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Oh JH, Jo S, Park KW, Lee EJ, Lee SH, Hwang YS, Jeon HR, Ryu Y, Yoon HJ, Chun SM, Kim CJ, Kim TW, Sung CO, Chae S, Chung SJ. Whole-genome sequencing reveals an association between small genomic deletions and an increased risk of developing Parkinson's disease. Exp Mol Med 2023; 55:555-564. [PMID: 36869069 PMCID: PMC10073127 DOI: 10.1038/s12276-023-00952-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 03/05/2023] Open
Abstract
Single-nucleotide variants (SNVs) associated with Parkinson's disease (PD) have been investigated mainly through genome-wide association studies. However, other genomic alterations, including copy number variations, remain less explored. In this study, we conducted whole-genome sequencing of primary (310 PD patients and 100 healthy individuals) and independent (100 PD patients and 100 healthy individuals) cohorts from the Korean population to identify high-resolution small genomic deletions, gains, and SNVs. Global small genomic deletions and gains were found to be associated with an increased and decreased risk of PD development, respectively. Thirty significant locus deletions were identified in PD, with most being associated with an increased PD risk in both cohorts. Small genomic deletions in clustered loci located in the GPR27 region had high enhancer signals and showed the closest association with PD. GPR27 was found to be expressed specifically in brain tissue, and GPR27 copy number loss was associated with upregulated SNCA expression and downregulated dopamine neurotransmitter pathways. Clustering of small genomic deletions on chr20 in exon 1 of the GNAS isoform was detected. In addition, we found several PD-associated SNVs, including one in the enhancer region of the TCF7L2 intron, which exhibited a cis-acting regulatory mode and an association with the beta-catenin signaling pathway. These findings provide a global, whole-genome view of PD and suggest that small genomic deletions in regulatory domains contribute to the risk of PD development.
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Affiliation(s)
- Ji-Hye Oh
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sungyang Jo
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kye Won Park
- Department of Neurology, Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu-si, Gyeonggi-do, Republic of Korea
| | - Eun-Jae Lee
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seung Hyun Lee
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yun Su Hwang
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ha Ra Jeon
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yeonjin Ryu
- Korea Brain Bank, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hee Jeong Yoon
- Korea Brain Bank, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Sung-Min Chun
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chong Jai Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chang Ohk Sung
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea. .,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Sehyun Chae
- Korea Brain Bank, Korea Brain Research Institute, Daegu, Republic of Korea.
| | - Sun Ju Chung
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Park SH, Bennett-Baker P, Ahmed S, Arlt MF, Ljungman M, Glover TW, Wilson TE. Locus-specific transcription silencing at the FHIT gene suppresses replication stress-induced copy number variant formation and associated replication delay. Nucleic Acids Res 2021; 49:7507-7524. [PMID: 34181717 PMCID: PMC8287918 DOI: 10.1093/nar/gkab559] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 12/11/2022] Open
Abstract
Impaired replication progression leads to de novo copy number variant (CNV) formation at common fragile sites (CFSs). We previously showed that these hotspots for genome instability reside in late-replicating domains associated with large transcribed genes and provided indirect evidence that transcription is a factor in their instability. Here, we compared aphidicolin (APH)-induced CNV and CFS frequency between wild-type and isogenic cells in which FHIT gene transcription was ablated by promoter deletion. Two promoter-deletion cell lines showed reduced or absent CNV formation and CFS expression at FHIT despite continued instability at the NLGN1 control locus. APH treatment led to critical replication delays that remained unresolved in G2/M in the body of many, but not all, large transcribed genes, an effect that was reversed at FHIT by the promoter deletion. Altering RNase H1 expression did not change CNV induction frequency and DRIP-seq showed a paucity of R-loop formation in the central regions of large genes, suggesting that R-loops are not the primary mediator of the transcription effect. These results demonstrate that large gene transcription is a determining factor in replication stress-induced genomic instability and support models that CNV hotspots mainly result from the transcription-dependent passage of unreplicated DNA into mitosis.
