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Pfeifer GP. DNA Damage and Parkinson's Disease. Int J Mol Sci 2024; 25:4187. [PMID: 38673772 PMCID: PMC11050701 DOI: 10.3390/ijms25084187] [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: 02/25/2024] [Revised: 03/20/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
The etiology underlying most sporadic Parkinson's' disease (PD) cases is unknown. Environmental exposures have been suggested as putative causes of the disease. In cell models and in animal studies, certain chemicals can destroy dopaminergic neurons. However, the mechanisms of how these chemicals cause the death of neurons is not understood. Several of these agents are mitochondrial toxins that inhibit the mitochondrial complex I of the electron transport chain. Familial PD genes also encode proteins with important functions in mitochondria. Mitochondrial dysfunction of the respiratory chain, in combination with the presence of redox active dopamine molecules in these cells, will lead to the accumulation of reactive oxygen species (ROS) in dopaminergic neurons. Here, I propose a mechanism regarding how ROS may lead to cell killing with a specificity for neurons. One rarely considered hypothesis is that ROS produced by defective mitochondria will lead to the formation of oxidative DNA damage in nuclear DNA. Many genes that encode proteins with neuron-specific functions are extraordinary long, ranging in size from several hundred kilobases to well over a megabase. It is predictable that such long genes will contain large numbers of damaged DNA bases, for example in the form of 8-oxoguanine (8-oxoG), which is a major DNA damage type produced by ROS. These DNA lesions will slow down or stall the progression of RNA polymerase II, which is a term referred to as transcription stress. Furthermore, ROS-induced DNA damage may cause mutations, even in postmitotic cells such as neurons. I propose that the impaired transcription and mutagenesis of long, neuron-specific genes will lead to a loss of neuronal integrity, eventually leading to the death of these cells during a human lifetime.
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Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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2
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Gerovska D, Fernández Moreno P, Zabala A, Araúzo-Bravo MJ. Cell-Free Genic Extrachromosomal Circular DNA Profiles of DNase Knockouts Associated with Systemic Lupus Erythematosus and Relation with Common Fragile Sites. Biomedicines 2023; 12:80. [PMID: 38255187 PMCID: PMC10813657 DOI: 10.3390/biomedicines12010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Cell-free extrachromosomal circular DNA (cf-eccDNA) has been proposed as a promising early biomarker for disease diagnosis, progression and drug response. Its established biomarker features are changes in the number and length distribution of cf-eccDNA. Another novel promising biomarker is a set of eccDNA excised from a panel of genes specific to a condition compared to a control. Deficiencies in two endonucleases that specifically target DNA, Dnase1 and Dnase1l3, are associated with systemic lupus erythematosus (SLE). To study the genic eccDNA profiles in the case of their deficiencies, we mapped sequenced eccDNA data from plasma, liver and buffy coat from Dnase1 and Dnase1l3 knockouts (KOs), and wild type controls in mouse. Next, we performed an eccDNA differential analysis between KO and control groups using our DifCir algorithm. We found a specific genic cf-eccDNA fingerprint of the Dnase1l3 group compared to the wild type controls involving 131 genes; 26% of them were associated with human chromosomal fragile sites (CFSs) and with a statistically significant enrichment of CFS-associated genes. We found six genes in common with the genic cf-eccDNA profile of SLE patients with DNASE1L3 deficiency, namely Rorb, Mvb12b, Osbpl10, Fto, Tnik and Arhgap10; all of them were specific and present in all human plasma samples, and none of them were associated with CFSs. A not so distinctive genic cf-eccDNA difference involving only seven genes was observed in the case of the Dnase1 group compared to the wild type. In tissue-liver and buffy coat-we did not detect the same genic eccDNA difference observed in the plasma samples. These results point to a specific role of a set of genic eccDNA in plasma from DNase KOs, as well as a relation with CFS genes, confirming the promise of the genic cf-eccDNA in studying diseases and the need for further research on the relationship between eccDNA and CFSs.
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Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Patricia Fernández Moreno
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Aitor Zabala
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
- Basque Foundation for Science, IKERBASQUE, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
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3
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease. Mov Disord 2023; 38:2249-2257. [PMID: 37926948 PMCID: PMC10843047 DOI: 10.1002/mds.29610] [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: 06/27/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Parkin RBR E3 ubiquitin-protein ligase (PRKN) mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E, which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. OBJECTIVES To identify complex structural variants in PRKN using long-read sequencing. METHODS We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read sequencing. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of Accelerating Medicines Partnership Parkinson's disease (AMP-PD) and United Kingdom (UK)-Biobank datasets. RESULTS Multiple ligation probe amplification identified a heterozygous exon three deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7 Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN expression. CONCLUSIONS This is the first report describing a large 7 Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read sequencing for structural variant analysis in unresolved young-onset PD cases. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo Tokyo Koto Geriatric Medical Center 3-3-20 Shinsuna, Koto-ku, Tokyo 136-0075
| | - Risa Nonaka
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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Wang N, Xu S, Egli D. Replication stress in mammalian embryo development, differentiation, and reprogramming. Trends Cell Biol 2023; 33:872-886. [PMID: 37202286 DOI: 10.1016/j.tcb.2023.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/20/2023]
Abstract
Duplicating a genome of 3 billion nucleotides is challenged by a variety of obstacles that can cause replication stress and affect the integrity of the genome. Recent studies show that replication fork slowing and stalling is prevalent in early mammalian development, resulting in genome instability and aneuploidy, and constituting a barrier to development in human reproduction. Genome instability resulting from DNA replication stress is a barrier to the cloning of animals and to the reprogramming of differentiated cells to induced pluripotent stem cells, as well as a barrier to cell transformation. Remarkably, the regions most impacted by replication stress are shared in these different cellular contexts, affecting long genes and flanking intergenic areas. In this review we integrate our knowledge of DNA replication stress in mammalian embryos, in programming, and in reprogramming, and we discuss a potential role for fragile sites in sensing replication stress and restricting cell cycle progression in health and disease.
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Affiliation(s)
- Ning Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shuangyi Xu
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA.
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5
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-read sequencing resolves a complex structural variant in PRKN Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.14.23293948. [PMID: 37790330 PMCID: PMC10543050 DOI: 10.1101/2023.08.14.23293948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background PRKN mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. Objectives To identify complex structural variants in PRKN using long-read sequencing. Methods We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of AMP-PD and UK-Biobank datasets. Results Multiple ligation probe amplification identified a heterozygous exon 3 deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4,941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN isoforms. Conclusions This is the first report describing a large 7Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read whole genome sequencing for structural variant analysis in unresolved young-onset PD cases.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Risa Nonaka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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Hill HJ, Bonser D, Golic KG. Dicentric chromosome breakage in Drosophila melanogaster is influenced by pericentric heterochromatin and occurs in nonconserved hotspots. Genetics 2023; 224:iyad052. [PMID: 37010100 PMCID: PMC10213500 DOI: 10.1093/genetics/iyad052] [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: 10/18/2022] [Revised: 10/18/2022] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Chromosome breakage plays an important role in the evolution of karyotypes and can produce deleterious effects within a single individual, such as aneuploidy or cancer. Forces that influence how and where chromosomes break are not fully understood. In humans, breakage tends to occur in conserved hotspots called common fragile sites (CFS), especially during replication stress. By following the fate of dicentric chromosomes in Drosophila melanogaster, we find that breakage under tension also tends to occur in specific hotspots. Our experimental approach was to induce sister chromatid exchange in a ring chromosome to generate a dicentric chromosome with a double chromatid bridge. In the following cell division, the dicentric bridges may break. We analyzed the breakage patterns of 3 different ring-X chromosomes. These chromosomes differ by the amount and quality of heterochromatin they carry as well as their genealogical history. For all 3 chromosomes, breakage occurs preferentially in several hotspots. Surprisingly, we found that the hotspot locations are not conserved between the 3 chromosomes: each displays a unique array of breakage hotspots. The lack of hotspot conservation, along with a lack of response to aphidicolin, suggests that these breakage sites are not entirely analogous to CFS and may reveal new mechanisms of chromosome fragility. Additionally, the frequency of dicentric breakage and the durability of each chromosome's spindle attachment vary significantly between the 3 chromosomes and are correlated with the origin of the centromere and the amount of pericentric heterochromatin. We suggest that different centromere strengths could account for this.
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Affiliation(s)
- Hunter J Hill
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Danielle Bonser
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kent G Golic
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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7
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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8
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Kałuzińska-Kołat Ż, Kośla K, Kołat D, Płuciennik E, Bednarek AK. Antineoplastic Nature of WWOX in Glioblastoma Is Mainly a Consequence of Reduced Cell Viability and Invasion. BIOLOGY 2023; 12:biology12030465. [PMID: 36979157 PMCID: PMC10045224 DOI: 10.3390/biology12030465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023]
Abstract
Following the discovery of WWOX, research has moved in many directions, including the role of this putative tumor suppressor in the central nervous system and related diseases. The task of determining the nature of WWOX in glioblastoma (GBM) is still considered to be at the initial stage; however, the influence of this gene on the GBM malignant phenotype has already been reported. Because most of the available in vitro research does not consider several cellular GBM models or a wide range of investigated biological assays, the present study aimed to determine the main processes by which WWOX exhibits anticancer properties in GBM, while taking into account the phenotypic heterogeneity between cell lines. Ectopic WWOX overexpression was studied in T98G, DBTRG-05MG, U251MG, and U87MG cell lines that were compared with the use of assays investigating cell viability, proliferation, apoptosis, adhesion, clonogenicity, three-dimensional and anchorage-independent growth, and invasiveness. Observations presenting the antineoplastic properties of WWOX were consistent for T98G, U251MG, and U87MG. Increased proliferation and tumor growth were noted in WWOX-overexpressing DBTRG-05MG cells. A possible explanation for this, arrived at via bioinformatics tools, was linked to the TARDBP transcription factor and expression differences of USP25 and CPNE2 that regulate EGFR surface abundance. Collectively, and despite various cell line-specific circumstances, WWOX exhibits its anticancer nature mainly via a reduction of cell viability and invasiveness of glioblastoma.
