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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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2
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Irvin EM, Wang H. Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures. DNA Repair (Amst) 2023; 128:103528. [PMID: 37392578 PMCID: PMC10989508 DOI: 10.1016/j.dnarep.2023.103528] [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: 04/08/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
DNA repair pathways are tightly regulated processes that recognize specific hallmarks of DNA damage and coordinate lesion repair through discrete mechanisms, all within the context of a three-dimensional chromatin landscape. Dysregulation or malfunction of any one of the protein constituents in these pathways can contribute to aging and a variety of diseases. While the collective action of these many proteins is what drives DNA repair on the organismal scale, it is the interactions between individual proteins and DNA that facilitate each step of these pathways. In much the same way that ensemble biochemical techniques have characterized the various steps of DNA repair pathways, single-molecule imaging (SMI) approaches zoom in further, characterizing the individual protein-DNA interactions that compose each pathway step. SMI techniques offer the high resolving power needed to characterize the molecular structure and functional dynamics of individual biological interactions on the nanoscale. In this review, we highlight how our lab has used SMI techniques - traditional atomic force microscopy (AFM) imaging in air, high-speed AFM (HS-AFM) in liquids, and the DNA tightrope assay - over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance. We discuss how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated. For each highlighted project, we discuss novel findings made possible by the spatial and temporal resolution offered by these SMI techniques and unique DNA substrates.
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Affiliation(s)
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, NC, USA; Physics Department, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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3
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Wang Y, Zhou L, Guo H, Cheng H. Genome-Wide Analysis of the Rad21/ REC8 Gene Family in Cotton ( Gossypium spp.). Genes (Basel) 2023; 14:genes14050993. [PMID: 37239353 DOI: 10.3390/genes14050993] [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: 04/06/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Cohesin is a ring-shaped protein complex and plays a critical role in sister chromosome cohesion, which is a key event during mitosis and meiosis. Meiotic recombination protein REC8 is one of the subunits of the cohesion complex. Although REC8 genes have been characterized in some plant species, little is known about them in Gossypium. In this study, 89 REC8 genes were identified and analyzed in 16 plant species (including 4 Gossypium species); 12 REC8 genes were identified in Gossypium. hirsutum, 11 in Gossypium. barbadense, 7 in Gossypium. raimondii, and 5 in Gossypium. arboreum. In a phylogenetic analysis, the 89 RCE8 genes clustered into 6 subfamilies (I-VI). The chromosome location, exon-intron structure, and motifs of the REC8 genes in the Gossypium species were also analyzed. Expression patterns of GhREC8 genes in various tissues and under abiotic stress treatments were analyzed based on public RNA-seq data, which indicated that GhREC8 genes might have different functions in growth and development. Additionally, qRT-PCR analysis showed that MeJA, GA, SA, and ABA treatments could induce the expression of GhREC8 genes. In general, the genes of the REC8 gene family of cotton were systematically analyzed, and their potential function in cotton mitosis, meiosis, and in response to abiotic stress and hormones were preliminary predicted, which provided an important basis for further research on cotton development and resistance to abiotic stress.
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Affiliation(s)
- Yali Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lili Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huiming Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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4
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Yoon S, Choi EH, Park SJ, Kim KP. α-Kleisin subunit of cohesin preserves the genome integrity of embryonic stem cells. BMB Rep 2023; 56:108-113. [PMID: 36571142 PMCID: PMC9978357 DOI: 10.5483/bmbrep.2022-0106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 12/22/2022] [Indexed: 10/10/2023] Open
Abstract
Cohesin is a ring-shaped protein complex that comprises the SMC1, SMC3, and α-kleisin proteins, STAG1/2/3 subunits, and auxiliary factors. Cohesin participates in chromatin remodeling, chromosome segregation, DNA replication, and gene expression regulation during the cell cycle. Mitosis-specific α-kleisin factor RAD21 and meiosis-specific α-kleisin factor REC8 are expressed in embryonic stem cells (ESCs) to maintain pluripotency. Here, we demonstrated that RAD21 and REC8 were involved in maintaining genomic stability and modulating chromatin modification in murine ESCs. When the kleisin subunits were depleted, DNA repair genes were downregulated, thereby reducing cell viability and causing replication protein A (RPA) accumulation. This finding suggested that the repair of exposed single-stranded DNA was inefficient. Furthermore, the depletion of kleisin subunits induced DNA hypermethylation by upregulating DNA methylation proteins. Thus, we proposed that the cohesin complex plays two distinct roles in chromatin remodeling and genomic integrity to ensure the maintenance of pluripotency in ESCs. [BMB Reports 2023; 56(2): 108-113].
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Affiliation(s)
- Seobin Yoon
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
| | - Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - Seo Jung Park
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
| | - Keun Pil Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
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5
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Yoon S, Choi EH, Park SJ, Kim KP. α-Kleisin subunit of cohesin preserves the genome integrity of embryonic stem cells. BMB Rep 2023; 56:108-113. [PMID: 36571142 PMCID: PMC9978357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022] Open
Abstract
Cohesin is a ring-shaped protein complex that comprises the SMC1, SMC3, and α-kleisin proteins, STAG1/2/3 subunits, and auxiliary factors. Cohesin participates in chromatin remodeling, chromosome segregation, DNA replication, and gene expression regulation during the cell cycle. Mitosis-specific α-kleisin factor RAD21 and meiosis-specific α-kleisin factor REC8 are expressed in embryonic stem cells (ESCs) to maintain pluripotency. Here, we demonstrated that RAD21 and REC8 were involved in maintaining genomic stability and modulating chromatin modification in murine ESCs. When the kleisin subunits were depleted, DNA repair genes were downregulated, thereby reducing cell viability and causing replication protein A (RPA) accumulation. This finding suggested that the repair of exposed single-stranded DNA was inefficient. Furthermore, the depletion of kleisin subunits induced DNA hypermethylation by upregulating DNA methylation proteins. Thus, we proposed that the cohesin complex plays two distinct roles in chromatin remodeling and genomic integrity to ensure the maintenance of pluripotency in ESCs. [BMB Reports 2023; 56(2): 108-113].
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Affiliation(s)
- Seobin Yoon
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
| | - Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - Seo Jung Park
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
| | - Keun Pil Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
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6
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Bianco F, Lattanzio G, Lorenzini L, Mazzoni M, Clavenzani P, Calzà L, Giardino L, Sternini C, Costanzini A, Bonora E, De Giorgio R. Enteric Neuromyopathies: Highlights on Genetic Mechanisms Underlying Chronic Intestinal Pseudo-Obstruction. Biomolecules 2022; 12:biom12121849. [PMID: 36551277 PMCID: PMC9776039 DOI: 10.3390/biom12121849] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Severe gut motility disorders are characterized by the ineffective propulsion of intestinal contents. As a result, the patients develop disabling/distressful symptoms, such as nausea and vomiting along with altered bowel habits up to radiologically demonstrable intestinal sub-obstructive episodes. Chronic intestinal pseudo-obstruction (CIPO) is a typical clinical phenotype of severe gut dysmotility. This syndrome occurs due to changes altering the morpho-functional integrity of the intrinsic (enteric) innervation and extrinsic nerve supply (hence neuropathy), the interstitial cells of Cajal (ICC) (mesenchymopathy), and smooth muscle cells (myopathy). In the last years, several genes have been identified in different subsets of CIPO patients. The focus of this review is to cover the most recent update on enteric dysmotility related to CIPO, highlighting (a) forms with predominant underlying neuropathy, (b) forms with predominant myopathy, and (c) mitochondrial disorders with a clear gut dysfunction as part of their clinical phenotype. We will provide a thorough description of the genes that have been proven through recent evidence to cause neuro-(ICC)-myopathies leading to abnormal gut contractility patterns in CIPO. The discovery of susceptibility genes for this severe condition may pave the way for developing target therapies for enteric neuro-(ICC)-myopathies underlying CIPO and other forms of gut dysmotility.
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Affiliation(s)
- Francesca Bianco
- Department of Veterinary Sciences, University of Bologna, 40064 Ozzano Emilia, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Giulia Lattanzio
- Department of Veterinary Sciences, University of Bologna, 40064 Ozzano Emilia, Italy
| | - Luca Lorenzini
- Department of Veterinary Sciences, University of Bologna, 40064 Ozzano Emilia, Italy
| | - Maurizio Mazzoni
- Department of Veterinary Sciences, University of Bologna, 40064 Ozzano Emilia, Italy
| | - Paolo Clavenzani
- Department of Veterinary Sciences, University of Bologna, 40064 Ozzano Emilia, Italy
| | - Laura Calzà
- IRET Foundation, 40064 Ozzano Emilia, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Luciana Giardino
- Department of Veterinary Sciences, University of Bologna, 40064 Ozzano Emilia, Italy
- IRET Foundation, 40064 Ozzano Emilia, Italy
| | - Catia Sternini
- UCLA/DDRC, Division of Digestive Diseases, Departments Medicine and Neurobiology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90001, USA
| | - Anna Costanzini
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elena Bonora
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Correspondence: (E.B.); (R.D.G.); Tel.: +39-051-2094761 (E.B.); +39-0532-236631 (R.D.G.)
| | - Roberto De Giorgio
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: (E.B.); (R.D.G.); Tel.: +39-051-2094761 (E.B.); +39-0532-236631 (R.D.G.)
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7
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Saitta C, Rebellato S, Bettini LR, Giudici G, Panini N, Erba E, Massa V, Auer F, Friedrich U, Hauer J, Biondi A, Fazio G, Cazzaniga G. Potential role of STAG1 mutations in genetic predisposition to childhood hematological malignancies. Blood Cancer J 2022; 12:88. [PMID: 35654786 PMCID: PMC9163173 DOI: 10.1038/s41408-022-00683-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/11/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
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8
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Hou W, Li Y, Zhang J, Xia Y, Wang X, Chen H, Lou H. Cohesin in DNA damage response and double-strand break repair. Crit Rev Biochem Mol Biol 2022; 57:333-350. [PMID: 35112600 DOI: 10.1080/10409238.2022.2027336] [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: 08/05/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
Cohesin, a four-subunit ring comprising SMC1, SMC3, RAD21 and SA1/2, tethers sister chromatids by DNA replication-coupled cohesion (RC-cohesion) to guarantee correct chromosome segregation during cell proliferation. Postreplicative cohesion, also called damage-induced cohesion (DI-cohesion), is an emerging critical player in DNA damage response (DDR). In this review, we sum up recent progress on how cohesin regulates the DNA damage checkpoint activation and repair pathway choice, emphasizing postreplicative cohesin loading and DI-cohesion establishment in yeasts and mammals. DI-cohesion and RC-cohesion show distinct features in many aspects. DI-cohesion near or far from the break sites might undergo different regulations and execute different tasks in DDR and DSB repair. Furthermore, some open questions in this field and the significance of this new scenario to our understanding of genome stability maintenance and cohesinopathies are discussed.
