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Chen SC, Zhou XY, Li SY, Zhao MM, Huang HF, Jia J, Xu CM. Carrier burden of over 300 diseases in Han Chinese identified by expanded carrier testing of 300 couples using assisted reproductive technology. J Assist Reprod Genet 2023; 40:2157-2173. [PMID: 37450097 PMCID: PMC10440320 DOI: 10.1007/s10815-023-02876-y] [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: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Expanded carrier screening (ECS) has become a common practice for identifying carriers of monogenic diseases. However, existing large gene panels are not well-tailored to Chinese populations. In this study, ECS testing for pathogenic variants of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in 330 genes implicated in 342 autosomal recessive (AR) or X-linked diseases was carried out. We assessed the differences in allele frequencies specific to the Chinese population who have used assisted reproductive technology (ART) and the important genes to screen for in this population. METHODOLOGY A total of 300 heterosexual couples were screened by our ECS panel using next-generation sequencing. A customed bioinformatic algorithm was used to analyze SNVs and CNVs. Guidelines from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology were adapted for variant interpretation. Pathogenic or likely pathogenic (P/LP) SNVs located in high homology regions/deletions and duplications of one or more exons in length were independently verified with other methods. RESULTS 64.83% of the patients were identified to be carriers of at least one of 342 hereditary conditions. We identified 622 P/LP variants, 4.18% of which were flagged as CNVs. The rate of at-risk couples was 3%. A total of 149 AR diseases accounted for 64.05% of the cumulative carrier rate, and 48 diseases had a carrier rate above 1/200 in the test. CONCLUSION An expanded screening of inherited diseases by incorporating different variant types, especially CNVs, has the potential to reduce the occurrence of severe monogenic diseases in the offspring of patients using ART in China.
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Affiliation(s)
- Song-Chang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xuan-You Zhou
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shu-Yuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ming-Min Zhao
- Fujungenetics Biotechnology Co., Ltd., No. 70 of Tongchuan Road, Putuo District, Shanghai, 200333, China
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Jia Jia
- Fujungenetics Biotechnology Co., Ltd., No. 70 of Tongchuan Road, Putuo District, Shanghai, 200333, China.
| | - Chen-Ming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China.
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.
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2
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Nguyen MHT, Nguyen AHP, Ngo DN, Nguyen PMT, Tang HS, Giang H, Lu YT, Nguyen HN, Tran MD. The mutation spectrum of SLC25A13 gene in citrin deficiency: identification of novel mutations in Vietnamese pediatric cohort with neonatal intrahepatic cholestasis. J Hum Genet 2023; 68:305-312. [PMID: 36599957 DOI: 10.1038/s10038-022-01112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND Citrin deficiency (CD), a disorder caused by mutations in the SLC25A13 gene, may result in neonatal intrahepatic cholestasis. This study was purposely to explore the mutation spectrum of SLC25A13 gene in Vietnamese CD patients. METHODS The 292 unrelated CD patients were first screened for four high-frequency mutations by PCR/PCR-RFLP. Then, Sanger sequencing was performed directly for heterozygous or undetected patients. Novel mutations identified would need to be confirmed by their parents. RESULTS 12 pathogenic SLC25A13 mutations were identified in all probands, including three deletions c.851_854del (p.R284Rfs*3), c.70-63_133del (p.Y24_72Ifs*10), and c.[1956C>A;1962del] (p.[N652K;F654Lfs*45]), two splice-site mutations (IVS6+5G>A and IVS11+1G>A), one nonsense mutations c.1399C>T (p.R467*), one duplication mutation c.1638_1660dup (p.A554fs*570), one insertion IVSl6ins3kb (p.A584fs*585), and four missense mutation c.2T>C (p.M1T), c.1231G>A (p.V411M), c.1763G>A (p.R588Q), and c.135G>C (p.L45F). Among them, c.851_854del (mut I) was the most identified mutant allele (91.78%) with a total of 247 homozygous and 42 heterozygous genotypes of carriers. Interestingly, two novel mutations were identified: c.70-63_133del (p.Y24_72Ifs*10) and c.[1956C>A;1962del] (p.[N652K;F654Lfs*45]). CONCLUSION The SLC25A13 mutation spectrum related to intrahepatic cholestasis infants in Vietnam revealed a quite similar pattern to Asian countries' reports. This finding supports the use of targeted SLC25A13 mutation for CD screening in Vietnam and contributed to the SLC25A13 mutation spectra worldwide. It also helps emphasize the role of DNA analysis in treatment, genetic counseling, and prenatal diagnosis.
