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Xie S, Yuan L, Sui Y, Feng S, Li H, Li X. NME4 mediates metabolic reprogramming and promotes nonalcoholic fatty liver disease progression. EMBO Rep 2024; 25:378-403. [PMID: 38177901 PMCID: PMC10897415 DOI: 10.1038/s44319-023-00012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 01/06/2024] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is mainly characterized by excessive fat accumulation in the liver, and it is associated with liver-related complications and adverse systemic diseases. NAFLD has become the most prevalent liver disease; however, effective therapeutic agents for NAFLD are still lacking. We combined clinical data with proteomics and metabolomics data, and found that the mitochondrial nucleoside diphosphate kinase NME4 plays a central role in mitochondrial lipid metabolism. Nme4 is markedly upregulated in mice fed with high-fat diet, and its expression is positively correlated with the level of steatosis. Hepatic deletion of Nme4 suppresses the progression of hepatic steatosis. Further studies demonstrated that NME4 interacts with several key enzymes in coenzyme A (CoA) metabolism and increases the level of acetyl-CoA and malonyl-CoA, which are the major lipid components of the liver in NAFLD. Increased level of acetyl-CoA and malonyl-CoA lead to increased triglyceride levels and lipid accumulation in the liver. Taken together, these findings reveal that NME4 is a critical regulator of NAFLD progression and a potential therapeutic target for NAFLD.
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Affiliation(s)
- Shaofang Xie
- Westlake Institute for Advanced Study, Fudan University, 310018, Shanghai, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
| | - Lei Yuan
- Westlake Institute for Advanced Study, Fudan University, 310018, Shanghai, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
| | - Yue Sui
- Westlake Institute for Advanced Study, Fudan University, 310018, Shanghai, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
| | - Shan Feng
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
| | - Hengle Li
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xu Li
- Westlake Institute for Advanced Study, Fudan University, 310018, Shanghai, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China.
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2
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Lee JK, Oh A. Combined Malonic and Methylmalonic Aciduria Diagnosed by Recurrent and Severe Infections Mimicking a Primary Immunodeficiency Disease: A Case Report. J Korean Med Sci 2023; 38:e387. [PMID: 37987109 PMCID: PMC10659923 DOI: 10.3346/jkms.2023.38.e387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/04/2023] [Indexed: 11/22/2023] Open
Abstract
Combined malonic and methylmalonic aciduria is a rare genetic disorder caused by ACSF3 biallelic variants that results in impaired protein and fat metabolism and the accumulation of malonic and methylmalonic acids. A 52-day-old infant with a fever and a history of possible meningitis during the neonatal period was hospitalized. Multiple lesions of necrotizing lymphadenitis with abscesses in the left inguinal area were treated by incision and drainage along with appropriate antibiotic therapy, which revealed a methicillin-resistant Staphylococcus aureus infection. At 6 months of age, the patient was admitted with anal abscesses. Due to the increased suspicion of primary immunodeficiency disease, genetic testing was conducted, which revealed ACSF3 biallelic variants inherited from both parents. Urine organic acid analysis revealed elevated levels of malonic and methylmalonic acids. At 29 months, the patient showed normal growth and development without any dietary modifications. He had occasional colds, but severe bacterial infections were absent. The prognosis suggests a benign disease course. Here, we present the first reported case of ACSF3 compound heterozygote variants in Korea.
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Affiliation(s)
- Joon Kee Lee
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, Korea
- Department of Pediatrics, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Arum Oh
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, Korea.
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3
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da Silva-Buttkus P, Spielmann N, Klein-Rodewald T, Schütt C, Aguilar-Pimentel A, Amarie OV, Becker L, Calzada-Wack J, Garrett L, Gerlini R, Kraiger M, Leuchtenberger S, Östereicher MA, Rathkolb B, Sanz-Moreno A, Stöger C, Hölter SM, Seisenberger C, Marschall S, Fuchs H, Gailus-Durner V, Hrabě de Angelis M. Knockout mouse models as a resource for the study of rare diseases. Mamm Genome 2023; 34:244-261. [PMID: 37160609 PMCID: PMC10290595 DOI: 10.1007/s00335-023-09986-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/07/2023] [Indexed: 05/11/2023]
Abstract
Rare diseases (RDs) are a challenge for medicine due to their heterogeneous clinical manifestations and low prevalence. There is a lack of specific treatments and only a few hundred of the approximately 7,000 RDs have an approved regime. Rapid technological development in genome sequencing enables the mass identification of potential candidates that in their mutated form could trigger diseases but are often not confirmed to be causal. Knockout (KO) mouse models are essential to understand the causality of genes by allowing highly standardized research into the pathogenesis of diseases. The German Mouse Clinic (GMC) is one of the pioneers in mouse research and successfully uses (preclinical) data obtained from single-gene KO mutants for research into monogenic RDs. As part of the International Mouse Phenotyping Consortium (IMPC) and INFRAFRONTIER, the pan-European consortium for modeling human diseases, the GMC expands these preclinical data toward global collaborative approaches with researchers, clinicians, and patient groups.Here, we highlight proprietary genes that when deleted mimic clinical phenotypes associated with known RD targets (Nacc1, Bach2, Klotho alpha). We focus on recognized RD genes with no pre-existing KO mouse models (Kansl1l, Acsf3, Pcdhgb2, Rabgap1, Cox7a2) which highlight novel phenotypes capable of optimizing clinical diagnosis. In addition, we present genes with intriguing phenotypic data (Zdhhc5, Wsb2) that are not presently associated with known human RDs.This report provides comprehensive evidence for genes that when deleted cause differences in the KO mouse across multiple organs, providing a huge translational potential for further understanding monogenic RDs and their clinical spectrum. Genetic KO studies in mice are valuable to further explore the underlying physiological mechanisms and their overall therapeutic potential.
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Affiliation(s)
- Patricia da Silva-Buttkus
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Tanja Klein-Rodewald
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Christine Schütt
- Institute of Experimental Genetics, Applied Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Antonio Aguilar-Pimentel
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Lillian Garrett
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Markus Kraiger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Stefanie Leuchtenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Manuela A Östereicher
- Institute of Experimental Genetics, Applied Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen Strasse 25, 81377, Munich, Germany
| | - Adrián Sanz-Moreno
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Claudia Stöger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Sabine M Hölter
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Claudia Seisenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Susan Marschall
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany.
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany.
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4
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Han Y, Tan T, Li Z, Ma Z, Lan G, Liang J, Li K, Bai L. Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs. Genes (Basel) 2023; 14:genes14030655. [PMID: 36980926 PMCID: PMC10048629 DOI: 10.3390/genes14030655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future.
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Affiliation(s)
- Yachun Han
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Tao Tan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zixin Li
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Zheng Ma
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Lijing Bai
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Correspondence: ; Tel./Fax: +86-0755-2325-0160
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5
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Mortensen Ó, Thomsen E, Lydersen LN, Apol KD, Weihe P, Steig BÁ, Andorsdóttir G, Als TD, Gregersen NO. FarGen: Elucidating the distribution of coding variants in the isolated population of the Faroe Islands. Eur J Hum Genet 2023; 31:329-337. [PMID: 36404349 PMCID: PMC9995356 DOI: 10.1038/s41431-022-01227-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/30/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
Here we present results from FarGen Phase I exomes. This dataset is based on the FarGen cohort, which consists of 1,541 individuals from the isolated population of the Faroe Islands. The purpose of this cohort is to serve as a reference catalog of coding variants, and to conduct population genetic studies to better understand the genetic contribution to various diseases in the Faroese population. The first whole-exome data set comprise 465 individuals and a total of 148,267 genetic variants were discovered. Principle Component Analysis indicates that the population is isolated and weakly structured. The distribution of variants in various functional classes was compared with populations in the gnomAD dataset; the results indicated that the proportions were consistent across the cohorts, but probably due to a small sample size, the FarGen dataset contained relatively few rare variants. We identified 19 variants that are classified as pathogenic or likely pathogenic in ClinVar; several of these variants are associated with monogenetic diseases with increased prevalence in the Faroe Islands. The results support previous studies, which indicate that the Faroe Islands is an isolated and weakly structured population. Future studies may elucidate the significance of the 19 pathogenic variants that were identified. The FarGen Phase I dataset is an important step for genetic research in the Faroese population, and the next phase of FarGen will increase the sample size and broaden the scope.
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Affiliation(s)
- Ólavur Mortensen
- The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | - Elisabet Thomsen
- The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | | | - Katrin D Apol
- The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | - Pál Weihe
- Department of Occupational Medicine and Public Health, National Hospital of the Faroe Islands Tórshavn, Tórshavn, Faroe Islands
| | - Bjarni Á Steig
- Medical Department, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
| | - Guðrið Andorsdóttir
- The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
- Centre of Health Science, Faculty of Health, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Thomas D Als
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Noomi O Gregersen
- The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands.
- Centre of Health Science, Faculty of Health, University of the Faroe Islands, Tórshavn, Faroe Islands.
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6
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Jala A, Dutta R, Josyula JVN, Mutheneni SR, Borkar RM. Environmental phenol exposure associates with urine metabolome alteration in young Northeast Indian females. CHEMOSPHERE 2023; 317:137830. [PMID: 36640981 DOI: 10.1016/j.chemosphere.2023.137830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/12/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Urinary biomonitoring delivers the most accurate environmental phenols exposure assessment. However, environmental phenol exposure-related biomarkers are required to improve risk assessment to understand the internal processes perturbed, which may link exposure to specific health outcomes. This study aimed to investigate the association between environmental phenols exposure and the metabolome of young adult females from India. Urinary metabolomics was performed using liquid chromatography-mass spectrometry. Environmental phenols-related metabolic biomarkers were investigated by comparing the low and high exposure of environmental phenols. Seven potential biomarkers, namely histidine, cysteine-s-sulfate, 12-KETE, malonic acid, p-hydroxybenzoic acid, PE (36:2), and PS (36:0), were identified, revealing that environmental phenol exposure altered the metabolic pathways such as histidine metabolism, beta-Alanine metabolism, glycerophospholipid metabolism, and other pathways. This study also conceived an innovative strategy for the early prediction of diseases by combining urinary metabolomics with machine learning (ML) algorithms. The differential metabolites predictive accuracy by ML models was >80%. This is the first mass spectrometry-based metabolomics study on young adult females from India with environmental phenols exposure. The study is valuable in demonstrating multiple urine metabolic changes linked to environmental phenol exposure and a better understanding of the mechanisms behind environmental phenol-induced effects in young female adults.
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Affiliation(s)
- Aishwarya Jala
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Guwahati, 781101, Assam, India
| | - Ratul Dutta
- Down Town Hospital, Guwahati, Assam, 781106, India
| | | | - Srinivasa Rao Mutheneni
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, Telangana, India
| | - Roshan M Borkar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Guwahati, 781101, Assam, India.
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7
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Wilczewski CM, Obasohan J, Paschall JE, Zhang S, Singh S, Maxwell GL, Similuk M, Wolfsberg TG, Turner C, Biesecker LG, Katz AE. Genotype first: Clinical genomics research through a reverse phenotyping approach. Am J Hum Genet 2023; 110:3-12. [PMID: 36608682 PMCID: PMC9892776 DOI: 10.1016/j.ajhg.2022.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Although genomic research has predominantly relied on phenotypic ascertainment of individuals affected with heritable disease, the falling costs of sequencing allow consideration of genomic ascertainment and reverse phenotyping (the ascertainment of individuals with specific genomic variants and subsequent evaluation of physical characteristics). In this research modality, the scientific question is inverted: investigators gather individuals with a genomic variant and test the hypothesis that there is an associated phenotype via targeted phenotypic evaluations. Genomic ascertainment research is thus a model of predictive genomic medicine and genomic screening. Here, we provide our experience implementing this research method. We describe the infrastructure we developed to perform reverse phenotyping studies, including aggregating a super-cohort of sequenced individuals who consented to recontact for genomic ascertainment research. We assessed 13 studies completed at the National Institutes of Health (NIH) that piloted our reverse phenotyping approach. The studies can be broadly categorized as (1) facilitating novel genotype-disease associations, (2) expanding the phenotypic spectra, or (3) demonstrating ex vivo functional mechanisms of disease. We highlight three examples of reverse phenotyping studies in detail and describe how using a targeted reverse phenotyping approach (as opposed to phenotypic ascertainment or clinical informatics approaches) was crucial to the conclusions reached. Finally, we propose a framework and address challenges to building collaborative genomic ascertainment research programs at other institutions. Our goal is for more researchers to take advantage of this approach, which will expand our understanding of the predictive capability of genomic medicine and increase the opportunity to mitigate genomic disease.
