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Tong L, Li L, Wang W, Chen J. Case Report: Primary ciliary dyskinesia due to CCNO mutations: a Chinese pediatric case series and literature review. Front Pediatr 2024; 12:1458660. [PMID: 39380637 PMCID: PMC11458413 DOI: 10.3389/fped.2024.1458660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 09/04/2024] [Indexed: 10/10/2024] Open
Abstract
Primary ciliary dyskinesia (PCD) is a hereditary disorder characterized by defects in cilia that impair mucociliary clearance. This study focuses on PCD caused by mutations in the Cyclin O (CCNO) gene and reports on three cases involving Chinese children. Case 1 was an 8-year-and-3-month-old boy who presented with respiratory distress after birth and later developed a recurrent productive cough and purulent nasal discharge. He was initially diagnosed with diffuse panbronchiolitis (DPB) due to the presence of diffuse micronodules in lung CT scans. Case 2 was the younger sister of case 1. She also presented with respiratory distress after birth, with a chest radiograph revealing atelectasis. She required oxygen supplementation until the age of 2 months. Case 3 was a 4-year-and-4-month-old girl with a history of neonatal pneumonia, persistent pulmonary atelectasis, and recurrent lower respiratory tract infections. Her chest radiograph also showed diffuse micronodules. In all three cases, the final diagnosis of PCD was confirmed by genetic testing. Cases 1 and 2 exhibited homozygous c.248_252dup TGCCC (p.G85Cfs*11) mutations in the CCNO gene, while case 3 harbored a homozygous c.258_262dup GGCCC (p.Q88Rfs*8) mutation. A literature review indicated that the common clinical features of CCNO-PCD include neonatal respiratory distress (40/49, 81.6%), chronic cough (31/33, 93.9%), rhinosinusitis (30/35, 85.7%), bronchiectasis (26/35, 74.3%), and low nasal nitric oxide (nNO, 40/43, 93.0%). Notably, situs inversus has not been reported. In CCNO-PCD patients, cilia may appear structurally normal but were severely reduced in number or entirely absent. Lung CT scans in these patients may exhibit diffuse micronodules and "tree-in-bud" signs, which can lead to a clinical misdiagnosis of DPB. nNO screening combined with genetic testing is an optimized diagnostic strategy. Treatment options include the use of anti-infective and anti-inflammatory agent, along with daily airway clearance. This study underscores the importance of genetic testing in neonates and children with suspected PCD or those clinically diagnosed with DPB to enable an early diagnosis and prompt intervention, thereby enhancing the prognosis for these patients.
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Affiliation(s)
| | | | | | - Jiehua Chen
- Department of Respiratory Diseases, Shenzhen Children’s Hospital Affiliated to Shantou University Medical College, Shenzhen, China
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Justin Margret J, Jayasankaran C, Amritkumar P, Azaiez H, Srisailapathy CRS. Unraveling the Genetic Basis of Combined Deafness and Male Infertility Phenotypes through High-Throughput Sequencing in a Unique Cohort from South India. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300206. [PMID: 38884051 PMCID: PMC11170077 DOI: 10.1002/ggn2.202300206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/15/2024] [Indexed: 06/18/2024]
Abstract
The co-occurrence of sensorineural hearing loss and male infertility has been reported in several instances, suggesting potential shared genetic underpinnings. One such example is the contiguous gene deletion of CATSPER2 and STRC genes, previously associated with deafness-infertility syndrome (DIS) in males. Fifteen males with both hearing loss and infertility from southern India after exclusion for the DIS contiguous gene deletion and the FOXI1 gene mutations are subjected to exome sequencing. This resolves the genetic etiology in four probands for both the phenotypes; In the remaining 11 probands, two each conclusively accounted for deafness and male infertility etiologies. Genetic heterogeneity is well reflected in both phenotypes. Four recessive (TRIOBP, SLC26A4, GJB2, COL4A3) and one dominant (SOX10) for the deafness; six recessive genes (LRGUK, DNAH9, ARMC4, DNAH2, RSPH6A, and ACE) for male infertility can be conclusively ascribed. LRGUK and RSPH6A genes are implicated earlier only in mice models, while the ARMC4 gene is implicated in chronic destructive airway diseases due to primary ciliary dyskinesia. This study would be the first to document the role of these genes in the male infertility phenotype in humans. The result suggests that deafness and infertility are independent events and do not segregate together among the probands.
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Affiliation(s)
- Jeffrey Justin Margret
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Department of Pediatrics Louisiana State University Health Sciences Center Shreveport LA 71103 USA
| | - Chandru Jayasankaran
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Department of Personalized Health Care Roche Products India Pvt., Ltd. Bengaluru Karnataka 560 025 India
| | - Pavithra Amritkumar
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Meenakshi Academy of Higher Education and Research (MAHER) Chennai 600 078 India
| | - Hela Azaiez
- Department of Otolaryngology Carver College of Medicine University of Iowa Iowa City Iowa 52242 USA
| | - C R Srikumari Srisailapathy
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
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Xu Y, Ueda K, Nishikido T, Matsumoto T, Takeuchi K. Two Japanese Pediatric Patients With Primary Ciliary Dyskinesia Caused by Loss-of-Function Variants in the CCNO gene. Cureus 2024; 16:e58854. [PMID: 38784318 PMCID: PMC11115999 DOI: 10.7759/cureus.58854] [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] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Primary ciliary dyskinesia (PCD) is a rare congenital disorder caused by pathogenic variants of genes related to cilia. Here, we report two Japanese pediatric patients with PCD caused by pathogenic compound heterozygous variants in the cyclin O (CCNO) gene (Case 1, NM_021147.4:c.[262C>T];[781delC], p.[Gln88Ter];[Leu261fs]; Case 2, c.[262C>T];[c.248_252dupTGCCC], p.[Gln88Ter];[Gly85fs]). The clinical symptoms of the patients were varied. Neither of the patients had situs inversus. Transmission electron microscopy of the respiratory cilia from the nasal mucosa in Case 1 showed a remarkable reduction of cilia and the few residual cilia had central pair defects and microtubular disorganization.
