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Aleshin VA, Bunik VI. Protein-Protein Interfaces as Druggable Targets: A Common Motif of the Pyridoxal-5'-Phosphate-Dependent Enzymes to Receive the Coenzyme from Its Producers. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1022-1033. [PMID: 37751871 DOI: 10.1134/s0006297923070131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 09/28/2023]
Abstract
Pyridoxal-5'-phosphate (PLP), a phosphorylated form of vitamin B6, acts as a coenzyme for numerous reactions, including those changed in cancer and/or associated with the disease prognosis. Since highly reactive PLP can modify cellular proteins, it is hypothesized to be directly transferred from its donors to acceptors. Our goal is to validate the hypothesis by finding common motif(s) in the multitude of PLP-dependent enzymes for binding the limited number of PLP donors, namely pyridoxal kinase (PdxK), pyridox(am)in-5'-phosphate oxidase (PNPO), and PLP-binding protein (PLPBP). Experimentally confirmed interactions between the PLP donors and acceptors reveal that PdxK and PNPO interact with the most abundant PLP acceptors belonging to structural folds I and II, while PLPBP - with those belonging to folds III and V. Aligning sequences and 3D structures of the identified interactors of PdxK and PNPO, we have identified a common motif in the PLP-dependent enzymes of folds I and II. The motif extends from the enzyme surface to the neighborhood of the PLP binding site, represented by an exposed alfa-helix, a partially buried beta-strand, and residual loops. Pathogenicity of mutations in the human PLP-dependent enzymes within or in the vicinity of the motif, but outside of the active sites, supports functional significance of the motif that may provide an interface for the direct transfer of PLP from the sites of its synthesis to those of coenzyme binding. The enzyme-specific amino acid residues of the common motif may be useful to develop selective inhibitors blocking PLP delivery to the PLP-dependent enzymes critical for proliferation of malignant cells.
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Affiliation(s)
- Vasily A Aleshin
- Department of Biokinetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Biochemistry, Sechenov University, Moscow, 119048, Russia
| | - Victoria I Bunik
- Department of Biokinetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Department of Biochemistry, Sechenov University, Moscow, 119048, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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Ju X, Wang Z, Cai D, Xu H, Bello SF, Zhang S, Zhu W, Ji C, Nie Q. TAT gene polymorphism and its relationship with production traits in Muscovy ducks (Cairina Moschata). Poult Sci 2023; 102:102551. [PMID: 36972669 PMCID: PMC10050636 DOI: 10.1016/j.psj.2023.102551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
In a previous study, the laying pattern of Muscovy duck was explored by macro-fitting the laying curve of Muscovy duck, and transcriptome sequencing technique of the ovarian tissues was used to screen the egg-related gene "TAT." Moreover, recent results have shown that TAT is expressed in organs such as oviduct, ovary, and testis. The objective of this study is to examine the effect of TAT gene on egg production traits of Muscovy ducks. First, the expression levels of TAT gene in highest producing (HP) and lowest producing (LP) in 3 tissues related to reproduction were examined, and the results indicated that the expression of TAT gene in hypothalamus was significantly different between HP and LP groups. Then, 6 SNP loci (g. 120G>T, g, 122G>A, g, 254G> A, g. 270C >T, g, 312G>A, and g. 341C>A) were detected in TAT gene. Further, association analysis between the six SNP loci of TAT gene and egg production traits of 652 individual Muscovy ducks was done. The results showed that g. 254G>A and g. 270C>T were significantly correlated (P < 0.05 or 0.001) with the egg production traits of Muscovy ducks. This study elucidated the molecular mechanism that TAT gene might be regulating the egg production traits of Muscovy ducks.
