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Kannan A, Gangadharan Leela S, Branzei D, Gangwani L. Role of senataxin in R-loop-mediated neurodegeneration. Brain Commun 2024; 6:fcae239. [PMID: 39070547 PMCID: PMC11277865 DOI: 10.1093/braincomms/fcae239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/14/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
Senataxin is an RNA:DNA helicase that plays an important role in the resolution of RNA:DNA hybrids (R-loops) formed during transcription. R-loops are involved in the regulation of biological processes such as immunoglobulin class switching, gene expression and DNA repair. Excessive accumulation of R-loops results in DNA damage and loss of genomic integrity. Senataxin is critical for maintaining optimal levels of R-loops to prevent DNA damage and acts as a genome guardian. Within the nucleus, senataxin interacts with various RNA processing factors and DNA damage response and repair proteins. Senataxin interactors include survival motor neuron and zinc finger protein 1, with whom it co-localizes in sub-nuclear bodies. Despite its ubiquitous expression, mutations in senataxin specifically affect neurons and result in distinct neurodegenerative diseases such as amyotrophic lateral sclerosis type 4 and ataxia with oculomotor apraxia type 2, which are attributed to the gain-of-function and the loss-of-function mutations in senataxin, respectively. In addition, low levels of senataxin (loss-of-function) in spinal muscular atrophy result in the accumulation of R-loops causing DNA damage and motor neuron degeneration. Senataxin may play multiple functions in diverse cellular processes; however, its emerging role in R-loop resolution and maintenance of genomic integrity is gaining attention in the field of neurodegenerative diseases. In this review, we highlight the role of senataxin in R-loop resolution and its potential as a therapeutic target to treat neurodegenerative diseases.
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Affiliation(s)
| | - Shyni Gangadharan Leela
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Dana Branzei
- The AIRC Institute of Molecular Oncology Foundation, IFOM ETS, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia 27100, Italy
| | - Laxman Gangwani
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
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Guo T, Miao C, Liu Z, Duan J, Ma Y, Zhang X, Yang W, Xue M, Deng Q, Guo P, Xi Y, Yang X, Huang X, Ge W. Impaired dNKAP function drives genome instability and tumorigenic growth in Drosophila epithelia. J Mol Cell Biol 2024; 15:mjad078. [PMID: 38059855 PMCID: PMC11070879 DOI: 10.1093/jmcb/mjad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
Mutations or dysregulated expression of NF-kappaB-activating protein (NKAP) family genes have been found in human cancers. How NKAP family gene mutations promote tumor initiation and progression remains to be determined. Here, we characterized dNKAP, the Drosophila homolog of NKAP, and showed that impaired dNKAP function causes genome instability and tumorigenic growth in a Drosophila epithelial tumor model. dNKAP-knockdown wing imaginal discs exhibit tumorigenic characteristics, including tissue overgrowth, cell-invasive behavior, abnormal cell polarity, and cell adhesion defects. dNKAP knockdown causes both R-loop accumulation and DNA damage, indicating the disruption of genome integrity. Further analysis showed that dNKAP knockdown induces c-Jun N-terminal kinase (JNK)-dependent apoptosis and causes aberrant cell proliferation in distinct cell populations. Activation of the Notch and JAK/STAT signaling pathways contributes to the tumorigenic growth of dNKAP-knockdown tissues. Furthermore, JNK signaling is essential for dNKAP depletion-mediated cell invasion. Transcriptome analysis of dNKAP-knockdown tissues confirmed the misregulation of signaling pathways involved in promoting tumorigenesis and revealed abnormal regulation of metabolic pathways. dNKAP knockdown and oncogenic Ras, Notch, or Yki mutations show synergies in driving tumorigenesis, further supporting the tumor-suppressive role of dNKAP. In summary, this study demonstrates that dNKAP plays a tumor-suppressive role by preventing genome instability in Drosophila epithelia and thus provides novel insights into the roles of human NKAP family genes in tumor initiation and progression.
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Affiliation(s)
- Ting Guo
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Chen Miao
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Zhonghua Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingwei Duan
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yanbin Ma
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Xiao Zhang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Weiwei Yang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Maoguang Xue
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qiannan Deng
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Pengfei Guo
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yongmei Xi
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaohang Yang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
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Wheeler EC, Martin BJE, Doyle WC, Neaher S, Conway CA, Pitton CN, Gorelov RA, Donahue M, Jann JC, Abdel-Wahab O, Taylor J, Seiler M, Buonamici S, Pikman Y, Garcia JS, Belizaire R, Adelman K, Tothova Z. Splicing modulators impair DNA damage response and induce killing of cohesin-mutant MDS and AML. Sci Transl Med 2024; 16:eade2774. [PMID: 38170787 PMCID: PMC11222919 DOI: 10.1126/scitranslmed.ade2774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/08/2023] [Indexed: 01/05/2024]
Abstract
Splicing modulation is a promising treatment strategy pursued to date only in splicing factor-mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in cancer, including myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (AML), where they are associated with poor outcomes. Here, we showed that cohesin mutations are biomarkers of sensitivity to drugs targeting the splicing factor 3B subunit 1 (SF3B1) H3B-8800 and E-7107. We identified drug-induced alterations in splicing, and corresponding reduced gene expression, of a number of DNA repair genes, including BRCA1 and BRCA2, as the mechanism underlying this sensitivity in cell line models, primary patient samples and patient-derived xenograft (PDX) models of AML. We found that DNA damage repair genes are particularly sensitive to exon skipping induced by SF3B1 modulators due to their long length and large number of exons per transcript. Furthermore, we demonstrated that treatment of cohesin-mutant cells with SF3B1 modulators not only resulted in impaired DNA damage response and accumulation of DNA damage, but it sensitized cells to subsequent killing by poly(ADP-ribose) polymerase (PARP) inhibitors and chemotherapy and led to improved overall survival of PDX models of cohesin-mutant AML in vivo. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS and AML.
