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Watanabe D, Okamoto N, Kobayashi Y, Suzuki H, Kato M, Saitoh S, Kanemura Y, Takenouchi T, Yamada M, Nakato D, Sato M, Tsunoda T, Kosaki K, Miya F. Biallelic structural variants in three patients with ERCC8-related Cockayne syndrome and a potential pitfall of copy number variation analysis. Sci Rep 2024; 14:19741. [PMID: 39187681 PMCID: PMC11347644 DOI: 10.1038/s41598-024-70831-7] [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: 01/31/2024] [Accepted: 08/21/2024] [Indexed: 08/28/2024] Open
Abstract
Cockayne syndrome (CS) is a rare autosomal recessive disorder caused by mutations in ERCC8 or ERCC6. Most pathogenic variants in ERCC8 are single nucleotide substitutions. Structural variants (SVs) have been reported in patients with ERCC8-related CS. However, comprehensive molecular detection, including SVs of ERCC8, in CS patients remains problematic. Herein, we present three Japanese patients with ERCC8-related CS in whom causative SVs were identified using whole-exome-based copy number variation (CNV) detection tools. One patient showed compound heterozygosity for a 259-kb deletion and a deletion of exon 4 which has previously been reported as an Asia-specific variant. The other two patients were homozygous for the same exon 4 deletion. The exon 4 deletion was detected only by the ExomeDepth software. Intrigued by the discrepancy in the detection capability of various tools for the SVs, we evaluated the analytic performance of four whole-exome-based CNV detection tools using an exome data set from 337 healthy individuals. A total of 1,278,141 exons were predicted as being affected by the 4 CNV tools. Interestingly 95.1% of these affected exons were detected by one tool alone. Thus, we expect that the use of multiple tools may improve the detection rate of SVs from aligned exome data.
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Affiliation(s)
- Daisuke Watanabe
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
- Department of Pediatrics, Yamanashi University, Yamanashi, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yuichi Kobayashi
- Professional Development Center, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
- Department of Clinical Medicine, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
- Epilepsy Medical Center, Showa University Hospital, Tokyo, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yonehiro Kanemura
- Department of Biomedical Research and Innovation, Institute for Clinical Research, NHO Osaka National Hospital, Osaka, Japan
- Department of Neurosurgery, NHO Osaka National Hospital, Osaka, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Daisuke Nakato
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Masayuki Sato
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.
- Innovative Human Resource Development Division, Institute of Education, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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Chen Y, Yao L, Zhao S, Xu M, Ren S, Xie L, Liu L, Wang Y. The oxidative aging model integrated various risk factors in type 2 diabetes mellitus at system level. Front Endocrinol (Lausanne) 2023; 14:1196293. [PMID: 37293508 PMCID: PMC10244788 DOI: 10.3389/fendo.2023.1196293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is a chronic endocrine metabolic disease caused by insulin dysregulation. Studies have shown that aging-related oxidative stress (as "oxidative aging") play a critical role in the onset and progression of T2DM, by leading to an energy metabolism imbalance. However, the precise mechanisms through which oxidative aging lead to T2DM are yet to be fully comprehended. Thus, it is urgent to integrate the underlying mechanisms between oxidative aging and T2DM, where meaningful prediction models based on relative profiles are needed. Methods First, machine learning was used to build the aging model and disease model. Next, an integrated oxidative aging model was employed to identify crucial oxidative aging risk factors. Finally, a series of bioinformatic analyses (including network, enrichment, sensitivity, and pan-cancer analyses) were used to explore potential mechanisms underlying oxidative aging and T2DM. Results The study revealed a close relationship between oxidative aging and T2DM. Our results indicate that nutritional metabolism, inflammation response, mitochondrial function, and protein homeostasis are key factors involved in the interplay between oxidative aging and T2DM, even indicating key indices across different cancer types. Therefore, various risk factors in T2DM were integrated, and the theories of oxi-inflamm-aging and cellular senescence were also confirmed. Conclusion In sum, our study successfully integrated the underlying mechanisms linking oxidative aging and T2DM through a series of computational methodologies.
