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Ortigoza-Escobar JD, Zamani M, Dorison N, Sadeghian S, Azizimalamiri R, Alvi JR, Sultan T, Galehdari H, Shariati G, Saberi A, Leeuwen L, Zifarelli G, Bauer P, d'Hardemare V, Doummar D, Roze E, Travaglini L, Nicita F, Ojea Ponce N, Zahraei SM, Alabdi L, Tamim A, Hashem MO, Ababneh F, Morrow MM, Curry C, Tam A, Ruedy J, Bhambhani V, Veith R, Strømme P, Efthymiou S, Alkuraya FS, Moreno-De-Luca A, Burglen L, Houlden H, Maroofian R. Biallelic ZBTB11 Variants: A Neurodevelopmental Condition with Progressive Complex Movement Disorders. Mov Disord 2024. [PMID: 38899514 DOI: 10.1002/mds.29883] [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: 07/18/2023] [Revised: 05/08/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Biallelic ZBTB11 variants have previously been associated with an ultrarare subtype of autosomal recessive intellectual developmental disorder (MRT69). OBJECTIVE The aim was to provide insights into the clinical and genetic characteristics of ZBTB11-related disorders (ZBTB11-RD), with a particular emphasis on progressive complex movement abnormalities. METHODS Thirteen new and 16 previously reported affected individuals, ranging in age from 2 to 50 years, with biallelic ZBTB11 variants underwent clinical and genetic characterization. RESULTS All patients exhibited a range of neurodevelopmental phenotypes with varying severity, encompassing ocular and neurological features. Eleven new patients presented with complex abnormal movements, including ataxia, dystonia, myoclonus, stereotypies, and tremor, and 7 new patients exhibited cataracts. Deep brain stimulation was successful in treating 1 patient with generalized progressive dystonia. Our analysis revealed 13 novel variants. CONCLUSIONS This study provides additional insights into the clinical features and spectrum of ZBTB11-RD, highlighting the progressive nature of movement abnormalities in the background of neurodevelopmental phenotype. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Juan Darío Ortigoza-Escobar
- Movement Disorders Unit, Pediatric Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Barcelona, Spain
- European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Mina Zamani
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Nathalie Dorison
- Unité Dyspa, Neurochirurgie Pédiatrique, Hôpital Fondation Rothschild, Paris, France
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Centre, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Centre, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Javeria Raza Alvi
- Department of Pediatric Neurology, The Children's Hospital and the University of Child Health Sciences, Lahore, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, The Children's Hospital and the University of Child Health Sciences, Lahore, Pakistan
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Alihossein Saberi
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Lisette Leeuwen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | - Vincent d'Hardemare
- Unité Dyspa, Neurochirurgie Pédiatrique, Hôpital Fondation Rothschild, Paris, France
| | - Diane Doummar
- AP-HP. Sorbonne Université, Service de Neuropédiatrie et Centre de Référence Neurogénétique, Hôpital Armand Trousseau, FHU I2D2, Paris, France
| | - Emmanuel Roze
- Assistance Publique-Hôpitaux de Paris CHU Pitié-Salpêtrière DMU Neurosciences et Sorbonne Université, INSERM, CNRS, Institut du Cerveau, Paris, France
| | - Lorena Travaglini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Disorders, IRCCS, Bambino Gesù Children's Hospital of Rome, Rome, Italy
| | - Núria Ojea Ponce
- Department of Statistics, Institut de Recerca Sant Joan de Déu Barcelona, Barcelona, Spain
| | | | - Lama Alabdi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdullah Tamim
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Faroug Ababneh
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Cynthia Curry
- Department of Pediatrics, Genetic Medicine, UCSF/Fresno, Fresno, California, USA
| | - Allison Tam
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Jessica Ruedy
- Genetics Clinic, Children's MN, Minneapolis, Minnesota, USA
| | | | - Regan Veith
- Genetics Clinic, Children's MN, Minneapolis, Minnesota, USA
| | - Petter Strømme
- Division of Pediatrics and Adolescent Medicine, Oslo, University Hospital and Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology Section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Lydie Burglen
- Centre de Référence Maladies Rares "Malformations et Maladies Congénitales du Cervelet," Hôpital Trousseau, APHP, Sorbonne University, Paris, France
- Département de Génétique, APHP, Sorbonne University, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR, Paris, France
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
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Xia J, Li S, Liu S, Zhang L. Aldehyde dehydrogenase in solid tumors and other diseases: Potential biomarkers and therapeutic targets. MedComm (Beijing) 2023; 4:e195. [PMID: 36694633 PMCID: PMC9842923 DOI: 10.1002/mco2.195] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 01/18/2023] Open
Abstract
The family of aldehyde dehydrogenases (ALDHs) contains 19 isozymes and is involved in the oxidation of endogenous and exogenous aldehydes to carboxylic acids, which contributes to cellular and tissue homeostasis. ALDHs play essential parts in detoxification, biosynthesis, and antioxidants, which are of important value for cell proliferation, differentiation, and survival in normal body tissues. However, ALDHs are frequently dysregulated and associated with various diseases like Alzheimer's disease, Parkinson's disease, and especially solid tumors. Notably, the involvement of the ALDHs in tumor progression is responsible for the maintenance of the stem-cell-like phenotype, triggering rapid and aggressive clinical progressions. ALDHs have captured increasing attention as biomarkers for disease diagnosis and prognosis. Nevertheless, these require further longitudinal clinical studies in large populations for broad application. This review summarizes our current knowledge regarding ALDHs as potential biomarkers in tumors and several non-tumor diseases, as well as recent advances in our understanding of the functions and underlying molecular mechanisms of ALDHs in disease development. Finally, we discuss the therapeutic potential of ALDHs in diseases, especially in tumor therapy with an emphasis on their clinical implications.
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Affiliation(s)
- Jie Xia
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, The International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Siqin Li
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, The International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Suling Liu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, The International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer MedicineNanjing Medical UniversityNanjingChina
| | - Lixing Zhang
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Cancer Institutes, Key Laboratory of Breast Cancer in Shanghai, The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, The International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Shanghai Medical CollegeFudan UniversityShanghaiChina
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3
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Carneiro TJ, Vojtek M, Gonçalves-Monteiro S, Batista de Carvalho ALM, Marques MPM, Diniz C, Gil AM. Effect of Pd 2Spermine on Mice Brain-Liver Axis Metabolism Assessed by NMR Metabolomics. Int J Mol Sci 2022; 23:13773. [PMID: 36430252 PMCID: PMC9693583 DOI: 10.3390/ijms232213773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022] Open
Abstract
Cisplatin (cDDP)-based chemotherapy is often limited by severe deleterious effects (nephrotoxicity, hepatotoxicity and neurotoxicity). The polynuclear palladium(II) compound Pd2Spermine (Pd2Spm) has emerged as a potential alternative drug, with favorable pharmacokinetic/pharmacodynamic properties. This paper reports on a Nuclear Magnetic Resonance metabolomics study to (i) characterize the response of mice brain and liver to Pd2Spm, compared to cDDP, and (ii) correlate brain-liver metabolic variations. Multivariate and correlation analysis of the spectra of polar and lipophilic brain and liver extracts from an MDA-MB-231 cell-derived mouse model revealed a stronger impact of Pd2Spm on brain metabolome, compared to cDDP. This was expressed by changes in amino acids, inosine, cholate, pantothenate, fatty acids, phospholipids, among other compounds. Liver was less affected than brain, with cDDP inducing more metabolite changes. Results suggest that neither drug induces neuronal damage or inflammation, and that Pd2Spm seems to lead to enhanced brain anti-inflammatory and antioxidant mechanisms, regulation of brain bioactive metabolite pools and adaptability of cell membrane characteristics. The cDDP appears to induce higher extension of liver damage and an enhanced need for liver regeneration processes. This work demonstrates the usefulness of untargeted metabolomics in evaluating drug impact on multiple organs, while confirming Pd2Spm as a promising replacement of cDDP.
