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Pan F, Zhang R, Liu X, Shi X, Xin Q, Qiao D, Li C, Zhang Y, Chen M, Guo W, Luan S, Shao L. Three exonic variants in the PHEX gene cause aberrant splicing in a minigene assay. Front Genet 2024; 15:1353674. [PMID: 38841723 PMCID: PMC11150636 DOI: 10.3389/fgene.2024.1353674] [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: 12/11/2023] [Accepted: 04/24/2024] [Indexed: 06/07/2024] Open
Abstract
Background: X-linked hypophosphatemia (XLH, OMIM 307800) is a rare phosphorus metabolism disorder caused by PHEX gene variants. Many variants simply classified as missense or nonsense variants were only analyzed at the DNA level. However, growing evidence indicates that some of these variants may alter pre-mRNA splicing, causing diseases. Therefore, this study aimed to use bioinformatics tools and a minigene assay to ascertain the effects of PHEX variations on pre-mRNA splicing. Methods: We analyzed 174 variants in the PHEX gene described as missense or nonsense variants. Finally, we selected eight candidate variants using bioinformatics tools to evaluate their effects on pre-mRNA splicing using a minigene assay system. The complementary DNA (cDNA) sequence for the PHEX gene (RefSeq NM_000444.6) serves as the basis for DNA variant numbering. Results: Of the eight candidate variants, three were found to cause abnormal splicing. Variants c.617T>G p.(Leu206Trp) and c.621T>A p.(Tyr207*) in exon 5 altered the splicing of pre-mRNA, owing to the activation of a cryptic splice site in exon 5, which produced an aberrant transcript lacking a part of exon 5, whereas variant c.1700G>C p.(Arg567Pro) in exon 16 led to the activation of a cryptic splice site in intron 16, resulting in a partial inclusion of intron 16. Conclusion: Our study employed a minigene system, which has a great degree of flexibility to assess abnormal splicing patterns under the circumstances of patient mRNA samples that are not available, to explore the impact of the exonic variants on pre-mRNA splicing. Based on the aforementioned experimental findings, we demonstrated the importance of analyzing exonic variants at the mRNA level.
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Affiliation(s)
- Fengjiao Pan
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Ruixiao Zhang
- Department of Emergency, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xuyan Liu
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xiaomeng Shi
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Qing Xin
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Dan Qiao
- Department of Nephrology, Dalian Medical University, Dalian, China
| | - Changying Li
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yan Zhang
- Department of Nephrology, Weifang Medical University, Weifang, China
| | - Mengke Chen
- Department of Nephrology, Liaocheng Third People’s Hospital, Liaocheng, China
| | - Wencong Guo
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Shufang Luan
- Department of Medical Insurance Administration, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
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Fourikou M, Karipiadou A, Ververi A, Savvidou P, Laliotis N, Tsitouras V, Stabouli S, Roilides E, Kollios K. X-linked hypophosphatemia due to a de novo novel splice-site variant in a 7-year-old girl with scaphocephaly, Chiari syndrome type I and syringomyelia. Bone Rep 2024; 20:101731. [PMID: 38226334 PMCID: PMC10788211 DOI: 10.1016/j.bonr.2023.101731] [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: 08/24/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024] Open
Abstract
X-linked hypophosphatemia (XLH) is a rare X-linked dominant inherited disorder caused by loss-of-function variants in the PHEX gene and characterized by renal phosphate wasting, hypophosphatemia, abnormal vitamin D metabolism, growth retardation and lower limb deformities. We describe a case of XLH-rickets in a 7-year-old girl with scaphocephaly, Chiari syndrome type I and syringomyelia, with a de novo non-canonical splice variant (c.1080-3C > G) in intron 9 of the PHEX gene, that has not been previously described.
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Affiliation(s)
- Maria Fourikou
- 3rd Department of Paediatrics, Aristotle University of Thessaloniki, Hippokration General Hospital, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
| | - Aristea Karipiadou
- 3rd Department of Paediatrics, Aristotle University of Thessaloniki, Hippokration General Hospital, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
| | - Athina Ververi
- Centre for Genetics of Rare Diseases, Papageorgiou General Hospital, Agiou Pavlou 76, Pavlos Melas 564 29, Thessaloniki, Greece
| | - Parthena Savvidou
- 3rd Department of Paediatrics, Aristotle University of Thessaloniki, Hippokration General Hospital, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
| | - Nikolaos Laliotis
- Department of Orthopaedics, Inter Balkan Medical Center, Asklipiou 10, 57001 Pylaia, Thessaloniki, Greece
| | - Vassilios Tsitouras
- 2nd Neurosurgery Department, Aristotle University of Thessaloniki, Hippokration General Hospital, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
| | - Stella Stabouli
- 1st Department of Paediatrics, Aristotle University of Thessaloniki, Hippokration General Hospital, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
| | - Emmanuel Roilides
- 3rd Department of Paediatrics, Aristotle University of Thessaloniki, Hippokration General Hospital, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
| | - Konstantinos Kollios
- 3rd Department of Paediatrics, Aristotle University of Thessaloniki, Hippokration General Hospital, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
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Aiello F, Pasquali D, Baronio F, Cassio A, Rossi C, Di Fraia R, Carotenuto R, Digitale L, Festa A, Luongo C, Maltoni G, Schiano di Cola R, Del Giudice EM, Grandone A. Rare PHEX intron variant causes complete and severe phenotype in a family with hypophosphatemic rickets: a case report. J Pediatr Endocrinol Metab 2023; 36:91-95. [PMID: 36351286 DOI: 10.1515/jpem-2022-0365] [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: 07/30/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVES Lower limb deformities in children need careful orthopedic evaluation to distinguish physiological forms from pathological ones. X-linked hypophosphatemia (XLH) is a rare hereditary condition caused by PHEX gene mutations where tibial varum can be the first sign. CASE PRESENTATION We report a family presenting with severe tibial varum, harbouring a rare PHEX intron mutation, c.1586+6T>C. This is the first clinical description available in literature for this variant. Despite the previous prediction of a mild phenotype in functional study, our patients showed important bone deformities, rickets and impaired growth since infancy followed by severe bone pain, hearing loss and reduced life quality in adulthood. Burosumab therapy improved biochemical and radiological findings in children and ameliorated quality of life in adults. CONCLUSIONS This case demonstrated c.1586+6T>C causes a severe XLH phenotype, responsive to Burosumab. Familial genetic screening, enlarged to intronic region analysis, when XLH is suspected, allows precocious diagnosis to start timely the appropriate treatment.