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Affiliation(s)
| | - Katarzyna Kośla
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752 Lodz, Poland
| | - Damian Kołat
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752 Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, 90-752 Lodz, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752 Lodz, Poland
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9
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Huang Q, Baudis M. Candidate targets of copy number deletion events across 17 cancer types. Front Genet 2023; 13:1017657. [PMID: 36726722 PMCID: PMC9885371 DOI: 10.3389/fgene.2022.1017657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Genome variation is the direct cause of cancer and driver of its clonal evolution. While the impact of many point mutations can be evaluated through their modification of individual genomic elements, even a single copy number aberration (CNA) may encompass hundreds of genes and therefore pose challenges to untangle potentially complex functional effects. However, consistent, recurring and disease-specific patterns in the genome-wide CNA landscape imply that particular CNA may promote cancer-type-specific characteristics. Discerning essential cancer-promoting alterations from the inherent co-dependency in CNA would improve the understanding of mechanisms of CNA and provide new insights into cancer biology and potential therapeutic targets. Here we implement a model using segmental breakpoints to discover non-random gene coverage by copy number deletion (CND). With a diverse set of cancer types from multiple resources, this model identified common and cancer-type-specific oncogenes and tumor suppressor genes as well as cancer-promoting functional pathways. Confirmed by differential expression analysis of data from corresponding cancer types, the results show that for most cancer types, despite dissimilarity of their CND landscapes, similar canonical pathways are affected. In 25 analyses of 17 cancer types, we have identified 19 to 169 significant genes by copy deletion, including RB1, PTEN and CDKN2A as the most significantly deleted genes among all cancer types. We have also shown a shared dependence on core pathways for cancer progression in different cancers as well as cancer type separation by genome-wide significance scores. While this work provides a reference for gene specific significance in many cancers, it chiefly contributes a general framework to derive genome-wide significance and molecular insights in CND profiles with a potential for the analysis of rare cancer types as well as non-coding regions.
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Affiliation(s)
- Qingyao Huang
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland,Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Michael Baudis
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland,Swiss Institute of Bioinformatics, Zurich, Switzerland,*Correspondence: Michael Baudis,
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Weng A, Rabin EE, Flozak AS, Chiarella SE, Aillon RP, Gottardi CJ. Alpha-T-catenin is expressed in peripheral nerves as a constituent of Schwann cell adherens junctions. Biol Open 2022; 11:bio059634. [PMID: 36420826 PMCID: PMC9793867 DOI: 10.1242/bio.059634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022] Open
Abstract
The adherens junction component, alpha-T-catenin (αTcat) is an established contributor to cardiomyocyte junction structure and function, but recent genomic studies link CTNNA3 polymorphisms to diseases with no clear cardiac underpinning, including asthma, autism and multiple sclerosis, suggesting causal contributions from a different cell-type. We show Ctnna3 mRNA is highly expressed in peripheral nerves (e.g. vagus and sciatic), where αTcat protein enriches at paranodes and myelin incisure adherens junctions of Schwann cells. We validate αTcat immunodetection specificity using a new Ctnna3-knock-out fluorescence reporter mouse line yet find no obvious Schwann cell loss-of-function morphology at the light microscopic level. CTNNA3/Ctnna3 mRNA is also abundantly detected in oligodendrocytes of the central nervous system via public databases, supporting a general role for αTcat in these unique cell-cell junctions. These data suggest that the wide range of diseases linked to CTNNA3 may be through its role in maintaining neuroglial functions of central and peripheral nervous systems. This article has a corresponding First Person interview with the co-first authors of the paper.
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Affiliation(s)
- Anthea Weng
- Department of Pulmonary Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Erik E. Rabin
- Department of Pulmonary Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Annette S. Flozak
- Department of Pulmonary Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sergio E. Chiarella
- Department of Pulmonary Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Mayo Clinic, Rochester, MN 55902, USA
| | - Raul Piseaux Aillon
- Department of Pulmonary Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Cara J. Gottardi
- Department of Pulmonary Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Cell & Developmental Biology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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11
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Quereda C, Pastor À, Martín-Nieto J. Involvement of abnormal dystroglycan expression and matriglycan levels in cancer pathogenesis. Cancer Cell Int 2022; 22:395. [PMID: 36494657 PMCID: PMC9733019 DOI: 10.1186/s12935-022-02812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Dystroglycan (DG) is a glycoprotein composed of two subunits that remain non-covalently bound at the plasma membrane: α-DG, which is extracellular and heavily O-mannosyl glycosylated, and β-DG, an integral transmembrane polypeptide. α-DG is involved in the maintenance of tissue integrity and function in the adult, providing an O-glycosylation-dependent link for cells to their extracellular matrix. β-DG in turn contacts the cytoskeleton via dystrophin and participates in a variety of pathways transmitting extracellular signals to the nucleus. Increasing evidence exists of a pivotal role of DG in the modulation of normal cellular proliferation. In this context, deficiencies in DG glycosylation levels, in particular those affecting the so-called matriglycan structure, have been found in an ample variety of human tumors and cancer-derived cell lines. This occurs together with an underexpression of the DAG1 mRNA and/or its α-DG (core) polypeptide product or, more frequently, with a downregulation of β-DG protein levels. These changes are in general accompanied in tumor cells by a low expression of genes involved in the last steps of the α-DG O-mannosyl glycosylation pathway, namely POMT1/2, POMGNT2, CRPPA, B4GAT1 and LARGE1/2. On the other hand, a series of other genes acting earlier in this pathway are overexpressed in tumor cells, namely DOLK, DPM1/2/3, POMGNT1, B3GALNT2, POMK and FKTN, hence exerting instead a pro-oncogenic role. Finally, downregulation of β-DG, altered β-DG processing and/or impaired β-DG nuclear levels are increasingly found in human tumors and cell lines. It follows that DG itself, particular genes/proteins involved in its glycosylation and/or their interactors in the cell could be useful as biomarkers of certain types of human cancer, and/or as molecular targets of new therapies addressing these neoplasms.
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Affiliation(s)
- Cristina Quereda
- grid.5268.90000 0001 2168 1800Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Campus Universitario San Vicente, P.O. Box 99, 03080 Alicante, Spain
| | - Àngels Pastor
- grid.5268.90000 0001 2168 1800Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Campus Universitario San Vicente, P.O. Box 99, 03080 Alicante, Spain
| | - José Martín-Nieto
- grid.5268.90000 0001 2168 1800Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Campus Universitario San Vicente, P.O. Box 99, 03080 Alicante, Spain ,grid.5268.90000 0001 2168 1800Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’, Universidad de Alicante, 03080 Alicante, Spain
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12
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Shaikh N, Mazzagatti A, De Angelis S, Johnson SC, Bakker B, Spierings DCJ, Wardenaar R, Maniati E, Wang J, Boemo MA, Foijer F, McClelland SE. Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses. Genome Biol 2022; 23:223. [PMID: 36266663 PMCID: PMC9583511 DOI: 10.1186/s13059-022-02781-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major driver of cancer chromosomal instability is replication stress, the slowing or stalling of DNA replication. How replication stress and genomic instability are connected is not known. Aphidicolin-induced replication stress induces breakages at common fragile sites, but the exact causes of fragility are debated, and acute genomic consequences of replication stress are not fully explored. RESULTS We characterize DNA copy number alterations (CNAs) in single, diploid non-transformed cells, caused by one cell cycle in the presence of either aphidicolin or hydroxyurea. Multiple types of CNAs are generated, associated with different genomic regions and features, and observed copy number landscapes are distinct between aphidicolin and hydroxyurea-induced replication stress. Coupling cell type-specific analysis of CNAs to gene expression and single-cell replication timing analyses pinpointed the causative large genes of the most recurrent chromosome-scale CNAs in aphidicolin. These are clustered on chromosome 7 in RPE1 epithelial cells but chromosome 1 in BJ fibroblasts. Chromosome arm level CNAs also generate acentric lagging chromatin and micronuclei containing these chromosomes. CONCLUSIONS Chromosomal instability driven by replication stress occurs via focal CNAs and chromosome arm scale changes, with the latter confined to a very small subset of chromosome regions, potentially heavily skewing cancer genome evolution. Different inducers of replication stress lead to distinctive CNA landscapes providing the opportunity to derive copy number signatures of specific replication stress mechanisms. Single-cell CNA analysis thus reveals the impact of replication stress on the genome, providing insights into the molecular mechanisms which fuel chromosomal instability in cancer.
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Affiliation(s)
- Nadeem Shaikh
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alice Mazzagatti
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Simone De Angelis
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sarah C Johnson
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
- Current address: The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael A Boemo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Sarah E McClelland
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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13
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Dubois FPB, Shapira O, Greenwald NF, Zack T, Wala J, Tsai JW, Crane A, Baguette A, Hadjadj D, Harutyunyan AS, Kumar KH, Blattner-Johnson M, Vogelzang J, Sousa C, Kang KS, Sinai C, Wang DK, Khadka P, Lewis K, Nguyen L, Malkin H, Ho P, O'Rourke R, Zhang S, Gold R, Deng D, Serrano J, Snuderl M, Jones C, Wright KD, Chi SN, Grill J, Kleinman CL, Goumnerova LC, Jabado N, Jones DTW, Kieran MW, Ligon KL, Beroukhim R, Bandopadhayay P. Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. NATURE CANCER 2022; 3:994-1011. [PMID: 35788723 PMCID: PMC10365847 DOI: 10.1038/s43018-022-00403-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 05/23/2022] [Indexed: 12/13/2022]
Abstract
We analyzed the contributions of structural variants (SVs) to gliomagenesis across 179 pediatric high-grade gliomas (pHGGs). The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases (RTKs), including an SV amplifying a MYC enhancer in 12% of diffuse midline gliomas (DMG), indicating an underappreciated role for MYC in pHGG. SV signature analysis revealed that tumors with simple signatures were TP53 wild type (TP53WT) but showed alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A and RB1 early in tumor evolution and with later-occurring extrachromosomal amplicons. All pHGGs exhibited at least one simple-SV signature, but complex-SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with complex-SV signatures were associated with shorter overall survival independent of histone mutation and TP53 status. These data provide insight into the impact of SVs on gliomagenesis and the mechanisms that shape them.