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Affiliation(s)
- Tatiana J. Carneiro
- Department of Chemistry, CICECO—Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Martin Vojtek
- LAQV/REQUIMTE—Associated Laboratory for Green Chemistry of the Network of Chemistry and Technology, Laboratory of Pharmacology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, 4150-755 Porto, Portugal
| | - Salomé Gonçalves-Monteiro
- LAQV/REQUIMTE—Associated Laboratory for Green Chemistry of the Network of Chemistry and Technology, Laboratory of Pharmacology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, 4150-755 Porto, Portugal
| | | | - Maria Paula M. Marques
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Carmen Diniz
- LAQV/REQUIMTE—Associated Laboratory for Green Chemistry of the Network of Chemistry and Technology, Laboratory of Pharmacology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, 4150-755 Porto, Portugal
| | - Ana M. Gil
- Department of Chemistry, CICECO—Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
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Gao J, Hao Y, Piao X, Gu X. Aldehyde Dehydrogenase 2 as a Therapeutic Target in Oxidative Stress-Related Diseases: Post-Translational Modifications Deserve More Attention. Int J Mol Sci 2022; 23:ijms23052682. [PMID: 35269824 PMCID: PMC8910853 DOI: 10.3390/ijms23052682] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 02/07/2023] Open
Abstract
Aldehyde dehydrogenase 2 (ALDH2) has both dehydrogenase and esterase activity; its dehydrogenase activity is closely related to the metabolism of aldehydes produced under oxidative stress (OS). In this review, we recapitulate the enzyme activity of ALDH2 in combination with its protein structure, summarize and show the main mechanisms of ALDH2 participating in metabolism of aldehydes in vivo as comprehensively as possible; we also integrate the key regulatory mechanisms of ALDH2 participating in a variety of physiological and pathological processes related to OS, including tissue and organ fibrosis, apoptosis, aging, and nerve injury-related diseases. On this basis, the regulatory effects and application prospects of activators, inhibitors, and protein post-translational modifications (PTMs, such as phosphorylation, acetylation, S-nitrosylation, nitration, ubiquitination, and glycosylation) on ALDH2 are discussed and prospected. Herein, we aimed to lay a foundation for further research into the mechanism of ALDH2 in oxidative stress-related disease and provide a basis for better use of the ALDH2 function in research and the clinic.
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Affiliation(s)
- Jie Gao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (Y.H.)
| | - Yue Hao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (Y.H.)
| | - Xiangshu Piao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Xianhong Gu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (Y.H.)
- Correspondence:
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5
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Han X, Wang D, Zhao P, Liu C, Hao Y, Chang L, Zhao J, Zhao W, Mu L, Wang J, Li H, Kong Q, Han J. Inference of Subpathway Activity Profiles Reveals Metabolism Abnormal Subpathway Regions in Glioblastoma Multiforme. Front Oncol 2020; 10:1549. [PMID: 33072547 PMCID: PMC7533644 DOI: 10.3389/fonc.2020.01549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 07/20/2020] [Indexed: 11/24/2022] Open
Abstract
Glioblastoma, also known as glioblastoma multiforme (GBM), is the most malignant form of glioma and represents 81% of malignant brain and central nervous system (CNS) tumors. Like most cancers, GBM causes metabolic recombination to promote cell survival, proliferation, and invasion of cancer cells. In this study, we propose a method for constructing the metabolic subpathway activity score matrix to accurately identify abnormal targets of GBM metabolism. By integrating gene expression data from different sequencing methods, our method identified 25 metabolic subpathways that were significantly abnormal in the GBM patient population, and most of these subpathways have been reported to have an effect on GBM. Through the analysis of 25 GBM-related metabolic subpathways, we found that (S)-2,3-Epoxysqualene, which was at the central region of the sterol biosynthesis subpathway, may have a greater impact on the entire pathway, suggesting a potential high association with GBM. Analysis of CCK8 cell activity indicated that (S)-2,3-Epoxysqualene can indeed inhibit the activity of U87-MG cells. By flow cytometry, we demonstrated that (S)-2,3-Epoxysqualene not only arrested the U87-MG cell cycle in the G0/G1 phase but also induced cell apoptosis. These results confirm the reliability of our proposed metabolic subpathway identification method and suggest that (S)-2,3-Epoxysqualene has potential therapeutic value for GBM. In order to make the method more broadly applicable, we have developed an R system package crmSubpathway to perform disease-related metabolic subpathway identification and it is freely available on the GitHub (https://github.com/hanjunwei-lab/crmSubpathway).
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Affiliation(s)
- Xudong Han
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Donghua Wang
- Department of General Surgery, General Hospital of Heilongjiang Province Land Reclamation Bureau, Harbin, China
| | - Ping Zhao
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Chonghui Liu
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Yue Hao
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Lulu Chang
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Jiarui Zhao
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Wei Zhao
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Lili Mu
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Jinghua Wang
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China
| | - Hulun Li
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Qingfei Kong
- Department of Neurobiology, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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6
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Mingirulli N, Pyle A, Hathazi D, Alston CL, Kohlschmidt N, O'Grady G, Waddell L, Evesson F, Cooper SBT, Turner C, Duff J, Topf A, Yubero D, Jou C, Nascimento A, Ortez C, García‐Cazorla A, Gross C, O'Callaghan M, Santra S, Preece MA, Champion M, Korenev S, Chronopoulou E, Anirban M, Pierre G, McArthur D, Thompson K, Navas P, Ribes A, Tort F, Schlüter A, Pujol A, Montero R, Sarquella G, Lochmüller H, Jiménez‐Mallebrera C, Taylor RW, Artuch R, Kirschner J, Grünert SC, Roos A, Horvath R. Clinical presentation and proteomic signature of patients with TANGO2 mutations. J Inherit Metab Dis 2020; 43:297-308. [PMID: 31339582 PMCID: PMC7078914 DOI: 10.1002/jimd.12156] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
Abstract
Transport And Golgi Organization protein 2 (TANGO2) deficiency has recently been identified as a rare metabolic disorder with a distinct clinical and biochemical phenotype of recurrent metabolic crises, hypoglycemia, lactic acidosis, rhabdomyolysis, arrhythmias, and encephalopathy with cognitive decline. We report nine subjects from seven independent families, and we studied muscle histology, respiratory chain enzyme activities in skeletal muscle and proteomic signature of fibroblasts. All nine subjects carried autosomal recessive TANGO2 mutations. Two carried the reported deletion of exons 3 to 9, one homozygous, one heterozygous with a 22q11.21 microdeletion inherited in trans. The other subjects carried three novel homozygous (c.262C>T/p.Arg88*; c.220A>C/p.Thr74Pro; c.380+1G>A), and two further novel heterozygous (c.6_9del/p.Phe6del); c.11-13delTCT/p.Phe5del mutations. Immunoblot analysis detected a significant decrease of TANGO2 protein. Muscle histology showed mild variation of fiber diameter, no ragged-red/cytochrome c oxidase-negative fibers and a defect of multiple respiratory chain enzymes and coenzyme Q10 (CoQ10 ) in two cases, suggesting a possible secondary defect of oxidative phosphorylation. Proteomic analysis in fibroblasts revealed significant changes in components of the mitochondrial fatty acid oxidation, plasma membrane, endoplasmic reticulum-Golgi network and secretory pathways. Clinical presentation of TANGO2 mutations is homogeneous and clinically recognizable. The hemizygous mutations in two patients suggest that some mutations leading to allele loss are difficult to detect. A combined defect of the respiratory chain enzymes and CoQ10 with altered levels of several membrane proteins provides molecular insights into the underlying pathophysiology and may guide rational new therapeutic interventions.