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Affiliation(s)
| | | | - Diem-Ngoc Ngo
- Human Genetics Department, National Children's Hospital, Hanoi, Vietnam
| | | | - Hung-Sang Tang
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institutes, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institutes, Ho Chi Minh City, Vietnam
| | - Y-Thanh Lu
- Medical Genetics Institutes, Ho Chi Minh City, Vietnam
| | - Hoai-Nghia Nguyen
- Medical Genetics Institutes, Ho Chi Minh City, Vietnam.,University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Minh-Dien Tran
- Human Genetics Department, National Children's Hospital, Hanoi, Vietnam.,Hepatology Department, National Children's Hospital, Hanoi, Vietnam
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Tavoulari S, Lacabanne D, Thangaratnarajah C, Kunji ERS. Pathogenic variants of the mitochondrial aspartate/glutamate carrier causing citrin deficiency. Trends Endocrinol Metab 2022; 33:539-553. [PMID: 35725541 PMCID: PMC7614230 DOI: 10.1016/j.tem.2022.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/26/2022] [Accepted: 05/19/2022] [Indexed: 12/22/2022]
Abstract
Citrin deficiency is a pan-ethnic and highly prevalent mitochondrial disease with three different stages: neonatal intrahepatic cholestasis (NICCD), a relatively mild adaptation stage, and type II citrullinemia in adulthood (CTLN2). The cause is the absence or dysfunction of the calcium-regulated mitochondrial aspartate/glutamate carrier 2 (AGC2/SLC25A13), also called citrin, which imports glutamate into the mitochondrial matrix and exports aspartate to the cytosol. In citrin deficiency, these missing transport steps lead to impairment of the malate-aspartate shuttle, gluconeogenesis, amino acid homeostasis, and the urea cycle. In this review, we describe the geological spread and occurrence of citrin deficiency, the metabolic consequences and use our current knowledge of the structure to predict the impact of the known pathogenic mutations on the calcium-regulatory and transport mechanism of citrin.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Denis Lacabanne
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Chancievan Thangaratnarajah
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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4
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Lin WX, Yaqub MR, Zhang ZH, Mao M, Zeng HS, Chen FP, Li WM, Cai WZ, Li YQ, Tan ZY, Sheng W, Li ZM, Tao XL, Li YX, Zhang JP, Han YB, Li Y, Duan WQ, Ye BN, Li YR, Song YZ. Molecular epidemiologic study of citrin deficiency by screening for four reported pathogenic SLC25A13 variants in the Shaanxi and Guangdong provinces, China. Transl Pediatr 2021; 10:1658-1667. [PMID: 34295780 PMCID: PMC8261583 DOI: 10.21037/tp-21-58] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/19/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Citrin deficiency (CD) is an autosomal recessive disease resulting from biallelic mutations of the SLC25A13 gene. This study aimed to investigate the molecular epidemiological features of CD in the Guangdong and Shaanxi provinces of China. METHODS A total of 3,409 peripheral blood samples from Guangdong and 2,746 such samples from Shaanxi province were collected. Four prevalent SLC25A13 mutations NG_012247.2 (NM_014251.3): c.852_855del, c.1638_1660dup, c.615+5G>A, and c.1751-5_1751-4ins(2684) were screened by using the conventional polymerase chain reaction (PCR)/PCR-restriction fragment length polymorphism and newly-developed multiplex PCR methods, respectively. The mutated SLC25A13 allele frequencies, carrier frequencies, and CD morbidity rates were calculated and then compared with the Chi-square and Fisher's exact tests. RESULTS The mutations were detected in 68 out of 6,818 SLC25A13 alleles in Guangdong and 29 out of 5,492 alleles in the Shaanxi population. The carrier frequencies were subsequently calculated to be 1/51 and 1/95, while the CD morbidity rates were 1/10,053 and 1/35,865, in the 2 populations, respectively. When compared with the Shaanxi population, Guangdong exhibited a higher frequency of mutated SLC25A13 allele (68/6,818 vs. 29/5,492, χ2=8.570, P=0.003) in general, with higher c.852_855del (54/6,818 vs. 13/5,492, χ2=17.328, P=0.000) but lower c.1751-5_1751 -4ins(2684) (2/6,818 vs. 9/5,492, P=0.015) allele frequencies. The distribution of c.615+5G>A and c.1638_1660dup between the 2 provinces, as well as all 4 prevalent mutations among different geographic regions within the 2 provinces, did not differed significantly. CONCLUSIONS Our findings depicted the CD molecular epidemiological features in Guangdong and Shaanxi populations, providing preliminary but significant laboratory evidences for the subsequent CD diagnosis and management in the 2 provinces of mainland China.