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Affiliation(s)
- Yifei Xu
- Department of Otorhinolaryngology-Head and Neck Surgery, Mie University Graduate School of Medicine, Tsu, JPN
| | - Koki Ueda
- Department of Otorhinolaryngology-Head and Neck Surgery, Mie University Graduate School of Medicine, Tsu, JPN
| | - Tomoki Nishikido
- Department of Pediatric Pulmonology and Allergy, Osaka Women's and Children's Hospital, Izumi, JPN
| | - Tsubasa Matsumoto
- Department of Pediatric Infection and Immunology, Fukuoka Children's Hospital, Fukuoka, JPN
| | - Kazuhiko Takeuchi
- Department of Otorhinolaryngology-Head and Neck Surgery, Mie University Graduate School of Medicine, Tsu, JPN
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Xu Y, Wang J, Liu JH, Gao QQ, Wang B, Xu ZP. Identification of a novel splice site mutation in the DNAAF4 gene of a Chinese patient with primary ciliary dyskinesia. Asian J Androl 2023; 25:713-718. [PMID: 37147940 PMCID: PMC10715616 DOI: 10.4103/aja2022122] [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: 09/07/2022] [Accepted: 03/22/2023] [Indexed: 05/07/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a rare hereditary orphan condition that results in variable phenotypes, including infertility. About 50 gene variants are reported in the scientific literature to cause PCD, and among them, dynein axonemal assembly factor 4 ( DNAAF4 ) has been recently reported. DNAAF4 has been implicated in the preassembly of a multiunit dynein protein essential for the normal function of locomotory cilia as well as flagella. In the current study, a single patient belonging to a Chinese family was recruited, having been diagnosed with PCD and asthenoteratozoospermia. The affected individual was a 32-year-old male from a nonconsanguineous family. He also had abnormal spine structure and spinal cord bends at angles diagnosed with scoliosis. Medical reports, laboratory results, and imaging data were investigated. Whole-exome sequencing, Sanger sequencing, immunofluorescence analysis, hematoxylin-eosin staining, and in silico functional analysis, including protein modeling and docking studies, were used. The results identified DNAAF4 disease-related variants and confirmed their pathogenicity. Genetic analysis through whole-exome sequencing identified two pathogenic biallelic variants in the affected individual. The identified variants were a hemizygous splice site c.784-1G>A and heterozygous 20.1 Kb deletion at the DNAAF4 locus, resulting in a truncated and functionless DNAAF4 protein. Immunofluorescence analysis indicated that the inner dynein arm was not present in the sperm flagellum, and sperm morphological analysis revealed small sperm with twisted and curved flagella or lacking flagella. The current study found novel biallelic variants causing PCD and asthenoteratozoospermia, extending the range of DNAAF4 pathogenic variants in PCD and associated with the etiology of asthenoteratozoospermia. These findings will improve our understanding of the etiology of PCD.
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Affiliation(s)
- Yang Xu
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Jing Wang
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Ji-Hai Liu
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Qing-Qiang Gao
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Bing Wang
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Zhi-Peng Xu
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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Gong D, Tang Q, Yan LJ, Ye XM, Yang YC, Zou L, Ji Q, Wen XL. Case Report: A Novel Homozygous Mutation of Cyclin O Gene Mutation in Primary Ciliary Dyskinesia with Short Stature. Pharmgenomics Pers Med 2023; 16:443-448. [PMID: 37220549 PMCID: PMC10200132 DOI: 10.2147/pgpm.s406445] [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: 01/30/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023] Open
Abstract
Background Primary ciliary dyskinesia (PCD) is a group of autosomal recessive genetic diseases caused by abnormal ciliary ultrastructure and/or function, resulting in reduced ciliary clearance function or other dysfunctions. PCD is one of the causes of recurrent respiratory tract infections in children. At present, there is no gold standard for diagnosis. In patients clinically suspected with PCD, a variety of examination methods are available to assist in diagnosis, such as high-speed video microscopic imaging to analyze ciliary movement patterns, transmission electron microscopy to observe ciliary ultrastructure, genetic testing, and detection of nitric oxide content in nasal expiratory air. Case Description We present a case summary of the clinical data and treatment process of a child with PCD and short stature induced by Novel exon 1 of CCNO mutation (NM-021147.5) at c.323del, and the proband father and mother were heterozygous mutators, who was diagnosed and treated in the Pediatric Healthcare Department of our hospital. We treated the child with recombinant human growth hormone to increase the height, and the patient was also advised to improve nutrition, prevent and control infections, and encouraged sputum expectoration. We also recommended regular follow-up visits to the outpatient department, and to seek other symptomatic and supportive treatments as necessary. Conclusion The height and nutritional status of the child improved after treatment. We also reviewed relevant literature to help clinicians improve their understanding of this disease.
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Affiliation(s)
- Dai Gong
- Department of Children Health Care Center, Zhuzhou Hospital Affiliated to Xiangya Medical College, Central South University, Zhuzhou, Hunan, 412007, People’s Republic of China
| | - Qiong Tang
- Department of Children Health Care Center, Zhuzhou Hospital Affiliated to Xiangya Medical College, Central South University, Zhuzhou, Hunan, 412007, People’s Republic of China
| | - Li-Juan Yan
- Department of Children Health Care Center, Zhuzhou Hospital Affiliated to Xiangya Medical College, Central South University, Zhuzhou, Hunan, 412007, People’s Republic of China
| | - Xiao-Min Ye
- Department of Children Health Care Center, Zhuzhou Hospital Affiliated to Xiangya Medical College, Central South University, Zhuzhou, Hunan, 412007, People’s Republic of China
| | - Yi-Can Yang
- Department of Children Health Care Center, Zhuzhou Hospital Affiliated to Xiangya Medical College, Central South University, Zhuzhou, Hunan, 412007, People’s Republic of China
| | - Li Zou
- Department of Children Health Care Center, Zhuzhou Hospital Affiliated to Xiangya Medical College, Central South University, Zhuzhou, Hunan, 412007, People’s Republic of China
| | - Qing Ji
- Department of Children Health Care Center, Zhuzhou Hospital Affiliated to Xiangya Medical College, Central South University, Zhuzhou, Hunan, 412007, People’s Republic of China
| | - Xiang-Lan Wen
- Department of Children Health Care Center, Zhuzhou Hospital Affiliated to Xiangya Medical College, Central South University, Zhuzhou, Hunan, 412007, People’s Republic of China
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Prenatal diagnosis of fetuses with region of homozygosity detected by single nucleotide polymorphism array: a retrospective cohort study. J Hum Genet 2022; 67:629-638. [PMID: 35896820 DOI: 10.1038/s10038-022-01062-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/01/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Region of homozygosity (ROH) is classified as uniparental disomy (UPD) or identity by descent, depending on its origin. To explore the clinical relevance of ROH in prenatal diagnoses, we reviewed 5063 fetal samples subjected to single nucleotide polymorphism array at our center over 5 years. ROH cases meeting our reporting threshold were further analyzed. ROHs were detected in 22 fetuses (0.43%, 22/5063), of which, 77.3% (17/22) showed a ROH on a single chromosome and 22.7% (5/22) showed multiple ROHs on different chromosomes. Among 5063 fetuses undergoing invasive prenatal diagnoses owing to various indications, five cases were identified as UPDs with a rate of ~1/1000. We observed clinically relevant UPDs in two cases related to Prader-Willi syndrome and transient neonatal diabetes mellitus. Of note, one case showed 50% mosaicism for trisomy 2 in amniotic fluid, whereas a complete UPD (2) was observed in umbilical cord blood. Trio whole-exome sequencing was performed for three cases. Clinically relevant variants were identified in two cases, one of which, NM_000302:c.2071_2072insCC (p.R693Qfs*122) in PLOD1 located in the ROH, may be related to Ehlers-Danlos syndrome, kyphoscoliotic type, 1. Overall, 72.7% (16/22) of the ROH carriers showed ultrasound abnormalities, of whom eight (50%, 8/16) had adverse perinatal outcomes. Our study demonstrates that the clinical relevance of ROHs should be examined regarding fetuses with ROHs occurring on imprinted chromosomes or those derived from consanguineous parents in prenatal diagnoses; imprinting disorders and/or autosomal recessive diseases attributed to ROHs should be considered during genetic counseling.