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Affiliation(s)
- Francesca Aiello
- Department of Child, Woman, General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Daniela Pasquali
- Endocrinology, Department of Advanced Medical and Surgical Sciences, University "Luigi Vanvitelli", Naples, Italy
| | - Federico Baronio
- Department of Medical and Surgical Sciences-Unit of Paediatrics, University of Bologna, Bologna, Italy
| | - Alessandra Cassio
- Department of Medical and Surgical Sciences-Unit of Paediatrics, University of Bologna, Bologna, Italy
| | - Cesare Rossi
- Department of Medical and Surgical Sciences-Unit of Paediatrics, University of Bologna, Bologna, Italy
| | - Rosa Di Fraia
- Endocrinology, Department of Advanced Medical and Surgical Sciences, University "Luigi Vanvitelli", Naples, Italy
| | - Raffaela Carotenuto
- Endocrinology, Department of Advanced Medical and Surgical Sciences, University "Luigi Vanvitelli", Naples, Italy
| | - Lucia Digitale
- Endocrinology, Department of Advanced Medical and Surgical Sciences, University "Luigi Vanvitelli", Naples, Italy
| | - Adalgisa Festa
- Department of Child, Woman, General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Caterina Luongo
- Department of Child, Woman, General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giulio Maltoni
- Department of Medical and Surgical Sciences-Unit of Paediatrics, University of Bologna, Bologna, Italy
| | - Roberta Schiano di Cola
- Department of Child, Woman, General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Emanuele Miraglia Del Giudice
- Department of Child, Woman, General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anna Grandone
- Department of Child, Woman, General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
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Ma X, Pang Q, Zhang Q, Jiang Y, Wang O, Li M, Xing X, Xia W. A Novel Synonymous Variant of PHEX in a Patient with X-Linked Hypophosphatemia. Calcif Tissue Int 2022; 111:634-640. [PMID: 35831717 DOI: 10.1007/s00223-022-01003-w] [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] [Received: 05/20/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022]
Abstract
X-linked dominant hypophosphatemia (XLH), the most common form of hereditary hypophosphatemic rickets/osteomalacia, is caused by loss-of-function phosphate-regulating endopeptidase homolog X-linked gene (PHEX) variants. However, synonymous PHEX variants are rare in XLH. We report a 7-year-old boy with hypophosphatemia, short stature, and lower limb deformity. Whole-exome sequencing, reverse transcription-polymerase chain reaction, and Sanger sequencing were performed to identify the pathogenicity of the variant. A novel synonymous PHEX variant (NM_000444.4:c.1530 C>T, p.Arg510Arg) was detected in the proband. Further analysis revealed a 58-bp deletion at the 5' site of exon 14 during splicing. This study extends the genetic spectrum of XLH and confirms the rarity and significance of synonymous PHEX variants.
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Affiliation(s)
- Xiaosen Ma
- Department of Endocrinology, Key Laboratory of Endocrinology, National Commission of Health, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Qianqian Pang
- Department of Endocrinology, Key Laboratory of Endocrinology, National Commission of Health, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Qi Zhang
- Laboratory Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Jiang
- Department of Endocrinology, Key Laboratory of Endocrinology, National Commission of Health, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Ou Wang
- Department of Endocrinology, Key Laboratory of Endocrinology, National Commission of Health, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Mei Li
- Department of Endocrinology, Key Laboratory of Endocrinology, National Commission of Health, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Xiaoping Xing
- Department of Endocrinology, Key Laboratory of Endocrinology, National Commission of Health, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Weibo Xia
- Department of Endocrinology, Key Laboratory of Endocrinology, National Commission of Health, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China.