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Affiliation(s)
- Frank P B Dubois
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ofer Shapira
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noah F Greenwald
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Travis Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeremiah Wala
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jessica W Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Alexander Crane
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Audrey Baguette
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Djihad Hadjadj
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Kiran H Kumar
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cecilia Sousa
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kyung Shin Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claire Sinai
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dayle K Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Prasidda Khadka
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hayley Malkin
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Patricia Ho
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan O'Rourke
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rose Gold
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Davy Deng
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Chris Jones
- Division of Cancer Therapeutics and Department of Molecular Pathology, Institute of Cancer Research 15 Cotswold Road, Sutton, London, UK
| | - Karen D Wright
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan N Chi
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Jacques Grill
- Department of Pediatric and Adolescent Oncology and INSERM Unit 981, Gustave Roussy Institute and University of Paris Saclay, Villejuif, France
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Liliana C Goumnerova
- Department of Neurosurgery, Boston Children's Hospital; Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- LCG: Tromboprotea, MWK: Day One Biopharmaceuticals, San Francisco, CA, USA
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, Department of Medicine and Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mark W Kieran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- LCG: Tromboprotea, MWK: Day One Biopharmaceuticals, San Francisco, CA, USA
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham & Women's Hospital and Boston Children's Hospital, Boston, USA.
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
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14
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Ji F, Zhu X, Liao H, Ouyang L, Huang Y, Syeda MZ, Ying S. New Era of Mapping and Understanding Common Fragile Sites: An Updated Review on Origin of Chromosome Fragility. Front Genet 2022; 13:906957. [PMID: 35669181 PMCID: PMC9164283 DOI: 10.3389/fgene.2022.906957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic loci prone to forming gaps or breakages upon replication perturbation, which correlate well with chromosomal rearrangement and copy number variation. CFSs have been actively studied due to their important pathophysiological relevance in different diseases such as cancer and neurological disorders. The genetic locations and sequences of CFSs are crucial to understanding the origin of such unstable sites, which require reliable mapping and characterizing approaches. In this review, we will inspect the evolving techniques for CFSs mapping, especially genome-wide mapping and sequencing of CFSs based on current knowledge of CFSs. We will also revisit the well-established hypotheses on the origin of CFSs fragility, incorporating novel findings from the comprehensive analysis of finely mapped CFSs regarding their locations, sequences, and replication/transcription, etc. This review will present the most up-to-date picture of CFSs and, potentially, a new framework for future research of CFSs.
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Affiliation(s)
- Fang Ji
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinli Zhu
- Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Liao
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Liujian Ouyang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingfei Huang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Madiha Zahra Syeda
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Songmin Ying
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
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15
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Balzano E, Di Tommaso E, Antoccia A, Pelliccia F, Giunta S. Characterization of Chromosomal Instability in Glioblastoma. Front Genet 2022; 12:810793. [PMID: 35154254 PMCID: PMC8831864 DOI: 10.3389/fgene.2021.810793] [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: 11/07/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a malignant tumor of the central nervous system (CNS). The poor prognosis of GBM due to resistance to therapy has been associated with high chromosomal instability (CIN). Replication stress is a major cause of CIN that manifests as chromosome rearrangements, fragility, and breaks, including those cytologically expressed within specific chromosome regions named common fragile sites (CFSs). In this work, we characterized the expression of human CFSs in the glioblastoma U-251 MG cell line upon treatment with the inhibitor of DNA polymerase alpha aphidicolin (APH). We observed 52 gaps/breaks located within previously characterized CFSs. We found 17 to be CFSs in GBM cells upon treatment with APH, showing a frequency equal to at least 1% of the total gaps/breaks. We report that two CFSs localized to regions FRA2E (2p13/p12) and FRA2F (2q22) were only found in U-251 MG cells, but not lymphocytes or fibroblasts, after APH treatment. Notably, these glioblastoma-specific CFSs had a relatively high expression compared to the other CFSs with breakage frequency between ∼7 and 9%. Presence of long genes, incomplete replication, and delayed DNA synthesis during mitosis (MiDAS) after APH treatment suggest that an impaired replication process may contribute to this loci-specific fragility in U-251 MG cells. Altogether, our work offers a characterization of common fragile site expression in glioblastoma U-251 MG cells that may be further exploited for cytogenetic and clinical studies to advance our understanding of this incurable cancer.
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Affiliation(s)
- Elisa Balzano
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Elena Di Tommaso
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Antonio Antoccia
- Laboratory of Genetics and Cytogenetics, Dipartimento di Scienze, Università Degli Studi Roma Tre, Roma, Italy
| | - Franca Pelliccia
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- *Correspondence: Franca Pelliccia, ; Simona Giunta,
| | - Simona Giunta
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- *Correspondence: Franca Pelliccia, ; Simona Giunta,
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16
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Kodali S, Meyer-Nava S, Landry S, Chakraborty A, Rivera-Mulia JC, Feng W. Epigenomic signatures associated with spontaneous and replication stress-induced DNA double strand breaks. Front Genet 2022; 13:907547. [PMID: 36506300 PMCID: PMC9730818 DOI: 10.3389/fgene.2022.907547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Common fragile sites (CFSs) are specific regions of all individuals' genome that are predisposed to DNA double strand breaks (DSBs) and undergo subsequent rearrangements. CFS formation can be induced in vitro by mild level of DNA replication stress, such as DNA polymerase inhibition or nucleotide pool disturbance. The mechanisms of CFS formation have been linked to DNA replication timing control, transcription activities, as well as chromatin organization. However, it is unclear what specific cis- or trans-factors regulate the interplay between replication and transcription that determine CFS formation. We recently reported genome-wide mapping of DNA DSBs under replication stress induced by aphidicolin in human lymphoblastoids for the first time. Here, we systematically compared these DSBs with regards to nearby epigenomic features mapped in the same cell line from published studies. We demonstrate that aphidicolin-induced DSBs are strongly correlated with histone 3 lysine 36 trimethylation, a marker for active transcription. We further demonstrate that this DSB signature is a composite effect by the dual treatment of aphidicolin and its solvent, dimethylsulfoxide, the latter of which potently induces transcription on its own. We also present complementing evidence for the association between DSBs and 3D chromosome architectural domains with high density gene cluster and active transcription. Additionally, we show that while DSBs were detected at all but one of the fourteen finely mapped CFSs, they were not enriched in the CFS core sequences and rather demarcated the CFS core region. Related to this point, DSB density was not higher in large genes of greater than 300 kb, contrary to reported enrichment of CFS sites at these large genes. Finally, replication timing analyses demonstrate that the CFS core region contain initiation events, suggesting that altered replication dynamics are responsible for CFS formation in relatively higher level of replication stress.
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Affiliation(s)
- Sravan Kodali
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States
| | - Silvia Meyer-Nava
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Stephen Landry
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States
| | - Juan Carlos Rivera-Mulia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Wenyi Feng
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States
- *Correspondence: Wenyi Feng,
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17
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Mor-Shaked H, Paz-Ebstein E, Basal A, Ben-Haim S, Grobe H, Heymann S, Israel Z, Namnah M, Nitzan A, Rosenbluh C, Saada A, Tzur T, Yanovsky-Dagan S, Zaidel-Bar R, Harel T, Arkadir D. Levodopa-responsive dystonia caused by biallelic PRKN exon inversion invisible to exome sequencing. Brain Commun 2021; 3:fcab197. [PMID: 34514401 PMCID: PMC8421701 DOI: 10.1093/braincomms/fcab197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/20/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022] Open
Abstract
Biallelic pathogenic variants in PRKN (PARK2), encoding the E3 ubiquitin ligase parkin, lead to early-onset Parkinson's disease. Structural variants, including duplications or deletions, are common in PRKN due to their location within the fragile site FRA6E. These variants are readily detectable by copy number variation analysis. We studied four siblings with levodopa-responsive dystonia by exome sequencing followed by genome sequencing. Affected individuals developed juvenile levodopa-responsive dystonia with subsequent appearance of parkinsonism and motor fluctuations that improved by subthalamic stimulation. Exome sequencing and copy number variation analysis were not diagnostic, yet revealed a shared homozygous block including PRKN. Genome sequencing revealed an inversion within PRKN, with intronic breakpoints flanking exon 5. Breakpoint junction analysis implicated non-homologous end joining and possibly replicative mechanisms as the repair pathways involved. Analysis of cDNA indicated skipping of exon 5 (84 bp) that was replaced by 93 bp of retained intronic sequence, preserving the reading frame yet altering a significant number of residues. Balanced copy number inversions in PRKN are associated with a severe phenotype. Such structural variants, undetected by exome analysis and by copy number variation analysis, should be considered in the relevant clinical setting. These findings raise the possibility that PRKN structural variants are more common than currently estimated.
