research on NPHP1-associated deformity in the skin and the urinary system.
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Affiliation(s)
- Huajuan Tong
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Department of Nephrology, Rheumatology and Immunology, Fujian Children's Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Feng Zhao
- Department of Nephrology, Rheumatology and Immunology, Fujian Children's Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Yonghui Yang
- Department of Nephrology, Rheumatology and Immunology, Fujian Children's Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Xiaojian Qiu
- Department of Nephrology, Rheumatology and Immunology, Fujian Children's Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Liying Zhu
- Department of Nephrology, Rheumatology and Immunology, Fujian Children's Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Zihua Yu
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Department of Nephrology, Rheumatology and Immunology, Fujian Children's Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fuzhou, China
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5
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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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6
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Xin-Yi Z, Yang-Li D, Ling-Hui Z. Review of the phenotypes and genotypes of Bardet-Biedl syndrome from China. Front Genet 2023; 14:1247557. [PMID: 38034494 PMCID: PMC10684923 DOI: 10.3389/fgene.2023.1247557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Objective: To analyze the phenotypes, genotypes, and the relationship of phenotypes and genotypes for Chinese patients with Bardet-Biedl syndrome (BBS). Methods: The Chinese Wanfang and Weipu data, and PubMed were searched up to December 2022. Patients with detailed clinical feature data were involved in the analysis. Results: A total of 153 Chinese patients, including 87 males, 53 females, and 12 unknown, were enrolled. Their ages ranged from 1.2 to 44 years old with a mean of 16.70 ± 9.90 years old. Among these patients, 80 (52.29%) were reported by ophthalmologists, and only 24 (15.68%) reported by pediatricians. Most patients (132/137, 96.35%) had visual problems; 131/153 (85.62%) had polydactyly; 124/132 (93.93%) were overweight or obese; 63/114 (55.26%) had renal abnormalities; kidney dysfunction was found in 33 (21.57%); 83/104 (79.81%) had hypogonadism and/or genital hypoplasia; and 111/136 (81.62%) had mental retardation. In this series, genetic analysis was performed in 90 (58.82%) patients, including 22 BBS7 (24.71%), 20 BBS2 (22.73%), and 10 BBS10 (11.24%) patients. Moreover, 11 fetuses were diagnosed prenatally in the last 4 years except for one patient in 2004 year. It was noted that BBS7 had higher penetrance. BBS2 had higher hearing impairment and lower renal abnormality penetrance. BBS10 also had lower renal abnormality penetrance as well. Conclusion: Misdiagnosis or miss diagnosis of BBS may be common in China. In patients with polydactyly, visual impairment, obesity, renal abnormalities, hypogonadism, and mental retardation, or in fetuses with polydactyly and/or renal abnormalities, BBS should be considered in the differential diagnosis. Other deformities should be evaluated carefully and genetic analysis should be performed as early as possible.
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Affiliation(s)
- Zou Xin-Yi
- Department of Clinical Medicine, Medical School of Hangzhou City University, Hangzhou, China
| | - Dai Yang-Li
- Department of Endocrinology, The Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Zeng Ling-Hui
- Department of Clinical Medicine, Medical School of Hangzhou City University, Hangzhou, China
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7
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Reddy S, Simmers R, Shah A, Couser N. NPHP1-Related ciliopathies: A new case and major review of the ophthalmic manifestations of 147 reported cases. Clin Case Rep 2023; 11:e7818. [PMID: 37663822 PMCID: PMC10468586 DOI: 10.1002/ccr3.7818] [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: 06/26/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023] Open
Abstract
Our case report and review contribute to the understanding of ocular manifestations in NPHP1 ciliopathies by reinforcing the relationship between pathogenic genetic variants and a wide array of ophthalmic abnormalities.
