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Luan W, Cheng H, Xie H, Liu H, Wang Y, Wang S, Ye X, Zhu H, Tang F, Li Y, Chang X. PRKDC-Mediated NHEJ May Play a Crucial Role in Aneuploidy of Chromosome 8-Driven Progression of Ovarian Cancer. Int J Mol Sci 2024; 25:4825. [PMID: 38732044 PMCID: PMC11084440 DOI: 10.3390/ijms25094825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
High malignancy is a prominent characteristic of epithelial ovarian cancer (EOC), emphasizing the necessity for further elucidation of the potential mechanisms underlying cancer progression. Aneuploidy and copy number variation (CNV) partially contribute to the heightened malignancy observed in EOC; however, the precise features of aneuploidy and their underlying molecular patterns, as well as the relationship between CNV and aneuploidy in EOC, remain unclear. In this study, we employed single-cell sequencing data along with The Cancer Genome Atlas (TCGA) to investigate aneuploidy and CNV in EOC. The technique of fluorescence in situ hybridization (FISH) was employed using specific probes. The copy number variation within the genomic region of chromosome 8 (42754568-47889815) was assessed and utilized as a representative measure for the ploidy status of individual cells in chromosome 8. Differential expression analysis was performed between different subgroups based on chromosome 8 ploidy. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interaction (PPI), and hub-gene analyses were subsequently utilized to identify crucial genes involved. By classifying enriched tumor cells into distinct subtypes based on chromosome 8 ploidy combined with TCGA data integration, we identified key genes driving chromosome 8 aneuploidy in EOC, revealing that PRKDC gene involvement through the mediated non-homologous end-joining pathway may play a pivotal role in disease progression. Further validation through analysis of the GEO and TCGA database and survival assessment, considering both mRNA expression levels and CNV status of PRKDC, has confirmed its involvement in the progression of EOC. Further functional analysis revealed an upregulation of PRKDC in both ovarian EOC cells and tissues, with its expression showing a significant correlation with the extent of copy number variation (CNV) on chromosome 8. Taken together, CNV amplification and aneuploidy of chromosome 8 are important characteristics of EOC. PRKDC and the mediated NHEJ pathway may play a crucial role in driving aneuploidy on chromosome 8 during the progression of EOC.
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Affiliation(s)
- Wenqing Luan
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Hongyan Cheng
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Haoling Xie
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Huiping Liu
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Yicheng Wang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Shang Wang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Xue Ye
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Honglan Zhu
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Fuchou Tang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Yi Li
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Xiaohong Chang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
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Chen Y, Han X, Hua R, Li N, Zhang L, Hu W, Wang Y, Qian Z, Li S. Copy number variation sequencing for the products of conception: What is the optimal testing strategy. Clin Chim Acta 2024; 557:117884. [PMID: 38522821 DOI: 10.1016/j.cca.2024.117884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Copy number variation sequencing (CNV-seq) is crucial in prenatal diagnosis, but its limitations in detecting polyploidy, maternal cell contamination (MCC), and uniparental disomy (UPD) restrict its application in the analysis of products of conception (POCs). This study aimed to investigate an optimal genetic testing strategy for POCs in the era of CNV-seq. METHODS CNV-seq and quantitative fluorescent polymerase chain reaction (QF-PCR) were performed in all 4,211 spontaneous miscarriage cases. Different testing strategies were compared and the optimal testing strategies were proposed. RESULTS Of the 4,211 cases, 2561 (60.82%) exhibited clinically significant chromosomal abnormalities. CNV-seq alone, without QF-PCR, might misdiagnose 311 (7.39%) cases, including 278 polyploidy, 13 UPD, and 20 MCC. In 20 MCC cases identified by QF-PCR, CNV-seq successfully pinpointed the cause of miscarriage in 13 cases. Furthermore, in cases where QF-PCR suggested polyploidy, CNV-seq improved the diagnostic accuracy in 54 (1.28%) hypo/hypertriploidy cases. After comparing four different strategies, the sequential approach (initiating with CNV-seq followed by QF-PCR if necessary) emerged as advantageous, reducing approximately 70% of the cost associated with QF-PCR while maintaining result accuracy. CONCLUSIONS We propose an initial CNV-seq followed by QF-PCR if needed-an efficient and cost-effective strategy for the genetic analysis of POCs.
