1
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Zhang Z, Sun Y, Wang YY, Ma DY, Wang X, Cheng W, Jiang T. Retrospective analysis of isobutyryl CoA dehydrogenase deficiency. Minerva Pediatr (Torino) 2024; 76:645-651. [PMID: 34647701 DOI: 10.23736/s2724-5276.21.06179-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Isobutyryl-CoA dehydrogenase deficiency is a rare, autosomal recessive hereditary disease caused by a disorder in valine metabolism due to the deficiency of isobutyryl-CoA dehydrogenase. We provided two new mutations for ACAD8 and analyzed new sight to explore the association between the clinical phenotype and genotype of this disease. METHODS The concentration of butyrylcarnitine was tested by tandem mass spectrometry. Butyryl carnitine and isobutyryl glycine levels were determined based on urine organic acid analysis. Gene mutations were analyzed through gene sequencing. RESULTS Five individuals were diagnosed with isobutyryl-CoA dehydrogenase deficiency via newborn screening, and new mutations of ACAD8 encoding isobutyryl-CoA dehydrogenase were found. The mutations were c.1166G>A in exon 10 and c.986C>T in exon 9, which were analyzed as pathogenic sites. Both manifested as an increase in butyrylcarnitine and slightly elevated isobutyryl glycine levels. No abnormalities in growth and development were observed during follow-up. Additionally, we summarized 32 types of ACAD8 mutations reported worldwide, analyzed the distribution of mutations with clinical symptoms, and found them to be mainly concentrated in the N-terminal domain and C-terminal domain. These findings may provide new clues for the clinical diagnosis and management of isobutyryl-CoA dehydrogenase deficiency. CONCLUSIONS In this study, we reported new mutations of ACAD8 and performed a retrospective analysis of isobutyryl CoA dehydrogenase deficiency worldwide. Isobutyryl CoA dehydrogenase deficiency may pose a disease risk during the growth process, thereby requiring long-term follow-up.
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Affiliation(s)
- Zhilei Zhang
- Center of Newborn Screening, Center of Genetic Medicine, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yun Sun
- Center of Newborn Screening, Center of Genetic Medicine, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan-Yun Wang
- Center of Newborn Screening, Center of Genetic Medicine, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ding-Yuan Ma
- Center of Newborn Screening, Center of Genetic Medicine, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xin Wang
- Center of Newborn Screening, Center of Genetic Medicine, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Wei Cheng
- Center of Newborn Screening, Center of Genetic Medicine, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Tao Jiang
- Center of Newborn Screening, Center of Genetic Medicine, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China -
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2
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Teng J, Chen L, Yang F, Gao P, Yu P, Jiang Q, Xu Y, Xia W, Yu D. Selection of texture-associated biomarkers in chilled and iced grass carp (Ctenopharyngodon idella) fillets via DIA-based proteomics. Food Res Int 2024; 188:114505. [PMID: 38823848 DOI: 10.1016/j.foodres.2024.114505] [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: 03/26/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Consumers care about the texture of fresh fish flesh, but a rapid quantitative analytical method for this has not been properly established. In this study, texture-associated biomarkers were selected by DIA-based proteomics for possible future application. Results indicated a significant decline in texture and moisture characteristics with extended storage under chilled and iced conditions, and flesh quality was categorized into three intervals. A total of 8 texture-associated biomarkers were identified in the chilled storage group, and 3 distinct ones in the iced storage group. Biomarkers were further refined based on their expression levels. Isobutyryl-CoA dehydrogenase, mitochondrial and [Phosphatase 2A protein]-leucine-carboxy methyltransferase were identified as effective texture-associated biomarkers for chilled fish, and Staphylococcal nuclease domain-containing protein 1 for iced fish. This study provided suitable proteins as indicators of fresh fish flesh texture, which could help establish a rapid and convenient texture testing method in future studies.