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Affiliation(s)
- Wei-Xia Lin
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Muhammad Rauf Yaqub
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Zhan-Hui Zhang
- Clinical Medicine Research Institute, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Man Mao
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Han-Shi Zeng
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Feng-Ping Chen
- Department of Laboratory Science, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wei-Ming Li
- Department of Pediatrics, Maternal and Child Health Hospital of Qingyuan City, Qingyuan, China
| | - Wen-Zhe Cai
- Department of Internal Medicine, Central Hospital of Shantou City, Shantou, China
| | - Ying-Qiang Li
- Department of Internal Medicine, Maternal and Child Health Hospital of Yunfu City, Yunfu, China
| | - Zhi-Yong Tan
- Department of Pediatrics, Maternal and Child Health Hospital of Shaoguan City, Shaoguan, China
| | - Wei Sheng
- Department of Pediatrics, Weinan First Hospital, Weinan, China
| | - Zhi-Min Li
- Department of Pediatrics, San Er Ling Yi Hospital, Hanzhong, China
| | - Xiao-Ling Tao
- Department of Pediatrics, Xianyang Rainbow Hospital (Xianyang Children's Hospital), Xianyang, China
| | - Yuan-Xia Li
- Department of Pediatrics, Yan'an University Hospital, Yan'an, China
| | - Jun-Ping Zhang
- Clinical laboratory, Qishan County Hospital, Qishan, China
| | - Yao-Bin Han
- Department of Infectious Diseases, Shenmu Hospital of Northwestern University, Shenmu, China
| | - Yan Li
- Department of Pediatrics, Zhashui County Hospital, Zhashui, China
| | - Wu-Qiong Duan
- Department of Pediatrics, Ankang Central Hospital, Ankang, China
| | - Bao-Ni Ye
- Department of Pediatrics, Southern Campus of Tongchuan People's Hospital, Tongchuan, China
| | - Ya-Rong Li
- The Third Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Yuan-Zong Song
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
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5
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Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency: In vivo and in vitro studies of the aberrant transcription arising from two novel splice-site variants in SLC25A13. Eur J Med Genet 2021; 64:104145. [PMID: 33497767 DOI: 10.1016/j.ejmg.2021.104145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/09/2021] [Accepted: 01/20/2021] [Indexed: 11/22/2022]
Abstract
Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency (NICCD) is an autosomal recessive disease resulting from biallelic SLC25A13 mutations, and its diagnosis relies on genetic analysis. This study aimed to characterize the pathogenicity of 2 novel splice-site variants of SLC25A13 gene. Two patients (C0476 and C0556) suspected to have NICCD, their family members and 9 healthy volunteers were recruited as the research subjects. The SLC25A13 genotypes NG_012247.2(NM_014251.3): c.[852_855del]; [69+5G > A] in patient C0476 and c.[1453-1G > A]; [1751-5_1751-4ins (2684)] in patient C0556 were identified by means of polymerase chain reaction, long and accurate polymerase chain reaction, as well as Sanger sequencing. The 2 splice-site variants were absent in control databases and predicted to be pathogenic by computational analysis. The alternative splice variants in monocyte-derived macrophages from patient C0476 demonstrated exon 2 skipping [r.16_69del; p.(Val6_Lys23del)] in vivo, while minigene analysis revealed both exon 2-skipping and retained products from c.69+5G > A in vitro. In the patient C0556, an aberrant transcript [r.1453del; p.(Gly485Valfs*22)] resulting from c.1453-1G > A was detected on minigene splicing study. Thus, c.69+5G > A and c.1453-1G > A were both proved to be pathogenic. The 2 novel splice-site variants expanded the SLC25A13 mutation spectrum and provided reliable molecular markers for the definite diagnosis and genetic counseling of NICCD in the affected families.
