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Liu Y, Yang H, Gan S, He L, Zeng R, Xiao T, Wu L. A novel mutation of DNA2 regulates neuronal cell membrane potential and epileptogenesis. Cell Death Discov 2024; 10:259. [PMID: 38802339 PMCID: PMC11130173 DOI: 10.1038/s41420-024-02029-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/28/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Mesial temporal lobe epilepsy (MTLE) is one of the most intractable epilepsies. Previously, we reported that mitochondrial DNA deletions were associated with epileptogenesis. While the underlying mechanism of mitochondrial DNA deletions during epileptogenesis remain unknown. In this study, a novel somatic mutation of DNA2 gene was identified in the hippocampal tissue of two MTLE patients carrying mitochondrial DNA deletions, and this mutation decreased the full-length expression of DNA2 protein significantly, aborting its normal functions. Then, we knocked down the DNA2 protein in zebrafish, and we demonstrated that zebrafish with DNA2 deficiency showed decreased expression of mitochondrial complex II-IV, and exhibited hallmarks of epileptic seizures, including abnormal development of the zebrafish and epileptiform discharge signals in brain, compared to the Cas9-control group. Moreover, our cell-based assays showed that DNA2 deletion resulted in accumulated mitochondrial DNA damage, abnormal oxidative phosphorylation and decreased ATP production in cells. Inadequate ATP generation in cells lead to declined Na+, K+-ATPase activity and change of cell membrane potential. Together, these disorders caused by DNA2 depletion increased cell apoptosis and inhibited the differentiation of SH-SY5Y into branched neuronal phenotype. In conclusion, DNA2 deficiency regulated the cell membrane potential via affecting ATP production by mitochondria and Na+, K+-ATPase activity, and also affected neuronal cell growth and differentiation. These disorders caused by DNA2 dysfunction are important causes of epilepsy. In summary, we are the first to report the pathogenic somatic mutation of DNA2 gene in the patients with MTLE disease, and we uncovered the mechanism of DNA2 regulating the epilepsy. This study provides new insight into the pathogenesis of epilepsy and underscore the value of DNA2 in epilepsy.
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Affiliation(s)
- Yuting Liu
- Pediatrics Research Institute, The Affiliated Children's Hospital of Xiangya School of Medicine, Hunan Children's Hospital, Central South University, Changsha, Hunan, China
| | - Haiyan Yang
- Department of Neurology, The Affiliated Children's Hospital of Xiangya School of Medicine, Hunan Children's Hospital, Central South University, Changsha, Hunan, China
| | - Siyi Gan
- Department of Neurology, The Affiliated Children's Hospital of Xiangya School of Medicine, Hunan Children's Hospital, Central South University, Changsha, Hunan, China
| | - Lu He
- Department of Neurology, The Affiliated Children's Hospital of Xiangya School of Medicine, Hunan Children's Hospital, Central South University, Changsha, Hunan, China
| | - Rongrong Zeng
- Department of Neurology, The Affiliated Children's Hospital of Xiangya School of Medicine, Hunan Children's Hospital, Central South University, Changsha, Hunan, China
| | - Ting Xiao
- Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liwen Wu
- Department of Neurology, The Affiliated Children's Hospital of Xiangya School of Medicine, Hunan Children's Hospital, Central South University, Changsha, Hunan, China.
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2
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Martins DJ, Di Lazzaro Filho R, Bertola DR, Hoch NC. Rothmund-Thomson syndrome, a disorder far from solved. FRONTIERS IN AGING 2023; 4:1296409. [PMID: 38021400 PMCID: PMC10676203 DOI: 10.3389/fragi.2023.1296409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
Rothmund-Thomson syndrome (RTS) is a rare autosomal recessive disorder characterized by a range of clinical symptoms, including poikiloderma, juvenile cataracts, short stature, sparse hair, eyebrows/eyelashes, nail dysplasia, and skeletal abnormalities. While classically associated with mutations in the RECQL4 gene, which encodes a DNA helicase involved in DNA replication and repair, three additional genes have been recently identified in RTS: ANAPC1, encoding a subunit of the APC/C complex; DNA2, which encodes a nuclease/helicase involved in DNA repair; and CRIPT, encoding a poorly characterized protein implicated in excitatory synapse formation and splicing. Here, we review the clinical spectrum of RTS patients, analyze the genetic basis of the disease, and discuss molecular functions of the affected genes, drawing some novel genotype-phenotype correlations and proposing avenues for future studies into this enigmatic disorder.
