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Marioli C, Muzzi M, Colasuonno F, Fiorucci C, Cicolani N, Petrini S, Bertini E, Tartaglia M, Compagnucci C, Moreno S. Caspase-dependent apoptosis in Riboflavin Transporter Deficiency iPSCs and derived motor neurons. Cell Death Discov 2024; 10:54. [PMID: 38278809 PMCID: PMC10817897 DOI: 10.1038/s41420-024-01812-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
Riboflavin Transporter Deficiency (RTD) is a rare genetic, childhood-onset disease. This pathology has a relevant neurological involvement, being characterized by motor symptoms, ponto-bulbar paralysis and sensorineural deafness. Such clinical presentation is associated with muscle weakness and motor neuron (MN) degeneration, so that RTD is considered part of the MN disease spectrum. Based on previous findings demonstrating energy dysmetabolism and mitochondrial impairment in RTD induced Pluripotent Stem cells (iPSCs) and iPSC-derived MNs, here we address the involvement of intrinsic apoptotic pathways in disease pathogenesis using these patient-specific in vitro models by combined ultrastructural and confocal analyses. We show impaired neuronal survival of RTD iPSCs and MNs. Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) documents severe alterations in patients' cells, including deranged mitochondrial ultrastructure, and altered plasma membrane and nuclear organization. Occurrence of aberrantly activated apoptosis is confirmed by immunofluorescence and TUNEL assays. Overall, our work provides evidence of a role played by mitochondrial dysfunction in RTD, and identifies neuronal apoptosis as a contributing event in disease pathogenesis, indicating intrinsic apoptosis pathways as possible relevant targets for more effective therapeutical approaches.
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Affiliation(s)
- Chiara Marioli
- Department of Science, LIME, University Roma Tre, 00146, Rome, Italy
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Maurizio Muzzi
- Department of Science, LIME, University Roma Tre, 00146, Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 00179, Rome, Italy
| | - Fiorella Colasuonno
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Cristian Fiorucci
- Department of Science, LIME, University Roma Tre, 00146, Rome, Italy
| | - Nicolò Cicolani
- Confocal Microscopy Core Facility, Research Laboratories, IRCCS Ospedale Pediatrico Bambino Gesù, 00146, Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Laboratories, IRCCS Ospedale Pediatrico Bambino Gesù, 00146, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, IRCCS Ospedale Pediatrico Bambino Gesù, 00146, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Claudia Compagnucci
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy.
| | - Sandra Moreno
- Department of Science, LIME, University Roma Tre, 00146, Rome, Italy.
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 00179, Rome, Italy.
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Zhang W, Wu H, Li Z. Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach. Bioinformatics 2021; 37:1052-1059. [PMID: 33135072 PMCID: PMC8150138 DOI: 10.1093/bioinformatics/btaa930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION It is a common practice in epigenetics research to profile DNA methylation on tissue samples, which is usually a mixture of different cell types. To properly account for the mixture, estimating cell compositions has been recognized as an important first step. Many methods were developed for quantifying cell compositions from DNA methylation data, but they mostly have limited applications due to lack of reference or prior information. RESULTS We develop Tsisal, a novel complete deconvolution method which accurately estimate cell compositions from DNA methylation data without any prior knowledge of cell types or their proportions. Tsisal is a full pipeline to estimate number of cell types, cell compositions and identify cell-type-specific CpG sites. It can also assign cell type labels when (full or part of) reference panel is available. Extensive simulation studies and analyses of seven real datasets demonstrate the favorable performance of our proposed method compared with existing deconvolution methods serving similar purpose. AVAILABILITY AND IMPLEMENTATION The proposed method Tsisal is implemented as part of the R/Bioconductor package TOAST at https://bioconductor.org/packages/TOAST. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Weiwei Zhang
- School of Science, East China University of Technology, Nanchang, Jiangxi 330013, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Blossom SJ, Melnyk SB, Simmen FA. Complex epigenetic patterns in cerebellum generated after developmental exposure to trichloroethylene and/or high fat diet in autoimmune-prone mice. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:583-594. [PMID: 31894794 PMCID: PMC7350281 DOI: 10.1039/c9em00514e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichloroethylene (TCE) is an environmental contaminant associated with immune-mediated inflammatory disorders and neurotoxicity. Based on known negative effects of developmental overnutrition on neurodevelopment, we hypothesized that developmental exposure to high fat diet (HFD) consisting of 40% kcal fat would enhance neurotoxicity of low-level (6 μg per kg per day) TCE exposure in offspring over either stressor alone. Male offspring were evaluated at ∼6 weeks of age after exposure beginning 4 weeks preconception in the dams until weaning. TCE, whether used as a single exposure or together with HFD, appeared to be more robust than HFD alone in altering one-carbon metabolites involved in glutathione redox homeostasis and methylation capacity. In contrast, opposing effects of expression of key enzymes related to DNA methylation related to HFD and TCE exposure were observed. The mice generated unique patterns of anti-brain antibodies detected by western blotting attributable to both TCE and HFD. Taken together, developmental exposure to TCE and/or HFD appear to act in complex ways to alter brain biomarkers in offspring.
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Affiliation(s)
- Sarah J Blossom
- Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, AR 72202, USA.
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Deng L, Hou L, Zhang J, Tang X, Cheng Z, Li G, Fang X, Xu J, Zhang X, Xu R. Polymorphism of rs3737597 in DISC1 Gene on Chromosome 1q42.2 in sALS Patients: a Chinese Han Population Case-Control Study. Mol Neurobiol 2016; 54:3162-3179. [DOI: 10.1007/s12035-016-9869-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/17/2016] [Indexed: 01/10/2023]
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The expression of neurotrophins is differentially regulated by omega-3 polyunsaturated fatty acids at weaning and postweaning in C57BL/6 mice cerebral cortex. Neurochem Int 2014; 66:33-42. [DOI: 10.1016/j.neuint.2014.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/19/2013] [Accepted: 01/14/2014] [Indexed: 12/13/2022]
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Xu W, Zhu H, Gu M, Luo Q, Ding J, Yao Y, Chen F, Wang Z. DHTKD1 is essential for mitochondrial biogenesis and function maintenance. FEBS Lett 2013; 587:3587-92. [PMID: 24076469 DOI: 10.1016/j.febslet.2013.08.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
Abstract
Maintaining the functional integrity of mitochondria is crucial for cell function, signal transduction and overall cell activities. Mitochondrial dysfunctions may alter energy metabolism and in many cases are associated with neurological diseases. Recent studies have reported that mutations in dehydrogenase E1 and transketolase domain-containing 1 (DHTKD1), a mitochondrial protein encoding gene, could cause neurological abnormalities. However, the function of DHTKD1 in mitochondria remains unknown. Here, we report a strong correlation of DHTKD1 expression level with ATP production, revealing the fact that DHTKD1 plays a critical role in energy production in mitochondria. Moreover, suppression of DHTKD1 leads to impaired mitochondrial biogenesis and increased reactive oxygen species (ROS), thus leading to retarded cell growth and increased cell apoptosis. These findings demonstrate that DHTKD1 contributes to mitochondrial biogenesis and function maintenance.
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Affiliation(s)
- Wangyang Xu
- Department of Clinical Laboratories, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200011, China
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