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Affiliation(s)
- Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Han
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renyi Hua
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjing Hu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhida Qian
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Bai W, Zhang Q, Lin Z, Ye J, Shen X, Zhou L, Cai W. Analysis of copy number variations and possible candidate genes in spontaneous abortion by copy number variation sequencing. Front Endocrinol (Lausanne) 2023; 14:1218793. [PMID: 37916154 PMCID: PMC10616874 DOI: 10.3389/fendo.2023.1218793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/20/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction Embryonic chromosomal abnormalities represent a major causative factor in early pregnancy loss, highlighting the importance of understanding their role in spontaneous abortion. This study investigates the potential correlation between chromosomal abnormalities and spontaneous abortion using copy number variation sequencing (CNV-seq), a Next-Generation Sequencing (NGS) technology. Methods We analyzed Copy Number Variations (CNVs) in 395 aborted fetal specimens from spontaneous abortion patients by CNV-seq. And collected correlated data, including maternal age, gestational week, and Body Mass Index (BMI), and analyzed their relationship with the CNVs. Results Out of the 395 cases, 67.09% of the fetuses had chromosomal abnormalities, including numerical abnormalities, structural abnormalities, and mosaicisms. Maternal age was found to be an important risk factor for fetal chromosomal abnormalities, with the proportion of autosomal trisomy in abnormal karyotypes increasing with maternal age, while polyploidy decreased. The proportion of abnormal karyotypes with mosaic decreased as gestational age increased, while the frequency of polyploidy and sex chromosome monosomy increased. Gene enrichment analysis identified potential miscarriage candidate genes and functions, as well as pathogenic genes and pathways associated with unexplained miscarriage among women aged below or over 35 years old. Based on our study, it can be inferred that there is an association between BMI values and the risk of recurrent miscarriage caused by chromosomal abnormalities. Discussion Overall, these findings provide important insights into the understanding of spontaneous abortion and have implications for the development of personalized interventions for patients with abnormal karyotypes.
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Affiliation(s)
- Wei Bai
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Qi Zhang
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, China
| | - Zhi Lin
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Jin Ye
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Xiaoqi Shen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, China
| | - Linshuang Zhou
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Wenpin Cai
- Department of Laboratory Medicine, Wenzhou Traditional Chinese Medicine Hospital of Zhejiang Chinese Medical University, Zhejiang, China
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Chen Q, Zhang H, Li X, Li J, Chen H, Liu L, Zhou S, Xu Z. Sequential application of copy number variation sequencing and quantitative fluorescence polymerase chain reaction in genetic analysis of miscarriage and stillbirth. Mol Genet Genomic Med 2023; 11:e2187. [PMID: 37073418 PMCID: PMC10422063 DOI: 10.1002/mgg3.2187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 02/07/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Copy number variation sequencing (CNV-seq) could detect most chromosomal abnormalities except polyploidy, and quantitative fluorescence polymerase chain reaction (QF-PCR) is a supplementary method to CNV-seq in triploid detection. This study aimed to evaluate the feasibility of sequential application of CNV-seq and QF-PCR in genetic analysis of miscarriage and stillbirth. METHODS A total of 261 fetal specimens were analyzed by CNV-seq, and QF-PCR was only further performed for samples with normal female karyotype identified by CNV-seq. Cost and turnaround time (TAT) was analyzed for sequential detection strategy. Subgroup analysis and logistic regression were carried out to evaluate the relationship between clinical characteristics (maternal age, gestational age, and number of pregnancy losses) and the occurrence of chromosomal abnormalities. RESULTS Abnormal results were obtained in 120 of 261 (45.98%) cases. Aneuploidy was the most common abnormality (37.55%), followed by triploidy (4.98%) and pathogenic copy number variations (pCNVs) (3.45%). CNV-seq could detect the triploidy with male karyotype, and QF-PCR could further identify the remaining triploidy with female karyotype. In this study, we found more male triploidies than female triploidies. With the same ability in chromosomal abnormalities detection, the cost of sequential strategy decreased by 17.35% compared with combined strategy. In subgroup analysis, significant difference was found in the frequency of total chromosomal abnormalities between early abortion group and late abortion group. Results of logistic regression showed a trend that pregnant women with advanced age, first-time abortion, and abortion earlier than 12 weeks were more likely to detect chromosomal aberrations in their products of conception. CONCLUSION Sequential application of CNV-seq and QF-PCR is an economic and practical strategy to identify chromosomal abnormalities in fetal tissue.
