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Huang X, Huang J, Zhou X, Zhang C, Ding X, Wong PJC, Wang Y, Zhang R. Whole-exome sequencing has revealed novel genetic characteristics in intracranial germ cell tumours in the Chinese. Histopathology 2024; 84:1199-1211. [PMID: 38409885 DOI: 10.1111/his.15155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 12/02/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
AIMS Intracranial germ cell tumour (IGCT) is a type of rare central nervous system tumour that mainly occurs in children and adolescents, with great variation in its incidence rate and molecular characteristics in patients from different populations. The genetic alterations of IGCT in the Chinese population are still unknown. METHODS AND RESULTS In this study, 47 patients were enrolled and their tumour specimens were analysed by whole-exome sequencing (WES). We found that KIT was the most significantly mutated gene (15/47, 32%), which mainly occurred in the germinoma group (13/20, 65%), and less frequently in NGGCT (2/27, 7%). Copy number variations (CNVs) of FGF6 and TFE3 only appeared in NGGCT patients (P = 0.003 and 0.032, respectively), while CNVs of CXCR4, RAC2, PDGFA, and FEV only appeared in germinoma patients (P = 0.004 of CXCR4 and P = 0.027 for the last three genes). Compared with a previous Japanese cohort, the somatic mutation rates of RELN and SYNE1 were higher in the Chinese. Prognostic analysis showed that the NF1 mutation was associated with shorter overall survival and progression-free survival in IGCT patients. Clonal evolution analysis revealed an early branched evolutionary pattern in two IGCT patients who underwent changes in the histological subtype or degree of differentiation during disease surveillance. CONCLUSION This study indicated that Chinese IGCT patients may have distinct genetic characteristics and identified several possible genetic alterations that have the potential to become prognostic biomarkers of NGGCT patients.
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Affiliation(s)
- Xiang Huang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
| | - Jianhan Huang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
| | - Xiaoyu Zhou
- GenomiCare Biotechnology (Shanghai) Co. Ltd, Shanghai, China
| | - Chao Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
| | - Xinghua Ding
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
| | - Peter Jih Cheng Wong
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
| | - Yang Wang
- Department of Radiotherapy, Huashan Hospital, Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
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Ma L, Gao L, Hu Y, Li X, Liu C, Ji J, Shi X, Pan A, An Y, Luo N, Xia Y, Jiang Y. Feasibility of whole-exome sequencing in fine-needle aspiration specimens of papillary thyroid microcarcinoma for the identification of novel gene mutations. Clin Genet 2024; 105:567-572. [PMID: 38326996 DOI: 10.1111/cge.14494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/07/2024] [Accepted: 01/21/2024] [Indexed: 02/09/2024]
Abstract
Genetic profiling is important for assisting the management of papillary thyroid microcarcinoma (PTMC). Although whole-exome sequencing (WES) of surgically resected PTMC tissue has been performed and revealed potential prognostic biomarkers, its application in PTMC fine-needle aspiration (FNA) specimens has not been explored. This study aimed to evaluate the feasibility of WES using FNA specimens of PTMC. Five PTMC patients were enrolled with clinical characteristics gathered. Fine aspiration cytology needle (23 gauges) was used to collect FNA biopsy with ultrasound guidance. WES analysis of FNA specimens from five PTMC patients and matched blood samples was performed. The WES of FNA samples yielded an average sequencing depth of 281× and average coverage of 99.5%. We identified 534 somatic single-nucleotide variants and 13 indels in total, and per sample, we found a mean of 24 exonic mutations, which affected a total of 120 genes. In the PTMC FNA samples, the most frequently mutated genes were BRAF and ANKRD18B, and the four driver genes were BRAF, AFF3, SRCAP, and EGFR. We also identified several germline cancer predisposing gene mutations. The results suggest that WES of FNA specimens is feasible for PTMC and can identify novel genetic mutations.
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Affiliation(s)
- Liyuan Ma
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Luying Gao
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ya Hu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyi Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunhao Liu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Ji
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinlong Shi
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Aonan Pan
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuang An
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nengwen Luo
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Xia
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuxin Jiang
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Makino K, Ishii T, Takeda H, Saito Y, Fujiwara Y, Fujimoto M, Ito T, Wakama S, Kumagai K, Munekage F, Horie H, Tomofuji K, Oshima Y, Uebayashi EY, Kawai T, Ogiso S, Fukumitsu K, Takai A, Seno H, Hatano E. Integrated analyses of the genetic and clinicopathological features of cholangiolocarcinoma: cholangiolocarcinoma may be characterized by mismatch-repair deficiency. J Pathol 2024; 263:32-46. [PMID: 38362598 DOI: 10.1002/path.6257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/25/2023] [Accepted: 12/21/2023] [Indexed: 02/17/2024]
Abstract
Cholangiolocarcinoma (CLC) is a primary liver carcinoma that resembles the canals of Hering and that has been reported to be associated with stem cell features. Due to its rarity, the nature of CLC remains unclear, and its pathological classification remains controversial. To clarify the positioning of CLC in primary liver cancers and identify characteristics that could distinguish CLC from other liver cancers, we performed integrated analyses using whole-exome sequencing (WES), immunohistochemistry, and a retrospective review of clinical information on eight CLC cases and two cases of recurrent CLC. WES demonstrated that CLC includes IDH1 and BAP1 mutations, which are characteristic of intrahepatic cholangiocarcinoma (iCCA). A mutational signature analysis showed a pattern similar to that of iCCA, which was different from that of hepatocellular carcinoma (HCC). CLC cells, including CK7, CK19, and EpCAM, were positive for cholangiocytic differentiation markers. However, the hepatocytic differentiation marker AFP and stem cell marker SALL4 were completely negative. The immunostaining patterns of CLC with CD56 and epithelial membrane antigen were similar to those of the noncancerous bile ductules. In contrast, mutational signature cluster analyses revealed that CLC formed a cluster associated with mismatch-repair deficiency (dMMR), which was separate from iCCA. Therefore, to evaluate MMR status, we performed immunostaining of four MMR proteins (PMS2, MSH6, MLH1, and MSH2) and detected dMMR in almost all CLCs. In conclusion, CLC had highly similar characteristics to iCCA but not to HCC. CLC can be categorized as a subtype of iCCA. In contrast, CLC has characteristics of dMMR tumors that are not found in iCCA, suggesting that it should be treated distinctly from iCCA. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Kenta Makino
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takamichi Ishii
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Haruhiko Takeda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoichi Saito
- Laboratory of Bioengineering, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Yukio Fujiwara
- Department of Cell Pathology, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masakazu Fujimoto
- Department of Diagnostic Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Ito
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Wakama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Kumagai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumiaki Munekage
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Horie
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsuhiro Tomofuji
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yu Oshima
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Takayuki Kawai
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Surgery, Medical Research Institute Kitano Hospital, Osaka, Japan
| | - Satoshi Ogiso
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Fukumitsu
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Etsuro Hatano
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Chida-Nagai A, Akagawa H, Sawai S, Ma YJ, Yakuwa S, Muneuchi J, Yasuda K, Yamazawa H, Yamamoto T, Takakuwa E, Tomaru U, Furutani Y, Kato T, Harada G, Inai K, Nakanishi T, Manabe A, Takeda A, Jing ZC. Identification of Prostaglandin I2 Synthase Rare Variants in Patients With Williams Syndrome and Severe Peripheral Pulmonary Stenosis. J Am Heart Assoc 2024:e032872. [PMID: 38639351 DOI: 10.1161/jaha.123.032872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Peripheral pulmonary stenosis (PPS) is a condition characterized by the narrowing of the pulmonary arteries, which impairs blood flow to the lung. The mechanisms underlying PPS pathogenesis remain unclear. Thus, the aim of this study was to investigate the genetic background of patients with severe PPS to elucidate the pathogenesis of this condition. METHODS AND RESULTS We performed genetic testing and functional analyses on a pediatric patient with PPS and Williams syndrome (WS), followed by genetic testing on 12 patients with WS and mild-to-severe PPS, 50 patients with WS but not PPS, and 21 patients with severe PPS but not WS. Whole-exome sequencing identified a rare PTGIS nonsense variant (p.E314X) in a patient with WS and severe PPS. Prostaglandin I2 synthase (PTGIS) expression was significantly downregulated and cell proliferation and migration rates were significantly increased in cells transfected with the PTGIS p.E314X variant-encoding construct when compared with that in cells transfected with the wild-type PTGIS-encoding construct. p.E314X reduced the tube formation ability in human pulmonary artery endothelial cells and caspase 3/7 activity in both human pulmonary artery endothelial cells and human pulmonary artery smooth muscle cells. Compared with healthy controls, patients with PPS exhibited downregulated pulmonary artery endothelial prostaglandin I2 synthase levels and urinary prostaglandin I metabolite levels. We identified another PTGIS rare splice-site variant (c.1358+2T>C) in another pediatric patient with WS and severe PPS. CONCLUSIONS In total, 2 rare nonsense/splice-site PTGIS variants were identified in 2 pediatric patients with WS and severe PPS. PTGIS variants may be involved in PPS pathogenesis, and PTGIS represents an effective therapeutic target.
