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Qin Y, Godoy-Parejo C, Skowronska M, Verma A, Dejosez M, Zwaka TP. Generation of human pluripotent stem cell lines (WAe009-A) with THAP11 F80L cobalamin disorder-associated mutation. Stem Cell Res 2024; 79:103483. [PMID: 38943762 DOI: 10.1016/j.scr.2024.103483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Recent studies reported that the mutation in the THAP11 gene (THAP11F80L) could be responsible for the inborn vitamin deficiency known as cobalamin disorder, by affecting the expression of the enzyme MMACHC, key in the cobalamin metabolism. However, the specifics of the molecular mechanism are largely unknown. In here we generated genetically modified human pluripotent stem cell lines with THAP11F80L mutation, providing a new research tool for futher exploring the molecular mechanism. The established hPSC lines remain pluripotent, showing expression of OCT3/4, differentiation capacity to the three germ layers and displaying normal karyotype.
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Affiliation(s)
- Yiren Qin
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Godoy-Parejo
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Marta Skowronska
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angela Verma
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marion Dejosez
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas P Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Katayama K, Ito J, Murakami R, Yamashita A, Sasajima H, Narahashi S, Chiba J, Yamamoto I, Fujii W, Tochigi Y, Suzuki H. Mutation of the Thap4 gene causes dwarfism and testicular anomalies in rats and mice. Mamm Genome 2024; 35:149-159. [PMID: 38658415 DOI: 10.1007/s00335-024-10041-8] [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: 01/18/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The petit (pet) locus is associated with dwarfism, testicular anomalies, severe thymic hypoplasia, and high postnatal lethality, which are inherited in autosomal recessive mode of inheritance in rats with a Wistar strain genetic background. Linkage analysis localized the pet locus between 98.7 Mb and 101.2 Mb on rat chromosome 9. Nucleotide sequence analysis identified 2 bp deletion in exon 2 of the Thap4 gene as the causative mutation for pet. This deletion causes a frameshift and premature termination codon, resulting in a truncated THAP4 protein lacking approximately two-thirds of the C-terminal side. Thap4 is expressed in various organs, including the testis and thymus in rats. To elucidate the biological function of THAP4 in other species, we generated Thap4 knockout mice lacking exon 2 of the Thap4 gene through genome editing. Thap4 knockout mice also exhibited dwarfism and small testis but did not show high postnatal lethality. Thymus weights of adult Thap4 knockout male mice were significantly higher compared to wild-type male mice. Although Thap4 knockout male mice were fertile, their testis contained seminiferous tubules with spermatogenesis and degenerative seminiferous tubules lacking germ cells. Additionally, we observed vacuoles in seminiferous tubules, and clusters of cells in the lumen in seminiferous tubules in Thap4 knockout male mice. These results demonstrate that spontaneous mutation of Thap4 gene in rats and knockout of Thap4 gene in mice both cause dwarfism and testicular anomalies. Thap4 gene in rats and mice is essential for normal testicular development, maintaining spermatogenesis throughout the entire region of seminiferous tubules.
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Affiliation(s)
- Kentaro Katayama
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Junya Ito
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Rei Murakami
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Ayako Yamashita
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Hotaka Sasajima
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Satomi Narahashi
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Junko Chiba
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Ichiro Yamamoto
- Laboratory of Veterinary Biochemistry, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Wataru Fujii
- Laboratory of Biomedical Science, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuki Tochigi
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Hiroetsu Suzuki
- Laboratory of Veterinary Physiology, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan.
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Heinken A, El Kouche S, Guéant-Rodriguez RM, Guéant JL. Towards personalized genome-scale modeling of inborn errors of metabolism for systems medicine applications. Metabolism 2024; 150:155738. [PMID: 37981189 DOI: 10.1016/j.metabol.2023.155738] [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: 08/14/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023]
Abstract
Inborn errors of metabolism (IEMs) are a group of more than 1000 inherited diseases that are individually rare but have a cumulative global prevalence of 50 per 100,000 births. Recently, it has been recognized that like common diseases, patients with rare diseases can greatly vary in the manifestation and severity of symptoms. Here, we review omics-driven approaches that enable an integrated, holistic view of metabolic phenotypes in IEM patients. We focus on applications of Constraint-based Reconstruction and Analysis (COBRA), a widely used mechanistic systems biology approach, to model the effects of inherited diseases. Moreover, we review evidence that the gut microbiome is also altered in rare diseases. Finally, we outline an approach using personalized metabolic models of IEM patients for the prediction of biomarkers and tailored therapeutic or dietary interventions. Such applications could pave the way towards personalized medicine not just for common, but also for rare diseases.
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Affiliation(s)
- Almut Heinken
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France.
| | - Sandra El Kouche
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Rosa-Maria Guéant-Rodriguez
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France; National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
| | - Jean-Louis Guéant
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France; National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
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4
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Perez I, Reyes-Nava NG, Pinales BE, Quintana AM. Overexpression of MMACHC Prevents Craniofacial Phenotypes Caused by Knockdown of znf143b. AMERICAN JOURNAL OF UNDERGRADUATE RESEARCH 2023; 20:77-84. [PMID: 38617190 PMCID: PMC11013955 DOI: 10.33697/ajur.2023.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
ZNF143 is a sequence-specific DNA binding protein that regulates the expression of protein-coding genes and small RNA molecules. In humans, ZNF143 interacts with HCFC1, a transcriptional cofactor, to regulate the expression of downstream target genes, including MMACHC, which encodes an enzyme involved in cobalamin (cbl) metabolism. Mutations in HCFC1 or ZNF143 cause an inborn error of cobalamin metabolism characterized by abnormal cbl metabolism, intellectual disability, seizures, and mild to moderate craniofacial abnormalities. However, the mechanisms by which ZNF143 mutations cause individual phenotypes are not completely understood. Defects in metabolism and craniofacial development are hypothesized to occur because of decreased expression of MMACHC. But recent results have called into question this mechanism as the cause for craniofacial development. Therefore, in the present study, we implemented a loss of function analysis to begin to uncover the function of ZNF143 in craniofacial development using the developing zebrafish. The knockdown of znf143b, one zebrafish ortholog of ZNF143, caused craniofacial phenotypes of varied severity, which included a shortened and cleaved Meckel's cartilage, partial loss of ceratobranchial arches, and a distorted ceratohyal. These phenotypes did not result from a defect in the number of total chondrocytes but were associated with a mild to moderate decrease in mmachc expression. Interestingly, expression of human MMACHC via endogenous transgene prevented the onset of craniofacial phenotypes associated with znf143b knockdown. Collectively, our data establishes that knockdown of znf143b causes craniofacial phenotypes that can be alleviated by increased expression of MMACHC.
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Affiliation(s)
- Isaiah Perez
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX
| | | | - Briana E. Pinales
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX
| | - Anita M. Quintana
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX
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Castro VL, Paz D, Virrueta V, Estevao IL, Grajeda BI, Ellis CC, Quintana AM. Missense and nonsense mutations of the zebrafish hcfc1a gene result in contrasting mTor and radial glial phenotypes. Gene 2023; 864:147290. [PMID: 36804358 DOI: 10.1016/j.gene.2023.147290] [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: 11/01/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/20/2023]
Abstract
Mutations in the HCFC1 transcriptional co-factor protein are the cause of cblX syndrome and X-linked intellectual disability (XLID). cblX is the more severe disorder associated with intractable epilepsy, abnormal cobalamin metabolism, facial dysmorphia, cortical gyral malformations, and intellectual disability. In vitro, murine Hcfc1 regulates neural precursor (NPCs) proliferation and number, which has been validated in zebrafish. However, conditional deletion of mouse Hcfc1 in Nkx2.1 + cells increased cell death, reduced Gfap expression, and reduced numbers of GABAergic neurons. Thus, the role of this gene in brain development is not completely understood. Recently, knock-in of both a cblX (HCFC1) and cblX-like (THAP11) allele were created in mice. Knock-in of the cblX-like allele was associated with increased expression of proteins required for ribosome biogenesis. However, the brain phenotypes were not comprehensively studied due to sub-viability. Therefore, a mechanism underlying increased ribosome biogenesis was not described. We used a missense, a nonsense, and two conditional zebrafish alleles to further elucidate this mechanism during brain development. We observed contrasting phenotypes at the level of Akt/mTor activation, the number of radial glial cells, and the expression of two downstream target genes of HCFC1, asxl1 and ywhab. Despite these divergent phenotypes, each allele studied demonstrates with a high degree of face validity when compared to the phenotypes reported in the literature. Collectively, these data suggest that individual mutations in the HCFC1 protein result in differential mTOR activity which may be associated with contrasting cellular phenotypes.
