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Yamaguchi M, Cotterill S. Association of Mutations in Replicative DNA Polymerase Genes with Human Disease: Possible Application of Drosophila Models for Studies. Int J Mol Sci 2023; 24:ijms24098078. [PMID: 37175782 PMCID: PMC10178534 DOI: 10.3390/ijms24098078] [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: 03/21/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Replicative DNA polymerases, such as DNA polymerase α-primase, δ and ε, are multi-subunit complexes that are responsible for the bulk of nuclear DNA replication during the S phase. Over the last decade, extensive genome-wide association studies and expression profiling studies of the replicative DNA polymerase genes in human patients have revealed a link between the replicative DNA polymerase genes and various human diseases and disorders including cancer, intellectual disability, microcephalic primordial dwarfism and immunodeficiency. These studies suggest the importance of dissecting the mechanisms involved in the functioning of replicative DNA polymerases in understanding and treating a range of human diseases. Previous studies in Drosophila have established this organism as a useful model to understand a variety of human diseases. Here, we review the studies on Drosophila that explored the link between DNA polymerases and human disease. First, we summarize the recent studies linking replicative DNA polymerases to various human diseases and disorders. We then review studies on replicative DNA polymerases in Drosophila. Finally, we suggest the possible use of Drosophila models to study human diseases and disorders associated with replicative DNA polymerases.
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Affiliation(s)
| | - Sue Cotterill
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, UK
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Wang Y, Yan K, Wang L, Bi J. Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology. BMC Cancer 2021; 21:727. [PMID: 34167490 PMCID: PMC8229419 DOI: 10.1186/s12885-021-08356-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/29/2021] [Indexed: 12/04/2022] Open
Abstract
Background There is evidence that long non-coding RNA (lncRNA) is related to genetic stability. However, the complex biological functions of these lncRNAs are unclear. Method TCGA - KIRC lncRNAs expression matrix and somatic mutation information data were obtained from TCGA database. “GSVA” package was applied to evaluate the genomic related pathway in each samples. GO and KEGG analysis were performed to show the biological function of lncRNAs-mRNAs. “Survival” package was applied to determine the prognostic significance of lncRNAs. Multivariate Cox proportional hazard regression analysis was applied to conduct lncRNA prognosis model. Results In the present study, we applied computational biology to identify genome-related long noncoding RNA and identified 26 novel genomic instability-associated lncRNAs in clear cell renal cell carcinoma. We identified a genome instability-derived six lncRNA-based gene signature that significantly divided clear renal cell samples into high- and low-risk groups. We validated it in test cohorts. To further elucidate the role of the six lncRNAs in the model’s genome stability, we performed a gene set variation analysis (GSVA) on the matrix. We performed Pearson correlation analysis between the GSVA scores of genomic stability-related pathways and lncRNA. It was determined that LINC00460 and LINC01234 could be used as critical factors in this study. They may influence the genome stability of clear cell carcinoma by participating in mediating critical targets in the base excision repair pathway, the DNA replication pathway, homologous recombination, mismatch repair pathway, and the P53 signaling pathway. Conclusion subsections These data suggest that LINC00460 and LINC01234 are crucial for the stability of the clear cell renal cell carcinoma genome. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08356-9.
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Affiliation(s)
- Yutao Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Kexin Yan
- Department of Dermatology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Linhui Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianbin Bi
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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García-Cordero JM, Martínez-Palma NY, Madrigal-Bujaidar E, Jiménez-Martínez C, Madrigal-Santillán E, Morales-González JA, Paniagua-Pérez R, Álvarez-González I. Phaseolin, a Protein from the Seed of Phaseolus vulgaris, Has Antioxidant, Antigenotoxic, and Chemopreventive Properties. Nutrients 2021; 13:nu13061750. [PMID: 34063915 PMCID: PMC8224085 DOI: 10.3390/nu13061750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
The present report was designed to determine the antioxidant and antigenotoxic effects of phaseolin (isolated from Phaseolus vulgaris) against mouse colon and liver damage induced by azoxymethane (AOM) and its colon chemopreventive effect. Eight groups with 12 mice each were utilized for an eight-week experiment: the control group was intragastrically (ig) administered 0.9% saline solution; the positive control group was intraperitoneally (ip) injected with 7.5 mg/kg AOM twice a week (weeks three and four of the experiment); three groups were ig administered each day with phaseolin (40, 200, and 400 mg/kg); and three groups were ig administered phaseolin daily (40, 200, and 400 mg/kg) plus 7.5 mg/kg AOM twice a week in weeks three and four of the experiment. The results showed that phaseolin did not produce oxidative stress, DNA damage, or aberrant crypts; in contrast, 100% inhibition of lipoperoxidation, protein oxidation, and nitrites induction generated by AOM was found in both organs, and DPPH radical capture occurred. The two highest phaseolin doses reduced DNA damage induced by AOM in both organs by more than 90% and reduced the AOM-induced aberrant crypts by 84%. Therefore, our study demonstrated the strong in vivo antioxidant, antigenotoxic, and chemopreventive potential of phaseolin.
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Affiliation(s)
- Juan Manuel García-Cordero
- Laboratorio de Genética, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n. Zacatenco. Gustavo A. Madero, Ciudad de Mexico 07738, Mexico; (J.M.G.-C.); (N.Y.M.-P.); (E.M.-B.)
- Laboratorio de Compuestos Bioactivos, Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n. Zacatenco. Gustavo A. Madero, Ciudad de Mexico 07738, Mexico;
| | - Nikte Y. Martínez-Palma
- Laboratorio de Genética, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n. Zacatenco. Gustavo A. Madero, Ciudad de Mexico 07738, Mexico; (J.M.G.-C.); (N.Y.M.-P.); (E.M.-B.)