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Affiliation(s)
- Shivania Reddy
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Russell Simmers
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Arth Shah
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Natario Couser
- Department of Human and Molecular GeneticsVirginia Commonwealth University School of MedicineRichmondVirginiaUSA
- Department of OphthalmologyVirginia Commonwealth University School of MedicineRichmondVirginiaUSA
- Department of PediatricsVirginia Commonwealth University School of Medicine, Children's Hospital of Richmond at VCURichmondVirginiaUSA
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8
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Tauqeer Z, O'Neil EC, Brucker AJ, Aleman TS. NPHP1 FULL DELETION CAUSES NEPHRONOPHTHISIS AND A CONE-ROD DYSTROPHY. Retin Cases Brief Rep 2023; 17:352-358. [PMID: 36913617 DOI: 10.1097/icb.0000000000001208] [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: 11/25/2022]
Abstract
PURPOSE To describe in detail the structural and functional phenotypes of a patient with cone-rod dystrophy associated with a full deletion of the NPHP1 gene. METHODS A 30-year-old man with a history of end-stage renal disease presented with progressive vision loss in early adulthood prompting evaluation for retinal disease. Ophthalmic evaluation was performed including visual fields, electroretinography, spectral domain optical coherence tomography and short-wavelength and near-infrared fundus autofluorescence imaging. RESULTS The visual acuity was 20/60 in each eye. Fundus examination revealed a subtle bull's-eye maculopathy confirmed with fundus autofluorescence. Spectral domain optical coherence tomography demonstrated perifoveal loss of the outer retinal layers with structural preservation further peripherally. Static perimetry confirmed the loss of cone greater than rod sensitivities in a manner that colocalized to structural findings. Electroretinography revealed decreased cone- and rod-mediated responses. Genetic testing confirmed a homozygous whole-gene deletion of the NPHP1 gene. CONCLUSION NPHP1 -associated retinal degeneration may present as a cone-rod dystrophy in addition to the previously reported rod-predominant phenotypes and can notably be associated with systemic abnormalities, including renal disease. Our work further expands on the growing literature describing the retinal disease associated with systemic ciliopathies.
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Affiliation(s)
| | - Erin C O'Neil
- Scheie Eye Institute; and
- The Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Tomas S Aleman
- Scheie Eye Institute; and
- The Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania
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9
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Petzold F, Billot K, Chen X, Henry C, Filhol E, Martin Y, Avramescu M, Douillet M, Morinière V, Krug P, Jeanpierre C, Tory K, Boyer O, Burgun A, Servais A, Salomon R, Benmerah A, Heidet L, Garcelon N, Antignac C, Zaidan M, Saunier S. The genetic landscape and clinical spectrum of nephronophthisis and related ciliopathies. Kidney Int 2023:S0085-2538(23)00377-0. [PMID: 37230223 DOI: 10.1016/j.kint.2023.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
Nephronophthisis (NPH) is an autosomal-recessive ciliopathy representing one of the most frequent causes of kidney failure in childhood characterized by a broad clinical and genetic heterogeneity. Applied to one of the worldwide largest cohorts of patients with NPH, genetic analysis encompassing targeted and whole exome sequencing identified disease-causing variants in 600 patients from 496 families with a detection rate of 71%. Of 788 pathogenic variants, 40 known ciliopathy genes were identified. However, the majority of patients (53%) bore biallelic pathogenic variants in NPHP1. NPH-causing gene alterations affected all ciliary modules defined by structural and/or functional subdomains. Seventy six percent of these patients had progressed to kidney failure, of which 18% had an infantile form (under five years) and harbored variants affecting the Inversin compartment or intraflagellar transport complex A. Forty eight percent of patients showed a juvenile (5-15 years) and 34% a late-onset disease (over 15 years), the latter mostly carrying variants belonging to the Transition Zone module. Furthermore, while more than 85% of patients with an infantile form presented with extra-kidney manifestations, it only concerned half of juvenile and late onset cases. Eye involvement represented a predominant feature, followed by cerebellar hypoplasia and other brain abnormalities, liver and skeletal defects. The phenotypic variability were in a large part associated with mutation types, genes and corresponding ciliary modules with hypomorphic variants in ciliary genes playing a role in early steps of ciliogenesis associated with juvenile-to-late onset NPH forms. Thus, our data confirm a considerable proportion of late-onset NPH suggesting an underdiagnosis in adult chronic kidney disease.