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Affiliation(s)
- Victoria L Castro
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, USA.
| | - David Paz
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, USA
| | - Valeria Virrueta
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, USA
| | - Igor L Estevao
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, USA
| | - Brian I Grajeda
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, USA
| | - Cameron C Ellis
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, USA
| | - Anita M Quintana
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, USA.
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Tan D, Wei C, Chen Z, Huang Y, Deng J, Li J, Liu Y, Bao X, Xu J, Hu Z, Wang S, Fan Y, Jiang Y, Wu Y, Wu Y, Wang S, Liu P, Zhang Y, Yang Z, Jiang Y, Zhang H, Hong D, Zhong N, Jiang H, Xiong H. CAG Repeat Expansion in THAP11 Is Associated with a Novel Spinocerebellar Ataxia. Mov Disord 2023. [PMID: 37148549 DOI: 10.1002/mds.29412] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND More than 50 loci are associated with spinocerebellar ataxia (SCA), and the most frequent subtypes share nucleotide repeats expansion, especially CAG expansion. OBJECTIVE The objective of this study was to confirm a novel SCA subtype caused by CAG expansion. METHODS We performed long-read whole-genome sequencing combined with linkage analysis in a five-generation Chinese family, and the finding was validated in another pedigree. The three-dimensional structure and function of THAP11 mutant protein were predicted. Polyglutamine (polyQ) toxicity of THAP11 gene with CAG expansion was assessed in skin fibroblasts of patients, human embryonic kidney 293 and Neuro-2a cells. RESULTS We identified THAP11 as the novel causative SCA gene with CAG repeats ranging from 45 to 100 in patients with ataxia and from 20 to 38 in healthy control subjects. Among the patients, the number of CAA interruptions within CAG repeats was decreased to 3 (up to 5-6 in controls), whereas the number of 3' pure CAG repeats was up to 32 to 87 (4-16 in controls), suggesting that the toxicity of polyQ protein was length dependent on the pure CAG repeats. Intracellular aggregates were observed in cultured skin fibroblasts from patients. THAP11 polyQ protein was more intensely distributed in the cytoplasm of cultured skin fibroblasts from patients, which was replicated with in vitro cultured neuro-2a transfected with 54 or 100 CAG repeats. CONCLUSIONS This study identified a novel SCA subtype caused by intragenic CAG repeat expansion in THAP11 with intracellular aggregation of THAP11 polyQ protein. Our findings extended the spectrum of polyQ diseases and offered a new perspective in understanding polyQ-mediated toxic aggregation. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Dandan Tan
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Cuijie Wei
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yu Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, P.R. China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, P.R. China
| | | | - Yidan Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Xinhua Bao
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Jin Xu
- Center of Ultrastructural Pathology, Lab of Electron Microscopy, Peking University First Hospital, Beijing, P.R. China
| | - Zhengmao Hu
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, P.R. China
| | - Suxia Wang
- Center of Ultrastructural Pathology, Lab of Electron Microscopy, Peking University First Hospital, Beijing, P.R. China
| | - Yanbin Fan
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Yizheng Jiang
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, P.R. China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Yuan Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Shuang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Panyan Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Hong Zhang
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Daojun Hong
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - Nanbert Zhong
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, P.R. China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, P.R. China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, P.R. China
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, P.R. China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
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Paz D, Pinales BE, Castellanos BS, Perez I, Gil CB, Madrigal LJ, Reyes-Nava NG, Castro VL, Sloan JL, Quintana AM. Abnormal chondrocyte development in a zebrafish model of cblC syndrome restored by an MMACHC cobalamin binding mutant. Differentiation 2023; 131:74-81. [PMID: 37167860 DOI: 10.1016/j.diff.2023.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/13/2023]
Abstract
Variants in the MMACHC gene cause combined methylmalonic acidemia and homocystinuria cblC type, the most common inborn error of intracellular cobalamin (vitamin B12) metabolism. cblC is associated with neurodevelopmental, hematological, ocular, and biochemical abnormalities. In a subset of patients, mild craniofacial dysmorphia has also been described. Mouse models of Mmachc deletion are embryonic lethal but cause severe craniofacial phenotypes such as facial clefts. MMACHC encodes an enzyme required for cobalamin processing and variants in this gene result in the accumulation of two metabolites: methylmalonic acid (MMA) and homocysteine (HC). Interestingly, other inborn errors of cobalamin metabolism, such as cblX syndrome, are associated with mild facial phenotypes. However, the presence and severity of MMA and HC accumulation in cblX syndrome is not consistent with the presence or absence of facial phenotypes. Thus, the mechanisms by which mutations in MMACHC cause craniofacial defects are yet to be completely elucidated. Here we have characterized the craniofacial phenotypes in a zebrafish model of cblC (hg13) and performed restoration experiments with either a wildtype or a cobalamin binding deficient MMACHC protein. Homozygous mutants did not display gross morphological defects in facial development but did have abnormal chondrocyte nuclear organization and an increase in the average number of neighboring cell contacts, both phenotypes were fully penetrant. Abnormal chondrocyte nuclear organization was not associated with defects in the localization of neural crest specific markers, sox10 (RFP transgene) or barx1. Both nuclear angles and the number of neighboring cell contacts were fully restored by wildtype MMACHC and a cobalamin binding deficient variant of the MMACHC protein. Collectively, these data suggest that mutation of MMACHC causes mild to moderate craniofacial phenotypes that are independent of cobalamin binding.
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Affiliation(s)
- David Paz
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Briana E Pinales
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Barbara S Castellanos
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Isaiah Perez
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Claudia B Gil
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Lourdes Jimenez Madrigal
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Nayeli G Reyes-Nava
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Victoria L Castro
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Jennifer L Sloan
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anita M Quintana
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA.
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8
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Paz D, Pinales BE, Castellanos BS, Perez I, Gil CB, Madrigal LJ, Reyes-Nava NG, Castro VL, Sloan JL, Quintana AM. Abnormal chondrocyte intercalation in a zebrafish model of cblC syndrome restored by an MMACHC cobalamin binding mutant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524982. [PMID: 36711998 PMCID: PMC9882310 DOI: 10.1101/2023.01.20.524982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Variants in the MMACHC gene cause combined methylmalonic acidemia and homocystinuria cblC type, the most common inborn error of intracellular cobalamin (vitamin B12) metabolism. cblC is associated with neurodevelopmental, hematological, ocular, and biochemical abnormalities. In a subset of patients, mild craniofacial dysmorphia has also been described. Mouse models of Mmachc deletion are embryonic lethal but cause severe craniofacial phenotypes such as facial clefts. MMACHC encodes an enzyme required for cobalamin processing and variants in this gene result in the accumulation of two metabolites: methylmalonic acid (MMA) and homocysteine (HC). Interestingly, other inborn errors of cobalamin metabolism, such as cblX syndrome, are associated with mild facial phenotypes. However, the presence and severity of MMA and HC accumulation in cblX syndrome is not consistent with the presence or absence of facial phenotypes. Thus, the mechanisms by which mutation of MMACHC cause craniofacial defects have not been completely elucidated. Here we have characterized the craniofacial phenotypes in a zebrafish model of cblC ( hg13 ) and performed restoration experiments with either wildtype or a cobalamin binding deficient MMACHC protein. Homozygous mutants did not display gross morphological defects in facial development, but did have abnormal chondrocyte intercalation, which was fully penetrant. Abnormal chondrocyte intercalation was not associated with defects in the expression/localization of neural crest specific markers, sox10 or barx1 . Most importantly, chondrocyte organization was fully restored by wildtype MMACHC and a cobalamin binding deficient variant of MMACHC protein. Collectively, these data suggest that mutation of MMACHC causes mild to moderate craniofacial phenotypes that are independent of cobalamin binding.
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Affiliation(s)
- David Paz
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Briana E Pinales
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Barbara S Castellanos
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Isaiah Perez
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Claudia B Gil
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Lourdes Jimenez Madrigal
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Nayeli G Reyes-Nava
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Victoria L Castro
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Jennifer L Sloan
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Anita M Quintana
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
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9
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Elangovan R, Baruteau J. Inherited and acquired vitamin B12 deficiencies: Which administration route to choose for supplementation? Front Pharmacol 2022; 13:972468. [PMID: 36249776 PMCID: PMC9559827 DOI: 10.3389/fphar.2022.972468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Vitamin B12 or cobalamin deficiency is a commonly encountered clinical scenario and most clinicians will have familiarity prescribing Vitamin B12 to treat their patients. Despite the high prevalence of this condition, there is widespread heterogeneity regarding routes, schedules and dosages of vitamin B12 administration. In this review, we summarise the complex metabolic pathway of Vitamin B12, the inherited and acquired causes of Vitamin B12 deficiency and subsequently highlight the disparate international practice of prescribing Vitamin B12 replacement therapy. We describe the evidence base underpinning the novel sublingual, intranasal and subcutaneous modes of B12 replacement in comparison to intramuscular and oral routes, with their respective benefits for patient compliance and cost-saving.