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Affiliation(s)
- Emily C. Wheeler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Benjamin J. E. Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - William C. Doyle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Sofia Neaher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Caroline A. Conway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Caroline N. Pitton
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Rebecca A. Gorelov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Melanie Donahue
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Johann C. Jann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Justin Taylor
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael Seiler
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Silvia Buonamici
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02215 USA
| | - Jacqueline S. Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Roger Belizaire
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Karen Adelman
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
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4
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Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
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Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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5
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Hu MZ, Dai ZZ, Ji HY, Zheng AQ, Liang H, Shen MM, Liu JN, Tang KF, Zhu SJ, Wang KJ. Upregulation of FAM50A promotes cancer development. Med Oncol 2023; 40:217. [PMID: 37393403 DOI: 10.1007/s12032-023-02072-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/24/2023] [Indexed: 07/03/2023]
Abstract
FAM50A encodes a nuclear protein involved in mRNA processing; however, its role in cancer development remains unclear. Herein, we conducted an integrative pan-cancer analysis using The Cancer Genome Atlas, Genotype-Tissue Expression, and the Clinical Proteomic Tumor Analysis Consortium databases. Based on the gene expression data from TCGA and GTEx databases, we compared FAM50A mRNA levels in 33 types of human cancer tissues to those in corresponding normal tissues and found that FAM50A mRNA level was upregulated in 20 of the 33 types of common cancer tissues. Then, we compared the DNA methylation status of the FAM50A promoter in tumor tissues to that in corresponding normal tissues. FAM50A upregulation was accompanied by promoter hypomethylation in 8 of the 20 types of tumor tissues, suggesting that promoter hypomethylation contributes to the upregulation of FAM50A in these cancer tissues. Elevated FAM50A expression in 10 types of cancer tissues was associated with poor prognosis in patients with cancer. FAM50A expression was positively correlated with CD4+ T-lymphocyte and dendritic cell infiltration in cancer tissues but was negatively correlated with CD8+ T-cell infiltration in cancer tissues. FAM50A knockdown caused DNA damage, induced interferon beta and interleukin-6 expression, and repressed the proliferation, invasion, and migration of cancer cells. Our findings indicate that FAM50A might be useful in cancer detection, reveal insights into its role in cancer development, and may contribute to the development of cancer diagnostics and treatments.
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Affiliation(s)
- Mei-Zhen Hu
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Zhi-Zheng Dai
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Hong-Yu Ji
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - An-Qi Zheng
- The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, 325015, People's Republic of China
| | - Hang Liang
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Mei-Mei Shen
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Choqing, 400016, People's Republic of China
| | - Jun-Nan Liu
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Kai-Fu Tang
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Shu-Juan Zhu
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Ke-Jian Wang
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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6
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Liu C, Xu W, Wang L, Yang Z, Li K, Hu J, Chen Y, Zhang R, Xiao S, Liu W, Wei H, Chen JY, Sun Q, Li W. Dual roles of R-loops in the formation and processing of programmed DNA double-strand breaks during meiosis. Cell Biosci 2023; 13:82. [PMID: 37170281 PMCID: PMC10173651 DOI: 10.1186/s13578-023-01026-2] [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: 01/03/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Meiotic recombination is initiated by Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions called hotspots; however, the factor(s) that specify the positions of meiotic DSB hotspots remain unclear. RESULTS Here, we examined the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, during budding yeast meiosis and found that the R-loops were changed dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage and found that these R-loops were associated with meiotic recombination during yeast meiosis. We show that transcription-replication head-on collisions could promote R-loop formation during meiotic DNA replication, and these R-loops are associated with Spo11. Furthermore, meiotic recombination hotspots can be eliminated by reversing the direction of transcription or replication, and reversing both of these directions can reconstitute the hotspots. CONCLUSIONS Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication.
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Affiliation(s)
- Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Liying Wang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yinghong Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruidan Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sai Xiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenwen Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huafang Wei
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
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Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
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8
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Muzio L, Ghirelli A, Agosta F, Martino G. Novel therapeutic approaches for motor neuron disease. HANDBOOK OF CLINICAL NEUROLOGY 2023; 196:523-537. [PMID: 37620088 DOI: 10.1016/b978-0-323-98817-9.00027-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that leads to the neurodegeneration and death of upper and lower motor neurons (MNs). Although MNs are the main cells involved in the process of neurodegeneration, a growing body of evidence points toward other cell types as concurrent to disease initiation and propagation. Given the current absence of effective therapies, the quest for other therapeutic targets remains open and still challenges the scientific community. Both neuronal and extra-neuronal mechanisms of cellular stress and damage have been studied and have posed the basis for the development of novel therapies that have been investigated on both animal models and humans. In this chapter, a thorough review of the main mechanisms of cellular damage and the respective therapeutic attempts targeting them is reported. The main areas covered include neuroinflammation, protein aggregation, RNA metabolism, and oxidative stress.
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Affiliation(s)
- Luca Muzio
- San Raffaele Scientific Institute, Division of Neuroscience, InsPE, Milan, Italy
| | - Alma Ghirelli
- San Raffaele Scientific Institute, Division of Neuroscience, InsPE, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Agosta
- San Raffaele Scientific Institute, Division of Neuroscience, InsPE, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Gianvito Martino
- San Raffaele Scientific Institute, Division of Neuroscience, InsPE, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
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9
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Zhao W, Pei Q, Zhu Y, Zhan D, Mao G, Wang M, Qiu Y, Zuo K, Pei H, Sun LQ, Wen M, Tan R. The Association of R-Loop Binding Proteins Subtypes with CIN Implicates Therapeutic Strategies in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14225607. [PMID: 36428700 PMCID: PMC9688457 DOI: 10.3390/cancers14225607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022] Open
Abstract
Chromosomal instability (CIN) covers approximately 65 to 70% of colorectal cancer patients and plays an essential role in cancer progression. However, the molecular features and therapeutic strategies related to those patients are still controversial. R-loop binding proteins (RLBPs) exert significant roles in transcription and replication. Here, integrative colorectal cancer proteogenomic analysis identified two RLBPs subtypes correlated with distinct prognoses. Cluster I (CI), represented by high expression of RLBPs, was associated with the CIN phenotype. While Cluster II (CII) with the worst prognosis and low expression of RLBPs was composed of a high percentage of patients with mucinous adenocarcinoma or right-sided colon cancer. The molecular feature analysis revealed that the active RNA processing, ribosome synthesis, and aberrant DNA damage repair were shown in CI, a high inflammatory signaling pathway, and lymphocyte infiltration was enriched in CII. In addition, we revealed 42 tumor-associated RLBPs proteins. The CI with high expression of tumor-associated proteins was sensitive to drugs targeting genome integrity and EGFR in both cell and organoid models. Thus, our study unveils a significant molecular association of the CIN phenotype with RLBPs, and also provides a powerful resource for further functional exploration of RLBPs in cancer progression and therapeutic application.
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Affiliation(s)
- Wenchao Zhao
- General Surgery Department, Xiangya Hospital, Central South University, Changsha 410008, China
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qian Pei
- General Surgery Department, Xiangya Hospital, Central South University, Changsha 410008, China
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yongwei Zhu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Guo Mao
- Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha 410073, China
| | - Meng Wang
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
| | - Yanfang Qiu
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
| | - Ke Zuo
- Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha 410073, China
| | - Haiping Pei
- General Surgery Department, Xiangya Hospital, Central South University, Changsha 410008, China
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lun-Quan Sun
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha 410008, China
- Center for Molecular Imaging of Central South University, Xiangya Hospital, Changsha 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ming Wen
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha 410008, China
- Center for Molecular Imaging of Central South University, Xiangya Hospital, Changsha 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (M.W.); (R.T.); Tel.: +86-731-84327212 (M.W.); +86-731-84327212 (R.T.)
| | - Rong Tan
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha 410008, China
- Center for Molecular Imaging of Central South University, Xiangya Hospital, Changsha 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (M.W.); (R.T.); Tel.: +86-731-84327212 (M.W.); +86-731-84327212 (R.T.)