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Affiliation(s)
- Jialu Teng
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Lihua Chen
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Fang Yang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Pei Gao
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Peipei Yu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Qixing Jiang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Yanshun Xu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Wenshui Xia
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Dongxing Yu
- SoHao Fd-Tech Co., QingDao, ShanDong 266700, China.
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3
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Xue Q, Yang Y, Li H, Li X, Zou L, Li T, Ma H, Qi H, Wang J, Yu T. Functions and mechanisms of protein lysine butyrylation (Kbu): Therapeutic implications in human diseases. Genes Dis 2023; 10:2479-2490. [PMID: 37554202 PMCID: PMC10404885 DOI: 10.1016/j.gendis.2022.10.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/27/2022] [Accepted: 10/20/2022] [Indexed: 11/30/2022] Open
Abstract
Post-translational modifications (PTM) are covalent modifications of proteins or peptides caused by proteolytic cleavage or the attachment of moieties to one or more amino acids. PTMs play essential roles in biological function and regulation and have been linked with several diseases. Modifications of protein acylation (Kac), a type of PTM, are known to induce epigenetic regulatory processes that promote various diseases. Thus, an increasing number of studies focusing on acylation modifications are being undertaken. Butyrylation (Kbu) is a new acylation process found in animals and plants. Kbu has been recently linked to the onset and progression of several diseases, such as cancer, cardiovascular diseases, diabetes, and vascular dementia. Moreover, the mode of action of certain drugs used in the treatment of lymphoma and colon cancer is based on the regulation of butyrylation levels, suggesting that butyrylation may play a therapeutic role in these diseases. In addition, butyrylation is also commonly involved in rice gene expression and thus plays an important role in the growth, development, and metabolism of rice. The tools and analytical methods that could be utilized for the prediction and detection of lysine butyrylation have also been investigated. This study reviews the potential role of histone Kbu, as well as the mechanisms underlying this process. It also summarizes various enzymes and analytical methods associated with Kbu, with the goal of providing new insights into the role of Kbu in gene regulation and diseases.
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Affiliation(s)
- Qianqian Xue
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266021, China
| | - Hong Li
- Clinical Laboratory, Central Laboratory. The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Xiaoxin Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Lu Zou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Tianxiang Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Huibo Ma
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Hongzhao Qi
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Jianxun Wang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266021, China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
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4
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Tummolo A, Leone P, Tolomeo M, Solito R, Mattiuzzo M, Lepri FR, Lorè T, Cardinali R, De Giovanni D, Simonetti S, Barile M. Combined isobutyryl-CoA and multiple acyl-CoA dehydrogenase deficiency in a boy with altered riboflavin homeostasis. JIMD Rep 2022; 63:276-291. [PMID: 35822092 PMCID: PMC9259400 DOI: 10.1002/jmd2.12292] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/24/2022] Open
Abstract
In this report, we describe the case of an 11-year-old boy, who came to our attention for myalgia and muscle weakness, associated with inappetence and vomiting. Hypertransaminasemia was also noted, with ultrasound evidence of hepatomegaly. Biochemical investigations revealed acylcarnitine and organic acid profiles resembling those seen in MADD, that is, multiple acyl-CoA dehydrogenase deficiencies (OMIM #231680) a rare inherited disorder of fatty acids, amino acids, and choline metabolism. The patient carried a single pathogenetic variant in the ETFDH gene (c.524G>A, p.Arg175His) and no pathogenetic variant in the riboflavin (Rf) homeostasis related genes (SLC52A1, SLC52A2, SLC52A3, SLC25A32, FLAD1). Instead, compound heterozygosity was found in the ACAD8 gene (c.512C>G, p.Ser171Cys; c.822C>A, p.Asn274Lys), coding for isobutyryl-CoA dehydrogenase (IBD), whose pathogenic variants are associated to IBD deficiency (OMIM #611283), a rare autosomal recessive disorder of valine catabolism. The c.822C>A was never previously described in a patient. Subsequent further analyses of Rf homeostasis showed reduced levels of flavins in plasma and altered FAD-dependent enzymatic activities in erythrocytes, as well as a significant reduction in the level of the plasma membrane Rf transporter 2 in erythrocytes. The observed Rf/flavin scarcity in this patient, possibly associated with a decreased ETF:QO efficiency might be responsible for the observed MADD-like phenotype. The patient's clinical picture improved after supplementation of Rf, l-carnitine, Coenzyme Q10, and also 3OH-butyrate. This report demonstrates that, even in the absence of genetic defects in genes involved in Rf homeostasis, further targeted molecular analysis may reveal secondary and possibly treatable biochemical alterations in this pattern.
