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Zhang C, Huang G, Yang J, Jiang Y, Huang R, Ye Z, Huang Y, Hu H, Xi X. Overexpression of DBT suppresses the aggressiveness of renal clear cell carcinoma and correlates with immune infiltration. Front Immunol 2023; 14:1197011. [PMID: 37383233 PMCID: PMC10293648 DOI: 10.3389/fimmu.2023.1197011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/30/2023] Open
Abstract
Conventional therapy for kidney renal clear cell carcinoma (KIRC) is unpromising. The tumor microenvironment (TME) is intimately linked to the invasiveness of a variety of tumor forms, including KIRC. The purpose of this research is to establish the prognostic and immune-related significance of dihydrolipoamide branched chain transacylase E2 (DBT) in individuals with KIRC. In this investigation, we discovered that DBT expression was down-regulated in a range of human malignancies, and low DBT expression in KIRC was linked to higher-level clinicopathological characteristics as well as a poor prognosis for KIRC patients. Based on the findings of univariate and multivariate Cox regression analyses, DBT might be employed as an independent prognostic factor in KIRC patients. Furthermore, we developed a nomogram to better investigate DBT's predictive usefulness. To confirm DBT expression, we examined KIRC cell lines using RT-qPCR and Western blotting. We also examined the role of DBT in KIRC using colony formation, CCK-8, EdU, transwell, and wound healing assays. We discovered that plasmid-mediated overexpression of DBT in KIRC cells slowed cell proliferation and decreased migration and invasion. Multiple enrichment analyses revealed that DBT may be involved in processes and pathways related to immunotherapy and drug metabolism. We computed the immune infiltration score and discovered that the immunological score and the ESTIMATE score were both greater in the DBT low expression group. According to the CIBERSORT algorithm, DBT seems to promote anti-cancer immune responses in KIRC by activating M1 macrophages, mast cells, and dendritic cells while inhibiting regulatory T cells. Finally, in KIRC, DBT expression was found to be highly linked to immunological checkpoints, targeted medicines, and immunotherapeutic agents. Our findings suggest that DBT is a distinct predictive biomarker for KIRC patients, playing a significant role in the TME of KIRC and serving as a reference for the selection of targeted treatment and immunotherapy.
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Affiliation(s)
- Chiyu Zhang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Gaomin Huang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiale Yang
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yi Jiang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ruizhen Huang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenfeng Ye
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yawei Huang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Honglin Hu
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoqing Xi
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Mori T, Machida K, Kudou Y, Kimishima M, Sassa K, Goto-Inoue N, Minei R, Ogura A, Kobayashi Y, Kamiya K, Nakaya D, Yamamoto N, Kashiwagi A, Kashiwagi K. Novel predator-induced phenotypic plasticity by hemoglobin and physiological changes in the brain of Xenopus tropicalis. Front Physiol 2023; 14:1178869. [PMID: 37346489 PMCID: PMC10279953 DOI: 10.3389/fphys.2023.1178869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Organisms adapt to changes in their environment to survive. The emergence of predators is an example of environmental change, and organisms try to change their external phenotypic systems and physiological mechanisms to adapt to such changes. In general, prey exhibit different phenotypes to predators owing to historically long-term prey-predator interactions. However, when presented with a novel predator, the extent and rate of phenotypic plasticity in prey are largely unknown. Therefore, exploring the physiological adaptive response of organisms to novel predators is a crucial topic in physiology and evolutionary biology. Counterintuitively, Xenopus tropicalis tadpoles do not exhibit distinct external phenotypes when exposed to new predation threats. Accordingly, we examined the brains of X. tropicalis tadpoles to understand their response to novel predation pressure in the absence of apparent external morphological adaptations. Principal component analysis of fifteen external morphological parameters showed that each external morphological site varied nonlinearly with predator exposure time. However, the overall percentage change in principal components during the predation threat (24 h) was shown to significantly (p < 0.05) alter tadpole morphology compared with that during control or 5-day out treatment (5 days of exposure to predation followed by 5 days of no exposure). However, the adaptive strategy of the altered sites was unknown because the changes were not specific to a particular site but were rather nonlinear in various sites. Therefore, RNA-seq, metabolomic, Ingenuity Pathway Analysis, and Kyoto Encyclopedia of Genes and Genomes analyses were performed on the entire brain to investigate physiological changes in the brain, finding that glycolysis-driven ATP production was enhanced and ß-oxidation and the tricarboxylic acid cycle were downregulated in response to predation stress. Superoxide dismutase was upregulated after 6 h of exposure to new predation pressure, and radical production was reduced. Hemoglobin was also increased in the brain, forming oxyhemoglobin, which is known to scavenge hydroxyl radicals in the midbrain and hindbrain. These suggest that X. tropicalis tadpoles do not develop external morphological adaptations that are positively correlated with predation pressure, such as tail elongation, in response to novel predators; however, they improve their brain functionality when exposed to a novel predator.