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Peng B, Gao YH, Xie JQ, He XW, Wang CC, Xu JF, Zhang GJ. Clinical and genetic spectrum of primary ciliary dyskinesia in Chinese patients: a systematic review. Orphanet J Rare Dis 2022; 17:283. [PMID: 35854386 PMCID: PMC9295413 DOI: 10.1186/s13023-022-02427-1] [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: 03/05/2022] [Accepted: 06/30/2022] [Indexed: 11/15/2022] Open
Abstract
Background Primary ciliary dyskinesia (PCD) represents a highly heterogenous disorder with extensive clinical and genetic patterns among populations of different geographic location and ethnic origin. However, data about Chinese patients are limited. We aimed to summarize the clinical and genetic spectrum of Chinese PCD patients based on all available literatures. Methods We searched Embase, Pubmed, Web of Science and Chinese databases including CNKI, SinoMed and Wanfang from 1981 to 2021, to identify articles reporting patients with PCD in China, which had included information about transmission electron microscopy and/or genetic testing. Results A total of 244 Chinese PCD patients in 52 articles were included. Of these patients, the mean age was 13.1 years, and 55 patients (22.5%) were diagnosed with PCD after 18 years old. Compared with patients diagnosed with PCD in childhood or infancy, patients diagnosed with PCD in adulthood had a higher prevalence of chronic wet cough, sinusitis, Pseudomonas aeruginosa (PA) isolation and radiological bronchiectasis as well as worse lung function. 25 PCD-related genes were identified in 142 patients, and DNAH5, DNAH11, CCDC39 and CCDC40 were the most frequently detected mutations. More than half of genetic variants were loss-of-function mutations, and the majority of these variants were seen only once. Correlations between PCD phenotype, genotype and ciliary ultrastructure were also evidenced. Conclusions Diagnostic delay and under-recognition of PCD remain a big issue in China, which contributes to progressive lung disease and PA infection indicating worse outcome. Specialist equipment and expertise are urgently required to facilitate the early diagnosis and treatment of PCD. Trial registry PROSPERO; No.: CRD42021257804; URL:www.crd.york.ac.uk/prospero/ Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02427-1.
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Affiliation(s)
- Bo Peng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Yong-Hua Gao
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China.
| | - Jia-Qi Xie
- Department of Respiratory and Critical Care Medicine, Xiangyang Central Hospital, Xiangyang, China
| | - Xiao-Wen He
- Department of Respiratory and Critical Care Medicine, Xuchang Central Hospital, Xuchang, China
| | - Cong-Cong Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Jin-Fu Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China
| | - Guo-Jun Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China.
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Guo T, Lu C, Yang D, Lei C, Liu Y, Xu Y, Yang B, Wang R, Luo H. Case Report: DNAAF4 Variants Cause Primary Ciliary Dyskinesia and Infertility in Two Han Chinese Families. Front Genet 2022; 13:934920. [PMID: 35903363 PMCID: PMC9315306 DOI: 10.3389/fgene.2022.934920] [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: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Primary ciliary dyskinesia (PCD) is a rare genetic disorder, predominantly autosomal recessive. The dynein axonemal assembly factor 4 (DNAAF4) is mainly involved in the preassembly of multisubunit dynein protein, which is fundamental to the proper functioning of cilia and flagella. There are few reports of PCD-related pathogenic variants of DNAAF4, and almost no DNAAF4-related articles focused on sperm phenotype. Moreover, the association between DNAAF4 and scoliosis has never been reported, to the best of our knowledge.Materials and Methods: We recruited two patients with a clinical diagnosis of PCD. One came from a consanguineous and another from a non-consanguineous family. Clinical data, laboratory test results, and imaging data were analyzed. Through whole exome sequencing, immunofluorescence, electron microscopy, high-speed video microscopy analysis, and hematoxylin–eosin (HE) staining, we identified the disease-associated variants and validated the pathogenicity.Results: Proband 1 (P1, F1: II-1), a 19-year-old man, comes from a non-consanguineous family-I, and proband 2 (P2, F2: II-1), a 37-year-old woman, comes from a consanguineous family-II. Both had sinusitis, bronchiectasis, situs inversus, and scoliosis. P1 also had asthenoteratozoospermia, and P2 had an immature uterus. Two homozygous pathogenic variants in DNAAF4 (NM_130810.4), c.988C > T, p.(Arg330Trp), and DNAAF4 (NM_130810.4), c.733 C > T, p.(Arg245*), were identified through whole exome sequencing. High-speed microscopy analysis showed that most of the cilia were static in P1, with complete static of the respiratory cilia in P2. Immunofluorescence showed that the outer dynein arms (ODA) and inner dynein arms (IDA) were absent in the respiratory cilia of both probands, as well as in the sperm flagellum of P1. Transmission electron microscopy revealed the absence of ODA and IDA of respiratory cilia of P2, and HE staining showed irregular, short, absent, coiled, and bent flagella.Conclusion: Our study identified a novel variant c.733C > T, which expanded the spectrum of DNAAF4 variants. Furthermore, we linked DNAAF4 to asthenoteratozoospermia and likely scoliosis in patients with PCD. This study will contribute to a better understanding of PCD.
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Affiliation(s)
- Ting Guo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Chenyang Lu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Danhui Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Ying Liu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Yingjie Xu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Binyi Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Rongchun Wang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
- *Correspondence: Hong Luo, ; Rongchun Wang,
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
- *Correspondence: Hong Luo, ; Rongchun Wang,
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Wang L, Wang R, Yang D, Lu C, Xu Y, Liu Y, Guo T, Lei C, Luo H. Novel RSPH4A Variants Associated With Primary Ciliary Dyskinesia-Related Infertility in Three Chinese Families. Front Genet 2022; 13:922287. [PMID: 35812741 PMCID: PMC9257073 DOI: 10.3389/fgene.2022.922287] [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: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The radial spoke head component 4A (RSPH4A) is involved in the assembly of radial spokes, which is essential for motile cilia function. Asthenoteratozoospermia in primary ciliary dyskinesia (PCD) related to RSPH4A variants has not been reported. Materials and Methods: RSPH4A variants were identified and validated using whole-exome and Sanger sequencing in three unrelated Chinese families. High-speed video microscopy analysis (HSVA) was performed to measure the beating frequency and pattern of nasal cilia of the patients and healthy control. Papanicolaou staining and computer-aided sperm analysis were performed to analyze the morphology and motility of the sperm in patient 1. Immunofluorescence was adopted to confirm the structure deficiency of sperm and nasal cilia. Results: Patient 1 from family 1 is a 22-year-old unmarried male presented with bronchiectasis. Semen analysis and sperm Papanicolaou staining confirmed asthenoteratozoospermia. Novel compound heterozygous RSPH4A variants c.2T>C, p.(Met1Thr) and c.1774_1775del, p.(Leu592Aspfs*5) were detected in this patient. Patients 2 and 3 are from two unrelated consanguineous families; they are both females and exhibited bronchiectasis and infertility. Two homozygous RSPH4A variants c.2T>C, p.(Met1Thr) and c.351dupT, p.(Pro118Serfs*2) were detected, respectively. HSVA showed that most of the cilia in patients 1 and 3 were with abnormal rotational movement. The absence of RSPH4A and RSPH1 in patient 1's sperm and patient 3's respiratory cilia was indicated by immunofluorescence. Patient 2 died of pulmonary infection and respiratory failure at the age of 35 during follow-up. Conclusion: Dysfunctional sperm flagellum and motile cilia in the respiratory tract and the fallopian tube were found in patients with RSPH4A variants. Our study enriches the genetic spectrum and clinical phenotypes of RSPH4A variants in PCD, and c.2T>C, p.(Met1Thr) detected in our patients may be a hotspot RSPH4A variant in Chinese.