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Affiliation(s)
- Davi Jardim Martins
- Genomic Stability Unit, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Ricardo Di Lazzaro Filho
- Center for Human Genome Studies, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Dasa Genômica/Genera, Genômica, São Paulo, Brazil
| | - Debora Romeo Bertola
- Center for Human Genome Studies, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Genetics Unit, Department of Pediatrics, Faculty of Medicine, Children’s Institute, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - Nícolas Carlos Hoch
- Genomic Stability Unit, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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3
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DNA2 mutation causing multisystemic disorder with impaired mitochondrial DNA maintenance. J Hum Genet 2022; 67:691-699. [PMID: 36064591 DOI: 10.1038/s10038-022-01075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE To describe a novel DNA2 variant contributing to defects in mtDNA maintenance and mtDNA depletion syndrome (MDS), and the clinical and histological findings associated with this variation. METHODS Herein, we describe the case of a patient who presented with hearing loss and myopathy, given the family history of similar findings in the father, was evaluated by sequencing of the deafness gene panel, mitochondrial genome, and the exome. Furthermore, tissue staining, mtDNA copy number detection, mtDNA sequencing, and long-range polymerase chain reaction tests were also conducted on the muscle biopsy specimen. In vitro experiments, including analyses of the mtDNA copy number; levels of ATP, ATPase, and reactive oxygen species (ROS); and the membrane potential, were performed. RESULTS The DNA2 heterozygous truncating variant c. 2368C > T (p.Q790X) was identified and verified as the cause of an mtDNA copy number decrement in both functional experiments and muscle tissue analyses. These changes were accompanied by reductions in ATP, ATPase, and ROS levels. CONCLUSION The DNA2 variant was a likely cause of MDS in this patient. These findings expand the mutational spectrum of MDS and improve our understanding of the functions of DNA2 by revealing its novel role in mtDNA maintenance.
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4
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Kohzaki M. Mammalian Resilience Revealed by a Comparison of Human Diseases and Mouse Models Associated With DNA Helicase Deficiencies. Front Mol Biosci 2022; 9:934042. [PMID: 36032672 PMCID: PMC9403131 DOI: 10.3389/fmolb.2022.934042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 12/01/2022] Open
Abstract
Maintaining genomic integrity is critical for sustaining individual animals and passing on the genome to subsequent generations. Several enzymes, such as DNA helicases and DNA polymerases, are involved in maintaining genomic integrity by unwinding and synthesizing the genome, respectively. Indeed, several human diseases that arise caused by deficiencies in these enzymes have long been known. In this review, the author presents the DNA helicases associated with human diseases discovered to date using recent analyses, including exome sequences. Since several mouse models that reflect these human diseases have been developed and reported, this study also summarizes the current knowledge regarding the outcomes of DNA helicase deficiencies in humans and mice and discusses possible mechanisms by which DNA helicases maintain genomic integrity in mammals. It also highlights specific diseases that demonstrate mammalian resilience, in which, despite the presence of genomic instability, patients and mouse models have lifespans comparable to those of the general population if they do not develop cancers; finally, this study discusses future directions for therapeutic applications in humans that can be explored using these mouse models.