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Affiliation(s)
- Friederike Petzold
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Division of Nephrology, Department of Endocrinology, Nephrology, and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Katy Billot
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Xiaoyi Chen
- Université de Paris, Imagine Institute, Data Science Platform, INSERM UMR 1163, Paris, France; Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France
| | - Charline Henry
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Emilie Filhol
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Yoann Martin
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Marina Avramescu
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Maxime Douillet
- Université de Paris, Imagine Institute, Data Science Platform, INSERM UMR 1163, Paris, France; Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France
| | - Vincent Morinière
- APHP, Génétique moléculaire, Hôpital universitaire Necker-Enfants malades, Paris, France
| | - Pauline Krug
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Kalman Tory
- Ist Department of Pediatrics, Semmelweis University, 1083 Budapest, Hungary
| | - Olivia Boyer
- Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Nephrology and Transplantation Department, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, APHP, Université de Paris, France
| | - Anita Burgun
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France; Hôpital Necker-Enfants Malades, Department of Medical Informatics, AP-HP, Paris, France; PaRis Artificial Intelligence Research InstitutE (PRAIRIE), France
| | - Aude Servais
- Nephrology and Transplantation Department, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, APHP, Université de Paris, France
| | - Remi Salomon
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris, Paris, France
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Laurence Heidet
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France; Department of Pediatry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Nephrology and Transplantation Department, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, APHP, Université de Paris, France
| | - Nicolas Garcelon
- Université de Paris, Imagine Institute, Data Science Platform, INSERM UMR 1163, Paris, France; Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Mohamad Zaidan
- Assistance Publique des Hôpitaux de Paris (AP-HP), Université Paris-Saclay, Hôpital de Bicêtre, Service de Néphrologie et Transplantation, Le Kremlin-Bicêtre, France; Centre de Compétence Maladies Rares « Syndrome Néphrotique Idiopathique », Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France.
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10
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Liu CH, Li LJ, Tian M, Cao GH, Zhang SF, Li JT. Two rare copy number variants involving loss of NPHP1, MALL, and MTLN genes contribute to nephronophthisis-induced nephropathy progression in a family: A case report. Niger J Clin Pract 2023; 26:524-527. [PMID: 37203120 DOI: 10.4103/njcp.njcp_775_22] [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: 05/20/2023]
Abstract
Nephronophthisis (NPHP) is a common pediatric cystic kidney disease, accounting for approximately 10% of end-stage renal failure cases in children. NPHP is primarily diagnosed through the identification of indel mutations and copy number variants (CNVs), and patients carrying NPHP1 mutations usually progress to renal failure at a mean age of 13 years old. However, the association between CNVs containing NPHP1 variations and the progression of NPHP-induced disease remains unclear. Here, we report three NPHP patients in a family. The proband had developed stage 4 chronic kidney disease (CKD) at 9 years old, and her younger brother and older sister had developed renal failure at 8 and 10 years old, respectively. A genetic diagnosis showed that they carried two rare CNVs, including homozygous loss of NPHP1, MALL, ACTR1AP1, MTLN, and LOC100507334. Heterozygous deletions mainly consisted of non-coding RNA genes on both sides of the CNVs. The proband was in stage 4 of CKD while her brother had progressed to renal failure, probably due to more extensive heterozygous deletion of a 67.115 kbp fragment, which included LIMS3-LOC440895, LOC440895, GPAA1P1, ZBTB45P1, and LINC0112 genes. This report demonstrates that larger CNV deletions, including homozygous NPHP1, MALL, and MTLN mutations and heterozygous deletions, presumably accelerate disease progression. Therefore, early genetic diagnosis plays a crucial role in the intervention and prognosis of these patients.
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Affiliation(s)
- C H Liu
- Department of Nephrology and Rheumatology, Zhengzhou Key Laboratory of Pediatric Kidney Disease Research; Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - L J Li
- Department of Nephrology and Rheumatology, Zhengzhou Key Laboratory of Pediatric Kidney Disease Research, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - M Tian
- Department of Nephrology and Rheumatology, Zhengzhou Key Laboratory of Pediatric Kidney Disease Research, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - G H Cao
- Department of Nephrology and Rheumatology, Zhengzhou Key Laboratory of Pediatric Kidney Disease Research, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - S F Zhang
- Department of Nephrology and Rheumatology, Zhengzhou Key Laboratory of Pediatric Kidney Disease Research, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - J T Li