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Affiliation(s)
- Tsukasa Mori
- Nihon University College of Bioresource Sciences, Fujisawa, Japan
| | - Kazumasa Machida
- Nihon University College of Bioresource Sciences, Fujisawa, Japan
| | - Yuki Kudou
- Nihon University College of Bioresource Sciences, Fujisawa, Japan
| | - Masaya Kimishima
- Nihon University College of Bioresource Sciences, Fujisawa, Japan
| | - Kaito Sassa
- Nihon University College of Bioresource Sciences, Fujisawa, Japan
| | - Naoko Goto-Inoue
- Nihon University College of Bioresource Sciences, Fujisawa, Japan
| | - Ryuhei Minei
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Atsushi Ogura
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | | | | | | | - Naoyuki Yamamoto
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Keiko Kashiwagi
- Hiroshima University Amphibian Research Center, Hiroshima, Japan
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Li L, Mao X, Yang N, Ji T, Wang S, Ma Y, Yang H, Sang Y, Zhao J, Gong L, Tang Y, Kong Y. Identification of gene mutations in six Chinese patients with maple syrup urine disease. Front Genet 2023; 14:1132364. [PMID: 36911408 PMCID: PMC10001893 DOI: 10.3389/fgene.2023.1132364] [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: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
Background: Maple syrup urine disease (MSUD) is a rare autosomal recessive amino acid metabolic disease. This study is to identify the pathogenic genetic factors of six cases of MUSD and evaluates the application value of high-throughput sequencing technology in the early diagnosis of MUSD. Methods: Clinical examination was carried out for patients and used blood tandem mass spectrometry (MS/MS), urine gas chromatography-mass spectrometry (GC/MS), and the application of high-throughput sequencing technology for detection. Validate candidate mutations by polymerase chain reaction (PCR)-Sanger sequencing technology. Bioinformatics software analyzed the variants' pathogenicity. Using Swiss PDB Viewer software to predict the effect of mutation on the structure of BCKDHA and BCKDHB proteins. Result: A total of six MSUD patients were diagnosed, including four males and two females. Nine variants were found in three genes of six MSUD families by high-throughput sequencing, including four missense mutations: c.659C>T(p.A220V), c.818C>T(p.T273I), c.1134C>G(p.D378E), and c.1006G>A(p.G336S); two non-sense mutations: c.1291C>T(p.R431*) and c.331C>T(p.R111*); three deletion mutations: c.550delT (p.S184Pfs*46), c.718delC (p.P240Lfs*14), and c.795delG (p.N266Tfs*64). Sanger sequencing's results were consistent with the high-throughput sequencing. The bioinformatics software revealed that the mutations were harmful, and the prediction results of Swiss PDB Viewer suggest that variation affects protein conformation. Conclusion: This study identified nine pathogenic variants in the BCKDHA, BCKDHB, and DBT genes in six MSUD families, including two novel pathogenic variants in the BCKDHB gene, which enriched the genetic mutational spectrum of the disease. High-throughput sequencing is essential for the MSUD's differential diagnosis, early treatment, and prenatal diagnosis.