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10
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Idrissou M, Maréchal A. The PRP19 Ubiquitin Ligase, Standing at the Cross-Roads of mRNA Processing and Genome Stability. Cancers (Basel) 2022; 14:cancers14040878. [PMID: 35205626 PMCID: PMC8869861 DOI: 10.3390/cancers14040878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 12/07/2022] Open
Abstract
mRNA processing factors are increasingly being recognized as important regulators of genome stability. By preventing and resolving RNA:DNA hybrids that form co-transcriptionally, these proteins help avoid replication-transcription conflicts and thus contribute to genome stability through their normal function in RNA maturation. Some of these factors also have direct roles in the activation of the DNA damage response and in DNA repair. One of the most intriguing cases is that of PRP19, an evolutionarily conserved essential E3 ubiquitin ligase that promotes mRNA splicing, but also participates directly in ATR activation, double-strand break resection and mitosis. Here, we review historical and recent work on PRP19 and its associated proteins, highlighting their multifarious cellular functions as central regulators of spliceosome activity, R-loop homeostasis, DNA damage signaling and repair and cell division. Finally, we discuss open questions that are bound to shed further light on the functions of PRP19-containing complexes in both normal and cancer cells.
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Affiliation(s)
- Mouhamed Idrissou
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N3, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N3, Canada
- Correspondence:
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11
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Belliveau J, Papoutsakis ET. Extracellular Vesicles Facilitate Large-Scale Dynamic Exchange of Proteins and RNA Among Cultured Chinese Hamster Ovary (CHO) and Human Cells. Biotechnol Bioeng 2022; 119:1222-1238. [PMID: 35120270 DOI: 10.1002/bit.28053] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/11/2022]
Abstract
Cells in culture are viewed as unique individuals in a large population communicating through extracellular molecules and, more recently extracellular vesicles (EVs). Our data here paint a different picture: large-scale exchange of cellular material through EVs. To visualize the dynamic production and cellular uptake of EVs, we used correlative confocal microscopy and scanning electron microscopy, as well as flow cytometry to interrogate labeled cells. Using cells expressing fluorescent proteins (GFP, miRFP703) and cells tagged with protein and RNA dyes, we show that Chinese Hamster Ovary (CHO) cells dynamically produce and uptake EVs to exchange proteins and RNAs at a large scale. Applying a simple model to our data, we estimate, for the first time, the per cell specific rates of EV production (68 and 203 microparticles and exosomes, respectively, per day). This EV-mediated massive exchange of cellular material observed in CHO cultures was also observed in cultured human CHRF-288-11 and primary hematopoietic stem and progenitor cells. This study demonstrates an underappreciated massive protein and RNA exchange between cells mediated by EVs spanning cell type, suggesting that the proximity of cells in normal and tumor tissues may also result in prolific exchange of cellular material. This exchange would be expected to homogenize the cell-population cytosol and dynamically regulate cell proliferation and the cellular state. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jessica Belliveau
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19711.,Delaware Biotechnology Institute,, University of Delaware, Newark, DE, 19711
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19711.,Delaware Biotechnology Institute,, University of Delaware, Newark, DE, 19711.,Department of Biological Sciences, University of Delaware, Newark, DE, 19711
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12
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Guo CR, Mao Y, Jiang F, Juan CX, Zhou GP, Li N. Computational detection of a genome instability-derived lncRNA signature for predicting the clinical outcome of lung adenocarcinoma. Cancer Med 2021; 11:864-879. [PMID: 34866362 PMCID: PMC8817082 DOI: 10.1002/cam4.4471] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/30/2021] [Accepted: 10/03/2021] [Indexed: 12/13/2022] Open
Abstract
Evidence has been emerging of the importance of long non-coding RNAs (lncRNAs) in genome instability. However, no study has established how to classify such lncRNAs linked to genomic instability, and whether that connection poses a therapeutic significance. Here, we established a computational frame derived from mutator hypothesis by combining profiles of lncRNA expression and those of somatic mutations in a tumor genome, and identified 185 candidate lncRNAs associated with genomic instability in lung adenocarcinoma (LUAD). Through further studies, we established a six lncRNA-based signature, which assigned patients to the high- and low-risk groups with different prognosis. Further validation of this signature was performed in a number of separate cohorts of LUAD patients. In addition, the signature was found closely linked to genomic mutation rates in patients, indicating it could be a useful way to quantify genomic instability. In summary, this research offered a novel method by through which more studies may explore the function of lncRNAs and presented a possible new way for detecting biomarkers associated with genomic instability in cancers.
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Affiliation(s)
- Chen-Rui Guo
- Department of Abdominal Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yan Mao
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Jiang
- Department of Neonatology,, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chen-Xia Juan
- Department of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Guo-Ping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ning Li
- Department of Abdominal Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
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13
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Castillo-Guzman D, Chédin F. Defining R-loop classes and their contributions to genome instability. DNA Repair (Amst) 2021; 106:103182. [PMID: 34303066 PMCID: PMC8691176 DOI: 10.1016/j.dnarep.2021.103182] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/20/2023]
Abstract
R-loops are non-B DNA structures that form during transcription when the nascent RNA anneals to the template DNA strand forming a RNA:DNA hybrid. Understanding the genomic distribution and function of R-loops is an important goal, since R-loops have been implicated in a number of adaptive and maladaptive processes under physiological and pathological conditions. Based on R-loop mapping datasets, we propose the existence of two main classes of R-loops, each associated with unique characteristics. Promoter-paused R-loops (Class I) are short R-loops that form at high frequency during promoter-proximal pausing by RNA polymerase II. Elongation-associated R-loops (Class II) are long structures that occur throughout gene bodies at modest frequencies. We further discuss the relationships between each R-loop class with instances of genome instability and suggest that increased class I R-loops, resulting from enhanced promoter-proximal pausing, represent the main culprits for R-loop mediated genome instability under pathological conditions.
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Affiliation(s)
- Daisy Castillo-Guzman
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA, 95616, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA, 95616, United States.
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14
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Jiang M, Jia K, Wang L, Li W, Chen B, Liu Y, Wang H, Zhao S, He Y, Zhou C. Alterations of DNA damage response pathway: Biomarker and therapeutic strategy for cancer immunotherapy. Acta Pharm Sin B 2021; 11:2983-2994. [PMID: 34729299 PMCID: PMC8546664 DOI: 10.1016/j.apsb.2021.01.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/25/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
Genomic instability remains an enabling feature of cancer and promotes malignant transformation. Alterations of DNA damage response (DDR) pathways allow genomic instability, generate neoantigens, upregulate the expression of programmed death ligand 1 (PD-L1) and interact with signaling such as cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling. Here, we review the basic knowledge of DDR pathways, mechanisms of genomic instability induced by DDR alterations, impacts of DDR alterations on immune system, and the potential applications of DDR alterations as biomarkers and therapeutic targets in cancer immunotherapy.