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Affiliation(s)
- Lin Wang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Rongchun Wang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Danhui Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Chenyang Lu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Yingjie Xu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Ying Liu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Ting Guo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
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10
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Feng J, Li J, Du Y, Shi T, Sharma L, Jie Z. Case Report: Rare Dynein Axonemal Heavy Chain 9 Mutations in a Han-Chinese Patient With Kartagener Syndrome. Front Med (Lausanne) 2022; 9:893968. [PMID: 35770021 PMCID: PMC9234165 DOI: 10.3389/fmed.2022.893968] [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: 03/11/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
A 52-year-old woman presented with respiratory symptoms of productive cough and shortness of breath. She had suffered from repeated pneumonia. The CT scans revealed chronic sinusitis, tree bud signs in pulmonary imaging, and situs inversus. She received a primary diagnosis of Kartagener syndrome of primary ciliary dyskinesia (PCD) and a genetic examination was performed. Compound heterozygous mutations in dynein axonemal heavy chain 9 (DNAH9) were identified, which encoded outer dynein arms (ODAs) components. DNAH9 mutations are relatively rare events in PCD, and this is the first report of PCD patients with DNAH9 mutations in the Chinese population. Further, a literature review of mutations in PCD was conducted.
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Affiliation(s)
- Jingjing Feng
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Junqing Li
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Yong Du
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Tianyun Shi
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Center of Community-Based Health Research, Fudan University, Shanghai, China
- *Correspondence: Zhijun Jie,
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11
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Picchetta L, Caroselli S, Figliuzzi M, Cogo F, Zambon P, Costa M, Pergher I, Patassini C, Cortellessa F, Zuccarello D, Poli M, Capalbo A. Molecular tools for the genomic assessment of oocyte’s reproductive competence. J Assist Reprod Genet 2022; 39:847-860. [PMID: 35124783 PMCID: PMC9050973 DOI: 10.1007/s10815-022-02411-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
The most important factor associated with oocytes' developmental competence has been widely identified as the presence of chromosomal abnormalities. However, growing application of genome-wide sequencing (GS) in population diagnostics has enabled the identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting IVF outcomes and reproductive fitness. Indeed, GS analysis in families with history of isolated infertility has recently led to the discovery of new genes and variants involved in specific human infertility endophenotypes that impact the availability and the functionality of female gametes by altering unique mechanisms necessary for oocyte maturation and early embryo development. Ongoing advancements in analytical and bioinformatic pipelines for the study of the genetic determinants of oocyte competence may provide the biological evidence required not only for improving the diagnosis of isolated female infertility but also for the development of novel preventive and therapeutic approaches for reproductive failure. Here, we provide an updated discussion and review of the progresses made in preconception genomic medicine in the identification of genetic factors associated with oocyte availability, function, and competence.
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12
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Li Q, Tian S, Yan B, Liu CM, Lam TW, Li R, Luo R. Building a Chinese pan-genome of 486 individuals. Commun Biol 2021; 4:1016. [PMID: 34462542 PMCID: PMC8405635 DOI: 10.1038/s42003-021-02556-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Pan-genome sequence analysis of human population ancestry is critical for expanding and better defining human genome sequence diversity. However, the amount of genetic variation still missing from current human reference sequences is still unknown. Here, we used 486 deep-sequenced Han Chinese genomes to identify 276 Mbp of DNA sequences that, to our knowledge, are absent in the current human reference. We classified these sequences into individual-specific and common sequences, and propose that the common sequence size is uncapped with a growing population. The 46.646 Mbp common sequences obtained from the 486 individuals improved the accuracy of variant calling and mapping rate when added to the reference genome. We also analyzed the genomic positions of these common sequences and found that they came from genomic regions characterized by high mutation rate and low pathogenicity. Our study authenticates the Chinese pan-genome as representative of DNA sequences specific to the Han Chinese population missing from the GRCh38 reference genome and establishes the newly defined common sequences as candidates to supplement the current human reference.
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Affiliation(s)
- Qiuhui Li
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, China
| | - Bin Yan
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Chi Man Liu
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Tak-Wah Lam
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China.
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.
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13
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Xiong Y, Xia H, Yuan L, Deng S, Ding Z, Deng H. Identification of compound heterozygous DNAH11 variants in a Han-Chinese family with primary ciliary dyskinesia. J Cell Mol Med 2021; 25:9028-9037. [PMID: 34405951 PMCID: PMC8435457 DOI: 10.1111/jcmm.16866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/24/2021] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a group of genetically and clinically heterogeneous disorders with motile cilia dysfunction. It is clinically characterized by oto‐sino‐pulmonary diseases and subfertility, and half of the patients have situs inversus (Kartagener syndrome). To identify the genetic cause in a Han‐Chinese pedigree, whole‐exome sequencing was conducted in the 37‐year‐old proband, and then, Sanger sequencing was performed on available family members. Minigene splicing assay was applied to verify the impact of the splice‐site variant. Compound heterozygous variants including a splice‐site variant (c.1974‐1G>C, rs1359107415) and a missense variant (c.7787G>A, p.(Arg2596Gln), rs780492669), in the dynein axonemal heavy chain 11 gene (DNAH11) were identified and confirmed as the disease‐associated variants of this lineage. The minigene expression in vitro revealed that the c.1974‐1G>C variant could cause skipping over exon 12, predicted to result in a truncated protein. This discovery may enlarge the DNAH11 variant spectrum of PCD, promote accurate genetic counselling and contribute to PCD diagnosis.
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Affiliation(s)
- Ying Xiong
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hong Xia
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Disease Genome Research Center, Central South University, Changsha, China
| | - Sheng Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zerui Ding
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Disease Genome Research Center, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
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14
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Bu H, Sun G, Zhu Y, Yang Y, Tan Z, Zhao T, Hu S. The M310T mutation in the GATA4 gene is a novel pathogenic target of the familial atrial septal defect. BMC Cardiovasc Disord 2021; 21:12. [PMID: 33413087 PMCID: PMC7788758 DOI: 10.1186/s12872-020-01822-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although most cases of atrial septal defect (ASD) are sporadic, familial cases have been reported, which may be caused by mutation of transcription factor GATA binding protein 4 (GATA4). Herein we combined whole-exome sequencing and bioinformatics strategies to identify a novel mutation in GATA4 accounting for the etiology in a Chinese family with ASD. METHODS We identified kindred spanning 3 generations in which 3 of 12 (25.0%) individuals had ASD. Punctilious records for the subjects included complete physical examination, transthoracic echocardiography, electrocardiograph and surgical confirming. Whole-exome capture and high-throughput sequencing were performed on the proband III.1. Sanger sequencing was used to validate the candidate variants, and segregation analyses were performed in the family members. RESULTS Direct sequencing of GATA4 from the genomic DNA of family members identified a T-to-C transition at nucleotide 929 in exon 5 that predicted a methionine to threonine substitution at codon 310 (M310T) in the nuclear localization signal (NLS) region. Two affected members (II.2 and III.3) and the proband (III.1) who was recognized as a carrier exhibited this mutation, whereas the other unaffected family members or control individuals did not. More importantly, the mutation GATA4 (c.T929C: p.M310T) has not been reported previously in either familial or sporadic cases of congenital heart defects (CHD). CONCLUSIONS We identified for the first time a novel M310T mutation in the GATA4 gene that is located in the NLS region and leads to family ASD with arrhythmias. However, the mechanism by which this pathogenic mutation contributes to the development of heart defect and tachyarrhythmias remains to be ascertained.