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Affiliation(s)
- Ayako Chida-Nagai
- Department of Pediatrics Hokkaido University Hospital Sapporo Japan
- Department of Pediatric Cardiology and Adult Congenital Cardiology Tokyo Women's Medical University Tokyo Japan
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical Sciences Tokyo Women's Medical University Tokyo Japan
| | - Saori Sawai
- Department of Pediatrics Hokkaido University Hospital Sapporo Japan
| | - Yue-Jiao Ma
- Department of Cardiology, Peking Union Medical College Hospital Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Satoshi Yakuwa
- Department of Pediatrics Obihiro Kosei Hospital Obihiro Japan
| | - Jun Muneuchi
- Department of Pediatrics, Kyushu Hospital Japan Community Healthcare Organization Kitakyusyu Japan
| | - Kazushi Yasuda
- Department of Pediatric Cardiology Aichi Children's Health and Medical Center Obu Japan
| | | | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science Tokyo Women's Medical University Tokyo Japan
| | - Emi Takakuwa
- Department of Surgical Pathology Hokkaido University Hospital Sapporo Japan
| | - Utano Tomaru
- Department of Surgical Pathology Hokkaido University Hospital Sapporo Japan
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology and Adult Congenital Cardiology Tokyo Women's Medical University Tokyo Japan
| | - Tatsuya Kato
- Department of Thoracic Surgery Hokkaido University Hospital Sapporo Japan
| | - Gen Harada
- Department of Pediatric Cardiology and Adult Congenital Cardiology Tokyo Women's Medical University Tokyo Japan
| | - Kei Inai
- Department of Pediatric Cardiology and Adult Congenital Cardiology Tokyo Women's Medical University Tokyo Japan
| | - Toshio Nakanishi
- Department of Pediatric Cardiology and Adult Congenital Cardiology Tokyo Women's Medical University Tokyo Japan
| | - Atsushi Manabe
- Department of Pediatrics Hokkaido University Hospital Sapporo Japan
| | - Atsuhito Takeda
- Department of Pediatrics Hokkaido University Hospital Sapporo Japan
| | - Zhi-Cheng Jing
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital Guangdong Academy of Medical Sciences Southern Medical University Guangzhou China
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Yu J, Ling X, Chen L, Fang Y, Lin H, Lou J, Ren Y, Chen J. Genotypic and phenotypic features of 39 Chinese patients with glycogen storage diseases type I, VI, and IX. Clin Genet 2024. [PMID: 38576397 DOI: 10.1111/cge.14530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
Glycogen storage diseases (GSDs) are abnormally inherited glycogen metabolism mainly affecting the liver, muscles, and heart. Deficiency of proteins involved in glycogen metabolism caused by genetic mutations are responsible for different subtype of GSDs. However, there are still some challenges in diagnosing GSD. This study includes 39 suspected GSDs patients from unrelated families in China. Next-generation sequencing (NGS) was used to investigate the reason for their diseases at the genetic level. Finally, all 39 patients were diagnosed with GSDs, including 20 GSD-Ia, 4 GSD-VI, and 15 GSD IX (12 GSD-IXa patients and 3 GSD-IXb patients). Thirty-two mutations in G6PC1, PYGL, PHKA2, and PHKB genes were identified, with 14 of them being novel variants. The pathogenicity of novel variants was classified according to ACMG guildlines and predicted by in slico algorithms. Mutations p.L216L and p.R83H in G6PC1 gene may be the hot spot mutation in Chinese. Hearing impairment is a rare clinical feature of GSD Ia, which has also been observed in our cohort. The severity of GSD VI and IX was indicated by our patients. Close follow-up should be applied to GSD VI and IX patients. Our findings provided evidence for building the phenotype-genotype of GSDs and expanded the mutation spectrum of related genes.
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Affiliation(s)
- Jindan Yu
- Gastroenterology Department, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | | | - Lingli Chen
- Gastroenterology Department, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Youhong Fang
- Gastroenterology Department, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Haihua Lin
- Gastroenterology Department, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jingan Lou
- Gastroenterology Department, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yanqi Ren
- Grandomics Biosciences, Beijing, China
| | - Jie Chen
- Gastroenterology Department, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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Sasatani M, Xi Y, Daino K, Ishikawa A, Masuda Y, Kajimura J, Piao J, Zaharieva EK, Honda H, Zhou G, Hamasaki K, Kusunoki Y, Shimura T, Kakinuma S, Shimada Y, Doi K, Ishikawa-Fujiwara T, Sotomaru Y, Kamiya K. Rev1 overexpression accelerates N-methyl-N-nitrosourea (MNU)-induced thymic lymphoma by increasing mutagenesis. Cancer Sci 2024. [PMID: 38572512 DOI: 10.1111/cas.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 04/05/2024] Open
Abstract
Rev1 has two important functions in the translesion synthesis pathway, including dCMP transferase activity, and acts as a scaffolding protein for other polymerases involved in translesion synthesis. However, the role of Rev1 in mutagenesis and tumorigenesis in vivo remains unclear. We previously generated Rev1-overexpressing (Rev1-Tg) mice and reported that they exhibited a significantly increased incidence of intestinal adenoma and thymic lymphoma (TL) after N-methyl-N-nitrosourea (MNU) treatment. In this study, we investigated mutagenesis of MNU-induced TL tumorigenesis in wild-type (WT) and Rev1-Tg mice using diverse approaches, including whole-exome sequencing (WES). In Rev1-Tg TLs, the mutation frequency was higher than that in WT TL in most cases. However, no difference in the number of nonsynonymous mutations in the Catalogue of Somatic Mutations in Cancer (COSMIC) genes was observed, and mutations involved in Notch1 and MAPK signaling were similarly detected in both TLs. Mutational signature analysis of WT and Rev1-Tg TLs revealed cosine similarity with COSMIC mutational SBS5 (aging-related) and SBS11 (alkylation-related). Interestingly, the total number of mutations, but not the genotypes of WT and Rev1-Tg, was positively correlated with the relative contribution of SBS5 in individual TLs, suggesting that genetic instability could be accelerated in Rev1-Tg TLs. Finally, we demonstrated that preleukemic cells could be detected earlier in Rev1-Tg mice than in WT mice, following MNU treatment. In conclusion, Rev1 overexpression accelerates mutagenesis and increases the incidence of MNU-induced TL by shortening the latency period, which may be associated with more frequent DNA damage-induced genetic instability.
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Affiliation(s)
- Megumi Sasatani
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yang Xi
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, China
| | - Kazuhiro Daino
- Department of Radiation Effects Research, Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Atsuko Ishikawa
- Department of Radiation Effects Research, Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yuji Masuda
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Molecular Pharmaco-Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Junko Kajimura
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Biosample Research Center, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Jinlian Piao
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Gastroenterological and Transplant Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Elena Karamfilova Zaharieva
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hiroaki Honda
- Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Guanyu Zhou
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Kanya Hamasaki
- Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Yoichiro Kusunoki
- Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Tsutomu Shimura
- Department of Environmental Health, National Institute of Public Health, Saitama, Japan
| | - Shizuko Kakinuma
- Department of Radiation Effects Research, Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | | | - Kazutaka Doi
- Department of Radiation Regulatory Science Research, Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | | | - Yusuke Sotomaru
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Kenji Kamiya
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
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Wang L, Pan P, Ma H, He C, Qin Z, He W, Huang J, Tan S, Meng D, Wei H, Yin A. Malformations of cortical development: Fetal imaging and genetics. Mol Genet Genomic Med 2024; 12:e2440. [PMID: 38634212 PMCID: PMC11024634 DOI: 10.1002/mgg3.2440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/04/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Malformations of cortical development (MCD) are a group of congenital disorders characterized by structural abnormalities in the brain cortex. The clinical manifestations include refractory epilepsy, mental retardation, and cognitive impairment. Genetic factors play a key role in the etiology of MCD. Currently, there is no curative treatment for MCD. Phenotypes such as epilepsy and cerebral palsy cannot be observed in the fetus. Therefore, the diagnosis of MCD is typically based on fetal brain magnetic resonance imaging (MRI), ultrasound, or genetic testing. The recent advances in neuroimaging have enabled the in-utero diagnosis of MCD using fetal ultrasound or MRI. METHODS The present study retrospectively reviewed 32 cases of fetal MCD diagnosed by ultrasound or MRI. Then, the chromosome karyotype analysis, single nucleotide polymorphism array or copy number variation sequencing, and whole-exome sequencing (WES) findings were presented. RESULTS Pathogenic copy number variants (CNVs) or single-nucleotide variants (SNVs) were detected in 22 fetuses (three pathogenic CNVs [9.4%, 3/32] and 19 SNVs [59.4%, 19/32]), corresponding to a total detection rate of 68.8% (22/32). CONCLUSION The results suggest that genetic testing, especially WES, should be performed for fetal MCD, in order to evaluate the outcomes and prognosis, and predict the risk of recurrence in future pregnancies.
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Affiliation(s)
- Lin‐Lin Wang
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Jinan UniversityGuangzhouGuangdongChina
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Ping‐Shan Pan
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Hui Ma
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Chun He
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Zai‐Long Qin
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Wei He
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Jing Huang
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Shu‐Yin Tan
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Da‐Hua Meng
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Hong‐Wei Wei
- Prenatal Diagnosis CenterMaternal & Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningGuangxiChina
| | - Ai‐Hua Yin
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Jinan UniversityGuangzhouGuangdongChina
- Medical Genetic CenterGuangdong Women and Children HospitalGuangzhouGuangdongChina
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Du J, Nakachi Y, Murata Y, Kiyota E, Kato T, Bundo M, Iwamoto K. Exploration of cell type-specific somatic mutations in schizophrenia and the impact of maternal immune activation on the somatic mutation profile in the brain. Psychiatry Clin Neurosci 2024; 78:237-247. [PMID: 38334156 DOI: 10.1111/pcn.13640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024]
Abstract
AIM Schizophrenia (SZ) is a severe psychiatric disorder caused by the interaction of genetic and environmental factors. Although somatic mutations that occur in the brain after fertilization may play an important role in the cause of SZ, their frequencies and patterns in the brains of patients and related animal models have not been well studied. This study aimed to find somatic mutations related to the pathophysiology of SZ. METHODS We performed whole-exome sequencing (WES) of neuronal and nonneuronal nuclei isolated from the postmortem prefrontal cortex of patients with SZ (n = 10) and controls (n = 10). After detecting somatic mutations, we explored the similarities and differences in shared common mutations between two cell types and cell type-specific mutations. We also performed WES of prefrontal cortex samples from an animal model of SZ based on maternal immune activation (MIA) and explored the possible impact of MIA on the patterns of somatic mutations. RESULTS We did not find quantitative differences in somatic mutations but found higher variant allele fractions of neuron-specific mutations in patients with SZ. In the mouse model, we found a larger variation in the number of somatic mutations in the offspring of MIA mice, with the occurrence of somatic mutations in neurodevelopment-related genes. CONCLUSION Somatic mutations occurring at an earlier stage of brain cell differentiation toward neurons may be important for the cause of SZ. MIA may affect somatic mutation profiles in the brain.