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Affiliation(s)
- Yao Chen
- Department of Biomedical Engineering, School of Intelligent Medicine, China Medical University, Shenyang, Liaoning, China
| | - Lilin Yao
- Department of Biomedical Engineering, School of Intelligent Medicine, China Medical University, Shenyang, Liaoning, China
| | - Shuheng Zhao
- Department of Biomedical Engineering, School of Intelligent Medicine, China Medical University, Shenyang, Liaoning, China
| | - Mengchu Xu
- Department of Biomedical Engineering, School of Intelligent Medicine, China Medical University, Shenyang, Liaoning, China
| | - Siwei Ren
- Department of Biomedical Engineering, School of Intelligent Medicine, China Medical University, Shenyang, Liaoning, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics & Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Lei Liu
- Intelligent Medicine Institute, Fudan University, Shanghai, China
| | - Yin Wang
- Department of Biomedical Engineering, School of Intelligent Medicine, China Medical University, Shenyang, Liaoning, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
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Huerta Guevara AP, McGowan SJ, Kazantzis M, Stallons TR, Sano T, Mulder NL, Jurdzinski A, van Dijk TH, Eggen BJL, Jonker JW, Niedernhofer LJ, Kruit JK. Increased insulin sensitivity and diminished pancreatic beta-cell function in DNA repair deficient Ercc1 d/- mice. Metabolism 2021; 117:154711. [PMID: 33493548 PMCID: PMC8625516 DOI: 10.1016/j.metabol.2021.154711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/03/2021] [Accepted: 01/20/2021] [Indexed: 01/06/2023]
Abstract
BACKGROUND Type 2 diabetes (T2DM) is an age-associated disease characterized by hyperglycemia due to insulin resistance and decreased beta-cell function. DNA damage accumulation has been associated with T2DM, but whether DNA damage plays a role in the pathogenesis of the disease is unclear. Here, we used mice deficient for the DNA excision-repair gene Ercc1 to study the impact of persistent endogenous DNA damage accumulation on energy metabolism, glucose homeostasis and beta-cell function. METHODS ERCC1-XPF is an endonuclease required for multiple DNA repair pathways and reduced expression of ERCC1-XPF causes accelerated accumulation of unrepaired endogenous DNA damage and accelerated aging in humans and mice. In this study, energy metabolism, glucose metabolism, beta-cell function and insulin sensitivity were studied in Ercc1d/- mice, which model a human progeroid syndrome. RESULTS Ercc1d/- mice displayed suppression of the somatotropic axis and altered energy metabolism. Insulin sensitivity was increased, whereas, plasma insulin levels were decreased in Ercc1d/- mice. Fasting induced hypoglycemia in Ercc1d/- mice, which was the result of increased glucose disposal. Ercc1d/- mice exhibit a significantly reduced beta-cell area, even compared to control mice of similar weight. Glucose-stimulated insulin secretion in vivo was decreased in Ercc1d/- mice. Islets isolated from Ercc1d/- mice showed increased DNA damage markers, decreased glucose-stimulated insulin secretion and increased susceptibility to apoptosis. CONCLUSION Spontaneous DNA damage accumulation triggers an adaptive response resulting in improved insulin sensitivity. Loss of DNA repair, however, does negatively impacts beta-cell survival and function in Ercc1d/- mice.
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Affiliation(s)
- Ana P Huerta Guevara
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Sara J McGowan
- Institute on the Biology of Aging and Metabolism and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St., Minneapolis, MN 55455, USA; Department of Metabolism and Aging, Scripps Research Institute, Jupiter, FL 33458, USA
| | | | | | - Tokio Sano
- Department of Metabolism and Aging, Scripps Research Institute, Jupiter, FL 33458, USA
| | - Niels L Mulder
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Angelika Jurdzinski
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Theo H van Dijk
- Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Johan W Jonker
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Laura J Niedernhofer
- Institute on the Biology of Aging and Metabolism and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St., Minneapolis, MN 55455, USA; Department of Metabolism and Aging, Scripps Research Institute, Jupiter, FL 33458, USA
| | - Janine K Kruit
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands.
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Molecular spectrum of excision repair cross-complementation group 8 gene defects in Chinese patients with Cockayne syndrome type A. Sci Rep 2017; 7:13686. [PMID: 29057985 PMCID: PMC5651726 DOI: 10.1038/s41598-017-14034-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/05/2017] [Indexed: 01/09/2023] Open
Abstract
There are two genetics complementary groups Cockayne syndrome type A and B (CS-A and CS-B OMIM 216400, 133540), which is a rare autosomal recessive segmental progeroid syndrome. Homozygous or compound heterozygous mutations in the excision repair cross-complementation group 8 gene (ERCC8) result in CS-A, and mutations in ERCC6 result in CS-B. Homozygous ERCC6/ERCC8 mutations also result in UV-sensitive syndrome. In this study, twenty-one Han Chinese patients with CS were investigated to identify mutations in ERCC8/ERCC6, of which thirteen cases with CS-A were identified with the mutations of ERCC8. There are five types mutations of ERCC8 in our study, such as exon 4 rearrangement, c.394_398delTTACA, c.299insA, c.843 + 2 T > C, and c.2 T > A. An estimated frequency of exon 4 rearrangement accounts for 69.23% and c.394_398delTTACA accounts for 11.53% in our cohort. Haplotype analysis revealed that the exon 4 rearrangement and c.394_398delTTACA mutations originated from a common founder in the Chinese population respectively. With the identification of three novel ERCC8 mutations, this study expanded the molecular spectrum of known ERCC8 defects, and furthermore, suggests that the exon 4 rearrangement and c.394_398delTTACA mutations may be a common underlying cause of CS-A in the Chinese population, which is different from that in other populations.
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A complex intragenic rearrangement of ERCC8 in Chinese siblings with Cockayne syndrome. Sci Rep 2017; 7:44271. [PMID: 28333167 PMCID: PMC5363064 DOI: 10.1038/srep44271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/07/2017] [Indexed: 01/06/2023] Open
Abstract
Cockayne syndrome is an autosomal recessive disorder principally characterized by postnatal growth failure and progressive neurological dysfunction, due primarily to mutations in ERCC6 and ERCC8. Here, we report our diagnostic experience for two patients in a Chinese family suspected on clinical grounds to have Cockayne syndrome. Using multiple molecular techniques, including whole exome sequencing, array comparative genomic hybridization and quantitative polymerase chain reaction, we identified compound heterozygosity for a maternal splicing variant (chr5:60195556, NM_000082:c.618-2A > G) and a paternal complex deletion/inversion/deletion rearrangement removing exon 4 of ERCC8, confirming the suspected pathogenesis in these two subjects. Microhomology (TAA and AGCT) at the breakpoints indicated that microhomology-mediated FoSTeS events were involved in this complex ERCC8 rearrangement. This diagnostic experience illustrates the value of high-throughput genomic technologies combined with detailed phenotypic assessment in clinical genetic diagnosis.
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