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Affiliation(s)
- Caralynn M. Wilczewski
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Justice Obasohan
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Justin E. Paschall
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Suiyuan Zhang
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Sumeeta Singh
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - George L. Maxwell
- Women’s Health Integrated Research Center, Inova Health System, Falls Church, VA 22042, USA
| | - Morgan Similuk
- National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Tyra G. Wolfsberg
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Clesson Turner
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Leslie G. Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA,Corresponding author
| | - Alexander E. Katz
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
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8
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Forny P, Bonilla X, Lamparter D, Shao W, Plessl T, Frei C, Bingisser A, Goetze S, van Drogen A, Harshman K, Pedrioli PGA, Howald C, Poms M, Traversi F, Bürer C, Cherkaoui S, Morscher RJ, Simmons L, Forny M, Xenarios I, Aebersold R, Zamboni N, Rätsch G, Dermitzakis ET, Wollscheid B, Baumgartner MR, Froese DS. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency. Nat Metab 2023; 5:80-95. [PMID: 36717752 PMCID: PMC9886552 DOI: 10.1038/s42255-022-00720-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/01/2022] [Indexed: 01/31/2023]
Abstract
Methylmalonic aciduria (MMA) is an inborn error of metabolism with multiple monogenic causes and a poorly understood pathogenesis, leading to the absence of effective causal treatments. Here we employ multi-layered omics profiling combined with biochemical and clinical features of individuals with MMA to reveal a molecular diagnosis for 177 out of 210 (84%) cases, the majority (148) of whom display pathogenic variants in methylmalonyl-CoA mutase (MMUT). Stratification of these data layers by disease severity shows dysregulation of the tricarboxylic acid cycle and its replenishment (anaplerosis) by glutamine. The relevance of these disturbances is evidenced by multi-organ metabolomics of a hemizygous Mmut mouse model as well as through identification of physical interactions between MMUT and glutamine anaplerotic enzymes. Using stable-isotope tracing, we find that treatment with dimethyl-oxoglutarate restores deficient tricarboxylic acid cycling. Our work highlights glutamine anaplerosis as a potential therapeutic intervention point in MMA.
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Affiliation(s)
- Patrick Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ximena Bonilla
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - David Lamparter
- Health 2030 Genome Center, Geneva, Switzerland
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
| | - Wenguang Shao
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Tanja Plessl
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Caroline Frei
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Bingisser
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sandra Goetze
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Audrey van Drogen
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Keith Harshman
- Health 2030 Genome Center, Geneva, Switzerland
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
| | - Patrick G A Pedrioli
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | | | - Martin Poms
- Division of Clinical Chemistry, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Florian Traversi
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sarah Cherkaoui
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France
| | - Raphael J Morscher
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Luke Simmons
- Division of Child Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Merima Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ioannis Xenarios
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Agora Center, Lausanne, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Nicola Zamboni
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Gunnar Rätsch
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Medical Informatics Unit, University Hospital Zurich, Zurich, Switzerland.
- AI Center, ETH Zurich, Zurich, Switzerland.
| | - Emmanouil T Dermitzakis
- Health 2030 Genome Center, Geneva, Switzerland.
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
| | - Bernd Wollscheid
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
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9
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Li Y, Li J, Wu G, Yang H, Yang X, Wang D, He Y. Role of SIRT3 in neurological diseases and rehabilitation training. Metab Brain Dis 2023; 38:69-89. [PMID: 36374406 PMCID: PMC9834132 DOI: 10.1007/s11011-022-01111-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/17/2022] [Indexed: 11/16/2022]
Abstract
Sirtuin3 (SIRT3) is a deacetylase that plays an important role in normal physiological activities by regulating a variety of substrates. Considerable evidence has shown that the content and activity of SIRT3 are altered in neurological diseases. Furthermore, SIRT3 affects the occurrence and development of neurological diseases. In most cases, SIRT3 can inhibit clinical manifestations of neurological diseases by promoting autophagy, energy production, and stabilization of mitochondrial dynamics, and by inhibiting neuroinflammation, apoptosis, and oxidative stress (OS). However, SIRT3 may sometimes have the opposite effect. SIRT3 can promote the transfer of microglia. Microglia in some cases promote ischemic brain injury, and in some cases inhibit ischemic brain injury. Moreover, SIRT3 can promote the accumulation of ceramide, which can worsen the damage caused by cerebral ischemia-reperfusion (I/R). This review comprehensively summarizes the different roles and related mechanisms of SIRT3 in neurological diseases. Moreover, to provide more ideas for the prognosis of neurological diseases, we summarize several SIRT3-mediated rehabilitation training methods.
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Affiliation(s)
- Yanlin Li
- Department of Rehabilitation, Jinzhou Central Hospital, 51 Shanghai Road, Guta District, Jinzhou, 121000, Liaoning Province, People's Republic of China
| | - Jing Li
- Department of Rehabilitation, Jinzhou Central Hospital, 51 Shanghai Road, Guta District, Jinzhou, 121000, Liaoning Province, People's Republic of China
| | - Guangbin Wu
- Department of Rehabilitation, Jinzhou Central Hospital, 51 Shanghai Road, Guta District, Jinzhou, 121000, Liaoning Province, People's Republic of China
| | - Hua Yang
- Department of Rehabilitation, Jinzhou Central Hospital, 51 Shanghai Road, Guta District, Jinzhou, 121000, Liaoning Province, People's Republic of China
| | - Xiaosong Yang
- Department of Rehabilitation, Jinzhou Central Hospital, 51 Shanghai Road, Guta District, Jinzhou, 121000, Liaoning Province, People's Republic of China
| | - Dongyu Wang
- Department of Neurology, Jinzhou Central Hospital, 51 Shanghai Road, Guta District, Jinzhou, 121000, Liaoning Province, People's Republic of China
| | - Yanhui He
- Department of Radiology, Jinzhou Central Hospital, 51 Shanghai Road, Guta District, Jinzhou, 121000, Liaoning Province, People's Republic of China.
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10
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Head PE, Myung S, Chen Y, Schneller JL, Wang C, Duncan N, Hoffman P, Chang D, Gebremariam A, Gucek M, Manoli I, Venditti CP. Aberrant methylmalonylation underlies methylmalonic acidemia and is attenuated by an engineered sirtuin. Sci Transl Med 2022; 14:eabn4772. [PMID: 35613279 PMCID: PMC10468269 DOI: 10.1126/scitranslmed.abn4772] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Organic acidemias such as methylmalonic acidemia (MMA) are a group of inborn errors of metabolism that typically arise from defects in the catabolism of amino and fatty acids. Accretion of acyl-CoA species is postulated to underlie disease pathophysiology, but the mechanism(s) remain unknown. Here, we surveyed hepatic explants from patients with MMA and unaffected donors, in parallel with samples from various mouse models of methylmalonyl-CoA mutase deficiency. We found a widespread posttranslational modification, methylmalonylation, that inhibited enzymes in the urea cycle and glycine cleavage pathway in MMA. Biochemical studies and mouse genetics established that sirtuin 5 (SIRT5) controlled the metabolism of MMA-related posttranslational modifications. SIRT5 was engineered to resist acylation-driven inhibition via lysine to arginine mutagenesis. The modified SIRT5 was used to create an adeno-associated viral 8 (AAV8) vector and systemically delivered to mutant and control mice. Gene therapy ameliorated hyperammonemia and reduced global methylmalonylation in the MMA mice.
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Affiliation(s)
- PamelaSara E. Head
- National Institute of General Medical Sciences, NIH, 45 Center Drive MSC 6200 Bethesda, MD, 20892-6200 USA
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Sangho Myung
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Yong Chen
- National Heart Lung and Blood Institute, NIH, Building 31, 31 Center Drive Bethesda, MD 20892, USA
| | - Jessica L. Schneller
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Cindy Wang
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Nicholas Duncan
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Pauline Hoffman
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - David Chang
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Abigael Gebremariam
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Marjan Gucek
- National Heart Lung and Blood Institute, NIH, Building 31, 31 Center Drive Bethesda, MD 20892, USA
| | - Irini Manoli
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Charles P. Venditti
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
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11
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Algothmi K, Alqurashi A, Alrofaidi A, Alharbi M, Farsi R, Alburae N, Ganash M, Azhari S, Basingab F, Almuhammadi A, Alqosaibi A, Alkhatabi H, Elaimi A, Jan M, Aldhalaan H, Alrafiah A, Alhazmi S. DNA Methylation Level of Transcription Factor Binding Site in the Promoter Region of Acyl-CoA Synthetase Family Member 3 ( ACSF3) in Saudi Autistic Children. Pharmgenomics Pers Med 2022; 15:131-142. [PMID: 35221709 PMCID: PMC8865760 DOI: 10.2147/pgpm.s346187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) is one of the main epigenetic mechanisms that affects gene expression without changing the underlying DNA sequence. Aberrant DNAm has an implication in different human diseases such as cancer, schizophrenia, and autism spectrum disorder (ASD). ASD is a neurodevelopmental disorder that affects behavior, learning, and communication skills. Acyl-CoA synthetase family member 3 (ACSF3) encodes malonyl-CoA synthetase that is involved in the synthesis and oxidation of fatty acids. The dysregulation in such gene has been reported in combined malonic and methylmalonic aciduria associated with neurological symptoms such as memory problems, psychiatric diseases, and/or cognitive decline. This research aims to study DNAm in the transcription factor (TF) binding site of ACSF3 in Saudi autistic children. To determine whether the DNAm of the TF-binding site is a cause or a consequence of transcription regulation of ACSF3. METHODS RT-qPCR and DNA methylight qPCR were used to determine the expression and DNAm level in the promoter region of ACSF3, respectively. DNA and RNA were extracted from 19 cases of ASD children and 18 control samples from their healthy siblings. RESULTS The results showed a significant correlation between the gene expression of ACSF3 and specificity protein 1 (SP1) in 17 samples of ASD patients, where both genes were upregulated in 9 samples and downregulated in 8 samples. CONCLUSION Although this study found no DNAm in the binding site of SP1 within the ACSF3 promoter, the indicated correlation highlights a possible role of ACSF3 and SP1 in ASD patients.
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Affiliation(s)
- Khloud Algothmi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amal Alqurashi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Alrofaidi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Farsi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Alburae
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdah Ganash
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatemah Basingab
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Almuhammadi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amany Alqosaibi
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Heba Alkhatabi
- King Abdulaziz University, Centre of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia,Medical LaboratorySciencesDepartment,Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- King Abdulaziz University, Centre of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia,Medical LaboratorySciencesDepartment,Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia
| | - Mohammed Jan
- College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hesham Aldhalaan
- Center for Autism Research at King Faisal Specialist Hospital & Research Center (KFSH & RC), Riyadh, Saudi Arabia
| | - Aziza Alrafiah
- Medical LaboratorySciencesDepartment,Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia,Correspondence: Aziza Alrafiah, P.O Box 80200, Jeddah, 21589, Saudi Arabia, Tel +966 126401000 Ext. 23495, Fax +966 126401000 Ext. 21686, Email
| | - Safiah Alhazmi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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12
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Sumathipala D, Strømme P, Fattahi Z, Lüders T, Sheng Y, Kahrizi K, Einarsen IH, Sloan JL, Najmabadi H, van den Heuvel L, Wevers RA, Guerrero-Castillo S, Mørkrid L, Valayannopoulos V, Backe PH, Venditti CP, van Karnebeek CD, Nilsen H, Frengen E, Misceo D. ZBTB11 dysfunction: spectrum of brain abnormalities, biochemical signature and cellular consequences. Brain 2022; 145:2602-2616. [PMID: 35104841 PMCID: PMC9337812 DOI: 10.1093/brain/awac034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
Bi-allelic pathogenic variants in ZBTB11 have been associated with intellectual developmental disorder, autosomal recessive 69 (MRT69; OMIM 618383). We report five patients from three families with novel, bi-allelic variants in ZBTB11. We have expanded the clinical phenotype of MRT69, documenting varied severity of atrophy affecting different brain regions and described combined malonic and methylmalonic aciduria as a biochemical manifestation. As ZBTB11 encodes for a transcriptional regulator, we performeded chromatin immunoprecipitation-sequencing targeting ZBTB11 in fibroblasts from patients and controls. Chromatin immunoprecipitation-sequencing revealed binding of wild-type ZBTB11 to promoters in 238 genes, among which genes encoding proteins involved in mitochondrial functions and RNA processing are over-represented. Mutated ZBTB11 showed reduced binding to 61 of the targeted genes, indicating that the variants act as loss of function. Most of these genes are related to mitochondrial functions. Transcriptome analysis of the patient fibroblasts revealed dysregulation of mitochondrial functions. In addition, we uncovered that reduced binding of the mutated ZBTB11 to ACSF3 leads to decreased ACSF3 transcript level, explaining combined malonic and methylmalonic aciduria. Collectively, these results expand the clinical spectrum of ZBTB11-related neurological disease and give insight into the pathophysiology in which the dysfunctional ZBTB11 affect mitochondrial functions and RNA processing contributing to the neurological and biochemical phenotypes.
