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Wakasa T, Nonaka K, Harada A, Ohkawa Y, Kikutake C, Suyama M, Kobunai T, Tsunekuni K, Matsuoka K, Kataoka Y, Ochiiwa H, Miyadera K, Sagara T, Oki E, Ohdo S, Maehara Y, Iimori M, Kitao H. The anti-tumor effect of trifluridine via induction of aberrant mitosis is unaffected by mutations modulating p53 activity. Cell Death Discov 2024; 10:307. [PMID: 38956056 PMCID: PMC11219725 DOI: 10.1038/s41420-024-02083-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
The fluorinated thymidine analog trifluridine (FTD) is a chemotherapeutic drug commonly used to treat cancer; however, the mechanism by which FTD induces cytotoxicity is not fully understood. In addition, the effect of gain-of-function (GOF) missense mutations of the TP53 gene (encoding p53), which promote cancer progression and chemotherapeutic drug resistance, on the chemotherapeutic efficacy of FTD is unclear. Here, we revealed the mechanisms by which FTD-induced aberrant mitosis and contributed to cytotoxicity in both p53-null and p53-GOF missense mutant cells. In p53-null mutant cells, FTD-induced DNA double-stranded breaks, single-stranded DNA accumulation, and the associated DNA damage responses during the G2 phase. Nevertheless, FTD-induced DNA damage and the related responses were not sufficient to trigger strict G2/M checkpoint arrest. Thus, these features were carried over into mitosis, resulting in chromosome breaks and bridges, and subsequent cytokinesis failure. Improper mitotic exit eventually led to cell apoptosis, caused by the accumulation of extensive DNA damage and the presence of micronuclei encapsulated in the disrupted nuclear envelope. Upon FTD treatment, the behavior of the p53-GOF-missense mutant, isogenic cell lines, generated by CRISPR/Cas9 genome editing, was similar to that of p53-null mutant cells. Thus, our data suggest that FTD treatment overrode the effect on gene expression induced by p53-GOF mutants and exerted its anti-tumor activity in a manner that was independent of the p53 function.
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Affiliation(s)
- Takeshi Wakasa
- Department of Molecular Cancer Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
- Taiho Pharmaceutical Co. Ltd., Tokyo, Japan
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kentaro Nonaka
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Kyushu Central Hospital of the Mutual Aid Association of Public School Teachers, Fukuoka, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Chie Kikutake
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | | | | | | | | | | | | | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigehiro Ohdo
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Maehara
- Kyushu Central Hospital of the Mutual Aid Association of Public School Teachers, Fukuoka, Japan
| | - Makoto Iimori
- Department of Molecular Cancer Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
- Oral Medicine Research Center, Fukuoka Dental College, Fukuoka, Japan.
| | - Hiroyuki Kitao
- Department of Molecular Cancer Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
- Oral Medicine Research Center, Fukuoka Dental College, Fukuoka, Japan.
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2
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Hosea R, Hillary S, Naqvi S, Wu S, Kasim V. The two sides of chromosomal instability: drivers and brakes in cancer. Signal Transduct Target Ther 2024; 9:75. [PMID: 38553459 PMCID: PMC10980778 DOI: 10.1038/s41392-024-01767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 04/02/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and is associated with tumor cell malignancy. CIN triggers a chain reaction in cells leading to chromosomal abnormalities, including deviations from the normal chromosome number or structural changes in chromosomes. CIN arises from errors in DNA replication and chromosome segregation during cell division, leading to the formation of cells with abnormal number and/or structure of chromosomes. Errors in DNA replication result from abnormal replication licensing as well as replication stress, such as double-strand breaks and stalled replication forks; meanwhile, errors in chromosome segregation stem from defects in chromosome segregation machinery, including centrosome amplification, erroneous microtubule-kinetochore attachments, spindle assembly checkpoint, or defective sister chromatids cohesion. In normal cells, CIN is deleterious and is associated with DNA damage, proteotoxic stress, metabolic alteration, cell cycle arrest, and senescence. Paradoxically, despite these negative consequences, CIN is one of the hallmarks of cancer found in over 90% of solid tumors and in blood cancers. Furthermore, CIN could endow tumors with enhanced adaptation capabilities due to increased intratumor heterogeneity, thereby facilitating adaptive resistance to therapies; however, excessive CIN could induce tumor cells death, leading to the "just-right" model for CIN in tumors. Elucidating the complex nature of CIN is crucial for understanding the dynamics of tumorigenesis and for developing effective anti-tumor treatments. This review provides an overview of causes and consequences of CIN, as well as the paradox of CIN, a phenomenon that continues to perplex researchers. Finally, this review explores the potential of CIN-based anti-tumor therapy.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sumera Naqvi
