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Dougarem D, Chen Y, Sun Y, Huang H, Luo Q. A Novel Heterozygous Intronic FBN1 Variant Contributes to Aberrant RNA Splicing in Marfan Syndrome. Mol Genet Genomic Med 2024; 12:e70004. [PMID: 39219382 PMCID: PMC11366968 DOI: 10.1002/mgg3.70004] [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: 03/19/2024] [Revised: 08/03/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Marfan syndrome (MFS) is a complex genetic systemic connective tissue disorder. It is well known that genetic factors play a critical role in the progression of MFS, with nearly all cases attributed to variants in the FBN1 gene. METHODS We investigated a Chinese family with MFS spanning two generations. Whole exome sequencing, in silico analysis, minigene constructs, transfection, RT-PCR, and protein secondary structure analysis were used to analyze the genotype of the proband and his father. RESULTS The main clinical manifestations of the proband and his father were subluxation of the left lens and high myopia with pectus deformity. Whole exome sequencing identified a novel single nucleotide variant (SNV) in the FBN1 gene at a non-canonical splice site, c.443-3C>G. This variant resulted in two abnormal mRNA transcripts, leading to a frameshift and an in-frame insertion. Further in vitro experiments indicated that the c.443-3C>G variant in FBN1 was pathogenic and functionally harmful. CONCLUSION This research identified a novel intronic pathogenic FBN1: c.443-3C>G gene variant, which led to two different aberrant splicing effects. Further functional analysis expands the variant spectrum and provides a strong indication and sufficient basis for preimplantation genetic testing for monogenic disease (PGT-M).
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Affiliation(s)
| | - Yi‐Xiao Chen
- School of MedicineZhejiang UniversityHangzhouChina
| | - Yi‐Na Sun
- School of MedicineZhejiang UniversityHangzhouChina
| | - He‐Feng Huang
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive EndocrinologyWomen's Hospital, Zhejiang University School of MedicineHangzhouChina
- Shanghai Key Laboratory of Reproduction and DevelopmentShanghaiChina
- Obstetrics and Gynecology Hospital, Institute of Reproduction and DevelopmentFudan UniversityShanghaiChina
- Research Units of Embryo Original DiseasesChinese Academy of Medical Sciences (No. 2019RU056)ShanghaiChina
| | - Qiong Luo
- Women's Hospital, School of MedicineZhejiang UniversityHangzhouChina
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Zhang Y, Liu W, Shu Z, Li Y, Sun F, Li ZG, Han TX, Mao HW, Wang TY. Delayed-onset adenosine deaminase deficiency with a novel synonymous mutation and a case series from China. World J Pediatr 2023; 19:687-700. [PMID: 37154862 DOI: 10.1007/s12519-023-00729-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/11/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Adenosine deaminase (ADA) is a key enzyme in the purine salvage pathway. Genetic defects of the ADA gene can cause a subtype of severe combined immunodeficiency. To date, few Chinese cases have been reported. METHODS We retrospectively reviewed the medical records of patients diagnosed with ADA deficiency in Beijing Children's Hospital and summarized the previously published ADA deficiency cases from China in the literature. RESULTS Nine patients were identified with two novel mutations (W272X and Q202 =). Early-onset infection, thymic abnormalities and failure to thrive were the most common manifestations of Chinese ADA-deficient patients. The ADA genotype has a major effect on the clinical phenotype. Notably, a novel synonymous mutation (c.606G>A, p.Q202=) was identified in a delayed-onset patient, which affected pre-mRNA splicing leading to a frameshift and premature truncation of the protein. Furthermore, the patient showed γδT cells expansion with an increased effect or phenotype, which may be associated with the delayed onset of disease. In addition, we reported cerebral aneurysm and intracranial artery stenosis for the first time in ADA deficiency. Five patients died with a median age of four months, while two patients received stem cell transplantation and are alive. CONCLUSIONS This study described the first case series of Chinese ADA-deficient patients. Early-onset infection, thymic abnormalities and failure to thrive were the most common manifestations in our patients. We identified a synonymous mutation that affected pre-mRNA splicing in the ADA gene, which had never been reported in ADA deficiency. Furthermore, we reported cerebral aneurysm in a delayed-onset patient for the first time. Further study is warranted to investigate the underlying mechanisms.
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Affiliation(s)
- Yue Zhang
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Xicheng District, Beijing, 100045, China
| | - Wei Liu
- Hematology Oncology Center, Henan Children's Hospital, Children's Hospital Affiliated of Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Zhou Shu
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Xicheng District, Beijing, 100045, China
| | - Yan Li
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Xicheng District, Beijing, 100045, China
| | - Fei Sun
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Xicheng District, Beijing, 100045, China
| | - Zhi-Gang Li
- Hematologic Disease Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Xicheng District, Beijing, 100045, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Tong-Xin Han
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Xicheng District, Beijing, 100045, China
| | - Hua-Wei Mao
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Xicheng District, Beijing, 100045, China.
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China.
| | - Tian-You Wang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Xicheng District, Beijing, 100045, China.
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China.