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Affiliation(s)
- Wenya Hou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yan Li
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Jiaxin Zhang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yisui Xia
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xueting Wang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Hongxiang Chen
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Huiqiang Lou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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9
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Tuna M, Amos CI, Mills GB. Whole-chromosome arm acquired uniparental disomy in cancer development is a consequence of isochromosome formation. Neoplasia 2022; 25:9-17. [PMID: 35065533 PMCID: PMC8788198 DOI: 10.1016/j.neo.2021.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/09/2023]
Abstract
Using SNP-based microarray data from The Cancer Genome Atlas (TCGA), we investigated isochromosomes (deletion of one arm and duplication of the other arm) and related acquired uniparental disomy in 12 tumor types. We observed a high frequency of isochromosomes (25.98%) across all type of tumors except thyroid cancers. The highest frequency of isochromosomes was found in lung squamous cell carcinoma (54.18%). Moreover, whole-chromosome arm acquired uniparental disomy (aUPD) was common in the deleted arms of isochromosomes. These data are consistent with whole-chromosome arm aUPD likely being a consequence of isochromosomes formation. Our findings implicated aUPD as occurring through error-prone DNA repair of a deleted arm or segment of a chromosome that leads to homozygosity for existing alterations. Isochromosomes were significantly more frequent in TP53 mutated samples than wild types in 6 types of tumors with loss of TP53 function potentially contributing to development of isochromosomes. Isochromosomes are common alterations in cancer, and losing one arm of a chromosome could result in duplication of the lost arm. Duplication of the remaining arm leads promulgation of the effects on any defects in the remaining allele, due to subsequent homozygosity.
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Affiliation(s)
- Musaffe Tuna
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza room 100.23D, Houston, TX 77030, USA.
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza room 100.23D, Houston, TX 77030, USA; Institute of Clinical and Translational Medicine, Baylor College of Medicine, USA
| | - Gordon B Mills
- Department of Cell, Developmental & Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR, USA; Precision Oncology, Knight Cancer Institute, Portland, OR, USA
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10
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Clinical and Pathological Features of Severe Gut Dysmotility. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1383:9-17. [PMID: 36587142 DOI: 10.1007/978-3-031-05843-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Severe gut motility disorders are characterized by ineffective propulsion of intestinal contents. As a result, patients often develop extremely uncomfortable symptoms, ranging from nausea and vomiting along with alterations of bowel habits, up to radiologically confirmed subobstructive episodes. Chronic intestinal pseudo-obstruction (CIPO) is a typical clinical phenotype of severe gut dysmotility due to morphological and functional alterations of the intrinsic (enteric) innervation and extrinsic nerve supply (hence neuropathy), interstitial cells of Cajal (ICCs) (mesenchymopathy), and smooth muscle cells (myopathy). In this chapter, we highlight some molecular mechanisms of CIPO and review the clinical phenotypes and the genetics of the different types of CIPO. Specifically, we will detail the role of some of the most representative genetic mutations involving RAD21, LIG3, and ACTG2 to provide a better understanding of CIPO and related underlying neuropathic or myopathic histopathological abnormalities. This knowledge may unveil targeted strategies to better manage patients with such severe disease.
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11
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Long Q, Liu Z, Gullerova M. Sweet Melody or Jazz? Transcription Around DNA Double-Strand Breaks. Front Mol Biosci 2021; 8:655786. [PMID: 33959637 PMCID: PMC8096065 DOI: 10.3389/fmolb.2021.655786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/22/2021] [Indexed: 12/23/2022] Open
Abstract
Genomic integrity is continuously threatened by thousands of endogenous and exogenous damaging factors. To preserve genome stability, cells developed comprehensive DNA damage response (DDR) pathways that mediate the recognition of damaged DNA lesions, the activation of signaling cascades, and the execution of DNA repair. Transcription has been understood to pose a threat to genome stability in the presence of DNA breaks. Interestingly, accumulating evidence in recent years shows that the transient transcriptional activation at DNA double-strand break (DSB) sites is required for efficient repair, while the rest of the genome exhibits temporary transcription silencing. This genomic shut down is a result of multiple signaling cascades involved in the maintenance of DNA/RNA homeostasis, chromatin stability, and genome fidelity. The regulation of transcription of protein-coding genes and non-coding RNAs has been extensively studied; however, the exact regulatory mechanisms of transcription at DSBs remain enigmatic. These complex processes involve many players such as transcription-associated protein complexes, including kinases, transcription factors, chromatin remodeling complexes, and helicases. The damage-derived transcripts themselves also play an essential role in DDR regulation. In this review, we summarize the current findings on the regulation of transcription at DSBs and discussed the roles of various accessory proteins in these processes and consequently in DDR.
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Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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12
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Michelena J, Pellegrino S, Spegg V, Altmeyer M. Replicated chromatin curtails 53BP1 recruitment in BRCA1-proficient and BRCA1-deficient cells. Life Sci Alliance 2021; 4:4/6/e202101023. [PMID: 33811064 PMCID: PMC8046418 DOI: 10.26508/lsa.202101023] [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: 01/18/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
This study demonstrates how single cell normalization to genome size provides insight into genome function, here in the context of DNA double-strand break repair by 53BP1 versus BRCA1–BARD1. DNA double-strand breaks can be repaired by non-homologous end-joining or homologous recombination. Which pathway is used depends on the balance between the tumor suppressors 53BP1 and BRCA1 and on the availability of an undamaged template DNA for homology-directed repair. How cells switch from a 53BP1-dominated to a BRCA1-governed homologous recombination response as they progress through the cell cycle is incompletely understood. Here we reveal, using high-throughput microscopy and applying single cell normalization to control for increased genome size as cells replicate their DNA, that 53BP1 recruitment to damaged replicated chromatin is inefficient in both BRCA1-proficient and BRCA1-deficient cells. Our results substantiate a dual switch model from a 53BP1-dominated response in unreplicated chromatin to a BRCA1–BARD1–dominated response in replicated chromatin, in which replication-coupled dilution of 53BP1’s binding mark H4K20me2 functionally cooperates with BRCA1–BARD1–mediated suppression of 53BP1 binding. More generally, we suggest that appropriate normalization of single cell data, for example, to DNA content, provides additional layers of information, which can be critical for quantifying and interpreting cellular phenotypes.
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Affiliation(s)
- Jone Michelena
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Stefania Pellegrino
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School (LSZGS), Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School (LSZGS), Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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13
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Yi F, Zhang Y, Wang Z, Wang Z, Li Z, Zhou T, Xu H, Liu J, Jiang B, Li X, Wang L, Bai N, Guo Q, Guan Y, Feng Y, Mao Z, Fan G, Zhang S, Wang C, Cao L, O'Rourke BP, Wang Y, Wu Y, Wu B, You S, Zhang N, Guan J, Song X, Sun Y, Wei S, Cao L. The deacetylation-phosphorylation regulation of SIRT2-SMC1A axis as a mechanism of antimitotic catastrophe in early tumorigenesis. SCIENCE ADVANCES 2021; 7:7/9/eabe5518. [PMID: 33627431 PMCID: PMC7904255 DOI: 10.1126/sciadv.abe5518] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 01/12/2021] [Indexed: 05/05/2023]
Abstract
Improper distribution of chromosomes during mitosis can contribute to malignant transformation. Higher eukaryotes have evolved a mitotic catastrophe mechanism for eliminating mitosis-incompetent cells; however, the signaling cascade and its epigenetic regulation are poorly understood. Our analyses of human cancerous tissue revealed that the NAD-dependent deacetylase SIRT2 is up-regulated in early-stage carcinomas of various organs. Mass spectrometry analysis revealed that SIRT2 interacts with and deacetylates the structural maintenance of chromosomes protein 1 (SMC1A), which then promotes SMC1A phosphorylation to properly drive mitosis. We have further demonstrated that inhibition of SIRT2 activity or continuously increasing SMC1A-K579 acetylation causes abnormal chromosome segregation, which, in turn, induces mitotic catastrophe in cancer cells and enhances their vulnerability to chemotherapeutic agents. These findings suggest that regulation of the SIRT2-SMC1A axis through deacetylation-phosphorylation permits escape from mitotic catastrophe, thus allowing early precursor lesions to overcome oncogenic stress.
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Affiliation(s)
- Fei Yi
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Ying Zhang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Zhijun Wang
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Zhuo Wang
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Ziwei Li
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Tingting Zhou
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Hongde Xu
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Jingwei Liu
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Bo Jiang
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Xiaoman Li
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Liang Wang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Ning Bai
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Qiqiang Guo
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Yi Guan
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Yanling Feng
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Zhiyong Mao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200082, China
| | - Guangjian Fan
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Shengping Zhang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Chuangui Wang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Longyue Cao
- Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Brian P O'Rourke
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yang Wang
- Panjin Liaohe Oilfield Gem Flower Hospital, Panjin, Liaoning Province 124010, China
| | - Yanmei Wu
- Panjin Liaohe Oilfield Gem Flower Hospital, Panjin, Liaoning Province 124010, China
| | - Boquan Wu
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Shilong You
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Naijin Zhang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Junlin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiaoyu Song
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China.
| | - Yingxian Sun
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China.
| | - Shi Wei
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35249-7331, USA.
| | - Liu Cao
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China.
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14
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Idilli AI, Pazzi C, dal Pozzolo F, Roccuzzo M, Mione MC. Rad21 Haploinsufficiency Prevents ALT-Associated Phenotypes in Zebrafish Brain Tumors. Genes (Basel) 2020; 11:E1442. [PMID: 33266037 PMCID: PMC7760354 DOI: 10.3390/genes11121442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 01/17/2023] Open
Abstract
Cohesin is a protein complex consisting of four core subunits responsible for sister chromatid cohesion in mitosis and meiosis, and for 3D genome organization and gene expression through the establishment of long distance interactions regulating transcriptional activity in the interphase. Both roles are important for telomere integrity, but the role of cohesin in telomere maintenance mechanisms in highly replicating cancer cells in vivo is poorly studied. Here we used a zebrafish model of brain tumor, which uses alternative lengthening of telomeres (ALT) as primary telomere maintenance mechanism to test whether haploinsufficiency for Rad21, a member of the cohesin ring, affects ALT development. We found that a reduction in Rad21 levels prevents ALT-associated phenotypes in zebrafish brain tumors and triggers an increase in tert expression. Despite the rescue of ALT phenotypes, tumor cells in rad21+/- fish exhibit an increase in DNA damage foci, probably due to a reduction in double-strand breaks repair efficiency.