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Affiliation(s)
- Lulu Li
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Healthcare Hospital, Beijing, China
| | - Xinmei Mao
- Peking University First Hospital Ningxia Women and Children's Hospital (Ningxia Hui Autonomous Region Maternal and Child Health Hospital), Yinchuan, China
| | - Nan Yang
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Healthcare Hospital, Beijing, China
| | - Taoyun Ji
- Peking University First Hospital Ningxia Women and Children's Hospital (Ningxia Hui Autonomous Region Maternal and Child Health Hospital), Yinchuan, China
| | - Shunan Wang
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Healthcare Hospital, Beijing, China
| | - Yulan Ma
- Peking University First Hospital Ningxia Women and Children's Hospital (Ningxia Hui Autonomous Region Maternal and Child Health Hospital), Yinchuan, China
| | - Haihe Yang
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Healthcare Hospital, Beijing, China
| | - Yuting Sang
- Peking University First Hospital Ningxia Women and Children's Hospital (Ningxia Hui Autonomous Region Maternal and Child Health Hospital), Yinchuan, China
| | - Jinqi Zhao
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Healthcare Hospital, Beijing, China
| | - Lifei Gong
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Healthcare Hospital, Beijing, China
| | - Yue Tang
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Healthcare Hospital, Beijing, China
| | - Yuanyuan Kong
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Healthcare Hospital, Beijing, China
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Fang X, Zhu X, Feng Y, Bai Y, Zhao X, Liu N, Kong X. Genetic analysis by targeted next-generation sequencing and novel variation identification of maple syrup urine disease in Chinese Han population. Sci Rep 2021; 11:18939. [PMID: 34556729 PMCID: PMC8460745 DOI: 10.1038/s41598-021-98357-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022] Open
Abstract
Maple syrup urine disease (MSUD) is a rare autosomal recessive disorder that affects the degradation of branched chain amino acids (BCAAs). Only a few cases of MSUD have been documented in Mainland China. In this report, 8 patients (4 females and 4 males) with MSUD from 8 unrelated Chinese Han families were diagnosed at the age of 6 days to 4 months. All the coding regions and exon/intron boundaries of BCKDHA, BCDKHB, DBT and DLD genes were analyzed by targeted NGS in the 8 MSUD pedigrees. Targeted NGS revealed 2 pedigrees with MSUD Ia, 5 pedigrees with Ib, 1 pedigree with MSUD II. Totally, 13 variants were detected, including 2 variants (p.Ala216Val and p.Gly281Arg) in BCKDHA gene, 10 variants (p.Gly95Ala, p.Ser171Pro, p.Phe175Leu, p.Arg183Trp, p.Lys222Thr, p.Arg285Ter, p.Arg111Ter, p.S184Pfs*46, p.Arg170Cys, p.I160Ffs*25) in BCKDHB gene, 1 variant (p.Arg431Ter) in DBT gene. In addition, 4 previously unidentified variants (p.Gly281Arg in BCKDHA gene, p.Ser171Pro, p.Gly95Ala and p.Lys222Thr in BCKDHB gene) were identified. NGS plus Sanger sequencing detection is effective and accurate for gene diagnosis. Computational structural modeling indicated that these novel variations probably affect structural stability and considered as likely pathogenic variants.
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Affiliation(s)
- Xiaohua Fang
- Obstetrics and Gynecology Department, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Xiaofan Zhu
- Obstetrics and Gynecology Department, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Yin Feng
- Obstetrics and Gynecology Department, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Ying Bai
- Obstetrics and Gynecology Department, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Xuechao Zhao
- Obstetrics and Gynecology Department, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Ning Liu
- Obstetrics and Gynecology Department, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China.
| | - Xiangdong Kong
- Obstetrics and Gynecology Department, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China.