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Affiliation(s)
| | | | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Torben Lüders
- Department of Clinical Molecular Biology, Section of Clinical Molecular Biology (EpiGen), University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ingunn Holm Einarsen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Jennifer L Sloan
- Organic Acid Research Section, Medical Genomics and Metabolic Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Lambert van den Heuvel
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands,United for Metabolic Disease—UMD, The Netherlands
| | - Sergio Guerrero-Castillo
- University Children’s Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Lars Mørkrid
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Paul Hoff Backe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Charles P Venditti
- Organic Acid Research Section, Medical Genomics and Metabolic Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Clara D van Karnebeek
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands,United for Metabolic Disease—UMD, The Netherlands,Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Section of Clinical Molecular Biology (EpiGen), University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | | | - Doriana Misceo
- Correspondence to: Doriana Misceo Department of Medical Genetics Oslo University Hospital and University of Oslo Postboks 4956 Nydalen, 0424 Oslo, Norway E-mail:
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13
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He W, Fang X, Lu X, Liu Y, Li G, Zhao Z, Li J, Yang R. Function Identification of Bovine ACSF3 Gene and Its Association With Lipid Metabolism Traits in Beef Cattle. Front Vet Sci 2022; 8:766765. [PMID: 35071379 PMCID: PMC8770830 DOI: 10.3389/fvets.2021.766765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/13/2021] [Indexed: 11/24/2022] Open
Abstract
Acyl-CoA synthetase family member 3 (ACSF3) carries out the first step of mitochondrial fatty acid synthesis II, which is the linkage of malonate and, to a lesser extent, methylmalonate onto CoA. Malonyl-coenzyme A (malonyl-CoA) is a central metabolite in mammalian fatty acid biochemistry that is generated and utilized in the cytoplasm. In this research, we verified the relationship between expression of the ACSF3 and the production of triglycerides (TGs) at the cellular level by silencing and over-expressing ACSF3. Subsequently, through Sanger sequencing, five polymorphisms were found in the functional domain of the bovine ACSF3, and the relationship between ACSF3 polymorphism and the economic traits and fatty acid composition of Chinese Simmental cattle was analyzed by a means of variance analysis and multiple comparison. The results illustrated that the expression of ACSF3 promoted triglyceride synthesis in bovine mammary epithelial cells and bovine fetal fibroblast cells. Further association analysis also indicated that individuals with the AG genotype (g.14211090 G > A) of ACSF3 were significantly associated with the fatty acid composition of intramuscular fat (higher content of linoleic acid, α-linolenic acid, and arachidonic acid), and that CTCAG haplotype individuals were significantly related to the fatty acid composition of intramuscular fat (higher linoleic acid content). Individuals with the AA genotypes of g.14211055 A > G and g.14211090 G > A were substantially associated with a larger eye muscle area in the Chinese Simmental cattle population. ACSF3 played a pivotal role in the regulation of cellular triacylglycerol and long-chain polyunsaturated fatty acid levels, and polymorphism could serve as a useful molecular marker for future marker-assisted selection in the breeding of intramuscular fat deposition traits in beef cattle.
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Affiliation(s)
- Wei He
- College of Animal Science, Jilin University, Changchun, China
| | - Xibi Fang
- College of Animal Science, Jilin University, Changchun, China
| | - Xin Lu
- College of Animal Science, Jilin University, Changchun, China
| | - Yue Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Guanghui Li
- College of Animal Science, Jilin University, Changchun, China
| | - Zhihui Zhao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Junya Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Runjun Yang
- College of Animal Science, Jilin University, Changchun, China
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14
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Heterogenous Clinical Landscape in a Consanguineous Malonic Aciduria Family. Int J Mol Sci 2021; 22:ijms222312633. [PMID: 34884438 PMCID: PMC8658006 DOI: 10.3390/ijms222312633] [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: 10/16/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/27/2022] Open
Abstract
Malonic aciduria is an extremely rare inborn error of metabolism due to malonyl-CoA decarboxylase deficiency. This enzyme is encoded by the MLYCD (Malonyl-CoA Decarboxylase) gene, and the disease has an autosomal recessive inheritance. Malonic aciduria is characterized by systemic clinical involvement, including neurologic and digestive symptoms, metabolic acidosis, hypoglycemia, failure to thrive, seizures, developmental delay, and cardiomyopathy. We describe here two index cases belonging to the same family that, despite an identical genotype, present very different clinical pictures. The first case is a boy with neonatal metabolic symptoms, abnormal brain MRI, and dilated cardiomyopathy. The second case, the cousin of the first patient in a consanguineous family, showed later symptoms, mainly with developmental delay. Both patients showed high levels of malonylcarnitine on acylcarnitine profiles and malonic acid on urinary organic acid chromatographies. The same homozygous pathogenic variant was identified, c.346C > T; p. (Gln116*). We also provide a comprehensive literature review of reported cases. A review of the literature yielded 52 cases described since 1984. The most common signs were developmental delay and cardiomyopathy. Increased levels of malonic acid and malonylcarnitine were constant. Presentations ranged from neonatal death to patients surviving past adolescence. These two cases and reported patients in the literature highlight the inter- and intrafamilial variability of malonic aciduria.
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15
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Osborn LJ, Claesen J, Brown JM. Microbial Flavonoid Metabolism: A Cardiometabolic Disease Perspective. Annu Rev Nutr 2021; 41:433-454. [PMID: 34633856 DOI: 10.1146/annurev-nutr-120420-030424] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cardiometabolic disease (CMD) is a leading cause of death worldwide and encompasses the inflammatory metabolic disorders of obesity, type 2 diabetes mellitus, nonalcoholic fatty liver disease, and cardiovascular disease. Flavonoids are polyphenolic plant metabolites that are abundantly present in fruits and vegetables and have biologically relevant protective effects in a number of cardiometabolic disorders. Several epidemiological studies underscored a negative association between dietary flavonoid consumption and the propensity to develop CMD. Recent studies elucidated the contribution of the gut microbiota in metabolizing dietary intake as it relates to CMD. Importantly, the biological efficacy of flavonoids in humans and animal models alike is linked to the gut microbial community. Herein, we discuss the opportunities and challenges of leveraging flavonoid intake as a potential strategy to prevent and treat CMD in a gut microbe-dependent manner, with special emphasis on flavonoid-derived microbial metabolites.
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Affiliation(s)
- Lucas J Osborn
- Department of Cardiovascular and Metabolic Sciences and Center for Microbiome and Human Health, Lerner Research Institute of the Cleveland Clinic, Cleveland, Ohio 44195, USA; , , .,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Jan Claesen
- Department of Cardiovascular and Metabolic Sciences and Center for Microbiome and Human Health, Lerner Research Institute of the Cleveland Clinic, Cleveland, Ohio 44195, USA; , , .,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - J Mark Brown
- Department of Cardiovascular and Metabolic Sciences and Center for Microbiome and Human Health, Lerner Research Institute of the Cleveland Clinic, Cleveland, Ohio 44195, USA; , , .,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
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16
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Luciani A, Denley MCS, Govers LP, Sorrentino V, Froese DS. Mitochondrial disease, mitophagy, and cellular distress in methylmalonic acidemia. Cell Mol Life Sci 2021; 78:6851-6867. [PMID: 34524466 PMCID: PMC8558192 DOI: 10.1007/s00018-021-03934-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 01/09/2023]
Abstract
Mitochondria—the intracellular powerhouse in which nutrients are converted into energy in the form of ATP or heat—are highly dynamic, double-membraned organelles that harness a plethora of cellular functions that sustain energy metabolism and homeostasis. Exciting new discoveries now indicate that the maintenance of this ever changing and functionally pleiotropic organelle is particularly relevant in terminally differentiated cells that are highly dependent on aerobic metabolism. Given the central role in maintaining metabolic and physiological homeostasis, dysregulation of the mitochondrial network might therefore confer a potentially devastating vulnerability to high-energy requiring cell types, contributing to a broad variety of hereditary and acquired diseases. In this Review, we highlight the biological functions of mitochondria-localized enzymes from the perspective of understanding—and potentially reversing—the pathophysiology of inherited disorders affecting the homeostasis of the mitochondrial network and cellular metabolism. Using methylmalonic acidemia as a paradigm of complex mitochondrial dysfunction, we discuss how mitochondrial directed-signaling circuitries govern the homeostasis and physiology of specialized cell types and how these may be disturbed in disease. This Review also provides a critical analysis of affected tissues, potential molecular mechanisms, and novel cellular and animal models of methylmalonic acidemia which are being used to develop new therapeutic options for this disease. These insights might ultimately lead to new therapeutics, not only for methylmalonic acidemia, but also for other currently intractable mitochondrial diseases, potentially transforming our ability to regulate homeostasis and health.
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Affiliation(s)
- Alessandro Luciani
- Mechanisms of Inherited Kidney Diseases Group, Institute of Physiology, University of Zurich, 8032, Zurich, Switzerland.
| | - Matthew C S Denley
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland
| | - Larissa P Govers
- Mechanisms of Inherited Kidney Diseases Group, Institute of Physiology, University of Zurich, 8032, Zurich, Switzerland
| | - Vincenzo Sorrentino
- Department of Musculo-Skeletal Health, Nestlé Institute of Health Sciences, Nestlé Research, 1015, Lausanne, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland.
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17
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Gao Y, Tian R, Liu H, Xue H, Zhang R, Han S, Ji L, Huang W, Zhan J, You Y. Research progress on intervention effect and mechanism of protocatechuic acid on nonalcoholic fatty liver disease. Crit Rev Food Sci Nutr 2021; 62:9053-9075. [PMID: 34142875 DOI: 10.1080/10408398.2021.1939265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become a surge burden worldwide due to its high prevalence, with complicated deterioration symptoms such as liver fibrosis and cancer. No effective drugs are available for NALFD so far. The rapid growth of clinical demand has prompted the treatment of NAFLD to become a research hotspot. Protocatechuic acid (PCA) is a natural secondary metabolite commonly found in fruits, vegetables, grains, and herbal medicine. It is also the major internal metabolites of anthocyanins and other polyphenols. In the present manuscript, food sources, metabolic absorption, and efficacy of PCA were summarized while analyzing its role in improving NAFLD, as well as the mechanism involved. The results indicated that PCA could ameliorate NAFLD by regulating glucose and lipid metabolism, oxidative stress and inflammation, gut microbiota and metabolites. It was proposed for the first time that PCA might reduce NAFLD by enhancing the energy consumption of brown adipose tissue (BAT). However, the PCA administration mode and dose for NAFLD remain inconclusive. Fresh insights into the specific molecular mechanisms are required, while clinical trials are essential in the future. This review provides new targets and reasoning for the clinical application of PCA in the prevention and treatment of NAFLD.