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Affiliation(s)
- Jianbin Du
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yui Murata
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
| | - Emi Kiyota
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
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Cao Y, Zheng H, Zhu Z, Yao L, Tian W, Cao L. Clinical and Genetic Spectrum in a Large Cohort of Hereditary Spastic Paraplegia. Mov Disord 2024; 39:651-662. [PMID: 38291924 DOI: 10.1002/mds.29728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/23/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Next-generation sequencing-based molecular assessment has benefited the diagnosis of hereditary spastic paraplegia (HSP) subtypes. However, the clinical and genetic spectrum of HSP due to large fragment deletions/duplications has yet to be fully defined. OBJECTIVE We aim to better characterize the clinical phenotypes and genetic features of HSP and to provide new thoughts on diagnosis. METHODS Whole-exome sequencing (WES) was performed in patients with clinically suspected HSP, followed by multiple ligation-dependent probe amplification (MLPA) sequentially carried out for those with negative findings in known causative genes. Genotype-phenotype correlation analyses were conducted under specific genotypes. RESULTS We made a genetic diagnosis in 60% (162/270) of patients, of whom 48.9% (132/270) had 24 various subtypes due to point mutations (SPG4/SPG11/SPG35/SPG7/SPG10/SPG5/SPG3A/SPG2/SPG76/SPG30/SPG6/SPG9A/SPG12/SPG15/SPG17/SPG18/SPG26/SPG49/SPG55/SPG56/SPG57/SPG62/SPG78/SPG80). Thirty patients were found to have causative rearrangements by MLPA (11.1%), among which SPG4 was the most prevalent (73.3%), followed by SPG3A (16.7%), SPG6 (3.3%), SPG7 (3.3%), and SPG11 (3.3%). Clinical analysis showed that some symptoms were often related to specific subtypes, and rearrangement-related SPG3A patients seemingly had later onset. We observed a presumptive anticipation among SPG4 and SPG3A families due to rearrangement. CONCLUSIONS Based on the largest known Asian HSP cohort, including the largest subgroup of rearrangement-related pedigrees, we gain a comprehensive understanding of the clinical and genetic spectrum of HSP. We propose a diagnostic flowchart to sequentially detect the causative genes in practice. Large fragment mutations account for a considerable proportion of HSP, and thus, MLPA screening acts as a beneficial supplement to routine WES. © 2024 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Yuwen Cao
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Neurological Rare Disease Biobank and Precision Diagnostic Technical Service Platform, Shanghai, China
| | - Haoran Zheng
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Zeyu Zhu
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Yao
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Suzhou Hospital of Anhui Medical University, Suzhou Municipal Hospital of Anhui Province, Suzhou, China
| | - Wotu Tian
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Neurological Rare Disease Biobank and Precision Diagnostic Technical Service Platform, Shanghai, China
| | - Li Cao
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Neurological Rare Disease Biobank and Precision Diagnostic Technical Service Platform, Shanghai, China
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Wu WJ, Ma GC, Chang TY, Lee MH, Lin WH, Chen M. Outcome and etiology of fetal pleural effusion, fetal ascites and hydrops fetalis after fetal intervention: retrospective observational cohort from a single institution. Ultrasound Obstet Gynecol 2024; 63:536-543. [PMID: 37767652 DOI: 10.1002/uog.27501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
OBJECTIVES Non-immune hydrops fetalis (NIHF) is the pathological accumulation of fluids in fetal compartments, without maternal isoimmunization. Fetal interventions (e.g. shunting, fetal paracentesis, fetal thoracocentesis, fetal pleurodesis) are used to alleviate fluid accumulations, but the outcome is uncertain because the underlying causes of NIHF vary. We aimed to explore the etiology and long-term outcome of NIHF after fetal intervention. METHODS This was a retrospective review of fetuses with NIHF, defined by the presence of fetal ascites, pleural or pericardial effusion, skin edema or cystic hygroma, or a combination of these features, who underwent intervention at our institution during the period 2012-2021. Clinical surveillance, genetic analysis and viral infection screening were used to define the etiology. Chart reviews and telephone interviews were conducted to assess the long-term outcomes. RESULTS In total, 55 fetuses were enrolled and 46 cases had final follow-up data after delivery. Etiology was identified in 33 cases, including four for which the underlying causes were not identified initially using small-gene-panel tests but which were later diagnosed with monogenic disorders by whole-exome sequencing (WES). Twenty-three cases with follow-up survived, having a follow-up period of 2-11 years at the time of writing, of which 17 were healthy. All 11 cases initially presenting as congenital chylothorax survived with favorable outcome. CONCLUSIONS The etiologies of NIHF are heterogeneous, and the long-term (spanning 2-11 years) outcome of fetal intervention varies, according to the underlying etiology, with cases caused by congenital chylothorax having the best prognosis. Genome-wide tests, such as WES, may be helpful in determining the underlying condition in cases caused by a genetic disorder, and this may affect fetal therapy approaches in the future. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- W-J Wu
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
- Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan
| | - G-C Ma
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - T-Y Chang
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan, Taiwan
| | - M-H Lee
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
| | - W-H Lin
- Welgene Biotechnology Company, Nangang Business Park, Taipei, Taiwan
| | - M Chen
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
- Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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Chen Y, Yang R, Chen X, Lin N, Li C, Fu Y, He A, Wang Y, Zhang T, Ma J. Atypical mandibulofacial dysostosis with microcephaly diagnosed through the identification of a novel pathogenic mutation in EFTUD2. Mol Genet Genomic Med 2024; 12:e2426. [PMID: 38562046 PMCID: PMC10985408 DOI: 10.1002/mgg3.2426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Mandibulofacial dysostosis with microcephaly (MFDM, OMIM# 610536) is a rare monogenic disease that is caused by a mutation in the elongation factor Tu GTP binding domain containing 2 gene (EFTUD2, OMIM* 603892). It is characterized by mandibulofacial dysplasia, microcephaly, malformed ears, cleft palate, growth and intellectual disability. MFDM can be easily misdiagnosed due to its phenotypic overlap with other craniofacial dysostosis syndromes. The clinical presentation of MFDM is highly variable among patients. METHODS A patient with craniofacial anomalies was enrolled and evaluated by a multidisciplinary team. To make a definitive diagnosis, whole-exome sequencing was performed, followed by validation by Sanger sequencing. RESULTS The patient presented with extensive facial bone dysostosis, upward slanting palpebral fissures, outer and middle ear malformation, a previously unreported orbit anomaly, and spina bifida occulta. A novel, pathogenic insertion mutation (c.215_216insT: p.Tyr73Valfs*4) in EFTUD2 was identified as the likely cause of the disease. CONCLUSIONS We diagnosed this atypical case of MFDM by the detection of a novel pathogenetic mutation in EFTUD2. We also observed previously unreported features. These findings enrich both the genotypic and phenotypic spectrum of MFDM.
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Affiliation(s)
- Ying Chen
- Department of Facial Plastic and Reconstructive SurgeryEye & ENT Hospital of Fudan UniversityShanghaiChina
- ENT InstituteEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Run Yang
- Department of Facial Plastic and Reconstructive SurgeryEye & ENT Hospital of Fudan UniversityShanghaiChina
- ENT InstituteEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Xin Chen
- Department of Facial Plastic and Reconstructive SurgeryEye & ENT Hospital of Fudan UniversityShanghaiChina
- ENT InstituteEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Naier Lin
- Department of RadiologyEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Chenlong Li
- Department of Facial Plastic and Reconstructive SurgeryEye & ENT Hospital of Fudan UniversityShanghaiChina
- ENT InstituteEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Yaoyao Fu
- Department of Facial Plastic and Reconstructive SurgeryEye & ENT Hospital of Fudan UniversityShanghaiChina
- ENT InstituteEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Aijuan He
- Department of Facial Plastic and Reconstructive SurgeryEye & ENT Hospital of Fudan UniversityShanghaiChina
- ENT InstituteEye & ENT Hospital of Fudan UniversityShanghaiChina
| | - Yimin Wang
- GeneMind Biosciences Company LimitedShenzhenChina
| | - Tianyu Zhang
- Department of Facial Plastic and Reconstructive SurgeryEye & ENT Hospital of Fudan UniversityShanghaiChina
- ENT InstituteEye & ENT Hospital of Fudan UniversityShanghaiChina
- NHC Key Laboratory of Hearing MedicineFudan UniversityShanghaiChina
| | - Jing Ma
- Department of Facial Plastic and Reconstructive SurgeryEye & ENT Hospital of Fudan UniversityShanghaiChina
- ENT InstituteEye & ENT Hospital of Fudan UniversityShanghaiChina
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12
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Sun Q, Xie Z, Song L, Fu D. A case of polyglucosan body myopathy caused by an RBCK1 gene variant and literature review. Mol Genet Genomic Med 2024; 12:e2432. [PMID: 38588043 PMCID: PMC11000808 DOI: 10.1002/mgg3.2432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/28/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
OBJECTIVE To analyze the clinical and genetic characteristics of a patient with Polyglucosan body myopathy 1 (PGBM1) caused by a novel compound heterozygous variant in the RBCK1 gene. METHODS The clinical data of the patient were collected, next-generation sequencing technology was used to determine the exome sequence of the patient, and the suspected pathogenic locus was verified by Sanger sequencing. RESULTS Through whole-exome sequencing, we found that there were c.919G>T; p. (Glu307*) and c.723_730dup; p. (Glu244fs) variants of the RBCK1 gene in the patient, inherited from his parents, constituting a compound heterozygous variation. According to the guidelines of the American College of Medical Genetics and Genomics (ACMG), the two variants were rated as pathogenic, but there were no comparable cases. Previous literature reported 24 patients with RBCK1 gene variants, involving a total of 20 myocardial and 18 skeletal muscle cases. CONCLUSIONS The patient was twice diagnosed with cardiac insufficiency, neglecting the usual manifestations of muscle weakness, resulting in misdiagnosis. Later, novel variants in the RBCK1 gene were discovered through whole-exome sequencing, and symptomatic treatment was given after diagnosis. The importance of whole-exome sequencing technology in disease diagnosis and genetic counseling was emphasized.