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Affiliation(s)
- Albina Tummolo
- Metabolic Diseases and Clinical Genetics UnitChildren's Hospital “Giovanni XXIII”BariItaly
| | - Piero Leone
- Department of Biosciences, Biotechnology and BiopharmaceuticsUniversity of Bari “A. Moro”BariItaly
| | - Maria Tolomeo
- Department of Biosciences, Biotechnology and BiopharmaceuticsUniversity of Bari “A. Moro”BariItaly
| | - Rita Solito
- Department of Biosciences, Biotechnology and BiopharmaceuticsUniversity of Bari “A. Moro”BariItaly
| | - Matteo Mattiuzzo
- Laboratory of Medical GeneticsTranslational Cytogenomics Research Unit, Bambino Gesù Children HospitalRomeItaly
| | - Francesca Romana Lepri
- Laboratory of Medical GeneticsTranslational Cytogenomics Research Unit, Bambino Gesù Children HospitalRomeItaly
| | - Tania Lorè
- Regional Centre for Neonatal ScreeningChildren's Hospital “Giovanni XXIII”BariItaly
| | - Roberta Cardinali
- Regional Centre for Neonatal ScreeningChildren's Hospital “Giovanni XXIII”BariItaly
| | - Donatella De Giovanni
- Metabolic Diseases and Clinical Genetics UnitChildren's Hospital “Giovanni XXIII”BariItaly
| | - Simonetta Simonetti
- Regional Centre for Neonatal ScreeningChildren's Hospital “Giovanni XXIII”BariItaly
| | - Maria Barile
- Department of Biosciences, Biotechnology and BiopharmaceuticsUniversity of Bari “A. Moro”BariItaly
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5
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Zhuang DY, Ding SX, Wang F, Yang XC, Pan XL, Bao YW, Zhou LM, Li HB. Identification of Six Novel Variants of ACAD8 in Isobutyryl-CoA Dehydrogenase Deficiency With Increased C4 Carnitine Using Tandem Mass Spectrometry and NGS Sequencing. Front Genet 2022; 12:791869. [PMID: 35154245 PMCID: PMC8831754 DOI: 10.3389/fgene.2021.791869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Isobutyryl-CoA dehydrogenase deficiency (IBDHD, MIM: #611283) is a rare autosomal recessive hereditary disease, which is caused by genetic mutations of acyl-CoA dehydrogenase (ACAD) 8 and associated with valine catabolism. Here, tandem mass spectrometry (MS/MS) was applied to screen 302,993 neonates for inherited metabolic diseases (IMD) in Ningbo of China from 2017 to 2020. The results suggest that 198 newborns (0.7‰) were initially screened positive for IBDHD with C4-Carnitine, and 27 cases (0.1‰) were re-screened positive. Genetic diagnosis was performed on 21 of the 27 cases. Seven compound heterozygous variations, three biallelic variations, and one heterozygous variation of ACAD8 were found with a pathogenicity rate of 33.3% (7/21). In addition, seven biallelic variations, one heterozygous variation of acyl-CoA dehydrogenase short chain (ACADS), and one biallelic variation of acyl-CoA dehydrogenase short/branched chain (ACADSB) was detected. Further research showed that ACAD8 mutations of 11 IBDHD cases distributed in six different exons with total 14 mutation sites. Five of which were known suspected pathogenic sites (c.286G > A, c.553C > T, c.1000C > T, c.409G > A, c.500del) and six were novel mutation sites: c.911A > T, c.904C > T, c.826G > A, c.995T > C, c.1166G > A, c.1165C > T. This finding enriched the mutation spectrum of ACAD8 in IBDHD.