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Affiliation(s)
- Quan Chen
- Department of Reproductive and Genetic DiseasesDeyang People's HospitalDeyangSichuanChina
- Deyang Key Laboratory of Birth Defects Prevention and ControlDeyang People's HospitalDeyangSichuanChina
| | - Hao Zhang
- Department of Reproductive and Genetic DiseasesDeyang People's HospitalDeyangSichuanChina
- Deyang Key Laboratory of Birth Defects Prevention and ControlDeyang People's HospitalDeyangSichuanChina
| | - Xue Li
- Department of Reproductive and Genetic DiseasesDeyang People's HospitalDeyangSichuanChina
- Deyang Key Laboratory of Birth Defects Prevention and ControlDeyang People's HospitalDeyangSichuanChina
| | - Junxing Li
- Department of Obstetrics and GynecologyDeyang People's HospitalDeyangSichuanChina
| | - Huijuan Chen
- Department of Reproductive and Genetic DiseasesDeyang People's HospitalDeyangSichuanChina
- Deyang Key Laboratory of Birth Defects Prevention and ControlDeyang People's HospitalDeyangSichuanChina
| | - Lin Liu
- Department of Reproductive and Genetic DiseasesDeyang People's HospitalDeyangSichuanChina
- Deyang Key Laboratory of Birth Defects Prevention and ControlDeyang People's HospitalDeyangSichuanChina
| | - Shijie Zhou
- Department of Reproductive and Genetic DiseasesDeyang People's HospitalDeyangSichuanChina
- Deyang Key Laboratory of Birth Defects Prevention and ControlDeyang People's HospitalDeyangSichuanChina
| | - Zhihong Xu
- Department of Reproductive and Genetic DiseasesDeyang People's HospitalDeyangSichuanChina
- Deyang Key Laboratory of Birth Defects Prevention and ControlDeyang People's HospitalDeyangSichuanChina
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Zhuang J, Wang J, Luo Q, Zeng S, Chen Y, Jiang Y, Chen X, Wang Y, Xie Y, Wang G, Chen C. Case Report: Novel compound heterozygous variants in CHRNA1 gene leading to lethal multiple pterygium syndrome: A case report. Front Genet 2022; 13:964098. [PMID: 36092864 PMCID: PMC9459375 DOI: 10.3389/fgene.2022.964098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Lethal multiple pterygium syndrome (LMPS) is a rare autosomal recessive inherited disorder typically characterized by intrauterine growth retardation, multiple pterygia, and flexion contractures. Case presentation: We herein report a Chinese case with a history of three adverse pregnancies demonstrating the same ultrasonic phenotypes, including increased nuchal translucency, edema, fetal neck cystoma, reduced movement, joint contractures, and other congenital features. Whole-exome sequencing (WES) revealed novel compound heterozygous variants in the CHRNA1 gene NM_000079.4: c.[1128delG (p.Pro377LeufsTer10)]; [505T>C (p.Trp169Arg)] in the recruited individual, and subsequent familial segregation showed that both parents transmitted their respective mutation. Conclusion: For the first time, we identified an association between the CHRNA1 gene and the recurrent lethal multiple pterygium syndrome (LMPS) in a Chinese family. This finding may also enrich the mutation spectrum of the CHRNA1 gene and promote the applications of WES technology in etiologic diagnosis of ultrasound anomalies in prenatal examination.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Junyu Wang
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Qi Luo
- Department of Public Health for Women and Children, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Yu’e Chen
- Ultrasonography, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Xinying Chen
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Chunnuan Chen, ; Gaoxiong Wang, ; Yingjun Xie,
| | - Gaoxiong Wang
- Quanzhou Women’s and Children’s Hospital, Quanzhou, China
- *Correspondence: Chunnuan Chen, ; Gaoxiong Wang, ; Yingjun Xie,
| | - Chunnuan Chen
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- *Correspondence: Chunnuan Chen, ; Gaoxiong Wang, ; Yingjun Xie,
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