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Affiliation(s)
- Nadja Mingirulli
- Department of Neuropediatrics and Muscle DisordersMedical Center – University of Freiburg, Faculty of MedicineBreisgauGermany
- Department of General PediatricsAdolescent Medicine and Neonatology, Medical Center – University of Freiburg, Faculty of MedicineBreisgauGermany
| | - Angela Pyle
- Wellcome Centre for Mitochondrial ResearchInstitute of Genetic Medicine, Newcastle UniversityNewcastle upon TyneUK
| | - Denisa Hathazi
- Biomedical Research DepartmentLeibniz‐Institut für Analytische Wissenschaften – ISAS – e.VDortmundGermany
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial ResearchInstitute of Neuroscience, Newcastle UniversityNewcastle upon TyneUK
| | | | - Gina O'Grady
- Kid's Neuroscience Centre, Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Leigh Waddell
- Kid's Neuroscience Centre, Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Frances Evesson
- Kid's Neuroscience Centre, Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Child and Adolescent HealthThe University of SydneySydneyNew South WalesAustralia
| | - Sandra B. T. Cooper
- Kid's Neuroscience Centre, Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Child and Adolescent HealthThe University of SydneySydneyNew South WalesAustralia
| | - Christian Turner
- Discipline of Child and Adolescent HealthThe University of SydneySydneyNew South WalesAustralia
- CardiologyThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Jennifer Duff
- Wellcome Centre for Mitochondrial ResearchInstitute of Genetic Medicine, Newcastle UniversityNewcastle upon TyneUK
| | - Ana Topf
- John Walton Muscular Dystrophy Research CentreInstitute of Genetic Medicine, Newcastle UniversityNewcastle upon TyneUK
| | - Delia Yubero
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Cristina Jou
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Andrés Nascimento
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Carlos Ortez
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Angels García‐Cazorla
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Claudia Gross
- Wellcome Centre for Mitochondrial ResearchInstitute of Neuroscience, Newcastle UniversityNewcastle upon TyneUK
| | - Maria O'Callaghan
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Saikat Santra
- Birmingham Women's and Children's NHS Foundation TrustBirminghamUK
| | | | | | - Sergei Korenev
- Department of Inherited DiseaseSt Thomas HospitalLondonUK
| | | | - Majumdar Anirban
- South West Regional Metabolic DepartmentBristol Royal Hospital for ChildrenBristolUK
| | - Germaine Pierre
- South West Regional Metabolic DepartmentBristol Royal Hospital for ChildrenBristolUK
| | - Daniel McArthur
- Center for Mendelian Genomics and Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts
- Analytic and Translational Genetics UnitMassachusetts General HospitalBostonMassachusetts
| | - Kyle Thompson
- Kid's Neuroscience Centre, Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Placido Navas
- Centro Andaluz de Biología del DesarrolloUníversidad Pablo de Olavide‐CSIC‐JA and CIBERER, Instituto de Salud Carlos IIIMadridSpain
| | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme – IBCServei de Bioquímica I Genètìca Molecular, Hospital Clínìc, IDIBAPS, CIBERERBarcelonaSpain
| | - Frederic Tort
- Secció d'Errors Congènits del Metabolisme – IBCServei de Bioquímica I Genètìca Molecular, Hospital Clínìc, IDIBAPS, CIBERERBarcelonaSpain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Institut d'Investìgacío Biomedíca de Bellvitge (IDIBELL), and Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos IIIMadridSpain
| | - Aurora Pujol
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
| | - Raquel Montero
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Georgia Sarquella
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle DisordersMedical Center – University of Freiburg, Faculty of MedicineBreisgauGermany
- Children's Hospital of Eastern Ontario Research Institute, University of OttawaOttawaOntarioCanada
- Division of Neurology, Department of MedicineThe Ottawa HospitalOttawaOntarioCanada
| | - Cecilia Jiménez‐Mallebrera
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Robert W. Taylor
- Kid's Neuroscience Centre, Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Rafael Artuch
- Department of Clinical Biochemistry, Genetics, Pediatric Neurology and Cardiology and BiobankInstitut de Recerca Sant Joan de Déu and CIBERER, Instituto de Salud Carlos III BarcelonaBarcelonaSpain
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle DisordersMedical Center – University of Freiburg, Faculty of MedicineBreisgauGermany
| | - Sarah C. Grünert
- Department of General PediatricsAdolescent Medicine and Neonatology, Medical Center – University of Freiburg, Faculty of MedicineBreisgauGermany
| | - Andreas Roos
- Biomedical Research DepartmentLeibniz‐Institut für Analytische Wissenschaften – ISAS – e.VDortmundGermany
- Pediatric NeurologyUniversity Children's Hospital, University of Duisburg‐Essen, Faculty of MedicineEssenGermany
| | - Rita Horvath
- Wellcome Centre for Mitochondrial ResearchInstitute of Genetic Medicine, Newcastle UniversityNewcastle upon TyneUK
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
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7
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Dekker LJM, Wu S, Jurriëns C, Mustafa DAN, Grevers F, Burgers PC, Sillevis Smitt PAE, Kros JM, Luider TM. Metabolic changes related to the IDH1 mutation in gliomas preserve TCA-cycle activity: An investigation at the protein level. FASEB J 2020; 34:3646-3657. [PMID: 31960518 DOI: 10.1096/fj.201902352r] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/26/2019] [Accepted: 12/05/2019] [Indexed: 12/17/2022]
Abstract
The discovery of the IDH1 R132H (IDH1 mut) mutation in low-grade glioma and the associated change in function of the IDH1 enzyme has increased the interest in glioma metabolism. In an earlier study, we found that changes in expression of genes involved in the aerobic glycolysis and the TCA cycle are associated with IDH1 mut. Here, we apply proteomics to FFPE samples of diffuse gliomas with or without IDH1 mutations, to map changes in protein levels associated with this mutation. We observed significant changes in the enzyme abundance associated with aerobic glycolysis, glutamate metabolism, and the TCA cycle in IDH1 mut gliomas. Specifically, the enzymes involved in the metabolism of glutamate, lactate, and enzymes involved in the conversion of α-ketoglutarate were increased in IDH1 mut gliomas. In addition, the bicarbonate transporter (SLC4A4) was increased in IDH1 mut gliomas, supporting the idea that a mechanism preventing intracellular acidification is active. We also found that enzymes that convert proline, valine, leucine, and isoleucine into glutamate were increased in IDH1 mut glioma. We conclude that in IDH1 mut glioma metabolism is rewired (increased input of lactate and glutamate) to preserve TCA-cycle activity in IDH1 mut gliomas.
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Affiliation(s)
- Lennard J M Dekker
- Department of Neurology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Suying Wu
- Department of Neurology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Cherise Jurriëns
- Department of Neurology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Dana A N Mustafa
- Department of Pathology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Frederieke Grevers
- Department of Pathology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Peter C Burgers
- Department of Neurology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Peter A E Sillevis Smitt
- Department of Neurology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
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8
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Xue L, Shuyan T, Xiaoli L, Zilong L, Qiuling F, Lining W, Yanqiu L, Li Y. Glomerular Proteomic Profiles in the NZB/W F1 Hybrid Mouse Model of Lupus Nephritis. Med Sci Monit 2019; 25:2122-2131. [PMID: 30900683 PMCID: PMC6698093 DOI: 10.12659/msm.914365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Lupus nephritis is one of the most serious complications of systemic lupus erythematosus (SLE) and is associated with patient mortality. This study aimed to investigate the proteomic profiles of the glomerulus in the NZB/W F1 hybrid mouse model of mild and severe lupus nephritis using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) combined with matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Material/Methods Female NZB/WF1 mice (n=60) at 28 weeks of age were divided into the mild proteinuria group (+1), the moderate proteinuria group (+2), and the severe proteinuria group (+3) using paper strip urine testing, and then later divided into a mild (≤1+) and severe (≥3+) proteinuria group to allow comparison of upregulation and down-regulation of proteins between the two groups. Renal glomeruli were isolated following renal perfusion with magnetic beads. Protein expression was determined by Western blot, immunohistochemistry, 2D-DIGE, and MALDI-TOF-MS. Results A total of 56 differentially expressed proteins were identified from 133 protein spots, of which 18 were upregulated and 23 were down-regulated between groups 1 and 2. Expression of the proteins Ras-related GTP-binding protein B (RRAGB), serine/threonine-protein kinase 1 (SMG1), angiopoietin 2 (ANGP2), methylmalonate semialdehyde (MMSA), and ATP beta chain (ATPB) were identified by Western blot and SMG1, ANGP2, and MMSA were identified by immunohistochemistry. Conclusions In a mouse model of lupus nephritis, expression of SMG1, MMSA, and ATPB were down-regulated, and RRAGB and ANGP2 were upregulated.