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5
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Alhamoudi KM, Alghamdi B, Alswailem M, Nasir A, Aljomaiah A, Al-Hindi H, Alzahrani AS. A Unique Mechanism of a Novel Synonymous PHEX Variant Causing X-Linked Hypophosphatemia. J Clin Endocrinol Metab 2022; 107:2883-2891. [PMID: 35896147 DOI: 10.1210/clinem/dgac435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Synonymous mutations are usually nonpathogenic. OBJECTIVE We report here a family with X-linked hypophosphatemia (XLH) due to a novel synonymous PHEX variant with a unique mechanism. METHODS We studied a 4-member family (a mother, a son, and 2 daughters), all affected with XLH. Genomic DNA was extracted from peripheral leucocytes. Whole exome sequencing (WES) was used to identify the underlying genetic variant in the proband (the son). Sanger sequencing was used to confirm this variant in the proband and his family members. RT-PCR and sequencing of the cDNA revealed the effect of this variant on the PHEX structure and function. RESULTS A synonymous variant in the PHEX gene (c.1701A>C) was identified in all affected members. This variant changes the first nucleotide of exon 17 from adenine to cytosine. Using RT-PCR, this variant was shown to interfere with splicing of exons 16 with 17 resulting in a single shorter PHEX transcript in the proband compared to normal control. Sanger sequencing of the cDNA revealed a complete skipping of exon 17 and direct splicing of exons 16 and 18. This led to a frameshift and an introduction of a new stop codon in the next codon (codon 568), which ultimately led to truncation and loss of the final 183 amino acids of PHEX. CONCLUSION This novel variant shows how a synonymous exonic mutation may induce a complex series of changes in the transcription and translation of the gene and causes a disease, a mechanism that is not commonly recognized.
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Affiliation(s)
- Kheloud M Alhamoudi
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, MBC#03, PO BOX 3354, Riyadh, 11211, Saudi Arabia
| | - Balgees Alghamdi
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, MBC#03, PO BOX 3354, Riyadh, 11211, Saudi Arabia
| | - Meshael Alswailem
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, MBC#03, PO BOX 3354, Riyadh, 11211, Saudi Arabia
| | - Abdul Nasir
- Department of Molecular science and Technology, Ajou University, Suwon, 443-749, South Korea
| | - Abeer Aljomaiah
- Department of Medicine, King Faisal Specialist Hospital & Research Centre, P.O Box 3354, Riyadh 11211, Saudi Arabia
| | - Hindi Al-Hindi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital & Research Centre, P.O Box 3354, Riyadh 11211, Saudi Arabia
| | - Ali S Alzahrani
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, MBC#03, PO BOX 3354, Riyadh, 11211, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital & Research Centre, P.O Box 3354, Riyadh 11211, Saudi Arabia
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6
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Pathogenic Variants of the PHEX Gene. ENDOCRINES 2022. [DOI: 10.3390/endocrines3030040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Twenty-five years ago, a pathogenic variant of the phosphate-regulating endopeptidase homolog X-linked (PHEX) gene was identified as the cause of X-linked hypophosphatemic rickets (XLH). Subsequently, the overproduction of fibroblast growth factor 23 (FGF23) due to PHEX defects has been found to be associated with XLH pathophysiology. However, the mechanism by which PHEX deficiency contributes to the upregulation of FGF23 and the function of PHEX itself remain unclear. To date, over 700 pathogenic variants have been identified in patients with XLH, and functional assays and genotype–phenotype correlation analyses based on pathogenic variant data derived from XLH patients have been reported. Genetic testing for XLH is useful for the diagnosis. Not only have single-nucleotide variants causing missense, nonsense, and splicing variants and small deletion/insertion variants causing frameshift/non-frameshift alterations been observed, but also gross deletion/duplication variants causing copy number variants have been reported as pathogenic variants in PHEX. With the development of new technologies including next generation sequencing, it is expected that an increasing number of pathogenic variants will be identified. This chapter aimed to summarize the genotype of PHEX and related analyses and discusses the pathophysiology of PHEX defects to seek clues on unsolved questions.
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Cao Y, You Y, Wang Q, Ren X, Li S, Li L, Xia W, Guan X, Yang T, Ikegawa S, Wang Z, Zhao X. Identification of six novel variants from nine Chinese families with hypophosphatemic rickets. BMC Med Genomics 2022; 15:161. [PMID: 35842615 PMCID: PMC9287957 DOI: 10.1186/s12920-022-01305-w] [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: 05/21/2021] [Accepted: 06/27/2022] [Indexed: 11/25/2022] Open
Abstract
Background Hypophosphatemic rickets (HR) is a rare genetic disorder associated with renal phosphate wasting and characterized by bone defects. Inactivating mutations in the phosphate regulating endopeptidase homolog X‑linked gene (PHEX) account for most cases of HR. The aim of this study was to identify causative variants in nine unrelated Chinese families associated with HR, and to determine potential pathogenicity of the identified variants. Methods Genomic DNA was isolated from the peripheral blood of HR patients and their healthy relatives, followed by next-generation sequencing and/or Sanger sequencing. In silico prediction combined with conservation analysis was performed to assess the effects of the variants, and 3D protein modeling was conducted to predict the functional effects on the encoded protein. Results All HR patients recruited in this study displayed bone deformities and tooth agenesis, as well as reduced serum phosphate levels and elevated urine phosphate levels. Nine PHEX variants were identified in eight families, including four novel variants (c.1661_1726del, c.980A > G, c.1078A > T, and c.1017_1051dup). Of the nine identified PHEX variants, five caused a truncated protein, two caused an altered amino acid, and the other two were the canonical splicing variants. Novel variants c.1336G > A and c.1364 T > C in SLC34A3 were also found in one family. Conservation analysis showed that all the amino acids corresponding to the missense variants were highly conserved. In silico analysis and 3D protein structure modeling confirmed the pathogenicity of these variants. Conclusions This study identified four novel variants in PHEX and two novel variants in SLC34A3 in a Chinese cohort with HR. Our findings highlight the dominant role of PHEX in HR, and expand the genotypic and phenotypic spectra of this disorder. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01305-w.