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
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3
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Pinto LM, Pailas A, Bondarchenko M, Sharma AB, Neumann K, Rizzo AJ, Jeanty C, Nicot N, Racca C, Graham MK, Naughton C, Liu Y, Chen CL, Meakin PJ, Gilbert N, Britton S, Meeker AK, Heaphy CM, Larminat F, Van Dyck E. DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks. Nucleic Acids Res 2024; 52:1136-1155. [PMID: 38038252 PMCID: PMC10853780 DOI: 10.1093/nar/gkad1141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Maintaining chromatin integrity at the repetitive non-coding DNA sequences underlying centromeres is crucial to prevent replicative stress, DNA breaks and genomic instability. The concerted action of transcriptional repressors, chromatin remodelling complexes and epigenetic factors controls transcription and chromatin structure in these regions. The histone chaperone complex ATRX/DAXX is involved in the establishment and maintenance of centromeric chromatin through the deposition of the histone variant H3.3. ATRX and DAXX have also evolved mutually-independent functions in transcription and chromatin dynamics. Here, using paediatric glioma and pancreatic neuroendocrine tumor cell lines, we identify a novel ATRX-independent function for DAXX in promoting genome stability by preventing transcription-associated R-loop accumulation and DNA double-strand break formation at centromeres. This function of DAXX required its interaction with histone H3.3 but was independent of H3.3 deposition and did not reflect a role in the repression of centromeric transcription. DAXX depletion mobilized BRCA1 at centromeres, in line with BRCA1 role in counteracting centromeric R-loop accumulation. Our results provide novel insights into the mechanisms protecting the human genome from chromosomal instability, as well as potential perspectives in the treatment of cancers with DAXX alterations.
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Affiliation(s)
- Lia M Pinto
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
- Discovery & Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Alexandros Pailas
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Max Bondarchenko
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Abhishek Bharadwaj Sharma
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Katrin Neumann
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Anthony J Rizzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Céline Jeanty
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Nathalie Nicot
- Translational Medicine Operations Hub, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Carine Racca
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Mindy K Graham
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Catherine Naughton
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 1QY, UK
| | - Yaqun Liu
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75248 Paris Cedex 05, France
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75248 Paris Cedex 05, France
| | - Paul J Meakin
- Discovery & Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 1QY, UK
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Christopher M Heaphy
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Florence Larminat
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Eric Van Dyck
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
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4
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Bournaka S, Badra-Fajardo N, Arbi M, Taraviras S, Lygerou Z. The cell cycle revisited: DNA replication past S phase preserves genome integrity. Semin Cancer Biol 2024; 99:45-55. [PMID: 38346544 DOI: 10.1016/j.semcancer.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
Accurate and complete DNA duplication is critical for maintaining genome integrity. Multiple mechanisms regulate when and where DNA replication takes place, to ensure that the entire genome is duplicated once and only once per cell cycle. Although the bulk of the genome is copied during the S phase of the cell cycle, increasing evidence suggests that parts of the genome are replicated in G2 or mitosis, in a last attempt to secure that daughter cells inherit an accurate copy of parental DNA. Remaining unreplicated gaps may be passed down to progeny and replicated in the next G1 or S phase. These findings challenge the long-established view that genome duplication occurs strictly during the S phase, bridging DNA replication to DNA repair and providing novel therapeutic strategies for cancer treatment.
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Affiliation(s)
- Spyridoula Bournaka
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Nibal Badra-Fajardo
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Marina Arbi
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Stavros Taraviras
- Department of Physiology, Medical School, University of Patras, Patras 26504, Greece
| | - Zoi Lygerou
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece.