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Affiliation(s)
- Dan-Yan Zhuang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Shu-Xia Ding
- Department of Endocrinology and Genetic Metabolism of Pediatrics, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Fei Wang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Xiang-Chun Yang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Xiao-Li Pan
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, China
| | - You-Wei Bao
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Li-ming Zhou
- Reproductive Medicine Centre, Ningbo Women and Children’s Hospital, Ningbo, China
- *Correspondence: Hai-bo Li, ; Li-ming Zhou,
| | - Hai-bo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, China
- *Correspondence: Hai-bo Li, ; Li-ming Zhou,
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6
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Feng J, Yang C, Zhu L, Zhang Y, Zhao X, Chen C, Chen QX, Shu Q, Jiang P, Tong F. Phenotype, genotype and long-term prognosis of 40 Chinese patients with isobutyryl-CoA dehydrogenase deficiency and a review of variant spectra in ACAD8. Orphanet J Rare Dis 2021; 16:392. [PMID: 34544473 PMCID: PMC8454130 DOI: 10.1186/s13023-021-02018-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022] Open
Abstract
Background Isobutyryl-CoA dehydrogenase deficiency (IBDD) is a rare autosomal recessive metabolic disorder resulting from variants in ACAD8, and is poorly understood, as only dozens of cases have been reported previously. Based on a newborn screening program, we evaluated the incidence, phenotype and genotype of IBDD as well as the prognosis. Moreover, we reviewed the variant spectrum in ACAD8 associated with IBDD. Methods Forty unrelated patients with IBDD were retrospectively screened for newborns between Jan 2012 and Dec 2020. Tandem mass spectrometry (MS/MS) was used to determine the concentrations of C4-acylcarnitine, C4/C2 (acetylcarnitine), and C4/C3 (propionylcarnitine). All suspected cases were genetically tested by metabolic genes panel. Results The incidence of IBDD here was 1: 62,599. All patients presented continuously elevated C4-acylcarnitine levels with higher ratios of C4/C2 and C4/C3. Isobutyrylglycine occurred in only 8 patients. During follow-up, four patients had a transient motor delay, and two patients had growth delay. Notably, one case harbored both ACAD8 compound heterozygous variants and a KMT2A de novo variant (c.2739del, p.E914Rfs*35), with IBDD and Wiedemann–Steiner syndrome together, had exact severe global developmental delay. All patients were regularly monitored once they were diagnosed, and each patient gradually had a normal diet after 6 months of age. After 3–108 months of follow-up, most individuals were healthy except the case harboring the KMT2A variant. A total of 16 novel variants in ACAD8, c.4_5delCT, c.109C > T, c.110–2A > T, c.236G > A, c.259G > A, c.381–14G > A, c.413delA, c.473A > G, c.500delG, c.758 T > G, c.842–1G > A, c.911A > T, c.989G > A, c.1150G > C, c.1157A > G and c.1165C > T, were identified. Along with a literature review on 51 ACAD8 variants in 81 IBDD patients, we found that the most common variant was c.286G > A (27.2%), which has been observed solely in the Chinese population to date, followed by c.1000C > T (8.6%), c.1176G > T (3.7%) and c.455 T > C (3.1%). Conclusion The concentration of C4-acylcarnitine in NBS plus subsequent genetic testing is necessary for IBDD diagnosis. Both the genotypes and ACAD8 variants in IBDD are highly heterogeneous, and no significant correlations between genotype and phenotype are present here in patients with IBDD. Our IBDD cohort with detaied clinical characteristics, genotypes and long-term prognosis will be helpful for the diagnosis and management of patients with IBDD in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-02018-6.