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Affiliation(s)
- Aurora Irene Idilli
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Cecilia Pazzi
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Francesca dal Pozzolo
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Michela Roccuzzo
- Advanced Imaging Facility, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy;
| | - Maria Caterina Mione
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
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15
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The molecular basis and disease relevance of non-homologous DNA end joining. Nat Rev Mol Cell Biol 2020; 21:765-781. [PMID: 33077885 DOI: 10.1038/s41580-020-00297-8] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/26/2022]
Abstract
Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism of any type of DNA double-strand break (DSB) during most of the cell cycle and is essential for the development of antigen receptors. Defects in NHEJ result in sensitivity to ionizing radiation and loss of lymphocytes. The most critical step of NHEJ is synapsis, or the juxtaposition of the two DNA ends of a DSB, because all subsequent steps rely on it. Recent findings show that, like the end processing step, synapsis can be achieved through several mechanisms. In this Review, we first discuss repair pathway choice between NHEJ and other DSB repair pathways. We then integrate recent insights into the mechanisms of NHEJ synapsis with updates on other steps of NHEJ, such as DNA end processing and ligation. Finally, we discuss NHEJ-related human diseases, including inherited disorders and neoplasia, which arise from rare failures at different NHEJ steps.
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16
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The meiosis-specific cohesin component stromal antigen 3 promotes cell migration and chemotherapeutic resistance in colorectal cancer. Cancer Lett 2020; 497:112-122. [PMID: 33039558 DOI: 10.1016/j.canlet.2020.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/24/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022]
Abstract
Chromosome instability is one of the hallmarks of cancer. Stromal antigen (STAG) 3 is a core component of the meiosis-specific cohesin complex, which regulates sister chromatid cohesion. Although aberrantly activated genes encoding the cohesin complex have been identified in cancers, little is known about the role of STAG3 in colorectal cancer (CRC). Here, we evaluated the prognostic impact and role of STAG3 in CRC. Analysis of 172 CRC surgical specimens revealed that high STAG3 expression was associated with poor prognosis. STAG3 knockdown inhibited cell migration and increased drug sensitivity to oxaliplatin, 5-fluorouracil, irinotecan hydrochloride hydrate, and BRAF inhibitor in CRC cell lines. The enhanced drug sensitivity was also confirmed in a human organoid established from a CRC specimen. Moreover, suppression of STAG3 increased γH2AX foci. Particularly, in BRAF-mutant CRC cells, STAG3 silencing suppressed the expression of snail family transcriptional repressor 1 and phosphorylation of extracellular signal-regulated kinase via upregulation of dual-specificity phosphatase 6. Our findings suggest that STAG3 is related to poor clinical outcomes and promotes metastasis and chemotherapeutic resistance in CRC. STAG3 may be a novel prognostic marker and potential therapeutic target for CRC.
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17
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Persistent STAG2 mutation despite multimodal therapy in recurrent pediatric glioblastoma. NPJ Genom Med 2020; 5:23. [PMID: 32528726 PMCID: PMC7264170 DOI: 10.1038/s41525-020-0130-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/20/2020] [Indexed: 01/03/2023] Open
Abstract
Similar to their adult counterparts, the prognosis for pediatric patients with high-grade gliomas remains poor. At time of recurrence, treatment options are limited and remain without consensus. This report describes the genetic findings, obtained from whole-exome sequencing of a pediatric patient with glioblastoma who underwent multiple surgical resections and treatment with standard chemoradiation, as well as a novel recombinant poliovirus vaccine therapy. Strikingly, despite the variety of treatments, there was persistence of a tumor clone, characterized by a deleterious STAG2 mutation, whose deficiency in preclinical studies can cause aneuploidy and aberrant mitotic progression, but remains understudied in the clinical setting. There was near elimination of an EGFR mutated and amplified tumor clone after gross total resection, standard chemoradiation, and poliovirus therapy, followed by the emergence of a persistently STAG2 mutated clone, with rare mutations in PTPN11 and BRAF, the latter composed of a novel deleterious mutation previously not reported in pediatric glioblastoma (p.D594G). This was accompanied by a mutation signature shift towards one characterized by increased DNA damage repair defects, consistent with the known underlying STAG2 deficiency. As such, this case represents a novel report following the clinical and genetic progression of a STAG2 mutated glioblastoma, including treatment with a novel and emerging immunotherapy. Although STAG2 deficiency comprises only a small subset of gliomas, this case adds clinical evidence to existing preclinical data supporting a role for STAG2 mutations in gliomagenesis and resistance to standard therapies.
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18
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Lawrimore CJ, Lawrimore J, He Y, Chavez S, Bloom K. Polymer perspective of genome mobilization. Mutat Res 2020; 821:111706. [PMID: 32516654 DOI: 10.1016/j.mrfmmm.2020.111706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
Chromosome motion is an intrinsic feature of all DNA-based metabolic processes and is a particularly well-documented response to both DNA damage and repair. By using both biological and polymer physics approaches, many of the contributing factors of chromatin motility have been elucidated. These include the intrinsic properties of chromatin, such as stiffness, as well as the loop modulators condensin and cohesin. Various biological factors such as external tethering to nuclear domains, ATP-dependent processes, and nucleofilaments further impact chromatin motion. DNA damaging agents that induce double-stranded breaks also cause increased chromatin motion that is modulated by recruitment of repair and checkpoint proteins. Approaches that integrate biological experimentation in conjunction with models from polymer physics provide mechanistic insights into the role of chromatin dynamics in biological function. In this review we discuss the polymer models and the effects of both DNA damage and repair on chromatin motion as well as mechanisms that may underlie these effects.
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Affiliation(s)
- Colleen J Lawrimore
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Josh Lawrimore
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Yunyan He
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Sergio Chavez
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Kerry Bloom
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States.
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19
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Fan L, Xu S, Zhang F, Cui X, Fazli L, Gleave M, Clark DJ, Yang A, Hussain A, Rassool F, Qi J. Histone demethylase JMJD1A promotes expression of DNA repair factors and radio-resistance of prostate cancer cells. Cell Death Dis 2020; 11:214. [PMID: 32238799 PMCID: PMC7113292 DOI: 10.1038/s41419-020-2405-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 01/12/2023]
Abstract
The DNA damage response (DDR) pathway is a promising target for anticancer therapies. The androgen receptor and myeloblastosis transcription factors have been reported to regulate expression of an overlapping set of DDR genes in prostate cancer cells. Here, we found that histone demethylase JMJD1A regulates expression of a different set of DDR genes largely through c-Myc. Inhibition of JMJD1A delayed the resolution of γ-H2AX foci, reduced the formation of foci containing ubiquitin, 53BP1, BRCA1 or Rad51, and inhibited the reporter activity of double-strand break (DSB) repair. Mechanistically, JMJD1A regulated expression of DDR genes by increasing not only the level but also the chromatin recruitment of c-Myc through H3K9 demethylation. Further, we found that ubiquitin ligase HUWE1 induced the K27-/K29-linked noncanonical ubiquitination of JMJD1A at lysine-918. Ablation of the JMJD1A noncanonical ubiquitination lowered DDR gene expression, impaired DSB repair, and sensitized response of prostate cells to irradiation, topoisomerase inhibitors or PARP inhibitors. Thus, development of agents that target JMJD1A or its noncanonical ubiquitination may sensitize the response of prostate cancer to radiotherapy and possibly also genotoxic therapy.
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Affiliation(s)
- Lingling Fan
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Songhui Xu
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Fengbo Zhang
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.,Department of Urology, Beijing Friendship Hospital, Capital Medical University, 100050, Beijing, China
| | - Xiaolu Cui
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.,Department of Urology, First Hospital of China Medical University, 110001, Shenyang, China
| | - Ladan Fazli
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - David J Clark
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.,Department of Anatomy and Neurobiology, University of Maryland, Baltimore, MD, USA.,Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Austin Yang
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.,Department of Anatomy and Neurobiology, University of Maryland, Baltimore, MD, USA
| | - Arif Hussain
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.,Baltimore VA Medical Center, Baltimore, MD, USA
| | - Feyruz Rassool
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.,Department of Radiation Oncology, University of Maryland, Baltimore, MD, USA
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA. .,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.
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20
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Honda T, Nakayama R, Kawahara Y, Yuge L, Ueda K. Kaposi's sarcoma-associated herpesvirus is cell-intrinsically controlled in latency in microgravity. Virus Res 2020; 276:197821. [PMID: 31756357 DOI: 10.1016/j.virusres.2019.197821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
In the next several decades, humans will explore deep space, including Mars. During long-term space flight, astronauts will be exposed to various physical stressors. Among these stressors, microgravity may compromise the immune system. Consistently, the reactivation of several latent herpesviruses has been reported in astronauts. Although herpesvirus infection status is determined by both cell-intrinsic and -extrinsic factors, it remains unclear which factors play major roles in the virus reactivation in microgravity. Here, using Kaposi's sarcoma-associated herpesvirus (KSHV)-infected cells, we found that KSHV is cell-intrinsically controlled in latency in microgravity. Innate immunity appeared to be unaffected in microgravity, while the expression of some restriction factors against KSHV, such as CTCF and AMPK, was upregulated. Collectively, the infected cells in microgravity can control KSHV in latency, possibly by unimpaired innate immunity and upregulated KSHV restriction factors. This is the first pilot study of the conflicts between cell-intrinsic defense systems and viruses in microgravity and provides fundamental information regarding host-virus interactions in microgravity.