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Affiliation(s)
- Qiqing Sun
- Department of CardiologyChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Zhenhua Xie
- Henan Children's Neurodevelopment Engineering Research Center, Henan Provincial Clinical Research Center for Pediatric DiseasesChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouChina
| | - Lifang Song
- Department of NeurologyChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
| | - Dapeng Fu
- Department of CardiologyChildren's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's HospitalZhengzhouHenanChina
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Li J, Wei X, Sun Y, Chen X, Zhang Y, Cui X, Shu J, Li D, Cai C. Phosphoserine aminotransferase deficiency diagnosed by whole-exome sequencing and LC-MS/MS reanalysis: A case report and review of literature. Mol Genet Genomic Med 2024; 12:e2400. [PMID: 38546032 PMCID: PMC10976427 DOI: 10.1002/mgg3.2400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/26/2023] [Accepted: 02/05/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Phosphoserine aminotransferase deficiency (PSATD) is an autosomal recessive disorder associated with hypertonia, psychomotor retardation, and acquired microcephaly. Patients with PSATD have low concentrations of serine in plasma and cerebrospinal fluid. METHODS We reported a 2-year-old female child with developmental delay, dyskinesia, and microcephaly. LC-MS/MS was used to detect amino acid concentration in the blood and whole-exome sequencing (WES) was used to identify the variants. PolyPhen-2 web server and PyMol were used to predict the pathogenicity and changes in the 3D model molecular structure of protein caused by variants. RESULTS WES demonstrated compound heterozygous variants in PSAT1, which is associated with PSATD, with a paternal likely pathogenic variant (c.235G>A, Gly79Arg) and a maternal likely pathogenic variant (c.43G>C, Ala15Pro). Reduced serine concentration in LC-MS/MS further confirmed the diagnosis of PSATD in this patient. CONCLUSIONS Our findings demonstrate the importance of WES combined with LC-MS/MS reanalysis in the diagnosis of genetic diseases and expand the PSAT1 variant spectrum in PSATD. Moreover, we summarize all the cases caused by PSAT1 variants in the literature. This case provides a vital reference for the diagnosis of future cases.
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Affiliation(s)
- Jiaci Li
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Tianjin Pediatric Research InstituteTianjinChina
- Tianjin Key Laboratory of Birth Defects for Prevention and TreatmentTianjinChina
| | - Xinping Wei
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Department of NeurologyTianjin Children's HospitalTianjinChina
| | - Yuchen Sun
- College of Traditional Chinese medicineTianjin University of Traditional Chinese MedicineTianjinChina
| | - Xiaofang Chen
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
| | - Ying Zhang
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Tianjin Medical UniversityGraduate College of Tianjin Medical UniversityTianjinChina
| | - Xiaoyu Cui
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
| | - Jianbo Shu
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Tianjin Pediatric Research InstituteTianjinChina
- Tianjin Key Laboratory of Birth Defects for Prevention and TreatmentTianjinChina
| | - Dong Li
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Department of NeurologyTianjin Children's HospitalTianjinChina
| | - Chunquan Cai
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Tianjin Pediatric Research InstituteTianjinChina
- Tianjin Key Laboratory of Birth Defects for Prevention and TreatmentTianjinChina
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Li J, Liang X, Wang X, Yang P, Jian X, Fu L, Deng A, Liu C, Liu J. A missense GDF5 variant causes brachydactyly type A1 and multiple-synostoses syndrome 2. JOR Spine 2024; 7:e1302. [PMID: 38222807 PMCID: PMC10782059 DOI: 10.1002/jsp2.1302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/16/2023] [Accepted: 11/02/2023] [Indexed: 01/16/2024] Open
Abstract
Objective This study aimed to identify the molecular defects and clinical manifestations in a Chinese family with brachydactyly (BD) type A1 (BDA1) and multiple-synostoses syndrome 2 (SYNS2). Methods A Chinese family with BDA1 and SYNS2 was enrolled in this study. Whole-exome sequencing was used to analyze the gene variants in the proband. The sequences of the candidate pathogenic variant in GDF5 was validated via Sanger sequencing. I-TASSER and PyMOL were used to analyze the functional domains of the corresponding mutant proteins. Results The family was found to have an autosomal-dominantly inherited combination of BDA1 and SYNS2 caused by the S475N variant in the GDF5 gene. The variant was located within the functional region, and the mutated residue was found to be highly conserved among species. Via bioinformatic analyses, we predicted this variant to be deleterious, which perturb the protein function. The substitution of the negatively charged amino acid S475 with the neutral N475 was predicted to disrupt the formation of salt bridges with Y487 and impair the structure, stability, and function of the protein, consequently, the abnormalities in cartilage and bone development ensue. Conclusions A single genetic variant (S475N) which disrupt the formation of salt bridges with Y487, in the interface of the antagonist- and receptor-binding sites of GDF5 concurrently causes two pathological mechanisms. This is the first report of this variant, identified in a Chinese family with BDA1 and SYNS2.
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Affiliation(s)
- Juyi Li
- Department of Pharmacy, The Central Hospital of WuhanTongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Xiaofang Liang
- Department of Dermatology, The Central Hospital of WuhanTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Xiufang Wang
- Department of Pain, The Central Hospital of WuhanTongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Pei Yang
- Department of Radiology, The Central Hospital of WuhanTongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Xiaofei Jian
- Department of Orthopedics, The Central Hospital of WuhanTongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Lei Fu
- Department of Ultrasound, The Central Hospital of WuhanTongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Aiping Deng
- Department of Pharmacy, The Central Hospital of WuhanTongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Chao Liu
- Hubei Key Laboratory of Diabetes and AngiopathyHubei University of Science and TechnologyXianningHubeiChina
| | - Jianxin Liu
- Department of Ultrasound, The Central Hospital of WuhanTongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
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Mohammadi MF, Fateh ST, Aghajani H, Bahramy A, Zaheryani SMS, Behroozi J, Kahani SM, Mohammadi P, Garshasbi M. Expression assay of the COLQ in a family with congenital myasthenic syndrome and symptomatic carriers. Clin Case Rep 2023; 11:e8062. [PMID: 37881193 PMCID: PMC10593973 DOI: 10.1002/ccr3.8062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/20/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
Congenital myasthenic syndromes-5 (CMS5) is a rare autosomal recessive heterogeneous disorder, caused by pathogenic variants in the COLQ that lead to skeletal muscle weakness and abnormal fatigability. The onset is usually from birth to childhood. Disease-causing variants in the collagen-like tail subunit are the most explained etiology in synaptic CMS, causing defected acetylcholinesterase. In this study whole-exome sequencing (WES) was performed in an affected boy with muscle weakness, ophthalmoplegia, and bilateral ptosis and gene expression assay by qRT-PCR was performed in entire family. A homozygous nonsense variant in the COLQ [NM_005677.4:c.679C>T], (p.Arg227Ter) was identified in the proband. Segregation analysis by Sanger sequencing confirmed the homozygous state in the proband and heterozygous state in his parents and four of the siblings. The mRNA expression level in the proband was 0.02 of a healthy person, and in the carriers were 0.42 of a healthy person. This study presents an Iranian family with two affected children and eight symptomatic carriers with attenuated mRNA expression. This study provides evidence that carriers of the COLQ disease-causing variants could become symptomatic with some yet unknown pathogenesis mechanism and underscore the importance of further investigations to elucidate this mechanism.
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Affiliation(s)
- Mohammad Farid Mohammadi
- Department of Cell and Molecular Sciences, Faculty of Biological SciencesKharazmi UniversityTehranIran
| | | | - Hadi Aghajani
- Faculty of Medicine, Tehran Medical Sciences BranchIslamic Azad UniversityTehranIran
| | - Afshin Bahramy
- Department of Medical Genetics, Faculty of Medical SciencesTarbiat Modares UniversityTehranIran
| | | | - Javad Behroozi
- Department of Medical Genetics, Faculty of Medical SciencesTarbiat Modares UniversityTehranIran
- Research Center for Cancer Screening and EpidemiologyAJA University of Medical SciencesTehranIran
| | - Seyyed Mohammad Kahani
- Department of Medical Genetics, Faculty of Medical SciencesTarbiat Modares UniversityTehranIran
| | - Pouria Mohammadi
- Department of Medical Genetics, Faculty of Medical SciencesTarbiat Modares UniversityTehranIran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical SciencesTarbiat Modares UniversityTehranIran
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Fazelifar AF, Pourirahim M, Masoumi T, Biglari A, Maleki M, Kalayinia S. Identification of a novel pathogenic variant in KCNH2 in an Iranian family with long QT syndrome 2 by whole-exome sequencing. J Arrhythm 2023; 39:430-453. [PMID: 37324772 PMCID: PMC10264754 DOI: 10.1002/joa3.12857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 06/17/2023] Open
Abstract
Background Long QT syndrome (LQTS) is a lethal cardiac condition. However, the clinical implementation of genetic testing has now made LQTS eminently treatable. Next-generation sequencing has remarkable potential for both clinical diagnostics and research of LQTS. Here, we investigated the genetic etiology in an LQTS-suspected Iranian pedigree by whole-exome sequencing and collected all KCNH2 variants with consensus based on publications. Methods WES was performed on the proband of this pedigree to reveal the underlying cause of sudden cardiac death (SCD). The variant found was validated and segregated by polymerase chain reaction and Sanger sequencing. Based on the literature review, KCNH2 variants were retrospectively analyzed to identify pathogenic variants, likely pathogenic variants, and variants of uncertain significance by using different prediction tools. Results WES identified an autosomal dominant nonsense variant, c.1425C>A: p.Tyr475Ter, in the KCNH2 gene, which appeared to be the most likely cause of LQTS in this pedigree. Moreover, our comprehensive literature review yielded 511 KCNH2 variants in association with the LQTS phenotype, with c.3002G>A (CADD Phred=49) being the most pathogenic variant. Conclusions Variants in the KCNH2 gene are considered a major cause of LQTS worldwide. The detected c.1425C>A is a novel variant to be reported from Iran for the first time. This result indicates the importance of KCNH2 screening in a pedigree with SCD cases.
