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Misceo D, Strømme P, Bitarafan F, Chawla MS, Sheng Y, Bach de Courtade SM, Eide L, Frengen E. Biallelic NDUFA4 Deletion Causes Mitochondrial Complex IV Deficiency in a Patient with Leigh Syndrome. Genes (Basel) 2024; 15:500. [PMID: 38674434 PMCID: PMC11050323 DOI: 10.3390/genes15040500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Oxidative phosphorylation involves a complex multi-enzymatic mitochondrial machinery critical for proper functioning of the cell, and defects herein cause a wide range of diseases called "primary mitochondrial disorders" (PMDs). Mutations in about 400 nuclear and 37 mitochondrial genes have been documented to cause PMDs, which have an estimated birth prevalence of 1:5000. Here, we describe a 4-year-old female presenting from early childhood with psychomotor delay and white matter signal changes affecting several brain regions, including the brainstem, in addition to lactic and phytanic acidosis, compatible with Leigh syndrome, a genetically heterogeneous subgroup of PMDs. Whole genome sequencing of the family trio identified a homozygous 12.9 Kb deletion, entirely overlapping the NDUFA4 gene. Sanger sequencing of the breakpoints revealed that the genomic rearrangement was likely triggered by Alu elements flanking the gene. NDUFA4 encodes for a subunit of the respiratory chain Complex IV, whose activity was significantly reduced in the patient's fibroblasts. In one family, dysfunction of NDUFA4 was previously documented as causing mitochondrial Complex IV deficiency nuclear type 21 (MC4DN21, OMIM 619065), a relatively mild form of Leigh syndrome. Our finding confirms the loss of NDUFA4 function as an ultra-rare cause of Complex IV defect, clinically presenting as Leigh syndrome.
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Affiliation(s)
- Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (F.B.); (Y.S.); (E.F.)
| | - Petter Strømme
- Division of Pediatrics and Adolescent Medicine, Oslo University Hospital and Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
| | - Fatemeh Bitarafan
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (F.B.); (Y.S.); (E.F.)
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (F.B.); (Y.S.); (E.F.)
| | | | - Lars Eide
- Department of Biochemistry, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (S.M.B.d.C.); (L.E.)
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (F.B.); (Y.S.); (E.F.)
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Chung AK, Lin RT, Yeh CC, Yang CY, Wu CJ, Chen PL, Lin JT. Diagnostic rate of germline pathogenic variants in pancreatic ductal adenocarcinoma patients using whole genome sequencing. Front Genet 2023; 14:1172365. [PMID: 37234870 PMCID: PMC10205989 DOI: 10.3389/fgene.2023.1172365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Identification of germline pathogenic variants in cancer patients is critical for treatment planning, genetic counseling, and health policymaking. However, previous estimates of the prevalence of germline etiology of pancreatic ductal adenocarcinoma (PDAC) were biased because they were based only on sequencing data of protein-coding regions of known PDAC candidate genes. To determine the percentage of patients with PDAC carrying germline pathogenic variants, we enrolled the inpatients from the digestive health clinics, hematology and oncology clinics, and surgical clinics of a single tertiary medical center in Taiwan for whole genome sequencing (WGS) analysis of genomic DNA. The virtual gene panel of 750 genes comprised PDAC candidate genes and those listed in the COSMIC Cancer Gene Census. The genetic variant types under investigation included single nucleotide substitutions, small indels, structural variants, and mobile element insertions (MEIs). In 8 of 24 (33.3%) patients with PDAC, we identified pathogenic/likely pathogenic variants, including single nucleotide substitutions and small indels in ATM, BRCA1, BRCA2, POLQ, SPINK1 and CASP8, as well as structural variants in CDC25C and USP44. We identified additional patients carrying variants that could potentially affect splicing. This cohort study demonstrates that an extensive analysis of the abundant information yielded by the WGS approach can uncover many pathogenic variants that could be missed by traditional panel-based or whole exome sequencing-based approaches. The percentage of patients with PDAC carrying germline variants might be much higher than previously expected.