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Affiliation(s)
- Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Emuna Paz-Ebstein
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Adily Basal
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Simona Ben-Haim
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Nuclear Medicine, Hadassah Medical Organization, Jerusalem 91120, Israel.,Institute of Nuclear Medicine, University College London and UCL Hospitals, NHS Trust, London NW1 2BU, UK
| | - Hanna Grobe
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Sami Heymann
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurosurgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Zvi Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurosurgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Montaser Namnah
- Department of Neurology, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Anat Nitzan
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Chaggai Rosenbluh
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Ann Saada
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Tomer Tzur
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Plastic Surgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | | | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - David Arkadir
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurology, Hadassah Medical Organization, Jerusalem 91120, Israel
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18
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Rasnic R, Linial M. Chromoanagenesis Landscape in 10,000 TCGA Patients. Cancers (Basel) 2021; 13:4197. [PMID: 34439350 PMCID: PMC8392194 DOI: 10.3390/cancers13164197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022] Open
Abstract
During the past decade, whole-genome sequencing of tumor biopsies and individuals with congenital disorders highlighted the phenomenon of chromoanagenesis, a single chaotic event of chromosomal rearrangement. Chromoanagenesis was shown to be frequent in many types of cancers, to occur in early stages of cancer development, and significantly impact the tumor's nature. However, an in-depth, cancer-type dependent analysis has been somewhat incomplete due to the shortage in whole genome sequencing of cancerous samples. In this study, we extracted data from The Pan-Cancer Analysis of Whole Genome (PCAWG) and The Cancer Genome Atlas (TCGA) to construct and test a machine learning algorithm that can detect chromoanagenesis with high accuracy (86%). The algorithm was applied to ~10,000 unlabeled TCGA cancer patients. We utilize the chromoanagenesis assignment results, to analyze cancer-type specific chromoanagenesis characteristics in 20 TCGA cancer types. Our results unveil prominent genes affected in either chromoanagenesis or non-chromoanagenesis tumorigenesis. The analysis reveals a mutual exclusivity relationship between the genes impaired in chromoanagenesis versus non-chromoanagenesis cases. We offer the discovered characteristics as possible targets for cancer diagnostic and therapeutic purposes.
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Affiliation(s)
- Roni Rasnic
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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19
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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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20
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Meiotic recombination mirrors patterns of germline replication in mice and humans. Cell 2021; 184:4251-4267.e20. [PMID: 34260899 DOI: 10.1016/j.cell.2021.06.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/02/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
Genetic recombination generates novel trait combinations, and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots; however, megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns; therefore, we devised an approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis, and a distinctive replication pattern in human males underlies the subtelomeric increase in recombination. We detected a robust correlation between replication and both contemporary and historical recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.
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21
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Simpson BS, Pye H, Whitaker HC. The oncological relevance of fragile sites in cancer. Commun Biol 2021; 4:567. [PMID: 33980983 PMCID: PMC8115686 DOI: 10.1038/s42003-021-02020-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/12/2021] [Indexed: 01/15/2023] Open
Abstract
Recent developments in sequencing the cancer genome have provided the first in-depth mapping of structural variants (SV) across 38 tumour types. Sixteen signatures of structural variants have been proposed which broadly characterise the variation seen across cancer types. One signature shows increased duplications and deletions at fragile sites, with little association with the typical DNA repair defects. We discuss how, for many of these fragile sites, the clinical impacts are yet to be explored. One example is NAALADL2, one of the most frequently altered fragile sites in the cancer genome. The copy-number variations (CNVs) which occur at fragile sites, such as NAALADL2, may span many genes without typical DNA repair defects and could have a large impact on cell signalling. In this Perspective, Simpson, Pye, and Whitaker discuss recent research identifying structural genomic variants in human cancers with a particular focus on deletions and duplications at genomic fragile sites. They argue that tumours with predominantly fragile site structural variants represent a distinct mutational signature that warrants further research.
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Affiliation(s)
- Benjamin S Simpson
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Hayley Pye
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Hayley C Whitaker
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK.
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22
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Dionellis VS, Norkin M, Karamichali A, Rossetti GG, Huelsken J, Ordonez-Moran P, Halazonetis TD. Genomic Instability Profiles at the Single Cell Level in Mouse Colorectal Cancers of Defined Genotypes. Cancers (Basel) 2021; 13:cancers13061267. [PMID: 33809306 PMCID: PMC7999300 DOI: 10.3390/cancers13061267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
The genomes of many human CRCs have been sequenced, revealing a large number of genetic alterations. However, the molecular mechanisms underlying the accumulation of these alterations are still being debated. In this study, we examined colorectal tumours that developed in mice with Apclox/lox, LSL-KrasG12D, and Tp53lox/lox targetable alleles. Organoids were derived from single cells and the spectrum of mutations was determined by exome sequencing. The number of single nucleotide substitutions (SNSs) correlated with the age of the tumour, but was unaffected by the number of targeted cancer-driver genes. Thus, tumours that expressed mutant Apc, Kras, and Tp53 alleles had as many SNSs as tumours that expressed only mutant Apc. In contrast, the presence of large-scale (>10 Mb) copy number alterations (CNAs) correlated strongly with Tp53 inactivation. Comparison of the SNSs and CNAs present in organoids derived from the same tumour revealed intratumoural heterogeneity consistent with genomic lesions accumulating at significantly higher rates in tumour cells compared to normal cells. The rate of acquisition of SNSs increased from the early stages of cancer development, whereas large-scale CNAs accumulated later, after Tp53 inactivation. Thus, a significant fraction of the genomic instability present in cancer cells cannot be explained by aging processes occurring in normal cells before oncogenic transformation.
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Affiliation(s)
- Vasilis S. Dionellis
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland; (V.S.D.); (A.K.); (G.G.R.)
| | - Maxim Norkin
- Cancer Stem Cell Laboratory, Swiss Institute of Technology Lausanne (EPFL), ISREC, 1015 Lausanne, Switzerland;
| | - Angeliki Karamichali
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland; (V.S.D.); (A.K.); (G.G.R.)
| | - Giacomo G. Rossetti
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland; (V.S.D.); (A.K.); (G.G.R.)
| | - Joerg Huelsken
- Cancer Stem Cell Laboratory, Swiss Institute of Technology Lausanne (EPFL), ISREC, 1015 Lausanne, Switzerland;
- Correspondence: (J.H.); (P.O.-M.); (T.D.H.)
| | - Paloma Ordonez-Moran
- Division of Cancer & Stem Cells, School of Medicine, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
- Correspondence: (J.H.); (P.O.-M.); (T.D.H.)
| | - Thanos D. Halazonetis
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland; (V.S.D.); (A.K.); (G.G.R.)
- Correspondence: (J.H.); (P.O.-M.); (T.D.H.)
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23
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Brown LC, Tucker MD, Sedhom R, Schwartz EB, Zhu J, Kao C, Labriola MK, Gupta RT, Marin D, Wu Y, Gupta S, Zhang T, Harrison MR, George DJ, Alva A, Antonarakis ES, Armstrong AJ. LRP1B mutations are associated with favorable outcomes to immune checkpoint inhibitors across multiple cancer types. J Immunother Cancer 2021; 9:e001792. [PMID: 33653800 PMCID: PMC7929846 DOI: 10.1136/jitc-2020-001792] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Low-density lipoprotein receptor-related protein 1b (encoded by LRP1B) is a putative tumor suppressor, and preliminary evidence suggests LRP1B-mutated cancers may have improved outcomes with immune checkpoint inhibitors (ICI). METHODS We conducted a multicenter, retrospective pan-cancer analysis of patients with LRP1B alterations treated with ICI at Duke University, Johns Hopkins University (JHU) and University of Michigan (UM). The primary objective was to assess the association between overall response rate (ORR) to ICI and pathogenic or likely pathogenic (P/LP) LRP1B alterations compared with LRP1B variants of unknown significance (VUS). Secondary outcomes were the associations with progression-free survival (PFS) and overall survival (OS) by LRP1B status. RESULTS We identified 101 patients (44 Duke, 35 JHU, 22 UM) with LRP1B alterations who were treated with ICI. The most common tumor types by alteration (P/LP vs VUS%) were lung (36% vs 49%), prostate (9% vs 7%), sarcoma (5% vs 7%), melanoma (9% vs 0%) and breast cancer (3% vs 7%). The ORR for patients with LRP1B P/LP versus VUS alterations was 54% and 13%, respectively (OR 7.5, 95% CI 2.9 to 22.3, p=0.0009). P/LP LRP1B alterations were associated with longer PFS (HR 0.42, 95% CI 0.26 to 0.68, p=0.0003) and OS (HR 0.62, 95% CI 0.39 to 1.01, p=0.053). These results remained consistent when excluding patients harboring microsatellite instability (MSI) and controlling for tumor mutational burden (TMB). CONCLUSIONS This multicenter study shows significantly better outcomes with ICI therapy in patients harboring P/LP versus VUS LRP1B alterations, independently of TMB/MSI status. Further mechanistic and prospective validation studies are warranted.
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Affiliation(s)
- Landon C Brown
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Matthew D Tucker
- Internal Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ramy Sedhom
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Eric B Schwartz
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason Zhu
- Levine Cancer Institute, Charlotte, North Carolina, USA
| | - Chester Kao
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Matthew K Labriola
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Rajan T Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Daniele Marin
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Yuan Wu
- Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
| | - Santosh Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Tian Zhang
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Michael R Harrison
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Daniel J George
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Ajjai Alva
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Emmanuel S Antonarakis
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
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24
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FANCD2 modulates the mitochondrial stress response to prevent common fragile site instability. Commun Biol 2021; 4:127. [PMID: 33514811 PMCID: PMC7846573 DOI: 10.1038/s42003-021-01647-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 12/29/2020] [Indexed: 12/16/2022] Open
Abstract
Common fragile sites (CFSs) are genomic regions frequently involved in cancer-associated rearrangements. Most CFSs lie within large genes, and their instability involves transcription- and replication-dependent mechanisms. Here, we uncover a role for the mitochondrial stress response pathway in the regulation of CFS stability in human cells. We show that FANCD2, a master regulator of CFS stability, dampens the activation of the mitochondrial stress response and prevents mitochondrial dysfunction. Genetic or pharmacological activation of mitochondrial stress signaling induces CFS gene expression and concomitant relocalization to CFSs of FANCD2. FANCD2 attenuates CFS gene transcription and promotes CFS gene stability. Mechanistically, we demonstrate that the mitochondrial stress-dependent induction of CFS genes is mediated by ubiquitin-like protein 5 (UBL5), and that a UBL5-FANCD2 dependent axis regulates the mitochondrial UPR in human cells. We propose that FANCD2 coordinates nuclear and mitochondrial activities to prevent genome instability.