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Affiliation(s)
- Junqi Feng
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, 310052, China.,Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Chenxi Yang
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Ling Zhu
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, 310052, China
| | - Yuchen Zhang
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xiaoxu Zhao
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, 310052, China
| | - Chi Chen
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, 310052, China
| | - Qi-Xing Chen
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, 310052, China
| | - Qiang Shu
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, 310052, China.
| | - Pingping Jiang
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, 310052, China. .,Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, 310058, China.
| | - Fan Tong
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, 310052, China.
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7
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Zhu Z, Han Z, Halabelian L, Yang X, Ding J, Zhang N, Ngo L, Song J, Zeng H, He M, Zhao Y, Arrowsmith CH, Luo M, Bartlett MG, Zheng YG. Identification of lysine isobutyrylation as a new histone modification mark. Nucleic Acids Res 2021; 49:177-189. [PMID: 33313896 PMCID: PMC7797053 DOI: 10.1093/nar/gkaa1176] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/05/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Short-chain acylations of lysine residues in eukaryotic proteins are recognized as essential posttranslational chemical modifications (PTMs) that regulate cellular processes from transcription, cell cycle, metabolism, to signal transduction. Lysine butyrylation was initially discovered as a normal straight chain butyrylation (Knbu). Here we report its structural isomer, branched chain butyrylation, i.e. lysine isobutyrylation (Kibu), existing as a new PTM on nuclear histones. Uniquely, isobutyryl-CoA is derived from valine catabolism and branched chain fatty acid oxidation which is distinct from the metabolism of n-butyryl-CoA. Several histone acetyltransferases were found to possess lysine isobutyryltransferase activity in vitro, especially p300 and HAT1. Transfection and western blot experiments showed that p300 regulated histone isobutyrylation levels in the cell. We resolved the X-ray crystal structures of HAT1 in complex with isobutyryl-CoA that gleaned an atomic level insight into HAT-catalyzed isobutyrylation. RNA-Seq profiling revealed that isobutyrate greatly affected the expression of genes associated with many pivotal biological pathways. Together, our findings identify Kibu as a novel chemical modification mark in histones and suggest its extensive role in regulating epigenetics and cellular physiology.
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Affiliation(s)
- Zhesi Zhu
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Zhen Han
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Xiangkun Yang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Jun Ding
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Nawei Zhang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Liza Ngo
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Jiabao Song
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Maomao He
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 20021, USA
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
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8
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Eleftheriadou M, Medici-van den Herik E, Stuurman K, van Bever Y, Hellebrekers DMEI, van Slegtenhorst M, Ruijter G, Barakat TS. Isobutyryl-CoA dehydrogenase deficiency associated with autism in a girl without an alternative genetic diagnosis by trio whole exome sequencing: A case report. Mol Genet Genomic Med 2021; 9:e1595. [PMID: 33432785 PMCID: PMC8077115 DOI: 10.1002/mgg3.1595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023] Open
Abstract
Background Isobutyryl‐CoA dehydrogenase (IBD) is a mitochondrial enzyme catalysing the third step in the degradation of the essential branched‐chain amino acid valine and is encoded by ACAD8. ACAD8 mutations lead to isobutyryl‐CoA dehydrogenase deficiency (IBDD), which is identified by increased C4‐acylcarnitine levels. Affected individuals are either asymptomatic or display a variety of symptoms during infancy, including speech delay, cognitive impairment, failure to thrive, hypotonia, and emesis. Methods Here, we review all previously published IBDD patients and describe a girl diagnosed with IBDD who was presenting with autism as the main disease feature. Results To assess whether a phenotype‐genotype correlation exists that could explain the development or absence of clinical symptoms in IBDD, we compared CADD scores, in silico mutation predictions, LoF tolerance scores and C4‐acylcarnitine levels between symptomatic and asymptomatic individuals. Statistical analysis of these parameters did not establish significant differences amongst both groups. Conclusion As in our proband, trio whole exome sequencing did not establish an alternative secondary genetic diagnosis for autism, and reported long‐term follow‐up of IBDD patients is limited, it is possible that autism spectrum disorders could be one of the disease‐associated features. Further long‐term follow‐up is suggested in order to delineate the full clinical spectrum associated with IBDD.