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Affiliation(s)
- An-Ko Chung
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ro-Ting Lin
- Department of Occupational Safety and Health, College of Public Health, China Medical University, Taichung, Taiwan
| | - Chun-Chieh Yeh
- School of Medicine, China Medical University, Taichung, Taiwan
- Department of Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Chi-Ying Yang
- Department of Internal Medicine, Digestive Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Chang-Jiun Wu
- Department of Genomic Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Jaw-Town Lin
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, E-Da Hospital, Kaohsiung, Taiwan
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Schütte J, Reusch J, Khandanpour C, Eisfeld C. Structural Variants as a Basis for Targeted Therapies in Hematological Malignancies. Front Oncol 2019; 9:839. [PMID: 31555592 PMCID: PMC6722867 DOI: 10.3389/fonc.2019.00839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/14/2019] [Indexed: 11/13/2022] Open
Abstract
Structural variants (SV) are changes in the genomic landscape that can alter gene expression levels and thus lead to disease development. The most common and best studied SVs in hematological malignancies are chromosomal translocations. Here, parts of two genes that are normally on different chromosomes come into close proximity due to a failure in DNA repair. As a consequence, fusion proteins which show a different function and/or cellular localization compared to the two original proteins are expressed, sometimes even at different levels. The identification of chromosomal translocations is often used to identify the specific disease a patient is suffering from. In addition, SVs such as deletions, duplications, inversions and single nucleotide polymorphisms (SNPs) can occur in hematopoietic cells and lead to their malignant transformations. Changes in the 3D genome structure have also recently been shown to impact disease development. In this review, we describe a variety of SVs occurring in different subtypes of hematological malignancies. Currently, most therapeutic approaches target fusion proteins which are the cellular product of chromosomal translocations. However, amplifications and SNPs also play a role in disease progression and can be targeted. We present some examples for different types of structural variants and how they are currently treated.
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Affiliation(s)
- Judith Schütte
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Julia Reusch
- Medizinische Fakultät, Universität Münster, Münster, Germany
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Yang G, Luo W, Zhang J, Yan X, Du Y, Zhou L, Li W, Wang H, Chen Z, Guo T. Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants. Front Plant Sci 2019; 10:1514. [PMID: 31850019 PMCID: PMC6892775 DOI: 10.3389/fpls.2019.01514] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/31/2019] [Indexed: 05/19/2023]
Abstract
Physical mutagens, such as carbon-ion beams (CIBs) and gamma rays (GRs), induce mutations with high frequency at a relatively low dose and are more user-friendly and environment-friendly in mutation breeding. Previous studies showed that CIBs induced large sized deletions and insertions, and chromosomal rearrangements, whereas GRs induce shorter deletions and insertions, and more frequent base substitutions. However, the difference on the genomic level between CIB- and GR-induced mutations remains to be clarified. In the present study, we re-sequence six mutagenized lines derived from CIB irradiation and four mutagenized lines derived from GRs. A total of 283 and 381 variations are induced in these mutants by CIBs and GRs, respectively, including single base substitutions (SBSs), small insertion and deletions (InDels), multiple nucleotide variants (MNVs). SBSs are the most abundant type of mutation and single base transition is the main form for SBSs. CIB-induced InDels accounted for 25.44% of the total variations, while GR-induced InDels accounted for 17.85%. On the contrary, the frequency of MNVs induced by GRs was approximately 2.19 times that induced by CIBs, which indicates CIBs induced increased InDels, whereas GRs induced increased MNVs. Notably, multiple base deletions (≥5 bp) were induced at a much higher frequency by CIBs than by GRs. We also find mutations induced by CIBs and GRs are unevenly distributed on chromosomes. Unusual high-frequency (HF) and low-frequency (LF) mutation regions are discovered by analyzing mutations per 1Mb along the genome. The mutation frequency within the HF regions were significantly higher than the LF regions (P < 0.05). A large majority of SBSs, InDels, and MNVs induced by CIBs and GRs occurred in upstream and downstream regions. Our study compares difference of mutation profiles induced by the CIB irradiation and GR on rice genomes, and give some clues for understanding the mutagenesis mechanism of physical radiation and improving the mutagenesis efficiency.
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Affiliation(s)
- Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Wenlong Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Jian Zhang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Xiancheng Yan
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Yan Du
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Libin Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- *Correspondence: Tao Guo,
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