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Beyzaei Z, Nabavizadeh S, Karimzadeh S, Geramizadeh B. The mutation spectrum and ethnic distribution of non-hepatorenal tyrosinemia (types II, III). Orphanet J Rare Dis 2022; 17:424. [PMID: 36471409 PMCID: PMC9724276 DOI: 10.1186/s13023-022-02579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Different types of non-hepatorenal tyrosinemia are among the rare forms of tyrosinemia. Tyrosinemia type II and III are autosomal recessive disorders caused by pathogenic variants in the tyrosine aminotransferase (TAT), and 4-hydroxyphenyl-pyruvate dioxygenas (HPPD) genes, respectively. There are still unclarified aspects in their clinical presentations, mutational spectrum, and genotype-phenotype correlation. MAIN BODY In this study, we evaluated the spectrum of TAT and HHPD gene mutations in patients with tyrosinemia type II and III. Moreover, biochemical and clinical findings are evaluated to establish a genotype-phenotype relationship in the above-mentioned patients. Thirty-three TAT variants have been reported in 42 families, consisting of 21 missense variants, 5 frameshift variants, 4 nonsense variants, 2 variants that primarily cause splicing site, and 1 skipping complete exon (large deletion). The most common variant is p.Arg57Ter, causing a splicing defect, and resulting in premature termination of translation, which was found in 10 patients from 3 families. In HPPD gene, eleven variants in 16 patients have been reported including 7 missense variants, 2 nonsense variants, 1 splice defect, and 1 frameshift variant so far. All variants are unique, except for p.Tyr160Cys, which is a missense variant found in two different patients. Regarding genotype-phenotype correlations, in 90% of tyrosinemia type II patients, positive clinical and biochemical correlations with a detected variant are observed. In HPPD gene, due to the small number of patients, it is not possible to make a definite conclusion. CONCLUSION This is the first large review of variants in TAT and HPPD, highlighting the wide spectrum of disease-causing mutations. Such information is beneficial for the establishment of a privileged mutation screening process in a specific region or ethnic group.
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Affiliation(s)
- Zahra Beyzaei
- grid.412571.40000 0000 8819 4698Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Nabavizadeh
- grid.412571.40000 0000 8819 4698Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Karimzadeh
- grid.412571.40000 0000 8819 4698Shiraz Medical School Library, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bita Geramizadeh
- grid.412571.40000 0000 8819 4698Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran ,grid.412571.40000 0000 8819 4698Department of Pathology, Medical School of Shiraz University, Shiraz Transplant Research Center (STRC), Shiraz University of Medical Sciences, Khalili St., Research Tower, Seventh Floor, Shiraz, Iran
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Decreased SLC27A5 Suppresses Lipid Synthesis and Tyrosine Metabolism to Activate the Cell Cycle in Hepatocellular Carcinoma. Biomedicines 2022; 10:biomedicines10020234. [PMID: 35203444 PMCID: PMC8869743 DOI: 10.3390/biomedicines10020234] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
Tyrosine is an essential ketogenic and glycogenic amino acid for the human body, which means that tyrosine is not only involved in protein metabolism, but also participates in the metabolism of lipids and carbohydrates. The liver is an important place for metabolism of lipids, carbohydrates, and proteins. The metabolic process of biological macro-molecules is a basis for maintaining the physiological activities of organisms, but the cross-linking mechanism of these processes is still unclear. Here, we found that the tyrosine-metabolizing enzymes, which were specifically and highly expressed in the liver, were significantly down-regulated in hepatocellular carcinoma (HCC), and had a correlation with a poor prognosis of HCC patients. Further analysis found that the reduction of tyrosine metabolism would activate the cell cycle and promote cell proliferation. In addition, we also found that the solute carrier family 27 member 5 (SLC27A5) regulates the expression of tyrosine-metabolizing enzymes through nuclear factor erythroid 2-related factor 2 (NRF2). Therefore, the SLC27A5 and tyrosine-metabolizing enzymes that we have identified coordinate lipid and tyrosine metabolism, regulate the cell cycle, and are potential targets for cancer treatment.