- Department of Nephrology and Rheumatology, Zhengzhou Key Laboratory of Pediatric Kidney Disease Research; Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
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11
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Wang D, Chen X, Wen Q, Li Z, Chen W, Chen W, Wang X. A single heterozygous nonsense mutation in the TTC21B gene causes adult-onset nephronophthisis 12: A case report and review of literature. Mol Genet Genomic Med 2022; 10:e2076. [PMID: 36263627 PMCID: PMC9747551 DOI: 10.1002/mgg3.2076] [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: 06/16/2022] [Revised: 09/25/2022] [Accepted: 09/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Nephronophthisis type 12 (NPHP 12) is a rare cilia-related cystic kidney disease, caused by TTC21B mutation, mainly involving the kidneys, which generally occurs in children. Our study aimed to illustrate its clinical, pathological and genetic characteristics by reporting an adult-onset case of NPHP 12 caused by a single heterozygous nonsense mutation of TTC21B confirmed by renal histology and whole exome sequencing and reviewing related literature with a comparative analysis of the clinical features of each case. It will further increase the recognition of this rare kidney genetic disease, which sometimes can manifest as an adult disease. RESULTS A 33-years-old man showed a chronic disease course, and he exhibited slight renal dysfunction (CKD stage 3, eGFR = 49 ml/[min* 1.73 m2]) with renal tubular proteinuria, without any extrarenal manifestations, congenital malformation history of kidney disease, or family hereditary disease. Renal histological findings showed substantial interstitial fibrosis with some irregular and tortuous tubules with complex branches and segmental thickening and splitting of the tubular basement membrane. The patient was diagnosed with chronic interstitial nephritis for an unknown reason clinically. Further genetic analysis revealed a single heterozygous nonsense mutation in the TTC21B gene and NPHP 12 was diagnosed finally. CONCLUSION A single heterozygous mutation in the TTC21B gene may cause atypical NPHP12, which had a relatively later onset and milder clinical symptoms without developmental abnormalities. Therefore, for unexplained adult-onset chronic interstitial nephritis with unusual changes of renal tubules and interstitial fibrosis, even without a clear history of hereditary kidney disease, genetic testing is still recommended. The correct diagnosis of this rare adult-onset hereditary nephropathy can avoid unnecessary treatment.
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Affiliation(s)
- Dan Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Xionghui Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Qiong Wen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Zhijian Li
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Wei Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Wenfang Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,Department of PathologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Xin Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
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12
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Genotype and phenotype analysis and transplantation strategy in children with kidney failure caused by NPHP. Pediatr Nephrol 2022; 38:1609-1620. [PMID: 36227438 PMCID: PMC10060285 DOI: 10.1007/s00467-022-05763-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Nephronophthisis-related ciliopathies (NPHP-RC) have strong genotype and phenotype heterogeneity, and the transplantation strategy of Boichis syndrome is still controversial. Our purpose was to examine associations of genotype and phenotype in children with NPHP-RC and analyze the transplantation strategies of different phenotypes. METHODS The records of children with NPHP treated at our center from 01/2018 to 03/2021 were retrospectively reviewed. Inclusion criteria were a diagnosis of NPHP, received kidney transplantation, and received whole exome sequencing (WES) or nephropathy gene panel testing. RESULTS Twenty-nine children with NPHP were included. Nine children (31%) had NPHP1 mutations, and all presented with isolated nephropathy. Eighteen of 20 patients with non-NPHP1 mutations had compound heterozygous mutations, and 70% had extrarenal phenotype. Age at disease presentation (11.2 ± 1.94 years) and the development of kidney failure (12.4 ± 2.70 years) were later in children with NPHP1 mutations than those with non-NPHP1 mutations (5.2 ± 2.83 years and 5.7 ± 2.92 years, respectively). Four of six children with NPHP3 mutations were diagnosed with Boichis syndrome due to liver fibrosis. Isolated kidney transplantation resulted in good outcomes for patients with mild or moderate liver fibrosis without portal hypertension, while cholestasis was common postoperatively and could be resolved with ursodeoxycholic acid. CONCLUSIONS NPHP1 mutations are the most common in children with NPHP, and the phenotype of NPHP1 mutation is significantly different from that of non-NPHP1 mutation. For NPHP patients with mild to moderate liver fibrosis without portal hypertension, timely treatment of cholestasis could prevent the rapid progression of liver function damage after isolated kidney transplantation. A higher resolution version of the Graphical abstract is available as Supplementary information.