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Affiliation(s)
- Liu Xue
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Tian Shuyan
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Li Xiaoli
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Li Zilong
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Fan Qiuling
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Wang Lining
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Li Yanqiu
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Yao Li
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
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9
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Shaheen R, Maddirevula S, Ewida N, Alsahli S, Abdel-Salam GMH, Zaki MS, Tala SA, Alhashem A, Softah A, Al-Owain M, Alazami AM, Abadel B, Patel N, Al-Sheddi T, Alomar R, Alobeid E, Ibrahim N, Hashem M, Abdulwahab F, Hamad M, Tabarki B, Alwadei AH, Alhazzani F, Bashiri FA, Kentab A, Şahintürk S, Sherr E, Fregeau B, Sogati S, Alshahwan SAM, Alkhalifi S, Alhumaidi Z, Temtamy S, Aglan M, Otaify G, Girisha KM, Tulbah M, Seidahmed MZ, Salih MA, Abouelhoda M, Momin AA, Saffar MA, Partlow JN, Arold ST, Faqeih E, Walsh C, Alkuraya FS. Genomic and phenotypic delineation of congenital microcephaly. Genet Med 2019; 21:545-552. [PMID: 30214071 PMCID: PMC6986385 DOI: 10.1038/s41436-018-0140-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/09/2018] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Congenital microcephaly (CM) is an important birth defect with long term neurological sequelae. We aimed to perform detailed phenotypic and genomic analysis of patients with Mendelian forms of CM. METHODS Clinical phenotyping, targeted or exome sequencing, and autozygome analysis. RESULTS We describe 150 patients (104 families) with 56 Mendelian forms of CM. Our data show little overlap with the genetic causes of postnatal microcephaly. We also show that a broad definition of primary microcephaly -as an autosomal recessive form of nonsyndromic CM with severe postnatal deceleration of occipitofrontal circumference-is highly sensitive but has a limited specificity. In addition, we expand the overlap between primary microcephaly and microcephalic primordial dwarfism both clinically (short stature in >52% of patients with primary microcephaly) and molecularly (e.g., we report the first instance of CEP135-related microcephalic primordial dwarfism). We expand the allelic and locus heterogeneity of CM by reporting 37 novel likely disease-causing variants in 27 disease genes, confirming the candidacy of ANKLE2, YARS, FRMD4A, and THG1L, and proposing the candidacy of BPTF, MAP1B, CCNH, and PPFIBP1. CONCLUSION Our study refines the phenotype of CM, expands its genetics heterogeneity, and informs the workup of children born with this developmental brain defect.
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Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Saeed Al Tala
- Department of Pediatrics, Genetic Unit, Armed Forces Hospital Southern Region, Khamis Mushayt, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ameen Softah
- King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Basma Abadel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Al-Sheddi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Alomar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Muddathir Hamad
- Division of Pediatric Neurology, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ali H Alwadei
- Pediatric Neurology Department, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fahad Alhazzani
- Pediatrics Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fahad A Bashiri
- Division of Pediatric Neurology, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Amal Kentab
- Division of Pediatric Neurology, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Serdar Şahintürk
- Faculty of Medicine, Physiology Department, Bursa Uludag University, Bursa, Turkey
| | - Elliott Sherr
- Department of Neurology, University of California, San Francisco, California, USA
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, California, USA
| | - Samira Sogati
- Department of Medical Genetics, King Fahad General Hospital, Jeddah, Saudi Arabia
| | - Saad Ali M Alshahwan
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | | | | | - Samia Temtamy
- Clinical Genetics Department, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Mona Aglan
- Clinical Genetics Department, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Ghada Otaify
- Clinical Genetics Department, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Katta M Girisha
- Department of Medical Genetics Kasturba Medical College, Manipal University (currently Manipal Academy of Higher Education), Manipal, India
| | - Maha Tulbah
- Department of obstetrics and gynecology king Faisal specialist hospital and research center, Riyadh, Saudi Arabia
| | | | - Mustafa A Salih
- Division of Pediatric Neurology, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Afaque A Momin
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Muna Al Saffar
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Division of Genetics and Genomics, Department of Medicine, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jennifer N Partlow
- Division of Genetics and Genomics, Department of Medicine, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Eissa Faqeih
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Christopher Walsh
- Division of Genetics and Genomics, Department of Medicine, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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10
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Neinast MD, Jang C, Hui S, Murashige DS, Chu Q, Morscher RJ, Li X, Zhan L, White E, Anthony TG, Rabinowitz JD, Arany Z. Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids. Cell Metab 2019; 29:417-429.e4. [PMID: 30449684 PMCID: PMC6365191 DOI: 10.1016/j.cmet.2018.10.013] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 05/25/2018] [Accepted: 10/22/2018] [Indexed: 01/04/2023]
Abstract
Elevations in branched-chain amino acids (BCAAs) associate with numerous systemic diseases, including cancer, diabetes, and heart failure. However, an integrated understanding of whole-body BCAA metabolism remains lacking. Here, we employ in vivo isotopic tracing to systemically quantify BCAA oxidation in healthy and insulin-resistant mice. We find that most tissues rapidly oxidize BCAAs into the tricarboxylic acid (TCA) cycle, with the greatest quantity occurring in muscle, brown fat, liver, kidneys, and heart. Notably, pancreas supplies 20% of its TCA carbons from BCAAs. Genetic and pharmacologic suppression of branched-chain alpha-ketoacid dehydrogenase kinase, a clinically targeted regulatory kinase, induces BCAA oxidation primarily in skeletal muscle of healthy mice. While insulin acutely increases BCAA oxidation in cardiac and skeletal muscle, chronically insulin-resistant mice show blunted BCAA oxidation in adipose tissues and liver, shifting BCAA oxidation toward muscle. Together, this work provides a quantitative framework for understanding systemic BCAA oxidation in health and insulin resistance.
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Affiliation(s)
- Michael D Neinast
- Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Cholsoon Jang
- Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA; Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Sheng Hui
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Danielle S Murashige
- Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Qingwei Chu
- Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Raphael J Morscher
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Xiaoxuan Li
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Le Zhan
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Tracy G Anthony
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Joshua D Rabinowitz
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Zoltan Arany
- Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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11
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Bisen S, Kakhniashvili D, Johnson DL, Bukiya AN. Proteomic Analysis of Baboon Cerebral Artery Reveals Potential Pathways of Damage by Prenatal Alcohol Exposure. Mol Cell Proteomics 2019; 18:294-307. [PMID: 30413562 PMCID: PMC6356072 DOI: 10.1074/mcp.ra118.001047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/03/2018] [Indexed: 01/28/2023] Open
Abstract
Alcohol is one of the most widely misused substances in the world. Alcohol consumption by pregnant women often results in an array of fetal developmental abnormalities, but the damage to the fetus by alcohol remains poorly understood. The limited knowledge regarding the molecular targets of alcohol in the developing fetus constitutes one of the major obstacles in developing effective pharmacological interventions that could prevent fetal damage after alcohol consumption by pregnant women. The fetal cerebral artery is emerging as an important mediator of fetal cerebral damage by maternal alcohol drinking. In the present work, we conduct proteomics analysis of cerebral (basilar) artery lysates of near-term fetal baboons to search for protein targets of fetal alcohol exposure. Our study demonstrates that 3 episodes of binge alcohol exposure during the second trimester-equivalent of human pregnancy are sufficient to render profound changes in fetal cerebral artery proteome. These changes persisted, as they were detected in near-term fetuses. In particular, the relative abundance of 238 proteins differed significantly between control and alcohol-exposed fetuses. Enrichment analysis pointed at the group of metabolic activity proteins as a major class targeted by alcohol. Western blotting confirmed upregulation of the aldehyde dehydrogenase 6 family member A1 (ALDH6A1) in cerebral artery lysates from alcohol-exposed fetuses. This upregulation translated to greater ALDH activity of cerebral artery lysate of near-term fetuses following prenatal alcohol exposure when compared with controls.