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Affiliation(s)
- Amir Farjam Fazelifar
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Maryam Pourirahim
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Tannaz Masoumi
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Alireza Biglari
- Department of Genetics & Molecular Medicine, School of MedicineZanjan University of Medical SciencesZanjanIran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
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17
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Poquérusse J, Nolan M, Thorburn DR, Van Hove JLK, Friederich MW, Love DR, Taylor J, Powell CA, Minczuk M, Snell RG, Lehnert K, Glamuzina E, Jacobsen JC. Severe neonatal onset neuroregression with paroxysmal dystonia and apnoea: Expanding the phenotypic and genotypic spectrum of CARS2-related mitochondrial disease. JIMD Rep 2023; 64:223-232. [PMID: 37151360 PMCID: PMC10159863 DOI: 10.1002/jmd2.12360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Disorders of mitochondrial function are a collectively common group of genetic diseases in which deficits in core mitochondrial translation machinery, including aminoacyl tRNA synthetases, are key players. Biallelic variants in the CARS2 gene (NM_024537.4), which encodes the mitochondrial aminoacyl-tRNA synthetase for cysteine (CARS2, mt-aaRScys; MIM*612800), result in childhood onset epileptic encephalopathy and complex movement disorder with combined oxidative phosphorylation deficiency (MIM#616672). Prior to this report, eight unique pathogenic variants in the CARS2 gene had been reported in seven individuals. Here, we describe a male who presented in the third week of life with apnoea. He rapidly deteriorated with paroxysmal dystonic crises and apnoea resulting in death at 16 weeks. He had no evidence of seizure activity or multisystem disease and had normal brain imaging. Skeletal muscle biopsy revealed a combined disorder of oxidative phosphorylation. Whole-exome sequencing identified biallelic variants in the CARS2 gene: one novel (c.1478T>C, p.Phe493Ser), and one previously reported (c.655G>A, p.Ala219Thr; rs727505361). Northern blot analysis of RNA isolated from the patient's fibroblasts confirmed a clear defect in aminoacylation of the mitochondrial tRNA for cysteine (mt-tRNACys). To our knowledge, this is the earliest reported case of CARS2 deficiency with severe, early onset dystonia and apnoea, without epilepsy.
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Affiliation(s)
- Jessie Poquérusse
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Melinda Nolan
- Department of NeurologyStarship Children's HealthAucklandNew Zealand
| | - David R. Thorburn
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of PaediatricsThe University of MelbourneMelbourneVictoriaAustralia
| | - Johan L. K. Van Hove
- Department of Pediatrics, School of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Marisa W. Friederich
- Department of Pediatrics, School of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Donald R. Love
- Diagnostic GeneticsLabPLUS, Auckland City HospitalAucklandNew Zealand
- Present address:
Division Chief, Pathology GeneticsSidra MedicineDohaQatar
| | - Juliet Taylor
- Genetic Health Service New ZealandAuckland City HospitalAucklandNew Zealand
| | | | - Michal Minczuk
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Russell G. Snell
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Klaus Lehnert
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Emma Glamuzina
- Adult and Paediatric National Metabolic ServiceAuckland City HospitalAucklandNew Zealand
| | - Jessie C. Jacobsen
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
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18
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Yokoi K, Nakajima Y, Takahashi Y, Hamajima T, Tajima G, Saito K, Miyai S, Inagaki H, Yoshikawa T, Kurahashi H, Ito T. Transport and Golgi organization 2 deficiency with a prominent elevation of C14:1 during a metabolic crisis: A case report. JIMD Rep 2023; 64:3-9. [PMID: 36636595 PMCID: PMC9830013 DOI: 10.1002/jmd2.12275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 01/16/2023] Open
Abstract
Mutations in transport and Golgi organization 2 homolog (TANGO2) have recently been described as a cause of an autosomal recessive syndrome characterized by episodes of metabolic crisis associated with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration. Herein, we report a case of a one-and-a-half-year-old Japanese girl, born to nonconsanguineous parents, who presented with metabolic crisis characterized by hypoglycemia with hypoketonemia, rhabdomyolysis, lactic acidosis, and prolonged corrected QT interval (QTc) at the age of 6 months. Acylcarnitine analysis during the episode of crisis showed prominent elevation of C14:1, suggesting very-long-chain acyl-CoA dehydrogenase (VLCAD) deficiency. In addition, worsening rhabdomyolysis was observed after intravenous administration of L-carnitine. VLCAD deficiency was initially suspected; however, the enzyme activity in lymphocytes was only mildly decreased at the gene carrier level, and no mutation in the VLCAD gene (ADADVL) was detected. Subsequently, acylcarnitine analysis was nonspecific at 17-h fasting and almost normal during the stable phase. Eventually, a trio whole-exome sequencing revealed a compound heterozygous variant of two novel variants in the TANGO2 gene, a missense variant, and a deletion of exon 7. This is the first case of TANGO2 deficiency in Asians. Our case suggests that elevated C14:1 may be seen in severe metabolic crises and that the use of L-carnitine should be avoided during metabolic crises.
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Affiliation(s)
- Katsuyuki Yokoi
- Department of PediatricsFujita Health University School of MedicineToyoakeJapan
- Division of Molecular GeneticsInstitute for Comprehensive Medical Science, Fujita Health UniversityToyoakeJapan
| | - Yoko Nakajima
- Department of PediatricsFujita Health University School of MedicineToyoakeJapan
| | - Yoshihisa Takahashi
- Department of Endocrinology and MetabolismAichi Children's Health and Medical CenterOhbuJapan
| | - Takashi Hamajima
- Department of Endocrinology and MetabolismAichi Children's Health and Medical CenterOhbuJapan
| | - Go Tajima
- Division of Neonatal ScreeningResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Kazuyoshi Saito
- Department of PediatricsFujita Health University School of MedicineToyoakeJapan
| | - Shunsuke Miyai
- Division of Molecular GeneticsInstitute for Comprehensive Medical Science, Fujita Health UniversityToyoakeJapan
| | - Hidehito Inagaki
- Division of Molecular GeneticsInstitute for Comprehensive Medical Science, Fujita Health UniversityToyoakeJapan
| | - Tetsushi Yoshikawa
- Department of PediatricsFujita Health University School of MedicineToyoakeJapan
| | - Hiroki Kurahashi
- Division of Molecular GeneticsInstitute for Comprehensive Medical Science, Fujita Health UniversityToyoakeJapan
| | - Tetsuya Ito
- Department of PediatricsFujita Health University School of MedicineToyoakeJapan
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19
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Kurosawa S, Toya T, Sadato D, Hishima T, Hirama C, Najima Y, Kobayashi T, Haraguchi K, Okuyama Y, Oboki K, Harada H, Sakamaki H, Ohashi K, Harada Y, Doki N. Mutation profiles of diffuse large B-cell lymphoma transformation of splenic B-cell lymphoma/leukemia, unclassifiable on whole-exome sequencing. EJHaem 2021; 2:854-860. [PMID: 35845190 PMCID: PMC9175768 DOI: 10.1002/jha2.315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 02/06/2023]
Abstract
A 58-year-old male was diagnosed with splenic B-cell lymphoma/leukemia, unclassifiable (SPLL-U). The lymphoma transformed into diffuse large B-cell lymphoma (DLBCL), and multidrug chemotherapy and autologous stem cell transplantation achieved complete remission. Two years later, the lymphoma relapsed as SPLL-U. Serial whole-exome sequencing indicated that the mutation profiles were similar between the onset and relapsed samples while those in DLBCL were partially distinctive, which was in line with the clinical course. Hierarchical clustering revealed that an IGLL5 mutation was the founder mutation proceeding the development of the diseases and suggested that KRAS and other mutations might contribute to the transformation.
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Affiliation(s)
- Shuhei Kurosawa
- Hematology DivisionTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Takashi Toya
- Hematology DivisionTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Daichi Sadato
- Clinical Research Support CenterTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
- Research Center for Genome & Medical SciencesTokyo Metropolitan Institute of Medical ScienceSetagaya CityJapan
| | - Tsunekazu Hishima
- Department of PathologyTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Chizuko Hirama
- Clinical Research Support CenterTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
- Research Center for Genome & Medical SciencesTokyo Metropolitan Institute of Medical ScienceSetagaya CityJapan
| | - Yuho Najima
- Hematology DivisionTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Takeshi Kobayashi
- Hematology DivisionTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Kyoko Haraguchi
- Division of Transfusion and Cell TherapyTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Yoshiki Okuyama
- Division of Transfusion and Cell TherapyTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Keisuke Oboki
- Research Center for Genome & Medical SciencesTokyo Metropolitan Institute of Medical ScienceSetagaya CityJapan
| | - Hironori Harada
- Hematology DivisionTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
- Laboratory of OncologySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachiojiJapan
| | - Hisashi Sakamaki
- Hematology DivisionTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Kazuteru Ohashi
- Hematology DivisionTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Yuka Harada
- Clinical Research Support CenterTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
| | - Noriko Doki
- Hematology DivisionTokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalBunkyo CityJapan
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20
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Yu H, Gall B, Newman M, Hathaway Q, Brundage K, Ammer A, Mathers P, Siderovski D, Hull RW. Contribution of HCN1 variant to sinus bradycardia: A case report. J Arrhythm 2021; 37:1337-1347. [PMID: 34621433 PMCID: PMC8485797 DOI: 10.1002/joa3.12598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/08/2021] [Accepted: 06/26/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Missense mutations in the hyperpolarization-activated cyclic nucleotide-modulated (HCN) channel 4 (HCN4) are one of the genetic causes of cardiac sinus bradycardia. OBJECTIVE To investigate possible HCN4 channel mutation in a young patient with profound sinus bradycardia. METHODS Direct sequencing of HCN4 and whole-exome sequencing were performed on DNA samples from the indexed patient (P), the patient's son (PS), and a family unrelated healthy long-distance running volunteer (V). Resting heart rate was 31 bpm for P, 67 bpm for PS, and 50 bpm for V. Immunoblots, flow cytometry, and immunocytofluorescence confocal imaging were used to study cellular distribution of channel variants. Patch-clamp electrophysiology was used to investigate the properties of mutant HCN1 channels. RESULTS In P no missense mutations were found in the HCN4 gene; instead, we found two heterozygous variants in the HCN1 gene: deletion of an N-terminal glycine triplet (72GGG74, "N-del") and a novel missense variant, P851A, in the C-terminal region. N-del variant was found before and shared by PS. These two variations were not found in V. Compared to wild type, N-del and P851A reduced cell surface expression and negatively shifted voltage-activation with slower activation kinetics. CONCLUSION Decreased channel activity HCN1 mutant channel makes it unable to contribute to early depolarization of sinus node action potential, thus likely a main cause of the profound sinus bradycardia in this patient.