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Affiliation(s)
- Tomoyuki Honda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan.
| | - Ryota Nakayama
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yumi Kawahara
- Space Bio-Laboratories Co., Ltd., Minami-ku, Hiroshima 734-0037, Japan
| | - Louis Yuge
- Space Bio-Laboratories Co., Ltd., Minami-ku, Hiroshima 734-0037, Japan; Division of Bio-Environmental Adaptation Sciences, Graduate School of Biomedical and Health Sciences, Hiroshima University, Minami-ku, Hiroshima 734-0037, Japan
| | - Keiji Ueda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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21
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Tai HH, Lagüe M, Thomson S, Aurousseau F, Neilson J, Murphy A, Bizimungu B, Davidson C, Deveaux V, Bègue Y, Wang HY, Xiong X, Jacobs JME. Tuber transcriptome profiling of eight potato cultivars with different cold-induced sweetening responses to cold storage. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:163-176. [PMID: 31756603 DOI: 10.1016/j.plaphy.2019.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/01/2019] [Accepted: 11/02/2019] [Indexed: 05/19/2023]
Abstract
Tubers are vegetative reproduction organs formed from underground extensions of the plant stem. Potato tubers are harvested and stored for months. Storage under cold temperatures of 2-4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS). CIS is undesirable as it leads to darkened color with fry processing. The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance. Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage. Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage. The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases. It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.
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Affiliation(s)
- Helen H Tai
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada.
| | - Martin Lagüe
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - Frédérique Aurousseau
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Jonathan Neilson
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Agnes Murphy
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Benoit Bizimungu
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Charlotte Davidson
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Virginie Deveaux
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Yves Bègue
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Hui Ying Wang
- College of Horticulture and Landscape, Hunan Agriculture Univ, Hunan, Changsha, 410128, China
| | - Xingyao Xiong
- College of Horticulture and Landscape, Hunan Agriculture Univ, Hunan, Changsha, 410128, China
| | - Jeanne M E Jacobs
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, New Zealand
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22
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Dumas SJ, Meta E, Borri M, Goveia J, Rohlenova K, Conchinha NV, Falkenberg K, Teuwen LA, de Rooij L, Kalucka J, Chen R, Khan S, Taverna F, Lu W, Parys M, De Legher C, Vinckier S, Karakach TK, Schoonjans L, Lin L, Bolund L, Dewerchin M, Eelen G, Rabelink TJ, Li X, Luo Y, Carmeliet P. Single-Cell RNA Sequencing Reveals Renal Endothelium Heterogeneity and Metabolic Adaptation to Water Deprivation. J Am Soc Nephrol 2019; 31:118-138. [PMID: 31818909 DOI: 10.1681/asn.2019080832] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/01/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Renal endothelial cells from glomerular, cortical, and medullary kidney compartments are exposed to different microenvironmental conditions and support specific kidney processes. However, the heterogeneous phenotypes of these cells remain incompletely inventoried. Osmotic homeostasis is vitally important for regulating cell volume and function, and in mammals, osmotic equilibrium is regulated through the countercurrent system in the renal medulla, where water exchange through endothelium occurs against an osmotic pressure gradient. Dehydration exposes medullary renal endothelial cells to extreme hyperosmolarity, and how these cells adapt to and survive in this hypertonic milieu is unknown. METHODS We inventoried renal endothelial cell heterogeneity by single-cell RNA sequencing >40,000 mouse renal endothelial cells, and studied transcriptome changes during osmotic adaptation upon water deprivation. We validated our findings by immunostaining and functionally by targeting oxidative phosphorylation in a hyperosmolarity model in vitro and in dehydrated mice in vivo. RESULTS We identified 24 renal endothelial cell phenotypes (of which eight were novel), highlighting extensive heterogeneity of these cells between and within the cortex, glomeruli, and medulla. In response to dehydration and hypertonicity, medullary renal endothelial cells upregulated the expression of genes involved in the hypoxia response, glycolysis, and-surprisingly-oxidative phosphorylation. Endothelial cells increased oxygen consumption when exposed to hyperosmolarity, whereas blocking oxidative phosphorylation compromised endothelial cell viability during hyperosmotic stress and impaired urine concentration during dehydration. CONCLUSIONS This study provides a high-resolution atlas of the renal endothelium and highlights extensive renal endothelial cell phenotypic heterogeneity, as well as a previously unrecognized role of oxidative phosphorylation in the metabolic adaptation of medullary renal endothelial cells to water deprivation.
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Affiliation(s)
- Sébastien J Dumas
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Elda Meta
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Mila Borri
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Jermaine Goveia
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Katerina Rohlenova
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Nadine V Conchinha
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Kim Falkenberg
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Laure-Anne Teuwen
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Laura de Rooij
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Joanna Kalucka
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Rongyuan Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shawez Khan
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Federico Taverna
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Weisi Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Magdalena Parys
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Carla De Legher
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Stefan Vinckier
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Tobias K Karakach
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Luc Schoonjans
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Lin Lin
- Lars Bolund Institute of Regenerative Medicine, Beijing Genomics Institute (BGI)-Qingdao, BGI-Shenzhen, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Beijing Genomics Institute (BGI)-Qingdao, BGI-Shenzhen, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Mieke Dewerchin
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Guy Eelen
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Ton J Rabelink
- Division of Nephrology, Department of Internal Medicine, The Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China;
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Beijing Genomics Institute (BGI)-Qingdao, BGI-Shenzhen, Qingdao, China; .,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China; and.,Qingdao-Europe Advanced Institute for Life Sciences, Beijing Genomics Institute (BGI)-Qingdao, Qingdao, China
| | - Peter Carmeliet
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium; .,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
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23
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Arnould C, Legube G. The Secret Life of Chromosome Loops upon DNA Double-Strand Break. J Mol Biol 2019; 432:724-736. [PMID: 31401119 PMCID: PMC7057266 DOI: 10.1016/j.jmb.2019.07.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022]
Abstract
DNA double-strand breaks (DSBs) are harmful lesions that severely challenge genomic integrity, and recent evidence suggests that DSBs occur more frequently on the genome than previously thought. These lesions activate a complex and multilayered response called the DNA damage response, which allows to coordinate their repair with the cell cycle progression. While the mechanistic details of repair processes have been narrowed, thanks to several decades of intense studies, our knowledge of the impact of DSB on chromatin composition and chromosome architecture is still very sparse. However, the recent development of various tools to induce DSB at annotated loci, compatible with next-generation sequencing-based approaches, is opening a new framework to tackle these questions. Here we discuss the influence of initial and DSB-induced chromatin conformation and the strong potential of 3C-based technologies to decipher the contribution of chromosome architecture during DSB repair.
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Affiliation(s)
- Coline Arnould
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.
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24
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Mao Y, Xue P, Li L, Xu P, Cai Y, Chu X, Jiang P, Zhu S. Bioinformatics analysis of mRNA and miRNA microarray to identify the key miRNA‑gene pairs in small‑cell lung cancer. Mol Med Rep 2019; 20:2199-2208. [PMID: 31257520 PMCID: PMC6691276 DOI: 10.3892/mmr.2019.10441] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023] Open
Abstract
Small-cell lung cancer (SCLC) is a type of lung cancer with early metastasis, and high recurrence and mortality rates. The molecular mechanism is still unclear and further research is required. The aim of the present study was to examine the pathogenesis and potential molecular markers of SCLC by comparing the differential expression of mRNA and microRNA (miRNA) between SCLC tissue and normal lung tissue. A transcriptome sequencing dataset (GSE6044) and a non-coding RNA sequence dataset (GSE19945) were downloaded from the Gene Expression Omnibus (GEO) database. In total, 451 differentially expressed genes (DEGs) and 134 differentially expressed miRNAs (DEMs) were identified using the R limma software package and the GEO2R tool of the GEO, respectively. The Gene Ontology function was significantly enriched for 28 terms, and the Kyoto Encyclopedia of Genes and Genomes database had 19 enrichment pathways, mainly related to ‘cell cycle’, ‘DNA replication’ and ‘oocyte meiosis mismatch repair’. The protein-protein interaction network was constructed using Cytoscape software to identify the molecular mechanisms of key signaling pathways and cellular activities in SCLC. The 1,402 miRNA-gene pairs encompassed 602 target genes of the DEMs using miRNAWalk, which is a bioinformatics platform that predicts DEM target genes and miRNA-gene pairs. There were 19 overlapping genes regulated by 32 miRNAs between target genes of the DEMs and DEGs. Bioinformatics analysis may help to better understand the role of DEGs, DEMs and miRNA-gene pairs in cell proliferation and signal transduction. The related hub genes may be used as biomarkers for the diagnosis and prognosis of SCLC, and as potential drug targets.
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Affiliation(s)
- Yun Mao
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Peng Xue
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing 100102, P.R. China
| | - Linlu Li
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Pengpeng Xu
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Yafang Cai
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Xuelei Chu
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Pengyuan Jiang
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Shijie Zhu
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing 100102, P.R. China
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25
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MicroRNA Expression Changes in Women with Breast Cancer Stratified by DNA Repair Capacity Levels. JOURNAL OF ONCOLOGY 2019; 2019:7820275. [PMID: 31191653 PMCID: PMC6525916 DOI: 10.1155/2019/7820275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/15/2019] [Accepted: 04/17/2019] [Indexed: 12/20/2022]
Abstract
Breast cancer (BC) is the most commonly diagnosed cancer in women worldwide and is the leading cause of death among Hispanic women. Previous studies have shown that women with a low DNA repair capacity (DRC), measured through the nucleotide excision repair (NER) pathway, have an increased BC risk. Moreover, we previously reported an association between DRC levels and the expression of the microRNA (miRNA) let-7b in BC patients. MiRNAs can induce genomic instability by affecting the cell's DNA damage response while influencing the cancer pathobiology. The aim of this pilot study is to identify plasma miRNAs related to variations in DRC levels in BC cases. Hypothesis. Our hypothesis consists in testing whether DRC levels can be correlated with miRNA expression levels. Methods. Plasma samples were selected from 56 (27 cases and 29 controls) women recruited as part of our BC cohort. DRC values were measured in lymphocytes using the host-cell reactivation assay. The samples were divided into two categories: low (≤3.8%) and high (>3.8%) DRC levels. MiRNAs were extracted to perform an expression profile analysis. Results. Forty miRNAs were identified to be BC-related (p<0.05, MW), while 18 miRNAs were found to be differentially expressed among BC cases and controls with high and low DRC levels (p<0.05, KW). Among these candidates are miR-299-5p, miR-29b-3p, miR-302c-3p, miR-373-3p, miR-636, miR-331-5p, and miR-597-5p. Correlation analyses revealed that 4 miRNAs were negatively correlated within BC cases with low DRC (p<0.05, Spearman's correlation). Results from multivariate analyses revealed that the clinicopathological characteristics may not have a direct effect on specific miRNA expression. Conclusion. This pilot study provides evidence of four miRNAs that are negatively regulated in BC cases with low DRC levels. Additional studies are needed in order to have a complete framework regarding the overall DRC levels, miRNA expression profiles, and tumor characteristics.