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Affiliation(s)
- So Hae Park
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Samreen Ahmed
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas W Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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Fan X, Zhu Y, Wang N, Zhang B, Zhang C, Wang Y. Therapeutic Dose of Hydroxyurea-Induced Synaptic Abnormalities on the Mouse Spermatocyte. Front Physiol 2021; 12:666339. [PMID: 34305635 PMCID: PMC8299468 DOI: 10.3389/fphys.2021.666339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
Hydroxyurea (HU) is a widely used pharmacological therapy for sickle cell disease (SCD). However, replication stress caused by HU has been shown to inhibit premeiotic S-phase DNA, leading to reproductive toxicity in germ cells. In this study, we administered the therapeutic doses of HU (i.e., 25 and 50 mg/kg) to male mice to explore whether replication stress by HU affects pachytene spermatocytes and causes the abnormalities of homologous chromosomes pairing and recombination during prophase I of meiosis. In comparison with the control group, the proportions of spermatocyte gaps were significantly different in the experimental groups injected with 25 mg/kg (p < 0.05) and 50 mg/kg of HU (p < 0.05). Moreover, the proportions of unrepaired double-stranded breaks (DSBs) observed by γH2AX staining also corresponded to a higher HU dose with a greater number of breaks. Additionally, a reduction in the counts of recombination foci on the autosomal SCs was observed in the pachytene spermatocytes. Our results reveal that HU has some effects on synaptonemal complex (SC) formation and DSB repair which suggest possible problems in fertility. Therefore, this study provides new evidence of the mechanisms underlying HU reproductive toxicity.
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Affiliation(s)
- Xiaobo Fan
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
| | - Yunxia Zhu
- The Center of Reproductive Medicine, Xuzhou Maternity and Child Health Care Hospital, Xuzhou, China
| | - Naixin Wang
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
| | - Bing Zhang
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
| | - Cui Zhang
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
| | - Yanan Wang
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
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Hovhannisyan G, Harutyunyan T, Aroutiounian R, Liehr T. DNA Copy Number Variations as Markers of Mutagenic Impact. Int J Mol Sci 2019; 20:ijms20194723. [PMID: 31554154 PMCID: PMC6801639 DOI: 10.3390/ijms20194723] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/26/2022] Open
Abstract
DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution of environmental factors, such as mutagens, in the origin of CNVs, is poorly understood. In this review, we summarize current knowledge about mutagen-induced CNVs in human, animal and plant cells. Differences in CNV frequencies induced by radiation and chemical mutagens, distribution of CNVs in the genome, as well as adaptive effects in plants, are discussed. Currently available information concerning impact of mutagens in induction of CNVs in germ cells is presented. Moreover, the potential of CNVs as a new endpoint in mutagenicity test-systems is discussed.
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Affiliation(s)
- Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany.
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Beal MA, Meier MJ, Williams A, Rowan-Carroll A, Gagné R, Lindsay SJ, Fitzgerald T, Hurles ME, Marchetti F, Yauk CL. Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring. Commun Biol 2019; 2:228. [PMID: 31240266 PMCID: PMC6586636 DOI: 10.1038/s42003-019-0476-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/23/2019] [Indexed: 01/14/2023] Open
Abstract
Understanding the effects of environmental exposures on germline mutation rates has been a decades-long pursuit in genetics. We used next-generation sequencing and comparative genomic hybridization arrays to investigate genome-wide mutations in the offspring of male mice exposed to benzo(a)pyrene (BaP), a common environmental pollutant. We demonstrate that offspring developing from sperm exposed during the mitotic or post-mitotic phases of spermatogenesis have significantly more de novo single nucleotide variants (1.8-fold; P < 0.01) than controls. Both phases of spermatogenesis are susceptible to the induction of heritable mutations, although mutations arising from post-fertilization events are more common after post-mitotic exposure. In addition, the mutation spectra in sperm and offspring of BaP-exposed males are consistent. Finally, we report a significant increase in transmitted copy number duplications (P = 0.001) in BaP-exposed sires. Our study demonstrates that germ cell mutagen exposures induce genome-wide mutations in the offspring that may be associated with adverse health outcomes.
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Affiliation(s)
- Marc A. Beal
- Carleton University, Ottawa, Ontario K1S 5B6 Canada
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Sarah J. Lindsay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Tomas Fitzgerald
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
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