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13
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NPHP3 splice acceptor site variant is associated with infantile nephronophthisis and asphyxiating thoracic dystrophy; A rare combination. Eur J Med Genet 2022; 65:104578. [PMID: 35987473 DOI: 10.1016/j.ejmg.2022.104578] [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: 05/09/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022]
Abstract
Nephronophthisis (NPHP) is a group of rare inherited ciliopathy disorders characterized by the multicystic dysplastic kidney, oligohydramnios, and tubulointerstitial nephritis that progresses to end-stage renal disease (ESRD). NPHP is a clinically and genetically heterogeneous disorder with extrarenal symptoms including skeletal deformities, nervous system anomalies, and ophthalmologic features. Three clinical subtypes, infantile, juvenile, and adolescent, have been recognized based on age of onset of ESRD. Infantile nephronophthisis with asphyxiating thoracic dystrophy is a very rare association. Here, we investigated a consanguineous family having two neonates with a clinical phenotype of lethal infantile NPHP associated with asphyxiating thoracic dystrophy. Whole exome sequence data analysis identified a splice acceptor site variant (Chr3-132408107-CCT-C; NM_153240.4: c.2694-2_2694-1del) in the NPHP3 gene. The segregation of a variant in the family was confirmed by Sanger sequencing. The lethal phenotype in our case might be due to respiratory insufficiency secondary to a severely restricted thoracic cage. Present work is an exclusive depiction of lethal infantile NPHP phenotype in association with asphyxiating thoracic dystrophy that has not been reported before in families segregating NPHP3 mutations. Moreover, this work expands the phenotypic spectrum of NPHP3 variants. Overall, our findings add to the increasing body of evidence that mutations in ciliary genes/proteins show pleiotropic effects with phenotypic overlap between related disorders and apparently unrelated clinical entities.
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14
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Kim SY, Kim BJ, Oh DY, Han JH, Yi N, Kim NJ, Park MK, Keum C, Seo GH, Choi BY. Improving genetic diagnosis by disease-specific, ACMG/AMP variant interpretation guidelines for hearing loss. Sci Rep 2022; 12:12457. [PMID: 35864128 PMCID: PMC9304357 DOI: 10.1038/s41598-022-16661-x] [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: 08/04/2021] [Accepted: 07/13/2022] [Indexed: 12/29/2022] Open
Abstract
The 2018 Hearing Loss Expert Panel (HL-EP)-specific guidelines specified from the universal 2015 ACMG/AMP guidelines are proposed to be used in genetic HL, which prompted this study. A genetic HL cohort comprising 135 unrelated probands with available exome sequencing data was established. Overall, 169 variants were prioritized as candidates and interpreted using the 2015 ACMG/AMP and 2018 HL-EP guidelines. Changes in rule application and variant classification between the guidelines were compared. The concordance rate of variant classification of each variant between the guidelines was 71.60%, with significant difference. The proportion of pathogenic variants increased from 13.02% (2015) to 29.59% (2018). Variant classifications of autosomal recessive (AR) variants that previously belonged to VUS or likely pathogenic in the 2015 guidelines were changed toward pathogenic in the 2018 guidelines more frequently than those of autosomal dominant variants (29.17% vs. 6.38%, P = 0.005). Stratification of the PM3 and PP1 rules in the 2018 guidelines led to more substantial escalation than that in the 2015 guidelines. We compared the disease-specific guidelines (2018) with the universal guidelines (2015) using real-world data. Owing to the sophistication of case-level data, the HL-specific guidelines have more explicitly classified AR variants toward "likely pathogenic" or "pathogenic", serving as potential references for other recessive genetic diseases.
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Affiliation(s)
- So Young Kim
- grid.410886.30000 0004 0647 3511Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Bong Jik Kim
- grid.254230.20000 0001 0722 6377Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Doo Yi Oh
- grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jin Hee Han
- grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Nayoung Yi
- grid.254230.20000 0001 0722 6377Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Daejeon, South Korea ,grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Namju Justin Kim
- grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Moo Kyun Park
- grid.31501.360000 0004 0470 5905Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, South Korea
| | | | | | - Byung Yoon Choi
- grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
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15
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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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16
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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: 10] [Impact Index Per Article: 3.3] [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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17
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Li Y, Ma C, Li W, Yang Y, Li X, Liu J, Wang J, Li S, Liu Y, Li K, Li J, Huang D, Chen R, Lv L, Li M, Luo XJ. A missense variant in NDUFA6 confers schizophrenia risk by affecting YY1 binding and NAGA expression. Mol Psychiatry 2021; 26:6896-6911. [PMID: 33931730 DOI: 10.1038/s41380-021-01125-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/31/2021] [Accepted: 04/13/2021] [Indexed: 12/18/2022]
Abstract
Genome-wide association studies (GWASs) have revealed that genetic variants at the 22q13.2 risk locus were robustly associated with schizophrenia. However, the causal variants at this risk locus and their roles in schizophrenia remain elusive. Here we identify the risk missense variant rs1801311 (located in the 1st exon of NDUFA6 gene) as likely causal for schizophrenia at 22q13.2 by disrupting binding of YY1, TAF1, and POLR2A. We systematically elucidated the regulatory mechanisms of rs1801311 and validated the regulatory effect of this missense variant. Intriguingly, rs1801311 physically interacted with NAGA (encodes the alpha-N-acetylgalactosaminidase, which is mainly involved in regulating metabolisms of glycoproteins and glycolipids in lysosome) and showed the most significant association with NAGA expression in the human brain, with the risk allele (G) associated with higher NAGA expression. Consistent with eQTL analysis, expression analysis showed that NAGA was significantly upregulated in brains of schizophrenia cases compared with controls, further supporting that rs1801311 may confer schizophrenia risk by regulating NAGA expression. Of note, we found that NAGA regulates important neurodevelopmental processes, including proliferation and differentiation of neural stem cells. Transcriptome analysis corroborated that NAGA regulates pathways associated with neuronal differentiation. Finally, we independently confirmed the association between rs1801311 and schizophrenia in a large Chinese cohort. Our study elucidates the regulatory mechanisms of the missense schizophrenia risk variant rs1801311 and provides mechanistic links between risk variant and schizophrenia etiology. In addition, this study also revealed the novel role of coding variants in gene regulation and schizophrenia risk, i.e., genetic variant in coding region of a specific gene may confer disease risk through regulating distal genes (act as regulatory variant for distal genes).