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5
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Baron N, Purushotham R, Pullaiahgari D, Bose P, Zarivach R, Shapira M. LeishIF4E2 is a cap-binding protein that plays a role in Leishmania cell cycle progression. FASEB J 2024; 38:e23367. [PMID: 38095329 DOI: 10.1096/fj.202301665r] [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: 08/16/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023]
Abstract
Leishmania encode six paralogs of the cap-binding protein eIF4E and five eIF4G candidates, forming unique complexes. Two cap-binding proteins, LeishIF4E1 and LeishIF4E2, do not bind any identified LeishIF4Gs, thus their roles are intriguing. Here, we combine structural prediction, proteomic analysis, and interaction assays to shed light on LeishIF4E2 function. A nonconserved C-terminal extension was identified through structure prediction and sequence alignment. m7 GTP-binding assays involving both recombinant and transgenic LeishIF4E2 with and without the C-terminal extension revealed that this extension functions as a regulatory gate, modulating the cap-binding activity of LeishIF4E2. The interactomes of the two LeishIF4E2 versions were investigated, highlighting the role of the C-terminal extension in binding to SLBP2. SLBP2 is known to interact with a stem-loop structure in the 3' UTRs of histone mRNAs. Consistent with the predicted inhibitory effect of SLBP2 on histone expression in Xenopus laevis, a hemizygous deletion mutant of LeishIF4E2, exhibited an upregulation of several histones. We therefore propose that LeishIF4E2 is involved in histone expression, possibly through its interaction between SLBP2 and LeishIF4E2, thus affecting cell cycle progression. In addition, cell synchronization showed that LeishIF4E2 expression decreased during the S-phase, when histones are known to be synthesized. Previous studies in T. brucei also highlighted an association between TbEIF4E2 and SLBP2, and further reported on an interaction between TbIF4E2 and S-phase-abundant mRNAs. Our results show that overexpression of LeishIF4E2 correlates with upregulation of cell cycle and chromosome maintenance proteins. Along with its effect on histone expression, we propose that LeishIF4E2 is involved in cell cycle progression.
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Affiliation(s)
- Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Rajaram Purushotham
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Priyanka Bose
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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6
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Forte G, Boteva L, Conforto F, Gilbert N, Cook PR, Marenduzzo D. Bridging condensins mediate compaction of mitotic chromosomes. J Cell Biol 2024; 223:e202209113. [PMID: 37976091 PMCID: PMC10655892 DOI: 10.1083/jcb.202209113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 07/08/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Eukaryotic chromosomes compact during mitosis into elongated cylinders-and not the spherical globules expected of self-attracting long flexible polymers. This process is mainly driven by condensin-like proteins. Here, we present Brownian-dynamic simulations involving two types of such proteins with different activities. One, which we refer to as looping condensins, anchors long-lived chromatin loops to create bottlebrush structures. The second, referred to as bridging condensins, forms multivalent bridges between distant parts of these loops. We show that binding of bridging condensins leads to the formation of shorter and stiffer mitotic-like cylinders without requiring any additional energy input. These cylinders have several features matching experimental observations. For instance, the axial condensin backbone breaks up into clusters as found by microscopy, and cylinder elasticity qualitatively matches that seen in chromosome pulling experiments. Additionally, simulating global condensin depletion or local faulty condensin loading gives phenotypes seen experimentally and points to a mechanistic basis for the structure of common fragile sites in mitotic chromosomes.
