1
|
Liu YX, Ding MH, Sheng Y, Sun MF, Liu L, Zhang Y. Doubly bi-allelic variants of MTHFR and MTHFD1 in a Chinese patient with hyperhomocysteinemia and failure of folic acid therapy. Front Genet 2023; 13:964990. [PMID: 36685872 PMCID: PMC9845700 DOI: 10.3389/fgene.2022.964990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/30/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Hyperhomocysteinemia (HHcy) is a risk factor for thromboembolic disease. Defects in one-carbon metabolism (1-CM)-related genes, such as methylenetetrahydrofolate reductase (MTHFR), methylenetetrahydrofolate dehydrogenase, cyclohydrolase, and formyltetrahydrofolate synthetase 1 (MTHFD1), can cause HHcy and may also affect the efficacy of folic acid therapy. The details of mechanisms are yet to be further investigated. Method: We described a Chinese family with hereditary HHcy. The proband suffered from severe thromboembolic disease and experienced failure of folic acid therapy. Two sons of the proband were also diagnosed with HHcy but were sensitive to folic acid therapy. Whole-exome sequencing (WES) was conducted to evaluate the genetic lesion of this family. Results: Compound heterozygous variants (a common polymorphism, p. A222V, and a novel variant, p. C631*fs*1) of the MTHFR gene and a homozygous missense variant (p. K134R) of the MTHFD1 gene were identified in the proband. The two sons, with successful intervention, only harbored the homozygous p. A222V variant of the MTHFR gene. Conclusion: The clinical manifestations and genetic research synergistically confirmed the diagnosis of HHcy and clarified the failure of folic acid therapy in the proband caused by doubly bi-allelic variants of the MTHFR and MTHFD1 genes. Our study increased our understanding of the molecular basis of 1-CM-related gene defects on folic acid therapy in HHcy.
Collapse
Affiliation(s)
- Yu-Xing Liu
- Department of Neurology, Xuzhou Central Hospital, Xuzhou, China,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Man-Hua Ding
- Department of Radiotherapy, Xuzhou Cancer Hospital, Xuzhou, China
| | - Yue Sheng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Meng-Fei Sun
- Department of Neurology, Xuzhou Central Hospital, Xuzhou, China
| | - Lv Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China,*Correspondence: Lv Liu, ; Yang Zhang,
| | - Yang Zhang
- Department of Neurology, Xuzhou Central Hospital, Xuzhou, China,*Correspondence: Lv Liu, ; Yang Zhang,
| |
Collapse
|
2
|
Bezerra GA, Holenstein A, Foster WR, Xie B, Hicks KG, Bürer C, Lutz S, Mukherjee A, Sarkar D, Bhattacharya D, Rutter J, Talukdar A, Brown PJ, Luo M, Shi L, Froese DS, Yue WW. Identification of small molecule allosteric modulators of 5,10-methylenetetrahydrofolate reductase (MTHFR) by targeting its unique regulatory domain. Biochimie 2021; 183:100-107. [PMID: 33476699 PMCID: PMC8040968 DOI: 10.1016/j.biochi.2021.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
Abstract
The folate and methionine cycles, constituting one-carbon metabolism, are critical pathways for cell survival. Intersecting these two cycles, 5,10-methylenetetrahydrofolate reductase (MTHFR) directs one-carbon units from the folate to methionine cycle, to be exclusively used for methionine and S-adenosylmethionine (AdoMet) synthesis. MTHFR deficiency and upregulation result in diverse disease states, rendering it an attractive drug target. The activity of MTHFR is inhibited by the binding of AdoMet to an allosteric regulatory domain distal to the enzyme's active site, which we have previously identified to constitute a novel fold with a druggable pocket. Here, we screened 162 AdoMet mimetics using differential scanning fluorimetry, and identified 4 compounds that stabilized this regulatory domain. Three compounds were sinefungin analogues, closely related to AdoMet and S-adenosylhomocysteine (AdoHcy). The strongest thermal stabilisation was provided by (S)-SKI-72, a potent inhibitor originally developed for protein arginine methyltransferase 4 (PRMT4). Using surface plasmon resonance, we confirmed that (S)-SKI-72 binds MTHFR via its allosteric domain with nanomolar affinity. Assay of MTHFR activity in the presence of (S)-SKI-72 demonstrates inhibition of purified enzyme with sub-micromolar potency and endogenous MTHFR from HEK293 cell lysate in the low micromolar range, both of which are lower than AdoMet. Nevertheless, unlike AdoMet, (S)-SKI-72 is unable to completely abolish MTHFR activity, even at very high concentrations. Combining binding assays, kinetic characterization and compound docking, this work indicates the regulatory domain of MTHFR can be targeted by small molecules and presents (S)-SKI-72 as an excellent candidate for development of MTHFR inhibitors.