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26
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Litwin I, Pilarczyk E, Wysocki R. The Emerging Role of Cohesin in the DNA Damage Response. Genes (Basel) 2018; 9:genes9120581. [PMID: 30487431 PMCID: PMC6316000 DOI: 10.3390/genes9120581] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/23/2022] Open
Abstract
Faithful transmission of genetic material is crucial for all organisms since changes in genetic information may result in genomic instability that causes developmental disorders and cancers. Thus, understanding the mechanisms that preserve genome integrity is of fundamental importance. Cohesin is a multiprotein complex whose canonical function is to hold sister chromatids together from S-phase until the onset of anaphase to ensure the equal division of chromosomes. However, recent research points to a crucial function of cohesin in the DNA damage response (DDR). In this review, we summarize recent advances in the understanding of cohesin function in DNA damage signaling and repair. First, we focus on cohesin architecture and molecular mechanisms that govern sister chromatid cohesion. Next, we briefly characterize the main DDR pathways. Finally, we describe mechanisms that determine cohesin accumulation at DNA damage sites and discuss possible roles of cohesin in DDR.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Ewa Pilarczyk
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
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27
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Countryman P, Fan Y, Gorthi A, Pan H, Strickland E, Kaur P, Wang X, Lin J, Lei X, White C, You C, Wirth N, Tessmer I, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Cohesin SA2 is a sequence-independent DNA-binding protein that recognizes DNA replication and repair intermediates. J Biol Chem 2018; 293:1054-1069. [PMID: 29175904 PMCID: PMC5777247 DOI: 10.1074/jbc.m117.806406] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/22/2017] [Indexed: 11/06/2022] Open
Abstract
Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids, mediated by the cohesin protein complex, which also plays crucial roles in diverse genome maintenance pathways. Current models attribute DNA binding by cohesin to entrapment of dsDNA by the cohesin ring subunits (SMC1, SMC3, and RAD21 in humans). However, the biophysical properties and activities of the fourth core cohesin subunit SA2 (STAG2) are largely unknown. Here, using single-molecule atomic force and fluorescence microscopy imaging as well as fluorescence anisotropy measurements, we established that SA2 binds to both dsDNA and ssDNA, albeit with a higher binding affinity for ssDNA. We observed that SA2 can switch between the 1D diffusing (search) mode on dsDNA and stable binding (recognition) mode at ssDNA gaps. Although SA2 does not specifically bind to centromeric or telomeric sequences, it does recognize DNA structures often associated with DNA replication and double-strand break repair, such as a double-stranded end, single-stranded overhang, flap, fork, and ssDNA gap. SA2 loss leads to a defect in homologous recombination-mediated DNA double-strand break repair. These results suggest that SA2 functions at intermediate DNA structures during DNA transactions in genome maintenance pathways. These findings have important implications for understanding the function of cohesin in these pathways.
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Affiliation(s)
| | - Yanlin Fan
- the Department of BioSciences, Rice University, Houston, Texas 77251
| | - Aparna Gorthi
- the Greehey Children's Cancer Research Institute and
- Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, Texas 78229
| | | | | | | | | | - Jiangguo Lin
- From the Physics Department
- the Institute of Biomechanics, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaoying Lei
- the Department of BioSciences, Rice University, Houston, Texas 77251
- the School of Public Health, Shandong University, Jinan 250012, China
| | | | - Changjiang You
- the Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany, and
| | - Nicolas Wirth
- the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Jacob Piehler
- the Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany, and
| | | | - Alexander J R Bishop
- the Greehey Children's Cancer Research Institute and
- Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, Texas 78229
| | - Yizhi Jane Tao
- the Department of BioSciences, Rice University, Houston, Texas 77251
| | - Hong Wang
- From the Physics Department,
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
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28
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Jiang Y, Liu Y, Hu H. Studies on DNA Damage Repair and Precision Radiotherapy for Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:105-123. [PMID: 29282681 DOI: 10.1007/978-981-10-6020-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Radiotherapy acts as an important component of breast cancer management, which significantly decreases local recurrence in patients treated with conservative surgery or with radical mastectomy. On the foundation of technological innovation of radiotherapy setting, precision radiotherapy of cancer has been widely applied in recent years. DNA damage and its repair mechanism are the vital factors which lead to the formation of tumor. Moreover, the status of DNA damage repair in cancer cells has been shown to influence patient response to the therapy, including radiotherapy. Some genes can affect the radiosensitivity of tumor cell by regulating the DNA damage repair pathway. This chapter will describe the potential application of DNA damage repair in precision radiotherapy of breast cancer.
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Affiliation(s)
- Yanhui Jiang
- Department of Radiotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yimin Liu
- Department of Radiotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Hai Hu
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China
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29
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Yi F, Wang Z, Liu J, Zhang Y, Wang Z, Xu H, Li X, Bai N, Cao L, Song X. Structural Maintenance of Chromosomes protein 1: Role in Genome Stability and Tumorigenesis. Int J Biol Sci 2017; 13:1092-1099. [PMID: 28924389 PMCID: PMC5599913 DOI: 10.7150/ijbs.21206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 07/05/2017] [Indexed: 01/05/2023] Open
Abstract
SMC1 (Structural Maintenance of Chromosomes protein 1), well known as one of the SMC superfamily members, has been explored to function in many activities including chromosome dynamics, cell cycle checkpoint, DNA damage repair and genome stability. Upon being properly assembled as part of cohesin, SMC1 can be phosphorylated by ATM and mediate downstream DNA damage repair after ionizing irradiation. Abnormal gene expression or mutation of SMC1 can cause defect in the DNA damage repair pathway, which has been strongly associated with tumorigenesis. Here we focus to discuss SMC1's role in genome stability maintenance and tumorigenesis. Deciphering the underlying molecular mechanism can provide insight into novel strategies for cancer treatment.
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Affiliation(s)
- Fei Yi
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Zhuo Wang
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Jingwei Liu
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Ying Zhang
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Zhijun Wang
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Hongde Xu
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Xiaoman Li
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Ning Bai
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Liu Cao
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Xiaoyu Song
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
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30
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Abstract
Cellular chromosomal DNA is the principal target through which ionising radiation exerts it diverse biological effects. This chapter summarises the relevant DNA damage signalling and repair pathways used by normal and tumour cells in response to irradiation. Strategies for tumour radiosensitisation are reviewed which exploit tumour-specific DNA repair deficiencies or signalling pathway addictions, with a special focus on growth factor signalling, PARP, cancer stem cells, cell cycle checkpoints and DNA replication. This chapter concludes with a discussion of DNA repair-related candidate biomarkers of tumour response which are of crucial importance for implementing precision medicine in radiation oncology.
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31
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Abstract
The correct duplication and transmission of genetic material to daughter cells is the primary objective of the cell division cycle. DNA replication and chromosome segregation present both challenges and opportunities for DNA repair pathways that safeguard genetic information. As a consequence, there is a profound, two-way connection between DNA repair and cell cycle control. Here, we review how DNA repair processes, and DNA double-strand break repair in particular, are regulated during the cell cycle to optimize genomic integrity.
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32
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Cucco F, Musio A. Genome stability: What we have learned from cohesinopathies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2016; 172:171-8. [PMID: 27091086 DOI: 10.1002/ajmg.c.31492] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cohesin is a multiprotein complex involved in many DNA-related processes such as proper chromosome segregation, replication, transcription, and repair. Mutations in cohesin gene pathways are responsible for human diseases, collectively referred to as cohesinopathies. In addition, both cohesin gene expression dysregulation and mutations have been identified in cancer. Cohesinopathy cells are characterized by genome instability (GIN) visualized by a constellation of markers such as chromosome aneuploidies, chromosome aberrations, precocious sister chromatid separation, premature centromere separation, micronuclei formation, and sensitivity to genotoxic drugs. The emerging picture suggests that GIN observed in cohesinopathies may result from the synergistic effects of the multiple cohesin dysfunctions. © 2016 Wiley Periodicals, Inc.
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33
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Gelot C, Guirouilh-Barbat J, Le Guen T, Dardillac E, Chailleux C, Canitrot Y, Lopez BS. The Cohesin Complex Prevents the End Joining of Distant DNA Double-Strand Ends. Mol Cell 2016; 61:15-26. [PMID: 26687679 DOI: 10.1016/j.molcel.2015.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 09/25/2015] [Accepted: 11/02/2015] [Indexed: 02/07/2023]
Abstract
The end joining of distant DNA double-strand ends (DSEs) can produce potentially deleterious rearrangements. We show that depletion of cohesion complex proteins specifically stimulates the end joining (both C-NHEJ and A-EJ) of distant, but not close, I-SceI-induced DSEs in S/G2 phases. At the genome level, whole-exome sequencing showed that ablation of RAD21 or Sororin produces large chromosomal rearrangements (translocation, duplication, deletion). Moreover, cytogenetic analysis showed that RAD21 silencing leads to the formation of chromosome fusions synergistically with replication stress, which generates distant single-ended DSEs. These data reveal a role for the cohesin complex in protecting against genome rearrangements arising from the ligation of distant DSEs in S/G2 phases (both long-range DSEs and those that are only a few kilobases apart), while keeping end joining fully active for close DSEs. Therefore, this role likely involves limitation of DSE motility specifically in S phase, rather than inhibition of the end-joining machinery itself.
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Affiliation(s)
- Camille Gelot
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Josée Guirouilh-Barbat
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Tangui Le Guen
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Elodie Dardillac
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Catherine Chailleux
- Université de Toulouse UPS, CNRS UMR 5088, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), 31062 Toulouse, France
| | - Yvan Canitrot
- Université de Toulouse UPS, CNRS UMR 5088, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), 31062 Toulouse, France
| | - Bernard S Lopez
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France.