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Affiliation(s)
- Giada Forte
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Lora Boteva
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Filippo Conforto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter R. Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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7
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Irony-Tur Sinai M, Kerem B. Insights into common fragile site instability: DNA replication challenges at DNA repeat sequences. Emerg Top Life Sci 2023; 7:277-287. [PMID: 37876349 PMCID: PMC10754330 DOI: 10.1042/etls20230023] [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: 08/02/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023]
Abstract
Common fragile sites (CFS) are specific genomic regions prone to chromosomal instability under conditions of DNA replication stress. CFSs manifest as breaks, gaps, and constrictions on metaphase chromosomes under mild replication stress. These replication-sensitive CFS regions are preferentially unstable during cancer development, as reflected by their association with copy number variants (CNVs) frequently arise in most tumor types. Over the years, it became clear that a combination of different characteristics underlies the enhanced sensitivity of CFSs to replication stress. As of today, there is a strong evidence that the core fragility regions along CFSs overlap with actively transcribed large genes with delayed replication timing upon replication stress. Recently, the mechanistic basis for CFS instability was further extended to regions which span topologically associated domain (TAD) boundaries, generating a fragility signature composed of replication, transcription and genome organization. The presence of difficult-to-replicate AT-rich repeats was one of the early features suggested to characterize a subgroup of CFSs. These long stretches of AT-dinucleotide have the potential to fold into stable secondary structures which may impede replication fork progression, leaving the region under-replicated. Here, we focus on the molecular mechanisms underlying repeat instability at CFSs and on the proteins involved in the resolution of secondary structure impediments arising along repetitive sequence elements which are essential for the maintenance of genome stability.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
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8
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Traband EL, Hammerlund SR, Shameem M, Narayan A, Ramana S, Tella A, Sobeck A, Shima N. Mitotic DNA Synthesis in Untransformed Human Cells Preserves Common Fragile Site Stability via a FANCD2-Driven Mechanism That Requires HELQ. J Mol Biol 2023; 435:168294. [PMID: 37777152 PMCID: PMC10839910 DOI: 10.1016/j.jmb.2023.168294] [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: 06/12/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Faithful genome duplication is a challenging task for dividing mammalian cells, particularly under replication stress where timely resolution of late replication intermediates (LRIs) becomes crucial prior to cell division. In human cancer cells, mitotic DNA repair synthesis (MiDAS) is described as a final mechanism for the resolution of LRIs to avoid lethal chromosome mis-segregation. RAD52-driven MiDAS achieves this mission in part by generating gaps/breaks on metaphase chromosomes, which preferentially occur at common fragile sites (CFS). We previously demonstrated that a MiDAS mechanism also exists in untransformed and primary human cells, which is RAD52 independent but requires FANCD2. However, the properties of this form of MiDAS are not well understood. Here, we report that FANCD2-driven MiDAS in untransformed human cells: 1) requires a prerequisite step of FANCD2 mono-ubiquitination by a subset of Fanconi anemia (FA) proteins, 2) primarily acts to preserve CFS stability but not to prevent chromosome mis-segregation, and 3) depends on HELQ, which potentially functions at an early step. Hence, FANCD2-driven MiDAS in untransformed cells is built to protect CFS stability, whereas RAD52-driven MiDAS in cancer cells is likely adapted to prevent chromosome mis-segregation at the cost of CFS expression. Notably, we also identified a novel form of MiDAS, which surfaces to function when FANCD2 is absent in untransformed cells. Our findings substantiate the complex nature of MiDAS and a link between its deficiencies and the pathogenesis of FA, a human genetic disease.
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Affiliation(s)
- Emma L Traband
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Sarah R Hammerlund
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Mohammad Shameem
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Ananya Narayan
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Sanjiv Ramana
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Anika Tella
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Alexandra Sobeck
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, Minneapolis, MN 55455, USA
| | - Naoko Shima
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, Minneapolis, MN 55455, USA.
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9
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Abstract
Many cellular processes require large-scale rearrangements of chromatin structure. Structural maintenance of chromosomes (SMC) protein complexes are molecular machines that can provide structure to chromatin. These complexes can connect DNA elements in cis, walk along DNA, build and processively enlarge DNA loops and connect DNA molecules in trans to hold together the sister chromatids. These DNA-shaping abilities place SMC complexes at the heart of many DNA-based processes, including chromosome segregation in mitosis, transcription control and DNA replication, repair and recombination. In this Review, we discuss the latest insights into how SMC complexes such as cohesin, condensin and the SMC5-SMC6 complex shape DNA to direct these fundamental chromosomal processes. We also consider how SMC complexes, by building chromatin loops, can counteract the natural tendency of alike chromatin regions to cluster. SMC complexes thus control nuclear organization by participating in a molecular tug of war that determines the architecture of our genome.