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Bharadwaj A, Wahi N, Saxena A. Occurrence of Inborn Errors of Metabolism in Newborns, Diagnosis and Prophylaxis. Endocr Metab Immune Disord Drug Targets 2020; 21:592-616. [PMID: 33357204 DOI: 10.2174/1871530321666201223110918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 11/22/2022]
Abstract
Inborn errors of metabolism (IEM) are a heterogeneous group of rare genetic disorders that are generally transmitted as autosomal or X-linked recessive disorders. These defects arise due to mutations associated with specific gene(s), especially the ones associated with key metabolic enzymes. These enzymes or their product(s) are involved in various metabolic pathways, leading to the accumulation of intermediary metabolite(s), reflecting their toxic effects upon mutations. The diagnosis of these metabolic disorders is based on the biochemical analysis of the clinical manifestations produced and their molecular mechanism. Therefore, it is imperative to devise diagnostic tests with high sensitivity and specificity for early detection of IEM. Recent advances in biochemical and polymerase chain reaction-based genetic analysis along with pedigree and prenatal diagnosis can be life-saving in nature. The latest development in exome sequencing for rapid diagnosis and enzyme replacement therapy would facilitate the successful treatment of these metabolic disorders in the future. However, the longterm clinical implications of these genetic manipulations is still a matter of debate among intellectuals and requires further research.
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Affiliation(s)
- Alok Bharadwaj
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Nitin Wahi
- Department of Bioinformatics, Pathfinder Research and Training Foundation, Greater Noida - 201308, Uttar Pradesh, India
| | - Aditya Saxena
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
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Chen Y, Wu X, Hu D, Wang W. Importance of Mitochondrial-Related Genes in Dilated Cardiomyopathy Based on Bioinformatics Analysis. CARDIOVASCULAR INNOVATIONS AND APPLICATIONS 2020; 5. [DOI: 10.15212/cvia.2019.0588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We designed this study to identify potential key protein interaction networks, genes, and correlated pathways in dilated cardiomyopathy (DCM) via bioinformatics methods. We selected the GSE3586 microarray dataset, consisting of 15 dilated cardiomyopathic heart biopsy samples and 13 nonfailing heart biopsy samples. Initially, the GSE3586 dataset was downloaded and was analyzed with the limma package to identify differentially expressed genes (DEGs). A total of 172 DEGs consisting of 162 upregulated genes and ten downregulated genes in DCM were selected by the criterion of adjusted Pvalues less than 0.01 and the log2-fold change of 0.6 or greater. Gene Ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to view the biological processes, cellular components, molecular function, and KEGG pathways of the DEGs. Next, protein-protein interactions were constructed, and the hub protein modules were identified. Then we selected the key genes DLD, UQCRC2, DLAT, SUCLA2, ATP5A1, PRDX3, FH, SDHD, and NDUFV1, which are involved in a wide range of biological activities, such as the citrate cycle, oxidation-reduction processes and cellular respiration, and energy derivation by oxidation of organic compounds in mitochondria. Finally, we found that currently there are no related gene-targeting drugs after exploring the predicted interactions between key genes and drugs, and transcription factors. In conclusion, our study provides greater understanding of the pathogenesis and underlying molecular mechanisms in DCM. This contributes to the exploration of potential gene therapy targets.