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Affiliation(s)
- Yunxiao Gao
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Rongrong Tian
- Department of Biomedicine, Beijing City University, Beijing, China
| | - Haiyue Liu
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Huimin Xue
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Ruizhe Zhang
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Suping Han
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Lin Ji
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Weidong Huang
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Jicheng Zhan
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Yilin You
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
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18
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Kiessling E, Nötzli S, Todorova V, Forny M, Baumgartner MR, Samardzija M, Krijt J, Kožich V, Grimm C, Froese DS. Absence of MMACHC in peripheral retinal cells does not lead to an ocular phenotype in mice. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166201. [PMID: 34147638 DOI: 10.1016/j.bbadis.2021.166201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/25/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023]
Abstract
Combined methylmalonic aciduria with homocystinuria (cblC type) is a rare disease caused by mutations in the MMACHC gene. MMACHC encodes an enzyme crucial for intracellular vitamin B12 metabolism, leading to the accumulation of toxic metabolites e.g. methylmalonic acid (MMA) and homocysteine (Hcy), and secondary disturbances in folate and one-carbon metabolism when not fully functional. Patients with cblC deficiency often present in the neonatal or early childhood period with a severe multisystem pathology, which comprises a broad spectrum of treatment-resistant ophthalmological phenotypes, including retinal degeneration, impaired vision, and vascular changes. To examine the potential function of MMACHC in the retina and how its loss may impact disease, we performed gene expression studies in human and mouse, which showed that local expression of MMACHC in the retina and retinal pigment epithelium is relatively stable over time. To study whether functional MMACHC is required for retinal function and tissue integrity, we generated a transgenic mouse lacking Mmachc expression in cells of the peripheral retina. Characterization of this mouse revealed accumulation of cblC disease related metabolites, including MMA and the folate-dependent purine synthesis intermediates AICA-riboside and SAICA-riboside in the retina. Nevertheless, fundus appearance, morphology, vasculature, and cellular composition of the retina, as well as ocular function, remained normal in mice up to 6 or 12 months of age. Our data indicates that peripheral retinal neurons do not require intrinsic expression of Mmachc for survival and function and questions whether a local MMACHC deficiency is responsible for the retinal phenotypes in patients.
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Affiliation(s)
- Eva Kiessling
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland
| | - Sarah Nötzli
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland
| | - Vyara Todorova
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland
| | - Merima Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Marijana Samardzija
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland
| | - Jakub Krijt
- Dept. of Pediatrics and Inherited Metabolic Disorders, Charles University-First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Viktor Kožich
- Dept. of Pediatrics and Inherited Metabolic Disorders, Charles University-First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Christian Grimm
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland.
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19
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Altered Metabolic Flexibility in Inherited Metabolic Diseases of Mitochondrial Fatty Acid Metabolism. Int J Mol Sci 2021; 22:ijms22073799. [PMID: 33917608 PMCID: PMC8038842 DOI: 10.3390/ijms22073799] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 12/14/2022] Open
Abstract
In general, metabolic flexibility refers to an organism's capacity to adapt to metabolic changes due to differing energy demands. The aim of this work is to summarize and discuss recent findings regarding variables that modulate energy regulation in two different pathways of mitochondrial fatty metabolism: β-oxidation and fatty acid biosynthesis. We focus specifically on two diseases: very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) and malonyl-CoA synthetase deficiency (acyl-CoA synthetase family member 3 (ACSF3)) deficiency, which are both characterized by alterations in metabolic flexibility. On the one hand, in a mouse model of VLCAD-deficient (VLCAD-/-) mice, the white skeletal muscle undergoes metabolic and morphologic transdifferentiation towards glycolytic muscle fiber types via the up-regulation of mitochondrial fatty acid biosynthesis (mtFAS). On the other hand, in ACSF3-deficient patients, fibroblasts show impaired mitochondrial respiration, reduced lipoylation, and reduced glycolytic flux, which are compensated for by an increased β-oxidation rate and the use of anaplerotic amino acids to address the energy needs. Here, we discuss a possible co-regulation by mtFAS and β-oxidation in the maintenance of energy homeostasis.
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Abstract
Our ability to unravel the mysteries of human health and disease have changed dramatically over the past 2 decades. Decoding health and disease has been facilitated by the recent availability of high-throughput genomics and multi-omics analyses and the companion tools of advanced informatics and computational science. Understanding of the human genome and its influence on phenotype continues to advance through genotyping large populations and using “light phenotyping” approaches in combination with smaller subsets of the population being evaluated using “deep phenotyping” approaches. Using our capability to integrate and jointly analyze genomic data with other multi-omic data, the knowledge of genotype-phenotype relationships and associated genetic pathways and functions is being advanced. Understanding genotype-phenotype relationships that discriminate human health from disease is speculated to facilitate predictive, precision health care and change modes of health care delivery. The American Association for Dental Research Fall Focused Symposium assembled experts to discuss how studies of genotype-phenotype relationships are illuminating the pathophysiology of craniofacial diseases and developmental biology. Although the breadth of the topic did not allow all areas of dental, oral, and craniofacial research to be addressed (e.g., cancer), the importance and power of integrating genomic, phenomic, and other -omic data are illustrated using a variety of examples. The 8 Fall Focused talks presented different methodological approaches for ascertaining study populations and evaluating population variance and phenotyping approaches. These advances are reviewed in this summary.
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Affiliation(s)
- J T Wright
- Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M C Herzberg
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
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21
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Gabriel MC, Rice SM, Sloan JL, Mossayebi MH, Venditti CP, Al-Kouatly HB. Considerations of expanded carrier screening: Lessons learned from combined malonic and methylmalonic aciduria. Mol Genet Genomic Med 2021; 9:e1621. [PMID: 33625768 PMCID: PMC8123733 DOI: 10.1002/mgg3.1621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background Expanded carrier screening (ECS) utilizes high‐throughput next‐generation sequencing to evaluate an individual's carrier status for multiple conditions. Combined malonic and methylmalonic aciduria (CMAMMA) due to ACSF3 deficiency is a rare inherited disease included in such screening panels. Some cases have been reported with metabolic symptoms in childhood yet other cases describe a benign clinical course, suggesting the clinical phenotype is not well defined. Methods/Case Report Clinical and laboratory findings during the prenatal period were obtained retrospectively from medical records. Results A 37‐year‐old nulliparous woman and her partner were each identified as carriers of ACSF3 variants and presented at 9 weeks gestation for prenatal genetic consultation. The couple received extensive genetic counseling and proceeded with chorionic villus sampling at 11 weeks gestation. Subsequent analysis confirmed that the fetus inherited both parental ACSF variants. The couple was devastated by the results and after reviewing options of pregnancy continuation and termination, they decided to terminate the pregnancy. Following this decision, the patient was diagnosed with acute stress disorder. Conclusion This case highlights how expanded carrier screening adds complexity to reproductive decision‐making. Stronger guidelines and additional research are needed to direct and evaluate the timing, composition, and implementation of ECS panels.
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Affiliation(s)
- Marie Cosette Gabriel
- Department of Obstetrics and Gynecology, Cooper University Hospital, Camden, NJ, USA
| | - Stephanie M Rice
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| | - Jennifer L Sloan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew H Mossayebi
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| | - Charles P Venditti
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
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22
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Wang P, Shu J, Gu C, Yu X, Zheng J, Zhang C, Cai C. Combined Malonic and Methylmalonic Aciduria Due to ACSF3 Variants Results in Benign Clinical Course in Three Chinese Patients. Front Pediatr 2021; 9:751895. [PMID: 34900860 PMCID: PMC8658908 DOI: 10.3389/fped.2021.751895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: Combined malonic and methylmalonic aciduria (CMAMMA) is a rare metabolic disease caused by biallelic variants in ACSF3 gene. The clinical phenotype is highly heterogeneous in this disorder, ranging from asymptomatic to severe symptoms. No cases with CMAMMA were reported in China. Materials and Methods: In this study, three Chinese pediatric patients were diagnosed with CMAMMA unexpectedly while being treated for other ailments. To better characterize CMAMMA in a Chinese population, we made a multidimensional analysis with detailed clinical phenotype, semi-quantitative detection of urine organic acid, and analysis of ACSF3 gene variants. Results: The clinical presentation of these patients is quite different; their main complaints were anemia, jaundice, or abnormal urine test, respectively. They showed no symptoms of the classic methylmalonic academia, but urine organic acid analysis showed elevated malonic acid and methylmalonic acid in all the patients repeatedly. Variants were found at four sites in ACSF3 gene. Patient 1 carried the compound heterogeneous variant c.689G> A (p.Trp230*)/c.1456G> A (p.Ala486Thr). A compound heterozygous variant c.473C> T (p.Pro158Leu)/c.1456G> A (p.Ala486Thr) was identified in patient 2. Patient 3 harbored a novel homozygous variant c.1447A> G (p.Lys483Glu). Conclusions: Three Chinese patients were diagnosed with CMAMMA caused by ACSF3 variants. Their clinical course revealed that CMAMMA can be a benign condition that does not affect individual growth and development, but severe clinical phenotype may appear when other triggers exist. This study systematically elaborates CMAMMA in a Chinese population for the first time, broadens the spectrum of gene variant, and provides a strong basis for the etiological study of this disorder.
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Affiliation(s)
- Ping Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Chunyu Gu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China.,Graduate College of Tianjin Medical University, Tianjin, China
| | - Xiaoli Yu
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Jie Zheng
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Chunhua Zhang
- Matsumoto Institute of Life Science (MILS) International, Yokohama, Japan
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China.,Department of Neurosurgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
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23
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Suryaprakash S, George A, Langenburg S, Savaşan S. Pediatric recurrent Rosai-Dorfman disease with germline heterozygous SLC29A3 and somatic MAP2K1 mutations. Ann Hematol 2020; 99:2965-2967. [PMID: 32944792 DOI: 10.1007/s00277-020-04264-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Affiliation(s)
| | - Amy George
- Division of Hematology/Oncology, Children's Hospital of Michigan, Detroit, MI, USA
| | - Scott Langenburg
- Division of Pediatric Surgery, Children's Hospital of Michigan, Detroit, MI, USA
| | - Süreyya Savaşan
- Division of Hematology/Oncology, Children's Hospital of Michigan, Detroit, MI, USA. .,Division of Hematology/Oncology and Blood and Marrow Transplant Program, Department of Pediatrics, Barbara Ann Karmanos Cancer Center, Central Michigan University College of Medicine, Children's Hospital of Michigan, 3901 Beaubien Blvd, Detroit, MI, 48201, USA.
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24
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Sun R, Kang X, Zhao Y, Wang Z, Wang R, Fu R, Li Y, Hu Y, Wang Z, Shan W, Zhou J, Tian X, Yao J. Sirtuin 3-mediated deacetylation of acyl-CoA synthetase family member 3 by protocatechuic acid attenuates non-alcoholic fatty liver disease. Br J Pharmacol 2020; 177:4166-4180. [PMID: 32520409 DOI: 10.1111/bph.15159] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/30/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND PURPOSE Hepatic fatty acid metabolism disorder, a key pathogenic mechanism underlying non-alcoholic fatty liver disease (NAFLD), is associated with the hyperacetylation of mitochondrial enzymes. Acyl-CoA synthetase family member 3 (ACSF3), which is involved in the regulation of fatty acid metabolism, was predicted to contain lysine acetylation sites related to the mitochondrial deacetylase sirtuin 3 (SIRT3). The purpose of this study was to explore the underlying mechanism by which SIRT3 deacetylates ACSF3 in NAFLD and the protective effect of the natural phenolic compound protocatechuic acid (PCA) against fatty acid metabolism disorder via the SIRT3/ACSF3 pathway. EXPERIMENTAL APPROACH The role of protocatechuic acid and its molecular mechanism in NAFLD were detected in rats and SIRT3-knockout mice fed a high-fat diet (HFD) and in AML-12 cells treated with palmitic acid (PA). KEY RESULTS Pharmacological treatment with protocatechuic acid significantly attenuated high-fat diet-induced fatty acid metabolism disorder in NAFLD. Molecular docking assays showed that protocatechuic acid specifically bound SIRT3 as a substrate and increased SIRT3 protein expression. However, the protective role of protocatechuic acid was abolished by SIRT3 knockdown, which increased ACSF3 expression and exacerbated fatty acid metabolism disorder. Mechanistically, SIRT3 was shown to specifically regulate the acetylation and degradation of ACSF3, which govern the capacity of ACSF3 to mediate fatty acid metabolism disorder during NAFLD. CONCLUSION AND IMPLICATIONS SIRT3-mediated ACSF3 deacetylation is a novel molecular mechanism in NAFLD therapy and protocatechuic acid confers protection against high-fat diet- and palmitic acid-induced hepatic fatty acid metabolism disorder through the SIRT3/ACSF3 pathway.