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34
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Zhao J, Fu W, Liao H, Dai L, Jiang Z, Pan Y, Huang H, Mo Y, Li S, Yang G, Yin J. The regulatory and predictive functions of miR-17 and miR-92 families on cisplatin resistance of non-small cell lung cancer. BMC Cancer 2015; 15:731. [PMID: 26482648 PMCID: PMC4617718 DOI: 10.1186/s12885-015-1713-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 10/08/2015] [Indexed: 12/20/2022] Open
Abstract
Background Chemotherapy is an important therapeutic approach for non-small cell lung cancer (NSCLC). However, a successful long-term treatment can be prevented by the occurring of chemotherapy resistance frequently, and the molecular mechanisms of chemotherapy resistance in NSCLC remain unclear. In this study, abnormal expressions of miR-17 and miR-92 families are observed in cisplatin-resistant cells, suggesting that miR-17 and miR-92 families are involved in the regulation of cisplatin resistance in NSCLC. Methods miRNA microarray shows that miR-17 and miR-92 families are all down-regulated in cisplatin-resistant A549/DDP cells compared with cisplatin-sensitive A549 cells. The aim of this study is to investigate the regulatory functions of miR-17 and miR-92 families on the formation of cisplatin resistance and the predictive functions of them as biomarkers of platinum-based chemotherapy resistance in NSCLC. Results The low expressions of miR-17 and miR-92 families can maintain cisplatin resistance through the regulation of CDKN1A and RAD21. As a result of high expressions of CDKN1A and RAD21, the inhibition of DNA synthesis and the repair of DNA damage are achieved and these may be two major contributing factors to cisplatin resistance. Moreover, we demonstrate that the expressions of miR-17 and miR-92 families in NSCLC tissues are significantly associated with platinum-based chemotherapy response. Conclusion Our study indicates that miR-17 and miR-92 families play important roles in cisplatin resistance and can be used as potential biomarkers for better predicting the clinical response to platinum-based chemotherapy in NSCLC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1713-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Zhao
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Wenfan Fu
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Hongying Liao
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Lu Dai
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Zeyong Jiang
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Youguang Pan
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Haoda Huang
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Yijun Mo
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Siwen Li
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Guangping Yang
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Jun Yin
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
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Somaiah N, Rothkamm K, Yarnold J. Where Do We Look for Markers of Radiotherapy Fraction Size Sensitivity? Clin Oncol (R Coll Radiol) 2015; 27:570-8. [PMID: 26108884 DOI: 10.1016/j.clon.2015.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 03/31/2015] [Accepted: 06/06/2015] [Indexed: 02/06/2023]
Abstract
The response of human normal tissues to radiotherapy fraction size is often described in terms of cellular recovery, but the causal links between cellular and tissue responses to ionising radiation are not necessarily straightforward. This article reviews the evidence for a cellular basis to clinical fractionation sensitivity in normal tissues and discusses the significance of a long-established inverse association between fractionation sensitivity and proliferative indices. Molecular mechanisms of fractionation sensitivity involving DNA damage repair and cell cycle control are proposed that will probably require modification before being applicable to human cancer. The article concludes by discussing the kind of correlative research needed to test for and validate predictive biomarkers of tumour fractionation sensitivity.
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Affiliation(s)
- N Somaiah
- The Institute of Cancer Research & The Royal Marsden NHS Foundation Trust, London, UK.
| | - K Rothkamm
- University Medical Center, Hamburg-Eppendorf, Germany
| | - J Yarnold
- The Institute of Cancer Research & The Royal Marsden NHS Foundation Trust, London, UK
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Sand LGL, Szuhai K, Hogendoorn PCW. Sequencing Overview of Ewing Sarcoma: A Journey across Genomic, Epigenomic and Transcriptomic Landscapes. Int J Mol Sci 2015; 16:16176-215. [PMID: 26193259 PMCID: PMC4519945 DOI: 10.3390/ijms160716176] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 12/17/2022] Open
Abstract
Ewing sarcoma is an aggressive neoplasm occurring predominantly in adolescent Caucasians. At the genome level, a pathognomonic EWSR1-ETS translocation is present. The resulting fusion protein acts as a molecular driver in the tumor development and interferes, amongst others, with endogenous transcription and splicing. The Ewing sarcoma cell shows a poorly differentiated, stem-cell like phenotype. Consequently, the cellular origin of Ewing sarcoma is still a hot discussed topic. To further characterize Ewing sarcoma and to further elucidate the role of EWSR1-ETS fusion protein multiple genome, epigenome and transcriptome level studies were performed. In this review, the data from these studies were combined into a comprehensive overview. Presently, classical morphological predictive markers are used in the clinic and the therapy is dominantly based on systemic chemotherapy in combination with surgical interventions. Using sequencing, novel predictive markers and candidates for immuno- and targeted therapy were identified which were summarized in this review.
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Affiliation(s)
- Laurens G L Sand
- Department of Pathology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
| | - Pancras C W Hogendoorn
- Department of Pathology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
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Rothkamm K, Barnard S, Moquet J, Ellender M, Rana Z, Burdak-Rothkamm S. DNA damage foci: Meaning and significance. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:491-504. [PMID: 25773265 DOI: 10.1002/em.21944] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
The discovery of DNA damage response proteins such as γH2AX, ATM, 53BP1, RAD51, and the MRE11/RAD50/NBS1 complex, that accumulate and/or are modified in the vicinity of a chromosomal DNA double-strand break to form microscopically visible, subnuclear foci, has revolutionized the detection of these lesions and has enabled studies of the cellular machinery that contributes to their repair. Double-strand breaks are induced directly by a number of physical and chemical agents, including ionizing radiation and radiomimetic drugs, but can also arise as secondary lesions during replication and DNA repair following exposure to a wide range of genotoxins. Here we aim to review the biological meaning and significance of DNA damage foci, looking specifically at a range of different settings in which such markers of DNA damage and repair are being studied and interpreted.
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Affiliation(s)
- Kai Rothkamm
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
- Department of Radiotherapy, Laboratory of Radiation Biology and Experimental Radiation Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen Barnard
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
| | - Jayne Moquet
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
| | - Michele Ellender
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
| | - Zohaib Rana
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
| | - Susanne Burdak-Rothkamm
- Department of Cellular Pathology, Oxford University Hospitals, Headley Way, Headington, Oxford, United Kingdom
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Thompson LL, McManus KJ. A novel multiplexed, image-based approach to detect phenotypes that underlie chromosome instability in human cells. PLoS One 2015; 10:e0123200. [PMID: 25893404 PMCID: PMC4404342 DOI: 10.1371/journal.pone.0123200] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/19/2015] [Indexed: 11/30/2022] Open
Abstract
Chromosome instability (CIN) is characterized by a progressive change in chromosome numbers. It is a characteristic common to virtually all tumor types, and is commonly observed in highly aggressive and drug resistant tumors. Despite this information, the majority of human CIN genes have yet to be elucidated. In this study, we developed and validated a multiplexed, image-based screen capable of detecting three different phenotypes associated with CIN. Large-scale chromosome content changes were detected by quantifying changes in nuclear volumes following RNAi-based gene silencing. Using a DsRED-LacI reporter system to fluorescently label chromosome 11 within a human fibrosarcoma cell line, we were able to detect deviations from the expected number of two foci per nucleus (one focus/labelled chromosome) that occurred following CIN gene silencing. Finally, micronucleus enumeration was performed, as an increase in micronucleus formation is a classic hallmark of CIN. To validate the ability of each assay to detect phenotypes that underlie CIN, we silenced the established CIN gene, SMC1A. Following SMC1A silencing we detected an increase in nuclear volumes, a decrease in the number of nuclei harboring two DsRED-LacI foci, and an increase in micronucleus formation relative to controls (untreated and siGAPDH). Similar results were obtained in an unrelated human fibroblast cell line. The results of this study indicate that each assay is capable of detecting CIN-associated phenotypes, and can be utilized in future experiments to uncover novel human CIN genes, which will provide novel insight into the pathogenesis of cancer.
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Affiliation(s)
- Laura L. Thompson
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Institute of Cell Biology, Winnipeg, Manitoba, Canada
| | - Kirk J. McManus
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Institute of Cell Biology, Winnipeg, Manitoba, Canada
- * E-mail:
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da Costa-Nunes JA, Capitão C, Kozak J, Costa-Nunes P, Ducasa GM, Pontes O, Angelis KJ. The AtRAD21.1 and AtRAD21.3 Arabidopsis cohesins play a synergistic role in somatic DNA double strand break damage repair. BMC PLANT BIOLOGY 2014; 14:353. [PMID: 25511710 PMCID: PMC4273318 DOI: 10.1186/s12870-014-0353-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 11/26/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND The RAD21 cohesin plays, besides its well-recognised role in chromatid cohesion, a role in DNA double strand break (dsb) repair. In Arabidopsis there are three RAD21 paralog genes (AtRAD21.1, AtRAD21.2 and AtRAD21.3), yet only AtRAD21.1 has been shown to be required for DNA dsb damage repair. Further investigation of the role of cohesins in DNA dsb repair was carried out and is here reported. RESULTS We show for the first time that not only AtRAD21.1 but also AtRAD21.3 play a role in somatic DNA dsb repair. Comet data shows that the lack of either cohesins induces a similar high basal level of DNA dsb in the nuclei and a slower DNA dsb repair kinetics in both cohesin mutants. The observed AtRAD21.3 transcriptional response to DNA dsb induction reinforces further the role of this cohesin in DNA dsb repair. The importance of AtRAD21.3 in DNA dsb damage repair, after exposure to DNA dsb damage inducing agents, is notorious and recognisably evident at the phenotypical level, particularly when the AtRAD21.1 gene is also disrupted. CONCLUSIONS Our data demonstrates that both Arabidopsis cohesin (AtRAD21.1 and AtRAD21.3) play a role in somatic DNA dsb repair. Furthermore, the phenotypical data from the atrad21.1 atrad21.3 double mutant indicates that these two cohesins function synergistically in DNA dsb repair. The implications of this data are discussed.