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Affiliation(s)
- Yukuan Chen
- Shantou University Medical College, Shantou, 515041 Guangdong, People’s Republic of China
- Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong, People’s Republic of China
| | - Xiaohui Wu
- Shantou University Medical College, Shantou, 515041 Guangdong, People’s Republic of China
- Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong, People’s Republic of China
| | - Danchun Hu
- Shantou University Medical College, Shantou, 515041 Guangdong, People’s Republic of China
- Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong, People’s Republic of China
| | - Wei Wang
- Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong, People’s Republic of China
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Pickens CA, Sternberg M, Seeterlin M, De Jesús VR, Morrissey M, Manning A, Bhakta S, Held PK, Mei J, Cuthbert C, Petritis K. Harmonizing Newborn Screening Laboratory Proficiency Test Results Using the CDC NSQAP Reference Materials. Int J Neonatal Screen 2020; 6:75. [PMID: 33123642 PMCID: PMC7570198 DOI: 10.3390/ijns6030075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/12/2020] [Indexed: 11/16/2022] Open
Abstract
Newborn screening (NBS) laboratories cannot accurately compare mass spectrometry-derived results and cutoff values due to differences in testing methodologies. The objective of this study was to assess harmonization of laboratory proficiency test (PT) results using quality control (QC) data. Newborn Screening Quality Assurance Program (NSQAP) QC and PT data reported from 302 laboratories in 2019 were used to compare results among laboratories. QC materials were provided as dried blood spot cards which included a base pool and the base pool enriched with specific concentrations of metabolites in a linear range. QC data reported by laboratories were regressed on QC data reported by the Centers for Disease Control and Prevention (CDC), and laboratory's regression parameters were used to harmonize their PT result. In general, harmonization tended to reduce overall variation in PT data across laboratories. The metabolites glutarylcarnitine (C5DC), tyrosine, and phenylalanine were displayed to highlight inter- and intra-method variability in NBS results. Several limitations were identified using retrospective data for harmonization, and future studies will address these limitations to further assess feasibility of using NSQAP QC data to harmonize PT data. Harmonizing NBS data using common QC materials appears promising to aid result comparison between laboratories.
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Affiliation(s)
- Charles Austin Pickens
- Centers for Disease Control and Prevention, Division of Laboratory Sciences, Newborn Screening and Molecular Biology Branch, MS F19, Atlanta, GA 30341, USA; (C.A.P.); (M.S.); (J.M.); (C.C.)
| | - Maya Sternberg
- Centers for Disease Control and Prevention, Division of Laboratory Sciences, Newborn Screening and Molecular Biology Branch, MS F19, Atlanta, GA 30341, USA; (C.A.P.); (M.S.); (J.M.); (C.C.)
| | - Mary Seeterlin
- Michigan Department of Community Health, Lansing, MI 49221, USA;
| | - Víctor R De Jesús
- Centers for Disease Control and Prevention, Division of Laboratory Sciences, Tobacco and Volatiles Branch, Atlanta, GA 30341, USA;
| | - Mark Morrissey
- Wadsworth Center/New York State Department of Health, Albany, NY 12201-0509, USA;
| | - Adrienne Manning
- Katherine A. Kelley State Public Health Laboratory, Connecticut Department of Public Health, Rocky Hill, CT 06067, USA;
| | - Sonal Bhakta
- Arizona Department of Health Services, Office of Newborn Screening, Phoenix, AZ 85007, USA;
| | - Patrice K Held
- Wisconsin State Laboratory of Hygiene, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA;
| | - Joanne Mei
- Centers for Disease Control and Prevention, Division of Laboratory Sciences, Newborn Screening and Molecular Biology Branch, MS F19, Atlanta, GA 30341, USA; (C.A.P.); (M.S.); (J.M.); (C.C.)
| | - Carla Cuthbert
- Centers for Disease Control and Prevention, Division of Laboratory Sciences, Newborn Screening and Molecular Biology Branch, MS F19, Atlanta, GA 30341, USA; (C.A.P.); (M.S.); (J.M.); (C.C.)
| | - Konstantinos Petritis
- Centers for Disease Control and Prevention, Division of Laboratory Sciences, Newborn Screening and Molecular Biology Branch, MS F19, Atlanta, GA 30341, USA; (C.A.P.); (M.S.); (J.M.); (C.C.)