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Affiliation(s)
- Ruimin Sun
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Xiaohui Kang
- Department of Pharmacy, Dalian Medical University, Dalian, China
| | - Yan Zhao
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Zhanyu Wang
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ruiwen Wang
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Rong Fu
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Yang Li
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yan Hu
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Zhecheng Wang
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Wen Shan
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Junjun Zhou
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Xiaofeng Tian
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jihong Yao
- Department of Pharmacology, Dalian Medical University, Dalian, China
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25
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Tucci S. Brain metabolism and neurological symptoms in combined malonic and methylmalonic aciduria. Orphanet J Rare Dis 2020; 15:27. [PMID: 31969167 PMCID: PMC6977288 DOI: 10.1186/s13023-020-1299-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/09/2020] [Indexed: 01/03/2023] Open
Abstract
Combined malonic and methylmalonic aciduria (CMAMMA) is an inborn error of metabolism which has been proposed being a benign condition. However, older patients may present with neurological manifestations such as seizures, memory problems, psychiatric problems and/ or cognitive decline. In fibroblasts from CMAMMA patients we have recently demonstrated a dysregulation of energy metabolism with increased dependency on β-oxidation for energy production. Because of the inability of the brain to rely efficiently on this pathway to retrieve the required energy to a great extent, we hypothesize an alternative disease-causing mechanism that does not only include the accumulation of the metabolites malonic and methylmalonic acids. Here, we suggest a novel hypothesis on the possible pathophysiological mechanism responsible for the development of neurological symptoms in the long-run.
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Affiliation(s)
- Sara Tucci
- Department of General Pediatrics and Adolescent Medicine, Laboratory of Clinical Biochemistry and Metabolism, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Mathildenstrasse 1, 79106, Freiburg, Germany.
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26
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Yang H, Zhao C, Tang MC, Wang Y, Wang SP, Allard P, Furtos A, Mitchell GA. Inborn errors of mitochondrial acyl-coenzyme a metabolism: acyl-CoA biology meets the clinic. Mol Genet Metab 2019; 128:30-44. [PMID: 31186158 DOI: 10.1016/j.ymgme.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/30/2019] [Accepted: 05/05/2019] [Indexed: 12/18/2022]
Abstract
The last decade saw major advances in understanding the metabolism of Coenzyme A (CoA) thioesters (acyl-CoAs) and related inborn errors (CoA metabolic diseases, CAMDs). For diagnosis, acylcarnitines and organic acids, both derived from acyl-CoAs, are excellent markers of most CAMDs. Clinically, each CAMD is unique but strikingly, three main patterns emerge: first, systemic decompensations with combinations of acidosis, ketosis, hypoglycemia, hyperammonemia and fatty liver; second, neurological episodes, particularly acute "stroke-like" episodes, often involving the basal ganglia but sometimes cerebral cortex, brainstem or optic nerves and third, especially in CAMDs of long chain fatty acyl-CoA metabolism, lipid myopathy, cardiomyopathy and arrhythmia. Some patients develop signs from more than one category. The pathophysiology of CAMDs is not precisely understood. Available data suggest that signs may result from CoA sequestration, toxicity and redistribution (CASTOR) in the mitochondrial matrix has been suggested to play a role. This predicts that most CAMDs cause deficiency of CoA, limiting mitochondrial energy production, and that toxic effects from the abnormal accumulation of acyl-CoAs and from extramitochondrial functions of acetyl-CoA may also contribute. Recent progress includes the following. (1) Direct measurements of tissue acyl-CoAs in mammalian models of CAMDs have been related to clinical features. (2) Inborn errors of CoA biosynthesis were shown to cause clinical changes similar to those of inborn errors of acyl-CoA degradation. (3) CoA levels in cells can be influenced pharmacologically. (4) Roles for acetyl-CoA are increasingly identified in all cell compartments. (5) Nonenzymatic acyl-CoA-mediated acylation of intracellular proteins occurs in mammalian tissues and is increased in CAMDs.
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Affiliation(s)
- Hao Yang
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Chen Zhao
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada; College of Animal Science and Technology, Northwest A&F University, China
| | | | - Youlin Wang
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Shu Pei Wang
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Pierre Allard
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | | | - Grant A Mitchell
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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27
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Laubach ZM, Perng W, Cardenas A, Rifas-Shiman SL, Oken E, DeMeo D, Litonjua AA, Duca RC, Godderis L, Baccarelli A, Hivert MF. Socioeconomic status and DNA methylation from birth through mid-childhood: a prospective study in Project Viva. Epigenomics 2019; 11:1413-1427. [PMID: 31509016 PMCID: PMC6802709 DOI: 10.2217/epi-2019-0040] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/20/2018] [Indexed: 12/28/2022] Open
Abstract
Aim: We investigated associations of prenatal socioeconomic status (SES) with DNA methylation at birth, and to explore persistence of associations into early (∼3 years) and mid-childhood (∼7 years) among 609 mother-child pairs in a Boston-area prebirth cohort. Materials & methods: First, we created a prenatal SES index comprising individual- and neighborhood-level metrics and examined associations of low (lowest 10%) versus high (upper 90%) SES with genome-wide DNA methylation in cord blood via the Infinium HumanMethylation450 BeadChip. Next, we evaluated persistence of associations detected in cord blood with DNA methylation of the same CpG sites measured in peripheral leukocytes in early- and mid-childhood. Results & conclusion: Low prenatal SES was associated with methylation at CpG sites near ACSF3, TNRC6C-AS1, MTMR4 and LRRN4. The relationship with LRRN4 persisted into early childhood.
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Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Wei Perng
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Center, Aurora, CO 80045, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Dawn DeMeo
- Center for Chest Diseases, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Augusto A Litonjua
- Division of Pediatric Pulmonary Medicine, Golisano Children's Hospital at Strong, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Radu-Corneliu Duca
- Centre for Environment & Health, Department of Public Health & Primary Care, University of Leuven (KU Leuven), 3000, Belgium
| | - Lode Godderis
- Centre for Environment & Health, Department of Public Health & Primary Care, University of Leuven (KU Leuven), 3000, Belgium
- IDEWE, External Service for Prevention at Protection at Work, Heverlee, 3001, Belgium
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY 10032, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
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28
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Wolffenbuttel BH, Wouters HJ, Heiner-Fokkema MR, van der Klauw MM. The Many Faces of Cobalamin (Vitamin B 12) Deficiency. Mayo Clin Proc Innov Qual Outcomes 2019; 3:200-214. [PMID: 31193945 PMCID: PMC6543499 DOI: 10.1016/j.mayocpiqo.2019.03.002] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Although cobalamin (vitamin B12) deficiency was described over a century ago, it is still difficult to establish the correct diagnosis and prescribe the right treatment. Symptoms related to vitamin B12 deficiency may be diverse and vary from neurologic to psychiatric. A number of individuals with vitamin B12 deficiency may present with the classic megaloblastic anemia. In clinical practice, many cases of vitamin B12 deficiency are overlooked or sometimes even misdiagnosed. In this review, we describe the heterogeneous disease spectrum of patients with vitamin B12 deficiency in whom the diagnosis was either based on low serum B12 levels, elevated biomarkers like methylmalonic acid and/or homocysteine, or the improvement of clinical symptoms after the institution of parenteral vitamin B12 therapy. We discuss the possible clinical signs and symptoms of patients with B12 deficiency and the various pitfalls of diagnosis and treatment.
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Affiliation(s)
- Bruce H.R. Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, NL-9700 RB, The Netherlands
| | - Hanneke J.C.M. Wouters
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, NL-9700 RB, The Netherlands
- Department of Haematology, University of Groningen, University Medical Center Groningen, Groningen, NL-9700 RB, The Netherlands
| | - M. Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, NL-9700 RB, The Netherlands
| | - Melanie M. van der Klauw
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, NL-9700 RB, The Netherlands
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Li G, Zhao Y, Li Y, Chen Y, Jin W, Sun G, Han R, Tian Y, Li H, Kang X. Weighted gene coexpression network analysis identifies specific transcriptional modules and hub genes related to intramuscular fat traits in chicken breast muscle. J Cell Biochem 2019; 120:13625-13639. [PMID: 30937957 DOI: 10.1002/jcb.28636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/15/2019] [Accepted: 02/28/2019] [Indexed: 12/31/2022]
Abstract
Intramuscular fat (IMF) traits are important factors that influence meat quality. However, the molecular regulatory mechanisms that underlie this trait in chickens are still poorly understood at the gene coexpression level. Here, we performed a weighted gene coexpression network analysis between IMF traits and transcriptome profile in breast muscle in the Chinese domestic Gushi chicken breed at 6, 14, 22, and 30 weeks. A total of 26 coexpressed gene modules were identified. Six modules, which included the dark gray, purple, cyan, pink, light cyan, and blue modules, showed a significant positive correlation (P < 0.05) with IMF traits. The strongest correlation was observed between the dark gray module and IMF content (r = 0.85; P = 4e-04) and between the blue module and different fatty acid content (r = 0.87~0.91; P = 5e-05~2e-04). Enrichment analysis showed that the enrichment of biological processes, such as fatty acid metabolic process, fat cell differentiation, acylglycerol metabolic process, and glycerolipid metabolism were significantly different in the six modules. In addition, the 32, 24, 4, 7, 6, and 25 hub genes were identified from the blue, pink, light cyan, cyan, dark gray, and purple modules, respectively. These hub genes are involved in multiple links to fatty acid metabolism, phospholipid metabolism, cholesterol metabolism, diverse cellular behaviors, and cell events. These results provide novel insights into the molecular regulatory mechanisms for IMF-related traits in chicken and may also help to uncover the formation mechanism for excellent meat quality traits in local breeds of Chinese chicken.
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Affiliation(s)
- Guoxi Li
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Yinli Zhao
- Department of Animal Science, College of Biological Engineering, Henan University of Technology, Zheng Zhou, Henan, P. R. China
| | - Yuanfang Li
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Yi Chen
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Wenjiao Jin
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Guirong Sun
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Ruili Han
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Yadong Tian
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Hong Li
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Xiangtao Kang
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
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Levtova A, Waters PJ, Buhas D, Lévesque S, Auray-Blais C, Clarke JTR, Laframboise R, Maranda B, Mitchell GA, Brunel-Guitton C, Braverman NE. Combined malonic and methylmalonic aciduria due to ACSF3 mutations: Benign clinical course in an unselected cohort. J Inherit Metab Dis 2019; 42:107-116. [PMID: 30740739 DOI: 10.1002/jimd.12032] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND The clinical significance of combined malonic and methylmalonic aciduria due to ACSF3 deficiency (CMAMMA) is controversial. In most publications, affected patients were identified during the investigation of various complaints. METHODS Using a cross-sectional multicenter retrospective natural history study, we describe the course of all known CMAMMA individuals in the province of Quebec. RESULTS We identified 25 CMAMMA patients (6 months to 30 years old) with a favorable outcome regardless of treatment. All but one came to clinical attention through the Provincial Neonatal Urine Screening Program (screening on day 21 of life). Median methylmalonic acid (MMA) levels ranged from 107 to 857 mmol/mol creatinine in urine (<10) and from 8 to 42 μmol/L in plasma (<0.4); median urine malonic acid (MA) levels ranged from 9 to 280 mmol/mol creatinine (<5). MMA was consistently higher than MA. These findings are comparable to those previously reported in CMAMMA. Causal ACSF3 mutations were identified in all patients for whom genotyping was performed (76% of cases). The most common ACSF3 mutations in our cohort were c.1075G > A (p.E359K) and c.1672C > T (p.R558W), representing 38.2 and 20.6% of alleles in genotyped families, respectively; we also report several novel mutations. CONCLUSION Because our province still performs urine newborn screening, our patient cohort is the only one free of selection bias. Therefore, the favorable clinical course observed suggests that CMAMMA is probably a benign condition, although we cannot exclude the possibility that a small minority of patients may present symptoms attributable to CMAMMA, perhaps as a result of interactions with other genetic or environmental factors.