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25
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Pentzold C, Kokal M, Pentzold S, Weise A. Sites of chromosomal instability in the context of nuclear architecture and function. Cell Mol Life Sci 2020; 78:2095-2103. [PMID: 33219838 PMCID: PMC7966619 DOI: 10.1007/s00018-020-03698-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/02/2020] [Accepted: 10/31/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal fragile sites are described as areas within the tightly packed mitotic chromatin that appear as breaks or gaps mostly tracing back to a loosened structure and not a real nicked break within the DNA molecule. Most facts about fragile sites result from studies in mitotic cells, mainly during metaphase and mainly in lymphocytes. Here, we synthesize facts about the genomic regions that are prone to form gaps and breaks on metaphase chromosomes in the context of interphase. We conclude that nuclear architecture shapes the activity profile of the cell, i.e. replication timing and transcriptional activity, thereby influencing genomic integrity during interphase with the potential to cause fragility in mitosis. We further propose fragile sites as examples of regions specifically positioned in the interphase nucleus with putative anchoring points at the nuclear lamina to enable a tightly regulated replication–transcription profile and diverse signalling functions in the cell. Consequently, fragility starts before the actual display as chromosomal breakage in metaphase to balance the initial contradiction of cellular overgrowth or malfunctioning and maintaining diversity in molecular evolution.
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Affiliation(s)
- Constanze Pentzold
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany.
| | - Miriam Kokal
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Stefan Pentzold
- Research Center Lobeda, Jena University Hospital, 07747, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
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26
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Macheret M, Bhowmick R, Sobkowiak K, Padayachy L, Mailler J, Hickson ID, Halazonetis TD. High-resolution mapping of mitotic DNA synthesis regions and common fragile sites in the human genome through direct sequencing. Cell Res 2020; 30:997-1008. [PMID: 32561860 PMCID: PMC7784693 DOI: 10.1038/s41422-020-0358-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/31/2020] [Indexed: 12/22/2022] Open
Abstract
DNA replication stress, a feature of human cancers, often leads to instability at specific genomic loci, such as the common fragile sites (CFSs). Cells experiencing DNA replication stress may also exhibit mitotic DNA synthesis (MiDAS). To understand the physiological function of MiDAS and its relationship to CFSs, we mapped, at high resolution, the genomic sites of MiDAS in cells treated with the DNA polymerase inhibitor aphidicolin. Sites of MiDAS were evident as well-defined peaks that were largely conserved between cell lines and encompassed all known CFSs. The MiDAS peaks mapped within large, transcribed, origin-poor genomic regions. In cells that had been treated with aphidicolin, these regions remained unreplicated even in late S phase; MiDAS then served to complete their replication after the cells entered mitosis. Interestingly, leading and lagging strand synthesis were uncoupled in MiDAS, consistent with MiDAS being a form of break-induced replication, a repair mechanism for collapsed DNA replication forks. Our results provide a better understanding of the mechanisms leading to genomic instability at CFSs and in cancer cells.
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Affiliation(s)
- Morgane Macheret
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Katarzyna Sobkowiak
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Laura Padayachy
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Jonathan Mailler
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark.
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland.
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27
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Soheili-Nezhad S, van der Linden RJ, Olde Rikkert M, Sprooten E, Poelmans G. Long genes are more frequently affected by somatic mutations and show reduced expression in Alzheimer's disease: Implications for disease etiology. Alzheimers Dement 2020; 17:489-499. [PMID: 33075204 PMCID: PMC8048495 DOI: 10.1002/alz.12211] [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: 04/30/2020] [Revised: 10/11/2020] [Accepted: 10/21/2020] [Indexed: 12/17/2022]
Abstract
Aging, the greatest risk factor for Alzheimer's disease (AD), may lead to the accumulation of somatic mutations in neurons. We investigated whether somatic mutations, specifically in longer genes, are implicated in AD etiology. First, we modeled the theoretical likelihood of genes being affected by aging‐induced somatic mutations, dependent on their length. We then tested this model and found that long genes are indeed more affected by somatic mutations and that their expression is more frequently reduced in AD brains. Furthermore, using gene‐set enrichment analysis, we investigated the potential consequences of such long gene disruption. We found that long genes are involved in synaptic adhesion and other synaptic pathways that are predicted to be inhibited in the brains of AD patients. Taken together, our findings indicate that long gene–dependent synaptic impairment may contribute to AD pathogenesis.
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Affiliation(s)
- Sourena Soheili-Nezhad
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Marcel Olde Rikkert
- Department of Geriatric Medicine, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboudumc Alzheimer Center, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emma Sprooten
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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28
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Under-Replicated DNA: The Byproduct of Large Genomes? Cancers (Basel) 2020; 12:cancers12102764. [PMID: 32992928 PMCID: PMC7601121 DOI: 10.3390/cancers12102764] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/28/2022] Open
Abstract
In this review, we provide an overview of how proliferating eukaryotic cells overcome one of the main threats to genome stability: incomplete genomic DNA replication during S phase. We discuss why it is currently accepted that double fork stalling (DFS) events are unavoidable events in higher eukaryotes with large genomes and which responses have evolved to cope with its main consequence: the presence of under-replicated DNA (UR-DNA) outside S phase. Particular emphasis is placed on the processes that constrain the detrimental effects of UR-DNA. We discuss how mitotic DNA synthesis (MiDAS), mitotic end joining events and 53BP1 nuclear bodies (53BP1-NBs) deal with such specific S phase DNA replication remnants during the subsequent phases of the cell cycle.
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29
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Ji F, Liao H, Pan S, Ouyang L, Jia F, Fu Z, Zhang F, Geng X, Wang X, Li T, Liu S, Syeda MZ, Chen H, Li W, Chen Z, Shen H, Ying S. Genome-wide high-resolution mapping of mitotic DNA synthesis sites and common fragile sites by direct sequencing. Cell Res 2020; 30:1009-1023. [PMID: 32561861 DOI: 10.1038/s41422-020-0357-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/31/2020] [Indexed: 01/13/2023] Open
Abstract
Common fragile sites (CFSs) are genomic loci prone to the formation of breaks or gaps on metaphase chromosomes. They are hotspots for chromosome rearrangements and structural variations, which have been extensively implicated in carcinogenesis, aging, and other pathological processes. Although many CFSs were identified decades ago, a consensus is still lacking for why they are particularly unstable and sensitive to replication perturbations. This is in part due to the lack of high-resolution mapping data for the vast majority of the CFSs, which has hindered mechanistic interrogations. Here, we seek to map human CFSs with high resolution on a genome-wide scale by sequencing the sites of mitotic DNA synthesis (MiDASeq) that are specific for CFSs. We generated a nucleotide-resolution atlas of MiDAS sites (MDSs) that covered most of the known CFSs, and comprehensively analyzed their sequence characteristics and genomic features. Our data on MDSs tallied well with long-standing hypotheses to explain CFS fragility while highlighting the contributions of late replication timing and large transcription units. Notably, the MDSs also encompassed most of the recurrent double-strand break clusters previously identified in mouse neural stem/progenitor cells, thus bridging evolutionarily conserved break points across species. Moreover, MiDAseq provides an important resource that can stimulate future research on CFSs to further unravel the mechanisms and biological relevance underlying these labile genomic regions.
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Affiliation(s)
- Fang Ji
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Hongwei Liao
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Sheng Pan
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Liujian Ouyang
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Fang Jia
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Zaiyang Fu
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Fengjiao Zhang
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Xinwei Geng
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Xinming Wang
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Tingting Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Shuangying Liu
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.,Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
| | - Madiha Zahra Syeda
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China
| | - Haixia Chen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Zhihua Chen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China. .,State Key Laboratory of Respiratory Diseases, Guangzhou, Guangdong, 510120, China.
| | - Songmin Ying
- Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang, 310009, China.
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30
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Satas G, Zaccaria S, Mon G, Raphael BJ. SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses. Cell Syst 2020; 10:323-332.e8. [PMID: 32864481 PMCID: PMC7451135 DOI: 10.1016/j.cels.2020.04.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A small number of somatic mutations drive the development of cancer, but all somatic mutations are markers of the evolutionary history of a tumor. Prominent methods to construct phylogenies from single-cell sequencing data use single-nucleotide variants (SNVs) as markers but fail to adequately account for copy-number aberrations (CNAs), which can overlap SNVs and result in SNV losses. Here, we introduce SCARLET, an algorithm that infers tumor phylogenies from single-cell DNA sequencing data while accounting for both CNA-driven loss of SNVs and sequencing errors. SCARLET outperforms existing methods on simulated data, with more accurate inference of the order in which mutations were acquired and the mutations present in individual cells. Using a single-cell dataset from a patient with colorectal cancer, SCARLET constructs a tumor phylogeny that is consistent with the observed CNAs and suggests an alternate origin for the patient's metastases. SCARLET is available at: github.com/raphael-group/scarlet.