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Affiliation(s)
- Yixuan Cao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Yi You
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Qiong Wang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Xiuzhi Ren
- The People's Hospital of Wuqing District, Tianjin, 301700, China
| | - Shan Li
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Lulu Li
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Weibo Xia
- Department of Endocrinology, Key Laboratory of Endocrinology of the Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Xin Guan
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Tao Yang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences (IMS), Tokyo, 108-8639, Japan
| | - Zheng Wang
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences (IMS), Tokyo, 108-8639, Japan
| | - Xiuli Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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Albader N, Zou M, BinEssa HA, Abdi S, Al-Enezi AF, Meyer BF, Alzahrani AS, Shi Y. Insights of Noncanonical Splice-site Variants on RNA Splicing in Patients With Congenital Hypothyroidism. J Clin Endocrinol Metab 2022; 107:e1263-e1276. [PMID: 34632506 DOI: 10.1210/clinem/dgab737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Congenital hypothyroidism (CH) is caused by mutations in the genes for thyroid hormone synthesis. In our previous investigation of CH patients, approximately 53% of patients had mutations in either coding exons or canonical splice sites of causative genes. Noncanonical splice-site variants in the intron were detected but their pathogenic significance was not known. OBJECTIVE This work aims to evaluate noncanonical splice-site variants on pre-messenger RNA (pre-mRNA) splicing of CH-causing genes. METHODS Next-generation sequencing data of 55 CH cases in 47 families were analyzed to identify rare intron variants. The effects of variants on pre-mRNA splicing were investigated by minigene RNA-splicing assay. RESULTS Four intron variants were found in 3 patients: solute carrier family 26 member 4 (SLC26A4) c.1544+9C>T and c.1707+94C>T in one patient, and solute carrier family 5 member 5 (SLC5A5) c.970-48G>C and c.1652-97A>C in 2 other patients. The c.1707+94C>T and c.970-48G>C caused exons 15 and 16 skipping, and exon 8 skipping, respectively. The remaining variants had no effect on RNA splicing. Furthermore, we analyzed 28 previously reported noncanonical splice-site variants (4 in TG and 24 in SLC26A4). Among them, 15 variants (~ 54%) resulted in aberrant splicing and 13 variants had no effect on RNA splicing. These data were compared with 3 variant-prediction programs (FATHMM-XF, FATHMM-MKL, and CADD). Among 32 variants, FATHMM-XF, FATHMM-MKL, and CADD correctly predicted 20 (63%), 17 (53%), and 26 (81%) variants, respectively. CONCLUSION Two novel deep intron mutations have been identified in SLC26A4 and SLC5A5, bringing the total number of solved families with disease-causing mutations to approximately 45% in our cohort. Approximately 46% (13/28) of reported noncanonical splice-site mutations do not disrupt pre-mRNA splicing. CADD provides highest prediction accuracy of noncanonical splice-site variants.
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Affiliation(s)
- Najla Albader
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - Minjing Zou
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Huda A BinEssa
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Saba Abdi
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - Anwar F Al-Enezi
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Brian F Meyer
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ali S Alzahrani
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Yufei Shi
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
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Xu T, Tao X, Zhang Z, Yue H. Clinical and genetic characteristics of 29 Chinese patients with X-linked hypophosphatemia. Front Endocrinol (Lausanne) 2022; 13:956646. [PMID: 36060934 PMCID: PMC9437435 DOI: 10.3389/fendo.2022.956646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE The aim of this study was to fully describe the clinical and genetic characteristics, including clinical manifestations, intact fibroblast growth factor 23 (iFGF23) levels, and presence of PHEX gene mutations, of 22 and 7 patients with familial and sporadic X-linked dominant hypophosphatemia (XLH), respectively. METHODS Demographic data, clinical features, biochemical indicators, and imaging data of 29 patients were collected. All 22 exons and exon-intron boundaries of the PHEX gene were amplified by polymerase chain reaction (PCR) and directly sequenced. The serum level of iFGF23 was measured in 15 of the patients. RESULTS Twenty-nine patients (male/female: 13:16, juvenile/adult: 15:14) with XLH were included. The main symptoms were bowed lower extremities (89.7%), abnormal gait (89.7%), and short stature/growth retardation (78.6%). Hypophosphatemia with a high alkaline phosphatase level was the main biochemical feature and the median value of serum iFGF23 was 55.7 pg/ml (reference range: 16.1-42.2 pg/ml). Eight novel mutations in the PHEX gene were identified by Sanger sequencing, including two missense mutations (p. Gln682Leu and p. Phe312Ser), two deletions (c.350_356del and c.755_761del), one insertion (c.1985_1986insTGAC), and three splice mutations (c.1700+5G>C, c.1966-1G>T, and c.350-14_350-1del). Additionally, the recurrence rate after the first orthopedic surgery was 77.8% (7/9), and five of them had their first surgery before puberty. CONCLUSION Our study expanded the clinical phenotypes and gene mutation spectrum of XLH and provided a reference for the optimal timing of orthopedic surgeries.