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Affiliation(s)
- Alina Levtova
- Division of Medical Genetics, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM) and Université de Montréal, Tour Viger, 900 rue St-Denis, R07-462, Montreal, Quebec H2X 0A9, Canada
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, 3175 Côte-Sainte-Catherine, Montreal, Quebec H3T 1C5, Canada
| | - Paula J Waters
- Division of Medical Genetics, Department of Pediatrics, Université de Sherbrooke, CHUS, 3001 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada
| | - Daniela Buhas
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Departments of Medical Genetics and Pediatrics, Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Sébastien Lévesque
- Division of Medical Genetics, Department of Pediatrics, Université de Sherbrooke, CHUS, 3001 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada
| | - Christiane Auray-Blais
- Division of Medical Genetics, Department of Pediatrics, Université de Sherbrooke, CHUS, 3001 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada
| | - Joe T R Clarke
- Division of Medical Genetics, Department of Pediatrics, Université de Sherbrooke, CHUS, 3001 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada
| | - Rachel Laframboise
- Department of Pediatrics, Laval University Hospital Centre, Quebec, Quebec, Canada
| | - Bruno Maranda
- Division of Medical Genetics, Department of Pediatrics, Université de Sherbrooke, CHUS, 3001 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada
- Department of Pediatrics, Laval University Hospital Centre, Quebec, Quebec, Canada
| | - Grant A Mitchell
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, 3175 Côte-Sainte-Catherine, Montreal, Quebec H3T 1C5, Canada
| | - Catherine Brunel-Guitton
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, 3175 Côte-Sainte-Catherine, Montreal, Quebec H3T 1C5, Canada
| | - Nancy E Braverman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Departments of Medical Genetics and Pediatrics, Montreal Children's Hospital, Montreal, Quebec, Canada
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Bowman CE, Wolfgang MJ. Role of the malonyl-CoA synthetase ACSF3 in mitochondrial metabolism. Adv Biol Regul 2019; 71:34-40. [PMID: 30201289 PMCID: PMC6347522 DOI: 10.1016/j.jbior.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 12/26/2022]
Abstract
Malonyl-CoA is a central metabolite in fatty acid biochemistry. It is the rate-determining intermediate in fatty acid synthesis but is also an allosteric inhibitor of the rate-setting step in mitochondrial long-chain fatty acid oxidation. While these canonical cytoplasmic roles of malonyl-CoA have been well described, malonyl-CoA can also be generated within the mitochondrial matrix by an alternative pathway: the ATP-dependent ligation of malonate to Coenzyme A by the malonyl-CoA synthetase ACSF3. Malonate, a competitive inhibitor of succinate dehydrogenase of the TCA cycle, is a potent inhibitor of mitochondrial respiration. A major role for ACSF3 is to provide a metabolic pathway for the clearance of malonate by the generation of malonyl-CoA, which can then be decarboxylated to acetyl-CoA by malonyl-CoA decarboxylase. Additionally, ACSF3-derived malonyl-CoA can be used to malonylate lysine residues on proteins within the matrix of mitochondria, possibly adding another regulatory layer to post-translational control of mitochondrial metabolism. The discovery of ACSF3-mediated generation of malonyl-CoA defines a new mitochondrial metabolic pathway and raises new questions about how the metabolic fates of this multifunctional metabolite intersect with mitochondrial metabolism.
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Affiliation(s)
- Caitlyn E Bowman
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michael J Wolfgang
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Costanzo M, Cevenini A, Marchese E, Imperlini E, Raia M, Del Vecchio L, Caterino M, Ruoppolo M. Label-Free Quantitative Proteomics in a Methylmalonyl-CoA Mutase-Silenced Neuroblastoma Cell Line. Int J Mol Sci 2018; 19:ijms19113580. [PMID: 30428564 PMCID: PMC6275031 DOI: 10.3390/ijms19113580] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 11/09/2018] [Indexed: 02/06/2023] Open
Abstract
Methylmalonic acidemias (MMAs) are inborn errors of metabolism due to the deficient activity of methylmalonyl-CoA mutase (MUT). MUT catalyzes the formation of succinyl-CoA from methylmalonyl-CoA, produced from propionyl-CoA catabolism and derived from odd chain fatty acids β-oxidation, cholesterol, and branched-chain amino acids degradation. Increased methylmalonyl-CoA levels allow for the presymptomatic diagnosis of the disease, even though no approved therapies exist. MMA patients show hyperammonemia, ketoacidosis, lethargy, respiratory distress, cognitive impairment, and hepatomegaly. The long-term consequences concern neurologic damage and terminal kidney failure, with little chance of survival. The cellular pathways affected by MUT deficiency were investigated using a quantitative proteomics approach on a cellular model of MUT knockdown. Currently, a consistent reduction of the MUT protein expression was obtained in the neuroblastoma cell line (SH-SY5Y) by using small-interfering RNA (siRNA) directed against an MUT transcript (MUT siRNA). The MUT absence did not affect the cell viability and apoptotic process in SH-SY5Y. In the present study, we evaluate and quantify the alterations in the protein expression profile as a consequence of MUT-silencing by a mass spectrometry-based label-free quantitative analysis, using two different quantitative strategies. Both quantitative methods allowed us to observe that the expression of the proteins involved in mitochondrial oxido-reductive homeostasis balance was affected by MUT deficiency. The alterated functional mitochondrial activity was observed in siRNA_MUT cells cultured with a propionate-supplemented medium. Finally, alterations in the levels of proteins involved in the metabolic pathways, like carbohydrate metabolism and lipid metabolism, were found.
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Affiliation(s)
- Michele Costanzo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
- Associazione Culturale DiSciMuS RFC, Casoria, 80026 Naples, Italy.
| | - Armando Cevenini
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
| | - Emanuela Marchese
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
- Dipartimento di Salute Mentale e Fisica e Medicina Preventiva, Università degli Studi della Campania "L. Vanvitelli", 80138 Naples, Italy.
| | | | - Maddalena Raia
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
| | | | - Marianna Caterino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
- Associazione Culturale DiSciMuS RFC, Casoria, 80026 Naples, Italy.
| | - Margherita Ruoppolo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
- Associazione Culturale DiSciMuS RFC, Casoria, 80026 Naples, Italy.
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Brasil S, Leal F, Vega A, Navarrete R, Ecay MJ, Desviat LR, Riera C, Padilla N, de la Cruz X, Couce ML, Martin-Hernández E, Morais A, Pedrón C, Peña-Quintana L, Rigoldi M, Specola N, de Almeida IT, Vives I, Yahyaoui R, Rodríguez-Pombo P, Ugarte M, Pérez-Cerda C, Merinero B, Pérez B. Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants. Orphanet J Rare Dis 2018; 13:125. [PMID: 30041674 PMCID: PMC6057060 DOI: 10.1186/s13023-018-0862-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/29/2018] [Indexed: 12/04/2022] Open
Abstract
Background Cellular cobalamin defects are a locus and allelic heterogeneous disorder. The gold standard for coming to genetic diagnoses of cobalamin defects has for some time been gene-by-gene Sanger sequencing of individual DNA fragments. Enzymatic and cellular methods are employed before such sequencing to help in the selection of the gene defects to be sought, but this is time-consuming and laborious. Furthermore some cases remain undiagnosed because no biochemical methods have been available to test for cobalamin absorption and transport defects. Results This paper reports the use of massive parallel sequencing of DNA (exome analysis) for the accurate and rapid genetic diagnosis of cobalamin-related defects in a cohort of affected patients. The method was first validated in an initial cohort with different cobalamin defects. Mendelian segregation, the frequency of mutations, and the comprehensive structural and functional analysis of gene variants, identified disease-causing mutations in 12 genes involved in the absorption and synthesis of active cofactors of vitamin B12 (22 cases), and in the non-cobalamin metabolism-related genes ACSF3 (in four biochemically misdiagnosed patients) and SUCLA2 (in one patient with an unusual presentation). We have identified thirteen new variants all classified as pathogenic according to the ACGM recommendation but four were classified as variant likely pathogenic in MUT and SUCLA2. Functional and structural analysis provided evidences to classify them as pathogenic variants. Conclusions The present findings suggest that the technology used is sufficiently sensitive and specific, and the results it provides sufficiently reproducible, to recommend its use as a second-tier test after the biochemical detection of cobalamin disorder markers in the first days of life. However, for accurate diagnoses to be made, biochemical and functional tests that allow comprehensive clinical phenotyping are also needed. Electronic supplementary material The online version of this article (10.1186/s13023-018-0862-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra Brasil
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Ana Vega
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - María Jesús Ecay
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Lourdes R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Casandra Riera
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natàlia Padilla
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Mari Luz Couce
- Hospital Clínico Universitario de Santiago, Santiago de Compostela, CIBERER, Santiago de Compostela, Spain
| | | | - Ana Morais
- Hospital Universitario La Paz, Madrid, Spain
| | | | - Luis Peña-Quintana
- Hospital Universitario Materno Infantil, CIBEROBN, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Miriam Rigoldi
- Center for Rare Disorders, ASST- Monza, Ospedale San Gerardo, Monza, Italy
| | - Norma Specola
- Unidad de Metabolismo Hospital de Niños de La Plata, La Plata, Argentina
| | | | | | - Raquel Yahyaoui
- Hospital Universitario Regional de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Celia Pérez-Cerda
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Begoña Merinero
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain.
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Roberts BS, Hardigan AA, Moore DE, Ramaker RC, Jones AL, Fitz-Gerald MB, Cooper GM, Wilcox CM, Kimberly RP, Myers RM. Discovery and Validation of Circulating Biomarkers of Colorectal Adenoma by High-Depth Small RNA Sequencing. Clin Cancer Res 2018; 24:2092-2099. [PMID: 29490987 PMCID: PMC5932113 DOI: 10.1158/1078-0432.ccr-17-1960] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 01/02/2018] [Accepted: 02/21/2018] [Indexed: 12/18/2022]
Abstract
Purpose: Colorectal cancer is the third most common cancer worldwide, causing approximately 700,000 deaths each year. The majority of colorectal cancers begin as adenomas. Definitive screening for colorectal adenomas is currently accomplished through colonoscopy but, owing largely to costs and invasiveness, is typically limited to patient groups at higher risk by virtue of age or family history. We sought to determine if blood-based small RNA markers could detect colorectal adenoma.Experimental Design: We applied high-depth small RNA sequencing to plasma from a large (n = 189) cohort of patients, balanced for age, sex, and ancestry. Our analytical methodology allowed for the detection of both microRNAs and other small RNA species. We replicated sequencing results by qPCR on plasma samples from an independent cohort (n = 140).Results: We found several small RNA species with significant associations to colorectal adenoma, including both microRNAs and non-microRNA small RNAs. These associations were robust to correction for patient covariates, including age. Among the adenoma-associated small RNAs, two, a miR-335-5p isoform and an un-annotated small RNA, were validated by qPCR in an independent cohort. A classifier trained on measures of these two RNAs in the discovery cohort yields an AUC of 0.755 (0.775 with age) for adenoma detection in the independent cohort. This classifier accurately detects adenomas in patients under 50 and is robust to sex or ancestry.Conclusions: Circulating small RNAs (including but not limited to miRNAs) discovered by sequencing and validated by qPCR identify patients with colorectal adenomas effectively. Clin Cancer Res; 24(9); 2092-9. ©2018 AACR.
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Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Dianna E Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Meredith B Fitz-Gerald
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - C Mel Wilcox
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Robert P Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.