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Affiliation(s)
- Ramyia Elangovan
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Julien Baruteau
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- National Institute of Health Research Great Ormond Street Biomedical Research Centre, London, United Kingdom
- *Correspondence: Julien Baruteau,
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10
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Esser AJ, Mukherjee S, Dereven‘kov IA, Makarov SV, Jacobsen DW, Spiekerkoetter U, Hannibal L. Versatile Enzymology and Heterogeneous Phenotypes in Cobalamin Complementation Type C Disease. iScience 2022; 25:104981. [PMID: 36105582 PMCID: PMC9464900 DOI: 10.1016/j.isci.2022.104981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nutritional deficiency and genetic errors that impair the transport, absorption, and utilization of vitamin B12 (B12) lead to hematological and neurological manifestations. The cblC disease (cobalamin complementation type C) is an autosomal recessive disorder caused by mutations and epi-mutations in the MMACHC gene and the most common inborn error of B12 metabolism. Pathogenic mutations in MMACHC disrupt enzymatic processing of B12, an indispensable step before micronutrient utilization by the two B12-dependent enzymes methionine synthase (MS) and methylmalonyl-CoA mutase (MUT). As a result, patients with cblC disease exhibit plasma elevation of homocysteine (Hcy, substrate of MS) and methylmalonic acid (MMA, degradation product of methylmalonyl-CoA, substrate of MUT). The cblC disorder manifests early in childhood or in late adulthood with heterogeneous multi-organ involvement. This review covers current knowledge on the cblC disease, structure–function relationships of the MMACHC protein, the genotypic and phenotypic spectra in humans, experimental disease models, and promising therapies.
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11
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Wang F, Liang L, Ling S, Yu Y, Chen T, Xu F, Gong Z, Han L. Clinical characteristics and genotype analysis of five infants with cblX type of methylmalonic acidemia. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:298-305. [PMID: 36207831 PMCID: PMC9511482 DOI: 10.3724/zdxbyxb-2022-0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/30/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE To investigate the clinical and genetic characteristics of infants with cobalamin (cbl) X type of methylmalonic acidemia (MMA). METHODS The clinical data of 5 infants with cblX type of MMA diagnosed in Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine and Shanghai Children's Hospital from the year 2016 to 2020 were collected. The levels of blood acylcarnitines were detected by tandem mass spectrometry, the levels of urinary organic acids were detected by gas-chromatography mass spectrometry, the pathogenic genes were detected by whole exon gene sequencing, and the effect of new pathogenic mutations on three-dimensional protein structure was predicted by bioinformatics analysis. RESULTS Five infants with cblX type were diagnosed, including 4 males and 1 female, and the onset age was 0-6 months. The main clinical manifestations of 4 males were intractable epilepsy, mental and motor retardation, metabolic abnormalities presented mild increase of blood homocysteine level. Among them, 3 cases were accompanied by slight increase of urinary methylmalonic acid, and 1 case was accompanied by increase of blood propionylcarnitine (C3) and C3/acetylcarnitine (C2). Gene detection found that 2 cases carried a same hemizygous mutation c.344C>T (p.A115V) of HCFC1 gene, which was the most reported mutation, and the other 2 cases carried novel pathogenic mutations, c.92G>A (p.R31Q) and c.166G>C (p.V56L). These 3 gene mutations located in the Kelch domain of HCFC1 protein. One female infant carried a benign mutation of c.3731G>T (p.R1244L). Her clinical symptoms were mild, and only the urinary methylmalonic acid was slightly increased. CONCLUSIONS The clinical manifestations of children with cblX type of MMA are intractable epilepsy, mental and motor retardation, and other serious neurological symptoms. Their metabolic abnormalities present the increase of blood homocysteine with methylmalonic acid (urinary methylmalonic acid or/and blood C3, C3/C2). The clinical and biochemical phenotypes are separated, so the diagnosis should be in combination with the results of gene testing.
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Affiliation(s)
- Fei Wang
- 1. Department of Endocrinology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Lili Liang
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Shiying Ling
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Yue Yu
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Ting Chen
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Feng Xu
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Zhuwen Gong
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Lianshu Han
- 2. Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
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12
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Wiedemann A, Oussalah A, Lamireau N, Théron M, Julien M, Mergnac JP, Augay B, Deniaud P, Alix T, Frayssinoux M, Feillet F, Guéant JL. Clinical, phenotypic and genetic landscape of case reports with genetically proven inherited disorders of vitamin B 12 metabolism: A meta-analysis. Cell Rep Med 2022; 3:100670. [PMID: 35764087 PMCID: PMC9381384 DOI: 10.1016/j.xcrm.2022.100670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/22/2021] [Accepted: 06/02/2022] [Indexed: 10/31/2022]
Abstract
Inherited disorders of B12 metabolism produce a broad spectrum of manifestations, with limited knowledge of the influence of age and the function of related genes. We report a meta-analysis on 824 patients with a genetically proven diagnosis of an inherited disorder of vitamin B12 metabolism. Gene clusters and age categories are associated with patients' manifestations. The "cytoplasmic transport" cluster is associated with neurological and ophthalmological manifestations, the "mitochondrion" cluster with hypotonia, acute metabolic decompensation, and death, and the "B12 availability" and "remethylation" clusters with anemia and cytopenia. Hypotonia, EEG abnormalities, nystagmus, and strabismus are predominant in the younger patients, while neurological manifestations, such as walking difficulties, peripheral neuropathy, pyramidal syndrome, cerebral atrophy, psychiatric disorders, and thromboembolic manifestations, are predominant in the older patients. These results should prompt systematic checking of markers of vitamin B12 status, including homocysteine and methylmalonic acid, when usual causes of these manifestations are discarded in adult patients.
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Affiliation(s)
- Arnaud Wiedemann
- Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000 Nancy, France; Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France; Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Abderrahim Oussalah
- Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000 Nancy, France; Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France; Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, 54000 Nancy, France
| | - Nathalie Lamireau
- Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France
| | - Maurane Théron
- Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France
| | - Melissa Julien
- Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, 54000 Nancy, France
| | | | - Baptiste Augay
- Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France
| | - Pauline Deniaud
- Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France
| | - Tom Alix
- Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, 54000 Nancy, France
| | - Marine Frayssinoux
- Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, 54000 Nancy, France
| | - François Feillet
- Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000 Nancy, France; Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France; Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Louis Guéant
- Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000 Nancy, France; Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France; Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, 54000 Nancy, France.
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13
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Kiessling E, Peters F, Ebner LJ, Merolla L, Samardzija M, Baumgartner MR, Grimm C, Froese DS. HIF1 and DROSHA are involved in MMACHC repression in hypoxia. Biochim Biophys Acta Gen Subj 2022; 1866:130175. [DOI: 10.1016/j.bbagen.2022.130175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/03/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022]
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14
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Watkins D, Rosenblatt DS. Inherited defects of cobalamin metabolism. VITAMINS AND HORMONES 2022; 119:355-376. [PMID: 35337626 DOI: 10.1016/bs.vh.2022.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cobalamin (vitamin B12) is required for activity of the enzymes methylmalonyl-CoA mutase and methionine synthase in human cells. Inborn errors affecting cobalamin uptake or metabolism are characterized by accumulation of the substrates for these enzymes, methylmalonic acid and homocysteine, in blood and urine. Inborn errors affecting synthesis of the adenosylcobalamin coenzyme required by methylmalonyl-CoA mutase (cblA and cblB) result in isolated methylmalonic aciduria; inborn errors affecting synthesis of the methylcobalamin coenzyme required by methionine synthase (cblE and cblG) result in isolated homocystinuria. Combined methylmalonic aciduria and homocystinuria is seen in patients with impaired intestinal cobalamin absorption (intrinsic factor deficiency, Imerslund-Gräsbeck syndrome) and with defects affecting synthesis of both cobalamin coenzymes (cblC, cblD, cblF and cblJ). A series of disorders caused by pathogenic variant mutations affecting gene regulators (transcription factors) of the MMACHC gene have recently been described (HCFC1 [cblX disorder] and deficiencies of THAP11, and ZNF143 [the cblK disorder]).