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Key Words
- ATM, ataxia-telangiectasia mutated
- ATR, ataxia telangiectasia and Rad3 related
- BAP1, BRCA1-associated protein 1
- BER, base excision repair
- BRAF, v-RAF murine sarcoma viral oncogene homologue B
- BRCA, breast cancer susceptibility gene
- CHEK, cell-cycle checkpoint kinase
- CHK1, checkpoint kinase 1
- DAMP, damage-associated molecular patterns
- DDR, DNA damage response
- DNA damage response
- DNA repair
- DR, direct repair
- DSBs, double-strand breaks
- FDA, United State Food and Drug Administration
- GSK3β, glycogen synthase kinase 3β
- Genomic instability
- HMGB1, high mobility group box-1
- HRR, homologous recombination repair
- ICI, immune checkpoint inhibitor
- IFNγ, interferon gamma
- IHC, immunohistochemistry
- IRF1, interferon regulatory factor 1
- Immunotherapy
- JAK, Janus kinase
- MAD1, mitotic arrest deficient-like 1
- MGMT, O6-methylguanine methyltransferase
- MLH1, MutL homolog 1
- MMR, mismatch repair
- MNT, MAX network transcriptional repressor
- MSH2/6, MutS protein homologue-2/6
- MSI, microsatellite instability
- MUTYH, MutY homolog
- MyD88, myeloid differentiation factor 88
- NEK1, NIMA-related kinase 1
- NER, nucleotide excision repair
- NGS, next generation sequencing
- NHEJ, nonhomologous end-joining
- NIMA, never-in-mitosis A
- NSCLC, non-small cell lung cancer
- ORR, objective response rate
- OS, overall survival
- PALB2, partner and localizer of BRCA2
- PARP, poly-ADP ribose polymerase
- PCR, polymerase chain reaction
- PD-1
- PD-1, programmed death 1
- PD-L1
- PD-L1, programmed death ligand 1
- PFS, progression-free survival
- RAD51C, RAD51 homolog C
- RB1, retinoblastoma 1
- RPA, replication protein A
- RSR, replication stress response
- SCNAs, somatic copy number alterations
- STAT, signal transducer and activator of transcription
- STING, stimulator of interferon genes
- TBK1, TANK-binding kinase 1
- TILs, tumor-infiltrating lymphocytes
- TLR4, Toll-like receptor 4
- TMB, tumor mutational burden
- TME, tumor microenvironment
- TP53, tumor protein P53
- TRIF, Toll-interleukin 1 receptor domain-containing adaptor inducing INF-β
- Tumor microenvironment
- XRCC4, X-ray repair cross complementing protein 4
- cGAS, cyclic GMP–AMP synthase
- cGAS–STING
- ssDNA, single-stranded DNA
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Affiliation(s)
- Minlin Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Keyi Jia
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Lei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Yu Liu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
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15
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Cargill M, Venkataraman R, Lee S. DEAD-Box RNA Helicases and Genome Stability. Genes (Basel) 2021; 12:1471. [PMID: 34680866 PMCID: PMC8535883 DOI: 10.3390/genes12101471] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 02/06/2023] Open
Abstract
DEAD-box RNA helicases are important regulators of RNA metabolism and have been implicated in the development of cancer. Interestingly, these helicases constitute a major recurring family of RNA-binding proteins important for protecting the genome. Current studies have provided insight into the connection between genomic stability and several DEAD-box RNA helicase family proteins including DDX1, DDX3X, DDX5, DDX19, DDX21, DDX39B, and DDX41. For each helicase, we have reviewed evidence supporting their role in protecting the genome and their suggested mechanisms. Such helicases regulate the expression of factors promoting genomic stability, prevent DNA damage, and can participate directly in the response and repair of DNA damage. Finally, we summarized the pathological and therapeutic relationship between DEAD-box RNA helicases and cancer with respect to their novel role in genome stability.
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Affiliation(s)
- Michael Cargill
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
| | - Rasika Venkataraman
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Stanley Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
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16
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St Germain C, Zhao H, Barlow JH. Transcription-Replication Collisions-A Series of Unfortunate Events. Biomolecules 2021; 11:1249. [PMID: 34439915 PMCID: PMC8391903 DOI: 10.3390/biom11081249] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Transcription-replication interactions occur when DNA replication encounters genomic regions undergoing transcription. Both replication and transcription are essential for life and use the same DNA template making conflicts unavoidable. R-loops, DNA supercoiling, DNA secondary structure, and chromatin-binding proteins are all potential obstacles for processive replication or transcription and pose an even more potent threat to genome integrity when these processes co-occur. It is critical to maintaining high fidelity and processivity of transcription and replication while navigating through a complex chromatin environment, highlighting the importance of defining cellular pathways regulating transcription-replication interaction formation, evasion, and resolution. Here we discuss how transcription influences replication fork stability, and the safeguards that have evolved to navigate transcription-replication interactions and maintain genome integrity in mammalian cells.
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Affiliation(s)
- Commodore St Germain
- School of Mathematics and Science, Solano Community College, 4000 Suisun Valley Road, Fairfield, CA 94534, USA
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
| | - Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
| | - Jacqueline H. Barlow
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
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17
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Goyal M, Singh BK, Simantov K, Kaufman Y, Eshar S, Dzikowski R. An SR protein is essential for activating DNA repair in malaria parasites. J Cell Sci 2021; 134:271848. [PMID: 34291805 PMCID: PMC8435287 DOI: 10.1242/jcs.258572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/14/2021] [Indexed: 11/24/2022] Open
Abstract
Plasmodium falciparum, the parasite responsible for the deadliest form of human malaria, replicates within the erythrocytes of its host, where it encounters numerous pressures that cause extensive DNA damage, which must be repaired efficiently to ensure parasite survival. Malaria parasites, which have lost the non-homologous end joining (NHEJ) pathway for repairing DNA double-strand breaks, have evolved unique mechanisms that enable them to robustly maintain genome integrity under such harsh conditions. However, the nature of these adaptations is unknown. We show that a highly conserved RNA splicing factor, P. falciparum (Pf)SR1, plays an unexpected and crucial role in DNA repair in malaria parasites. Using an inducible and reversible system to manipulate PfSR1 expression, we demonstrate that this protein is recruited to foci of DNA damage. Although loss of PfSR1 does not impair parasite viability, the protein is essential for their recovery from DNA-damaging agents or exposure to artemisinin, the first-line antimalarial drug, demonstrating its necessity for DNA repair. These findings provide key insights into the evolution of DNA repair pathways in malaria parasites as well as the ability of the parasite to recover from antimalarial treatment. Summary: There is an unexpected role for the alternative splicing factor PfSR1 in activating the DNA damage response in the human malaria parasite Plasmodium falciparum.