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Affiliation(s)
- Yifan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Changguo Ma
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wenqiang Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yongfeng Yang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Junyang Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shiwu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yixing Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Kaiqin Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jiao Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Di Huang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Rui Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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18
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Olinger E, Al Alawi I, Al Riyami MS, Al Salmi I, Molinari E, Faqeih EA, Al Hamed M, Barroso-Gil M, Powell L, Al-Hussaini AA, Rahim KA, Almontashiri N, Miles C, Shril S, Hildebrandt F, Wilson IJ, Sayer JA. A discarded synonymous variant in NPHP3 explains nephronophthisis and congenital hepatic fibrosis in several families. Hum Mutat 2021; 42:1221-1228. [PMID: 34212438 PMCID: PMC8434971 DOI: 10.1002/humu.24251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 02/05/2023]
Abstract
Half of patients with a ciliopathy syndrome remain unsolved after initial analysis of whole exome sequencing (WES) data, highlighting the need for improved variant filtering and annotation. By candidate gene curation of WES data, combined with homozygosity mapping, we detected a homozygous predicted synonymous allele in NPHP3 in two children with hepatorenal fibrocystic disease from a consanguineous family. Analyses on patient-derived RNA shows activation of a cryptic mid-exon splice donor leading to frameshift. Remarkably, the same rare variant was detected in four additional families with hepatorenal disease from UK, US, and Saudi patient cohorts and in addition, another synonymous NPHP3 variant was identified in an unsolved case from the Genomics England 100,000 Genomes data set. We conclude that synonymous NPHP3 variants, not reported before and discarded by pathogenicity pipelines, solved several families with a ciliopathy syndrome. These findings prompt careful reassessment of synonymous variants, especially if they are rare and located in candidate genes.
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Affiliation(s)
- Eric Olinger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Intisar Al Alawi
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
- National Genetic Center, Ministry of Health, Oman
| | | | - Isa Al Salmi
- National Genetic Center, Ministry of Health, Oman
| | - Elisa Molinari
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Eissa Ali Faqeih
- Department of Medical Genetics, Children’s Specialist Hospital, King Fahad Medical City, Riyadh Saudi Arabia
| | - Mohamed Al Hamed
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Laura Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Abdulrahman A. Al-Hussaini
- Department of Medical Genetics, Children’s Specialist Hospital, King Fahad Medical City, Riyadh Saudi Arabia
| | - Khawla A. Rahim
- Department of Medical Genetics, Children’s Specialist Hospital, King Fahad Medical City, Riyadh Saudi Arabia
| | - Naif Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Colin Miles
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ian J. Wilson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - John A. Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom
- Renal Services, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, United Kingdom
- NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, NE4 5PL, United Kingdom
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19
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Li D, Hu M, Chen H, Wu X, Wei X, Lin H, Gao X, Wang H, Li M, Ong ACM, Yue Z, Sun L. An Nphp1 knockout mouse model targeting exon 2-20 demonstrates characteristic phenotypes of human Nephronophthisis. Hum Mol Genet 2021; 31:232-243. [PMID: 34415307 DOI: 10.1093/hmg/ddab239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/30/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Nephronophthisis (NPH) is the most prevalent monogenetic disorder leading to end-stage renal failure (ESRD) in childhood. Mutations in Nphp1, encoding a cilia-localized protein, account for the majority of NPH cases. Despite its identification many years ago, Nphp1 deletions targeting exon 4 or exon 20 have not reproduced the histological features of human NPH in murine models. In this study, we deleted exon 2-20 of Nphp1 by CRISPR/Cas9 gene editing to create a near-total knockout (KO) mouse model (Nphp1del2-20/del2-20). Nphp1del2-20/del2-20 mice faithfully reproduced the renal and extrarenal phenotypes associated with human NPH, including renal cyst development, tubular basement membrane thickening, retinal degeneration and abnormal spermatogenesis. Importantly, Nphp1 re-expression using an adenoviral-associated-virus-9 (AAV9) vector could partially rescue both renal and retinal phenotypes in Nphp1del2-20/del2-20 mice. Our results reported the first relevant Nphp1 mouse model with renal phenotypes for human disease. It will be a valuable model for future studies of Nphp1 function and to develop novel treatments for this common childhood disease.