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Affiliation(s)
- David Watkins
- Department of Human Genetics, McGill University, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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15
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Oussalah A, Siblini Y, Hergalant S, Chéry C, Rouyer P, Cavicchi C, Guerrini R, Morange PE, Trégouët D, Pupavac M, Watkins D, Pastinen T, Chung WK, Ficicioglu C, Feillet F, Froese DS, Baumgartner MR, Benoist JF, Majewski J, Morrone A, Rosenblatt DS, Guéant JL. Epimutations in both the TESK2 and MMACHC promoters in the Epi-cblC inherited disorder of intracellular metabolism of vitamin B 12. Clin Epigenetics 2022; 14:52. [PMID: 35440018 PMCID: PMC9020039 DOI: 10.1186/s13148-022-01271-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/05/2022] [Indexed: 03/14/2023] Open
Abstract
Background epi-cblC is a recently discovered inherited disorder of intracellular vitamin B12 metabolism associating hematological, neurological, and cardiometabolic outcomes. It is produced by an epimutation at the promoter common to CCDC163P and MMACHC, which results from an aberrant antisense transcription due to splicing mutations in the antisense PRDX1 gene neighboring MMACHC. We studied whether the aberrant transcription produced a second epimutation by encompassing the CpG island of the TESK2 gene neighboring CCDC163P.
Methods We unraveled the methylome architecture of the CCDC163P–MMACHC CpG island (CpG:33) and the TESK2 CpG island (CpG:51) of 17 epi-cblC cases. We performed an integrative analysis of the DNA methylome profiling, transcriptome reconstruction of RNA-sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-Seq) of histone H3, and transcription expression of MMACHC and TESK2.
Results The PRDX1 splice mutations and activation of numerous cryptic splice sites produced antisense readthrough transcripts encompassing the bidirectional MMACHC/CCDC163P promoter and the TESK2 promoter, resulting in the silencing of both the MMACHC and TESK2 genes through the deposition of SETD2-dependent H3K36me3 marks and the generation of epimutations in the CpG islands of the two promoters. Conclusions The antisense readthrough transcription of the mutated PRDX1 produces an epigenetic silencing of MMACHC and TESK2. We propose using the term 'epi-digenism' to define this epigenetic disorder that affects two genes. Epi-cblC is an entity that differs from cblC. Indeed, the PRDX1 and TESK2 altered expressions are observed in epi-cblC but not in cblC, suggesting further evaluating the potential consequences on cancer risk and spermatogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01271-1.
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Affiliation(s)
- Abderrahim Oussalah
- INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France.,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology and Nutrition, University Hospital of Nancy, 54000, Nancy, France
| | - Youssef Siblini
- INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France
| | - Sébastien Hergalant
- INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France
| | - Céline Chéry
- INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France.,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology and Nutrition, University Hospital of Nancy, 54000, Nancy, France
| | - Pierre Rouyer
- INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France
| | - Catia Cavicchi
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy
| | - Renzo Guerrini
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy.,Department of NEUROFARBA, University of Florence, Florence, Italy
| | - Pierre-Emmanuel Morange
- INSERM UMR_S 1263, Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, 13385, Marseille, France
| | - David Trégouët
- INSERM, BPH, U1219, Université Bordeaux, 33000, Bordeaux, France
| | - Mihaela Pupavac
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - David Watkins
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, USA
| | - Can Ficicioglu
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - François Feillet
- INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France.,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France
| | - D Sean Froese
- Division of Metabolism, University Children's Hospital, University of Zürich, Zürich, Switzerland
| | - Matthias R Baumgartner
- Division of Metabolism, University Children's Hospital, University of Zürich, Zürich, Switzerland
| | - Jean-François Benoist
- Biochemistry Hormonology Laboratory, Robert-Debré University Hospital, APHP, 48 bd Serurier, 75019, Paris, France
| | - Jacek Majewski
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Amelia Morrone
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy.,Department of NEUROFARBA, University of Florence, Florence, Italy
| | - David S Rosenblatt
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Jean-Louis Guéant
- INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France. .,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology and Nutrition, University Hospital of Nancy, 54000, Nancy, France. .,Department of Hepato-Gastroenterology, University Hospital of Nancy, 54000, Nancy, France.
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16
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Hannibal L, Jacobsen DW. Intracellular processing of vitamin B 12 by MMACHC (CblC). VITAMINS AND HORMONES 2022; 119:275-298. [PMID: 35337623 DOI: 10.1016/bs.vh.2022.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Vitamin B12 (cobalamin, Cbl, B12) is a water-soluble micronutrient synthesized exclusively by a group of microorganisms. Human beings are unable to make B12 and thus obtain the vitamin via intake of animal products, fermented plant-based foods or supplements. Vitamin B12 obtained from the diet comprises three major chemical forms, namely hydroxocobalamin (HOCbl), methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl). The most common form of B12 present in supplements is cyanocobalamin (CNCbl). Yet, these chemical forms cannot be utilized directly as they come, but instead, they undergo chemical processing by the MMACHC protein, also known as CblC. Processing of dietary B12 by CblC involves removal of the upper-axial ligand (beta-ligand) yielding the one-electron reduced intermediate cob(II)alamin. Newly formed cob(II)alamin undergoes trafficking and delivery to the two B12-dependent enzymes, cytosolic methionine synthase (MS) and mitochondrial methylmalonyl-CoA mutase (MUT). The catalytic cycles of MS and MUT incorporate cob(II)alamin as a precursor to regenerate the coenzyme forms MeCbl and AdoCbl, respectively. Mutations and epimutations in the MMACHC gene result in cblC disease, the most common inborn error of B12 metabolism, which manifests with combined homocystinuria and methylmalonic aciduria. Elevation of metabolites homocysteine and methylmalonic acid occurs because the lack of an active CblC blocks formation of the indispensable precursor cob(II)alamin that is necessary to activate MS and MUT. Thus, in patients with cblC disease, vitamin B12 is absorbed and present in circulation in normal to high concentrations, yet, cells are unable to make use of it. Mutations in seemingly unrelated genes that modify MMACHC gene expression also result in clinical phenotypes that resemble cblC disease. We review current knowledge on structural and functional aspects of intracellular processing of vitamin B12 by the versatile protein CblC, its partners and possible regulators.
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Affiliation(s)
- Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany.
| | - Donald W Jacobsen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
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17
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Chern T, Achilleos A, Tong X, Hill MC, Saltzman AB, Reineke LC, Chaudhury A, Dasgupta SK, Redhead Y, Watkins D, Neilson JR, Thiagarajan P, Green JBA, Malovannaya A, Martin JF, Rosenblatt DS, Poché RA. Mutations in Hcfc1 and Ronin result in an inborn error of cobalamin metabolism and ribosomopathy. Nat Commun 2022; 13:134. [PMID: 35013307 PMCID: PMC8748873 DOI: 10.1038/s41467-021-27759-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Combined methylmalonic acidemia and homocystinuria (cblC) is the most common inborn error of intracellular cobalamin metabolism and due to mutations in Methylmalonic Aciduria type C and Homocystinuria (MMACHC). Recently, mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) were shown to result in cellular phenocopies of cblC. Since HCFC1/RONIN jointly regulate MMACHC, patients with mutations in these factors suffer from reduced MMACHC expression and exhibit a cblC-like disease. However, additional de-regulated genes and the resulting pathophysiology is unknown. Therefore, we have generated mouse models of this disease. In addition to exhibiting loss of Mmachc, metabolic perturbations, and developmental defects previously observed in cblC, we uncovered reduced expression of target genes that encode ribosome protein subunits. We also identified specific phenotypes that we ascribe to deregulation of ribosome biogenesis impacting normal translation during development. These findings identify HCFC1/RONIN as transcriptional regulators of ribosome biogenesis during development and their mutation results in complex syndromes exhibiting aspects of both cblC and ribosomopathies. Combined methylmalonic acidemia (MMA) and hyperhomocysteinemias are inborn errors of vitamin B12 metabolism, and mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) underlie some forms of these disorders. Here the authors generated mouse models of a human syndrome due to mutations in RONIN (THAP11) and HCFC1, and show that this syndrome is both an inborn error of vitamin B12 metabolism and displays some features of ribosomopathy.
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Affiliation(s)
- Tiffany Chern
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Annita Achilleos
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus.
| | - Xuefei Tong
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Hill
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alexander B Saltzman
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lucas C Reineke
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arindam Chaudhury
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Swapan K Dasgupta
- Department of Pathology, Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, 77030, USA
| | - Yushi Redhead
- The Francis Crick Institute, London, NW1 1AT, UK.,Centre for Craniofacial Biology and Regeneration, King's College London, London, SE1 9RT, UK
| | - David Watkins
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Perumal Thiagarajan
- Department of Pathology, Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeremy B A Green
- Centre for Craniofacial Biology and Regeneration, King's College London, London, SE1 9RT, UK
| | - Anna Malovannaya
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Heart Institute, Houston, TX, 77030, USA
| | - David S Rosenblatt
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Ross A Poché
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.