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Affiliation(s)
- Claire Hoencamp
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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10
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Casimir L, Zimmer S, Racine-Brassard F, Goudreau F, Jacques PÉ, Maréchal A. Chronic treatment with ATR and CHK1 inhibitors does not substantially increase the mutational burden of human cells. Mutat Res 2023; 827:111834. [PMID: 37531716 DOI: 10.1016/j.mrfmmm.2023.111834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023]
Abstract
DNA replication stress (RS) entails the frequent slow down and arrest of replication forks by a variety of conditions that hinder accurate and processive genome duplication. Elevated RS leads to genome instability, replication catastrophe and eventually cell death. RS is particularly prevalent in cancer cells and its exacerbation to unsustainable levels by chemotherapeutic agents remains a cornerstone of cancer treatments. The adverse consequences of RS are normally prevented by the ATR and CHK1 checkpoint kinases that stabilize stressed forks, suppress origin firing and promote cell cycle arrest when replication is perturbed. Specific inhibitors of these kinases have been developed and shown to potentiate RS and cell death in multiple in vitro cancer settings. Ongoing clinical trials are now probing their efficacy against various cancer types, either as single agents or in combination with mainstay chemotherapeutics. Despite their promise as valuable additions to the anti-cancer pharmacopoeia, we still lack a genome-wide view of the potential mutagenicity of these new drugs. To investigate this question, we performed chronic long-term treatments of TP53-depleted human cancer cells with ATR and CHK1 inhibitors (ATRi, AZD6738/ceralasertib and CHK1i, MK8776/SCH-900776). ATR or CHK1 inhibition did not significantly increase the mutational burden of cells, nor generate specific mutational signatures. Indeed, no notable changes in the numbers of base substitutions, short insertions/deletions and larger scale rearrangements were observed despite induction of replication-associated DNA breaks during treatments. Interestingly, ATR inhibition did induce a slight increase in closely-spaced mutations, a feature previously attributed to translesion synthesis DNA polymerases. The results suggest that ATRi and CHK1i do not have substantial mutagenic effects in vitro when used as standalone agents.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Goudreau
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
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11
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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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12
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Li JSZ, Abbasi A, Kim DH, Lippman SM, Alexandrov LB, Cleveland DW. Chromosomal fragile site breakage by EBV-encoded EBNA1 at clustered repeats. Nature 2023; 616:504-509. [PMID: 37046091 PMCID: PMC10328181 DOI: 10.1038/s41586-023-05923-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/07/2023] [Indexed: 04/14/2023]
Abstract
Epstein-Barr virus (EBV) is an oncogenic herpesvirus associated with several cancers of lymphocytic and epithelial origin1-3. EBV encodes EBNA1, which binds to a cluster of 20 copies of an 18-base-pair palindromic sequence in the EBV genome4-6. EBNA1 also associates with host chromosomes at non-sequence-specific sites7, thereby enabling viral persistence. Here we show that the sequence-specific DNA-binding domain of EBNA1 binds to a cluster of tandemly repeated copies of an EBV-like, 18-base-pair imperfect palindromic sequence encompassing a region of about 21 kilobases at human chromosome 11q23. In situ visualization of the repetitive EBNA1-binding site reveals aberrant structures on mitotic chromosomes characteristic of inherently fragile DNA. We demonstrate that increasing levels of EBNA1 binding trigger dose-dependent breakage at 11q23, producing a fusogenic centromere-containing fragment and an acentric distal fragment, with both mis-segregated into micronuclei in the next cell cycles. In cells latently infected with EBV, elevating EBNA1 abundance by as little as twofold was sufficient to trigger breakage at 11q23. Examination of whole-genome sequencing of EBV-associated nasopharyngeal carcinomas revealed that structural variants are highly enriched on chromosome 11. Presence of EBV is also shown to be associated with an enrichment of chromosome 11 rearrangements across 2,439 tumours from 38 cancer types. Our results identify a previously unappreciated link between EBV and genomic instability, wherein EBNA1-induced breakage at 11q23 triggers acquisition of structural variations in chromosome 11.
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MESH Headings
- Humans
- Binding Sites
- DNA/chemistry
- DNA/metabolism
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/metabolism
- Herpesvirus 4, Human/pathogenicity
- Viral Proteins/genetics
- Viral Proteins/metabolism
- DNA Breaks, Double-Stranded
- Chromosomes, Human, Pair 11/chemistry
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 11/metabolism
- Genomic Instability
- Mitosis
- Chromosome Breakage
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Affiliation(s)
- Julia Su Zhou Li
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Dong Hyun Kim
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Oncology Research Unit, Pfizer Inc., San Diego, CA, USA
| | | | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA.
