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Al-Jarf R, Karmakar M, Myung Y, Ascher DB. Uncovering the Molecular Drivers of NHEJ DNA Repair-Implicated Missense Variants and Their Functional Consequences. Genes (Basel) 2023; 14:1890. [PMID: 37895239 PMCID: PMC10606680 DOI: 10.3390/genes14101890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/24/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Variants in non-homologous end joining (NHEJ) DNA repair genes are associated with various human syndromes, including microcephaly, growth delay, Fanconi anemia, and different hereditary cancers. However, very little has been done previously to systematically record the underlying molecular consequences of NHEJ variants and their link to phenotypic outcomes. In this study, a list of over 2983 missense variants of the principal components of the NHEJ system, including DNA Ligase IV, DNA-PKcs, Ku70/80 and XRCC4, reported in the clinical literature, was initially collected. The molecular consequences of variants were evaluated using in silico biophysical tools to quantitatively assess their impact on protein folding, dynamics, stability, and interactions. Cancer-causing and population variants within these NHEJ factors were statistically analyzed to identify molecular drivers. A comprehensive catalog of NHEJ variants from genes known to be mutated in cancer was curated, providing a resource for better understanding their role and molecular mechanisms in diseases. The variant analysis highlighted different molecular drivers among the distinct proteins, where cancer-driving variants in anchor proteins, such as Ku70/80, were more likely to affect key protein-protein interactions, whilst those in the enzymatic components, such as DNA-PKcs, were likely to be found in intolerant regions undergoing purifying selection. We believe that the information acquired in our database will be a powerful resource to better understand the role of non-homologous end-joining DNA repair in genetic disorders, and will serve as a source to inspire other investigations to understand the disease further, vital for the development of improved therapeutic strategies.
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Affiliation(s)
- Raghad Al-Jarf
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville, VIC 3052, Australia (M.K.)
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Malancha Karmakar
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville, VIC 3052, Australia (M.K.)
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Yoochan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville, VIC 3052, Australia (M.K.)
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - David B. Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville, VIC 3052, Australia (M.K.)
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
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Peake JD, Noguchi E. Fanconi anemia: current insights regarding epidemiology, cancer, and DNA repair. Hum Genet 2022; 141:1811-1836. [PMID: 35596788 DOI: 10.1007/s00439-022-02462-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Fanconi anemia is a genetic disorder that is characterized by bone marrow failure, as well as a predisposition to malignancies including leukemia and squamous cell carcinoma (SCC). At least 22 genes are associated with Fanconi anemia, constituting the Fanconi anemia DNA repair pathway. This pathway coordinates multiple processes and proteins to facilitate the repair of DNA adducts including interstrand crosslinks (ICLs) that are generated by environmental carcinogens, chemotherapeutic crosslinkers, and metabolic products of alcohol. ICLs can interfere with DNA transactions, including replication and transcription. If not properly removed and repaired, ICLs cause DNA breaks and lead to genomic instability, a hallmark of cancer. In this review, we will discuss the genetic and phenotypic characteristics of Fanconi anemia, the epidemiology of the disease, and associated cancer risk. The sources of ICLs and the role of ICL-inducing chemotherapeutic agents will also be discussed. Finally, we will review the detailed mechanisms of ICL repair via the Fanconi anemia DNA repair pathway, highlighting critical regulatory processes. Together, the information in this review will underscore important contributions to Fanconi anemia research in the past two decades.
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Affiliation(s)
- Jasmine D Peake
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.
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Deng X, Tchieu J, Higginson DS, Hsu KS, Feldman R, Studer L, Shaham S, Powell SN, Fuks Z, Kolesnick R. Disabling the Fanconi Anemia Pathway in Stem Cells Leads to Radioresistance and Genomic Instability. Cancer Res 2021; 81:3706-3716. [PMID: 33941615 DOI: 10.1158/0008-5472.can-20-3309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/15/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
Fanconi anemia is an inherited genome instability syndrome characterized by interstrand cross-link hypersensitivity, congenital defects, bone marrow failure, and cancer predisposition. Although DNA repair mediated by Fanconi anemia genes has been extensively studied, how inactivation of these genes leads to specific cellular phenotypic consequences associated with Fanconi anemia is not well understood. Here we report that Fanconi anemia stem cells in the C. elegans germline and in murine embryos display marked nonhomologous end joining (NHEJ)-dependent radiation resistance, leading to survival of progeny cells carrying genetic lesions. In contrast, DNA cross-linking does not induce generational genomic instability in Fanconi anemia stem cells, as widely accepted, but rather drives NHEJ-dependent apoptosis in both species. These findings suggest that Fanconi anemia is a stem cell disease reflecting inappropriate NHEJ, which is mutagenic and carcinogenic as a result of DNA misrepair, while marrow failure represents hematopoietic stem cell apoptosis. SIGNIFICANCE: This study finds that Fanconi anemia stem cells preferentially activate error-prone NHEJ-dependent DNA repair to survive irradiation, thereby conferring generational genomic instability that is instrumental in carcinogenesis.
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Affiliation(s)
- Xinzhu Deng
- Laboratory of Signal Transduction, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason Tchieu
- Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel S Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kuo-Shun Hsu
- Laboratory of Signal Transduction, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Regina Feldman
- Laboratory of Signal Transduction, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lorenz Studer
- Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shai Shaham
- The Rockefeller University, New York, New York
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zvi Fuks
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard Kolesnick
- Laboratory of Signal Transduction, Memorial Sloan Kettering Cancer Center, New York, New York.
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