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Affiliation(s)
- Gryte Satas
- Department of Computer Science, Brown University, Providence, RI 02912
- Department of Computer Science, Princeton University, Princeton, NJ 08540
| | - Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, NJ 08540
| | - Geoffrey Mon
- Department of Computer Science, Princeton University, Princeton, NJ 08540
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ 08540
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31
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Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites. Genes (Basel) 2020; 11:genes11030326. [PMID: 32204553 PMCID: PMC7140878 DOI: 10.3390/genes11030326] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022] Open
Abstract
Common fragile sites (CFSs) are particularly vulnerable regions of the genome that become visible as breaks, gaps, or constrictions on metaphase chromosomes when cells are under replicative stress. Impairment in DNA replication, late replication timing, enrichment of A/T nucleotides that tend to form secondary structures, the paucity of active or inducible replication origins, the generation of R-loops, and the collision between replication and transcription machineries on particularly long genes are some of the reported characteristics of CFSs that may contribute to their tissue-specific fragility. Here, we validated the induction of two CFSs previously found in the human fetal lung fibroblast line, Medical Research Council cell strain 5 (MRC-5), in another cell line derived from the same fetal tissue, Institute for Medical Research-90 cells (IMR-90). After induction of CFSs through aphidicolin, we confirmed the expression of the CFS 1p31.1 on chromosome 1 and CFS 3q13.3 on chromosome 3 in both fetal lines. Interestingly, these sites were found to not be fragile in lymphocytes, suggesting a role for epigenetic or transcriptional programs for this tissue specificity. Both these sites contained late-replicating genes NEGR1 (neuronal growth regulator 1) at 1p31.1 and LSAMP (limbic system-associated membrane protein) at 3q13.3, which are much longer, 0.880 and 1.4 Mb, respectively, than the average gene length. Given the established connection between long genes and CFS, we compiled information from the literature on all previously identified CFSs expressed in fibroblasts and lymphocytes in response to aphidicolin, including the size of the genes contained in each fragile region. Our comprehensive analysis confirmed that the genes found within CFSs are longer than the average human gene; interestingly, the two longest genes in the human genome are found within CFSs: Contactin Associated Protein 2 gene (CNTNAP2) in a lymphocytes’ CFS, and Duchenne muscular dystrophy gene (DMD) in a CFS expressed in both lymphocytes and fibroblasts. This indicates that the presence of very long genes is a unifying feature of all CFSs. We also obtained replication profiles of the 1p31.1 and 3q13.3 sites under both perturbed and unperturbed conditions using a combination of fluorescent in situ hybridization (FISH) and immunofluorescence against bromodeoxyuridine (BrdU) on interphase nuclei. Our analysis of the replication dynamics of these CFSs showed that, compared to lymphocytes where these regions are non-fragile, fibroblasts display incomplete replication of the fragile alleles, even in the absence of exogenous replication stress. Our data point to the existence of intrinsic features, in addition to the presence of long genes, which affect DNA replication of the CFSs in fibroblasts, thus promoting chromosomal instability in a tissue-specific manner.
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32
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Sugimoto N, Maehara K, Yoshida K, Ohkawa Y, Fujita M. Genome-wide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells. Nucleic Acids Res 2019; 46:6683-6696. [PMID: 29893900 PMCID: PMC6061783 DOI: 10.1093/nar/gky476] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/16/2018] [Indexed: 12/25/2022] Open
Abstract
In metazoan cells, only a limited number of mini chromosome maintenance (MCM) complexes are fired during S phase, while the majority remain dormant. Several methods have been used to map replication origins, but such methods cannot identify dormant origins. Herein, we determined MCM7-binding sites in human cells using ChIP-Seq, classified them into firing and dormant origins using origin data and analysed their association with various chromatin signatures. Firing origins, but not dormant origins, were well correlated with open chromatin regions and were enriched upstream of transcription start sites (TSSs) of transcribed genes. Aggregation plots of MCM7 signals revealed minimal difference in the efficacy of MCM loading between firing and dormant origins. We also analysed common fragile sites (CFSs) and found a low density of origins at these sites. Nevertheless, firing origins were enriched upstream of the TSSs. Based on the results, we propose a model in which excessive MCMs are actively loaded in a genome-wide manner, irrespective of chromatin status, but only a fraction are passively fired in chromatin areas with an accessible open structure, such as regions upstream of TSSs of transcribed genes. This plasticity in the specification of replication origins may minimize collisions between replication and transcription.
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Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
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33
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Lyu X, Chastain M, Chai W. Genome-wide mapping and profiling of γH2AX binding hotspots in response to different replication stress inducers. BMC Genomics 2019; 20:579. [PMID: 31299901 PMCID: PMC6625122 DOI: 10.1186/s12864-019-5934-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Replication stress (RS) gives rise to DNA damage that threatens genome stability. RS can originate from different sources that stall replication by diverse mechanisms. However, the mechanism underlying how different types of RS contribute to genome instability is unclear, in part due to the poor understanding of the distribution and characteristics of damage sites induced by different RS mechanisms. RESULTS We use ChIP-seq to map γH2AX binding sites genome-wide caused by aphidicolin (APH), hydroxyurea (HU), and methyl methanesulfonate (MMS) treatments in human lymphocyte cells. Mapping of γH2AX ChIP-seq reveals that APH, HU, and MMS treatments induce non-random γH2AX chromatin binding at discrete regions, suggesting that there are γH2AX binding hotspots in the genome. Characterization of the distribution and sequence/epigenetic features of γH2AX binding sites reveals that the three treatments induce γH2AX binding at largely non-overlapping regions, suggesting that RS may cause damage at specific genomic loci in a manner dependent on the fork stalling mechanism. Nonetheless, γH2AX binding sites induced by the three treatments share common features including compact chromatin, coinciding with larger-than-average genes, and depletion of CpG islands and transcription start sites. Moreover, we observe significant enrichment of SINEs in γH2AX sites in all treatments, indicating that SINEs may be a common barrier for replication polymerases. CONCLUSIONS Our results identify the location and common features of genome instability hotspots induced by different types of RS, and help in deciphering the mechanisms underlying RS-induced genetic diseases and carcinogenesis.
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Affiliation(s)
- Xinxing Lyu
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Megan Chastain
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Weihang Chai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA.
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34
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Genome reorganization in different cancer types: detection of cancer specific breakpoint regions. Mol Cytogenet 2019; 12:25. [PMID: 31249626 PMCID: PMC6585066 DOI: 10.1186/s13039-019-0435-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/15/2019] [Indexed: 01/11/2023] Open
Abstract
Background Tumorigenesis is a multi-step process which is accompanied by substantial changes in genome organization. The development of these changes is not only a random process, but rather comprise specific DNA regions that are prone to the reorganization process. Results We have analyzed previously published SNP arrays from three different cancer types (pancreatic adenocarcinoma, breast cancer and metastatic melanoma) and from non-malignant control samples. We calculated segmental copy number variations as well as breakpoint regions. Some of these regions were not randomly involved in genome reorganization since we detected fifteen of them in at least 20% of all tumor samples and one region on chromosome 9 where 43% of tumors have a breakpoint. Further, the top-15 breakpoint regions show an association to known fragile sites. The relevance of these common breakpoint regions was further confirmed by analyzing SNP arrays from 917 cancer cell lines. Conclusion Our analyses suggest that genome reorganization is common in tumorigenesis and that some breakpoint regions can be found across all cancer types, while others exclusively occur in specific entities.
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35
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Abstract
Genome replication involves dealing with obstacles that can result from DNA damage but also from chromatin alterations, topological stress, tightly bound proteins or non-B DNA structures such as R loops. Experimental evidence reveals that an engaged transcription machinery at the DNA can either enhance such obstacles or be an obstacle itself. Thus, transcription can become a potentially hazardous process promoting localized replication fork hindrance and stress, which would ultimately cause genome instability, a hallmark of cancer cells. Understanding the causes behind transcription-replication conflicts as well as how the cell resolves them to sustain genome integrity is the aim of this review.
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36
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Chen H, Chong W, Wu Q, Yao Y, Mao M, Wang X. Association of LRP1B Mutation With Tumor Mutation Burden and Outcomes in Melanoma and Non-small Cell Lung Cancer Patients Treated With Immune Check-Point Blockades. Front Immunol 2019; 10:1113. [PMID: 31164891 PMCID: PMC6536574 DOI: 10.3389/fimmu.2019.01113] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/01/2019] [Indexed: 01/04/2023] Open
Abstract
Background: Tumor mutation burden (TMB) have been served as the most prevalent biomarkers to predict immunotherapy response. LRP1B (low-density lipoprotein receptor-related protein 1B) is frequently mutated in melanoma, non-small cell lung cancer (NSCLC) and other tumors; however, its association with TMB and survival in patients with immunotherapy remains unknown. Methods: We curated somatic mutation data and clinicopathologic information from 332 melanoma immunotherapy samples for discovery and 113 NSCLC samples for further corroboration. Bayesian variants non-negative matrix factorization was used to extract tumor mutational signatures. Multivariate Cox and logistic regression models were applied to adjust confounding factors. The CIBERSORT and GSEA algorithm were separately used to infer leukocyte relative abundance and significantly enriched pathways. Results: Patients with LRP1B mutation were identified to be associated with prolonged survival in both immunotherapy cohort. Higher tumor mutation burden was found in LRP1B mutated patients, and the association remained significant after controlling for age, gender, stage, mutations in TP53 and ATR, and mutational signatures. Immune response and cell cycle regulation circuits were among the top enriched pathways in samples with LRP1B mutations. Conclusion: Our studies suggested sequencing even a single, frequently mutated gene may provide insight into genome-wide mutational burden, and may serve as a biomarker to predict immune response.
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Affiliation(s)
- Hao Chen
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China.,Key Laboratory of Cancer Prevention and Therapy of Tianjin, Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wei Chong
- Key Laboratory of Cancer Prevention and Therapy, Department of Breast Cancer Pathology and Research Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Qian Wu
- Department of Respiratory Medicine, Central Hospital of Zibo, Zibo, China
| | - Yueliang Yao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Min Mao
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xin Wang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China
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37
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Kaushal S, Freudenreich CH. The role of fork stalling and DNA structures in causing chromosome fragility. Genes Chromosomes Cancer 2019; 58:270-283. [PMID: 30536896 DOI: 10.1002/gcc.22721] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022] Open
Abstract
Alternative non-B form DNA structures, also called secondary structures, can form in certain DNA sequences under conditions that produce single-stranded DNA, such as during replication, transcription, and repair. Direct links between secondary structure formation, replication fork stalling, and genomic instability have been found for many repeated DNA sequences that cause disease when they expand. Common fragile sites (CFSs) are known to be AT-rich and break under replication stress, yet the molecular basis for their fragility is still being investigated. Over the past several years, new evidence has linked both the formation of secondary structures and transcription to fork stalling and fragility of CFSs. How these two events may synergize to cause fragility and the role of nuclease cleavage at secondary structures in rare and CFSs are discussed here. We also highlight evidence for a new hypothesis that secondary structures at CFSs not only initiate fragility but also inhibit healing, resulting in their characteristic appearance.