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Affiliation(s)
- Haisong Bu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China.,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Guowen Sun
- Department of Cardiothoracic Surgery, Chenzhou No. 1 People's Hospital, Chenzhou, 423000, Hunan, People's Republic of China
| | - Yun Zhu
- Department of Cardiothoracic Surgery, Chenzhou No. 1 People's Hospital, Chenzhou, 423000, Hunan, People's Republic of China
| | - Yifeng Yang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China.,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Zhiping Tan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China.,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Tianli Zhao
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China.,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Shijun Hu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China. .,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China. .,Department of Cardiovascular Surgery, The German Heart Centre, 80636, Munich, Germany.
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15
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Bi-allelic BRWD1 variants cause male infertility with asthenoteratozoospermia and likely primary ciliary dyskinesia. Hum Genet 2021; 140:761-773. [PMID: 33389130 DOI: 10.1007/s00439-020-02241-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022]
Abstract
Genetics-associated asthenoteratozoospermia is often seen in patients with multiple morphological abnormalities of the sperm flagella (MMAF). Although 24 causative genes have been identified, these explain only approximately half of patients with MMAF. Since sperm flagella and motile cilia (especially respiratory cilia) have similar axonemal structures, many patients with MMAF also exhibit respiratory symptoms, such as recurrent airway infection, chronic sinusitis, and bronchiectasis, which are frequently associated with primary ciliary dyskinesia (PCD), another recessive disorder. Here, exome sequencing was conducted to evaluate the genetic cause in 53 patients with MMAF and classic PCD/PCD-like symptoms. Two homozygous missense variants and a compound-heterozygous variant in the BRWD1 gene were identified in three unrelated individuals. BRWD1 staining was detected in the whole flagella and respiratory cilia of normal controls but was absent in BRWD1-mutated individuals. Transmission electron microscopy and immunostaining demonstrated that BRWD1 deficiency in human affected respiratory cilia and sperm flagella differently, as the absence of outer and inner dynein arms in sperm flagellum and respiratory cilia, while with a decreased number and outer doublet microtubule defects of respiratory cilia. To our knowledge, this is the first report of a BRWD1-variant-related disease in humans, manifesting as an autosomal recessive form of MMAF and PCD/PCD-like symptoms. Our data provide a basis for further exploring the molecular mechanism of BRWD1 gene during spermatogenesis and ciliogenesis.
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16
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Liu L, Liu YJ, Guo T, Luo H. Identification of a Missense Mutation in the Surfactant Protein A2 Gene in a Chinese Family with Interstitial Lung Disease. DNA Cell Biol 2020; 40:126-131. [PMID: 33181027 DOI: 10.1089/dna.2020.6045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Interstitial lung disease (ILD) is a large group of disorders, most of which lead to progressive scarring of lung tissue. The scarring associated with ILD eventually affects your ability to breathe and get enough oxygen into your bloodstream. The typical symptoms of ILD are shortness of breath at rest or aggravated by exertion and dry cough. In this study, we enrolled a family with ILDs from central south region of China. Three patients suffered from repeated cough and shortness of breath. The high resolution computed tomography (HRCT) testing further confirmed the diagnosis of interstitial lung lesions. Whole exome sequencing (WES) and Sanger sequencing were applied to detect the genetic lesion of the family. By employing WES, a novel heterozygous mutation (NM_001098668: c.554C>T/p.A185V) of surfactant protein A2 (SFTPA2) was identified in the affected individuals and absent in the healthy members. Bioinformatics analysis predicted that this mutation is disease-causing mutation and located in an evolutionarily conserved site of SFTPA2 protein. The novel mutation may disrupt the stability of SFTPA2 protein and induce endoplasmic reticulum stress, finally leading to ILD under the influence of microorganisms. Our study not only expands the spectrum of SFTPA2 mutations but also helps the family members to mitigate ILD risk factors. The study also supplements and improves genetic testing strategies and ILD risk estimation methodologies for China.
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Affiliation(s)
- Lv Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yi-Jie Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ting Guo
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hong Luo
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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17
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Shamseldin HE, Al Mogarri I, Alqwaiee MM, Alharbi AS, Baqais K, AlSaadi M, AlAnzi T, Alhashem A, Saghier A, Ameen W, Ibrahim N, Yang J, Abdulwahab F, Hashem M, Chivukula RR, Alkuraya FS. An exome-first approach to aid in the diagnosis of primary ciliary dyskinesia. Hum Genet 2020; 139:1273-1283. [PMID: 32367404 DOI: 10.1007/s00439-020-02170-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/25/2020] [Indexed: 01/31/2023]
Abstract
Unlike disorders of primary cilium, primary ciliary dyskinesia (PCD) has a much narrower clinical spectrum consistent with the limited tissue distribution of motile cilia. Nonetheless, PCD diagnosis can be challenging due to the overlapping features with other disorders and the requirement for sophisticated tests that are only available in specialized centers. We performed exome sequencing on all patients with a clinical suspicion of PCD but for whom no nasal nitric oxide test or ciliary functional assessment could be ordered. Among 81 patients (56 families), in whom PCD was suspected, 68% had pathogenic or likely pathogenic variants in established PCD-related genes that fully explain the phenotype (20 variants in 11 genes). The major clinical presentations were sinopulmonary infections (SPI) (n = 58), neonatal respiratory distress (NRD) (n = 2), laterality defect (LD) (n = 6), and combined LD/SPI (n = 15). Biallelic likely deleterious variants were also encountered in AKNA and GOLGA3, which we propose as novel candidates in a lung phenotype that overlaps clinically with PCD. We also encountered a PCD phenocopy caused by a pathogenic variant in ITCH, and a pathogenic variant in CEP164 causing Bardet-Biedl syndrome and PCD presentation as a very rare example of the dual presentation of these two disorders of the primary and motile cilia. Exome sequencing is a powerful tool that can help "democratize" the diagnosis of PCD, which is currently limited to highly specialized centers.