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Affiliation(s)
- José A da Costa-Nunes
- />Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa (UNL), Av. República, Apartado 127, 2781-901 Oeiras, Portugal
| | - Cláudio Capitão
- />Laboratório de Biotecnologia de Células Vegetais, ITQB, UNL, Av. República, Apartado 127, 2781-901 Oeiras, Portugal
- />Current address: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Jaroslav Kozak
- />Molecular Farming Lab., Institute of Experimental Botany AS CR, Na Karlovce 1, 160 00 Praha 6, Czech Republic
| | - Pedro Costa-Nunes
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
- />Current address: Nuclear Organization and Epigenetics Lab., Shanghai Center for Plant Stress Biology (PSC), No. 3888 Chenhua Road, Shanghai, 201602 P. R. China
| | - Gloria M Ducasa
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
| | - Olga Pontes
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
- />Current address: Nuclear Organization and Epigenetics Lab., Shanghai Center for Plant Stress Biology (PSC), No. 3888 Chenhua Road, Shanghai, 201602 P. R. China
| | - Karel J Angelis
- />Molecular Farming Lab., Institute of Experimental Botany AS CR, Na Karlovce 1, 160 00 Praha 6, Czech Republic
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Chen H, Wang ZD, Chen MS, Zhang XQ, Shen LP, Zhang JX, Chen Y. Activation of Toll-like receptors by intestinal microflora reduces radiation-induced DNA damage in mice. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 774:22-8. [PMID: 25440907 DOI: 10.1016/j.mrgentox.2014.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/24/2014] [Accepted: 09/03/2014] [Indexed: 11/19/2022]
Abstract
Activation of Toll-like receptors (TLRs) signaling by intestinal microflora-derived bacterial products plays a key role in injury defence for the host. We investigated the role of TLRs activated by intestinal microflora in radiation-induced DNA damage in mice. We analyzed DNA damage induced by 2Gy γ-ray radiation in an intestinal commensal bacteria-depleted mouse model (CD group), in which TLRs (TLR2/6, TLR4 and TLR5) ligand levels in serum were reduced. Chromosomal aberrations were measured in bone marrow cells and peripheral blood leukocyte comet assays were performed. DNA damage was increased in the CD group compared with the control group. Treatment of mice with TLR agonists (CBLB502, LPS and lipopeptide) 1h before radiation resulted in a significant decrease in DNA damage. Genes induced by TLR5 activation were analyzed; activation of TLRs regulated the expression of Gadd45b, Sod2, and Rad21, which are involved in DNA damage repair. In summary, our data indicate that TLRs activation by intestinal microflora reduces DNA damage induced by radiation and regulates expression of several DNA repair genes.
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Affiliation(s)
- Hong Chen
- Department of Developmental Biology, School of Life Sciences, Central South University, 172 Tong Zipo Road, Changsha 410013, China; Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China
| | - Zhi-Dong Wang
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China.
| | - Mao-Sheng Chen
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China
| | - Xue-Qing Zhang
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China
| | - Li-Ping Shen
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China
| | - Jian-Xiang Zhang
- Department of Developmental Biology, School of Life Sciences, Central South University, 172 Tong Zipo Road, Changsha 410013, China
| | - Ying Chen
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China.
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The genomic landscape of the Ewing Sarcoma family of tumors reveals recurrent STAG2 mutation. PLoS Genet 2014; 10:e1004475. [PMID: 25010205 PMCID: PMC4091782 DOI: 10.1371/journal.pgen.1004475] [Citation(s) in RCA: 299] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/15/2014] [Indexed: 01/19/2023] Open
Abstract
The Ewing sarcoma family of tumors (EFT) is a group of highly malignant small round blue cell tumors occurring in children and young adults. We report here the largest genomic survey to date of 101 EFT (65 tumors and 36 cell lines). Using a combination of whole genome sequencing and targeted sequencing approaches, we discover that EFT has a very low mutational burden (0.15 mutations/Mb) but frequent deleterious mutations in the cohesin complex subunit STAG2 (21.5% tumors, 44.4% cell lines), homozygous deletion of CDKN2A (13.8% and 50%) and mutations of TP53 (6.2% and 71.9%). We additionally note an increased prevalence of the BRCA2 K3326X polymorphism in EFT patient samples (7.3%) compared to population data (OR 7.1, p = 0.006). Using whole transcriptome sequencing, we find that 11% of tumors pathologically diagnosed as EFT lack a typical EWSR1 fusion oncogene and that these tumors do not have a characteristic Ewing sarcoma gene expression signature. We identify samples harboring novel fusion genes including FUS-NCATc2 and CIC-FOXO4 that may represent distinct small round blue cell tumor variants. In an independent EFT tissue microarray cohort, we show that STAG2 loss as detected by immunohistochemistry may be associated with more advanced disease (p = 0.15) and a modest decrease in overall survival (p = 0.10). These results significantly advance our understanding of the genomic and molecular underpinnings of Ewing sarcoma and provide a foundation towards further efforts to improve diagnosis, prognosis, and precision therapeutics testing. The Ewing sarcoma family of tumors is a group of aggressive cancers that primarily affects the pediatric and young adult population. Increasingly, genomics are being used to better define the disease biology and to identify targets for therapy in many cancer types. Here, we report one of the first and largest genomic studies to date in the Ewing sarcoma family of tumors. Using a combination of modern sequencing techniques in >100 samples, we discover that Ewing sarcomas have a genome that is less complex compared to most cancer types previously surveyed. We find that this cancer is frequently affected by mutations in STAG2, a gene that has recently gained attention due to its importance in the biology of several cancer types. We show that Ewing sarcoma patients whose tumors are affected by STAG2 loss may have a worse prognosis. Additionally, we identify a subset of tumors that were diagnosed as Ewing sarcoma that appear to be distinct from the majority based on genetic and molecular characteristics. Our findings help to define the genetic landscape of Ewing sarcoma and provide a starting point for improving individualization of diagnosis, prognosis and treatment in this cancer.
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Solomon DA, Kim JS, Waldman T. Cohesin gene mutations in tumorigenesis: from discovery to clinical significance. BMB Rep 2014; 47:299-310. [PMID: 24856830 PMCID: PMC4163871 DOI: 10.5483/bmbrep.2014.47.6.092] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 12/30/2022] Open
Abstract
Cohesin is a multi-protein complex composed of four core subunits (SMC1A, SMC3, RAD21, and either STAG1 or STAG2) that is responsible for the cohesion of sister chromatids following DNA replication until its cleavage during mitosis thereby enabling faithful segregation of sister chromatids into two daughter cells. Recent cancer genomics analyses have discovered a high frequency of somatic mutations in the genes encoding the core cohesin subunits as well as cohesin regulatory factors (e.g. NIPBL, PDS5B, ESPL1) in a select subset of human tumors including glioblastoma, Ewing sarcoma, urothelial carcinoma, acute myeloid leukemia, and acute megakaryoblastic leukemia. Herein we review these studies including discussion of the functional significance of cohesin inactivation in tumorigenesis and potential therapeutic mechanisms to selectively target cancers harboring cohesin mutations.
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MESH Headings
- Carcinogenesis
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Humans
- Leukemia, Megakaryoblastic, Acute/genetics
- Leukemia, Megakaryoblastic, Acute/metabolism
- Leukemia, Megakaryoblastic, Acute/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mutation
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Protein Subunits/genetics
- Protein Subunits/metabolism
- Urologic Neoplasms/genetics
- Urologic Neoplasms/metabolism
- Urologic Neoplasms/pathology
- Cohesins
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Affiliation(s)
- David A. Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, United States
| | - Jung-Sik Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, United States
| | - Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, United States
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Becker A, Durante M, Taucher-Scholz G, Jakob B. ATM alters the otherwise robust chromatin mobility at sites of DNA double-strand breaks (DSBs) in human cells. PLoS One 2014; 9:e92640. [PMID: 24651490 PMCID: PMC3961414 DOI: 10.1371/journal.pone.0092640] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/23/2014] [Indexed: 11/18/2022] Open
Abstract
Ionizing radiation induces DNA double strand breaks (DSBs) which can lead to the formation of chromosome rearrangements through error prone repair. In mammalian cells the positional stability of chromatin contributes to the maintenance of genome integrity. DSBs exhibit only a small, submicron scale diffusive mobility, but a slight increase in the mobility of chromatin domains by the induction of DSBs might influence repair fidelity and the formation of translocations. The radiation-induced local DNA decondensation in the vicinity of DSBs is one factor potentially enhancing the mobility of DSB-containing chromatin domains. Therefore in this study we focus on the influence of different chromatin modifying proteins, known to be activated by the DNA damage response, on the mobility of DSBs. IRIF (ionizing radiation induced foci) in U2OS cells stably expressing 53BP1-GFP were used as a surrogate marker of DSBs. Low angle charged particle irradiation, known to trigger a pronounced DNA decondensation, was used for the defined induction of linear tracks of IRIF. Our results show that movement of IRIF is independent of the investigated chromatin modifying proteins like ACF1 or PARP1 and PARG. Also depletion of proteins that tether DNA strands like MRE11 and cohesin did not alter IRIF dynamics significantly. Inhibition of ATM, a key component of DNA damage response signaling, resulted in a pronounced confinement of DSB mobility, which might be attributed to a diminished radiation induced decondensation. This confinement following ATM inhibition was confirmed using X-rays, proving that this effect is not restricted to densely ionizing radiation. In conclusion, repair sites of DSBs exhibit a limited mobility on a small spatial scale that is mainly unaffected by depletion of single remodeling or DNA tethering proteins. However, it relies on functional ATM kinase which is considered to influence the chromatin structure after irradiation.
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Affiliation(s)
- Annabelle Becker
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Marco Durante
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- Technical University of Darmstadt, Darmstadt, Germany
| | - Gisela Taucher-Scholz
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- Technical University of Darmstadt, Darmstadt, Germany
| | - Burkhard Jakob
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
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Bailey ML, O'Neil NJ, van Pel DM, Solomon DA, Waldman T, Hieter P. Glioblastoma cells containing mutations in the cohesin component STAG2 are sensitive to PARP inhibition. Mol Cancer Ther 2014; 13:724-32. [PMID: 24356817 PMCID: PMC4130349 DOI: 10.1158/1535-7163.mct-13-0749] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Recent data have identified STAG2, a core subunit of the multifunctional cohesin complex, as a highly recurrently mutated gene in several types of cancer. We sought to identify a therapeutic strategy to selectively target cancer cells harboring inactivating mutations of STAG2 using two independent pairs of isogenic glioblastoma cell lines containing either an endogenous mutant STAG2 allele or a wild-type STAG2 allele restored by homologous recombination. We find that mutations in STAG2 are associated with significantly increased sensitivity to inhibitors of the DNA repair enzyme PARP. STAG2-mutated, PARP-inhibited cells accumulated in G2 phase and had a higher percentage of micronuclei, fragmented nuclei, and chromatin bridges compared with wild-type STAG2 cells. We also observed more 53BP1 foci in STAG2-mutated glioblastoma cells, suggesting that these cells have defects in DNA repair. Furthermore, cells with mutations in STAG2 were more sensitive than cells with wild-type STAG2 when PARP inhibitors were used in combination with DNA-damaging agents. These data suggest that PARP is a potential target for tumors harboring inactivating mutations in STAG2, and strongly recommend that STAG2 status be determined and correlated with therapeutic response to PARP inhibitors, both prospectively and retrospectively, in clinical trials.