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5
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Mitchell C, Becker V, DeLoach J, Nestore E, Bolterstein E, Kohl KP. The Drosophila Mutagen-Sensitivity Gene mus109 Encodes DmDNA2. Genes (Basel) 2022; 13:genes13020312. [PMID: 35205357 PMCID: PMC8872385 DOI: 10.3390/genes13020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 02/05/2023] Open
Abstract
The identification of mutants through forward genetic screens is the backbone of Drosophila genetics research, yet many mutants identified through these screens have yet to be mapped to the Drosophila genome. This is especially true of mutants that have been identified as mutagen-sensitive (mus), but have not yet been mapped to their associated molecular locus. Our study addressed the need for additional mus gene identification by determining the locus and exploring the function of the X-linked mutagen-sensitive gene mus109 using three available mutant alleles: mus109D1, mus109D2, and mus109lS. After first confirming that all three mus109 alleles were sensitive to methyl methanesulfonate (MMS) using complementation analysis, we used deletion mapping to narrow the candidate genes for mus109. Through DNA sequencing, we were able to determine that mus109 is the uncharacterized gene CG2990, which encodes the Drosophila ortholog of the highly conserved DNA2 protein that is important for DNA replication and repair. We further used the sequence and structure of DNA2 to predict the impact of the mus109 allele mutations on the final gene product. Together, these results provide a tool for researchers to further investigate the role of DNA2 in DNA repair processes in Drosophila.
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Affiliation(s)
- Chandani Mitchell
- Biology Department, Winthrop University, Rock Hill, SC 29733, USA; (C.M.); (J.D.); (E.N.)
| | - Vada Becker
- Biology Department, Northeastern Illinois University, Chicago, IL 60625, USA; (V.B.); (E.B.)
| | - Jordan DeLoach
- Biology Department, Winthrop University, Rock Hill, SC 29733, USA; (C.M.); (J.D.); (E.N.)
| | - Erica Nestore
- Biology Department, Winthrop University, Rock Hill, SC 29733, USA; (C.M.); (J.D.); (E.N.)
| | - Elyse Bolterstein
- Biology Department, Northeastern Illinois University, Chicago, IL 60625, USA; (V.B.); (E.B.)
| | - Kathryn P. Kohl
- Biology Department, Winthrop University, Rock Hill, SC 29733, USA; (C.M.); (J.D.); (E.N.)
- Correspondence:
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6
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Tsutakawa SE, Bacolla A, Katsonis P, Bralić A, Hamdan SM, Lichtarge O, Tainer JA, Tsai CL. Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication. Front Mol Biosci 2021; 8:791792. [PMID: 34966786 PMCID: PMC8710748 DOI: 10.3389/fmolb.2021.791792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
All tumors have DNA mutations, and a predictive understanding of those mutations could inform clinical treatments. However, 40% of the mutations are variants of unknown significance (VUS), with the challenge being to objectively predict whether a VUS is pathogenic and supports the tumor or whether it is benign. To objectively decode VUS, we mapped cancer sequence data and evolutionary trace (ET) scores onto crystallography and cryo-electron microscopy structures with variant impacts quantitated by evolutionary action (EA) measures. As tumors depend on helicases and nucleases to deal with transcription/replication stress, we targeted helicase–nuclease–RPA complexes: (1) XPB-XPD (within TFIIH), XPF-ERCC1, XPG, and RPA for transcription and nucleotide excision repair pathways and (2) BLM, EXO5, and RPA plus DNA2 for stalled replication fork restart. As validation, EA scoring predicts severe effects for most disease mutations, but disease mutants with low ET scores not only are likely destabilizing but also disrupt sophisticated allosteric mechanisms. For sites of disease mutations and VUS predicted to be severe, we found strong co-localization to ordered regions. Rare discrepancies highlighted the different survival requirements between disease and tumor mutations, as well as the value of examining proteins within complexes. In a genome-wide analysis of 33 cancer types, we found correlation between the number of mutations in each tumor and which pathways or functional processes in which the mutations occur, revealing different mutagenic routes to tumorigenesis. We also found upregulation of ancient genes including BLM, which supports a non-random and concerted cancer process: reversion to a unicellular, proliferation-uncontrolled, status by breaking multicellular constraints on cell division. Together, these genes and global analyses challenge the binary “driver” and “passenger” mutation paradigm, support a gradient impact as revealed by EA scoring from moderate to severe at a single gene level, and indicate reduced regulation as well as activity. The objective quantitative assessment of VUS scoring and gene overexpression in the context of functional interactions and pathways provides insights for biology, oncology, and precision medicine.