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Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts.,Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
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38
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Transcription-dependent regulation of replication dynamics modulates genome stability. Nat Struct Mol Biol 2018; 26:58-66. [PMID: 30598553 DOI: 10.1038/s41594-018-0170-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023]
Abstract
Common fragile sites (CFSs) are loci that are hypersensitive to replication stress and hotspots for chromosomal rearrangements in cancers. CFSs replicate late in S phase, are cell-type specific and nest in large genes. The relative impact of transcription-replication conflicts versus a low density in initiation events on fragility is currently debated. Here we addressed the relationships between transcription, replication, and instability by manipulating the transcription of endogenous large genes in chicken and human cells. We found that inducing low transcription with a weak promoter destabilized large genes, whereas stimulating their transcription with strong promoters alleviated instability. Notably, strong promoters triggered a switch to an earlier replication timing, supporting a model in which high transcription levels give cells more time to complete replication before mitosis. Transcription could therefore contribute to maintaining genome integrity, challenging the dominant view that it is exclusively a threat.
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39
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Palumbo E, Russo A. Common fragile site instability in normal cells: Lessons and perspectives. Genes Chromosomes Cancer 2018; 58:260-269. [PMID: 30387295 DOI: 10.1002/gcc.22705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/26/2022] Open
Abstract
Mechanisms and events related to common fragile site (CFS) instability are well known in cancer cells. Here, we argue that normal cells remain an important experimental model to address questions related to CFS instability in the absence of alterations in cell cycle and DNA damage repair pathways, which are common features acquired in cancer. Furthermore, a major gap of knowledge concerns the stability of CFSs during gametogenesis. CFS instability in meiotic or postmeiotic stages of the germ cell line could generate chromosome deletions or large rearrangements. This in turn can lead to the functional loss of the several CFS-associated genes with tumor suppressor function. Our hypothesis is that such mutations can potentially result in genetic predisposition to develop cancer. Indirect evidence for CFS instability in human germ cells has been provided by genomic investigations in family pedigrees associated with genetic disease. The issue of CFS instability in the germ cell line should represent one of the future efforts, and may take advantage of the existence of sequence and functional conservation of CFSs between rodents and humans.
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Affiliation(s)
- Elisa Palumbo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
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40
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Zheglo D, Brueckner LM, Sepman O, Wecht EM, Kuligina E, Suspitsin E, Imyanitov E, Savelyeva L. The FRA14B
common fragile site maps to a region prone to somatic and germline rearrangements within the large GPHN
gene. Genes Chromosomes Cancer 2018; 58:284-294. [DOI: 10.1002/gcc.22706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/27/2023] Open
Affiliation(s)
- Diana Zheglo
- FSBI Research Centre for Medical Genetics; Moscow Russia
| | - Lena M. Brueckner
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Olga Sepman
- Klinik fuer Allgemein-, Viszeral-, Thorax- und minimal-invasive Chirurgie; Pforzheim Germany
| | - Elisa M. Wecht
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | | | - Evgenij Suspitsin
- Petrov Institute of Oncology; St Petersburg Russia
- St. Petersburg Pediatric Medical University; Sankt-Peterburg Russia
| | - Evgenij Imyanitov
- Petrov Institute of Oncology; St Petersburg Russia
- Mechnikov North-Western Medical University; Saint Petersburg Russia
| | - Larissa Savelyeva
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
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41
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Rebolledo-Jaramillo B, Ziegler A. Teneurins: An Integrative Molecular, Functional, and Biomedical Overview of Their Role in Cancer. Front Neurosci 2018; 12:937. [PMID: 30618566 PMCID: PMC6297388 DOI: 10.3389/fnins.2018.00937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/28/2018] [Indexed: 12/16/2022] Open
Abstract
Teneurins are large transmembrane proteins originally identified in Drosophila. Their essential role in development of the central nervous system is conserved throughout species, and evidence supports their involvement in organogenesis of additional tissues. Homophilic and heterophilic interactions between Teneurin paralogues mediate cellular adhesion in crucial processes such as neuronal pathfinding and synaptic organization. At the molecular level, Teneurins are proteolytically processed into distinct subdomains that have been implicated in extracellular and intracellular signaling, and in transcriptional regulation. Phylogenetic studies have shown a high degree of intra- and interspecies conservation of Teneurin genes. Accordingly, the occurrence of genetic variants has been associated with functional and phenotypic alterations in experimental systems, and with some inherited or sporadic conditions. Recently, tumor-related variations in Teneurin gene expression have been associated with patient survival in different cancers. Although these findings were incidental and molecular mechanisms were not addressed, they suggested a potential utility of Teneurin transcript levels as biomarkers for disease prognosis. Mutations and chromosomal alterations affecting Teneurin genes have been found occasionally in tumors, but literature remains scarce. The analysis of open-access molecular and clinical datasets derived from large oncologic cohorts provides an invaluable resource for the identification of additional somatic mutations. However, Teneurin variants have not been classified in terms of pathogenic risk and their phenotypic impact remains unknown. On this basis, is it plausible to hypothesize that Teneurins play a role in carcinogenesis? Does current evidence support a tumor suppressive or rather oncogenic function for these proteins? Here, we comprehensively discuss available literature with integration of molecular evidence retrieved from open-access databases. We show that Teneurins undergo somatic changes comparable to those of well-established cancer genes, and discuss their involvement in cancer-related signaling pathways. Current data strongly suggest a functional contribution of Teneurins to human carcinogenesis.
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Affiliation(s)
| | - Annemarie Ziegler
- Center for Genetics and Genomics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
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42
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Cao RJ, Li K, Xing WY, Du S, Li Q, Zhu XJ, Cui SS. Disabled-1 is down-regulated in clinical breast cancer and regulates cell apoptosis through NF-κB/Bcl-2/caspase-9. J Cell Mol Med 2018; 23:1622-1627. [PMID: 30484953 PMCID: PMC6349202 DOI: 10.1111/jcmm.14047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/20/2018] [Accepted: 11/05/2018] [Indexed: 11/29/2022] Open
Abstract
Disabled‐1 (Dab1) is best known as an adaptor protein regulating neuron migration and lamination during development. However, the exact function of Dab1 in breast cancer is unknown. In this study, we examined the expression of Dab1 in 38 breast cancer paraffin sections, as well as 60 paired frozen breast cancer and their adjacent tissues. Our results showed that Dab1 was reduced in breast cancer, and its compromised expression correlated with triple negative breast cancer phenotype, poor differentiation, as well as lymph node metastasis. Functional analysis in breast cancer cell lines demonstrated that Dab1 promoted cell apoptosis, which, at least partially, depended on its regulation of NF‐κB/Bcl‐2/caspase‐9 pathway. Our study strongly suggests that Dab1 may be a potential tumour suppressor gene in breast cancer.
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Affiliation(s)
- Rang-Juan Cao
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Kai Li
- Department of Anesthesia, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Wan-Ying Xing
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Shuang Du
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Qiang Li
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xiao-Juan Zhu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Shu-Sen Cui
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
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43
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Voutsinos V, Munk SHN, Oestergaard VH. Common Chromosomal Fragile Sites-Conserved Failure Stories. Genes (Basel) 2018; 9:E580. [PMID: 30486458 PMCID: PMC6315858 DOI: 10.3390/genes9120580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022] Open
Abstract
In order to pass on an intact copy of the genome during cell division, complete and faithful DNA replication is crucial. Yet, certain areas of the genome are intrinsically challenging to replicate, which manifests as high local mutation propensity. Such regions include trinucleotide repeat sequences, common chromosomal fragile sites (CFSs), and early replicating fragile sites (ERFSs). Despite their genomic instability CFSs are conserved, suggesting that they have a biological function. To shed light on the potential function of CFSs, this review summarizes the similarities and differences of the regions that challenge DNA replication with main focus on CFSs. Moreover, we review the mechanisms that operate when CFSs fail to complete replication before entry into mitosis. Finally, evolutionary perspectives and potential physiological roles of CFSs are discussed with emphasis on their potential role in neurogenesis.
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Affiliation(s)
- Vasileios Voutsinos
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Sebastian H N Munk
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Vibe H Oestergaard
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
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44
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The role of monogenic genes in idiopathic Parkinson's disease. Neurobiol Dis 2018; 124:230-239. [PMID: 30448284 DOI: 10.1016/j.nbd.2018.11.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/01/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022] Open
Abstract
In the past two decades, mutations in multiple genes have been linked to autosomal dominant or recessive forms of monogenic Parkinson's disease (PD). Collectively, these monogenic (often familial) cases account for less than 5% of all PD, the majority being apparently sporadic cases. More recently, large-scale genome-wide association studies have identified over 40 loci that increase risk of PD. Importantly, there is overlap between monogenic and sporadic PD genes, particularly for the loci that contain the genes SNCA and LRRK2, which are mutated in monogenic dominant PD. There have also been reports of idiopathic PD cases with heterozygous variants in autosomal recessive genes suggesting that these mutations may increase risk of PD. These observations suggest that monogenic and idiopathic PD may have shared pathogenic mechanisms. Here, we focus mainly on the role of monogenic PD genes that represent pleomorphic risk loci for idiopathic PD. We also discuss the functional mechanisms that may play a role in increasing risk of disease in both monogenic and idiopathic forms.