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Affiliation(s)
- Shivantika Bisen
- Department of Pharmacology, College of Medicine, University of Tennessee Health Science Center, 71 S. Manassas St., #205, Memphis, TN, 38103
| | - David Kakhniashvili
- Proteomics Core, University of Tennessee Health Science Center, 71 S. Manassas St., #110, Memphis, TN, 38103
| | - Daniel L Johnson
- Molecular Bioinformatics Core, University of Tennessee Health Science Center, 71 S. Manassas St., #110, Memphis, TN, 38103
| | - Anna N Bukiya
- Department of Pharmacology, College of Medicine, University of Tennessee Health Science Center, 71 S. Manassas St., #205, Memphis, TN, 38103;.
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12
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Chen P, Wang F, Feng J, Zhou R, Chang Y, Liu J, Zhao Q. Co-expression network analysis identified six hub genes in association with metastasis risk and prognosis in hepatocellular carcinoma. Oncotarget 2018; 8:48948-48958. [PMID: 28430663 PMCID: PMC5564739 DOI: 10.18632/oncotarget.16896] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/21/2017] [Indexed: 12/31/2022] Open
Abstract
Hepatocellular carcinoma (HCC) has a high incidence and mortality worldwide, and its carcinogenesis and progression are influenced by a complex network of gene interactions. A weighted gene co-expression network was constructed to identify gene modules associated with the clinical traits in HCC (n = 214). Among the 13 modules, high correlation was only found between the red module and metastasis risk (classified by the HCC metastasis gene signature) (R2 = −0.74). Moreover, in the red module, 34 network hub genes for metastasis risk were identified, six of which (ABAT, AGXT, ALDH6A1, CYP4A11, DAO and EHHADH) were also hub nodes in the protein-protein interaction network of the module genes. Thus, a total of six hub genes were identified. In validation, all hub genes showed a negative correlation with the four-stage HCC progression (P for trend < 0.05) in the test set. Furthermore, in the training set, HCC samples with any hub gene lowly expressed demonstrated a higher recurrence rate and poorer survival rate (hazard ratios with 95% confidence intervals > 1). RNA-sequencing data of 142 HCC samples showed consistent results in the prognosis. Gene set enrichment analysis (GSEA) demonstrated that in the samples with any hub gene highly expressed, a total of 24 functional gene sets were enriched, most of which focused on amino acid metabolism and oxidation. In conclusion, co-expression network analysis identified six hub genes in association with HCC metastasis risk and prognosis, which might improve the prognosis by influencing amino acid metabolism and oxidation.
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Affiliation(s)
- Pengfei Chen
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.,Department of Gastroenterology, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Juerong Feng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Rui Zhou
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
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13
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Miyazaki T, Nagasaka H, Komatsu H, Inui A, Morioka I, Tsukahara H, Kaji S, Hirayama S, Miida T, Kondou H, Ihara K, Yagi M, Kizaki Z, Bessho K, Kodama T, Iijima K, Yorifuji T, Matsuzaki Y, Honda A. Serum Amino Acid Profiling in Citrin-Deficient Children Exhibiting Normal Liver Function During the Apparently Healthy Period. JIMD Rep 2018; 43:53-61. [PMID: 29654547 DOI: 10.1007/8904_2018_99] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Citrin (mitochondrial aspartate-glutamate transporter) deficiency causes the failures in both carbohydrate-energy metabolism and the urea cycle, and the alterations in the serum levels of several amino acids in the stages of newborn (NICCD) and adult (CTLN2). However, the clinical manifestations are resolved between the NICCD and CTLN2, but the reasons are still unclear. This study evaluated the serum amino acid profile in citrin-deficient children during the healthy stage. METHODS Using HPLC-MS/MS analysis, serum amino acids were evaluated among 20 citrin-deficient children aged 5-13 years exhibiting normal liver function and 35 age-matched healthy controls. RESULTS The alterations in serum amino acids characterized in the NICCD and CTLN2 stages were not observed in the citrin-deficient children. Amino acids involved in the urea cycle, including arginine, ornithine, citrulline, and aspartate, were comparable in the citrin-deficient children to the respective control levels, but serum urea was twofold higher, suggestive of a functional urea cycle. The blood sugar level was normal, but glucogenic amino acids and glutamine were significantly decreased in the citrin-deficient children compared to those in the controls. In addition, significant increases of ketogenic amino acids, branched-chain amino acids (BCAAs), a valine intermediate 3-hydroxyisobutyrate, and β-alanine were also found in the citrin-deficient children. CONCLUSION The profile of serum amino acids in the citrin-deficient children during the healthy stage showed different characteristics from the NICCD and CTLN2 stages, suggesting that the failures in both urea cycle function and energy metabolism might be compensated by amino acid metabolism. SYNOPSIS In the citrin-deficient children during the healthy stage, the characteristics of serum amino acids, including decrease of glucogenic amino acids, and increase of ketogenic amino acids, BCAAs, valine intermediate, and β-alanine, were found by comparison to the age-matched healthy control children, and it suggested that the characteristic alteration of serum amino acids may be resulted from compensation for energy metabolism and ammonia detoxification.
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Affiliation(s)
- Teruo Miyazaki
- Division of Gastroenterology, Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Ami, Ibaraki, Japan.
| | - Hironori Nagasaka
- Department of Pediatrics, Takarazuka City Hospital, Takarazuka, Hyogo, Japan
| | - Haruki Komatsu
- Department of Pediatrics, Toho University Sakura Medical Center, Chiba, Japan
| | - Ayano Inui
- Department of Pediatric Hepatology and Gastroenterology, Saiseikai Yokohamashi Tobu Hospital, Yokohama, Kanagawa, Japan
| | - Ichiro Morioka
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Hirokazu Tsukahara
- Department of Pediatrics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Shunsaku Kaji
- Department of Pediatrics, Tsuyama-Chuo Hospital, Tsuyama, Okayama, Japan
| | - Satoshi Hirayama
- Department of Clinical Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Hiroki Kondou
- Department of Pediatrics, Kindai University Nara Hospital, Nara, Japan
| | - Kenji Ihara
- Department of Pediatrics, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
- Department of Pediatrics, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Mariko Yagi
- Department of Pediatrics, Nikoniko House Medical and Welfare Center, Kobe, Hyogo, Japan
| | - Zenro Kizaki
- Department of Pediatrics, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Kazuhiko Bessho
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takahiro Kodama
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tohru Yorifuji
- Division of Pediatric Endocrinology and Metabolism, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - Yasushi Matsuzaki
- Division of Gastroenterology, Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Ami, Ibaraki, Japan
| | - Akira Honda
- Division of Gastroenterology, Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Ami, Ibaraki, Japan
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14
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Patel N, Khan AO, Alsahli S, Abdel-Salam G, Nowilaty SR, Mansour AM, Nabil A, Al-Owain M, Sogati S, Salih MA, Kamal AM, Alsharif H, Alsaif HS, Alzahrani SS, Abdulwahab F, Ibrahim N, Hashem M, Faquih T, Shah ZA, Abouelhoda M, Monies D, Dasouki M, Shaheen R, Wakil SM, Aldahmesh MA, Alkuraya FS. Genetic investigation of 93 families with microphthalmia or posterior microphthalmos. Clin Genet 2018; 93:1210-1222. [PMID: 29450879 DOI: 10.1111/cge.13239] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/12/2018] [Accepted: 02/12/2018] [Indexed: 01/24/2023]
Abstract
Microphthalmia is a developmental eye defect that is highly variable in severity and in its potential for systemic association. Despite the discovery of many disease genes in microphthalmia, at least 50% of patients remain undiagnosed genetically. Here, we describe a cohort of 147 patients (93 families) from our highly consanguineous population with various forms of microphthalmia (including the distinct entity of posterior microphthalmos) that were investigated using a next-generation sequencing multi-gene panel (i-panel) as well as whole exome sequencing and molecular karyotyping. A potentially causal mutation was identified in the majority of the cohort with microphthalmia (61%) and posterior microphthalmos (82%). The identified mutations (55 point mutations, 15 of which are novel) spanned 24 known disease genes, some of which have not or only very rarely been linked to microphthalmia (PAX6, SLC18A2, DSC3 and CNKSR1). Our study has also identified interesting candidate variants in 2 genes that have not been linked to human diseases (MYO10 and ZNF219), which we present here as novel candidates for microphthalmia. In addition to revealing novel phenotypic aspects of microphthalmia, this study expands its allelic and locus heterogeneity and highlights the need for expanded testing of patients with this condition.