- Laboratorio de Compuestos Bioactivos, Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n. Zacatenco. Gustavo A. Madero, Ciudad de Mexico 07738, Mexico;
| | - Eduardo Madrigal-Bujaidar
- Laboratorio de Genética, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n. Zacatenco. Gustavo A. Madero, Ciudad de Mexico 07738, Mexico; (J.M.G.-C.); (N.Y.M.-P.); (E.M.-B.)
| | - Cristian Jiménez-Martínez
- Laboratorio de Compuestos Bioactivos, Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n. Zacatenco. Gustavo A. Madero, Ciudad de Mexico 07738, Mexico;
| | - Eduardo Madrigal-Santillán
- Laboratorio de Medicina de la Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n. Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (E.M.-S.); (J.A.M.-G.)
| | - José A. Morales-González
- Laboratorio de Medicina de la Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n. Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (E.M.-S.); (J.A.M.-G.)
| | - Rogelio Paniagua-Pérez
- Servicio de Bioquímica, Instituto Nacional de Rehabilitación, Av. Mexico-Xochimilco 289, Ciudad de Mexico 14389, Mexico;
| | - Isela Álvarez-González
- Laboratorio de Genética, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n. Zacatenco. Gustavo A. Madero, Ciudad de Mexico 07738, Mexico; (J.M.G.-C.); (N.Y.M.-P.); (E.M.-B.)
- Correspondence: ; Tel.: +52-(1)-5557296300 (ext. 57883)
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Hanasaki M, Yaku K, Yamauchi M, Nakagawa T, Masumoto H. Deletion of the GAPDH gene contributes to genome stability in Saccharomyces cerevisiae. Sci Rep 2020; 10:21146. [PMID: 33273685 PMCID: PMC7713361 DOI: 10.1038/s41598-020-78302-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 11/17/2020] [Indexed: 12/30/2022] Open
Abstract
Cellular metabolism is directly or indirectly associated with various cellular processes by producing a variety of metabolites. Metabolic alterations may cause adverse effects on cell viability. However, some alterations potentiate the rescue of the malfunction of the cell system. Here, we found that the alteration of glucose metabolism suppressed genome instability caused by the impairment of chromatin structure. Deletion of the TDH2 gene, which encodes glyceraldehyde 3-phospho dehydrogenase and is essential for glycolysis/gluconeogenesis, partially suppressed DNA damage sensitivity due to chromatin structure, which was persistently acetylated histone H3 on lysine 56 in cells with deletions of both HST3 and HST4, encoding NAD+-dependent deacetylases. tdh2 deletion also restored the short replicative lifespan of cells with deletion of sir2, another NAD+-dependent deacetylase, by suppressing intrachromosomal recombination in rDNA repeats increased by the unacetylated histone H4 on lysine 16. tdh2 deletion also suppressed recombination between direct repeats in hst3∆ hst4∆ cells by suppressing the replication fork instability that leads to both DNA deletions among repeats. We focused on quinolinic acid (QUIN), a metabolic intermediate in the de novo nicotinamide adenine dinucleotide (NAD+) synthesis pathway, which accumulated in the tdh2 deletion cells and was a candidate metabolite to suppress DNA replication fork instability. Deletion of QPT1, quinolinate phosphoribosyl transferase, elevated intracellular QUIN levels and partially suppressed the DNA damage sensitivity of hst3∆ hst4∆ cells as well as tdh2∆ cells. qpt1 deletion restored the short replicative lifespan of sir2∆ cells by suppressing intrachromosomal recombination among rDNA repeats. In addition, qpt1 deletion could suppress replication fork slippage between direct repeats. These findings suggest a connection between glucose metabolism and genomic stability.
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Affiliation(s)
- Miki Hanasaki
- Biomedical Research Support Center (BRSC), Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Keisuke Yaku
- Department of Metabolism and Nutrition, Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan
| | - Motohiro Yamauchi
- Department of Radiation Biology and Protection, Atomic Bomb Disease Institute, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Takashi Nakagawa
- Department of Metabolism and Nutrition, Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan
| | - Hiroshi Masumoto
- Biomedical Research Support Center (BRSC), Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan.
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Passemard S, Perez F, Gressens P, El Ghouzzi V. Endoplasmic reticulum and Golgi stress in microcephaly. Cell Stress 2019; 3:369-384. [PMID: 31832602 PMCID: PMC6883743 DOI: 10.15698/cst2019.12.206] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Microcephaly is a neurodevelopmental condition characterized by a small brain size associated with intellectual deficiency in most cases and is one of the most frequent clinical sign encountered in neurodevelopmental disorders. It can result from a wide range of environmental insults occurring during pregnancy or postnatally, as well as from various genetic causes and represents a highly heterogeneous condition. However, several lines of evidence highlight a compromised mode of division of the cortical precursor cells during neurogenesis, affecting neural commitment or survival as one of the common mechanisms leading to a limited production of neurons and associated with the most severe forms of congenital microcephaly. In this context, the emergence of the endoplasmic reticulum (ER) and the Golgi apparatus as key guardians of cellular homeostasis, especially through the regulation of proteostasis, has raised the hypothesis that pathological ER and/or Golgi stress could contribute significantly to cortical impairments eliciting microcephaly. In this review, we discuss recent findings implicating ER and Golgi stress responses in early brain development and provide an overview of microcephaly-associated genes involved in these pathways.
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Affiliation(s)
- Sandrine Passemard
- Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,Service de Génétique Clinique, AP-HP, Hôpital Robert Debré, F-75019 Paris, France
| | - Franck Perez
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France
| | - Pierre Gressens
- Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,Centre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King's College London, King's Health Partners, St. Thomas'Hospital, London, United Kingdom
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