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Affiliation(s)
- Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States.,Department of Cancer Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
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7
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DNA2 in Chromosome Stability and Cell Survival-Is It All about Replication Forks? Int J Mol Sci 2021; 22:ijms22083984. [PMID: 33924313 PMCID: PMC8069077 DOI: 10.3390/ijms22083984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/08/2021] [Accepted: 04/10/2021] [Indexed: 01/16/2023] Open
Abstract
The conserved nuclease-helicase DNA2 has been linked to mitochondrial myopathy, Seckel syndrome, and cancer. Across species, the protein is indispensable for cell proliferation. On the molecular level, DNA2 has been implicated in DNA double-strand break (DSB) repair, checkpoint activation, Okazaki fragment processing (OFP), and telomere homeostasis. More recently, a critical contribution of DNA2 to the replication stress response and recovery of stalled DNA replication forks (RFs) has emerged. Here, we review the available functional and phenotypic data and propose that the major cellular defects associated with DNA2 dysfunction, and the links that exist with human disease, can be rationalized through the fundamental importance of DNA2-dependent RF recovery to genome duplication. Being a crucial player at stalled RFs, DNA2 is a promising target for anti-cancer therapy aimed at eliminating cancer cells by replication-stress overload.
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8
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Parry DA, Tamayo-Orrego L, Carroll P, Marsh JA, Greene P, Murina O, Uggenti C, Leitch A, Káposzta R, Merő G, Nagy A, Orlik B, Kovács-Pászthy B, Quigley AJ, Riszter M, Rankin J, Reijns MAM, Szakszon K, Jackson AP. PRIM1 deficiency causes a distinctive primordial dwarfism syndrome. Genes Dev 2020; 34:1520-1533. [PMID: 33060134 PMCID: PMC7608753 DOI: 10.1101/gad.340190.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022]
Abstract
DNA replication is fundamental for cell proliferation in all organisms. Nonetheless, components of the replisome have been implicated in human disease, and here we report PRIM1 encoding the catalytic subunit of DNA primase as a novel disease gene. Using a variant classification agnostic approach, biallelic mutations in PRIM1 were identified in five individuals. PRIM1 protein levels were markedly reduced in patient cells, accompanied by replication fork asymmetry, increased interorigin distances, replication stress, and prolonged S-phase duration. Consequently, cell proliferation was markedly impaired, explaining the patients' extreme growth failure. Notably, phenotypic features distinct from those previously reported with DNA polymerase genes were evident, highlighting differing developmental requirements for this core replisome component that warrant future investigation.
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Affiliation(s)
- David A Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Lukas Tamayo-Orrego
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paula Carroll
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Philip Greene
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Olga Murina
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Carolina Uggenti
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Andrea Leitch
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | | | - Rita Káposzta
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Gabriella Merő
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Andrea Nagy
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Brigitta Orlik
- Institute of Pathology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Balázs Kovács-Pászthy
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Alan J Quigley
- Department of Radiology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, United Kingdom
| | - Magdolna Riszter
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Julia Rankin
- Department Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter EX1 2ED, United Kingdom
| | - Martin A M Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Katalin Szakszon
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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9
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Falquet B, Ölmezer G, Enkner F, Klein D, Challa K, Appanah R, Gasser SM, Rass U. Disease-associated DNA2 nuclease-helicase protects cells from lethal chromosome under-replication. Nucleic Acids Res 2020; 48:7265-7278. [PMID: 32544229 PMCID: PMC7367196 DOI: 10.1093/nar/gkaa524] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/21/2020] [Accepted: 06/09/2020] [Indexed: 01/28/2023] Open
Abstract
DNA2 is an essential nuclease–helicase implicated in DNA repair, lagging-strand DNA synthesis, and the recovery of stalled DNA replication forks (RFs). In Saccharomyces cerevisiae, dna2Δ inviability is reversed by deletion of the conserved helicase PIF1 and/or DNA damage checkpoint-mediator RAD9. It has been suggested that Pif1 drives the formation of long 5′-flaps during Okazaki fragment maturation, and that the essential function of Dna2 is to remove these intermediates. In the absence of Dna2, 5′-flaps are thought to accumulate on the lagging strand, resulting in DNA damage-checkpoint arrest and cell death. In line with Dna2’s role in RF recovery, we find that the loss of Dna2 results in severe chromosome under-replication downstream of endogenous and exogenous RF-stalling. Importantly, unfaithful chromosome replication in Dna2-mutant cells is exacerbated by Pif1, which triggers the DNA damage checkpoint along a pathway involving Pif1’s ability to promote homologous recombination-coupled replication. We propose that Dna2 fulfils its essential function by promoting RF recovery, facilitating replication completion while suppressing excessive RF restart by recombination-dependent replication (RDR) and checkpoint activation. The critical nature of Dna2’s role in controlling the fate of stalled RFs provides a framework to rationalize the involvement of DNA2 in Seckel syndrome and cancer.