Collapse
Affiliation(s)
- Gustavo A Bezerra
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Alexander Holenstein
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - William R Foster
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Bing Xie
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, USA
| | - Kevin G Hicks
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Seraina Lutz
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Ayan Mukherjee
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Dipika Sarkar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Debomita Bhattacharya
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, USA
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland.
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK.
| |
Collapse
|
3
|
Bhatia M, Thakur J, Suyal S, Oniel R, Chakraborty R, Pradhan S, Sharma M, Sengupta S, Laxman S, Masakapalli SK, Bachhawat AK. Allosteric inhibition of MTHFR prevents futile SAM cycling and maintains nucleotide pools in one-carbon metabolism. J Biol Chem 2020; 295:16037-16057. [PMID: 32934008 PMCID: PMC7681022 DOI: 10.1074/jbc.ra120.015129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/12/2020] [Indexed: 01/05/2023] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) links the folate cycle to the methionine cycle in one-carbon metabolism. The enzyme is known to be allosterically inhibited by SAM for decades, but the importance of this regulatory control to one-carbon metabolism has never been adequately understood. To shed light on this issue, we exchanged selected amino acid residues in a highly conserved stretch within the regulatory region of yeast MTHFR to create a series of feedback-insensitive, deregulated mutants. These were exploited to investigate the impact of defective allosteric regulation on one-carbon metabolism. We observed a strong growth defect in the presence of methionine. Biochemical and metabolite analysis revealed that both the folate and methionine cycles were affected in these mutants, as was the transsulfuration pathway, leading also to a disruption in redox homeostasis. The major consequences, however, appeared to be in the depletion of nucleotides. 13C isotope labeling and metabolic studies revealed that the deregulated MTHFR cells undergo continuous transmethylation of homocysteine by methyltetrahydrofolate (CH3THF) to form methionine. This reaction also drives SAM formation and further depletes ATP reserves. SAM was then cycled back to methionine, leading to futile cycles of SAM synthesis and recycling and explaining the necessity for MTHFR to be regulated by SAM. The study has yielded valuable new insights into the regulation of one-carbon metabolism, and the mutants appear as powerful new tools to further dissect out the intersection of one-carbon metabolism with various pathways both in yeasts and in humans.
Collapse
Affiliation(s)
- Muskan Bhatia
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Jyotika Thakur
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Shradha Suyal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Ruchika Oniel
- Institute for Stem Cell Science and Regenerative Medicine (inStem), NCBS-TIFR Campus, Bangalore, India
| | - Rahul Chakraborty
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shalini Pradhan
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Shantanu Sengupta
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), NCBS-TIFR Campus, Bangalore, India
| | - Shyam Kumar Masakapalli
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Anand Kumar Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India.
| |
Collapse
|
4
|
Massadeh S, Umair M, Alaamery M, Alfadhel M. A Novel Homozygous Non-sense Mutation in the Catalytic Domain of MTHFR Causes Severe 5,10-Methylenetetrahydrofolate Reductase Deficiency. Front Neurol 2019; 10:411. [PMID: 31068897 PMCID: PMC6491806 DOI: 10.3389/fneur.2019.00411] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Severe 5,10-methylenetetrahydrofolate reductase (MTHFR) deficiency is a heterogeneous metabolic disorder inherited in an autosomal recessive manner. Pathogenic mutations in MTHFR gene have been associated with severe MTHFR deficiency. The clinical presentation of MTHFR deficiency is highly variable and associated with several neurological anomalies. Methods: Direct whole-exome sequencing (WES) was performed in all the five available individuals from the family, including the affected individual (III-7) using standard procedures. Results: We observed a proband (III-7) with an abnormality in the cerebral white matter, apnoea, and microcephaly. WES analysis identified a novel homozygous non-sense mutation (c.154C>T; p.Arg52*) in MTHFR gene that segregated with the disease phenotype within the family. Conclusion: We identified a novel non-sense mutation in MTHFR gene in a single Egyptian family with severe MTHFR deficiency. The present investigation is clinically important, as it adds to the growing list of MTHFR mutations, which might help in genetic counseling of families of affected children and proper genotype-phenotype correlation.