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6
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Chalermwat C, Thosapornvichai T, Wongkittichote P, Phillips JD, Cox JE, Jensen AN, Wattanasirichaigoon D, Jensen LT. Overexpression of the peroxin Pex34p suppresses impaired acetate utilization in yeast lacking the mitochondrial aspartate/glutamate carrier Agc1p. FEMS Yeast Res 2020; 19:5621492. [PMID: 31711143 DOI: 10.1093/femsyr/foz078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/10/2019] [Indexed: 12/19/2022] Open
Abstract
PEX34, encoding a peroxisomal protein implicated in regulating peroxisome numbers, was identified as a high copy suppressor, capable of bypassing impaired acetate utilization of agc1∆ yeast. However, improved growth of agc1∆ yeast on acetate is not mediated through peroxisome proliferation. Instead, stress to the endoplasmic reticulum and mitochondria from PEX34 overexpression appears to contribute to enhanced acetate utilization of agc1∆ yeast. The citrate/2-oxoglutarate carrier Yhm2p is required for PEX34 stimulated growth of agc1∆ yeast on acetate medium, suggesting that the suppressor effect is mediated through increased activity of a redox shuttle involving mitochondrial citrate export. Metabolomic analysis also revealed redirection of acetyl-coenzyme A (CoA) from synthetic reactions for amino acids in PEX34 overexpressing yeast. We propose a model in which increased formation of products from the glyoxylate shunt, together with enhanced utilization of acetyl-CoA, promotes the activity of an alternative mitochondrial redox shuttle, partially substituting for loss of yeast AGC1.
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Affiliation(s)
- Chalongchai Chalermwat
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
| | - Thitipa Thosapornvichai
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
| | - Parith Wongkittichote
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand.,Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - John D Phillips
- Department of Internal Medicine, Division of Hematology, University of Utah, 30 N 1900 E, Salt Lake City, UT 84132, USA
| | - James E Cox
- Metabolomics Core Research Facility, University of Utah, 15 N Medical Drive East, Salt Lake City, UT 84112, USA.,Department of Biochemistry, University of Utah, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Amornrat N Jensen
- Department of Pathobiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Laran T Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
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7
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Na Nakorn C, Waisayarat J, Dejthevaporn C, Srisawasdi P, Wongwaisayawan S, Sukasem C. Genetic Variations and Frequencies of the Two Functional Single Nucleotide Polymorphisms of SLCO1B1 in the Thai Population. Front Pharmacol 2020; 11:728. [PMID: 32581780 PMCID: PMC7289979 DOI: 10.3389/fphar.2020.00728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/01/2020] [Indexed: 11/22/2022] Open
Abstract
Aim To investigate the variations and the frequencies of the SLCO1B1 gene in the Thai population. Methods Collected samples were categorized into five regions of Thailand. DNA samples were genotyped for two variants, c.388A>G and c.521T>C of the SLCO1B1, using TaqMan® real-time PCR. Results The minor allele frequencies (MAFs) of two single nucleotide polymorphisms (SNPs) were not significantly different among the five regions. The most frequent haplotype was SLCO1B1*1b (frequency: 0.654), followed by *1a (frequency: 0.217), *15 (frequency: 0.128), and *5 (frequency: 0.001). We observed a similar frequency of OATP1B1 transporter phenotypes compared to other populations. 75.85% of the Thai subjects showed normal OATP1B1 activity, 22.5% showed intermediate OATP1B1 activity, and 1.58% showed low OATP1B1 activity. Conclusion This study reported the frequencies of the SLCO1B1 variants and the subsequent OATP1B1 activity in a large cohort of Thais that can provide important information for the guidance of personalized drug therapy.