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Affiliation(s)
- Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ibrahim Al Mogarri
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mansour M Alqwaiee
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Adel S Alharbi
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Khaled Baqais
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Muslim AlSaadi
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Talal AlAnzi
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Afaf Saghier
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Waleed Ameen
- Department of Pediatrics, King Saud Medical City, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jason Yang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Raghu R Chivukula
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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18
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Guo Z, Chen W, Wang L, Qian L. Clinical and Genetic Spectrum of Children with Primary Ciliary Dyskinesia in China. J Pediatr 2020; 225:157-165.e5. [PMID: 32502479 DOI: 10.1016/j.jpeds.2020.05.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To report detailed knowledge about the clinical manifestations, ciliary phenotypes, genetic spectrum as well as phenotype/genotype correlation in primary ciliary dyskinesia (PCD) in Chinese children. STUDY DESIGN We recruited 50 Chinese children with PCD. Extensive clinical assessments, nasal nitric oxide, high-speed video analysis, transmission electron microscopy, and genetic testing were performed to characterize the phenotypes and genotypes of these patients. RESULTS Common clinical features included chronic wet cough (85.4%), laterality defects (70.0%), and neonatal respiratory distress (55.8%). A high prevalence of congenital abnormalities (30.2%, 13/43), observed in patients who underwent comprehensive examination for comorbidities, included thoracic deformity (11.6%, 5/43), congenital heart disease (9.3%, 4/43), and sensorineural deafness (2.3%, 1/43). For 24 children age >6 years, the mean predicted values of forced expiratory volume in 1 second were 87.2%. Bronchiectasis evident on high-resolution computed tomography was reported in 38.1% of patients (16/42). Biallelic mutations (81 total; 57 novel) were identified in 13 genes: DNAAF3, DNAAF1, DNAH5, DNAH11, CCDC39, CCDC40, CCDC114, CCDC103, HYDIN, CCNO, DNAI1, OFD1, and SPAG1. Overall, ciliary ultrastructural and beat pattern correlated well with the genotype. However, variable phenotypes were also observed in CCDC39 and DNAH5 mutant cilia. CONCLUSIONS This large PCD cohort in China broadens the clinical, ciliary phenotypes, and genetic characteristics of children with PCD. Our findings are roughly consistent with previous studies besides some peculiarities such as high prevalence of associated abnormalities.
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Affiliation(s)
- Zhuoyao Guo
- Respirology Department, Children's Hospital of Fudan University, Shanghai, P.R. China
| | - Weicheng Chen
- Cardiothoracic Surgery Department, Children's Hospital of Fudan University, Shanghai, China
| | - Libo Wang
- Respirology Department, Children's Hospital of Fudan University, Shanghai, P.R. China
| | - Liling Qian
- Respirology Department, Children's Hospital of Fudan University, Shanghai, P.R. China.
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19
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Colas P. Cyclin-dependent kinases and rare developmental disorders. Orphanet J Rare Dis 2020; 15:203. [PMID: 32762766 PMCID: PMC7410148 DOI: 10.1186/s13023-020-01472-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Extensive studies in the past 30 years have established that cyclin-dependent kinases (CDKs) exert many diverse, important functions in a number of molecular and cellular processes that are at play during development. Not surprisingly, mutations affecting CDKs or their activating cyclin subunits have been involved in a variety of rare human developmental disorders. These recent findings are reviewed herein, giving a particular attention to the discovered mutations and their demonstrated or hypothesized functional consequences, which can account for pathological human phenotypes. The review highlights novel, important CDK or cyclin functions that were unveiled by their association with human disorders, and it discusses the shortcomings of mouse models to reveal some of these functions. It explains how human genetics can be used in combination with proteome-scale interaction databases to loom regulatory networks around CDKs and cyclins. Finally, it advocates the use of these networks to profile pathogenic CDK or cyclin variants, in order to gain knowledge on protein function and on pathogenic mechanisms.
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Affiliation(s)
- Pierre Colas
- Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université / CNRS, Roscoff, France.
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20
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Sironen A, Shoemark A, Patel M, Loebinger MR, Mitchison HM. Sperm defects in primary ciliary dyskinesia and related causes of male infertility. Cell Mol Life Sci 2020; 77:2029-2048. [PMID: 31781811 PMCID: PMC7256033 DOI: 10.1007/s00018-019-03389-7] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 01/22/2023]
Abstract
The core axoneme structure of both the motile cilium and sperm tail has the same ultrastructural 9 + 2 microtubular arrangement. Thus, it can be expected that genetic defects in motile cilia also have an effect on sperm tail formation. However, recent studies in human patients, animal models and model organisms have indicated that there are differences in components of specific structures within the cilia and sperm tail axonemes. Primary ciliary dyskinesia (PCD) is a genetic disease with symptoms caused by malfunction of motile cilia such as chronic nasal discharge, ear, nose and chest infections and pulmonary disease (bronchiectasis). Half of the patients also have situs inversus and in many cases male infertility has been reported. PCD genes have a role in motile cilia biogenesis, structure and function. To date mutations in over 40 genes have been identified cause PCD, but the exact effect of these mutations on spermatogenesis is poorly understood. Furthermore, mutations in several additional axonemal genes have recently been identified to cause a sperm-specific phenotype, termed multiple morphological abnormalities of the sperm flagella (MMAF). In this review, we discuss the association of PCD genes and other axonemal genes with male infertility, drawing particular attention to possible differences between their functions in motile cilia and sperm tails.
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Affiliation(s)
- Anu Sironen
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK.
| | - Amelia Shoemark
- Department of Paediatrics, Royal Brompton Hospital, London, UK
- School of Medicine, University of Dundee, Dundee, UK
| | - Mitali Patel
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Michael R Loebinger
- Host Defence Unit, Royal Brompton and Harefield NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
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21
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Quandt E, Ribeiro MPC, Clotet J. Atypical cyclins: the extended family portrait. Cell Mol Life Sci 2020; 77:231-242. [PMID: 31420702 PMCID: PMC6971155 DOI: 10.1007/s00018-019-03262-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 12/12/2022]
Abstract
Regulation of cell division is orchestrated by cyclins, which bind and activate their catalytic workmates, the cyclin-dependent kinases (CDKs). Cyclins have been traditionally defined by an oscillating (cyclic) pattern of expression and by the presence of a characteristic "cyclin box" that determines binding to the CDKs. Noteworthy, the Human Genome Sequence Project unveiled the existence of several other proteins containing the "cyclin box" domain. These potential "cyclins" have been named new, orphan or atypical, creating a conundrum in cyclins nomenclature. Moreover, although many years have passed after their discovery, the scarcity of information regarding these possible members of the family has hampered the establishment of criteria for systematization. Here, we discuss the criteria that define cyclins and we propose a classification and nomenclature update based on structural features, interactors, and phylogenetic information. The application of these criteria allows to systematically define, for the first time, the subfamily of atypical cyclins and enables the use of a common nomenclature for this extended family.
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Affiliation(s)
- Eva Quandt
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, Sant Cugat del Vallès, 08195, Barcelona, Spain
| | - Mariana P C Ribeiro
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, Sant Cugat del Vallès, 08195, Barcelona, Spain.
| | - Josep Clotet
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, Sant Cugat del Vallès, 08195, Barcelona, Spain.