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Wang X, Liao X, Yang C, Huang K, Yu T, Yu L, Han C, Zhu G, Zeng X, Liu Z, Zhou X, Qin W, Su H, Ye X, Peng T. Identification of prognostic biomarkers for patients with hepatocellular carcinoma after hepatectomy. Oncol Rep 2019; 41:1586-1602. [PMID: 30628708 PMCID: PMC6365689 DOI: 10.3892/or.2019.6953] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/28/2018] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a lethal malignancy with high morbidity and mortality rates worldwide. The identification of prognosis-associated biomarkers is crucial to improve HCC patient survival. The present study aimed to explore potential predictive biomarkers for HCC. Differentially expressed genes (DEGs) were analyzed in the GSE36376 dataset using GEO2R. Hub genes were identified and further investigated for prognostic value in HCC patients. A risk score model and nomogram were constructed to predict HCC prognosis using the prognosis-associated genes and clinical factors. Pearson's correlation was employed to show interactions among hub genes. Gene enrichment analysis was performed to identify detailed biological processes and pathways. A total of 71 DEGs were obtained and seven (ADH4, CYP2C8, CYP2C9, CYP8B1, SLC22A1, TAT and HSD17B13, all adjusted P≤0.05) of the 10 hub genes were identified as prognosis-related genes for survival analysis in HCC patients, including alcohol dehydrogenase 4 (class II), pi polypeptide (ADH4), cytochrome p450 family 2 subfamily C member 8 (CYP2C8), cytochrome P450 family 2 subfamily C member 9 (CYP2C9), cytochrome P450 family 8 subfamily B member 1 (CYP8B1), solute carrier family 22 member 1 (SLC22A1), tyrosine aminotransferase (TAT) and hydroxysteroid 17-β dehydrogenase 13 (HSD17B13). The risk score model could predict HCC prognosis and the nomogram visualized gene expression and clinical factors of probability for HCC prognosis. The majority of genes showed significant Pearson's correlations with others (41 Pearson correlations P≤0.01, four Pearson correlations P>0.05). GO analysis revealed that terms such as ‘chemical carcinogenesis’ and ‘drug metabolism-cytochrome P450’ were enriched and may prove helpful to elucidate the mechanisms of hepatocarcinogenesis. Hub genes ADH4, CYP2C8, CYP2C9, CYP8B1, SLC22A1, TAT and HSD17B13 may be useful as predictive biomarkers for HCC prognosis.
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Affiliation(s)
- Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Ketuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Long Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xianmin Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Zhengqian Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Wei Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Hao Su
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xinping Ye
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Elloumi-Zghal H, Chaabouni Bouhamed H. Genetics and genomic medicine in Tunisia. Mol Genet Genomic Med 2018; 6:134-159. [PMID: 29663716 PMCID: PMC5902400 DOI: 10.1002/mgg3.392] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 01/19/2023] Open
Abstract
Genetics and genomic medicine in Tunisia.
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Caregiver Quality of Life with Tyrosinemia Type 1. J Genet Couns 2017; 27:723-731. [DOI: 10.1007/s10897-017-0157-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
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Peña-Quintana L, Scherer G, Curbelo-Estévez ML, Jiménez-Acosta F, Hartmann B, La Roche F, Meavilla-Olivas S, Pérez-Cerdá C, García-Segarra N, Giguère Y, Huppke P, Mitchell GA, Mönch E, Trump D, Vianey-Saban C, Trimble ER, Vitoria-Miñana I, Reyes-Suárez D, Ramírez-Lorenzo T, Tugores A. Tyrosinemia type II: Mutation update, 11 novel mutations and description of 5 independent subjects with a novel founder mutation. Clin Genet 2017; 92:306-317. [PMID: 28255985 DOI: 10.1111/cge.13003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 01/27/2017] [Accepted: 02/27/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND Tyrosinemia type II, also known as Richner-Hanhart Syndrome, is an extremely rare autosomal recessive disorder, caused by mutations in the gene encoding hepatic cytosolic tyrosine aminotransferase, leading to the accumulation of tyrosine and its metabolites which cause ocular and skin lesions, that may be accompanied by neurological manifestations, mostly intellectual disability. AIMS To update disease-causing mutations and current clinical knowledge of the disease. MATERIALS AND METHODS Genetic and clinical information were obtained from a collection of both unreported and previously reported cases. RESULTS We report 106 families, represented by 143 individuals, carrying a total of 36 genetic variants, 11 of them not previously known to be associated with the disease. Variants include 3 large deletions, 21 non-synonymous and 5 nonsense amino-acid changes, 5 frameshifts and 2 splice variants. We also report 5 patients from Gran Canaria, representing the largest known group of unrelated families sharing the same P406L mutation. CONCLUSIONS Data analysis did not reveal a genotype-phenotype correlation, but stressed the need of early diagnosis: All patients improved the oculocutaneous lesions after dietary treatment but neurological symptoms prevailed. The discovery of founder mutations in isolated populations, and the benefits of early intervention, should increase diagnostic awareness in newborns.