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Affiliation(s)
| | | | | | - Hua Yue
- *Correspondence: Hua Yue, ; Zhenlin Zhang,
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Alikasifoglu A, Unsal Y, Gonc EN, Ozon ZA, Kandemir N, Alikasifoglu M. Long-term effect of conventional phosphate and calcitriol treatment on metabolic recovery and catch-up growth in children with PHEX mutation. J Pediatr Endocrinol Metab 2021; 34:1573-1584. [PMID: 34525271 DOI: 10.1515/jpem-2021-0387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/30/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Hereditary hypophosphatemic rickets (HR) is conventionally treated with phosphate and calcitriol. Exploring genotype and phenotypic spectrum of X-linked hypophosphatemic rickets (XLHR), focusing on short-term, long-term, and pubertal impact of conventional treatment was aimed. METHODS Sixteen patients from 12 unrelated families with HR were analyzed for phosphate regulating endopeptidase homolog X-linked (PHEX) mutation. Initially Sanger sequencing analysis was performed. If PHEX mutation was not detected, multiplex ligation-dependent probe amplification (MLPA) was performed. If molecular defect was detected, first-degree relatives were analyzed. Thirteen patients (81%) and five first-degree relatives with XLHR were evaluated for genotype-phenotype or gender-phenotype correlation. Clinical characteristics and response to conventional treatment were determined retrospectively. RESULTS Nine different PHEX mutations were identified; four splice-site, three point mutations, and two single exon deletions. Four were novel mutations. Despite conventional treatment, median adult height was lower than median height on admission (-3.8 and -2.3 SDS, respectively), metabolic and radiographic recovery were not achieved, adherence was low (30%). Although mean adult height was better in compliant patients than noncompliants (-2.6 vs. -3.7 SDS, respectively), they were still short. Correlation between phenotype and genotype or gender could not be shown. Median phosphate decreased significantly throughout puberty (p=0.014). Median pubertal height was lower than prepubertal height (-4.4 vs. -3.6 SDS; respectively), pubertal growth spurt was not observed. Among five patients with a follow-up longer than five years, three had nephrocalcinosis (60%), two had hyperparathyroidism (40%), 4/6 (33%) required correction osteotomy. CONCLUSIONS Conventional treatment appears to have limited effect on metabolic, clinical and radiographic recovery in XLHR. Metabolic control and growth worsened during puberty. Although, long-term adverse effects are yet to be seen, introduction of burosumab as first-line treatment may be an alternative after infancy.
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Affiliation(s)
- Ayfer Alikasifoglu
- Division of Pediatric Endocrinology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yagmur Unsal
- Division of Pediatric Endocrinology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Elmas Nazli Gonc
- Division of Pediatric Endocrinology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Zeynep Alev Ozon
- Division of Pediatric Endocrinology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Nurgun Kandemir
- Division of Pediatric Endocrinology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Mehmet Alikasifoglu
- Division of Medical Genetics, Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
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11
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Yang C, Harafuji N, O'Connor AK, Kesterson RA, Watts JA, Majmundar AJ, Braun DA, Lek M, Laricchia KM, Fathy HM, Mane S, Shril S, Hildebrandt F, Guay-Woodford LM. Cystin genetic variants cause autosomal recessive polycystic kidney disease associated with altered Myc expression. Sci Rep 2021; 11:18274. [PMID: 34521872 PMCID: PMC8440558 DOI: 10.1038/s41598-021-97046-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
Mutation of the Cys1 gene underlies the renal cystic disease in the Cys1cpk/cpk (cpk) mouse that phenocopies human autosomal recessive polycystic kidney disease (ARPKD). Cystin, the protein product of Cys1, is expressed in the primary apical cilia of renal ductal epithelial cells. In previous studies, we showed that cystin regulates Myc expression via interaction with the tumor suppressor, necdin. Here, we demonstrate rescue of the cpk renal phenotype by kidney-specific expression of a cystin-GFP fusion protein encoded by a transgene integrated into the Rosa26 locus. In addition, we show that expression of the cystin-GFP fusion protein in collecting duct cells down-regulates expression of Myc in cpk kidneys. Finally, we report the first human patient with an ARPKD phenotype due to homozygosity for a deleterious splicing variant in CYS1. These findings suggest that mutations in Cys1/CYS1 cause an ARPKD phenotype in mouse and human, respectively, and that the renal cystic phenotype in the mouse is driven by overexpression of the Myc proto-oncogene.
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Affiliation(s)
- Chaozhe Yang
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Naoe Harafuji
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Amber K O'Connor
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Jacob A Watts
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hanan M Fathy
- Alexandria Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, CT, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lisa M Guay-Woodford
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA.