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13
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Benitez A, Sebald M, Kanagaraj R, Rodrigo-Brenni MC, Chan YW, Liang CC, West SC. GEN1 promotes common fragile site expression. Cell Rep 2023; 42:112062. [PMID: 36729836 DOI: 10.1016/j.celrep.2023.112062] [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: 02/23/2022] [Revised: 11/01/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
Our genomes harbor conserved DNA sequences, known as common fragile sites (CFSs), that are difficult to replicate and correspond to regions of genome instability. Following replication stress, CFS loci give rise to breaks or gaps (termed CFS expression) where under-replicated DNA subsequently undergoes mitotic DNA synthesis (MiDAS). We show that loss of the structure-selective endonuclease GEN1 reduces CFS expression, leading to defects in MiDAS, ultrafine anaphase bridge formation, and DNA damage in the ensuing cell cycle due to aberrant chromosome segregation. GEN1 knockout cells also exhibit an elevated frequency of bichromatid constrictions consistent with the presence of unresolved regions of under-replicated DNA. Previously, the role of GEN1 was thought to be restricted to the nucleolytic resolution of recombination intermediates. However, its ability to cleave under-replicated DNA at CFS loci indicates that GEN1 plays a dual role resolving both DNA replication and recombination intermediates before chromosome segregation.
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Affiliation(s)
- Anaid Benitez
- The Francis Crick Institute, DNA Recombination and Repair Laboratory, 1 Midland Road, London NW1 1AT, UK
| | - Marie Sebald
- The Francis Crick Institute, DNA Recombination and Repair Laboratory, 1 Midland Road, London NW1 1AT, UK
| | - Radhakrishnan Kanagaraj
- The Francis Crick Institute, DNA Recombination and Repair Laboratory, 1 Midland Road, London NW1 1AT, UK
| | - Monica C Rodrigo-Brenni
- The Francis Crick Institute, DNA Recombination and Repair Laboratory, 1 Midland Road, London NW1 1AT, UK
| | - Ying Wai Chan
- The Francis Crick Institute, DNA Recombination and Repair Laboratory, 1 Midland Road, London NW1 1AT, UK
| | - Chih-Chao Liang
- The Francis Crick Institute, DNA Recombination and Repair Laboratory, 1 Midland Road, London NW1 1AT, UK
| | - Stephen C West
- The Francis Crick Institute, DNA Recombination and Repair Laboratory, 1 Midland Road, London NW1 1AT, UK.
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14
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Mitotic DNA synthesis in response to replication stress requires the sequential action of DNA polymerases zeta and delta in human cells. Nat Commun 2023; 14:706. [PMID: 36759509 PMCID: PMC9911744 DOI: 10.1038/s41467-023-35992-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
Oncogene activation creates DNA replication stress (RS) in cancer cells, which can generate under-replicated DNA regions (UDRs) that persist until cells enter mitosis. UDRs also have the potential to generate DNA bridges in anaphase cells or micronuclei in the daughter cells, which could promote genomic instability. To suppress such damaging changes to the genome, human cells have developed a strategy to conduct 'unscheduled' DNA synthesis in mitosis (termed MiDAS) that serves to rescue under-replicated loci. Previous studies have shown that MiDAS proceeds via a POLD3-dependent pathway that shows some features of break-induced replication. Here, we define how human cells utilize both DNA gap filling (REV1 and Pol ζ) and replicative (Pol δ) DNA polymerases to complete genome duplication following a perturbed S-phase. We present evidence for the existence of a polymerase-switch during MiDAS that is required for new DNA synthesis at UDRs. Moreover, we reveal that, upon oncogene activation, cancer cell survival is significantly compromised when REV1 is depleted, suggesting that REV1 inhibition might be a feasible approach for the treatment of some human cancers.