Collapse
Affiliation(s)
- Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Joint Centers of Excellence Program, KACST-BWH/Harvard Center of Excellence for Biomedicine, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Joint Centers of Excellence Program, KACST-BWH/Harvard Center of Excellence for Biomedicine, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| |
Collapse
|
5
|
Froese DS, Kopec J, Rembeza E, Bezerra GA, Oberholzer AE, Suormala T, Lutz S, Chalk R, Borkowska O, Baumgartner MR, Yue WW. Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition. Nat Commun 2018; 9:2261. [PMID: 29891918 DOI: 10.1038/s41467-018-04735-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/16/2018] [Indexed: 11/08/2022] Open
Abstract
The folate and methionine cycles are crucial for biosynthesis of lipids, nucleotides and proteins, and production of the methyl donor S-adenosylmethionine (SAM). 5,10-methylenetetrahydrofolate reductase (MTHFR) represents a key regulatory connection between these cycles, generating 5-methyltetrahydrofolate for initiation of the methionine cycle, and undergoing allosteric inhibition by its end product SAM. Our 2.5 Å resolution crystal structure of human MTHFR reveals a unique architecture, appending the well-conserved catalytic TIM-barrel to a eukaryote-only SAM-binding domain. The latter domain of novel fold provides the predominant interface for MTHFR homo-dimerization, positioning the N-terminal serine-rich phosphorylation region near the C-terminal SAM-binding domain. This explains how MTHFR phosphorylation, identified on 11 N-terminal residues (16 in total), increases sensitivity to SAM binding and inhibition. Finally, we demonstrate that the 25-amino-acid inter-domain linker enables conformational plasticity and propose it to be a key mediator of SAM regulation. Together, these results provide insight into the molecular regulation of MTHFR. The human enzyme MTHFR links the folate and methionine cycles, which are essential for the biosynthesis of nucleotides and proteins. Here, the authors present the crystal structure and biochemical analysis of human MTHFR, providing molecular insights into its function and regulation in higher eukaryotes.
Collapse
|
6
|
Froese DS, Huemer M, Suormala T, Burda P, Coelho D, Guéant J, Landolt MA, Kožich V, Fowler B, Baumgartner MR. Mutation Update and Review of Severe Methylenetetrahydrofolate Reductase Deficiency. Hum Mutat 2016; 37:427-38. [DOI: 10.1002/humu.22970] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 02/03/2016] [Indexed: 11/07/2022]
|
7
|
Huemer M, Mulder-Bleile R, Burda P, Froese DS, Suormala T, Zeev BB, Chinnery PF, Dionisi-Vici C, Dobbelaere D, Gökcay G, Demirkol M, Häberle J, Lossos A, Mengel E, Morris AA, Niezen-Koning KE, Plecko B, Parini R, Rokicki D, Schiff M, Schimmel M, Sewell AC, Sperl W, Spiekerkoetter U, Steinmann B, Taddeucci G, Trejo-Gabriel-Galán JM, Trefz F, Tsuji M, Vilaseca MA, von Kleist-Retzow JC, Walker V, Zeman J, Baumgartner MR, Fowler B. Clinical pattern, mutations and in vitro residual activity in 33 patients with severe 5, 10 methylenetetrahydrofolate reductase (MTHFR) deficiency. J Inherit Metab Dis 2016; 39:115-24. [PMID: 26025547 PMCID: PMC6551224 DOI: 10.1007/s10545-015-9860-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 01/13/2023]
Abstract
BACKGROUND Severe methylenetetrahydrofolate reductase (MTHFR) deficiency is a rare inborn defect disturbing the remethylation of homocysteine to methionine (<200 reported cases). This retrospective study evaluates clinical, biochemical genetic and in vitro enzymatic data in a cohort of 33 patients. METHODS Clinical, biochemical and treatment data was obtained from physicians by using a questionnaire. MTHFR activity was measured in primary fibroblasts; genomic DNA was extracted from cultured fibroblasts. RESULTS Thirty-three patients (mean age at follow-up 11.4 years; four deceased; median age at first presentation 5 weeks; 17 females) were included. Patients with very low (<1.5%) mean control values of enzyme activity (n = 14) presented earlier and with a pattern of feeding problems, encephalopathy, muscular hypotonia, neurocognitive impairment, apnoea, hydrocephalus, microcephaly and epilepsy. Patients with higher (>1.7-34.8%) residual enzyme activity had mainly psychiatric symptoms, mental retardation, myelopathy, ataxia and spasticity. Treatment with various combinations of betaine, methionine, folate and cobalamin improved the biochemical and clinical phenotype. During the disease course, patients with very low enzyme activity showed a progression of feeding problems, neurological symptoms, mental retardation, and psychiatric disease while in patients with higher residual enzyme activity, myelopathy, ataxia and spasticity increased. All other symptoms remained stable or improved in both groups upon treatment as did brain imaging in some cases. No clear genotype-phenotype correlation was obvious. DISCUSSION MTHFR deficiency is a severe disease primarily affecting the central nervous system. Age at presentation and clinical pattern are correlated with residual enzyme activity. Treatment alleviates biochemical abnormalities and clinical symptoms partially.