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Affiliation(s)
- Hangang Yu
- Department of Physiology and PharmacologySchool of MedicineWest Virginia UniversityMorgantownWVUSA
| | - Bryan Gall
- Department of Physiology and PharmacologySchool of MedicineWest Virginia UniversityMorgantownWVUSA
- Present address:
Variant Curator at NateraSan CarlosCAUSA
| | - Mackenzie Newman
- Department of Physiology and PharmacologySchool of MedicineWest Virginia UniversityMorgantownWVUSA
| | - Quincy Hathaway
- Department of Exercise PhysiologySchool of MedicineWest Virginia UniversityMorgantownWVUSA
| | - Kathleen Brundage
- Department of Microbiology, Immunology & Cell BiologySchool of MedicineWest Virginia UniversityMorgantownWVUSA
| | - Amanda Ammer
- Department of Microbiology, Immunology & Cell BiologySchool of MedicineWest Virginia UniversityMorgantownWVUSA
| | - Peter Mathers
- Department of NeuroscienceSchool of MedicineWest Virginia UniversityMorgantownWVUSA
| | - David Siderovski
- Department of Physiology and PharmacologySchool of MedicineWest Virginia UniversityMorgantownWVUSA
- Present address:
Pharmacology & NeuroscienceUniversity of North TexasDentonTXUSA
| | - Robert W. Hull
- Department of CardiologySchool of MedicineWest Virginia UniversityMorgantownWVUSA
- Present address:
Department of CardiologyMon General HospitalMorgantownWVUSA
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21
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Farajzadeh Valilou S, Karimzad Hagh J, Salimi Asl M, Abdi Rad I, Edizadeh M, Pooladi A. A novel biallelic LMNB2 variant in a patient with progressive myoclonus epilepsy and ataxia: A case of laminopathy. Clin Case Rep 2021; 9:e04520. [PMID: 34466237 PMCID: PMC8381754 DOI: 10.1002/ccr3.4520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/20/2021] [Accepted: 05/30/2021] [Indexed: 12/26/2022] Open
Abstract
The report of LMNB2-related progressive myoclonus epilepsy and ataxia due to missense homozygous c.473G>T variant.
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Affiliation(s)
- Saeed Farajzadeh Valilou
- Department of Medical Genetics and Sarem Cell Research Center (SCRC)Sarem Womens' HospitalTehranIran
- Medical Genetics Network (MeGeNe)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Javad Karimzad Hagh
- Department of Medical Genetics and Sarem Cell Research Center (SCRC)Sarem Womens' HospitalTehranIran
- IVF CenterCuypers & Cuypers Fertility Center Heinsberger HöfeHeinsbergGermany
| | - Mohammad Salimi Asl
- Department of Medical Genetics and Sarem Cell Research Center (SCRC)Sarem Womens' HospitalTehranIran
| | - Isa Abdi Rad
- Departament of Medical GeneticsSchool of MedicineUrmia University of Medical SciencesUrmiaIran
| | - Masoud Edizadeh
- Biotechnology DepartmentSchool of MedicineLorestan University of Medical SciencesKhorramabadLorestanIran
| | - Arash Pooladi
- Cancer and Immunology Research CenterResearch Institute for Health DevelopmentKurdistan University of Medical SciencesSanandajIran
- Department of Medical GeneticsFaculty of MedicineKurdistan University of Medical SciencesSanandajIran
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22
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Flynn K, Feben C, Lamola L, Carstens N, Krause A, Lombard Z. Ending a diagnostic odyssey-The first case of Takenouchi-Kosaki syndrome in an African patient. Clin Case Rep 2021; 9:2144-2148. [PMID: 33936654 PMCID: PMC8077267 DOI: 10.1002/ccr3.3966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
First reported case of Takenouchi-Kosaki syndrome in an African patient with a de novo likely pathogenic missense variant identified in the CDC42 gene.
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Affiliation(s)
- Kaitlyn Flynn
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Lindiwe Lamola
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
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23
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Shinya Y, Hiraide T, Momoi M, Goto S, Suzuki H, Katsumata Y, Kurebayashi Y, Endo J, Sano M, Fukuda K, Kosaki K, Kataoka M. TNFRSF13B c.226G>A (p.Gly76Ser) as a Novel Causative Mutation for Pulmonary Arterial Hypertension. J Am Heart Assoc 2021; 10:e019245. [PMID: 33586470 PMCID: PMC8174299 DOI: 10.1161/jaha.120.019245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Recently, some studies reported the pulmonary artery hypertension (PAH)–associated genes. However, a majority of patients with familial or sporadic PAH lack variants in the known pathogenic genes. In this study, we investigated the new causative gene variants associated with PAH. Methods and Results Whole‐exome sequencing in 242 Japanese patients with familial or sporadic PAH identified a heterozygous substitution change involving c.226G>A (p.Gly76Ser) in tumor necrotic factor receptor superfamily 13B gene (TNFRSF13B) in 6 (2.5%) patients. TNFRSF13B controls the differentiation of B cell and secretion of inflammatory cytokines and may be involved in vascular inflammation. In silico structural analysis simulation demonstrated the structural instability of the N‐terminal region of the protein synthesized from TNFRSF13B p.Gly76Ser variant. These suggest that the TNFRSF13B p.Gly76Ser variant may be involved in the development of PAH via aberrant inflammation in pulmonary vessels. Conclusions TNFRSF13B p.Gly76Ser variant is a candidate of novel causative gene variant for PAH.
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Affiliation(s)
- Yoshiki Shinya
- Department of Cardiology Keio University School of Medicine Tokyo Japan
| | - Takahiro Hiraide
- Department of Cardiology Keio University School of Medicine Tokyo Japan
| | - Mizuki Momoi
- Department of Cardiology Keio University School of Medicine Tokyo Japan
| | - Shinichi Goto
- Department of Cardiology Keio University School of Medicine Tokyo Japan
| | - Hisato Suzuki
- Center for Medical Genetics Keio University School of Medicine Tokyo Japan
| | | | - Yutaka Kurebayashi
- Institute for Integrated Sports Medicine Keio University School of Medicine Tokyo Japan
| | - Jin Endo
- Department of Cardiology Keio University School of Medicine Tokyo Japan
| | - Motoaki Sano
- Department of Cardiology Keio University School of Medicine Tokyo Japan
| | - Keiichi Fukuda
- Department of Cardiology Keio University School of Medicine Tokyo Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics Keio University School of Medicine Tokyo Japan
| | - Masaharu Kataoka
- Department of Cardiology Keio University School of Medicine Tokyo Japan.,Second Department of Internal Medicine University of Occupational and Environmental Health Kitakyushu Japan
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24
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Naumova OY, Rychkov SY, Burenkova OV, Solodunova MY, Polyanskaya IV, Arintcina IA, Zhukova MA, Ovchinnikova IV, Zhukova OV, Grigorenko EL. Male pseudohermaphroditism: A case study of 46,XY disorder of sexual development using whole-exome sequencing. Clin Case Rep 2020; 8:2889-2894. [PMID: 33363845 PMCID: PMC7752474 DOI: 10.1002/ccr3.3286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/24/2020] [Accepted: 08/05/2020] [Indexed: 11/12/2022] Open
Abstract
The study shows that whole-exome sequencing is a promising approach to detect novel variants-and gene candidates in DSD, that, as a future direction, may improve the diagnostic gene panels for this heterogeneous disorder.