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Affiliation(s)
- Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Brajesh Kumar Singh
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yotam Kaufman
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Shiri Eshar
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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18
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Li J, Xiao L, Yan N, Li Y, Wang Y, Qin X, Zhao D, Liu M, Li N, Lin Y. The Neuroprotective Effect of MicroRNA‐22‐3p Modified Tetrahedral Framework Nucleic Acids on Damaged Retinal Neurons Via TrkB/BDNF Signaling Pathway. ADVANCED FUNCTIONAL MATERIALS 2021. [DOI: 10.1002/adfm.202104141] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jiajie Li
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 China
| | - Lirong Xiao
- Department of Ophthalmology West China Hospital Sichuan University Chengdu 610041 China
| | - Naihong Yan
- Department of Ophthalmology West China Hospital Sichuan University Chengdu 610041 China
| | - Yanjing Li
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 China
| | - Yun Wang
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 China
| | - Xin Qin
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 China
| | - Dan Zhao
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 China
| | - Mengting Liu
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 China
| | - Ni Li
- Department of Ophthalmology West China Hospital Sichuan University Chengdu 610041 China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 China
- College of Biomedical Engineering Sichuan University Chengdu 610041 China
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19
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Daily intake of Lactobacillus gasseri CP2305 ameliorates psychological premenstrual symptoms in young women: A randomized, double-blinded, placebo-controlled study. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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20
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Patel PS, Abraham KJ, Guturi KKN, Halaby MJ, Khan Z, Palomero L, Ho B, Duan S, St-Germain J, Algouneh A, Mateo F, El Ghamrasni S, Barbour H, Barnes DR, Beesley J, Sanchez O, Berman HK, Brown GW, El Bachir Affar, Chenevix-Trench G, Antoniou AC, Arrowsmith CH, Raught B, Pujana MA, Mekhail K, Hakem A, Hakem R. RNF168 regulates R-loop resolution and genomic stability in BRCA1/2-deficient tumors. J Clin Invest 2021; 131:140105. [PMID: 33529165 PMCID: PMC7843228 DOI: 10.1172/jci140105] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA1/2) genes considerably increase breast and ovarian cancer risk. Given that tumors with these mutations have elevated genomic instability, they exhibit relative vulnerability to certain chemotherapies and targeted treatments based on poly (ADP-ribose) polymerase (PARP) inhibition. However, the molecular mechanisms that influence cancer risk and therapeutic benefit or resistance remain only partially understood. BRCA1 and BRCA2 have also been implicated in the suppression of R-loops, triple-stranded nucleic acid structures composed of a DNA:RNA hybrid and a displaced ssDNA strand. Here, we report that loss of RNF168, an E3 ubiquitin ligase and DNA double-strand break (DSB) responder, remarkably protected Brca1-mutant mice against mammary tumorigenesis. We demonstrate that RNF168 deficiency resulted in accumulation of R-loops in BRCA1/2-mutant breast and ovarian cancer cells, leading to DSBs, senescence, and subsequent cell death. Using interactome assays, we identified RNF168 interaction with DHX9, a helicase involved in the resolution and removal of R-loops. Mechanistically, RNF168 directly ubiquitylated DHX9 to facilitate its recruitment to R-loop-prone genomic loci. Consequently, loss of RNF168 impaired DHX9 recruitment to R-loops, thereby abrogating its ability to resolve R-loops. The data presented in this study highlight a dependence of BRCA1/2-defective tumors on factors that suppress R-loops and reveal a fundamental RNF168-mediated molecular mechanism that governs cancer development and vulnerability.
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Affiliation(s)
- Parasvi S. Patel
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Karan Joshua Abraham
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Kiran Kumar Naidu Guturi
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Marie-Jo Halaby
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Zahra Khan
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Luis Palomero
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Brandon Ho
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Arash Algouneh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Francesca Mateo
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Haithem Barbour
- Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Daniel R. Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Beesley
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Otto Sanchez
- University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - Hal K. Berman
- Toronto General Research Institute, Toronto, Ontario, Canada
| | - Grant W. Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - El Bachir Affar
- Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | | | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Miquel Angel Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Anne Hakem
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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21
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Fraga de Andrade I, Mehta C, Bresnick EH. Post-transcriptional control of cellular differentiation by the RNA exosome complex. Nucleic Acids Res 2020; 48:11913-11928. [PMID: 33119769 PMCID: PMC7708067 DOI: 10.1093/nar/gkaa883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.
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Affiliation(s)
- Isabela Fraga de Andrade
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
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22
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Milbury KL, Paul B, Lari A, Fowler C, Montpetit B, Stirling PC. Exonuclease domain mutants of yeast DIS3 display genome instability. Nucleus 2020; 10:21-32. [PMID: 30724665 PMCID: PMC6380420 DOI: 10.1080/19491034.2019.1578600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated DIS3 allele, dis3E729K, provides evidence for DIS3 functioning in mitotic fidelity in yeast. This dis3E729K allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these DIS3 mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific DIS3 activities support mitotic fidelity in yeast.
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Affiliation(s)
- Karissa L Milbury
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Biplab Paul
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Azra Lari
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Claire Fowler
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Ben Montpetit
- b Department of Cell Biology , University of Alberta , Edmonton , Canada.,c Department of Viticulture and Enology , University of California , Davis , CA , USA
| | - Peter C Stirling
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada.,d Department of Medical Genetics , University of British Columbia , Vancouver , BC , Canada
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23
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Massonneau J, Lacombe-Burgoyne C, Boissonneault G. pH-induced variations in the TK1 gene model. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 849:503128. [PMID: 32087849 DOI: 10.1016/j.mrgentox.2019.503128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/09/2019] [Accepted: 11/25/2019] [Indexed: 12/31/2022]
Abstract
A physiological decrease in extracellular pH (pHe) alters the efficiency of DNA repair and increases formation of DNA double-strand breaks (DSBs). Whether this could translate into genetic instability and variations, was investigated using the TK6 cell model, in which positive selection of the TK1 gene loss-of-function mutations can be achieved from resistance to trifluorothymidine. Cell exposure to suboptimal pH (down to 6.9) for 3 weeks resulted in the 100 % frequency of a stronger frameshift mutation that has spread to both TK1 alleles, whereas weaker frameshift mutations within the 3'exon were eliminated during the selection. Suboptimal pHe values were also found to alter the proportion of the TK1 splicing variant expressed as percent spliced in index values and promote selection of truncated exons as well as intron retention. Although recovery at pH 7.4 did not reverse the selected frameshift mutation, reversal of splice variants and exon truncation towards control values were observed. Hence, suboptimal pHe can induce a combination of mutational events and splicing alterations within the same gene in the resistant clones. This model of positive selection for loss-of-function clearly demonstrates that suboptimal pHe may confer a similar growth advantage when such instability occurs within tumor suppressor genes.
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Affiliation(s)
- Julien Massonneau
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Chloë Lacombe-Burgoyne
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Guylain Boissonneault
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.