Collapse
Affiliation(s)
- Martina Huemer
- Division of Metabolism and Children's Research Center, University Childrens' Hospital Zürich, Zürich, Switzerland
- radiz - Rare Disease Initiative Zürich, Clinical Research Priority Program, University of Zürich, Zürich, Switzerland
- Department of Paediatrics, Landeskrankenhaus Bregenz, Bregenz, Austria
| | | | - Patricie Burda
- Division of Metabolism and Children's Research Center, University Childrens' Hospital Zürich, Zürich, Switzerland
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Childrens' Hospital Zürich, Zürich, Switzerland
| | - Terttu Suormala
- Division of Metabolism and Children's Research Center, University Childrens' Hospital Zürich, Zürich, Switzerland
| | - Bruria Ben Zeev
- Edmond and Lilly Safra Pediatric Hospital, Sheba Med Center and Sackler School of Medicine Tel Aviv, Tel Aviv, Israel
| | - Patrick F Chinnery
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Dries Dobbelaere
- Centre de Référence Maladies Héréditaires du Métabolisme de l'enfant et de l'adulte, Hôpital Jeanne de Flandre, Lille, France
| | - Gülden Gökcay
- Istanbul Medical Faculty, Children's Hospital, Pediatric Nutrition and Metabolism, Istanbul University, Istanbul, Turkey
| | - Mübeccel Demirkol
- Istanbul Medical Faculty, Children's Hospital, Pediatric Nutrition and Metabolism, Istanbul University, Istanbul, Turkey
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Childrens' Hospital Zürich, Zürich, Switzerland
| | - Alexander Lossos
- Villa metabolica, Center for Pediatric and Adolescent Medicine, MC Johannes-Gutenberg-University Mainz, Mainz, Germany
| | - Eugen Mengel
- Villa metabolica, Center for Pediatric and Adolescent Medicine, MC Johannes-Gutenberg-University Mainz, Mainz, Germany
| | - Andrew A Morris
- Willink Unit, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, Manchester, UK
| | - Klary E Niezen-Koning
- Laboratory Metabolic Diseases, University Medical Center Groningen, Groningen, The Netherlands
| | - Barbara Plecko
- radiz - Rare Disease Initiative Zürich, Clinical Research Priority Program, University of Zürich, Zürich, Switzerland
- Division of Child Neurology and Children's Research Center, University Children's Hospital Zürich, Zürich, Switzerland
| | - Rossella Parini
- Unit for rare metabolic diseases, Department of Pediatrics, Fondazione MBBM/San Gerardo Hospital, Monza, Italy
| | - Dariusz Rokicki
- Department of Pediatrics, Nutrition and Metabolic Diseases, The Children's Memorial Health Institute, Warsaw, Poland
| | - Manuel Schiff
- Reference Center for Inborn Errors of Metabolism, Hôpital Robert Debré, APHP, INSERM U1141 and Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Adrian C Sewell
- Department of Paediatrics, University Children's Hospital, Frankfurt am Main, Germany
- Bioscientia Institute for Laboratory Diagnostics, Ingelheim, Germany
| | - Wolfgang Sperl
- Department of Pediatrics, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Ute Spiekerkoetter
- Department of General Pediatrics and Adolescent Medicine, University Children's Hospital, Freiburg, Germany
| | - Beat Steinmann
- Division of Metabolism and Children's Research Center, University Childrens' Hospital Zürich, Zürich, Switzerland
| | - Grazia Taddeucci
- Department of Pediatrics, Section of Paediatric Neurology, University of Pisa, Pisa, Italy
| | | | - Friedrich Trefz
- Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
| | - Megumi Tsuji
- Department of Neuroscience, Jikei University School of Medicine, Minato, Tokyo, Japan
| | - María Antònia Vilaseca
- Laboratori de Malalties Metabòliques Hereditàrias, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Valerie Walker
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Jiri Zeman
- Department of Paediatrics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Childrens' Hospital Zürich, Zürich, Switzerland.