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18
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Shen Y, Hu Z, Yang J, Yang R, Huang X. A case of methylmalonic acidemia and homocysteinemia cblX type with negative tandem mass spectrometry testing. Zhejiang Da Xue Xue Bao Yi Xue Ban 2021; 50:795-798. [PMID: 35347920 PMCID: PMC8931597 DOI: 10.3724/zdxbyxb-2021-0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/10/2021] [Indexed: 06/14/2023]
Abstract
A child with methylmalonic acidemia and homocysteinemia cblX type presented focal seizures and epileptic spasms in early infancy, but the tandem mass spectrometry tests showed negative results during neonatal screening or acute attack. Despite treated with a variety of antiepileptic drugs, the child died at age of The blood spot sample of the patient was retrospectively tested with ultrahigh performance liquid chromatography-tandem mass spectrometry, and the increased levels of methylmalonic acid and homocysteine were revealed. Whole exome sequencing showed that the proband had a c.202C>G(p.Q68E) hemizygous mutation in gene, which was inherited from his mother.
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Zwaka TP, Skowronska M, Richman R, Dejosez M. Ronin overexpression induces cerebellar degeneration in a mouse model of ataxia. Dis Model Mech 2021; 14:269269. [PMID: 34165550 PMCID: PMC8246265 DOI: 10.1242/dmm.044834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/18/2021] [Indexed: 11/26/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) are a group of genetically heterogeneous inherited neurodegenerative disorders characterized by progressive ataxia and cerebellar degeneration. Here, we used a mouse model to test a possible connection between SCA and Ronin (Thap11), a polyglutamine-containing transcriptional regulator encoded in a region of human chromosome 16q22.1 that has been genetically linked to SCA type 4. We report that transgenic expression of Ronin in mouse cerebellar Purkinje cells leads to detrimental loss of these cells and the development of severe ataxia as early as 10 weeks after birth. Mechanistically, we find that several SCA-causing genes harbor Ronin DNA-binding motifs and are transcriptionally deregulated in transgenic animals. In addition, ectopic expression of Ronin in embryonic stem cells significantly increases the protein level of Ataxin-1, the protein encoded by Atxn1, alterations of which cause SCA type 1. This increase is also seen in the cerebellum of transgenic animals, although the latter was not statistically significant. Hence, our data provide evidence for a link between Ronin and SCAs, and suggest that Ronin may be involved in the development of other neurodegenerative diseases. Summary: Ronin is a polyglutamine protein encoded in a region of human chromosome 16q22.1 linked to spinocerebellar ataxia type 4. Overexpression of Ronin in mouse cerebellar Purkinje cells leads to their loss and ataxia.
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Affiliation(s)
- Thomas P Zwaka
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marta Skowronska
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ronald Richman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marion Dejosez
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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20
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Zanandrea R, Wiprich MT, Altenhofen S, Rubensam G, Dos Santos TM, Wyse ATS, Bonan CD. Paternal exposure to excessive methionine altered behavior and neurochemical activities in zebrafish offspring. Amino Acids 2021; 53:1153-1167. [PMID: 34156542 DOI: 10.1007/s00726-021-03019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
An increase in plasma L-methionine (Met) levels, even if transitory, can cause important toxicological alterations in the affected individuals. Met is essential in the regulation of epigenetic mechanisms and its influence on the subsequent generation has been investigated. However, few studies have explored the influence of a temporary increase in Met levels in parents on their offspring. This study evaluated the behavioral and neurochemical effects of parental exposure to high Met concentration (3 mM) in zebrafish offspring. Adult zebrafish were exposed to Met for 7 days, maintained for additional 7 days in tanks that contained only water, and then used for breeding. The offspring obtained from these fish (F1) were tested in this study. During the early stages of offspring development, morphology, heart rate, survival, locomotion, and anxiety-like behavior were assessed. When these animals reached the adult stage, locomotion, anxiety, aggression, social interaction, memory, oxidative stress, and levels of amino acids and neurotransmitters were analyzed. F1 larvae Met group presented an increase in the distance and mean speed when compared to the control group. F1 adult Met group showed decreased anxiety-like behavior and locomotion. An increase in reactive oxygen species was also observed in the F1 adult Met group whereas lipid peroxidation and antioxidant enzymes did not change when compared to the control group. Dopamine, serotonin, glutamate, and glutathione levels were increased in the F1 adult Met group. Taken together, our data show that even a transient increase in Met in parents can cause behavioral and neurochemical changes in the offspring, promoting transgenerational effects.
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Affiliation(s)
- Rodrigo Zanandrea
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Escola de Medicina, Pontifícia Universidade Católica Do Rio Grande Do Sul, Porto Alegre, RS, Brazil.,Laboratório de Neuroquímica e Psicofarmacologia, Escola de Ciências de Saúde e da Vida, Pontifícia Universidade Católica Do Rio Grande Do Sul, Avenida Ipiranga, 6681-Prédio 12, Bloco D, Sala 301, Porto Alegre, RS, Brazil
| | - Melissa Talita Wiprich
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Escola de Medicina, Pontifícia Universidade Católica Do Rio Grande Do Sul, Porto Alegre, RS, Brazil.,Laboratório de Neuroquímica e Psicofarmacologia, Escola de Ciências de Saúde e da Vida, Pontifícia Universidade Católica Do Rio Grande Do Sul, Avenida Ipiranga, 6681-Prédio 12, Bloco D, Sala 301, Porto Alegre, RS, Brazil
| | - Stefani Altenhofen
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Escola de Medicina, Pontifícia Universidade Católica Do Rio Grande Do Sul, Porto Alegre, RS, Brazil.,Laboratório de Neuroquímica e Psicofarmacologia, Escola de Ciências de Saúde e da Vida, Pontifícia Universidade Católica Do Rio Grande Do Sul, Avenida Ipiranga, 6681-Prédio 12, Bloco D, Sala 301, Porto Alegre, RS, Brazil
| | - Gabriel Rubensam
- Centro de Pesquisa em Toxicologia e Farmacologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Tiago Marcon Dos Santos
- Programa de Pós-Graduação Em Ciências Biológicas-Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Angela T S Wyse
- Programa de Pós-Graduação Em Ciências Biológicas-Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Carla Denise Bonan
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Escola de Medicina, Pontifícia Universidade Católica Do Rio Grande Do Sul, Porto Alegre, RS, Brazil. .,Laboratório de Neuroquímica e Psicofarmacologia, Escola de Ciências de Saúde e da Vida, Pontifícia Universidade Católica Do Rio Grande Do Sul, Avenida Ipiranga, 6681-Prédio 12, Bloco D, Sala 301, Porto Alegre, RS, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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21
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Sanghavi HM, Majumdar S. Oligomerization of THAP9 Transposase via Amino-Terminal Domains. Biochemistry 2021; 60:1822-1835. [PMID: 34033475 DOI: 10.1021/acs.biochem.1c00010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Active DNA transposases like the Drosophila P element transposase (DmTNP) undergo oligomerization as a prerequisite for transposition. Human THAP9 (hTHAP9) is a catalytically active but functionally uncharacterized homologue of DmTNP. Here we report (using co-immunoprecipitation, pull down, colocalization, and proximity ligation assays) that both full length and truncated hTHAP9 (corresponding to amino-terminal DNA binding and predicted coiled coil domains) undergo homo-oligomerization, predominantly in the nuclei of HEK293T cells. Interestingly, the oligomerization is shown to be partially mediated by DNA. However, mutating the leucines (either individually or together) or deleting the predicted coiled coil region did not significantly affect oligomerization. Thus, we highlight the importance of DNA and the amino-terminal regions of hTHAP9 for their ability to form higher-order oligomeric states. We also report that Hcf-1, THAP1, THAP10, and THAP11 are possible protein interaction partners of hTHAP9. Elucidating the functional relevance of the different putative oligomeric state(s) of hTHAP9 would help answer questions about its interaction partners as well as its unknown physiological roles.