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Affiliation(s)
- Melanie L Bailey
- Corresponding Author: Philip Hieter, Michael Smith Laboratories, 2185 East Mall, Room 323, University of British Columbia, Vancouver, British Columbia, Canada V6T1Z4.
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Yuan L, Yang X, Auman D, Makaroff CA. Expression of Epitope-Tagged SYN3 Cohesin Proteins Can Disrupt Meiosis in Arabidopsis. J Genet Genomics 2014; 41:153-64. [DOI: 10.1016/j.jgg.2013.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 11/23/2013] [Accepted: 11/26/2013] [Indexed: 12/13/2022]
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RAD21 cohesin overexpression is a prognostic and predictive marker exacerbating poor prognosis in KRAS mutant colorectal carcinomas. Br J Cancer 2014; 110:1606-13. [PMID: 24548858 PMCID: PMC3960611 DOI: 10.1038/bjc.2014.31] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/26/2013] [Accepted: 01/07/2014] [Indexed: 12/27/2022] Open
Abstract
Background: RAD21 is a component of the cohesion complex and is integral to chromosome segregation and error-free DNA repair. RAD21 is functionally important in tumour progression but its role in colorectal carcinoma (CRC) is unclear. We therefore assessed its clinicopathological and prognostic significance in CRC, as well as its effect on chemosensitivity. Methods: A retrospective observation study examined RAD21 expression in 652 CRCs using a tissue microarray approach. Correlation with clinicopathological factors including gender, tumour grade, mucinous subtype, TNM stage, disease-specific survival (DSS), BRAF and KRAS mutation status, tumour p53 immunostaining, tumour microsatellite instability and tumour CpG island methylator phenotype was performed. Colorectal cancer cell clones with stable RAD21 knockdown were generated and tested for cellular sensitivity to conventional chemotherapeutic drugs. Results: RAD21 expression was significantly correlated with male gender (56.7% vs 43.3%, P=0.02), well-differentiated histology (14.4% vs 4.0%, P=0.0001), higher T-stage (36.1% vs 27.0%, P=0.01), presence of metastasis (18.8% vs 12.6%, P=0.03), and shorter DSS (hazard ratio (HR) 1.4, 95% CI 1.1 to 1.9, P=0.01) in both univariate and multivariate analysis. RAD21 expression was associated with shorter DSS in patients with KRAS mutant tumours (HR:2.6, 95% CI:1.4–4.3, P=0.001) and in patients receiving adjuvant chemoradiotherapy (HR:1.9, 95% CI:1.2–3.0, P=0.008). Colorectal cancer cells with RAD21 knockdown exhibited enhanced sensitivity to 5-fluorouracil, either alone or in combination with oxaliplatin. Conclusions: RAD21 expression in CRC is associated with aggressive disease especially in KRAS mutant tumours and resistance to chemoradiotherapy. RAD21 may be an important novel therapeutic target.
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Covo S, Puccia CM, Argueso JL, Gordenin DA, Resnick MA. The sister chromatid cohesion pathway suppresses multiple chromosome gain and chromosome amplification. Genetics 2014; 196:373-84. [PMID: 24298060 PMCID: PMC3914611 DOI: 10.1534/genetics.113.159202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/11/2013] [Indexed: 11/18/2022] Open
Abstract
Gain or loss of chromosomes resulting in aneuploidy can be important factors in cancer and adaptive evolution. Although chromosome gain is a frequent event in eukaryotes, there is limited information on its genetic control. Here we measured the rates of chromosome gain in wild-type yeast and sister chromatid cohesion (SCC) compromised strains. SCC tethers the newly replicated chromatids until anaphase via the cohesin complex. Chromosome gain was measured by selecting and characterizing copper-resistant colonies that emerged due to increased copies of the metallothionein gene CUP1. Although all defective SCC diploid strains exhibited increased rates of chromosome gain, there were 15-fold differences between them. Of all mutants examined, a hypomorphic mutation at the cohesin complex caused the highest rate of chromosome gain while disruption of WPL1, an important regulator of SCC and chromosome condensation, resulted in the smallest increase in chromosome gain. In addition to defects in SCC, yeast cell type contributed significantly to chromosome gain, with the greatest rates observed for homozygous mating-type diploids, followed by heterozygous mating type, and smallest in haploids. In fact, wpl1-deficient haploids did not show any difference in chromosome gain rates compared to wild-type haploids. Genomic analysis of copper-resistant colonies revealed that the "driver" chromosome for which selection was applied could be amplified to over five copies per diploid cell. In addition, an increase in the expected driver chromosome was often accompanied by a gain of a small number of other chromosomes. We suggest that while chromosome gain due to SCC malfunction can have negative effects through gene imbalance, it could also facilitate opportunities for adaptive changes. In multicellular organisms, both factors could lead to somatic diseases including cancer.
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Affiliation(s)
- Shay Covo
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Christopher M. Puccia
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Dmitry A. Gordenin
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael A. Resnick
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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Mahmood SF, Gruel N, Chapeaublanc E, Lescure A, Jones T, Reyal F, Vincent-Salomon A, Raynal V, Pierron G, Perez F, Camonis J, Del Nery E, Delattre O, Radvanyi F, Bernard-Pierrot I. A siRNA screen identifies RAD21, EIF3H, CHRAC1 and TANC2 as driver genes within the 8q23, 8q24.3 and 17q23 amplicons in breast cancer with effects on cell growth, survival and transformation. Carcinogenesis 2013; 35:670-82. [PMID: 24148822 DOI: 10.1093/carcin/bgt351] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
RNA interference has boosted the field of functional genomics, by making it possible to carry out 'loss-of-function' screens in cultured cells. Here, we performed a small interfering RNA screening, in three breast cancer cell lines, for 101 candidate driver genes overexpressed in amplified breast tumors and belonging to eight amplicons on chromosomes 8q and 17q, investigating their role in cell survival/proliferation. This screening identified eight driver genes that were amplified, overexpressed and critical for breast tumor cell proliferation or survival. They included the well-described oncogenic driver genes for the 17q12 amplicon, ERBB2 and GRB7. Four of six other candidate driver genes-RAD21 and EIF3H, both on chromosome 8q23, CHRAC1 on chromosome 8q24.3 and TANC2 on chromosome 17q23-were confirmed to be driver genes regulating the proliferation/survival of clonogenic breast cancer cells presenting an amplification of the corresponding region. Indeed, knockdown of the expression of these genes decreased cell viability, through both cell cycle arrest and apoptosis induction, and inhibited the formation of colonies in anchorage-independent conditions, in soft agar. Strategies for inhibiting the expression of these genes or the function of the proteins they encode are therefore of potential value for the treatment of breast cancers presenting amplifications of the corresponding genomic region.
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Laugsch M, Seebach J, Schnittler H, Jessberger R. Imbalance of SMC1 and SMC3 cohesins causes specific and distinct effects. PLoS One 2013; 8:e65149. [PMID: 23776448 PMCID: PMC3680458 DOI: 10.1371/journal.pone.0065149] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 04/23/2013] [Indexed: 11/24/2022] Open
Abstract
SMC1 and SMC3 form a high-affinity heterodimer, which provides an open backbone of the cohesin ring, to be closed by a kleisin protein. RNAi mediated knock-down of either one heterodimer partner, SMC1 or SMC3, is expected to cause very similar if not identical phenotypes. However, we observed highly distinct, protein-specific phenotypes. Upon knock-down of human SMC1, much of SMC3 remains stable, accumulates in the cytoplasm and does not associate with other cohesin proteins. Most of the excess nuclear SMC3 is highly mobile and not or only weakly chromosome-associated. In contrast, human SMC3 knock-down rendered SMC1 instable without cytoplasmic accumulation. As observed by differential protein extraction and in FRAP experiments the remaining SMC1 or SMC3 proteins in the respective SMC1 or SMC3 knock-down experiments constituted a cohesin pool, which is associated with chromatin with highest affinity, likely the least expendable. Expression of bovine EGFP-SMC1 or mouse EGFP-SMC3 in human cells under conditions of human SMC1 or SMC3 knock-down rescued the respective phenotypes, but in untreated cells over-expressed exogenous SMC proteins mis-localized. Paucity of either one of the SMC proteins causes RAD21 degradation. These results argue for great caution in interpreting SMC1 and SMC3 RNAi or over-expression experiments. Under challenged conditions these two proteins unexpectedly behave differently, which may have biological consequences for regulation of cohesin-associated functions and for human cohesin pathologies.
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Affiliation(s)
- Magdalena Laugsch
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Jochen Seebach
- Dept. of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Hans Schnittler
- Dept. of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
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Homologous recombination mediates cellular resistance and fraction size sensitivity to radiation therapy. Radiother Oncol 2013; 108:155-61. [PMID: 23746696 DOI: 10.1016/j.radonc.2013.05.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/30/2013] [Accepted: 05/02/2013] [Indexed: 01/07/2023]
Abstract
PURPOSE Cellular sensitivity to radiotherapy total dose and fraction size is strongly influenced by DNA double strand break (DSB) repair. Here, we investigate response to radiotherapy fraction size using CHO cell lines deficient in specific DNA repair pathways in response to radiation induced DNA double strand breaks (DSB). EXPERIMENTAL DESIGN We irradiated CHO cell lines, AA8 (WT), irs1SF (XRCC3-), V3-3 (DNA-PKcs-) and EM9 (XRCC1-) with 16 Gy in 1 Gy daily fractions over 3 weeks or 16 Gy in 4 Gy daily fractions over 4 days, and studied clonogenic survival, DNA DSB repair kinetics (RAD51 and 53BP1 foci staining) and cell cycle profiles (flow cytometry). RESULTS In response to fractionated radiotherapy, wild-type and DNA repair defective cells accumulated in late S/G2 phase. In cells proficient in homologous recombination (HR), accumulation in S/G2 resulted in reduced sensitivity to fraction size and increased cellular resistance (clonogenic survival). Sensitivity to fraction size was also lost in NHEJ-defective V3-3 cells, which likely rely on functional HR. By contrast, HR-defective irs1SF cells, with functional NHEJ, remained equally sensitive to fractionation throughout the 3-week treatment. CONCLUSIONS The high fidelity of HR, which is independent of induced DNA damage level, is postulated to explain the low fractionation sensitivity and cellular resistance of cells in S/G2 phase. In conclusion, our results suggest that HR mediates resistance to fractionated radiotherapy, an observation that may help future efforts to improve radiotherapy outcome.
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