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Affiliation(s)
- N Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - A O Khan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - S Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | | | - S R Nowilaty
- Vitreo-retinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - A M Mansour
- Department of Ophthalmology, American University of Beirut, Beirut, Lebanon
| | - A Nabil
- Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - M Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - S Sogati
- Department of Medical Genetics, King Fahad General Hospital, Jeddah, Saudi Arabia
| | - M A Salih
- Division of Pediatrics Neurology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - A M Kamal
- Department of Ophthalmology, Cairo University, Cairo, Egypt
| | - H Alsharif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - H S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - S S Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - F Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - N Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - M Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - T Faquih
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Z A Shah
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - M Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - D Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - M Dasouki
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - R Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - S M Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - M A Aldahmesh
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - F S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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15
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Gipson AB, Morton KJ, Rhee RJ, Simo S, Clayton JA, Perrett ME, Binkley CG, Jensen EL, Oakes DL, Rouhier MF, Rouhier KA. Disruptions in valine degradation affect seed development and germination in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1029-1039. [PMID: 28321931 PMCID: PMC5461199 DOI: 10.1111/tpj.13538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 05/20/2023]
Abstract
We have functionally characterized the role of two putative mitochondrial enzymes in valine degradation using insertional mutants. Prior to this study, the relationship between branched-chain amino acid degradation (named for leucine, valine and isoleucine) and seed development was limited to leucine catabolism. Using a reverse genetics approach, we show that disruptions in the mitochondrial valine degradation pathway affect seed development and germination in Arabidopsis thaliana. A null mutant of 3-hydroxyisobutyryl-CoA hydrolase (CHY4, At4g31810) resulted in an embryo lethal phenotype, while a null mutant of methylmalonate semialdehyde dehydrogenase (MMSD, At2g14170) resulted in seeds with wrinkled coats, decreased storage reserves, elevated valine and leucine, and reduced germination rates. These data highlight the unique contributions CHY4 and MMSD make to the overall growth and viability of plants. It also increases our knowledge of the role branched-chain amino acid catabolism plays in seed development and amino acid homeostasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Kerry A. Rouhier
- Kenyon College 200 N. College Rd, Gambier, OH 43022
- Doan University 1014 Boswell Ave, Crete, NE 68333
- Corresponding author: Kerry A. Rouhier, 200 N. College Rd, Gambier, OH 43022, USA tel: (740) 427-5359, fax: (740) 427-5731,
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16
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Enzymes involved in branched-chain amino acid metabolism in humans. Amino Acids 2017; 49:1005-1028. [DOI: 10.1007/s00726-017-2412-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/15/2017] [Indexed: 12/27/2022]
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17
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Chursa U, Nuñez-Durán E, Cansby E, Amrutkar M, Sütt S, Ståhlman M, Olsson BM, Borén J, Johansson ME, Bäckhed F, Johansson BR, Sihlbom C, Mahlapuu M. Overexpression of protein kinase STK25 in mice exacerbates ectopic lipid accumulation, mitochondrial dysfunction and insulin resistance in skeletal muscle. Diabetologia 2017; 60:553-567. [PMID: 27981357 PMCID: PMC6518105 DOI: 10.1007/s00125-016-4171-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/14/2016] [Indexed: 12/11/2022]
Abstract
AIMS/HYPOTHESIS Understanding the molecular networks controlling ectopic lipid deposition and insulin responsiveness in skeletal muscle is essential for developing new strategies to treat type 2 diabetes. We recently identified serine/threonine protein kinase 25 (STK25) as a critical regulator of liver steatosis, hepatic lipid metabolism and whole body glucose and insulin homeostasis. Here, we assessed the role of STK25 in control of ectopic fat storage and insulin responsiveness in skeletal muscle. METHODS Skeletal muscle morphology was studied by histological examination, exercise performance and insulin sensitivity were assessed by treadmill running and euglycaemic-hyperinsulinaemic clamp, respectively, and muscle lipid metabolism was analysed by ex vivo assays in Stk25 transgenic and wild-type mice fed a high-fat diet. Lipid accumulation and mitochondrial function were also studied in rodent myoblasts overexpressing STK25. Global quantitative phosphoproteomics was performed in skeletal muscle of Stk25 transgenic and wild-type mice fed a high-fat diet to identify potential downstream mediators of STK25 action. RESULTS We found that overexpression of STK25 in transgenic mice fed a high-fat diet increases intramyocellular lipid accumulation, impairs skeletal muscle mitochondrial function and sarcomeric ultrastructure, and induces perimysial and endomysial fibrosis, thereby reducing endurance exercise capacity and muscle insulin sensitivity. Furthermore, we observed enhanced lipid accumulation and impaired mitochondrial function in rodent myoblasts overexpressing STK25, demonstrating an autonomous action for STK25 within cells. Global phosphoproteomic analysis revealed alterations in the total abundance and phosphorylation status of different target proteins located predominantly to mitochondria and sarcomeric contractile elements in Stk25 transgenic vs wild-type muscle, respectively, providing a possible molecular mechanism for the observed phenotype. CONCLUSIONS/INTERPRETATION STK25 emerges as a new regulator of the complex interplay between lipid storage, mitochondrial energetics and insulin action in skeletal muscle, highlighting the potential of STK25 antagonists for type 2 diabetes treatment.
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Affiliation(s)
- Urszula Chursa
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Esther Nuñez-Durán
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Emmelie Cansby
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Manoj Amrutkar
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Silva Sütt
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Marcus Ståhlman
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Jan Borén
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria E Johansson
- Department of Physiology, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Bengt R Johansson
- Institute of Biomedicine, Electron Microscopy Unit, University of Gothenburg, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Margit Mahlapuu
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden.
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18
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Popławski P, Tohge T, Bogusławska J, Rybicka B, Tański Z, Treviño V, Fernie AR, Piekiełko-Witkowska A. Integrated transcriptomic and metabolomic analysis shows that disturbances in metabolism of tumor cells contribute to poor survival of RCC patients. Biochim Biophys Acta Mol Basis Dis 2016; 1863:744-752. [PMID: 28012969 DOI: 10.1016/j.bbadis.2016.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 10/20/2022]
Abstract
PURPOSE Cellular metabolism of renal cell carcinoma (RCC) tumors is disturbed. The clinical significance of these alterations is weakly understood. We aimed to find if changes in metabolic pathways contribute to survival of RCC patients. MATERIAL AND METHODS 35 RCC tumors and matched controls were used for metabolite profiling using gas chromatography-mass spectrometry and transcriptomic analysis with qPCR-arrays targeting the expression of 93 metabolic genes. The clinical significance of obtained data was validated on independent cohort of 468 RCC patients with median follow-up of 43.22months. RESULTS The levels of 31 metabolites were statistically significantly changed in RCC tumors compared with controls. The top altered metabolites included beta-alanine (+4.2-fold), glucose (+3.4-fold), succinate (-11.0-fold), myo-inositol (-4.6-fold), adenine (-4.2-fold), uracil (-3.7-fold), and hypoxanthine (-3.0-fold). These disturbances were associated with altered expression of 53 metabolic genes. ROC curve analysis revealed that the top metabolites discriminating between tumor and control samples included succinate (AUC=0.91), adenine (AUC=0.89), myo-inositol (AUC=0.87), hypoxanthine (AUC=0.85), urea (AUC=0.85), and beta-alanine (AUC=0.85). Poor survival of RCC patients correlated (p<0.0001) with altered expression of genes involved in metabolism of succinate (HR=2.7), purines (HR=2.4), glucose (HR=2.4), beta-alanine (HR=2.5), and myo-inositol (HR=1.9). CONCLUSIONS We found that changes in metabolism of succinate, beta-alanine, purines, glucose and myo-inositol correlate with poor survival of RCC patients.