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Affiliation(s)
- Hiral M Sanghavi
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Sharmistha Majumdar
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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22
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Novel exon-skipping variant disrupting the basic domain of HCFC1 causes intellectual disability without metabolic abnormalities in both male and female patients. J Hum Genet 2021; 66:717-724. [PMID: 33517344 DOI: 10.1038/s10038-020-00892-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/09/2022]
Abstract
HCFC1, a global transcriptional regulator, has been shown to associate with MMACHC expression. Pathogenic variants in HCFC1 cause X-linked combined methylmalonic acidemia and hyperhomocysteinemia, CblX type (MIM# 309541). Recent studies showed that certain variants in HCFC1 are associated with X-linked intellectual disability with mild or absent metabolic abnormalities. Here, we report five subjects (three males, two females) from the same family with a novel predicted loss of function HCFC1 variant. All five patients exhibit developmental delay or intellectual disability/learning difficulty and some dysmorphic features; findings were milder in the female as compared to male subjects. Biochemical studies in all patients did not show methylmalonic acidemia or hyperhomocysteinemia but revealed elevated vitamin B12 levels. Trio exome sequencing of the proband and his parents revealed a maternally inherited novel variant in HCFC1 designated as c.1781_1803 + 3del26insCA (NM_005334). Targeted testing confirmed the presence of the same variant in two half-siblings and maternal great uncle. In silico analysis showed that the variant is expected to reduce the quality of the splice donor site in intron 10 and causes abnormal splicing. Sequencing of proband's cDNA revealed exon 10 skipping. Further molecular studies in the two manifesting females revealed moderate and high skewing of X inactivation. Our results support previous observation that HCFC1 variants located outside the Kelch domain exhibit dissociation of the clinical and biochemical phenotype and cause milder or no metabolic changes. We also show that this novel variant can be associated with a phenotype in females, although with milder severity, but further studies are needed to understand the role of skewed X inactivation among females in this rare disorder. Our work expands the genotypes and phenotypes associated with HCFC1-related disorder.
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23
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Kaur R, Attri SV, Saini AG, Sankhyan N. A high frequency and geographical distribution of MMACHC R132* mutation in children with cobalamin C defect. Amino Acids 2021; 53:253-264. [PMID: 33515116 DOI: 10.1007/s00726-021-02942-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022]
Abstract
Cobalamin C defect is caused by pathogenic variants in the MMACHC gene leading to impaired conversion of dietary vitamin B12 into methylcobalamin and adenosylcobalamin. Variants in the MMACHC gene cause accumulation of methylmalonic acid and homocysteine along with decreased methionine synthesis. The spectrum of MMACHC gene variants differs in various populations. A total of 19 North Indian children (age 0-18 years) with elevated methylmalonic acid and homocysteine were included in the study, and their DNA samples were subjected to Sanger sequencing of coding exons with flanking intronic regions of MMACHC gene. The genetic analysis resulted in the identification of a common pathogenic nonsense mutation, c.394C > T (R132*) in 85.7% of the unrelated cases with suspected cobalamin C defect. Two other known mutations c.347T > C (7%) and c.316G > A were also detected. Plasma homocysteine was significantly elevated (> 100 µmol/L) in 75% of the cases and methionine was decreased in 81% of the cases. Propionyl (C3)-carnitine, the primary marker for cobalamin C defect, was found to be elevated in only 43.75% of cases. However, the secondary markers such as C3/C2 and C3/C16 ratios were elevated in 87.5% and 100% of the cases, respectively. Neurological manifestations were the most common in our cohort. Our findings of the high frequency of a single MMACHC R132* mutation in cases with combined homocystinuria and methylmalonic aciduria may be proven helpful in designing a cost-effective and time-saving diagnostic strategy for resource-constraint settings. Since the R132* mutation is located near the last exon-exon junction, this is a potential target for the read-through therapeutics.
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Affiliation(s)
- Rajdeep Kaur
- Pediatric Biochemistry Unit, Department of Pediatrics, PGIMER, Chandigarh, 160012, India
| | - Savita Verma Attri
- Pediatric Biochemistry Unit, Department of Pediatrics, PGIMER, Chandigarh, 160012, India.
| | - Arushi Gahlot Saini
- Pediatric Neurology Unit, Department of Pediatrics, PGIMER, Chandigarh, India
| | - Naveen Sankhyan
- Pediatric Neurology Unit, Department of Pediatrics, PGIMER, Chandigarh, India
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24
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Castro VL, Quintana AM. The role of HCFC1 in syndromic and non-syndromic intellectual disability. ACTA ACUST UNITED AC 2020; 8. [PMID: 34164576 DOI: 10.18103/mra.v8i6.2122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mutations in the HCFC1 gene are associated with cases of syndromic (cblX) and non-syndromic intellectual disability. Syndromic individuals present with severe neurological defects including intractable epilepsy, facial dysmorphia, and intellectual disability. Non-syndromic individuals have also been described and implicate a role for HCFC1 during brain development. The penetrance of phenotypes and the presence of an overall syndrome is associated with the location of the mutation within the HCFC1 protein. Thus, one could hypothesize that the positioning of HCFC1 mutations lead to different neurological phenotypes that include but are not restricted to intellectual disability. The HCFC1 protein is comprised of multiple domains that function in cellular proliferation/metabolism. Several reports of HCFC1 disease variants have been identified, but a comprehensive review of each variant and its associated phenotypes has not yet been compiled. Here we perform a detailed review of HCFC1 function, model systems, variant location, and accompanying phenotypes to highlight current knowledge and the future status of the field.
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Affiliation(s)
- Victoria L Castro
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968
| | - Anita M Quintana
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968
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25
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Zanandrea R, Wiprich MT, Altenhofen S, Rubensam G, Dos Santos TM, Wyse ATS, Bonan CD. Withdrawal Effects Following Methionine Exposure in Adult Zebrafish. Mol Neurobiol 2020; 57:3485-3497. [PMID: 32533465 DOI: 10.1007/s12035-020-01970-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/01/2020] [Indexed: 12/14/2022]
Abstract
Methionine (Met) has important functions for homeostasis of various species, including zebrafish. However, the increased levels of this amino acid in plasma, a condition known as hypermethioninemia, can lead to cell alterations. Met is crucial for the methylation process and its excesses interfere with the cell cycle, an effect that persists even after the removal of this amino acid. Some conditions may lead to a transient increase of this amino acid with unexplored persistent effects of Met exposure. In the present study, we investigated the behavioral and neurochemical effects after the withdrawal of Met exposure. Zebrafish were divided into two groups: control and Met-treated group (3 mM) for 7 days and after maintained for 8 days in tanks containing only water. In the eighth day post-exposure, we evaluated locomotion, anxiety, aggression, social interaction, and memory, as well as oxidative stress parameters, amino acid, and neurotransmitter levels in the zebrafish brain. Our results showed that 8 days after Met exposure, the treated group showed decreased locomotion and aggressive responses, as well as impaired aversive memory. The Met withdrawal did not change thiobarbituric acid reactive substances, reactive oxygen species, and nitrite levels; however, we observed a decrease in antioxidant enzymes superoxide dismutase, catalase, and total thiols. Epinephrine and cysteine levels were decreased after the Met withdrawal whereas carnitine and creatine levels were elevated. Our findings indicate that a transient increase in Met causes persistent neurotoxicity, observed by behavioral and cognitive changes after Met withdrawal and that the mechanisms underlying these effects are related to changes in antioxidant system, amino acid, and neurotransmitter levels.
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Affiliation(s)
- Rodrigo Zanandrea
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Neuroquímica e Psicofarmacologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Melissa Talita Wiprich
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Neuroquímica e Psicofarmacologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Stefani Altenhofen
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Neuroquímica e Psicofarmacologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriel Rubensam
- Centro de Pesquisa em Toxicologia e Farmacologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tiago Marcon Dos Santos
- Programa de Pós-Graduação em Ciências Biológicas-Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Angela T S Wyse
- Programa de Pós-Graduação em Ciências Biológicas-Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Carla Denise Bonan
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.
- Laboratório de Neuroquímica e Psicofarmacologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.
- Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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26
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Castro VL, Reyes JF, Reyes-Nava NG, Paz D, Quintana AM. Hcfc1a regulates neural precursor proliferation and asxl1 expression in the developing brain. BMC Neurosci 2020; 21:27. [PMID: 32522152 PMCID: PMC7288482 DOI: 10.1186/s12868-020-00577-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Background Precise regulation of neural precursor cell (NPC) proliferation and differentiation is essential to ensure proper brain development and function. The HCFC1 gene encodes a transcriptional co-factor that regulates cell proliferation, and previous studies suggest that HCFC1 regulates NPC number and differentiation. However, the molecular mechanism underlying these cellular deficits has not been completely characterized. Methods Here we created a zebrafish harboring mutations in the hcfc1a gene (the hcfc1aco60/+ allele), one ortholog of HCFC1, and utilized immunohistochemistry and RNA-sequencing technology to understand the function of hcfc1a during neural development. Results The hcfc1aco60/+ allele results in an increased number of NPCs and increased expression of neuronal and glial markers. These neural developmental deficits are associated with larval hypomotility and the abnormal expression of asxl1, a polycomb transcription factor, which we identified as a downstream effector of hcfc1a. Inhibition of asxl1 activity and/or expression in larvae harboring the hcfc1aco60/+ allele completely restored the number of NPCs to normal levels. Conclusion Collectively, our data demonstrate that hcfc1a regulates NPC number, NPC proliferation, motor behavior, and brain development.