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24
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Dong X, Chen R. Understanding aberrant RNA splicing to facilitate cancer diagnosis and therapy. Oncogene 2019; 39:2231-2242. [PMID: 31819165 DOI: 10.1038/s41388-019-1138-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
Almost all genes in normal cells undergo alternative RNA splicing to generate a greater extent of diversification of gene products for normal cellular functions. RNA splicing is tightly regulated and closely interplays with genetic and epigenetic machinery. While DNA polymorphism and somatic mutations modulate alternative splicing patterns, RNA splicing also controls genomic stability, chromatin organization, and transcriptome. Tumor cells, in turn, often take advantage of aberrant RNA splicing to develop, grow and progress into therapy-resistant tumors. Understanding alternative RNA splicing in tumor cells would, therefore, provide us opportunities to gain further insights into tumor biology, identify diagnostic or prognosis biomarkers, as well as to design effective therapeutic means to control tumor progression. Here, we provide an overview of RNA splicing mechanisms and use prostate cancer as an example to review recent advancements in our understanding of RNA splicing in cancer progression and therapy resistance. We also discuss emerging diagnostic and therapeutic potentials of RNA splicing events or RNA splicing factors.
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Affiliation(s)
- Xuesen Dong
- Department of Urologic Sciences, Faculty of Medicine, The University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada. .,The Vancouver Prostate Centre, Vancouver General Hospital, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada.
| | - Ruiqi Chen
- Faculty of Medicine, University of Toronto, 27 King's College Circle 8, Toronto, ON, M5S 1A1, Canada
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25
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Li S, Sun Y, Tian T, Qin X, Lin S, Zhang T, Zhang Q, Zhou M, Zhang X, Zhou Y, Zhao H, Zhu B, Cai X. MicroRNA-214-3p modified tetrahedral framework nucleic acids target survivin to induce tumour cell apoptosis. Cell Prolif 2019; 53:e12708. [PMID: 31642557 PMCID: PMC6985659 DOI: 10.1111/cpr.12708] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/15/2019] [Accepted: 08/24/2019] [Indexed: 02/05/2023] Open
Abstract
Objectives Due to the instability of microRNAs, the applications of microRNA are currently limited. Thus, we utilized tetrahedral framework nucleic acids and a targeted microRNAs to form a stable nanocomposite to explore whether this nanocomposite can promote apoptosis of tumour cells. Materials and methods In our study, the survivin gene, which is expressed only in tumour cells and embryonic cells, was selected as the target gene; miRNA‐214‐3p, which can reduce the expression of survivin, was modified onto tetrahedral framework nucleic acid, thereby producing a reduction in the expression of survivin upon intracellular delivery and eventually leading to tumour cell apoptosis. Results By comparing the stability of microRNAs with that of microRNA‐tetrahedral framework nucleic acid, we proved the superiority of this carrier system. The results of flow cytometry showed that after treated with this complex, the ratio of A549 cells in both late and early period of apoptosis in miRNA‐214‐3p‐tetrahedral framework nucleic acid group had doubled and the cell cycle in the G2‐M phase had declined. The decrease in the expression of anti‐apoptotic protein and the increase in the expression of pro‐apoptotic protein indicate that the ability of this complex to function in cells also makes it attractive as a new targeted therapy for cancer. Conclusion The unique expression of survivin in tumour cells and embryonic cells makes microRNA‐tetrahedral framework nucleic acid a new targeted therapy. In addition, due to the functional diversity of microRNAs, this delivery system approach can be applied to a wide variety of fields, such as targeted therapy and tissue regeneration.
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Affiliation(s)
- Songhang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yue Sun
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Qin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shiyu Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qi Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mi Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaolin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Zhou
- College of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hu Zhao
- Department of Restorative Sciences, College of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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26
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Wells JP, White J, Stirling PC. R Loops and Their Composite Cancer Connections. Trends Cancer 2019; 5:619-631. [DOI: 10.1016/j.trecan.2019.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022]
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27
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Pillon MC, Lo YH, Stanley RE. IT'S 2 for the price of 1: Multifaceted ITS2 processing machines in RNA and DNA maintenance. DNA Repair (Amst) 2019; 81:102653. [PMID: 31324529 PMCID: PMC6764878 DOI: 10.1016/j.dnarep.2019.102653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cells utilize sophisticated RNA processing machines to ensure the quality of RNA. Many RNA processing machines have been further implicated in regulating the DNA damage response signifying a strong link between RNA processing and genome maintenance. One of the most intricate and highly regulated RNA processing pathways is the processing of the precursor ribosomal RNA (pre-rRNA), which is paramount for the production of ribosomes. Removal of the Internal Transcribed Spacer 2 (ITS2), located between the 5.8S and 25S rRNA, is one of the most complex steps of ribosome assembly. Processing of the ITS2 is initiated by the newly discovered endoribonuclease Las1, which cleaves at the C2 site within the ITS2, generating products that are further processed by the polynucleotide kinase Grc3, the 5'→3' exonuclease Rat1, and the 3'→5' RNA exosome complex. In addition to their defined roles in ITS2 processing, these critical cellular machines participate in other stages of ribosome assembly, turnover of numerous cellular RNAs, and genome maintenance. Here we summarize recent work defining the molecular mechanisms of ITS2 processing by these essential RNA processing machines and highlight their emerging roles in transcription termination, heterochromatin function, telomere maintenance, and DNA repair.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Yu-Hua Lo
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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28
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Sugaya K. Chromosome instability caused by mutations in the genes involved in transcription and splicing. RNA Biol 2019; 16:1521-1525. [PMID: 31385554 DOI: 10.1080/15476286.2019.1652523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Mutations in molecules involved in transcription and splicing can cause chromosome instability such as sister chromatid exchanges. We isolated and characterized responsible genes from mammalian temperature-sensitive mutant cells showing chromosome instability. A mutation in the largest subunit of RNA polymerase II affected DNA synthesis in S phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges. The yeast mutant harboring a homologous mutation showed very similar phenotype to that of the mammalian mutant. A mutation in Smu1, which is involved in splicing, also affected DNA synthesis in S and G2 phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges and chromosomal aberrations. These cells showed a connection between defects of RNA metabolism and induction of chromosome instability. Genome instability appeared to be caused by links between RNA metabolism and replication resulting in genomic recombination. RNA metabolism can be regarded as one possible driver of genome modification triggering genome evolution.