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Khalifa OA, Imtiaz F, Ramzan K, Zaki O, Gamal R, Elbaik L, Rihan S, Salam E, Abdul-Mawgoud R, Hassan M, Hassan N, Saleh E, Seoudi D, Moustafa AS. Genotype-phenotype correlation of 33 patients with maple syrup urine disease. Am J Med Genet A 2020; 182:2486-2500. [PMID: 32812330 DOI: 10.1002/ajmg.a.61806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/16/2022]
Abstract
Maple syrup urine disease (MSUD) is a rare autosomal recessive inherited disorder due to defects in the branched-chain α-ketoacid dehydrogenase complex (BCKDC). MSUD varies in severity and its clinical spectrum is quite broad, ranging from mild to severe phenotypes. Thirty-three MSUD patients were recruited into this study for molecular genetic variant profiling and genotype-phenotype correlation. Except for one patient, all other patients presented with the classic neonatal form of the disease. Seventeen different variants were detected where nine were novel. The detected variants spanned across the entire BCKDHA, BCKDHB and DBT genes. All variants were in homozygous forms. The commonest alterations were nonsense and frameshift variants, followed by missense variants. For the prediction of variant's pathogenicity, we used molecular modeling and several in silico tools including SIFT, Polyphen2, Condel, and Provean. In addition, six other tools were used for the prediction of the conservation of the variants' sites including Eigen-PC, GERP++, SiPhy, PhastCons vertebrates and primates, and PhyloP100 rank scores. Herein, we presented a comprehensive characterization of a large cohort of patients with MSUD. The clinical severity of the variants' phenotypes was well correlated with the genotypes. The study underscores the importance of the use of in silico analysis of MSUD genotypes for the prediction of the clinical outcomes in patients with MSUD.
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Affiliation(s)
- Ola A Khalifa
- Genetics Unit, Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Faiqa Imtiaz
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Osama Zaki
- Genetics Unit, Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Radwa Gamal
- Genetics Unit, Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lina Elbaik
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Shaimaa Rihan
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Ehab Salam
- Genetics Unit, Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Rehab Abdul-Mawgoud
- Genetics Unit, Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Magdy Hassan
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Nahla Hassan
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Eman Saleh
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Dina Seoudi
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Amr S Moustafa
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Mordaunt D, Cox D, Fuller M. Metabolomics to Improve the Diagnostic Efficiency of Inborn Errors of Metabolism. Int J Mol Sci 2020; 21:ijms21041195. [PMID: 32054038 PMCID: PMC7072749 DOI: 10.3390/ijms21041195] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/08/2020] [Accepted: 02/09/2020] [Indexed: 12/21/2022] Open
Abstract
Early diagnosis of inborn errors of metabolism (IEM)—a large group of congenital disorders—is critical, given that many respond well to targeted therapy. Newborn screening programs successfully capture a proportion of patients enabling early recognition and prompt initiation of therapy. For others, the heterogeneity in clinical presentation often confuses diagnosis with more common conditions. In the absence of family history and following clinical suspicion, the laboratory diagnosis typically begins with broad screening tests to circumscribe specialised metabolite and/or enzyme assays to identify the specific IEM. Confirmation of the biochemical diagnosis is usually achieved by identifying pathogenic genetic variants that will also enable cascade testing for family members. Unsurprisingly, this diagnostic trajectory is too often a protracted and lengthy process resulting in delays in diagnosis and, importantly, therapeutic intervention for these rare conditions is also postponed. Implementation of mass spectrometry technologies coupled with the expanding field of metabolomics is changing the landscape of diagnosing IEM as numerous metabolites, as well as enzymes, can now be measured collectively on a single mass spectrometry-based platform. As the biochemical consequences of impaired metabolism continue to be elucidated, the measurement of secondary metabolites common across groups of IEM will facilitate algorithms to further increase the efficiency of diagnosis.
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Affiliation(s)
- Dylan Mordaunt
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - David Cox
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
| | - Maria Fuller
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
- Correspondence: ; Tel.: +61-8-8161-6741
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