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Affiliation(s)
- Victoria L Castro
- Department of Biological Sciences and Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Joel F Reyes
- Department of Biological Sciences and Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Nayeli G Reyes-Nava
- Department of Biological Sciences and Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - David Paz
- Department of Biological Sciences and Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Anita M Quintana
- Department of Biological Sciences and Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA.
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27
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Rashka C, Hergalant S, Dreumont N, Oussalah A, Camadro JM, Marchand V, Hassan Z, Baumgartner MR, Rosenblatt DS, Feillet F, Guéant JL, Flayac J, Coelho D. Analysis of fibroblasts from patients with cblC and cblG genetic defects of cobalamin metabolism reveals global dysregulation of alternative splicing. Hum Mol Genet 2020; 29:1969-1985. [DOI: 10.1093/hmg/ddaa027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
Vitamin B12 or cobalamin (Cbl) metabolism can be affected by genetic defects leading to defective activity of either methylmalonyl-CoA mutase or methionine synthase or both enzymes. Patients usually present with a wide spectrum of pathologies suggesting that various cellular processes could be affected by modifications in gene expression. We have previously demonstrated that these genetic defects are associated with subcellular mislocalization of RNA-binding proteins (RBP) and subsequent altered nucleo-cytoplasmic shuttling of mRNAs. In order to characterize the possible changes of gene expression in these diseases, we have investigated global gene expression in fibroblasts from patients with cblC and cblG inherited disorders by RNA-seq. The most differentially expressed genes are strongly associated with developmental processes, neurological, ophthalmologic and cardiovascular diseases. These associations are consistent with the clinical presentation of cblC and cblG disorders. Multivariate analysis of transcript processing revaled splicing alterations that led to dramatic changes in cytoskeleton organization, response to stress, methylation of macromolecules and RNA binding. The RNA motifs associated with this differential splicing reflected a potential role of RBP such as HuR and HNRNPL. Proteomic analysis confirmed that mRNA processing was significantly disturbed. This study reports a dramatic alteration of gene expression in fibroblasts of patients with cblC and cblG disorders, which resulted partly from disturbed function of RBP. These data suggest to evaluate the rescue of the mislocalization of RBP as a potential strategy in the treatment of severe cases who are resistant to classical treatments with co-enzyme supplements.
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Affiliation(s)
- Charif Rashka
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Sébastien Hergalant
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Natacha Dreumont
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Abderrahim Oussalah
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
| | | | - Virginie Marchand
- University of Lorraine, CNRS, INSERM, UMS2008, IBSLor, Epitranscriptomics and RNA Sequencing Core Facility, Nancy F-54000, France
| | - Ziad Hassan
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Matthias R Baumgartner
- Radiz – Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases, University of Zürich, Zürich, Switzerland
| | | | - François Feillet
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
| | - Jean-Louis Guéant
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
| | - Justine Flayac
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - David Coelho
- Inserm UMRS 1256 NGERE – Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
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Dehaene H, Praz V, Lhôte P, Lopes M, Herr W. THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation. PLoS One 2020; 15:e0224646. [PMID: 31905202 PMCID: PMC6944463 DOI: 10.1371/journal.pone.0224646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Twelve human THAP proteins share the THAP domain, an evolutionary conserved zinc-finger DNA-binding domain. Studies of different THAP proteins have indicated roles in gene transcription, cell proliferation and development. We have analyzed this protein family, focusing on THAP7 and THAP11. We show that human THAP proteins possess differing homo- and heterodimer formation properties and interaction abilities with the transcriptional co-regulator HCF-1. HEK-293 cells lacking THAP7 were viable but proliferated more slowly. In contrast, HEK-293 cells were very sensitive to THAP11 alteration. Nevertheless, HEK-293 cells bearing a THAP11 mutation identified in a patient suffering from cobalamin disorder (THAP11F80L) were viable although proliferated more slowly. Cobalamin disorder is an inborn vitamin deficiency characterized by neurodevelopmental abnormalities, most often owing to biallelic mutations in the MMACHC gene, whose gene product MMACHC is a key enzyme in the cobalamin (vitamin B12) metabolic pathway. We show that THAP11F80L selectively affected promoter binding by THAP11, having more deleterious effects on a subset of THAP11 targets, and resulting in altered patterns of gene expression. In particular, THAP11F80L exhibited a strong effect on association with the MMACHC promoter and led to a decrease in MMACHC gene transcription, suggesting that the THAP11F80L mutation is directly responsible for the observed cobalamin disorder.
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Affiliation(s)
- Harmonie Dehaene
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Viviane Praz
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Philippe Lhôte
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Maykel Lopes
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Winship Herr
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Abdrabo LS, Watkins D, Wang SR, Lafond-Lapalme J, Riviere JB, Rosenblatt DS. Genome and RNA sequencing in patients with methylmalonic
aciduria of unknown cause. Genet Med 2019; 22:432-436. [DOI: 10.1038/s41436-019-0640-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/13/2019] [Indexed: 01/13/2023] Open
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Froese DS, Fowler B, Baumgartner MR. Vitamin B 12 , folate, and the methionine remethylation cycle-biochemistry, pathways, and regulation. J Inherit Metab Dis 2019; 42:673-685. [PMID: 30693532 DOI: 10.1002/jimd.12009] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/27/2018] [Accepted: 10/19/2018] [Indexed: 12/16/2022]
Abstract
Vitamin B12 (cobalamin, Cbl) is a nutrient essential to human health. Due to its complex structure and dual cofactor forms, Cbl undergoes a complicated series of absorptive and processing steps before serving as cofactor for the enzymes methylmalonyl-CoA mutase and methionine synthase. Methylmalonyl-CoA mutase is required for the catabolism of certain (branched-chain) amino acids into an anaplerotic substrate in the mitochondrion, and dysfunction of the enzyme itself or in production of its cofactor adenosyl-Cbl result in an inability to successfully undergo protein catabolism with concomitant mitochondrial energy disruption. Methionine synthase catalyzes the methyl-Cbl dependent (re)methylation of homocysteine to methionine within the methionine cycle; a reaction required to produce this essential amino acid and generate S-adenosylmethionine, the most important cellular methyl-donor. Disruption of methionine synthase has wide-ranging implications for all methylation-dependent reactions, including epigenetic modification, but also for the intracellular folate pathway, since methionine synthase uses 5-methyltetrahydrofolate as a one-carbon donor. Folate-bound one-carbon units are also required for deoxythymidine monophosphate and de novo purine synthesis; therefore, the flow of single carbon units to each of these pathways must be regulated based on cellular needs. This review provides an overview on Cbl metabolism with a brief description of absorption and intracellular metabolic pathways. It also provides a description of folate-mediated one-carbon metabolism and its intersection with Cbl at the methionine cycle. Finally, a summary of recent advances in understanding of how both pathways are regulated is presented.
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Affiliation(s)
- D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Brian Fowler
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
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Huemer M, Baumgartner MR. The clinical presentation of cobalamin-related disorders: From acquired deficiencies to inborn errors of absorption and intracellular pathways. J Inherit Metab Dis 2019; 42:686-705. [PMID: 30761552 DOI: 10.1002/jimd.12012] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
This review gives an overview of clinical characteristics, treatment and outcome of nutritional and acquired cobalamin (Cbl; synonym: vitamin B12) deficiencies, inborn errors of Cbl absorption and intracellular trafficking, as well as methylenetetrahydrofolate dehydrogenase (MTHFD1) and methylene tetrahydrofolate reductase (MTHFR) deficiencies, which impair Cbl-dependent remethylation. Acquired and inborn Cbl-related disorders and MTHFR deficiency cause multisystem, often severe disease. Failure to thrive, neurocognitive or psychiatric symptoms, eye disease, bone marrow alterations, microangiopathy and thromboembolic events are characteristic. The recently identified MTHFD1 defect additionally presents with severe immune deficiency. Deficient Cbl-dependent enzymes cause reduced methylation capacity and metabolite toxicity. Further net-effects of perturbed Cbl function or reduced Cbl supply causing oxidative stress, altered cytokine regulation or immune functions are discussed.