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45
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Carruthers RD, Ahmed SU, Ramachandran S, Strathdee K, Kurian KM, Hedley A, Gomez-Roman N, Kalna G, Neilson M, Gilmour L, Stevenson KH, Hammond EM, Chalmers AJ. Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells. Cancer Res 2018; 78:5060-5071. [PMID: 29976574 PMCID: PMC6128404 DOI: 10.1158/0008-5472.can-18-0569] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/25/2018] [Accepted: 06/28/2018] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) is a lethal primary brain tumor characterized by treatment resistance and inevitable tumor recurrence, both of which are driven by a subpopulation of GBM cancer stem-like cells (GSC) with tumorigenic and self-renewal properties. Despite having broad implications for understanding GSC phenotype, the determinants of upregulated DNA-damage response (DDR) and subsequent radiation resistance in GSC are unknown and represent a significant barrier to developing effective GBM treatments. In this study, we show that constitutive DDR activation and radiation resistance are driven by high levels of DNA replication stress (RS). CD133+ GSC exhibited reduced DNA replication velocity and a higher frequency of stalled replication forks than CD133- non-GSC in vitro; immunofluorescence studies confirmed these observations in a panel of orthotopic xenografts and human GBM specimens. Exposure of non-GSC to low-level exogenous RS generated radiation resistance in vitro, confirming RS as a novel determinant of radiation resistance in tumor cells. GSC exhibited DNA double-strand breaks, which colocalized with "replication factories" and RNA: DNA hybrids. GSC also demonstrated increased expression of long neural genes (>1 Mbp) containing common fragile sites, supporting the hypothesis that replication/transcription collisions are the likely cause of RS in GSC. Targeting RS by combined inhibition of ATR and PARP (CAiPi) provided GSC-specific cytotoxicity and complete abrogation of GSC radiation resistance in vitro These data identify RS as a cancer stem cell-specific target with significant clinical potential.Significance: These findings shed new light on cancer stem cell biology and reveal novel therapeutics with the potential to improve clinical outcomes by overcoming inherent radioresistance in GBM. Cancer Res; 78(17); 5060-71. ©2018 AACR.
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Affiliation(s)
- Ross D Carruthers
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom.
| | - Shafiq U Ahmed
- School of Pharmacy and Pharmaceutical Sciences, Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Shaliny Ramachandran
- Cancer Research UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Karen Strathdee
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Kathreena M Kurian
- Department of Neuropathology, Brain Tumour Research Group, Frenchay Hospital, North Bristol NHS Trust Bristol, Bristol, United Kingdom
| | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Natividad Gomez-Roman
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Gabriela Kalna
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Mathew Neilson
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Lesley Gilmour
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Katrina H Stevenson
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Ester M Hammond
- Cancer Research UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Anthony J Chalmers
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
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46
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Alt FW, Schwer B. DNA double-strand breaks as drivers of neural genomic change, function, and disease. DNA Repair (Amst) 2018; 71:158-163. [PMID: 30195640 DOI: 10.1016/j.dnarep.2018.08.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Early work from about two decades ago implicated DNA double-strand break (DSB) formation and repair in neuronal development. Findings emerging from recent studies of DSBs in proliferating neural progenitors and in mature, non-dividing neurons suggest important roles of DSBs in brain physiology, aging, cancer, psychiatric and neurodegenerative disorders. We provide an overview of some findings and speculate on what may lie ahead.
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Affiliation(s)
- Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States.
| | - Bjoern Schwer
- Department of Neurological Surgery and Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94158, United States.
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47
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Liu C, Deng H, Yang C, Li X, Zhu Y, Chen X, Li H, Li S, Cui H, Zhang X, Tan X, Li D, Zhang Z. A resolved discrepancy between multiplex PCR and multiplex ligation-dependent probe amplification by targeted next-generation sequencing discloses a novel partial exonic deletion in the Duchenne muscular dystrophy gene. J Clin Lab Anal 2018; 32:e22575. [PMID: 29802662 DOI: 10.1002/jcla.22575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/25/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The genetic diagnosis of Duchenne muscular dystrophy (DMD) has been complicated by the large size of the gene and its heterogeneous mutational spectrum. Multiplex PCR and multiplex ligation-dependent probe amplification (MLPA) are two well-established mutation screening methods. Here, we applied targeted next-generation sequencing (NGS) to clarify discrepant results between multiplex PCR and MLPA in a Chinese patient with DMD. METHODS MLPA was performed to confirm multiplex PCR results obtained previously. Targeted NGS was then used to analyze the full-length DMD gene including introns. RESULTS Multiplex PCR had previously identified an apparent deletion of exon 43 in the patient with DMD, but current MLPA indicated that exon 43 was present. Targeted NGS to clarify the genetic diagnosis identified a novel mutation, c.6241_c.6290 + 1109del1159insAC, which caused partial deletion of exon 43. This mutation removed the annealing sequence of the exon 43 reverse primer in multiplex PCR but had no influence on the hybridization site of the MLPA probe. Therefore, the discrepancy between the two methods was caused by partial exonic deletion that escaped MLPA detection. CONCLUSION Targeted NGS disclosed a novel partial exonic deletion in the DMD gene as the cause of discrepancy between multiplex PCR and MLPA. Targeted NGS could be used to provide a more accurate genetic diagnosis of DMD, particularly in cases of partial exonic deletions, which will be of benefit in patient management and the identification of disease carriers.
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Affiliation(s)
- Chang Liu
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Huiting Deng
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Cheng Yang
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Xixi Li
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Yanrong Zhu
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Xiangfa Chen
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Hui Li
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Shuo Li
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Hao Cui
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Xiaoyan Zhang
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Xiaoyue Tan
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
| | - Dong Li
- Department of Neurology, Tianjin Children's Hospital, Tianjin, China
| | - Zhujun Zhang
- Department of Pathology, School of Medicine, Nankai University, Tianjin, China
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48
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Chiarella SE, Rabin EE, Ostilla LA, Flozak AS, Gottardi CJ. αT-catenin: A developmentally dispensable, disease-linked member of the α-catenin family. Tissue Barriers 2018; 6:e1463896. [PMID: 29746206 PMCID: PMC6179130 DOI: 10.1080/21688370.2018.1463896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 02/07/2023] Open
Abstract
α-Catenins are actin-filament binding proteins and critical subunits of the cadherin-catenin cell-cell adhesive complex. They are found in nominally-defined epithelial (E), neural (N), and testis (T) forms transcribed from three distinct genes. While most of α-catenin research has focused on the developmentally essential founding member, αE-catenin, this review discusses recent studies on αT-catenin (CTNNA3), a developmentally dispensable isoform that is emerging as relevant to cardiac, allergic and neurological diseases.
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Affiliation(s)
- Sergio E. Chiarella
- Department of Medicine
- Cellular and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Erik E. Rabin
- Department of Medicine
- Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL
| | - Lorena A. Ostilla
- Department of Medicine
- Cellular and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Annette S. Flozak
- Department of Medicine
- Cellular and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Cara J. Gottardi
- Department of Medicine
- Cellular and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, IL
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49
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Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet 2018; 50:682-692. [PMID: 29662167 PMCID: PMC6372064 DOI: 10.1038/s41588-018-0086-z] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 02/22/2018] [Indexed: 12/18/2022]
Abstract
Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.
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Affiliation(s)
- David C Wedge
- Oxford Big Data Institute, University of Oxford, Oxford, UK.
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thomas Mitchell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Dan J Woodcock
- Oxford Big Data Institute, University of Oxford, Oxford, UK
| | | | - Mohammed Ghori
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jorge Zamora
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Hayley Whitaker
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | | | | | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Early Detection Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stefan Dentro
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Clare Verrill
- Oxford NIHR Biomedical Research Centre, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan M Berney
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nening Dennis
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Sue Merson
- The Institute of Cancer Research, London, UK
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - William Howat
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam Lambert
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jonathan Kay
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Katalin Karaszi
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Hayley Luxton
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Niedzica Camacho
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- The Institute of Cancer Research, London, UK
| | - Luke Marsden
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Lucy Matthews
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Valeria Bo
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Daniel Leongamornlert
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- The Institute of Cancer Research, London, UK
| | - Stuart McLaren
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anthony Ng
- The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yongwei Yu
- Second Military Medical University, Shanghai, China
| | | | | | - Sarah Thomas
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Elizabeth Bancroft
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Cyril Fisher
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Naomi Livni
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Nicol
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Simon Tavaré
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Pelvender Gill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Vincent Khoo
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Pardeep Kumar
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Declan Cahill
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Alan Thompson
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Erik Mayer
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Edward Rowe
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Tim Dudderidge
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Vincent Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Nimish C Shah
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | | | | | | | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | | | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Andrew G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
- School of Mathematics and Statistics/School of Medicine, University of St. Andrews, Fife, UK
| | - G Steven Bova
- Johns Hopkins School of Medicine, Baltimore, MD, USA
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Daniel S Brewer
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Colin S Cooper
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK.
- Royal Marsden NHS Foundation Trust, London and Sutton, UK.
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50
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DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression. Genetics 2017; 207:29-47. [PMID: 28874453 PMCID: PMC5586379 DOI: 10.1534/genetics.115.186627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 05/19/2017] [Indexed: 12/11/2022] Open
Abstract
Proper control of DNA replication is critical to ensure genomic integrity during cell proliferation. In addition, differential regulation of the DNA replication program during development can change gene copy number to influence cell size and gene expression. Drosophila melanogaster serves as a powerful organism to study the developmental control of DNA replication in various cell cycle contexts in a variety of differentiated cell and tissue types. Additionally, Drosophila has provided several developmentally regulated replication models to dissect the molecular mechanisms that underlie replication-based copy number changes in the genome, which include differential underreplication and gene amplification. Here, we review key findings and our current understanding of the developmental control of DNA replication in the contexts of the archetypal replication program as well as of underreplication and differential gene amplification. We focus on the use of these latter two replication systems to delineate many of the molecular mechanisms that underlie the developmental control of replication initiation and fork elongation.
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