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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12
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Formosa MM, Bergen DJM, Gregson CL, Maurizi A, Kämpe A, Garcia-Giralt N, Zhou W, Grinberg D, Ovejero Crespo D, Zillikens MC, Williams GR, Bassett JHD, Brandi ML, Sangiorgi L, Balcells S, Högler W, Van Hul W, Mäkitie O. A Roadmap to Gene Discoveries and Novel Therapies in Monogenic Low and High Bone Mass Disorders. Front Endocrinol (Lausanne) 2021; 12:709711. [PMID: 34539568 PMCID: PMC8444146 DOI: 10.3389/fendo.2021.709711] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022] Open
Abstract
Genetic disorders of the skeleton encompass a diverse group of bone diseases differing in clinical characteristics, severity, incidence and molecular etiology. Of particular interest are the monogenic rare bone mass disorders, with the underlying genetic defect contributing to either low or high bone mass phenotype. Extensive, deep phenotyping coupled with high-throughput, cost-effective genotyping is crucial in the characterization and diagnosis of affected individuals. Massive parallel sequencing efforts have been instrumental in the discovery of novel causal genes that merit functional validation using in vitro and ex vivo cell-based techniques, and in vivo models, mainly mice and zebrafish. These translational models also serve as an excellent platform for therapeutic discovery, bridging the gap between basic science research and the clinic. Altogether, genetic studies of monogenic rare bone mass disorders have broadened our knowledge on molecular signaling pathways coordinating bone development and metabolism, disease inheritance patterns, development of new and improved bone biomarkers, and identification of novel drug targets. In this comprehensive review we describe approaches to further enhance the innovative processes taking discoveries from clinic to bench, and then back to clinic in rare bone mass disorders. We highlight the importance of cross laboratory collaboration to perform functional validation in multiple model systems after identification of a novel disease gene. We describe the monogenic forms of rare low and high rare bone mass disorders known to date, provide a roadmap to unravel the genetic determinants of monogenic rare bone mass disorders using proper phenotyping and genotyping methods, and describe different genetic validation approaches paving the way for future treatments.
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Affiliation(s)
- Melissa M. Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Dylan J. M. Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- The Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Celia L. Gregson
- The Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Antonio Maurizi
- Department of Applied Clinical Sciences and Biotechnological, University of L’Aquila, L’Aquila, Italy
| | - Anders Kämpe
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Natalia Garcia-Giralt
- IMIM (Hospital del Mar Research Institute), Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Barcelona, Spain
| | - Wei Zhou
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain
| | - Diana Ovejero Crespo
- IMIM (Hospital del Mar Research Institute), Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Barcelona, Spain
| | - M. Carola Zillikens
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - J. H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Maria Luisa Brandi
- Department of Surgery and Translational Medicine (M.L.B.), University of Florence, Florence, Italy
| | - Luca Sangiorgi
- Department of Medical Genetics and Skeletal Rare Diseases, IRCCS Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain
| | - Wolfgang Högler
- Department of Paediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Outi Mäkitie
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Centre, Folkhälsan Institute of Genetics, Helsinki, Finland
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13
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Lin X, Li S, Zhang Z, Yue H. Clinical and Genetic Characteristics of 153 Chinese Patients With X-Linked Hypophosphatemia. Front Cell Dev Biol 2021; 9:617738. [PMID: 34141703 PMCID: PMC8204109 DOI: 10.3389/fcell.2021.617738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/16/2021] [Indexed: 11/27/2022] Open
Abstract
X-linked hypophosphatemia (XLH) is caused by inactivating mutations in the phosphate-regulating endopeptidase homolog, X-linked (PHEX) gene, resulting in an excess of circulating intact fibroblast growth factor-23 (iFGF-23) and a waste of renal phosphate. In the present study, we retrospectively reviewed the clinical and molecular features of 153 Chinese patients, representing 87 familial and 66 sporadic cases with XLH. A total of 153 patients with XLH presented with signs or symptoms at a median age of 18.0 months (range, 9.0 months–26.0 years). Lower-limb deformity was the most frequent clinical manifestation, accounting for 79.1% (121/153). Biochemical screening showed increased serum levels of iFGF23 in patients with XLH, with a wide variation ranging from 14.39 to 730.70 pg/ml. Median values of serum iFGF23 in pediatric and adult patients were 94.87 pg/ml (interquartile range: 74.27–151.86 pg/ml) and 72.82 pg/ml (interquartile range: 39.42–136.00 pg/ml), respectively. Although no difference in circulating iFGF23 levels between these two groups was observed (P = 0.062), the proportion of patients with high levels of circulating iFGF23 (>42.2 pg/ml) was greater in the pediatric group than in the adult group (P = 0.026). Eighty-eight different mutations in 153 patients were identified, with 27 (30.7%) being novel. iFGF23 levels and severity of the disease did not correlate significantly with truncating and non-truncating mutations or N-terminal and C-terminal PHEX mutations. This study provides a comprehensive description of the clinical profiles, circulating levels of iFGF23 and gene mutation features of patients with XLH, further enriching the genotypic spectrum of the diseases. The findings show no evident correlation of circulating iFGF23 levels with the age or disease severity in patients with XLH.