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Li W, He XD, Yang ZT, Han DM, Sun Y, Chen YX, Han XT, Guo SC, Ma YT, Jin X, Yang HM, Gao Y, Wang ZS, Li JK, He W. De Novo Mutations Contributes Approximately 7% of Pathogenicity in Inherited Eye Diseases. Invest Ophthalmol Vis Sci 2023; 64:5. [PMID: 36729443 PMCID: PMC9907368 DOI: 10.1167/iovs.64.2.5] [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] [Indexed: 02/03/2023] Open
Abstract
Purpose The purpose of this study was to describe genotype-phenotype associations and novel insights into genetic characteristics in a trio-based cohort of inherited eye diseases (IEDs). Methods To determine the etiological role of de novo mutations (DNMs) and genetic profile in IEDs, we retrospectively reviewed a large cohort of proband-parent trios of Chinese origin. The patients underwent a detailed examination and was clinically diagnosed by an ophthalmologist. Panel-based targeted exome sequencing was performed on DNA extracted from blood samples, containing coding regions of 792 IED-causative genes and their flanking exons. All participants underwent genetic testing. Results All proband-parent trios were divided into 22 subgroups, the overall diagnostic yield was 48.67% (605/1243), ranging from 4% to 94.44% for each of the subgroups. A total of 108 IED-causative genes were identified, with the top 24 genes explaining 67% of the 605 genetically solved trios. The genetic etiology of 6.76% (84/1243) of the trio was attributed to disease-causative DNMs, and the top 3 subgroups with the highest incidence of DNM were aniridia (n = 40%), Marfan syndrome/ectopia lentis (n = 38.78%), and retinoblastoma (n = 37.04%). The top 10 genes have a diagnostic yield of DNM greater than 3.5% in their subgroups, including PAX6 (40.00%), FBN1 (38.78%), RB1 (37.04%), CRX (10.34%), CHM (9.09%), WFS1 (8.00%), RP1L1 (5.88%), RS1 (5.26%), PCDH15 (4.00%), and ABCA4 (3.51%). Additionally, the incidence of DNM in offspring showed a trend of correlation with paternal age at reproduction, but not statistically significant with paternal (P = 0.154) and maternal (P = 0.959) age at reproduction. Conclusions Trios-based genetic analysis has high accuracy and validity. Our study helps to quantify the burden of the full spectrum IED caused by each gene, offers novel potential for elucidating etiology, and plays a crucial role in genetic counseling and patient management.
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Affiliation(s)
- Wei Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | | | - Zheng-Tao Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | - Dong-Ming Han
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | - Yan Sun
- He University, Shenyang, China
| | - Yan-Xian Chen
- Department of Ophthalmology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Xiao-Tong Han
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Si-Cheng Guo
- BGI-Shenzhen, Shenzhen, China,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Yu-Ting Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
| | - Huan-Ming Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Wei He
- He University, Shenyang, China
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Sarkar A, Panati K, Narala VR. Code inside the codon: The role of synonymous mutations in regulating splicing machinery and its impact on disease. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108444. [PMID: 36307006 DOI: 10.1016/j.mrrev.2022.108444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
In eukaryotes, precise pre-mRNA processing, including alternative splicing, is essential to carry out the intricate protein translation process. Both point mutations (that alter the translated protein sequence) and synonymous mutations (that do not alter the translated protein sequence) are capable of affecting the splicing process. Synonymous mutations are known to affect gene expression via altering mRNA stability, mRNA secondary structure, splicing processes, and translational kinetics. In higher eukaryotes, precise splicing is regulated by three weakly conserved cis-elements, 5' and 3' splice sites and the branch site. Many other cis-acting elements (exonic/intronic splicing enhancers and silencers) and trans-acting splicing factors (serine and arginine-rich proteins and heterogeneous nuclear ribonucleoproteins) have also been found to enhance or suppress the splicing process. The appearance of synonymous mutations in cis-acting elements can alter the splicing process by changing the binding pattern of splicing factors to exonic splicing enhancers or silencer motifs. This results in exon skipping, intron retention, and various other forms of alternative splicing, eventually leading to the emergence of a wide range of diseases. The focus of this review is to elucidate the role of synonymous mutations and their impact on abnormal splicing mechanisms. Further, this study highlights the function of synonymous mutation in mediating abnormal splicing in cancer and development of X-linked, and autosomal inherited diseases.
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Affiliation(s)
- Avik Sarkar
- Department of Zoology, Vidyasagar University, Midnapore, West Bengal 721102, India
| | - Kalpana Panati
- Department of Biotechnology, Government College for Men, Kadapa 516004, India
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Bi-allelic SMO variants in hypothalamic hamartoma: a recessive cause of Pallister-Hall syndrome. Eur J Hum Genet 2022; 30:384-388. [PMID: 35034092 PMCID: PMC8904774 DOI: 10.1038/s41431-021-01023-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/21/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022] Open
Abstract
Pallister-Hall syndrome, typically caused by germline or de novo variants within the GLI3 gene, has key features of hypothalamic hamartoma and polydactyly. Recently, a few similar cases have been described with bi-allelic SMO variants. We describe two siblings born to non-consanguineous unaffected parents presenting with hypothalamic hamartoma, post-axial polydactyly, microcephaly amongst other developmental anomalies. Previous clinical diagnostic exome analysis had excluded a pathogenic variant in GLI3. We performed exome sequencing re-analysis and identified bi-allelic SMO variants including a missense and synonymous variant in both affected siblings. We functionally characterised this synonymous variant showing it induces exon 8 skipping within the SMO transcript. Our results confirm bi-allelic SMO variants as an uncommon cause of Pallister-Hall syndrome and describe a novel exon-skipping mechanism, expanding the molecular architecture of this new clinico-molecular disorder.
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