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Affiliation(s)
- Chalitpon Na Nakorn
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Division of Pharmacogenomics and Personalized Medicine, Somdech Phra Debaratana Medical Center (SDMC), Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Jariya Waisayarat
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Charungthai Dejthevaporn
- Division of Neurology, Department of Internal Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornpen Srisawasdi
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sansanee Wongwaisayawan
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chonlaphat Sukasem
- Laboratory for Pharmacogenomics, Division of Pharmacogenomics and Personalized Medicine, Somdech Phra Debaratana Medical Center (SDMC), Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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8
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Lin Y, Liu Y, Zhu L, Le K, Shen Y, Yang C, Chen X, Hu H, Ma Q, Shi X, Hu Z, Yang J, Shen Y, Lin CH, Huang C, Huang X. Combining newborn metabolic and genetic screening for neonatal intrahepatic cholestasis caused by citrin deficiency. J Inherit Metab Dis 2020; 43:467-477. [PMID: 31845334 DOI: 10.1002/jimd.12206] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/08/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022]
Abstract
To evaluate the feasibility of incorporating genetic screening for neonatal intrahepatic cholestasis, caused by citrin deficiency (NICCD), into the current newborn screening (NBS) program. We designed a high-throughput iPLEX genotyping assay to detect 28 SLC25A13 mutations in the Chinese population. From March 2018 to June 2018, 237 630 newborns were screened by tandem mass spectrometry at six hospitals. Newborns with citrulline levels between 1/2 cutoff and cutoff values of the upper limit were recruited for genetic screening using the newly developed assay. The sensitivity and specificity of the iPLEX genotyping assay both reached 100% in clinical practice. Overall, 29 364 (12.4%) newborns received further genetic screening. Five patients with conclusive genotypes were successfully identified. The most common SLC25A13 mutation was c.851_854del, with an allele frequency of 60%. In total, 658 individuals with one mutant allele were identified as carriers. Eighteen different mutations were observed, yielding a carrier rate of 1/45. Notably, Quanzhou in southern China had a carrier rate of up to 1/28, whereas Jining in northern China had a carrier rate higher than that of other southern and border cities. The high throughput iPLEX genotyping assay is an effective and reliable approach for NICCD genotyping. The combined genetic screening could identify an additional subgroup of patients with NICCD, undetectable by conventional NBS. Therefore, this study demonstrates the viability of incorporating genetic screening for NICCD into the current NBS program.
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Affiliation(s)
- Yiming Lin
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Yaru Liu
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Lin Zhu
- Department of Translational Medicine, Hangzhou Genuine Clinical Laboratory Co. Ltd, Hangzhou, China
| | - Kaixing Le
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Yuyan Shen
- Neonatal Disease Screening Center, Huaihua Maternal and Child Health Hospital, Huaihua, China
| | - Chiju Yang
- Neonatal Disease Screening Center, Jining Maternal and Child Health Family Service Center, Jining, China
| | - Xigui Chen
- Neonatal Disease Screening Center, Jining Maternal and Child Health Family Service Center, Jining, China
| | - Haili Hu
- Neonatal Disease Screening Center, Hefei Women and Children's Health Care Hospital, Hefei, China
| | - Qingqing Ma
- Neonatal Disease Screening Center, Hefei Women and Children's Health Care Hospital, Hefei, China
| | - Xueqin Shi
- Department of Pediatrics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Zhenzhen Hu
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jianbin Yang
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yaping Shen
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Chien-Hsing Lin
- Department of Research and Development, Feng Chi Biotech Corp, Taipei, Taiwan
| | - Chenggang Huang
- Research and Development Center, Zhejiang Biosan Biochemical Technologies Co., Ltd, Hangzhou, China
| | - Xinwen Huang
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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9
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Genetic Analysis of Peroxisomal Genes Required for Longevity in a Yeast Model of Citrin Deficiency. Diseases 2020; 8:diseases8010002. [PMID: 31936501 PMCID: PMC7151034 DOI: 10.3390/diseases8010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/23/2019] [Accepted: 01/07/2020] [Indexed: 12/02/2022] Open
Abstract
Citrin is a liver-specific mitochondrial aspartate–glutamate carrier encoded by SLC25A13. Citrin deficiency caused by SLC25A13 mutation results in carbohydrate toxicity, citrullinemia type II, and fatty liver diseases, the mechanisms of some of which remain unknown. Citrin shows a functional homolog in yeast aspartate-glutamate carrier (Agc1p) and agc1Δ yeasts are used as a model organism of citrin deficiency. Here, we found that agc1Δ yeasts decreased fat utilization, impaired NADH balance in peroxisomes, and decreased chronological lifespan. The activation of GPD1-mediated NAD+ regeneration in peroxisomes by GPD1 over-expression or activation of the malate–oxaloacetate NADH peroxisomal shuttle, by increasing flux in this NADH shuttle and over-expression of MDH3, resulted in lifespan extension of agc1Δ yeasts. In addition, over-expression of PEX34 restored longevity of agc1Δ yeasts as well as wild-type cells. The effect of PEX34-mediated longevity required the presence of the GPD1-mediated NADH peroxisomal shuttle, which was independent of the presence of the peroxisomal malate–oxaloacetate NADH shuttle and PEX34-induced peroxisome proliferation. These data confirm that impaired NAD+ regeneration in peroxisomes is a key defect in the yeast model of citrin deficiency, and enhancing peroxisome function or inducing NAD+ regeneration in peroxisomes is suggested for further study in patients’ hepatocytes.