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Affiliation(s)
- Oxana Yu. Naumova
- Vavilov Institute of General GeneticsRussian Academy of SciencesMoscowRussia
- Saint Petersburg State UniversitySaint PetersburgRussia
- University of HoustonHoustonTXUSA
| | - Sergey Yu. Rychkov
- Vavilov Institute of General GeneticsRussian Academy of SciencesMoscowRussia
| | | | - Maria Yu. Solodunova
- Saint Petersburg State UniversitySaint PetersburgRussia
- Specialized Neuropsychiatric Baby Home #13Saint PetersburgRussia
| | | | | | - Marina A. Zhukova
- Saint Petersburg State UniversitySaint PetersburgRussia
- University of HoustonHoustonTXUSA
| | - Irina V. Ovchinnikova
- Saint Petersburg State UniversitySaint PetersburgRussia
- University of HoustonHoustonTXUSA
| | - Olga V. Zhukova
- Vavilov Institute of General GeneticsRussian Academy of SciencesMoscowRussia
| | - Elena L. Grigorenko
- Saint Petersburg State UniversitySaint PetersburgRussia
- University of HoustonHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
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25
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Katsuragawa H, Yamada Y, Ishida Y, Kaku Y, Fujimoto M, Kataoka TR, Haga H. A case of Langerhans cell sarcoma on the scalp: Whole-exome sequencing reveals a role of ultraviolet in the pathogenesis. Pathol Int 2020; 70:881-887. [PMID: 33410565 DOI: 10.1111/pin.13007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 11/28/2022]
Abstract
Langerhans cell sarcoma (LCS) is a high-grade neoplasm with overtly malignant cytological features and a Langerhans cell phenotype. The underlying genetic features are poorly understood, and only a few alterations, such as those of the MARK pathway-related genes, CDKN2A and TP53 have been reported. Here we present a 70-year-old male with LCS on the scalp and pulmonary metastasis. The multinodular tumor, 3.0 cm in diameter, consisted of diffusely proliferated pleomorphic cells with numerous mitoses (53/10 HPFs). Immunohistochemically, the tumor cells were positive for CD1a, Langerin and PD-L1, and the Ki-67 labeling index was 50%. These pathological features were consistent with LCS, and were also observed in the metastatic tumor. Whole-exome sequencing revealed that both the primary and metastatic tumors harbored a large number of mutations (>20 mutations/megabase), with deletion of CDKN2A and TP53 mutation, and highlighted that the mutational signature was predominantly characteristic of ultraviolet (UV) exposure (W = 0.828). Our results suggest, for the first time, that DNA damage by UV could accumulate in Langerhans cells and play a role in the pathogenesis of LCS. The high mutational burden and PD-L1 expression in the tumor would provide a rationale for the use of immune checkpoint inhibitors for treatment of unresectable LCS.
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Affiliation(s)
| | - Yosuke Yamada
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Yoshihiro Ishida
- Department of Dermatology, Kyoto University Hospital, Kyoto, Japan
| | - Yo Kaku
- Department of Dermatology, Kyoto University Hospital, Kyoto, Japan
| | - Masakazu Fujimoto
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Tatsuki R Kataoka
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
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26
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Hiraide T, Hattori A, Ieda D, Hori I, Saitoh S, Nakashima M, Saitsu H. De novo variants in SETD1B cause intellectual disability, autism spectrum disorder, and epilepsy with myoclonic absences. Epilepsia Open 2019; 4:476-481. [PMID: 31440728 PMCID: PMC6698685 DOI: 10.1002/epi4.12339] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/27/2019] [Accepted: 05/09/2019] [Indexed: 02/02/2023] Open
Abstract
Epilepsy with myoclonic absences is a specific seizure type characterized by bilateral rhythmic clonic jerks with impairment of consciousness. Here, we report an individual with epilepsy with myoclonic absences, mild intellectual disabilities, language disorder, and autism spectrum disorder. His interictal electroencephalogram revealed a spike-and-slow wave complex dominant in the frontal area. His ictal polygraphic and video-electroencephalogram showed a characteristic diffuse synchronous 3-Hz spike-and-wave burst associated with bilateral upper limb myoclonic jerks with impairment of consciousness. Using whole-exome sequencing, we found a novel de novo variant, c.386T>G, p.(Val129Gly), in SETD1B (SET domain containing 1B). We previously reported that two individuals with a de novo SETD1B variant showed intellectual disability, epilepsy, and autism. Of note, one of those individuals and the present case showed epilepsy with myoclonic absences. Therefore, this report supports the indication that SETD1B may be a causative gene for neurodevelopmental disorders and suggests that epilepsy with myoclonic absences may be a characteristic feature of SETD1B-related disorders.
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Affiliation(s)
- Takuya Hiraide
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
- Department of PediatricsHamamatsu University School of MedicineHamamatsuJapan
| | - Ayako Hattori
- Department of Pediatrics and NeonatologyNagoya City University, Graduate School of Medical SciencesAichiJapan
| | - Daisuke Ieda
- Department of Pediatrics and NeonatologyNagoya City University, Graduate School of Medical SciencesAichiJapan
| | - Ikumi Hori
- Department of Pediatrics and NeonatologyNagoya City University, Graduate School of Medical SciencesAichiJapan
| | - Shinji Saitoh
- Department of Pediatrics and NeonatologyNagoya City University, Graduate School of Medical SciencesAichiJapan
| | - Mitsuko Nakashima
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Hirotomo Saitsu
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
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27
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Shimizu D, Iwashima S, Sato K, Hayano S, Fukami M, Saitsu H, Ogata T. GATA4 variant identified by whole-exome sequencing in a Japanese family with atrial septal defect: Implications for male sex development. Clin Case Rep 2018; 6:2229-2233. [PMID: 30455927 PMCID: PMC6230668 DOI: 10.1002/ccr3.1851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/20/2018] [Accepted: 09/19/2018] [Indexed: 01/21/2023] Open
Abstract
We identified a heterozygous p.(R284H) variant of GATA4 in a Japanese family with atrial septal defect, including boys with apparently normal male sex development. The findings, together with the previous data, imply that GATA4 variants primarily cause congenital heart disease and rarely result in 46,XY disorder of sex development.
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Affiliation(s)
- Daisuke Shimizu
- Department of PediatricsHamamatsu University School of MedicineHamamatsuJapan
| | - Satoru Iwashima
- Department of PediatricsChutoen General Medical CenterKakegawaJapan
| | - Keisuke Sato
- Cardiac Intensive Care UnitShizuoka Children’s HospitalShizuokaJapan
| | - Satoshi Hayano
- Department of PediatricsChutoen General Medical CenterKakegawaJapan
| | - Maki Fukami
- Department of Molecular EndocrinologyNational Research Institute for Child health and DevelopmentTokyoJapan
| | - Hirotomo Saitsu
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Tsutomu Ogata
- Department of PediatricsHamamatsu University School of MedicineHamamatsuJapan
- Department of Molecular EndocrinologyNational Research Institute for Child health and DevelopmentTokyoJapan
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28
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Nelin S, Hussey R, Faux BM, Rohena L. Youngest presenting patient with dystonia 24 and review of the literature. Clin Case Rep 2018; 6:2070-2074. [PMID: 30455893 PMCID: PMC6230669 DOI: 10.1002/ccr3.1671] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/21/2018] [Accepted: 06/11/2018] [Indexed: 12/25/2022] Open
Abstract
Dystonia 24 was first reported in 2000 as an autosomal dominant cause of dystonia caused by variants in the ANO3 gene. Although many adults have been described with dystonia 24, since 2014, an increasing number of children have also been reported. Dystonia 24 should also be considered in the differential of a child with unexplained dystonia.
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29
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Uittenbogaard M, Gropman A, Brantner CA, Chiaramello A. Novel metabolic signatures of compound heterozygous Szt2 variants in a case of early-onset of epileptic encephalopathy. Clin Case Rep 2018; 6:2376-2384. [PMID: 30564332 PMCID: PMC6293145 DOI: 10.1002/ccr3.1868] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/25/2018] [Indexed: 01/06/2023] Open
Abstract
Our study reports the case of a patient with early onset of epileptic encephalopathy harboring compound heterozygous Szt2 variants. We provide the first evidence that these Szt2 variants impair mitochondrial energy metabolism. Our results shed light on their pathogenic molecular mechanism and clinical implications for brain development and disease progression.
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Affiliation(s)
- Martine Uittenbogaard
- Department of Anatomy and Regenerative Biology George Washington University School of Medicine and Health Sciences Washington District of Columbia
| | - Andrea Gropman
- Division of Neurogenetics and Developmental Pediatrics Children's National Medical Center Washington District of Columbia
| | - Christine A Brantner
- GW Nanofabrication and Imaging Center Office of the Vice President for Research George Washington University Washington District of Columbia
| | - Anne Chiaramello
- Department of Anatomy and Regenerative Biology George Washington University School of Medicine and Health Sciences Washington District of Columbia
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30
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Abstract
Undoubtedly, intratumor heterogeneity (ITH) is one of the causes of the intractability of cancers. Recently, technological innovation in genomics has promoted studies on ITH in solid tumors and on the pattern and level of diversity, which varies among malignancies. We profiled the genome in multiple regions of nine colorectal cancer (CRC) cases. The most impressive finding was that in the late phase, a parental clone branched into numerous subclones. We found that minor mutations were dominant in advanced CRC named neutral evolution; that is, driver gene aberrations were observed with high proportion in the early-acquired phase, but low in the late-acquired phase. Then, we validated that neutral evolution could cause ITH in advanced CRC by super-computational analysis. According to the clinical findings, we explored a branching evolutionary process model in cancer evolution, which assumes that each tumor cell has cellular automaton. According to the model, we verified factors to foster ITH with neutral evolution in advanced CRC. In this review, we introduce recent advances in the field of ITH including the general component of ITH, clonal selective factors that consolidate the evolutionary process, and a representative clinical application of ITH.
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Affiliation(s)
- Koshi Mimori
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Tomoko Saito
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Atsushi Niida
- Division of Health Medical Computational ScienceHealth Intelligence CenterInstitute of Medical ScienceThe University of TokyoTokyoJapan
| | - Satoru Miyano
- Laboratory of Sequence AnalysisHuman Genome CenterInstitute of Medical ScienceUniversity of TokyoTokyoJapan
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31
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DeMeo NN, Burgess JD, Blackburn PR, Gass JM, Richter J, Atwal HK, van Gerpen JA, Atwal PS. Co-occurrence of a novel PDGFRB variant and likely pathogenic variant in CASR in an individual with extensive intracranial calcifications and hypocalcaemia. Clin Case Rep 2017; 6:8-13. [PMID: 29375828 PMCID: PMC5771904 DOI: 10.1002/ccr3.1265] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/20/2017] [Accepted: 10/08/2017] [Indexed: 12/12/2022] Open
Abstract
This case report describes an individual with brain calcifications, cognitive decline, motor dysfunction, and hypocalcaemia. Exome sequencing revealed a previously reported variant in the CASR gene and a variant of uncertain significance in PDGFRB. The clinical phenotype is likely explained by the CASR variant, but we discuss how the PDGFRB variant could also participate in the phenotype.