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Affiliation(s)
- Maria Eleftheriadou
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | | | - Kyra Stuurman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Debby M E I Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - George Ruijter
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
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9
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Liu K, Jia B, Zhou L, Xing L, Wu L, Li Y, Lu J, Zhang L, Guan S. Ultraperformance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Mass Spectrometry-Based Metabolomics and Lipidomics Identify Biomarkers for Efficacy Evaluation of Mesalazine in a Dextran Sulfate Sodium-Induced Ulcerative Colitis Mouse Model. J Proteome Res 2020; 20:1371-1381. [PMID: 33356298 DOI: 10.1021/acs.jproteome.0c00757] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This study aims to identify biomarkers for evaluating the therapeutic efficacy of mesalazine on ulcerative colitis by metabolomics and lipidomics. A dextran sulfate sodium-induced mouse model was used. The disease status was assessed by a disease activity index, the TNF-α level of colon was measured by an enzyme-linked immunosorbent assay, and the pathological changes of colon tissue was examined by hematoxylin-eosin staining. Serum metabolomics and lipidomics analysis based on ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry were applied to decipher the metabolic profile changes. Multivariate analysis was applied to differentiate the metabolites of controls, models, and mesalazine-treated mice. By the receiver operating characteristic (ROC) analysis, 40 differential metabolites with an area under curve (AUC) >0.80 were screened out between control and model groups. Among them, four potential biomarkers (palmitoyl glucuronide, isobutyrylglycine, PC (20:3 (5Z, 8Z, 11Z)/15:0) and L-arginine) had a signficantly reversed level of peak areas in the mesalazine group, and three of them were closely correlated with mesalazine efficacy by linear regression analysis. Furthermore, metabolic pathway analysis revealed several dysregulated pathways in colitis mice, including glycerophospholipid metabolism, pyrimidine metabolism, linoleic acid metabolism, arginine biosynthesis, etc. This study indicates that serum metabolomics is a useful approach that can noninvasively evaluate the therapeutic effect and provide unique insights into the underlying mechanism of mesalazine.
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Affiliation(s)
- Kun Liu
- MOE Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Bingjie Jia
- MOE Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Liping Zhou
- Evaluation and Monitoring Center of Occupational Health, Guangzhou Twelfth People's Hospital, Guangzhou 510620, P.R. China
| | - Lei Xing
- MOE Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Lvying Wu
- MOE Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Yuanyuan Li
- MOE Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Jungang Lu
- Agilent Technologies (China) Co., Ltd., Guangzhou 510613, P.R. China
| | - Lei Zhang
- MOE Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Su Guan
- MOE Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
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10
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Sadat R, Hall PL, Wittenauer AL, Vengoechea ED, Park K, Hagar AF, Singh R, Moore RH, Gambello MJ. Increased parental anxiety and a benign clinical course: Infants identified with short-chain acyl-CoA dehydrogenase deficiency and isobutyryl-CoA dehydrogenase deficiency through newborn screening in Georgia. Mol Genet Metab 2020; 129:20-25. [PMID: 31813752 DOI: 10.1016/j.ymgme.2019.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/29/2022]
Abstract