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Affiliation(s)
- Martina Huemer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, Zürich, Switzerland
- Department of Paediatrics, Landeskrankenhaus Bregenz, Bregenz, Austria
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, Zürich, Switzerland
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32
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Tomar S, Sethi R, Lai PS. Specific phenotype semantics facilitate gene prioritization in clinical exome sequencing. Eur J Hum Genet 2019; 27:1389-1397. [PMID: 31053788 DOI: 10.1038/s41431-019-0412-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 02/21/2019] [Accepted: 04/15/2019] [Indexed: 12/13/2022] Open
Abstract
Selection and prioritization of phenotype-centric variants remains a challenging part of variant analysis and interpretation in clinical exome sequencing. Phenotype-driven shortlisting of patient-specific gene lists can avoid missed diagnosis. Here, we analyzed the relevance of using primary Human Phenotype Ontology identifiers (HPO IDs) in prioritizing Mendelian disease genes across 30 in-house, 10 previously reported, and 10 recently published cases using three popular web-based gene prioritization tools (OMIMExplorer, VarElect & Phenolyzer). We assessed partial HPO-based gene prioritization using randomly chosen and top 10%, 30%, and 50% HPO IDs based on information content and found high variance within rank ratios across the former vs the latter. This signified that randomly selected less-specific HPO IDs for a given disease phenotype performed poorly by ranking probe gene farther away from the top rank. In contrast, the use of top 10%, 30%, and 50% HPO IDs individually could rank the probe gene among the top 1% in the ranked list of genes that was equivalent to the results when the full list of HPO IDs were used. Hence, we conclude that use of just the top 10% of HPO IDs chosen based on information content is sufficient for ranking the probe gene at top position. Our findings provide practical guidance for utilizing structured phenotype semantics and web-based gene-ranking tools to aid in identifying known as well unknown candidate gene associations in Mendelian disorders.
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Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System (NUHS), 1E Kent Ridge Road, 119228, Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System (NUHS), 1E Kent Ridge Road, 119228, Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System (NUHS), 1E Kent Ridge Road, 119228, Singapore.
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Value of genetic analysis for confirming inborn errors of metabolism detected through the Spanish neonatal screening program. Eur J Hum Genet 2019; 27:556-562. [PMID: 30626930 DOI: 10.1038/s41431-018-0330-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/16/2018] [Accepted: 11/27/2018] [Indexed: 11/09/2022] Open
Abstract
The present work describes the value of genetic analysis as a confirmatory measure following the detection of suspected inborn errors of metabolism in the Spanish newborn mass spectrometry screening program. One hundred and forty-one consecutive DNA samples were analyzed by next-generation sequencing using a customized exome sequencing panel. When required, the Illumina extended clinical exome panel was used, as was Sanger sequencing or transcriptional profiling. Biochemical tests were used to confirm the results of the genetic analysis. Using the customized panel, the metabolic disease suspected in 83 newborns (59%) was confirmed. In three further cases, two monoallelic variants were detected for two genes involved in the same biochemical pathway. In the remainder, either a single variant or no variant was identified. Given the persistent absence of biochemical alterations, carrier status was assigned in 39 cases. False positives were recorded for 11. In five cases in which the biochemical pattern was persistently altered, further genetic analysis allowed the detection of two variants affecting the function of BCAT2, ACSF3, and DNAJC12, as well as a second, deep intronic variant in ETFDH or PTS. The present results suggest that genetic analysis using extended next-generation sequencing panels can be used as a confirmatory test for suspected inborn errors of metabolism detected in newborn screening programs. Biochemical tests can be very helpful when a diagnosis is unclear. In summary, simultaneous genomic and metabolomic analyses can increase the number of inborn errors of metabolism that can be confirmed following suggestive newborn screening results.
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Kozyraki R, Cases O. Cubilin, the Intrinsic Factor-Vitamin B12 Receptor in Development and Disease. Curr Med Chem 2018; 27:3123-3150. [PMID: 30295181 DOI: 10.2174/0929867325666181008143945] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/11/2018] [Accepted: 08/21/2018] [Indexed: 12/29/2022]
Abstract
Gp280/Intrinsic factor-vitamin B12 receptor/Cubilin (CUBN) is a large endocytic receptor serving multiple functions in vitamin B12 homeostasis, renal reabsorption of protein or toxic substances including albumin, vitamin D-binding protein or cadmium. Cubilin is a peripheral membrane protein consisting of 8 Epidermal Growth Factor (EGF)-like repeats and 27 CUB (defined as Complement C1r/C1s, Uegf, BMP1) domains. This structurally unique protein interacts with at least two molecular partners, Amnionless (AMN) and Lrp2/Megalin. AMN is involved in appropriate plasma membrane transport of Cubilin whereas Lrp2 is essential for efficient internalization of Cubilin and its ligands. Observations gleaned from animal models with Cubn deficiency or human diseases demonstrate the importance of this protein. In this review addressed to basic research and medical scientists, we summarize currently available data on Cubilin and its implication in renal and intestinal biology. We also discuss the role of Cubilin as a modulator of Fgf8 signaling during embryonic development and propose that the Cubilin-Fgf8 interaction may be relevant in human pathology, including in cancer progression, heart or neural tube defects. We finally provide experimental elements suggesting that some aspects of Cubilin physiology might be relevant in drug design.
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Affiliation(s)
- Renata Kozyraki
- INSERM UMRS 1138, Centre de Recherche des Cordeliers, Paris-Diderot University, Paris, France
| | - Olivier Cases
- INSERM UMRS 1138, Centre de Recherche des Cordeliers, Paris-Diderot University, Paris, France
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35
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Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L, Davis RW, Enns GM, Zhao H, Cowan TM, Scharfe C. Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia. Genet Med 2018; 21:896-903. [PMID: 30209273 PMCID: PMC6416784 DOI: 10.1038/s41436-018-0272-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/03/2018] [Indexed: 11/27/2022] Open
Abstract
Purpose Improved second-tier tools are needed to reduce false-positive outcomes in newborn screening (NBS) for inborn metabolic disorders on the Recommended Universal Screening Panel (RUSP). Methods We designed an assay for multiplex sequencing of 72 metabolic genes (RUSPseq) from newborn dried blood spots. Analytical and clinical performance was evaluated in 60 screen-positive newborns for methylmalonic acidemia (MMA) reported by the California Department of Public Health NBS program. Additionally, we trained a Random Forest machine learning classifier on NBS data to improve prediction of true and false-positive MMA cases. Results Of 28 MMA patients sequenced, we found two pathogenic or likely pathogenic (P/LP) variants in a MMA-related gene in 24 patients, and one pathogenic variant and a variant of unknown significance (VUS) in 1 patient. No such variant combinations were detected in MMA false positives and healthy controls. Random Forest–based analysis of the entire NBS metabolic profile correctly identified the MMA patients and reduced MMA false-positive cases by 51%. MMA screen-positive newborns were more likely of Hispanic ethnicity. Conclusion Our two-pronged approach reduced false positives by half and provided a reportable molecular finding for 89% of MMA patients. Challenges remain in newborn metabolic screening and DNA variant interpretation in diverse multiethnic populations.
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Affiliation(s)
- Gang Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Peidong Shen
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony Le
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eula Fung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Tina M Cowan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
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36
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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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Fujita J, Freire P, Coarfa C, Benham AL, Gunaratne P, Schneider MD, Dejosez M, Zwaka TP. Ronin Governs Early Heart Development by Controlling Core Gene Expression Programs. Cell Rep 2018; 21:1562-1573. [PMID: 29117561 PMCID: PMC5695914 DOI: 10.1016/j.celrep.2017.10.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/01/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022] Open
Abstract
Ronin (THAP11), a DNA-binding protein that evolved from a primordial DNA transposon by molecular domestication, recognizes a hyperconserved promoter sequence to control developmentally and metabolically essential genes in pluripotent stem cells. However, it remains unclear whether Ronin or related THAP proteins perform similar functions in development. Here, we present evidence that Ronin functions within the nascent heart as it arises from the mesoderm and forms a four-chambered organ. We show that Ronin is vital for cardiogenesis during midgestation by controlling a set of critical genes. The activity of Ronin coincided with the recruitment of its cofactor, Hcf-1, and the elevation of H3K4me3 levels at specific target genes, suggesting the involvement of an epigenetic mechanism. On the strength of these findings, we propose that Ronin activity during cardiogenesis offers a template to understand how important gene programs are sustained across different cell types within a developing organ such as the heart. Ronin displays complex expression patterns during embryogenesis Ronin is critical for heart growth Ronin regulates genetic growth programs Ronin binding influences H3K4me3 levels at target genes
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Affiliation(s)
- Jun Fujita
- Department of Cardiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Pablo Freire
- Department of Cellular and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ashley L Benham
- Stem Cell Engineering Department, Texas Heart Institute at St. Luke's Episcopal Hospital, Houston, TX 77225, USA
| | - Preethi Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Michael D Schneider
- British Heart Foundation Centre of Research Excellence, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Marion Dejosez
- Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Thomas P Zwaka
- Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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