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15
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Sorokin M, Rabushko E, Rozenberg JM, Mohammad T, Seryakov A, Sekacheva M, Buzdin A. Clinically relevant fusion oncogenes: detection and practical implications. Ther Adv Med Oncol 2022; 14:17588359221144108. [PMID: 36601633 PMCID: PMC9806411 DOI: 10.1177/17588359221144108] [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: 06/09/2022] [Accepted: 11/22/2022] [Indexed: 12/28/2022] Open
Abstract
Mechanistically, chimeric genes result from DNA rearrangements and include parts of preexisting normal genes combined at the genomic junction site. Some rearranged genes encode pathological proteins with altered molecular functions. Those which can aberrantly promote carcinogenesis are called fusion oncogenes. Their formation is not a rare event in human cancers, and many of them were documented in numerous study reports and in specific databases. They may have various molecular peculiarities like increased stability of an oncogenic part, self-activation of tyrosine kinase receptor moiety, and altered transcriptional regulation activities. Currently, tens of low molecular mass inhibitors are approved in cancers as the drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins, that is, including ALK, ABL, EGFR, FGFR1-3, NTRK1-3, MET, RET, ROS1 moieties. Therein, the presence of the respective RTK fusion in the cancer genome is the diagnostic biomarker for drug prescription. However, identification of such fusion oncogenes is challenging as the breakpoint may arise in multiple sites within the gene, and the exact fusion partner is generally unknown. There is no gold standard method for RTK fusion detection, and many alternative experimental techniques are employed nowadays to solve this issue. Among them, RNA-seq-based methods offer an advantage of unbiased high-throughput analysis of only transcribed RTK fusion genes, and of simultaneous finding both fusion partners in a single RNA-seq read. Here we focus on current knowledge of biology and clinical aspects of RTK fusion genes, related databases, and laboratory detection methods.
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Affiliation(s)
| | - Elizaveta Rabushko
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia,I.M. Sechenov First Moscow State Medical
University, Moscow, Russia
| | | | - Tharaa Mohammad
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia
| | | | - Marina Sekacheva
- I.M. Sechenov First Moscow State Medical
University, Moscow, Russia
| | - Anton Buzdin
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia,I.M. Sechenov First Moscow State Medical
University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic
Chemistry, Moscow, Russia,PathoBiology Group, European Organization for
Research and Treatment of Cancer (EORTC), Brussels, Belgium
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16
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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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17
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Pommier Y, Nussenzweig A, Takeda S, Austin C. Human topoisomerases and their roles in genome stability and organization. Nat Rev Mol Cell Biol 2022; 23:407-427. [PMID: 35228717 PMCID: PMC8883456 DOI: 10.1038/s41580-022-00452-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA–protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer. Topoisomerases have essential roles in transcription, DNA replication, chromatin remodelling and, as recently revealed, 3D genome organization. However, topoisomerases also generate DNA–protein crosslinks coupled with DNA breaks, which are increasingly recognized as a source of disease-causing genomic damage.
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18
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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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19
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Connolly C, Takahashi S, Miura H, Hiratani I, Gilbert N, Donaldson AD, Hiraga SI. SAF-A promotes origin licensing and replication fork progression to ensure robust DNA replication. J Cell Sci 2022; 135:jcs258991. [PMID: 34888666 DOI: 10.1242/jcs.258991] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
The organisation of chromatin is closely intertwined with biological activities of chromosome domains, including transcription and DNA replication status. Scaffold-attachment factor A (SAF-A), also known as heterogeneous nuclear ribonucleoprotein U (HNRNPU), contributes to the formation of open chromatin structure. Here, we demonstrate that SAF-A promotes the normal progression of DNA replication and enables resumption of replication after inhibition. We report that cells depleted of SAF-A show reduced origin licensing in G1 phase and, consequently, reduced origin activation frequency in S phase. Replication forks also progress less consistently in cells depleted of SAF-A, contributing to reduced DNA synthesis rate. Single-cell replication timing analysis revealed two distinct effects of SAF-A depletion: first, the boundaries between early- and late-replicating domains become more blurred; and second, SAF-A depletion causes replication timing changes that tend to bring regions of discordant domain compartmentalisation and replication timing into concordance. Associated with these defects, SAF-A-depleted cells show elevated formation of phosphorylated histone H2AX (γ-H2AX) and tend to enter quiescence. Overall, we find that SAF-A protein promotes robust DNA replication to ensure continuing cell proliferation.