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Affiliation(s)
- Dantong Li
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Miaoyue Hu
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Huamu Chen
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaohong Wu
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaoya Wei
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hongrong Lin
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xuefei Gao
- Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haiyan Wang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Min Li
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Albert C M Ong
- Kidney Genetics Group, Academic Nephrology Unit, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK
| | - Zhihui Yue
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Liangzhong Sun
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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20
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Wang X, Xiao H, Yao Y, Xu K, Liu X, Su B, Zhang H, Guan N, Zhong X, Zhang Y, Ding J, Wang F. Spectrum of Mutations in Pediatric Non-glomerular Chronic Kidney Disease Stages 2-5. Front Genet 2021; 12:697085. [PMID: 34295353 PMCID: PMC8290170 DOI: 10.3389/fgene.2021.697085] [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: 04/18/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Renal hypodysplasia and cystic kidney diseases, the common non-glomerular causes of pediatric chronic kidney disease (CKD), are usually diagnosed by their clinical and imaging characteristics. The high degree of phenotypic heterogeneity, in both conditions, makes the correct final diagnosis dependent on genetic testing. It is not clear, however, whether the frequencies of damaged alleles vary among different ethnicities in children with non-glomerular CKD, and this will influence the strategy used for genetic testing. In this study, 69 unrelated children (40 boys, 29 girls) of predominantly Han Chinese ethnicity with stage 2-5 non-glomerular CKD caused by suspected renal hypodysplasia or cystic kidney diseases were enrolled and assessed by molecular analysis using proband-only targeted exome sequencing and array-comparative genomic hybridization. Targeted exome sequencing discovered genetic etiologies in 33 patients (47.8%) covering 10 distinct genetic disorders. The clinical diagnoses in 13/48 patients (27.1%) with suspected renal hypodysplasia were confirmed, and two patients were reclassified carrying mutations in nephronophthisis (NPHP) genes. The clinical diagnoses in 16/20 patients (80%) with suspected cystic kidney diseases were confirmed, and one patient was reclassified as carrying a deletion in the hepatocyte nuclear factor-1-beta gene (HNF1B). The diagnosis of one patient with unknown non-glomerular disease was elucidated. No copy number variations were identified in the 20 patients with negative targeted exome sequencing results. NPHP genes were the most common disease-causing genes in the patients with disease onsets above 6 years of age (14/45, 31.1%). The children with stage 2 and 3 CKD at onset were found to carry causative mutations in paired box gene 2 (PAX2) and HNF1B gene (11/24, 45.8%), whereas those with stage 4 and 5 CKD mostly carried causative mutations in NPHP genes (19/45, 42.2%). The causative genes were not suspected by the kidney imaging patterns at disease onset. Thus, our data show that in Chinese children with non-glomerular renal dysfunction caused by renal hypodysplasia and cystic kidney diseases, the common causative genes vary with age and CKD stage at disease onset. These findings have the potential to improve management and genetic counseling of these diseases in clinical practice.