The long-term consequences and need for therapy in children with short-chain acyl-CoA dehydrogenase deficiency (SCADD) or isobutyryl-CoA dehydrogenase deficiency (IBDD) identified via newborn screening (NBS) remains controversial. Initial clinical descriptions were severe; however, while most cases identified through NBS have remained asymptomatic, clinical concerns have been raised in these populations. It is not clear whether these children are asymptomatic because of the success of NBS, or because the normal clinical course of these disorders is relatively benign. To evaluate these possibilities in our program, we evaluated the clinical outcomes of children with SCADD or IBDD identified by the Georgia NBS compared to the health status of a healthy age-matched control group. We also assessed parental anxiety during a phone interview both subjectively and objectively using the Pediatric Inventory for Parents (PIP), a validated measure of illness-related parental stress. The general health of 52 SCADD and nine IBDD cases from 2007 to 2016 were compared to the general health of unaffected control children obtained through the Centers for Disease Control and Prevention (CDC) parent listserv. We also collected statements from parents who participated in a phone survey regarding events they experienced during and after their diagnostic process. Overall, the children with SCADD and IBDD had no major health problems. There was no significant difference in cognitive development (p = .207). We identified a slightly higher incidence of reported neonatal hypoglycemia in the SCADD group; two of these occurred in the context of maternal diabetes. All interviewed parents reported extreme anxiety during the diagnostic period and current feelings of uncertainty about their child's future. PIP scores for all six caregivers who responded to that portion of the survey were consistent with some degree of parental stress. The greatest reported stressor was the unknown long-term impact of the illness. All children with SCADD and IBDD had no significant long-term sequelae. The phone interviews revealed substantial parental anxiety about the identification and follow-up of SCADD and IBDD. Based on our findings, the anxiety parents experience may be unwarranted given that we see no disease-associated morbidity or mortality in these children. Consideration should be given to the removal of these conditions from NBS panels, or if that is not possible, clinicians could educate parents on the benign nature of these diagnoses and release them from follow-up without treatment.
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Affiliation(s)
- Roa Sadat
- Genetic Counseling Program, Emory University Emory University School of Medicine, Atlanta, GA, USA
| | - Patricia L Hall
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Angela L Wittenauer
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Kevin Park
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Rani Singh
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Reneé H Moore
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Michael J Gambello
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
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11
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Wang T, Ma J, Zhang Q, Gao A, Wang Q, Li H, Xiang J, Wang B. Expanded Newborn Screening for Inborn Errors of Metabolism by Tandem Mass Spectrometry in Suzhou, China: Disease Spectrum, Prevalence, Genetic Characteristics in a Chinese Population. Front Genet 2019; 10:1052. [PMID: 31737040 PMCID: PMC6828960 DOI: 10.3389/fgene.2019.01052] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/01/2019] [Indexed: 12/30/2022] Open
Abstract
Expanded newborn screening for inborn errors of metabolism (IEMs) by tandem mass spectrometry (MS/MS) could simultaneously analyze more than 40 metabolites and identify about 50 kinds of IEMs. Next generation sequencing (NGS) targeting hundreds of IMEs-associated genes as a follow-up test in expanded newborn screening has been used for genetic analysis of patients. The spectrum, prevalence, and genetic characteristic of IEMs vary dramatically in different populations. To determine the spectrum, prevalence, and gene mutations of IEMs in newborns in Suzhou, China, 401,660 newborns were screened by MS/MS and 138 patients were referred to genetic analysis by NGS. The spectrum of 22 IEMs were observed in Suzhou population of newborns, and the overall incidence (excluding short chain acyl-CoA dehydrogenase deficiency (SCADD) and 3-Methylcrotonyl-CoA carboxylase deficiency (3-MCCD)) was 1/3,163. The prevalence of each IEM ranged from 1/401,660 to 1/19,128, while phenylketonuria (PKU) (1/19,128) and Mild hyperphenylalaninemia (M-HPA) (1/19,128) were the most common IEMs, followed by primary carnitine uptake defect (PCUD) (1/26,777), SCADD (1/28,690), hypermethioninemia (H-MET) (1/30,893), 3-MCCD (1/33,412) and methylmalonic acidemia (MMA) (1/40,166). Moreover, 89 reported mutations and 51 novel mutations in 25 IMEs-associated genes were detected in 138 patients with one of 22 IEMs. Some hotspot