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22
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Yue Y, Huang Q, Zhu P, Zhao P, Tan X, Liu S, Li S, Han X, Cheng L, Li B, Fu Y. Identification of Pathogenic Mutations and Investigation of the NOTCH Pathway Activation in Kartagener Syndrome. Front Genet 2019; 10:749. [PMID: 31507630 PMCID: PMC6713718 DOI: 10.3389/fgene.2019.00749] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
Primary ciliary dyskinesia (PCD), a rare genetic disorder, is mostly caused by defects in more than 40 known cilia structure-related genes. However, in approximately 20-35% of patients, it is caused by unknown genetic factors, and the inherited pathogenic factors are difficult to confirm. Kartagener syndrome (KTS) is a subtype of PCD associated with situs inversus, presenting more complex genetic heterogeneity. The aim of this study was to identify pathogenic mutations of candidate genes in Chinese patients with KTS and investigate the activation of the heterotaxy-related NOTCH pathway. Whole-exome sequencing was conducted in five patients with KTS. Pathogenic variants were identified using bioinformatics analysis. Candidate variants were validated by Sanger sequencing. The expression of the NOTCH pathway target genes was detected in patients with KTS. We identified 10 KTS-associated variants in six causative genes, namely, CCDC40, DNAH1, DNAH5, DNAH11, DNAI1, and LRRC6. Only one homozygote mutation was identified in LRRC6 (c.64dupT). Compound heterozygous mutations were found in DNAH1 and DNAH5. Six novel mutations were identified in four genes. Further analyses showed that the NOTCH pathway might be activated in patients with KTS. Overall, our study showed that compound heterozygous mutations widely exist in Chinese KTS patients. Our results demonstrated that the activation of the NOTCH pathway might play a role in the situs inversus pathogenicity of KTS. These findings highlight that Kartagener syndrome might be a complex genetic heterogeneous disorder mediated by heterozygous mutations in multiple PCD- or cilia-related genes.
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Affiliation(s)
- Yongjian Yue
- Key Laboratory of Shenzhen Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Disease, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Qijun Huang
- Key Laboratory of Shenzhen Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Disease, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Peng Zhu
- Central Lab of Shenzhen Pingshan People's Hospital, Shenzhen, China
| | - Pan Zhao
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Xinjuan Tan
- Key Laboratory of Shenzhen Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Disease, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Shengguo Liu
- Key Laboratory of Shenzhen Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Disease, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Shulin Li
- Key Laboratory of Shenzhen Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Disease, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Xuemei Han
- Key Laboratory of Shenzhen Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Disease, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Linling Cheng
- State Key Laboratory of Respiration Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Li
- Department of Pediatric, First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Yingyun Fu
- Key Laboratory of Shenzhen Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Disease, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
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23
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Liang Y, Jiang L, Zhong X, Hochwald SN, Wang Y, Huang L, Nie Q, Huang H, Xu JF. Discovery of Aberrant Alteration of Genome in Colorectal Cancer by Exome Sequencing. Am J Med Sci 2019; 358:340-349. [PMID: 31445671 DOI: 10.1016/j.amjms.2019.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/27/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND This study analyzed multiple parameters including somatic single nucleotide variations (SNVs), Insertion/Deletions, significantly mutated genes (SMGs), copy number variations and frequently altered pathways aims to discover novel aberrances in the tumorigenesis of colorectal cancer (CRC). MATERIALS AND METHODS Exome sequencing was performed on an Illumina platform to identify novel potential somatic variances in 34 paired tumor and adjacent normal tissues from 17 CRC patients. Results were compared with databases (dbSNP138, 1000 genomes SNP, Hapmap, Catalogue of Somatic Mutation of Cancer and ESP6500) and analyzed. MuSic software was used to identify SMGs. RESULTS In total, 1,637 somatic SNVs in 17 analyzed tumors were identified. Only 7 SNVs were shared by more than 1 tumor, suggesting that over 99% of the analyzed SNVs were independent events. Mutation of KRAS p. G12D and ZNF717 p. L39V were the most common SNVs. Moreover, 10 SMGs namely KRAS, TP53, SMAD4, ZNF717, FBXW7, APC, ZNF493, CDR1, the Armadillo repeat containing 4 (ARMC4) and sulfate-modifying factor 2 (SUMF2) were found. Among those, ZNF717, ZNF493, CDR1, ARMC4 and SUMF2 were novel frequent genes in CRC. For copy number variations analysis, gains in 10q25.3, 1p31.1, 1q44, 10q23.33, 11p15.4 and 20q13.33, and loss of 3q21.3 and 3q29 were frequent aberrations identified in our results. CONCLUSIONS We frequently found novel genes ZNF717, ZNF493, CDR1, ARMC4 and SUMF2 and gains in 10q25.3, which may be functional mutation in CRC. The high-frequency private events such as SNVs confirm the highly heterogeneous mutations found in CRCs. The mutated genes sites in different patients may vary significantly, which may also be more challenging for clinical treatment.
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Affiliation(s)
- Yuanzi Liang
- Department of Clinical Immunology, Institute of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, China
| | | | - Xiaogang Zhong
- Department of Gastrointestinal Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Steven N Hochwald
- Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, New York
| | - Yongsi Wang
- Division of Genome Sequencing, Huayin Medical Laboratory, Guangzhou, Guangdong, China
| | - Lihe Huang
- Department of Laboratory Medicine, Debao County Hospital, Baise, Guangxi, China
| | - Qiumiao Nie
- Wilking Biotechnology Co., Ltd, Nanning, Guangxi, China
| | - Huayi Huang
- Department of Laboratory Medicine and; Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, New York.
| | - Jun-Fa Xu
- Department of Clinical Immunology, Institute of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, China.
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24
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Bu H, Liu L, Hu S, Tan Z, Zhao T. Targeted next‑generation sequencing for research and diagnostics in congenital heart disease, and cleft lip and/or palate. Mol Med Rep 2019; 19:3831-3840. [PMID: 30896870 DOI: 10.3892/mmr.2019.10043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/08/2019] [Indexed: 11/06/2022] Open
Abstract
Congenital heart disease (CHD), and cleft lip and palate (CLP) are currently the most common types of structural malformation in infants. Various methods have been used to identify the disease‑associated genes. However, targeted next‑generation sequencing (NGS) is not yet considered an option for routine use. Thus, the present study aimed to assess the safety and feasibility of using targeted NGS in patients with CHD concomitant with CLP. Between November 2015 and May 2017, a total of 17 patients with CHD concomitant with CLP, who were excluded from a diagnosis of trisomy syndrome, were selected at The Second Xiangya Hospital of Central South University (Changsha, China). Genomic DNA was extracted from peripheral blood samples of the patients. The copy number variants (CNVs) were determined by conducting a single nucleotide polymorphism (SNP) array with Illumina HumanOmni1‑Quad Beadchip, while information on other gene mutations was obtained from targeted sequencing. The functions of gene mutations were then predicted using the PolyPhen‑2, SIFT and Mutation Taster tools. Finally, Sanger sequencing was used to verify the mutations. The results identified no pathogenic mutations in CNVs analyzed by high‑throughput SNP sequencing. Targeted NGS results demonstrated that 10 patients (58.8%) carried gene mutations, including 4 (23.5%) genetically diagnosed cases and 6 (35.3%) cases with unknown etiology. The 4 known diseases were Opitz G/BBB syndrome caused by MID1 gene mutation, Loeys‑Dietz syndrome caused by TGFBR1 gene mutation, Ritscher‑Schinzel/3C syndrome caused by KIAA0196 gene mutation and CHARGE syndrome caused by CHD7 gene mutation. The remaining 6 cases were not genetically diagnosed, although they carried candidate genes. In conclusion, the present study demonstrated that targeted NGS was an effective and accurate candidate gene detection method in patients with CHD concomitant with CLP.