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Affiliation(s)
- Xiaoyun Lin
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Shanshan Li
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Zhenlin Zhang
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Hua Yue
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
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14
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Zhong J, Xie Y, Dang Y, Zhang J, Song Y, Lan D. Use of RNA‑sequencing to detect abnormal transcription of the collagen α‑2 (VI) chain gene that can lead to Bethlem myopathy. Int J Mol Med 2021; 47:28. [PMID: 33537799 PMCID: PMC7895517 DOI: 10.3892/ijmm.2021.4861] [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: 03/15/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Bethlem myopathy (BM) is an autosomal dominant or autosomal recessive disorder and is usually associated with mutations in the collagen VI genes. In the present study, the pathogenicity of a novel splice-site mutation was explored using RNA-sequencing in a family with suspected BM, and a myopathy panel was performed in the proband. The genetic status of all family members was confirmed using Sanger sequencing. Clinical data and magnetic resonance imaging (MRI) features were also documented. In silico analysis was performed to predict the effects of the splice mutation. RNA-sequencing and reverse transcription (RT)-PCR were used to assess aberrant splicing. Immunocytochemistry was conducted to measure collagen VI protein levels within the gastrocnemius and in cultured skin fibroblasts. The results revealed that three patients in the family shared a similar classic BM presentation. MRI revealed distinct patterns of fatty infiltration in the lower extremities. A novel splicing mutation c.736-1G>C in the collagen α-2 (VI) chain (COL6A2) gene was found in all three patients. In silico analysis predicted that the mutation would destroy the normal splice acceptor site. RNA-sequencing detected two abnormal splicing variants adjacent to the mutation site, and RT-PCR confirmed the RNA-sequencing findings. Furthermore, a defect in the collagen protein within cultured fibroblasts was detected using immunocytochemistry. The mutation c.736-1G>C in the COL6A2 gene caused aberrant splicing and led to premature termination of protein translation. In conclusion, these findings may improve our knowledge of mutations of the COL6A2 gene associated with BM and demonstrated that RNA-sequencing can be a powerful tool for finding the underlying mechanism of a disease-causing mutations at a splice site.
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Affiliation(s)
- Jingzi Zhong
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Yanshu Xie
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Yiwu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jiapeng Zhang
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Yingru Song
- Department of Radiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Dan Lan
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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15
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Zou M, Guven A, BinEssa HA, Al-Rijjal RA, Meyer BF, Alzahrani AS, Shi Y. Molecular Analysis of CYP27B1 Mutations in Vitamin D-Dependent Rickets Type 1A: c.590G > A (p.G197D) Missense Mutation Causes a RNA Splicing Error. Front Genet 2020; 11:607517. [PMID: 33329754 PMCID: PMC7729158 DOI: 10.3389/fgene.2020.607517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/10/2020] [Indexed: 11/22/2022] Open
Abstract
Context Vitamin D-dependent rickets type 1A (VDDR1A) is a rare autosomal recessively inherited disorder due to loss-of-function mutations in the CYP27B1 gene. CYP27B1 encodes an enzyme of 25-hydroxyvitamin D-1α-hydroxylase for converting inactive 25-OHD to biologically active 1,25-(OH)2D. Objective To identify underlying genetic defects in patients with VDDR1A. Methods Twelve patients from 7 Turkish and 2 Saudi families were investigated. The coding exons and intron-exon boundaries of the CYP27B1 gene were amplified by Polymerase Chain Reaction (PCR) from peripheral lymphocyte DNA. PCR products were directly sequenced. The consequences of c.590G > A mutation were analyzed by in silico and functional analysis. Results CYP27B1 mutations were identified in all the patients. Two novel mutations were identified in two separate families: c.171delG (family 7) and c.398_400dupAAT (family 8). The intra-exon deletion of c.171delG resulted in a frameshift and premature stop codon 20 amino acids downstream from the mutation (p.L58Cfs∗20). The intra-exon duplication of c.398_400dupAAT generated a premature stop codon at the mutation site (p.W134∗). A missense c.590G > A (p.G197D) mutation was found in a patient from family 4 and caused a defect in pre-mRNA splicing. As a result, two populations of transcripts were detected: the majority of them with intron 3 retention (83%), and the minority (17%) being properly spliced transcripts with about 16% of wild-type enzymatic activity. The remaining nine patients from six families carried a previously reported c.1319_1325dupCCCACCC (F443Pfs∗24) mutation. Clinically, all the patients need continued calcitriol treatment, which was consistent with inactivation of 25-hydroxy vitamin D1α-hydroxylase activity. Conclusion Two novel frameshift CYP27B1 mutations were identified and predicted to inactivate 25-hydroxyvitamin D-1α-hydroxylase. The loss of enzymatic activity by c.590G > A missense mutation was mainly caused by aberrant pre-mRNA splicing.