- radiz - Rare Disease Initiative Zürich, Clinical Research Priority Program, University of Zürich, Zürich, Switzerland.
| | - Brian Fowler
- Division of Metabolism and Children's Research Center, University Childrens' Hospital Zürich, Zürich, Switzerland.
- University Childrens' Hospital Basel (UKBB), Basel, Switzerland.
| |
Collapse
|
8
|
Burda P, Schäfer A, Suormala T, Rummel T, Bürer C, Heuberger D, Frapolli M, Giunta C, Sokolová J, Vlášková H, Kožich V, Koch HG, Fowler B, Froese DS, Baumgartner MR. Insights into Severe 5,10-Methylenetetrahydrofolate Reductase Deficiency: Molecular Genetic and Enzymatic Characterization of 76 Patients. Hum Mutat 2015; 36:611-21. [DOI: 10.1002/humu.22779] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/20/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Patricie Burda
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Alexandra Schäfer
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Terttu Suormala
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Till Rummel
- Department of Pediatrics; University Hospital; Münster D-48149 Germany
| | - Céline Bürer
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Dorothea Heuberger
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Michele Frapolli
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Cecilia Giunta
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Jitka Sokolová
- Institute of Inherited Metabolic Disorders; First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Hana Vlášková
- Institute of Inherited Metabolic Disorders; First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Viktor Kožich
- Institute of Inherited Metabolic Disorders; First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Hans Georg Koch
- Department of Pediatrics; University Hospital; Münster D-48149 Germany
- Klinikum für Kinder- und Jugendmedizin; Klinikum Braunschweig; Braunschweig D-38118 Germany
| | - Brian Fowler
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - D. Sean Froese
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
- radiz - Rare Disease Initiative Zurich; Clinical Research Priority Program for Rare Diseases, University of Zurich; Switzerland
| | - Matthias R. Baumgartner
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
- radiz - Rare Disease Initiative Zurich; Clinical Research Priority Program for Rare Diseases, University of Zurich; Switzerland
- Zurich Center for Integrative Human Physiology; University of Zurich; Switzerland
| |
Collapse
|
9
|
Bao R, Huang L, Andrade J, Tan W, Kibbe WA, Jiang H, Feng G. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Inform 2014; 13:67-82. [PMID: 25288881 PMCID: PMC4179624 DOI: 10.4137/cin.s13779] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 12/21/2022] Open
Abstract
The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, pre-processing, alignment, post-processing, and variant analysis (detection, annotation, and prioritization). We evaluate the performance of open-source alignment programs and variant calling tools using simulated and benchmark datasets, and highlight the challenges posed by the lack of concordance among variant detection tools. Based on these results, we recommend adopting multiple tools and resources to reduce false positives and increase the sensitivity of variant calling. In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics.
Collapse
Affiliation(s)
- Riyue Bao
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Lei Huang
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Wei Tan
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York, USA
| | - Warren A Kibbe
- Biomedical Informatics Center (NUBIC), Clinical and Translational Sciences Institute (NUCATS), Northwestern University, Chicago, IL, USA
| | - Hongmei Jiang
- Department of Statistics, Northwestern University, Evanston, IL, USA
| | - Gang Feng
- Biomedical Informatics Center (NUBIC), Clinical and Translational Sciences Institute (NUCATS), Northwestern University, Chicago, IL, USA
| |
Collapse
|
10
|
Cullen CE, Carter GT, Weiss MD, Grant PA, Saperstein DS. Hypohomocysteinemia: a potentially treatable cause of peripheral neuropathology? Phys Med Rehabil Clin N Am 2012; 23:59-65, x. [PMID: 22239874 DOI: 10.1016/j.pmr.2011.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Perturbations of homocysteine metabolism are associated with increased risk for cardiovascular disease, stroke, dementia, and depression, among other major diseases. To assess the relationship between hypohomocysteinemia (HH) and idiopathic peripheral neuropathy (IPN), a retrospective review of 37,442 patients from a tertiary medical clinic was performed. Of patients with HH, 5.9% had IPN versus 0.6% of patients without IPN. Overall, 41% of patients with HH had IPN. These observations indicate that although HH is uncommon in the general population, there is a striking relationship between HH and the incidence of IPN. This article discusses the clinical ramifications of these findings.
Collapse
|