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Affiliation(s)
- Caitlin Connolly
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Saori Takahashi
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Hisashi Miura
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Ichiro Hiratani
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Nick Gilbert
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK
| | - Anne D Donaldson
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Shin-Ichiro Hiraga
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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20
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Gönenc II, Wolff A, Schmidt J, Zibat A, Müller C, Cyganek L, Argyriou L, Räschle M, Yigit G, Wollnik B. OUP accepted manuscript. Hum Mol Genet 2022; 31:2185-2193. [PMID: 35099000 PMCID: PMC9262399 DOI: 10.1093/hmg/ddab373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/02/2021] [Accepted: 12/27/2021] [Indexed: 11/12/2022] Open
Abstract
Bloom syndrome (BS) is an autosomal recessive disease clinically characterized by primary microcephaly, growth deficiency, immunodeficiency and predisposition to cancer. It is mainly caused by biallelic loss-of-function mutations in the BLM gene, which encodes the BLM helicase, acting in DNA replication and repair processes. Here, we describe the gene expression profiles of three BS fibroblast cell lines harboring causative, biallelic truncating mutations obtained by single-cell (sc) transcriptome analysis. We compared the scRNA transcription profiles from three BS patient cell lines to two age-matched wild-type controls and observed specific deregulation of gene sets related to the molecular processes characteristically affected in BS, such as mitosis, chromosome segregation, cell cycle regulation and genomic instability. We also found specific upregulation of genes of the Fanconi anemia pathway, in particular FANCM, FANCD2 and FANCI, which encode known interaction partners of BLM. The significant deregulation of genes associated with inherited forms of primary microcephaly observed in our study might explain in part the molecular pathogenesis of microcephaly in BS, one of the main clinical characteristics in patients. Finally, our data provide first evidence of a novel link between BLM dysfunction and transcriptional changes in condensin complex I and II genes. Overall, our study provides novel insights into gene expression profiles in BS on an sc level, linking specific genes and pathways to BLM dysfunction.
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Affiliation(s)
| | | | - Julia Schmidt
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Arne Zibat
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Christian Müller
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Lukas Cyganek
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Loukas Argyriou
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Markus Räschle
- Department of Molecular Genetics, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Bernd Wollnik
- To whom correspondence should be addressed at: Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany. Tel: +49 5513960606; Fax: +49 5513969303;
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Epum EA, Haber JE. DNA replication: the recombination connection. Trends Cell Biol 2022; 32:45-57. [PMID: 34384659 PMCID: PMC8688190 DOI: 10.1016/j.tcb.2021.07.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 01/03/2023]
Abstract
Failure to complete DNA replication is one of the major sources of genome instability leading to aneuploidy, chromosome breakage, and chromosome rearrangements that are associated with human cancer. One of the surprising revelations of the past decade is that the completion of replication at so-called common fragile sites (CFS) occurs very late in the cell cycle - at mitosis - through a process termed MiDAS (mitotic DNA synthesis). MiDAS is strongly related to another cancer-promoting phenomenon: the activation of alternative lengthening of telomeres (ALT). Our understanding of the mechanisms of ALT and MiDAS in mammalian cells has drawn heavily from recent advances in the study of break-induced replication (BIR), especially in budding yeast. We provide new insights into the BIR, MiDAS, and ALT pathways and their shared similarities.
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22
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Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation. Sci Rep 2021; 11:24437. [PMID: 34952909 PMCID: PMC8709867 DOI: 10.1038/s41598-021-04077-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/15/2021] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1 gene in the cheetah, several species of galliform birds, and rodents. The genomic region containing COA1 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and the occasional dispensability of the chaperone-like role of the COA1 gene.
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Abstract
Unlike bacteria, mammalian cells need to complete DNA replication before segregating their chromosomes for the maintenance of genome integrity. Thus, cells have evolved efficient pathways to restore stalled and/or collapsed replication forks during S-phase, and when necessary, also to delay cell cycle progression to ensure replication completion. However, strong evidence shows that cells can proceed to mitosis with incompletely replicated DNA when under mild replication stress (RS) conditions. Consequently, the incompletely replicated genomic gaps form, predominantly at common fragile site regions, where the converging fork-like DNA structures accumulate. These branched structures pose a severe threat to the faithful disjunction of chromosomes as they physically interlink the partially duplicated sister chromatids. In this review, we provide an overview discussing how cells respond and deal with the under-replicated DNA structures that escape from the S/G2 surveillance system. We also focus on recent research of a mitotic break-induced replication pathway (also known as mitotic DNA repair synthesis), which has been proposed to operate during prophase in an attempt to finish DNA synthesis at the under-replicated genomic regions. Finally, we discuss recent data on how mild RS may cause chromosome instability and mutations that accelerate cancer genome evolution.
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Affiliation(s)
- Camelia Mocanu
- Chromosome Dynamics and Stability Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 7BG, UK
| | - Kok-Lung Chan
- Chromosome Dynamics and Stability Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 7BG, UK
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24
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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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