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Affiliation(s)
- Minjing Zou
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ayla Guven
- Pediatric Endocrinology Clinic, Zeynep Kamil Women and Children Hospital, University of Health Science, Istanbul, Turkey
| | - Huda A BinEssa
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Roua A Al-Rijjal
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Brian F Meyer
- Pediatric Endocrinology Clinic, Zeynep Kamil Women and Children Hospital, University of Health Science, Istanbul, Turkey
| | - Ali S Alzahrani
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Yufei Shi
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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16
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Cebeci AN, Zou M, BinEssa HA, Alzahrani AS, Al-Rijjal RA, Al-Enezi AF, Al-Mohanna FA, Cavalier E, Meyer BF, Shi Y. Mutation of SGK3, a Novel Regulator of Renal Phosphate Transport, Causes Autosomal Dominant Hypophosphatemic Rickets. J Clin Endocrinol Metab 2020; 105:5672651. [PMID: 31821448 DOI: 10.1210/clinem/dgz260] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/09/2019] [Indexed: 11/19/2022]
Abstract
CONTEXT Hypophosphatemic rickets (HR) is a group of rare hereditary renal phosphate wasting disorders caused by mutations in PHEX, FGF23, DMP1, ENPP1, CLCN5, SLC9A3R1, SLC34A1, or SLC34A3. OBJECTIVE A large kindred with 5 HR patients was recruited with dominant inheritance. The study was undertaken to investigate underlying genetic defects in HR patients. DESIGN Patients and their family members were initially analyzed for PHEX and FGF23 mutations using polymerase chain reaction sequencing and copy number analysis. Exome sequencing was subsequently performed to identify novel candidate genes. RESULTS PHEX and FGF23 mutations were not detected in the patients. No copy number variation was observed in the genome using CytoScan HD array analysis. Mutations in DMP1, ENPP1, CLCN5, SLC9A3R1, SLC34A1, or SLC34A3 were also not found by exome sequencing. A novel c.979-96 T>A mutation in the SGK3 gene was found to be strictly segregated in a heterozygous pattern in patients and was not present in normal family members. The mutation is located 1 bp downstream of a highly conserved adenosine branch point, resulted in exon 13 skipping and in-frame deletion of 29 amino acids, which is part of the protein kinase domain and contains a Thr-320 phosphorylation site that is required for its activation. Protein tertiary structure modelling showed significant structural change in the protein kinase domain following the deletion. CONCLUSIONS The c.979-96 T>A splice mutation in the SGK3 gene causes exon 13 skipping and deletion of 29 amino acids in the protein kinase domain. The SGK3 mutation may cause autosomal dominant HR.
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Affiliation(s)
- Ayşe Nurcan Cebeci
- Department of Pediatric Endocrinology, Istanbul Bilim University, Istanbul, Turkey
| | - Minjing Zou
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Huda A BinEssa
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Ali S Alzahrani
- Department of Medicine King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Roua A Al-Rijjal
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Anwar F Al-Enezi
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Futwan A Al-Mohanna
- Department of Cell Biology, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Etienne Cavalier
- Department of Clinical Chemistry, University of Liège, CHU de Liège, Liège, Belgium
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Yufei Shi
- Department of Genetics, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
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17
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Yamamoto A, Nakamura T, Ohata Y, Kubota T, Ozono K. Phenotypes of a family with XLH with a novel PHEX mutation. Hum Genome Var 2020; 7:8. [PMID: 32257293 PMCID: PMC7109063 DOI: 10.1038/s41439-020-0095-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 11/22/2022] Open
Abstract
X-linked hypophosphatemia (XLH) is the most common form of heritable hypophosphatemic rickets. We encountered a 4-year-old boy with a novel variant in the phosphate-regulating neutral endopeptidase homolog X-linked (PHEX) gene who presented with a short stature, genu valgum, and scaphocephaly. The same mutation was identified in his mother and sister; however, the patient presented with a more severe case.
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Affiliation(s)
- Akiko Yamamoto
- Department of Pediatrics, Kumamoto Chuo Hospital, Kumamoto, Japan
| | - Toshiro Nakamura
- Department of Pediatrics, Kumamoto Chuo Hospital, Kumamoto, Japan
| | - Yasuhisa Ohata
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takuo Kubota
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Keiichi Ozono
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
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18
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Kuitche E, Jammali S, Ouangraoua A. SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution. BMC Bioinformatics 2019; 20:640. [PMID: 31842741 PMCID: PMC6916212 DOI: 10.1186/s12859-019-3207-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background It is now well established that eukaryotic coding genes have the ability to produce more than one type of transcript thanks to the mechanisms of alternative splicing and alternative transcription. Because of the lack of gold standard real data on alternative splicing, simulated data constitute a good option for evaluating the accuracy and the efficiency of methods developed for splice-aware sequence analysis. However, existing sequence evolution simulation methods do not model alternative splicing, and so they can not be used to test spliced sequence analysis methods. Results We propose a new method called SimSpliceEvol for simulating the evolution of sets of alternative transcripts along the branches of an input gene tree. In addition to traditional sequence evolution events, the simulation also includes gene exon-intron structure evolution events and alternative splicing events that modify the sets of transcripts produced from genes. SimSpliceEvol was implemented in Python. The source code is freely available at https://github.com/UdeS-CoBIUS/SimSpliceEvol. Conclusions Data generated using SimSpliceEvol are useful for testing spliced RNA sequence analysis methods such as methods for spliced alignment of cDNA and genomic sequences, multiple cDNA alignment, orthologous exons identification, splicing orthology inference, transcript phylogeny inference, which requires to know the real evolutionary relationships between the sequences.
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Affiliation(s)
- Esaie Kuitche
- Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l'Université, Quebec, J1K2R1, Canada.
| | - Safa Jammali
- Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l'Université, Quebec, J1K2R1, Canada.,Department of Biochemistry, University of Sherbrooke, 3001 12e avenue Nord, Quebec, J1H5N4, Canada
| | - Aïda Ouangraoua
- Department of Computer Science, University of Sherbrooke, 2500 Boulevard de l'Université, Quebec, J1K2R1, Canada
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