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Affiliation(s)
- Kimihiko Sugaya
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST) , Chiba , Japan.,Group of Quantum-state Controlled MRI, QST , Chiba , Japan
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29
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Infantino V, Stutz F. The functional complexity of the RNA-binding protein Yra1: mRNA biogenesis, genome stability and DSB repair. Curr Genet 2019; 66:63-71. [PMID: 31292684 DOI: 10.1007/s00294-019-01011-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/21/2022]
Abstract
The mRNA export adaptor Yra1 is essential in S. cerevisiae, and conserved from yeast to human (ALY/REF). It is well characterized for its function during transcription elongation, 3' processing and mRNA export. Recently, different studies linked Yra1 to genome stability showing that Yra1 overexpression causes DNA Double Strand Breaks through DNA:RNA hybrids stabilization, and that Yra1 depletion affects DSB repair. However, the mechanisms through which Yra1 contributes to genome stability maintenance are not fully understood. Interestingly, our results showed that the Yra1 C-box domain is required for Yra1 recruitment to an HO-induced irreparable DSB following extensive resection, and that it is essential to repair an HO-induced reparable DSB. Furthermore, we defined that the C-box domain of Yra1 plays a crucial role in DSB repair through homologous recombination but not through non-homologous end joining. Future studies aim at deciphering the mechanism by which Yra1 contributes to DSB repair by searching for Yra1 partners important for this process. This review focuses on the functional complexity of the Yra1 protein, not only summarizing its role in mRNA biogenesis but also emphasizing its auto-regulation and implication in genome integrity either through DNA:RNA hybrids stabilization or DNA double strand break repair in S. cerevisiae.
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Affiliation(s)
- Valentina Infantino
- Department of Cell Biology, University of Geneva, 30 Quai E. Ansermet, 1211, Geneva, Switzerland
| | - Françoise Stutz
- Department of Cell Biology, University of Geneva, 30 Quai E. Ansermet, 1211, Geneva, Switzerland.
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30
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Martinez-Macias MI, Moore DA, Green RL, Gomez-Herreros F, Naumann M, Hermann A, Van Damme P, Hafezparast M, Caldecott KW. FUS (fused in sarcoma) is a component of the cellular response to topoisomerase I-induced DNA breakage and transcriptional stress. Life Sci Alliance 2019; 2:2/2/e201800222. [PMID: 30808650 PMCID: PMC6391683 DOI: 10.26508/lsa.201800222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/11/2022] Open
Abstract
This work shows that the ALS-associated protein FUS is a component of the cellular response to transcriptional stress induced by topoisomerase I–induced DNA breakage, thereby accumulating at sites of nucleolar rRNA synthesis. FUS (fused in sarcoma) plays a key role in several steps of RNA metabolism, and dominant mutations in this protein are associated with neurodegenerative diseases. Here, we show that FUS is a component of the cellular response to topoisomerase I (TOP1)–induced DNA breakage; relocalising to the nucleolus in response to RNA polymerase II (Pol II) stalling at sites of TOP1-induced DNA breaks. This relocalisation is rapid and dynamic, reversing following the removal of TOP1-induced breaks and coinciding with the recovery of global transcription. Importantly, FUS relocalisation following TOP1-induced DNA breakage is associated with increased FUS binding at sites of RNA polymerase I transcription in ribosomal DNA and reduced FUS binding at sites of RNA Pol II transcription, suggesting that FUS relocates from sites of stalled RNA Pol II either to regulate pre-mRNA processing during transcriptional stress or to modulate ribosomal RNA biogenesis. Importantly, FUS-mutant patient fibroblasts are hypersensitive to TOP1-induced DNA breakage, highlighting the possible relevance of these findings to neurodegeneration.
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Affiliation(s)
| | - Duncan Aq Moore
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Ryan L Green
- Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Fernando Gomez-Herreros
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, England.,Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocio-Centro Superior de Investigaciones Cientificas-Universidad de Sevilla, Seville, Spain
| | - Marcel Naumann
- Department of Neurology, Technische Universität Dresden, and German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Andreas Hermann
- Department of Neurology, Technische Universität Dresden, and German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Transdisciplinary Neurosciences Rostock, University Medical Center Rostock, University of Rostock, Rostock, Germany.,Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | | | - Majid Hafezparast
- Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, England
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31
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Anufrieva KS, Shender VO, Arapidi GP, Lagarkova MA, Govorun VM. The Diverse Roles of Spliceosomal Proteins in the Regulation of Cell Processes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Tam AS, Sihota TS, Milbury KL, Zhang A, Mathew V, Stirling PC. Selective defects in gene expression control genome instability in yeast splicing mutants. Mol Biol Cell 2018; 30:191-200. [PMID: 30462576 PMCID: PMC6589566 DOI: 10.1091/mbc.e18-07-0439] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA processing mutants have been broadly implicated in genome stability, but mechanistic links are often unclear. Two predominant models have emerged: one involving changes in gene expression that perturb other genome maintenance factors and another in which genotoxic DNA:RNA hybrids, called R-loops, impair DNA replication. Here we characterize genome instability phenotypes in yeast splicing factor mutants and find that mitotic defects, and in some cases R-loop accumulation, are causes of genome instability. In both cases, alterations in gene expression, rather than direct cis effects, are likely to contribute to instability. Genome instability in splicing mutants is exacerbated by loss of the spindle-assembly checkpoint protein Mad1. Moreover, removal of the intron from the α-tubulin gene TUB1 restores genome integrity. Thus, differing penetrance and selective effects on the transcriptome can lead to a range of phenotypes in conditional mutants of the spliceosome, including multiple routes to genome instability.
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Affiliation(s)
- Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Tianna S Sihota
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Karissa L Milbury
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Anni Zhang
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Veena Mathew
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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Richard P, Ogami K, Chen Y, Feng S, Moresco JJ, Yates JR, Manley JL. NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells. RNA Biol 2018; 15:868-876. [PMID: 29902117 DOI: 10.1080/15476286.2018.1467180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RNA helicase Mtr4 is a versatile protein that is a crucial component of several distinct RNA surveillance complexes. Here we describe a novel complex that contains Mtr4, but has a role distinct from any of those previously described. We found that Mtr4 association with the human homolog of fission yeast Nrl1, NRDE-2, defines a novel function for Mtr4 in the DNA damage response pathway. We provide biochemical evidence that Mtr4 and NRDE-2 are part of the same complex and show that both proteins play a role in the DNA damage response by maintaining low DNA double-strand break levels. Importantly, the DNA damage response function of the Mtr4/NRDE-2 complex does not depend on the formation of R loops. We show however that NRDE-2 and Mtr4 can affect R-loop signals at a subset of distinct genes, possibly regulating their expression. Our work not only expands the wide range of Mtr4 functions, but also elucidates an important role of the less characterized human NRDE-2 protein.