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Affiliation(s)
- Piotr Popławski
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Warsaw, Poland
| | - Takayuki Tohge
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Joanna Bogusławska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Warsaw, Poland
| | - Beata Rybicka
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Warsaw, Poland
| | - Zbigniew Tański
- Masovian Specialist Hospital in Ostroleka, Ostroleka, Poland
| | - Victor Treviño
- Cátedra de Bioinformática, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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19
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Abstract
The three essential branched-chain amino acids (BCAAs), leucine, isoleucine and valine, share the first enzymatic steps in their metabolic pathways, including a reversible transamination followed by an irreversible oxidative decarboxylation to coenzyme-A derivatives. The respective oxidative pathways subsequently diverge and at the final steps yield acetyl- and/or propionyl-CoA that enter the Krebs cycle. Many disorders in these pathways are diagnosed through expanded newborn screening by tandem mass spectrometry. Maple syrup urine disease (MSUD) is the only disorder of the group that is associated with elevated body fluid levels of the BCAAs. Due to the irreversible oxidative decarboxylation step distal enzymatic blocks in the pathways do not result in the accumulation of amino acids, but rather to CoA-activated small carboxylic acids identified by gas chromatography mass spectrometry analysis of urine and are therefore classified as organic acidurias. Disorders in these pathways can present with a neonatal onset severe-, or chronic intermittent- or progressive forms. Metabolic instability and increased morbidity and mortality are shared between inborn errors in the BCAA pathways, while treatment options remain limited, comprised mainly of dietary management and in some cases solid organ transplantation.
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Affiliation(s)
- I Manoli
- Organic Acid Research Section, Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - C P Venditti
- Organic Acid Research Section, Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
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20
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Villani GRD, Gallo G, Scolamiero E, Salvatore F, Ruoppolo M. “Classical organic acidurias”: diagnosis and pathogenesis. Clin Exp Med 2016; 17:305-323. [DOI: 10.1007/s10238-016-0435-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/23/2016] [Indexed: 12/11/2022]
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21
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Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJ. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. eLife 2016; 5. [PMID: 27383050 PMCID: PMC4951191 DOI: 10.7554/elife.17670] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/20/2016] [Indexed: 12/20/2022] Open
Abstract
Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with metabolic plasticity and thus a selective advantage on different diets in the wild.
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Affiliation(s)
- Emma Watson
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | | | - Michael J Hoy
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Chi-Hua Li
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Timo Louisse
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Victoria Yao
- Department of Computer Science, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Akihiro Mori
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Amy D Holdorf
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States.,Simons Center for Data Analysis, Simons Foundation, New York, United States
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Albertha Jm Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
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22
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Hannibal L, Lysne V, Bjørke-Monsen AL, Behringer S, Grünert SC, Spiekerkoetter U, Jacobsen DW, Blom HJ. Biomarkers and Algorithms for the Diagnosis of Vitamin B12 Deficiency. Front Mol Biosci 2016; 3:27. [PMID: 27446930 PMCID: PMC4921487 DOI: 10.3389/fmolb.2016.00027] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/07/2016] [Indexed: 12/12/2022] Open
Abstract
Vitamin B12 (cobalamin, Cbl, B12) is an indispensable water-soluble micronutrient that serves as a coenzyme for cytosolic methionine synthase (MS) and mitochondrial methylmalonyl-CoA mutase (MCM). Deficiency of Cbl, whether nutritional or due to inborn errors of Cbl metabolism, inactivate MS and MCM leading to the accumulation of homocysteine (Hcy) and methylmalonic acid (MMA), respectively. In conjunction with total B12 and its bioactive protein-bound form, holo-transcobalamin (holo-TC), Hcy, and MMA are the preferred serum biomarkers utilized to determine B12 status. Clinically, vitamin B12 deficiency leads to neurological deterioration and megaloblastic anemia, and, if left untreated, to death. Subclinical vitamin B12 deficiency (usually defined as a total serum B12 of <200 pmol/L) presents asymptomatically or with rather subtle generic symptoms that oftentimes are mistakenly ascribed to unrelated disorders. Numerous studies have now established that serum vitamin B12 has limited diagnostic value as a stand-alone marker. Low serum levels of vitamin B12 not always represent deficiency, and likewise, severe functional deficiency of the micronutrient has been documented in the presence of normal and even high levels of serum vitamin B12. This review discusses the usefulness and limitations of current biomarkers of B12 status in newborn screening, infant and adult diagnostics, the algorithms utilized to diagnose B12 deficiency and unusual findings of vitamin B12 status in various human disorders.
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Affiliation(s)
- Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department for Pediatrics, Medical Center, University of Freiburg Freiburg, Germany
| | - Vegard Lysne
- Department of Clinical Sciences, University of Bergen Bergen, Norway
| | | | - Sidney Behringer
- Laboratory of Clinical Biochemistry and Metabolism, Department for Pediatrics, Medical Center, University of Freiburg Freiburg, Germany
| | - Sarah C Grünert
- Laboratory of Clinical Biochemistry and Metabolism, Department for Pediatrics, Medical Center, University of Freiburg Freiburg, Germany
| | - Ute Spiekerkoetter
- Laboratory of Clinical Biochemistry and Metabolism, Department for Pediatrics, Medical Center, University of Freiburg Freiburg, Germany
| | - Donald W Jacobsen
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Cleveland, OH, USA
| | - Henk J Blom
- Laboratory of Clinical Biochemistry and Metabolism, Department for Pediatrics, Medical Center, University of Freiburg Freiburg, Germany
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23
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Jurnak F. The Pivotal Role of Aldehyde Toxicity in Autism Spectrum Disorder: The Therapeutic Potential of Micronutrient Supplementation. Nutr Metab Insights 2016; 8:57-77. [PMID: 27330305 PMCID: PMC4910734 DOI: 10.4137/nmi.s29531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/20/2016] [Accepted: 03/30/2016] [Indexed: 12/11/2022] Open
Abstract
Autism spectrum disorder (ASD) is characterized by social and communication impairments as well as by restricted, repetitive patterns of behavior and interests. Genomic studies have not revealed dominant genetic errors common to all forms of ASD. So ASD is assumed to be a complex disorder due to mutations in hundreds of common variants. Other theories argue that spontaneous DNA mutations and/or environmental factors contribute to as much as 50% of ASD. In reviewing potential genetic linkages between autism and alcoholism, it became apparent that all theories of ASD are consistent with aldehyde toxicity, in which endogenous and exogenous aldehydes accumulate as a consequence of mutations in key enzymes. Aldehyde toxicity is characterized by cell-localized, micronutrient deficiencies in sulfur-containing antioxidants, thiamine (B1), pyridoxine (B6), folate, Zn2+, possibly Mg2+, and retinoic acid, causing oxidative stress and a cascade of metabolic disturbances. Aldehydes also react with selective cytosolic and membrane proteins in the cell of origin; then some types migrate to damage neighboring cells. Reactive aldehydes also form adducts with DNA, selectively mutating bases and inducing strand breakage. This article reviews the relevant genomic, biochemical, and nutritional literature, which supports the central hypothesis that most ASD symptoms are consistent with symptoms of aldehyde toxicity. The hypothesis represents a paradigm shift in thinking and has profound implications for clinical detection, treatment, and even prevention of ASD. Insight is offered as to which neurologically afflicted children might successfully be treated with micronutrients and which children are unlikely to be helped. The aldehyde toxicity hypothesis likely applies to other neurological disorders.