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Affiliation(s)
- Xiaoyuan Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Huijie Xiao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yong Yao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ke Xu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoyu Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Baige Su
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hongwen Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Na Guan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xuhui Zhong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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21
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Meng X, Long Y, Ren J, Wang G, Yin X, Li S. Ocular Characteristics of Patients With Bardet-Biedl Syndrome Caused by Pathogenic BBS Gene Variation in a Chinese Cohort. Front Cell Dev Biol 2021; 9:635216. [PMID: 33777945 PMCID: PMC7991091 DOI: 10.3389/fcell.2021.635216] [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: 11/30/2020] [Accepted: 02/08/2021] [Indexed: 12/29/2022] Open
Abstract
Bardet–Biedl syndrome (BBS; OMIM 209900) is a rare genetic disease causing damage to multiple organs and affecting patients’ quality of life in late adolescence or early adulthood. In this study, the ocular characteristics including morphology and function, were analyzed in 12 BBS patients from 10 Chinese families by molecular diagnostics. A total of five known and twelve novel variants in four BBS genes (BBS2, 58.33%; BBS4, 8.33%; BBS7, 16.67%; and BBS9, 16.67%) were identified in 10 Chinese families with BBS. All patients had typical phenotypes of retinitis pigmentosa with unrecordable or severely damaged cone and rod responses on full-field flash electroretinography (ffERG). Most of the patients showed unremarkable reactions in pattern visual evoked potential (PVEP) and multifocal electroretinography (mfERG), while their flash visual evoked potentials (FVEP) indicated display residual visual function. Changes in the fundus morphology, including color fundus photography and autofluorescence (AF) imaging, were heterogeneous and not consistent with the patients’ functional tests. Overall, our study expands the variation spectrum of the BBS gene, showing that the ocular characteristics of BBS patients are clinically highly heterogeneous, and demonstrates the usefulness of a combination of the ffERG and FVEP assessments of visual function in the advanced stage of retinopathy in BBS.
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Affiliation(s)
- Xiaohong Meng
- Department of Ophthalmology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of Visual Damage and Regeneration and Restoration of Chongqing, Chongqing, China
| | - Yanling Long
- Department of Ophthalmology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of Visual Damage and Regeneration and Restoration of Chongqing, Chongqing, China
| | - Jiayun Ren
- Department of Ophthalmology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of Visual Damage and Regeneration and Restoration of Chongqing, Chongqing, China
| | - Gang Wang
- Department of Ophthalmology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of Visual Damage and Regeneration and Restoration of Chongqing, Chongqing, China
| | - Xin Yin
- Department of Ophthalmology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of Visual Damage and Regeneration and Restoration of Chongqing, Chongqing, China
| | - Shiying Li
- Department of Ophthalmology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of Visual Damage and Regeneration and Restoration of Chongqing, Chongqing, China
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22
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Al Alawi I, Powell L, Rice SJ, Al Riyami MS, Al-Riyami M, Al Salmi I, Sayer JA. Case Report: A Novel In-Frame Deletion of GLIS2 Leading to Nephronophthisis and Early Onset Kidney Failure. Front Genet 2021; 12:791495. [PMID: 34917135 PMCID: PMC8669607 DOI: 10.3389/fgene.2021.791495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/28/2021] [Indexed: 02/05/2023] Open
Abstract
Variants in the GLIS family zinc finger protein 2 (GLIS2) are a rare cause of nephronophthisis-related ciliopathies (NPHP-RC). A reduction in urinary concentration and a progressive chronic tubulointerstitial nephropathy with corticomedullary cysts are the major characteristic features of NPHP. NPHP demonstrates phenotypic and genetic heterogeneity with at least 25 different recessive genes associated with the disease. We report a female, from a consanguineous family, who presented age 9 years with echogenic kidneys with loss of cortico-medullary differentiation and progressive chronic kidney disease reaching kidney failure by 10 years of age. A novel homozygous in-frame deletion (NM_032,575.3: c.560_574delACCATGTCAACGATT, p.H188_Y192del) in GLIS2 was identified using whole exome sequencing (WES) that segregated from each parent. The five amino acid deletion disrupts the alpha-helix of GLIS2 zinc-finger motif with predicted misfolding of the protein leading to its predicted pathogenicity. This study broadens the variant spectrum of GLIS2 variants leading to NPHP-RC. WES is a suitable molecular tool for children with kidney failure suggestive of NPHP-RC and should be part of routine diagnostics in kidney failure of unknown cause, especially in consanguineous families.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Laura Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sarah J. Rice
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mohammed S. Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Marwa Al-Riyami
- Department of Pathology, College of Medicine, Sultan Qaboos University, Muscat, Oman
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Internal Medicine, Oman Medical Specialty Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- Renal Services, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, United Kingdom
- *Correspondence: John A. Sayer,
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