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Affiliation(s)
- Benoît Falquet
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Gizem Ölmezer
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Franz Enkner
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Dominique Klein
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Rowin Appanah
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Ulrich Rass
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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10
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Appanah R, Jones D, Falquet B, Rass U. Limiting homologous recombination at stalled replication forks is essential for cell viability: DNA2 to the rescue. Curr Genet 2020; 66:1085-1092. [PMID: 32909097 PMCID: PMC7599155 DOI: 10.1007/s00294-020-01106-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022]
Abstract
The disease-associated nuclease–helicase DNA2 has been implicated in DNA end-resection during DNA double-strand break repair, Okazaki fragment processing, and the recovery of stalled DNA replication forks (RFs). Its role in Okazaki fragment processing has been proposed to explain why DNA2 is indispensable for cell survival across organisms. Unexpectedly, we found that DNA2 has an essential role in suppressing homologous recombination (HR)-dependent replication restart at stalled RFs. In the absence of DNA2-mediated RF recovery, excessive HR-restart of stalled RFs results in toxic levels of abortive recombination intermediates that lead to DNA damage-checkpoint activation and terminal cell-cycle arrest. While HR proteins protect and restart stalled RFs to promote faithful genome replication, these findings show how HR-dependent replication restart is actively constrained by DNA2 to ensure cell survival. These new insights disambiguate the effects of DNA2 dysfunction on cell survival, and provide a framework to rationalize the association of DNA2 with cancer and the primordial dwarfism disorder Seckel syndrome based on its role in RF recovery.
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Affiliation(s)
- Rowin Appanah
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - David Jones
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Benoît Falquet
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, 4056, Basel, Switzerland
| | - Ulrich Rass
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
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11
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Olthof AM, Rasmussen JS, Campeau PM, Kanadia RN. Disrupted minor intron splicing is prevalent in Mendelian disorders. Mol Genet Genomic Med 2020; 8:e1374. [PMID: 32573973 PMCID: PMC7507305 DOI: 10.1002/mgg3.1374] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
Background Splicing is crucial for proper gene expression, and is predominately executed by the major spliceosome. Conversely, 722 introns in 699 human minor intron‐containing genes (MIGs) are spliced by the minor spliceosome. Splicing of these minor introns is disrupted in diseases caused by pathogenic variants in the minor spliceosome, ultimately leading to the aberrant expression of a subset of these MIGs. However, the effect of variants in minor introns and MIGs on diseases remains unexplored. Methods Variants in MIGs and associated clinical manifestations were identified using ClinVar. The HPO database was then used to curate the related symptoms and affected organ systems. Results: We found pathogenic variants in 211 MIGs, which commonly resulted in intellectual disability, seizures and microcephaly. This revealed a subset of MIGs whose aberrant splicing may contribute to the pathogenesis of minor spliceosome‐related diseases. Moreover, we identified 51 pathogenic variants in minor intron splice sites that reduce the splice site strength and can induce alternative splicing. Conclusion These findings highlight that disrupted minor intron splicing has a broader impact on human diseases than previously appreciated. The hope is that this knowledge will aid in the development of therapeutic strategies that incorporate the minor intron splicing pathway.