mutations were observed for ten IEMs, including PAH gene c.728G > A, c.611A > G, and c.721C > T for Phenylketonuria, PAH gene c.158G > A, c.1238G > C, c.728G > A, and c.1315+6T > A for M-HPA, SLC22A5 gene c.1400C > G, c.51C > G, and c.760C > T for PCUD, ACADS gene c.1031A > G, c.164C > T, and c.1130C > T for SCAD deficiency, MAT1A gene c.791G > A for H-MET, MCCC1 gene c.639+2T > A and c.863A > G for 3-MCCD, MMUT gene c.1663G > A for MMA, SLC25A13 gene c.IVS16ins3Kb and c.852_855delTATG for cittrullinemia II, PTS gene c.259C > T and c.166G > A for Tetrahydrobiopterin deficiency, and ACAD8 gene c.1000C > T and c.286C > A for Isobutyryl coa dehydrogenase deficiency. All these hotspot mutations were reported to be pathogenic or likely pathogenic, except a novel mutation of ACAD8 gene c.286C > A. These mutational hotspots could be potential candidates for gene screening and these novel mutations expanded the mutational spectrum of IEMs. Therefore, our findings could be of value for genetic counseling and genetic diagnosis of IEMs.
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Affiliation(s)
- Ting Wang
- Newborn Screening Laboratory, Center for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jun Ma
- Newborn Screening Laboratory, Center for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Qin Zhang
- Genetic Clinic, Center for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ang Gao
- Genetic Clinic, Center for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Qi Wang
- Newborn Screening Laboratory, Center for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Hong Li
- Infertility Clinic, Center for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jingjing Xiang
- Genetic Laboratory, Center for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Benjing Wang
- Newborn Screening Laboratory, Center for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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12
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Lin Y, Peng W, Jiang M, Lin C, Lin W, Zheng Z, Li M, Fu Q. Clinical, biochemical and genetic analysis of Chinese patients with isobutyryl-CoA dehydrogenase deficiency. Clin Chim Acta 2018; 487:133-138. [PMID: 30253142 DOI: 10.1016/j.cca.2018.09.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/24/2018] [Accepted: 09/21/2018] [Indexed: 11/17/2022]
Abstract
Isobutyryl-CoA dehydrogenase deficiency (IBDHD) is a rare autosomal recessive metabolic disorder related to valine catabolism and results from variants in ACAD8. Here, we present the clinical, biochemical, and genotypes of seven patients with IBDHD in China for the first time. Five patients remained asymptomatic during follow-up, whereas one juvenile had speech delay and one newborn exhibited clinical symptoms. All patients showed remarkably increased concentrations of C4-aclycarnitine with elevated C4/C2 and C4/C3 ratios. In urine organic acid tests, only one patient presented with an increased concentration of isobutyrylglycine excretion. Genetic testing was performed to detect the causative variants. Five previously unreported variants, c.235C > G, c.286G > A, c.444G > T c.1092 + 1G > A, and c.1176G > T, and one known variant, c.1000C > T, in ACAD8 were identified. These previously unreported variants in ACAD8 were predicted to be disease-causing and the c.1092 + 1G > A variant was confirmed to cause skipping of exon 9 by reverse transcription PCR. The most common variant was c.286G > A, which showed an allelic frequency of 50% (7/14), and thus may be a prevalent variant among Chinese patients. Our results broaden the mutational spectrum of ACAD8 and improve the understanding of the clinical phenotype of IBDHD.
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Affiliation(s)
- Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Weilin Peng
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Mengyi Jiang
- Genuine Diagnostics Company Limited, Hangzhou, Zhejiang Province 310007, China
| | - Chunmei Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Weihua Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Zhenzhu Zheng
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China
| | - Min Li
- Genuine Diagnostics Company Limited, Hangzhou, Zhejiang Province 310007, China.
| | - Qingliu Fu
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Maternal and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province 362000, China.
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