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Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals. Hum Genet 2019; 138:389-409. [PMID: 30887117 DOI: 10.1007/s00439-019-01998-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/06/2019] [Indexed: 12/19/2022]
Abstract
Incidence rates of Mendelian diseases vary among ethnic groups, and frequencies of variant types of causative genes also vary among human populations. In this study, we examined to what extent we can predict population frequencies of recessive disorders from genomic data, and explored better strategies for variant interpretation and classification. We used a whole-genome reference panel from 3552 general Japanese individuals constructed by the Tohoku Medical Megabank Organization (ToMMo). Focusing on 32 genes for 17 congenital metabolic disorders included in newborn screening (NBS) in Japan, we identified reported and predicted pathogenic variants through variant annotation, interpretation, and multiple ways of classifications. The estimated carrier frequencies were compared with those from the Japanese NBS data based on 1,949,987 newborns from a previous study. The estimated carrier frequency based on genomic data with a recent guideline of variant interpretation for the PAH gene, in which defects cause hyperphenylalaninemia (HPA) and phenylketonuria (PKU), provided a closer estimate to that by the observed incidence than the other methods. In contrast, the estimated carrier frequencies for SLC25A13, which causes citrin deficiency, were much higher compared with the incidence rate. The results varied greatly among the 11 NBS diseases with single responsible genes; the possible reasons for departures from the carrier frequencies by reported incidence rates were discussed. Of note, (1) the number of pathogenic variants increases by including additional lines of evidence, (2) common variants with mild effects also contribute to the actual frequency of patients, and (3) penetrance of each variant remains unclear.
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11
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Lin WX, Zeng HS, Zhang ZH, Mao M, Zheng QQ, Zhao ST, Cheng Y, Chen FP, Wen WR, Song YZ. Molecular diagnosis of pediatric patients with citrin deficiency in China: SLC25A13 mutation spectrum and the geographic distribution. Sci Rep 2016; 6:29732. [PMID: 27405544 PMCID: PMC4942605 DOI: 10.1038/srep29732] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/21/2016] [Indexed: 12/21/2022] Open
Abstract
Citrin deficiency (CD) is a Mendelian disease due to biallelic mutations of SLC25A13 gene. Neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) is the major pediatric CD phenotype, and its definite diagnosis relies on SLC25A13 genetic analysis. China is a vast country with a huge population, but the SLC25A13 genotypic features of CD patients in our country remains far from being well clarified. Via sophisticated molecular analysis, this study diagnosed 154 new CD patients in mainland China and identified 9 novel deleterious SLC25A13 mutations, i.e. c.103A > G, [c.329 - 154_c.468 + 2352del2646; c.468 + 2392_c.468 + 2393ins23], c.493C > T, c.755 - 1G > C, c.845_c.848 + 1delG, c.933_c.933 + 1insGCAG, c.1381G > T, c.1452 + 1G > A and c.1706_1707delTA. Among the 274 CD patients diagnosed by our group thus far, 41 SLC25A13 mutations/variations were detected. The 7 mutations c.775C > T, c.851_854del4, c.1078C > T, IVS11 + 1G > A, c.1364G > T, c.1399C > T and IVS16ins3kb demonstrated significantly different geographic distribution. Among the total 53 identified genotypes, only c.851_854del4/c.851_854del4 and c.851_854del4/c.1399C > T presented different geographic distribution. The northern population had a higher level of SLC25A13 allelic heterogeneity than those in the south. These findings enriched the SLC25A13 mutation spectrum and brought new insights into the geographic distribution of the variations and genotypes, providing reliable evidences for NICCD definite diagnosis and for the determination of relevant molecular targets in different Chinese areas.