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Affiliation(s)
- L Peña-Quintana
- Department of Pediatrics, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain.,CIBER OBN, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - G Scherer
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
| | - M L Curbelo-Estévez
- Department of Pediatrics, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - F Jiménez-Acosta
- Mediteknia Dermatology and Hair Transplant Clinic, Medical Pathology Group, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - B Hartmann
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
| | - F La Roche
- Department of Endocrinology and Nutrition, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - S Meavilla-Olivas
- Section of Gastroenterology, Hepatology and Nutrition, Metabolopathies Unit Hospital Sant Joan de Déu, Barcelona, Spain
| | - C Pérez-Cerdá
- Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - N García-Segarra
- Center for Molecular Diseases, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Y Giguère
- Programme québécois de dépistage néonatal sanguin, CHU de Québec, and Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Quebec, Canada
| | - P Huppke
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - G A Mitchell
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montréal, Canada
| | - E Mönch
- Charité University Medical Center, Campus Virchow-Klinikum, Berlin, Germany
| | - D Trump
- Department of Medical Genetics, Addenbrooke's Hospital, Cambridge, UK
| | | | - E R Trimble
- Department of Clinical Biochemistry, Royal Victoria Hospital, Belfast, UK
| | - I Vitoria-Miñana
- Unidad de Nutrición y Metabolopatías, Hospital La Fe, Valencia, Spain
| | - D Reyes-Suárez
- Department of Pediatrics, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - T Ramírez-Lorenzo
- Research Unit, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - A Tugores
- Research Unit, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
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Gokay S, Kendirci M, Ustkoyuncu PS, Kardas F, Bayram AK, Per H, Poyrazoğlu HG. Tyrosinemia type II: Novel mutations in TAT in a boy with unusual presentation. Pediatr Int 2016; 58:1069-1072. [PMID: 27285949 DOI: 10.1111/ped.13062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/28/2016] [Accepted: 05/24/2016] [Indexed: 12/01/2022]
Abstract
Tyrosinemia type II is a rare autosomal recessive disorder caused by deficiency of tyrosine aminotransferase (TAT). It may occur with ocular and cutaneous symptoms with or without mental retardation, but epileptic seizure is a rare presentation of this disease. Herein we report the clinical, biochemical and genetic features of a 4-year-old boy who presented with afebrile seizure and photophobia. Genomic DNA was obtained from peripheral blood leukocytes from the whole family. Sequencing analysis was performed using the MiSeq next-generation sequencing platform. Sequencing of TAT indicated two new homozygous mutations p.L312P (c.935T>C) and p.T408M (c.1223C>T) for the proband and his asymptomatic sister. During a 2 year follow-up period, the patient had overall poor compliance with protein-restricted diet, but his asymptomatic sister had good compliance with the diet. Cognitive function of the patient worsened steadily, but his asymptomatic sister maintained normal mental status. Tyrosinemia type II should be considered in the differential diagnosis of children presenting with epileptic seizure and photophobia; furthermore, early diagnosis and protein-restricted regimen are important to reduce the risk of long-term complications of tyrosinemia type II such as mental disability.
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Affiliation(s)
- Songul Gokay
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey.
| | - Mustafa Kendirci
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Pembe Soylu Ustkoyuncu
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Fatih Kardas
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Ayse Kacar Bayram
- Division of Pediatric Neurology, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Hüseyin Per
- Division of Pediatric Neurology, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Hatice Gamze Poyrazoğlu
- Division of Pediatric Neurology, Department of Pediatrics, Faculty of Medicine, Fırat University, Elazığ, Turkey
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