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Affiliation(s)
- Anouk M Olthof
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, USA
| | - Jeffrey S Rasmussen
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, USA
| | | | - Rahul N Kanadia
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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12
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Zheng L, Meng Y, Campbell JL, Shen B. Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases. Nucleic Acids Res 2020; 48:16-35. [PMID: 31754720 PMCID: PMC6943134 DOI: 10.1093/nar/gkz1101] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/23/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022] Open
Abstract
DNA2 nuclease/helicase is a structure-specific nuclease, 5'-to-3' helicase, and DNA-dependent ATPase. It is involved in multiple DNA metabolic pathways, including Okazaki fragment maturation, replication of 'difficult-to-replicate' DNA regions, end resection, stalled replication fork processing, and mitochondrial genome maintenance. The participation of DNA2 in these different pathways is regulated by its interactions with distinct groups of DNA replication and repair proteins and by post-translational modifications. These regulatory mechanisms induce its recruitment to specific DNA replication or repair complexes, such as DNA replication and end resection machinery, and stimulate its efficient cleavage of various structures, for example, to remove RNA primers or to produce 3' overhangs at telomeres or double-strand breaks. Through these versatile activities at replication forks and DNA damage sites, DNA2 functions as both a tumor suppressor and promoter. In normal cells, it suppresses tumorigenesis by maintaining the genomic integrity. Thus, DNA2 mutations or functional deficiency may lead to cancer initiation. However, DNA2 may also function as a tumor promoter, supporting cancer cell survival by counteracting replication stress. Therefore, it may serve as an ideal target to sensitize advanced DNA2-overexpressing cancers to current chemo- and radiotherapy regimens.
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Affiliation(s)
- Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Yuan Meng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Judith L Campbell
- Divisions of Chemistry and Chemical Engineering and Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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13
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Tarnauskaitė Ž, Bicknell LS, Marsh JA, Murray JE, Parry DA, Logan CV, Bober MB, de Silva DC, Duker AL, Sillence D, Wise C, Jackson AP, Murina O, Reijns MAM. Biallelic variants in DNA2 cause microcephalic primordial dwarfism. Hum Mutat 2019; 40:1063-1070. [PMID: 31045292 PMCID: PMC6773220 DOI: 10.1002/humu.23776] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/15/2019] [Accepted: 04/28/2019] [Indexed: 11/11/2022]
Abstract
Microcephalic primordial dwarfism (MPD) is a group of rare single-gene disorders characterized by the extreme reduction in brain and body size from early development onwards. Proteins encoded by MPD-associated genes play important roles in fundamental cellular processes, notably genome replication and repair. Here we report the identification of four MPD individuals with biallelic variants in DNA2, which encodes an adenosine triphosphate (ATP)-dependent helicase/nuclease involved in DNA replication and repair. We demonstrate that the two intronic variants (c.1764-38_1764-37ins(53) and c.74+4A>C) found in these individuals substantially impair DNA2 transcript splicing. Additionally, we identify a missense variant (c.1963A>G), affecting a residue of the ATP-dependent helicase domain that is highly conserved between humans and yeast, with the resulting substitution (p.Thr655Ala) predicted to directly impact ATP/ADP (adenosine diphosphate) binding by DNA2. Our findings support the pathogenicity of these variants as biallelic hypomorphic mutations, establishing DNA2 as an MPD disease gene.
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Affiliation(s)
- Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Louise S. Bicknell
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jennie E. Murray
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - David A. Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Clare V. Logan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Michael B. Bober
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - Deepthi C. de Silva
- Department of Physiology, Faculty of MedicineUniversity of KelaniyaColomboSri Lanka
| | - Angela L. Duker
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - David Sillence
- Discipline of Genomic Medicine, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
- Western Sydney Genetics ProgramSydney Children's Hospitals NetworkWestmeadAustralia
| | - Carol Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal ResearchTexas Scottish, Rite Hospital for ChildrenDallasTexas
- McDermott Center for Human Growth and DevelopmentUniversity of Texas, Southwestern Medical CenterDallasTexas
- Department of Orthopaedic SurgeryUniversity of Texas Southwestern Medical CenterDallasTexas
- Department of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexas
| | - Andrew P. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Olga Murina
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Martin A. M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
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