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Laboratory analysis of organic acids, 2018 update: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2018. [DOI: 10.1038/gim.2018.45] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Kuster A, Arnoux JB, Barth M, Lamireau D, Houcinat N, Goizet C, Doray B, Gobin S, Schiff M, Cano A, Amsallem D, Barnerias C, Chaumette B, Plaze M, Slama A, Ioos C, Desguerre I, Lebre AS, de Lonlay P, Christa L. Diagnostic approach to neurotransmitter monoamine disorders: experience from clinical, biochemical, and genetic profiles. J Inherit Metab Dis 2018; 41:129-139. [PMID: 28924877 DOI: 10.1007/s10545-017-0079-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 07/10/2017] [Accepted: 07/27/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND AND AIM To improve the diagnostic work-up of patients with diverse neurological diseases, we have elaborated specific clinical and CSF neurotransmitter patterns. METHODS Neurotransmitter determinations in CSF from 1200 patients revealed abnormal values in 228 (19%) cases. In 54/228 (24%) patients, a final diagnosis was identified. RESULTS We have reported primary (30/54, 56%) and secondary (24/54, 44%) monoamine neurotransmitter disorders. For primary deficiencies, the most frequently mutated gene was DDC (n = 9), and the others included PAH with neuropsychiatric features (n = 4), PTS (n = 5), QDPR (n = 3), SR (n = 1), and TH (n = 1). We have also identified mutations in SLC6A3, FOXG1 (n = 1 of each), MTHFR (n = 3), FOLR1, and MTHFD (n = 1 of each), for dopamine transporter, neuronal development, and folate metabolism disorders, respectively. For secondary deficiencies, we have identified POLG (n = 3), ACSF3 (n = 1), NFU1, and SDHD (n = 1 of each), playing a role in mitochondrial function. Other mutated genes included: ADAR, RNASEH2B, RNASET2, SLC7A2-IT1 A/B lncRNA, and EXOSC3 involved in nuclear and cytoplasmic metabolism; RanBP2 and CASK implicated in post-traductional and scaffolding modifications; SLC6A19 regulating amino acid transport; MTM1, KCNQ2 (n = 2), and ATP1A3 playing a role in nerve cell electrophysiological state. Chromosome abnormalities, del(8)(p23)/dup(12) (p23) (n = 1), del(6)(q21) (n = 1), dup(17)(p13.3) (n = 1), and non-genetic etiologies (n = 3) were also identified. CONCLUSION We have classified the final 54 diagnoses in 11 distinctive biochemical profiles and described them through 20 clinical features. To identify the specific molecular cause of abnormal NT profiles, (targeted) genomics might be used, to improve diagnosis and allow early treatment of complex and rare neurological genetic diseases.
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Affiliation(s)
- Alice Kuster
- Neurometabolism department, Nantes Hospital and University, Nantes, France
| | - Jean-Baptiste Arnoux
- Reference center for inherited metabolic diseases, Necker Enfants-Malades Hospital, Assistance Publique Hôpitaux de Paris, Imagine Institute, Paris Descartes University, Paris, France
| | - Magalie Barth
- Neurometabolism department, Angers Hospital and University, Angers, France
| | - Delphine Lamireau
- Neuropediatric and Neurogenetic department, MRGM laboratory, National institute for health and medical research U1211, Pellegrin Hospital and University, Bordeaux, France
| | - Nada Houcinat
- Neuropediatric and Neurogenetic department, MRGM laboratory, National institute for health and medical research U1211, Pellegrin Hospital and University, Bordeaux, France
| | - Cyril Goizet
- Neuropediatric and Neurogenetic department, MRGM laboratory, National institute for health and medical research U1211, Pellegrin Hospital and University, Bordeaux, France
| | - Bérénice Doray
- Genetic department, Félix Guyon Hospital and University, Saint-Denis de la Réunion, France
| | - Stéphanie Gobin
- Genetic department, Necker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Manuel Schiff
- Neurometabolism and Biochemical department, Robert Debré Hospital and University, Paris, France
| | - Aline Cano
- Reference center for inherited metabolic diseases, la Timone-Marseille Hospital and University, Marseille, France
| | - Daniel Amsallem
- Neuropediatric department, Jean Minjoz Hospital, Besançon, France
| | - Christine Barnerias
- Neurology department, Necker Enfants Malades Hospital and Paris Descartes University, Paris, France
| | - Boris Chaumette
- Sainte Anne Hospital, University Hospital Department (SHU), Paris Descartes University and Institut National de la Santé et de la Recherche Médicale INSERM U894, CNRS GDR, 3557, Paris, France
| | - Marion Plaze
- Sainte Anne Hospital, University Hospital Department (SHU), Paris Descartes University and Institut National de la Santé et de la Recherche Médicale INSERM U894, CNRS GDR, 3557, Paris, France
| | - Abdelhamid Slama
- Biochemical department, Bicêtre Hospital, Assistance Publique Hôpitaux de Paris, Le Kremlin Bicêtre, France
| | - Christine Ioos
- Neuropediatric department, Raymond Poincaré Hospital, Garches, France
| | - Isabelle Desguerre
- Neurology department, Necker Enfants Malades Hospital and Paris Descartes University, Paris, France
| | - Anne-Sophie Lebre
- Genetic and Biological department, Reims University, Maison Blanche Hospital, F-51092, Reims, France
| | - Pascale de Lonlay
- Reference center for inherited metabolic diseases, Necker Enfants-Malades Hospital, Assistance Publique Hôpitaux de Paris, Imagine Institute, Paris Descartes University, Paris, France
| | - Laurence Christa
- Metabolomic and proteomic Biochemical department, Necker Enfants-Malades Hospital, Paris Descartes University, Paris, France.
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Reid ES, Papandreou A, Drury S, Boustred C, Yue WW, Wedatilake Y, Beesley C, Jacques TS, Anderson G, Abulhoul L, Broomfield A, Cleary M, Grunewald S, Varadkar SM, Lench N, Rahman S, Gissen P, Clayton PT, Mills PB. Advantages and pitfalls of an extended gene panel for investigating complex neurometabolic phenotypes. Brain 2017; 139:2844-2854. [PMID: 27604308 PMCID: PMC5091046 DOI: 10.1093/brain/aww221] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/14/2016] [Indexed: 12/15/2022] Open
Abstract
Neurometabolic disorders are markedly heterogeneous, both clinically and genetically, and are characterized by variable neurological dysfunction accompanied by suggestive neuroimaging or biochemical abnormalities. Despite early specialist input, delays in diagnosis and appropriate treatment initiation are common. Next-generation sequencing approaches still have limitations but are already enabling earlier and more efficient diagnoses in these patients. We designed a gene panel targeting 614 genes causing inborn errors of metabolism and tested its diagnostic efficacy in a paediatric cohort of 30 undiagnosed patients presenting with variable neurometabolic phenotypes. Genetic defects that could, at least partially, explain observed phenotypes were identified in 53% of cases. Where biochemical abnormalities pointing towards a particular gene defect were present, our panel identified diagnoses in 89% of patients. Phenotypes attributable to defects in more than one gene were seen in 13% of cases. The ability of in silico tools, including structure-guided prediction programmes to characterize novel missense variants were also interrogated. Our study expands the genetic, clinical and biochemical phenotypes of well-characterized (POMGNT1, TPP1) and recently identified disorders (PGAP2, ACSF3, SERAC1, AFG3L2, DPYS). Overall, our panel was accurate and efficient, demonstrating good potential for applying similar approaches to clinically and biochemically diverse neurometabolic disease cohorts.
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Affiliation(s)
- Emma S Reid
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Apostolos Papandreou
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Neurology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Suzanne Drury
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Christopher Boustred
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Wyatt W Yue
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Yehani Wedatilake
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Clare Beesley
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Developmental Biology and Cancer Programme, UCL Institute of Child Health, London, UK
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lara Abulhoul
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Alex Broomfield
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Maureen Cleary
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Stephanie Grunewald
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sophia M Varadkar
- Neurology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nick Lench
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Shamima Rahman
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Paul Gissen
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Peter T Clayton
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Philippa B Mills
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
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A conserved mammalian mitochondrial isoform of acetyl-CoA carboxylase ACC1 provides the malonyl-CoA essential for mitochondrial biogenesis in tandem with ACSF3. Biochem J 2017; 474:3783-3797. [PMID: 28986507 DOI: 10.1042/bcj20170416] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 01/06/2023]
Abstract
Mitochondrial fatty acid synthesis (mtFAS) is a highly conserved pathway essential for mitochondrial biogenesis. The mtFAS process is required for mitochondrial respiratory chain assembly and function, synthesis of the lipoic acid cofactor indispensable for the function of several mitochondrial enzyme complexes and essential for embryonic development in mice. Mutations in human mtFAS have been reported to lead to neurodegenerative disease. The source of malonyl-CoA for mtFAS in mammals has remained unclear. We report the identification of a conserved vertebrate mitochondrial isoform of ACC1 expressed from an ACACA transcript splicing variant. A specific knockdown (KD) of the corresponding transcript in mouse cells, or CRISPR/Cas9-mediated inactivation of the putative mitochondrial targeting sequence in human cells, leads to decreased lipoylation and mitochondrial fragmentation. Simultaneous KD of ACSF3, encoding a mitochondrial malonyl-CoA synthetase previously implicated in the mtFAS process, resulted in almost complete ablation of protein lipoylation, indicating that these enzymes have a redundant function in mtFAS. The discovery of a mitochondrial isoform of ACC1 required for lipoic acid synthesis has intriguing consequences for our understanding of mitochondrial disorders, metabolic regulation of mitochondrial biogenesis and cancer.
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The Mammalian Malonyl-CoA Synthetase ACSF3 Is Required for Mitochondrial Protein Malonylation and Metabolic Efficiency. Cell Chem Biol 2017; 24:673-684.e4. [PMID: 28479296 DOI: 10.1016/j.chembiol.2017.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/08/2017] [Accepted: 04/07/2017] [Indexed: 12/13/2022]
Abstract
Malonyl-coenzyme A (malonyl-CoA) is a central metabolite in mammalian fatty acid biochemistry generated and utilized in the cytoplasm; however, little is known about noncanonical organelle-specific malonyl-CoA metabolism. Intramitochondrial malonyl-CoA is generated by a malonyl-CoA synthetase, ACSF3, which produces malonyl-CoA from malonate, an endogenous competitive inhibitor of succinate dehydrogenase. To determine the metabolic requirement for mitochondrial malonyl-CoA, ACSF3 knockout (KO) cells were generated by CRISPR/Cas-mediated genome editing. ACSF3 KO cells exhibited elevated malonate and impaired mitochondrial metabolism. Unbiased and targeted metabolomics analysis of KO and control cells in the presence or absence of exogenous malonate revealed metabolic changes dependent on either malonate or malonyl-CoA. While ACSF3 was required for the metabolism and therefore detoxification of malonate, ACSF3-derived malonyl-CoA was specifically required for lysine malonylation of mitochondrial proteins. Together, these data describe an essential role for ACSF3 in dictating the metabolic fate of mitochondrial malonate and malonyl-CoA in mammalian metabolism.
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40
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Goebel K, Merner ND. A monograph proposing the use of canine mammary tumours as a model for the study of hereditary breast cancer susceptibility genes in humans. Vet Med Sci 2017; 3:51-62. [PMID: 28713573 PMCID: PMC5488221 DOI: 10.1002/vms3.61] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
Canines are excellent models for cancer studies due to their similar physiology and genomic sequence to humans, companion status and limited intra‐breed heterogeneity. Due to their affliction to mammary cancers, canines can serve as powerful genetic models of hereditary breast cancers. Variants within known human breast cancer susceptibility genes only explain a fraction of familial cases. Thus, further discovery is necessary but such efforts have been thwarted by genetic heterogeneity. Reducing heterogeneity is key, and studying isolated human populations have helped in the endeavour. An alternative is to study dog pedigrees, since artificial selection has resulted in extreme homogeneity. Identifying the genetic predisposition to canine mammary tumours can translate to human discoveries – a strategy currently underutilized. To explore this potential, we reviewed published canine mammary tumour genetic studies and proposed benefits of next generation sequencing canine cohorts to facilitate moving beyond incremental advances.
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Affiliation(s)
- Katie Goebel
- Department of Drug Discovery and DevelopmentHarrison School of PharmacyAuburn UniversityAuburnAlabama.,College of Veterinary MedicineAuburn UniversityAuburnAlabama
| | - Nancy D Merner
- Department of Drug Discovery and DevelopmentHarrison School of PharmacyAuburn UniversityAuburnAlabama
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41
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Abstract
PURPOSE OF REVIEW Recent clinical studies and management guidelines for the treatment of the organic acidopathies methylmalonic acidemia (MMA) and propionic acidemia address the scope of interventions to maximize health and quality of life. Unfortunately, these disorders continue to cause significant morbidity and mortality due to acute and chronic systemic and end-organ injury. RECENT FINDINGS Dietary management with medical foods has been a mainstay of therapy for decades, yet well controlled patients can manifest growth, development, cardiac, ophthalmological, renal, and neurological complications. Patients with organic acidopathies suffer metabolic brain injury that targets specific regions of the basal ganglia in a distinctive pattern, and these injuries may occur even with optimal management during metabolic stress. Liver transplantation has improved quality of life and metabolic stability, yet transplantation in this population does not entirely prevent brain injury or the development of optic neuropathy and cardiac disease. SUMMARY Management guidelines should identify necessary screening for patients with methylmalonic acidemia and propionic acidemia, and improve anticipatory management of progressive end-organ disease. Liver transplantation improves overall metabolic control, but injury to nonregenerative tissues may not be mitigated. Continued use of medical foods in these patients requires prospective studies to demonstrate evidence of benefit in a controlled manner.