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Affiliation(s)
- Haisong Bu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Lin Liu
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Shijun Hu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zhiping Tan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Tianli Zhao
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
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25
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Andjelkovic M, Minic P, Vreca M, Stojiljkovic M, Skakic A, Sovtic A, Rodic M, Skodric-Trifunovic V, Maric N, Visekruna J, Spasovski V, Pavlovic S. Genomic profiling supports the diagnosis of primary ciliary dyskinesia and reveals novel candidate genes and genetic variants. PLoS One 2018; 13:e0205422. [PMID: 30300419 PMCID: PMC6177184 DOI: 10.1371/journal.pone.0205422] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/25/2018] [Indexed: 11/18/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a rare inherited autosomal recessive or X-linked disorder that mainly affects lungs. Dysfunction of respiratory cilia causes symptoms such as chronic rhinosinusitis, coughing, rhinitis, conductive hearing loss and recurrent lung infections with bronchiectasis. It is now well known that pathogenic genetic changes lead to ciliary dysfunction. Here we report usage of clinical-exome based NGS approach in order to reveal underlying genetic causes in cohort of 21 patient with diagnosis of PCD. By detecting 18 (12 novel) potentially pathogenic genetic variants, we established the genetic cause of 11 (9 unrelated) patients. Genetic variants were detected in six PCD disease-causing genes, as well as in SPAG16 and SPAG17 genes, that were not detected in PCD patients so far, but were related to some symptoms of PCD. The most frequently mutated gene in our cohort was DNAH5 (27.77%). Identified variants were in homozygous, compound heterozygous and trans-heterozygous state. For detailed characterization of one novel homozygous genetic variant in DNAI1 gene (c. 947_948insG, p. Thr318TyrfsTer11), RT-qPCR and Western Blot analysis were performed. Molecular diagnostic approach applied in this study enables analysis of 29 PCD disease-causing and related genes. It resulted in mutation detection rate of 50% and enabled discovery of twelve novel mutations and pointed two possible novel PCD candidate genes.
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Affiliation(s)
- Marina Andjelkovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Predrag Minic
- Mother and Child Health Care Institute of Serbia „Dr Vukan Cupic“, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Misa Vreca
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Stojiljkovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Anita Skakic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Aleksandar Sovtic
- Mother and Child Health Care Institute of Serbia „Dr Vukan Cupic“, Belgrade, Serbia
| | - Milan Rodic
- Mother and Child Health Care Institute of Serbia „Dr Vukan Cupic“, Belgrade, Serbia
| | - Vesna Skodric-Trifunovic
- School of Medicine, University of Belgrade, Belgrade, Serbia
- Clinic for Pulmonology, Clinical Center of Serbia, Belgradе, Serbia
| | - Nina Maric
- Clinic for children diseases, University Clinical Center of the Republic of Srpska, Banja Luka, Bosnia and Herzegovina
| | - Jelena Visekruna
- Mother and Child Health Care Institute of Serbia „Dr Vukan Cupic“, Belgrade, Serbia
| | - Vesna Spasovski
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- * E-mail:
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26
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Yang L, Banerjee S, Cao J, Bai X, Peng Z, Chen H, Huang H, Han P, Feng S, Yi N, Song X, Wu J. Compound Heterozygous Variants in the Coiled-Coil Domain Containing 40 Gene in a Chinese Family with Primary Ciliary Dyskinesia Cause Extreme Phenotypic Diversity in Cilia Ultrastructure. Front Genet 2018; 9:23. [PMID: 29456554 PMCID: PMC5801289 DOI: 10.3389/fgene.2018.00023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Purpose: Primary ciliary dyskinesia (PCD) is a rare genetic disorder manifested with recurrent infections of respiratory tract and infertility. Mutations in more than 20 genes including the Coiled-Coil Domain Containing 40 (CCDC40) gene are associated with PCD. A Chinese proband with a clinical diagnosis of PCD was analyzed for mutations in these genes to identify the genetic basis of the disease in the family. The proband showed altered mucociliary clearance of the airways, various degree of hyperemia and edema of the mucous membrane, left/right body asymmetry, infertility and ultrastructural abnormality of cilia in both sperm and bronchioles. Methods: The DNA from the proband was analyzed for genetic variation in a subset of genes known to cause PCD using targeted next generation sequencing in order to understand the molecular and genetic basis of the PCD in present family. The result of targeted next generation sequencing has been validated by Sanger sequencing and q-PCR. Results: Targeted next-generation sequencing identified two novel mutations (c.1259delA and EX17_20 deletion) in CCDC40 gene that causes abnormal CCDC40 mRNA expression. These two novel variants cause disorganization of axoneme filaments, which resulted in reduction of sperm motility and phenotypic diversity in ultrastructure of cilia in the proband. Conclusion: These findings highlight the significance of the mutations in CCDC40 as novel candidates for genetic testing in PCD patients as well as the key role of ICSI treatment for the families affected by this ciliary dysmotility. Our findings showed that our work enriched the performance of cilia ultrastructure which were not previously reported in PCD patients.
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Affiliation(s)
- Lin Yang
- Centre for Reproductive Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | | | - Jie Cao
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaohong Bai
- Centre for Reproductive Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhijun Peng
- Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Haixia Chen
- Centre for Reproductive Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Peng Han
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Na Yi
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xueru Song
- Centre for Reproductive Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Jing Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
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27
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Whole-Exome Sequencing Identified a Novel Compound Heterozygous Mutation of LRRC6 in a Chinese Primary Ciliary Dyskinesia Patient. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1854269. [PMID: 29511670 PMCID: PMC5817365 DOI: 10.1155/2018/1854269] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/07/2017] [Indexed: 11/27/2022]
Abstract
Primary ciliary dyskinesia (PCD) is a clinical rare peculiar disorder, mainly featured by respiratory infection, tympanitis, nasosinusitis, and male infertility. Previous study demonstrated it is an autosomal recessive disease and by 2017 almost 40 pathologic genes have been identified. Among them are the leucine-rich repeat- (LRR-) containing 6 (LRRC6) codes for a 463-amino-acid cytoplasmic protein, expressed distinctively in motile cilia cells, including the testis cells and the respiratory epithelial cells. In this study, we applied whole-exome sequencing combined with PCD-known genes filtering to explore the genetic lesion of a PCD patient. A novel compound heterozygous mutation in LRRC6 (c.183T>G/p.N61K; c.179-1G>A) was identified and coseparated in this family. The missense mutation (c.183T>G/p.N61K) may lead to a substitution of asparagine by lysine at position 61 in exon 3 of LRRC6. The splice site mutation (c.179-1G>A) may cause a premature stop codon in exon 4 and decrease the mRNA levels of LRRC6. Both mutations were not present in our 200 local controls, dbSNP, and 1000 genomes. Three bioinformatics programs also predicted that both mutations are deleterious. Our study not only further supported the importance of LRRC6 in PCD, but also expanded the spectrum of LRRC6 mutations and will contribute to the genetic diagnosis and counseling of PCD patients.
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