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Affiliation(s)
- Wei-Xia Lin
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Han-Shi Zeng
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Zhan-Hui Zhang
- Clinical Medicine Research Institute, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Man Mao
- Department of Laboratory Science, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Qi-Qi Zheng
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Shu-Tao Zhao
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Ying Cheng
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Feng-Ping Chen
- Department of Laboratory Science, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Wang-Rong Wen
- Department of Laboratory Science, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Yuan-Zong Song
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
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12
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Zeng HS, Zhao ST, Deng M, Zhang ZH, Cai XR, Chen FP, Song YZ. Inspissated bile syndrome in an infant with citrin deficiency and congenital anomalies of the biliary tract and esophagus: identification and pathogenicity analysis of a novel SLC25A13 mutation with incomplete penetrance. Int J Mol Med 2014; 34:1241-8. [PMID: 25216257 PMCID: PMC4199400 DOI: 10.3892/ijmm.2014.1929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/05/2014] [Indexed: 01/14/2023] Open
Abstract
Biallelic mutations of the SLC25A13 gene result in citrin deficiency (CD) in humans. Neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) is the major CD phenotype in pediatrics; however, knowledge on its genotypic and phenotypic characteristics remains limited. The present study aimed to explore novel molecular and clinical characteristics of CD. An infant suspected to have NICCD as well as her parents were enrolled as the research subjects. SLC25A13 mutations were investigated using various methods, including cDNA cloning and sequencing. The pathogenicity of a novel mutation was analyzed bioinformatically and functionally with a yeast model. Both the infant and her father were heterozygous for c.2T>C and c.790G>A, while the mother was only a c.2T>C carrier. The novel c.790G>A mutation proved bioinformatically and functionally pathogenic. The infant had esophageal atresia and an accessory hepatic duct, along with bile plug formation confirmed by laparoscopic surgery. However, the father seemed to be healthy thus far. The findings of the present study enrich the genotypic and phenotypic characteristics of CD patients, and provided clinical and molecular evidence suggesting the possible non-penetrance of SLC25A13 mutations and the likely involvement of this gene in primitive foregut development during early embryonic life.
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Affiliation(s)
- Han-Shi Zeng
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Shu-Tao Zhao
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Mei Deng
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Zhan-Hui Zhang
- Central Laboratory, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Xiang-Ran Cai
- Medical Imaging Center, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Feng-Ping Chen
- Department of Laboratory Science, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Yuan-Zong Song
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China
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13
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Zhang ZH, Yang ZG, Chen FP, Kikuchi A, Liu ZH, Kuang LZ, Li WM, Song YZ, Kure S, Saheki T. Screening for Five Prevalent Mutations of SLC25A13 Gene in Guangdong, China: A Molecular Epidemiologic Survey of Citrin Deficiency. TOHOKU J EXP MED 2014; 233:275-81. [DOI: 10.1620/tjem.233.275] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Zhan-Hui Zhang
- Department of Pediatrics, The First Affiliated Hospital, Jinan University
- Central Laboratory, The First Affiliated Hospital, Jinan University
| | - Zhi-Gang Yang
- Department of Pediatrics, The First Affiliated Hospital, Jinan University
| | - Feng-Ping Chen
- Department of Laboratory Science, The First Affiliated Hospital, Jinan University
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Graduate School of Medicine
| | - Zhen-Huan Liu
- Department of Pediatric Neurorehabilitation, Nanhai Maternity and Child Care Hospital, Guangzhou University of Chinese Medicine
| | - Li-Zhen Kuang
- Department of Laboratory Science, Nanhai Maternity and Child Care Hospital, Guangzhou University of Chinese Medicine
| | - Wei-Ming Li
- Department of Pediatrics, Maternal and Child Health Hospital of Qingyuan City
| | - Yuan-Zong Song
- Department of Pediatrics, The First Affiliated Hospital, Jinan University
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University Graduate School of Medicine
| | - Takeyori Saheki
- Institute of Resource Development and Analysis, Kumamoto University
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