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42
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Engagement and communication among participants in the ClinSeq Genomic Sequencing Study. Genet Med 2016; 19:98-103. [PMID: 27763633 DOI: 10.1038/gim.2016.71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/21/2016] [Indexed: 12/15/2022] Open
Abstract
PURPOSE As clinical genome sequencing expand its reach, understanding how individuals engage with this process are of critical importance. In this study, we aimed to describe internal engagement and its correlates among a ClinSeq cohort of adults consented to genome sequencing and receipt of results. METHODS This study was framed using the precaution adoption process model (PAPM), in which knowledge predicts engagement and engagement predicts subsequent behaviors. Prior to receipt of sequencing results, 630 participants in the study completed a baseline survey. Engagement was assessed as the frequency with which participants thought about their participation in ClinSeq since enrollment. RESULTS Results were consistent with the PAPM: those with higher genomics knowledge reported higher engagement (r = 0.13, P = 0.001) and those who were more engaged reported more frequent communication with their physicians (r = 0.28, P < 0.001) and family members (r = 0.35, P < 0.001) about ClinSeq. Characteristics of those with higher engagement included poorer overall health (r = -0.13, P = 0.002), greater seeking of health information (r = 0.16, P < 0.001), and more recent study enrollment (r = -0.21, P < 0.001). CONCLUSION These data support the importance of internal engagement in communication related to genomic sequencing.Genet Med 19 1, 98-103.
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43
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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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44
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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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45
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Green RC, Goddard KAB, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, Garrett JR, Gray SW, Henderson GE, Hindorff LA, Holm IA, Lewis MH, Hutter CM, Janne PA, Joffe S, Kaufman D, Knoppers BM, Koenig BA, Krantz ID, Manolio TA, McCullough L, McEwen J, McGuire A, Muzny D, Myers RM, Nickerson DA, Ou J, Parsons DW, Petersen GM, Plon SE, Rehm HL, Roberts JS, Robinson D, Salama JS, Scollon S, Sharp RR, Shirts B, Spinner NB, Tabor HK, Tarczy-Hornoch P, Veenstra DL, Wagle N, Weck K, Wilfond BS, Wilhelmsen K, Wolf SM, Wynn J, Yu JH. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine. Am J Hum Genet 2016; 98:1051-1066. [PMID: 27181682 DOI: 10.1016/j.ajhg.2016.04.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/14/2016] [Indexed: 12/11/2022] Open
Abstract
Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.
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Affiliation(s)
- Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA.
| | - Katrina A B Goddard
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, NY 10032, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sawona Biswas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carrie L Blout
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kyle B Brothers
- Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Wylie Burke
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA; Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Departments of Pathology and Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Ann Arbor, MI 48109, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10029, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University, Nashville, TN 37203, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kelly East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jeremy R Garrett
- Children's Mercy Bioethics Center, Children's Mercy Hospital, Kansas City, MO 64108, USA; Departments of Pediatrics and Philosophy, University of Missouri - Kansas City, Kansas City, MO 64110, USA
| | - Stacy W Gray
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gail E Henderson
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ingrid A Holm
- Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Carolyn M Hutter
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Pasi A Janne
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Steven Joffe
- Department of Medical Ethics & Health Policy, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - David Kaufman
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Barbara A Koenig
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA 94118, USA
| | - Ian D Krantz
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Laurence McCullough
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean McEwen
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Amy McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey Ou
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Donald W Parsons
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sharon E Plon
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA; Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, MA 02139, USA
| | - J Scott Roberts
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
| | - Joseph S Salama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard R Sharp
- Biomedical Ethics Research Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Brian Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nancy B Spinner
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Holly K Tabor
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Peter Tarczy-Hornoch
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; University of Washington, Seattle, WA 98105, USA
| | - David L Veenstra
- Department of Pharmacy, University of Washington, Seattle, WA 98195, USA
| | - Nikhil Wagle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Karen Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Benjamin S Wilfond
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Kirk Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susan M Wolf
- Law School, Medical School, and Consortium on Law and Values in Health, Environment, & the Life Sciences, Minneapolis, University of Minnesota, MN 55455, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY 10029, USA
| | - Joon-Ho Yu
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
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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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Yu S, Wei W, Xia M, Jiang Z, He D, Li Z, Han H, Chu W, Liu H, Chen J. Molecular characterization, alternative splicing and expression analysis ofACSF2and its correlation with egg-laying performance in geese. Anim Genet 2016; 47:451-62. [DOI: 10.1111/age.12435] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2016] [Indexed: 01/07/2023]
Affiliation(s)
- S. Yu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - W. Wei
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - M. Xia
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Z. Jiang
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - D. He
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Z. Li
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - H. Han
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - W. Chu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - H. Liu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - J. Chen
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
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48
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Collison FT, Xie YA, Gambin T, Jhangiani S, Muzny D, Gibbs R, Lupski JR, Fishman GA, Allikmets R. Whole Exome Sequencing Identifies an Adult-Onset Case of Methylmalonic Aciduria and Homocystinuria Type C (cblC) with Non-Syndromic Bull's Eye Maculopathy. Ophthalmic Genet 2016; 36:270-5. [PMID: 25687216 PMCID: PMC4539287 DOI: 10.3109/13816810.2015.1010736] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Background: Methylmalonic aciduria and homocystinuria type C (cblC), a disorder of vitamin B12 (cobalamin) metabolism caused by mutations in the MMACHC gene, presents with many systemic symptoms, including neurological, cognitive, psychiatric, and thromboembolic events. Retinal phenotypes, including maculopathy, pigmentary retinopathy, and optic atrophy are common in early onset form of the disease but are rare in adult onset forms. Materials and Methods: An adult Hispanic female presented with decreased central vision, bilateral pericentral ring scotomas and bull’s eye-appearing macular lesions at 28 years of age. Her medical history was otherwise unremarkable except for iron deficiency anemia and both urinary tract and kidney infections. Screening of the ABCA4 gene, mutations in which frequently cause bull’s eye maculopathy, was negative. Subsequently, analysis with whole exome sequencing was performed. Results: Whole exome sequencing discovered compound heterozygous mutations in MMACHC, c.G482A:p.Arg161Gln and c.270_271insA:p.Arg91Lysfs*14, which segregated with the disease in the family. The genetic diagnosis was confirmed by biochemical laboratory testing, showing highly elevated urine methylmalonic acid/creatinine and homocysteine levels, and suggesting disease management with hydroxycobalamin injections and carnitine supplementation. Conclusions: In summary, a unique case of an adult patient with bull’s eye macular lesions and no clinically relevant systemic symptoms was diagnosed with cblC by genetic screening and follow-up biochemical laboratory tests.
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Affiliation(s)
- Frederick T Collison
- a The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who Are Blind or Visually Impaired , Chicago , IL , USA
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49
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Pupavac M, Tian X, Chu J, Wang G, Feng Y, Chen S, Fenter R, Zhang VW, Wang J, Watkins D, Wong LJ, Rosenblatt DS. Added value of next generation gene panel analysis for patients with elevated methylmalonic acid and no clinical diagnosis following functional studies of vitamin B12 metabolism. Mol Genet Metab 2016; 117:363-8. [PMID: 26827111 DOI: 10.1016/j.ymgme.2016.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 12/13/2022]
Abstract
Next generation sequencing (NGS) based gene panel testing is increasingly available as a molecular diagnostic approach for inborn errors of metabolism. Over the past 40 years patients have been referred to the Vitamin B12 Clinical Research Laboratory at McGill University for diagnosis of inborn errors of cobalamin metabolism by functional studies in cultured fibroblasts. DNA samples from patients in which no diagnosis was made by these studies were tested by a NGS gene panel to determine whether any molecular diagnoses could be made. 131 DNA samples from patients with elevated methylmalonic acid and no diagnosis following functional studies of cobalamin metabolism were analyzed using the 24 gene extended cobalamin metabolism NGS based panel developed by Baylor Miraca Genetics Laboratories. Gene panel testing identified two or more variants in a single gene in 16/131 patients. Eight patients had pathogenic findings, one had a finding of uncertain significance, and seven had benign findings. Of the patients with pathogenic findings, five had mutations in ACSF3, two in SUCLG1 and one in TCN2. Thus, the NGS gene panel allowed for the presumptive diagnosis of 8 additional patients for which a diagnosis was not made by the functional assays.
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Affiliation(s)
- Mihaela Pupavac
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Xia Tian
- Baylor Miraca Genetics Laboratories, Houston, TX, United States
| | - Jordan Chu
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Guoli Wang
- Baylor Miraca Genetics Laboratories, Houston, TX, United States
| | - Yanming Feng
- Baylor Miraca Genetics Laboratories, Houston, TX, United States
| | - Stella Chen
- Baylor Miraca Genetics Laboratories, Houston, TX, United States
| | | | - Victor W Zhang
- Baylor Miraca Genetics Laboratories, Houston, TX, United States; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Jing Wang
- Baylor Miraca Genetics Laboratories, Houston, TX, United States; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - David Watkins
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Lee-Jun Wong
- Baylor Miraca Genetics Laboratories, Houston, TX, United States; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
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50
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de Sain-van der Velden MGM, van der Ham M, Jans JJ, Visser G, Prinsen HCMT, Verhoeven-Duif NM, van Gassen KLI, van Hasselt PM. A New Approach for Fast Metabolic Diagnostics in CMAMMA. JIMD Rep 2016; 30:15-22. [PMID: 26915364 PMCID: PMC5110436 DOI: 10.1007/8904_2016_531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 12/09/2015] [Accepted: 12/17/2015] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND The presence of increased urinary concentrations of both methylmalonic acid (MMA) and malonic acid (MA) is assumed to differentiate combined malonic and methylmalonic aciduria (CMAMMA), due to mutations in the ACSF3 gene, from other causes of methylmalonic aciduria (classic MMAemia). Detection of MA in urine, however, is challenging since excretion of MA can be easily missed. The objective of the study was to develop a method for quantification of MA in plasma to allow differentiation between CMAMMA and classic MMAemia. METHODS Compound heterozygosity for mutations in the ACSF3 gene was detected in two female siblings using diagnostic exome sequencing. Urine (MMA and MA) was analyzed with GC/MS, while plasma was analyzed with UPLC-MS/MS. MA/MMA ratios were calculated. RESULTS Both patients had a severe psychiatric presentation (at the age of 6 years and 5.5 years, respectively) after a viral infection. MA excretion in the patients was only just above the highest control value in several samples. MA concentrations in plasma from the two patients were clearly above the highest value observed in control subjects. However, MA concentrations in plasma from patients with classic MMAemia were also elevated. Additional, calculation of MA/MMA ratio in plasma allowed to fully differentiate between CMAMMA and classic MMAemia. CONCLUSIONS Calculating the MA/MMA ratio in plasma allows differentiation between CMAMMA and classic MMAemia. The full clinical spectrum of CMAMMA remains to be delineated.
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Affiliation(s)
| | - Maria van der Ham
- Department of Medical Genetics, UMC Utrecht, 85090, 3508AB, Utrecht, The Netherlands
| | - Judith J Jans
- Department of Medical Genetics, UMC Utrecht, 85090, 3508AB, Utrecht, The Netherlands
| | - Gepke Visser
- Department of Pediatric Gastroenterology and Metabolic Diseases, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | | | | | - Koen L I van Gassen
- Department of Medical Genetics, UMC Utrecht, 85090, 3508AB, Utrecht, The Netherlands
| | - Peter M van Hasselt
- Department of Pediatric Gastroenterology and Metabolic Diseases, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
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