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Affiliation(s)
- Frances Jurnak
- Emerita Professor, Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, CA, USA
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24
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Molloy A, Pangilinan F, Mills J, Shane B, O’Neill M, McGaughey D, Velkova A, Abaan H, Ueland P, McNulty H, Ward M, Strain J, Cunningham C, Casey M, Cropp C, Kim Y, Bailey-Wilson J, Wilson A, Brody L. A Common Polymorphism in HIBCH Influences Methylmalonic Acid Concentrations in Blood Independently of Cobalamin. Am J Hum Genet 2016; 98:869-882. [PMID: 27132595 DOI: 10.1016/j.ajhg.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 03/08/2016] [Indexed: 12/20/2022] Open
Abstract
Methylmalonic acid (MMA) is a by-product of propionic acid metabolism through the vitamin B12 (cobalamin)-dependent enzyme methylmalonyl CoA mutase. Elevated MMA concentrations are a hallmark of several inborn errors of metabolism and indicators of cobalamin deficiency in older persons. In a genome-wide analysis of 2,210 healthy young Irish adults (median age 22 years) we identified a strong association of plasma MMA with SNPs in 3-hydroxyisobutyryl-CoA hydrolase (HIBCH, p = 8.42 × 10(-89)) and acyl-CoA synthetase family member 3 (ACSF3, p = 3.48 × 10(-19)). These loci accounted for 12% of the variance in MMA concentration. The most strongly associated SNP (HIBCH rs291466; c:2T>C) causes a missense change of the initiator methionine codon (minor-allele frequency = 0.43) to threonine. Surprisingly, the resulting variant, p.Met1?, is associated with increased expression of HIBCH mRNA and encoded protein. These homozygotes had, on average, 46% higher MMA concentrations than methionine-encoding homozygotes in young adults with generally low MMA concentrations (0.17 [0.14-0.21] μmol/L; median [25(th)-75(th) quartile]). The association between MMA levels and HIBCH rs291466 was highly significant in a replication cohort of 1,481 older individuals (median age 79 years) with elevated plasma MMA concentrations (0.34 [0.24-0.51] μmol/L; p = 4.0 × 10(-26)). In a longitudinal study of 185 pregnant women and their newborns, the association of this SNP remained significant across the gestational trimesters and in newborns. HIBCH is unique to valine catabolism. Studies evaluating flux through the valine catabolic pathway in humans should account for these variants. Furthermore, this SNP could help resolve equivocal clinical tests where plasma MMA values have been used to diagnose cobalamin deficiency.
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Sawyer SL, Hartley T, Dyment DA, Beaulieu CL, Schwartzentruber J, Smith A, Bedford HM, Bernard G, Bernier FP, Brais B, Bulman DE, Warman Chardon J, Chitayat D, Deladoëy J, Fernandez BA, Frosk P, Geraghty MT, Gerull B, Gibson W, Gow RM, Graham GE, Green JS, Heon E, Horvath G, Innes AM, Jabado N, Kim RH, Koenekoop RK, Khan A, Lehmann OJ, Mendoza-Londono R, Michaud JL, Nikkel SM, Penney LS, Polychronakos C, Richer J, Rouleau GA, Samuels ME, Siu VM, Suchowersky O, Tarnopolsky MA, Yoon G, Zahir FR, Majewski J, Boycott KM. Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care. Clin Genet 2015; 89:275-84. [PMID: 26283276 PMCID: PMC5053223 DOI: 10.1111/cge.12654] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/14/2015] [Accepted: 08/14/2015] [Indexed: 12/17/2022]
Abstract
An accurate diagnosis is an integral component of patient care for children with rare genetic disease. Recent advances in sequencing, in particular whole‐exome sequencing (WES), are identifying the genetic basis of disease for 25–40% of patients. The diagnostic rate is probably influenced by when in the diagnostic process WES is used. The Finding Of Rare Disease GEnes (FORGE) Canada project was a nation‐wide effort to identify mutations for childhood‐onset disorders using WES. Most children enrolled in the FORGE project were toward the end of the diagnostic odyssey. The two primary outcomes of FORGE were novel gene discovery and the identification of mutations in genes known to cause disease. In the latter instance, WES identified mutations in known disease genes for 105 of 362 families studied (29%), thereby informing the impact of WES in the setting of the diagnostic odyssey. Our analysis of this dataset showed that these known disease genes were not identified prior to WES enrollment for two key reasons: genetic heterogeneity associated with a clinical diagnosis and atypical presentation of known, clinically recognized diseases. What is becoming increasingly clear is that WES will be paradigm altering for patients and families with rare genetic diseases.
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Affiliation(s)
- S L Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - C L Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - A Smith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - H M Bedford
- Genetics Program, North York General Hospital, Toronto, Canada
| | - G Bernard
- Departments of Pediatrics, Neurology and Neurosurgery, Division of Pediatric Neurology, Montréal Children's Hospital, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - F P Bernier
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B Brais
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - D Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - J Deladoëy
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - B A Fernandez
- Disciplines of Genetics and Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - P Frosk
- Departments of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada
| | - M T Geraghty
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - B Gerull
- Cardiac Sciences and Medical Genetics, University of Calgary, Calgary, Canada
| | - W Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - R M Gow
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - G E Graham
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J S Green
- Disciplines of Genetics and Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - E Heon
- Department of Ophthalmology and Vision Sciences, Program of Genetics and Genomic Biology, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G Horvath
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - A M Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - N Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - R H Kim
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada
| | - R K Koenekoop
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Canada
| | - A Khan
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - O J Lehmann
- Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, Canada
| | - R Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - J L Michaud
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - S M Nikkel
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - L S Penney
- Medical Genetics, IWK Health Centre, Halifax, Canada
| | - C Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - J Richer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - G A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - M E Samuels
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - V M Siu
- Division of Medical Genetics, Department of Pediatrics, University of Western Ontario, London, Canada
| | - O Suchowersky
- Departments of Medicine, Medical Genetics, and Pediatrics, University of Alberta, Edmonton, Canada
| | - M A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - G Yoon
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - F R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | | | - J Majewski
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
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Oren Y, Nachshon A, Frishberg A, Wilentzik R, Gat-Viks I. Linking traits based on their shared molecular mechanisms. eLife 2015; 4. [PMID: 25781485 PMCID: PMC4362207 DOI: 10.7554/elife.04346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 02/20/2015] [Indexed: 12/29/2022] Open
Abstract
There is growing recognition that co-morbidity and co-occurrence of disease traits are often determined by shared genetic and molecular mechanisms. In most cases, however, the specific mechanisms that lead to such trait-trait relationships are yet unknown. Here we present an analysis of a broad spectrum of behavioral and physiological traits together with gene-expression measurements across genetically diverse mouse strains. We develop an unbiased methodology that constructs potentially overlapping groups of traits and resolves their underlying combination of genetic loci and molecular mechanisms. For example, our method predicts that genetic variation in the Klf7 gene may influence gene transcripts in bone marrow-derived myeloid cells, which in turn affect 17 behavioral traits following morphine injection; this predicted effect of Klf7 is consistent with an in vitro perturbation of Klf7 in bone marrow cells. Our analysis demonstrates the utility of studying hidden causative mechanisms that lead to relationships between complex traits.
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Affiliation(s)
- Yael Oren
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Aharon Nachshon
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amit Frishberg
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Roni Wilentzik
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Irit Gat-Viks
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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27
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FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. Am J Hum Genet 2014; 94:809-17. [PMID: 24906018 DOI: 10.1016/j.ajhg.2014.05.003] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 01/08/2023] Open
Abstract
Inherited monogenic disease has an enormous impact on the well-being of children and their families. Over half of the children living with one of these conditions are without a molecular diagnosis because of the rarity of the disease, the marked clinical heterogeneity, and the reality that there are thousands of rare diseases for which causative mutations have yet to be identified. It is in this context that in 2010 a Canadian consortium was formed to rapidly identify mutations causing a wide spectrum of pediatric-onset rare diseases by using whole-exome sequencing. The FORGE (Finding of Rare Disease Genes) Canada Consortium brought together clinicians and scientists from 21 genetics centers and three science and technology innovation centers from across Canada. From nation-wide requests for proposals, 264 disorders were selected for study from the 371 submitted; disease-causing variants (including in 67 genes not previously associated with human disease; 41 of these have been genetically or functionally validated, and 26 are currently under study) were identified for 146 disorders over a 2-year period. Here, we present our experience with four strategies employed for gene discovery and discuss FORGE's impact in a number of realms, from clinical diagnostics to the broadening of the phenotypic spectrum of many diseases to the biological insight gained into both disease states and normal human development. Lastly, on the basis of this experience, we discuss the way forward for rare-disease genetic discovery both in Canada and internationally.
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