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Affiliation(s)
| | | | - Patrick R Blackburn
- Center for Individualized Medicine Mayo Clinic Jacksonville Florida.,Department of Health Sciences Research Mayo Clinic Jacksonville Florida
| | - Jennifer M Gass
- Center for Individualized Medicine Mayo Clinic Jacksonville Florida
| | - John Richter
- Center for Individualized Medicine Mayo Clinic Jacksonville Florida.,Department of Clinical Genomics Mayo Clinic Jacksonville Florida
| | | | | | - Paldeep S Atwal
- Center for Individualized Medicine Mayo Clinic Jacksonville Florida.,Department of Clinical Genomics Mayo Clinic Jacksonville Florida
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32
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Menendez I, Carranza C, Herrera M, Marroquin N, Foster J, Cengiz FB, Bademci G, Tekin M. Dominant deafness-onychodystrophy syndrome caused by an ATP6V1B2 mutation. Clin Case Rep 2017; 5:376-379. [PMID: 28396750 PMCID: PMC5378843 DOI: 10.1002/ccr3.761] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 10/25/2016] [Accepted: 11/06/2016] [Indexed: 12/02/2022] Open
Abstract
Our report clarifies the role of ATP6V1B2 in patients with deafness and onycho‐osteodystrophy and confirms that a recurring ATP6V1B2 c.1516C>T [p.(Arg506*)], variant causes dominant deafness–onychodystrophy (DDOD) syndrome.
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Affiliation(s)
- Ibis Menendez
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami Florida USA
| | - Claudia Carranza
- Institute for Research on Genetic and Metabolic Diseases INVEGEM Guatemala City Guatemala
| | - Mariana Herrera
- Institute for Research on Genetic and Metabolic Diseases INVEGEM Guatemala City Guatemala
| | - Nely Marroquin
- Institute for Research on Genetic and Metabolic Diseases INVEGEM Guatemala City Guatemala
| | - Joseph Foster
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami Florida USA
| | - Filiz Basak Cengiz
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami Florida USA
| | - Guney Bademci
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami Florida USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami Florida USA; Department of Human Genetics Dr. John T. Macdonald Foundation University of Miami Miller School of Medicine Miami Florida USA
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33
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Sethi KD, Lang AE. Will New Genetic Techniques Like Exome Sequencing Obviate the Need for Clinical Expertise? No. Mov Disord Clin Pract 2016; 4:39-41. [PMID: 30713947 DOI: 10.1002/mdc3.12443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 11/06/2022] Open
Affiliation(s)
- Kapil D Sethi
- Medical College of Georgia at Augusta University Augusta Georgia USA
| | - Anthony E Lang
- Morton and Gloria Shulman Movement Disorders Clinic and the Edmond J. Safra Program in Parkinson's Disease Toronto Western Hospital and the University of Toronto Toronto Ontario Canada
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34
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Hamilton A, Tétreault M, Dyment DA, Zou R, Kernohan K, Geraghty MT, Hartley T, Boycott KM. Concordance between whole-exome sequencing and clinical Sanger sequencing: implications for patient care. Mol Genet Genomic Med 2016; 4:504-12. [PMID: 27652278 PMCID: PMC5023935 DOI: 10.1002/mgg3.223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 12/12/2022] Open
Abstract
The clinical translation of next‐generation sequencing has created a paradigm shift in the diagnostic assessment of individuals with suspected rare genetic diseases. Whole‐exome sequencing (WES) simultaneously examines the majority of the coding portion of the genome and is rapidly becoming accepted as an efficient alternative to clinical Sanger sequencing for diagnosing genetically heterogeneous disorders. Among reports of the clinical and diagnostic utility of WES, few studies to date have directly compared its concordance to Sanger sequencing, which is considered the clinical “gold standard”. We performed a direct comparison of 391 coding and noncoding polymorphisms and variants of unknown significance identified by clinical Sanger sequencing to the WES results of 26 patients. Of the 150 well‐covered coding variants identified by Sanger sequencing, 146 (97.3%) were also reported by WES. Nine genes were excluded from the comparison due to consistently low coverage in WES, which might be attributed to the use of older exome capture kits. We performed confirmatory Sanger sequencing of discordant variants; including five variants with discordant bases and four with discordant zygosity. Confirmatory Sanger sequencing supported the original Sanger report for three of the five discordant bases, one was shown to be a false positive supporting the WES data, and one result differed from both the Sanger and WES data. Two of the discordant zygosity results supported Sanger and the other two supported WES data. We report high concordance for well‐covered coding variants, supporting the use of WES as a screening tool for heterogeneous disorders, and recommend the use of supplementary Sanger sequencing for poorly‐covered genes when the clinical suspicion is high. Importantly, despite remaining difficulties with achieving complete coverage of the whole exome, 10 (38.5%) of the 26 compared patients were diagnosed through WES.
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Affiliation(s)
- Alison Hamilton
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Martine Tétreault
- Department of Human Genetics McGill UniversityMontréalQuébecCanada; McGill University and Genome Québec Innovation CenterMontréalQuébecCanada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaOntarioCanada; Department of GeneticsChildren's Hospital of Eastern Ontario ResearchOttawaOntarioCanada
| | - Ruobing Zou
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Michael T Geraghty
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaOntarioCanada; Division of Metabolics and Newborn ScreeningDepartment of PediatricsChildren's Hospital of Eastern OntarioOttawaOntarioCanada
| | | | | | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaOntarioCanada; Department of GeneticsChildren's Hospital of Eastern Ontario ResearchOttawaOntarioCanada
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35
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Dhamija R, Mink JW, Shah BB, Goodkin HP. GNAO1-Associated Movement Disorder. Mov Disord Clin Pract 2016; 3:615-617. [PMID: 30838255 DOI: 10.1002/mdc3.12344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 12/25/2022] Open
Affiliation(s)
- Radhika Dhamija
- Department of Neurology University of Virginia Charlottesville Virginia USA
| | - Jonathan W Mink
- Department of Neurology University of Rochester Rochester New York USA.,Department of Neurobiology & Anatomy University of Rochester Rochester New York USA.,Department of Brain & Cognitive Sciences University of Rochester Rochester New York USA.,Department of Pediatrics University of Rochester Rochester New York USA
| | - Binit B Shah
- Department of Neurology University of Virginia Charlottesville Virginia USA
| | - Howard P Goodkin
- Department of Neurology University of Virginia Charlottesville Virginia USA
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36
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Yang J, Kawasaki K, Lee M, Reid BM, Nunez SM, Choi M, Seymen F, Koruyucu M, Kasimoglu Y, Estrella-Yuson N, Lin BPJ, Simmer JP, Hu JCC. The dentin phosphoprotein repeat region and inherited defects of dentin. Mol Genet Genomic Med 2016; 4:28-38. [PMID: 26788535 PMCID: PMC4707025 DOI: 10.1002/mgg3.176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 11/12/2022] Open
Abstract
Nonsyndromic dentin defects classified as type II dentin dysplasia and types II and III dentinogenesis imperfecta are caused by mutations in DSPP (dentin sialophosphoprotein). Most reported disease‐causing DSPP mutations occur within the repetitive DPP (dentin phosphoprotein) coding sequence. We characterized the DPP sequences of five probands with inherited dentin defects using single molecule real‐time (SMRT) DNA sequencing. Eight of the 10 sequences matched previously reported DPP length haplotypes and two were novel. Alignment with known DPP sequences showed 32 indels arranged in 36 different patterns. Sixteen of the 32 indels were not represented in more than one haplotype. The 25 haplotypes with confirmed indels were aligned to generate a tree that describes how the length variations might have evolved. Some indels were independently generated in multiple lines. A previously reported disease‐causing DSPP mutation in Family 1 was confirmed and its position clarified (c.3135delC; p.Ser1045Argfs*269). A novel frameshift mutation (c.3504_3508dup; p.Asp1170Alafs*146) caused the dentin defects in Family 2. A COL1A2 (c.2027G>A or p.Gly676Asp) missense mutation, discovered by whole‐exome sequencing, caused the dentin defects in Family 3. We conclude that SMRT sequencing characterizes the DPP repeat region without cloning and can improve our understanding of normal and pathological length variations in DSPP alleles.
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Affiliation(s)
- Jie Yang
- Department of Biologic and Materials SciencesUniversity of Michigan School of Dentistry1210 Eisenhower PlaceAnn ArborMichigan; Department of Pediatric DentistrySchool and Hospital of StomatologyPeking University22 South AvenueZhongguancun Haidian DistrictBeijing100081China
| | - Kazuhiko Kawasaki
- Department of Anthropology Pennsylvania State University University Park Pennsylvania 16802
| | - Moses Lee
- Department of Biomedical Sciences Seoul National University College of Medicine 275-1 Yongon-dong, Chongno-gu Seoul 110-768 Korea
| | - Bryan M Reid
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan
| | - Stephanie M Nunez
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan
| | - Murim Choi
- Department of Biomedical Sciences Seoul National University College of Medicine 275-1 Yongon-dong, Chongno-gu Seoul 110-768 Korea
| | - Figen Seymen
- Department of Pedodontics Faculty of Dentistry Istanbul University Istanbul Turkey
| | - Mine Koruyucu
- Department of Pedodontics Faculty of Dentistry Istanbul University Istanbul Turkey
| | - Yelda Kasimoglu
- Department of Pedodontics Faculty of Dentistry Istanbul University Istanbul Turkey
| | - Ninna Estrella-Yuson
- Department of Paediatric Dentistry Women's and Children's Hospital 72 King William Road North Adelaide South Australia 5006 Australia
| | - Brent P J Lin
- Department of Pediatric Dentistry School of Dentistry University of California San Francisco California
| | - James P Simmer
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan
| | - Jan C-C Hu
- Department of Biologic and Materials Sciences University of Michigan School of Dentistry 1210 Eisenhower Place Ann Arbor Michigan
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