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Affiliation(s)
- Patricia Richard
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - Koichi Ogami
- a Department of Biological Sciences , Columbia University , New York , NY , USA.,b Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences , Nagoya City University , Nagoya , Japan
| | - Yaqiong Chen
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - Shuang Feng
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - James J Moresco
- c Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- c Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - James L Manley
- a Department of Biological Sciences , Columbia University , New York , NY , USA
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Anufrieva KS, Shender VО, Arapidi GP, Pavlyukov MS, Shakhparonov MI, Shnaider PV, Butenko IO, Lagarkova MA, Govorun VM. Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells. Genome Med 2018; 10:49. [PMID: 29950180 PMCID: PMC6020472 DOI: 10.1186/s13073-018-0557-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/07/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Abnormal pre-mRNA splicing regulation is common in cancer, but the effects of chemotherapy on this process remain unclear. METHODS To evaluate the effect of chemotherapy on slicing regulation, we performed meta-analyses of previously published transcriptomic, proteomic, phosphoproteomic, and secretome datasets. Our findings were verified by LC-MS/MS, western blotting, immunofluorescence, and FACS analyses of multiple cancer cell lines treated with cisplatin and pladienolide B. RESULTS Our results revealed that different types of chemotherapy lead to similar changes in alternative splicing by inducing intron retention in multiple genes. To determine the mechanism underlying this effect, we analyzed gene expression in 101 cell lines affected by ɣ-irradiation, hypoxia, and 10 various chemotherapeutic drugs. Strikingly, оnly genes involved in the cell cycle and pre-mRNA splicing regulation were changed in a similar manner in all 335 tested samples regardless of stress stimuli. We revealed significant downregulation of gene expression levels in these two pathways, which could be explained by the observed decrease in splicing efficiency and global intron retention. We showed that the levels of active spliceosomal proteins might be further post-translationally decreased by phosphorylation and export into the extracellular space. To further explore these bioinformatics findings, we performed proteomic analysis of cisplatin-treated ovarian cancer cells. Finally, we demonstrated that the splicing inhibitor pladienolide B impairs the cellular response to DNA damage and significantly increases the sensitivity of cancer cells to chemotherapy. CONCLUSIONS Decreased splicing efficiency and global intron retention is a novel stress response mechanism that may promote survival of malignant cells following therapy. We found that this mechanism can be inhibited by pladienolide B, which significantly increases the sensitivity of cancer cells to cisplatin which makes it a good candidate drug for improving the efficiency of cancer therapy.
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Affiliation(s)
- Ksenia S Anufrieva
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia.
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
- Systems Biology Lab, Moscow Institute of Physics and Technology (State University), Moscow, Region, 141701, Russia.
| | - Victoria О Shender
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia.
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
| | - Georgij P Arapidi
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
- Systems Biology Lab, Moscow Institute of Physics and Technology (State University), Moscow, Region, 141701, Russia
| | - Marat S Pavlyukov
- Laboratory of Membrane Bioenergetics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Michail I Shakhparonov
- Laboratory of Membrane Bioenergetics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Polina V Shnaider
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Ivan O Butenko
- Laboratory of Proteomic Analysis, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Maria A Lagarkova
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Vadim M Govorun
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Proteomic Analysis, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
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Jansen RW, de Jong MC, Kooi IE, Sirin S, Göricke S, Brisse HJ, Maeder P, Galluzzi P, van der Valk P, Cloos J, Eekhout I, Castelijns JA, Moll AC, Dorsman JC, de Graaf P. MR Imaging Features of Retinoblastoma: Association with Gene Expression Profiles. Radiology 2018; 288:506-515. [PMID: 29714679 DOI: 10.1148/radiol.2018172000] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Purpose To identify associations between magnetic resonance (MR) imaging features and gene expression in retinoblastoma. Materials and Methods A retinoblastoma MR imaging atlas was validated by using anonymized MR images from referral centers in Essen, Germany, and Paris, France. Images were from 39 patients with retinoblastoma (16 male and 18 female patients [the sex in five patients was unknown]; age range, 5-90 months; inclusion criterion: pretreatment MR imaging). This atlas was used to compare MR imaging features with genome-wide messenger RNA (mRNA) expression data from 60 consecutive patients obtained from 1995 to 2012 (35 male patients [58%]; age range, 2-69 months; inclusion criteria: pretreatment MR imaging, genome-wide mRNA expression data available). Imaging pathway associations were analyzed by means of gene enrichment. In addition, imaging features were compared with a predefined gene expression signature of photoreceptorness. Statistical analysis was performed with generalized linear modeling of radiology traits on normalized log2-transformed expression values. P values were corrected for multiple hypothesis testing. Results Radiogenomic analysis revealed 1336 differentially expressed genes for qualitative imaging features (threshold P = .05 after multiple hypothesis correction). Loss of photoreceptorness gene expression correlated with advanced stage imaging features, including multiple lesions (P = .03) and greater eye size (P < .001). The number of lesions on MR images was associated with expression of MYCN (P = .04). A newly defined radiophenotype of diffuse-growing, plaque-shaped, multifocal tumors displayed overexpression of SERTAD3 (P = .003, P = .049, and P = .06, respectively), a protein that stimulates cell growth by activating the E2F network. Conclusion Radiogenomic biomarkers can potentially help predict molecular features, such as photoreceptorness loss, that indicate tumor progression. Results imply a possible role for radiogenomics in future staging and treatment decision making in retinoblastoma.
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Affiliation(s)
- Robin W Jansen
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Marcus C de Jong
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Irsan E Kooi
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Selma Sirin
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Sophia Göricke
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Hervé J Brisse
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Philippe Maeder
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Paolo Galluzzi
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Paul van der Valk
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Jacqueline Cloos
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Iris Eekhout
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Jonas A Castelijns
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Annette C Moll
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Josephine C Dorsman
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
| | - Pim de Graaf
- From the Departments of Radiology and Nuclear Medicine (R.W.J., M.C.d.J., J.A.C., P.d.G.), Clinical Genetics (I.E.K., J.C.D.), Ophthalmology (A.C.M.), Pathology (P.v.d.V.), Pediatric Oncology (J.C.), and Epidemiology and Biostatistics (I.E.), VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands; European Retinoblastoma Imaging Collaboration (ERIC) (R.W.J., M.C.d.J., S.S., S.G., H.J.B., P.M., P.G., J.A.C., P.d.G.); Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany (S.S., S.G.); Department of Radiology, Institut Curie, Paris, France and Paris Sciences et Lettres Research University, Paris, France (H.J.B.); Department of Radiology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland (P.M.); and Unit of Neuroimaging and Neurointervention, Department of Neurosciences, Siena University Hospital, Siena, Italy (P.G.)
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Walker C, El-Khamisy SF. Perturbed autophagy and DNA repair converge to promote neurodegeneration in amyotrophic lateral sclerosis and dementia. Brain 2018; 141:1247-1262. [PMID: 29584802 PMCID: PMC5917746 DOI: 10.1093/brain/awy076] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/16/2018] [Accepted: 02/09/2018] [Indexed: 12/13/2022] Open
Abstract
Maintaining genomic stability constitutes a major challenge facing cells. DNA breaks can arise from direct oxidative damage to the DNA backbone, the inappropriate activities of endogenous enzymes such as DNA topoisomerases, or due to transcriptionally-derived RNA/DNA hybrids (R-loops). The progressive accumulation of DNA breaks has been linked to several neurological disorders. Recently, however, several independent studies have implicated nuclear and mitochondrial genomic instability, perturbed co-transcriptional processing, and impaired cellular clearance pathways as causal and intertwined mechanisms underpinning neurodegeneration. Here, we discuss this emerging paradigm in the context of amyotrophic lateral sclerosis and frontotemporal dementia, and outline how this knowledge paves the way to novel therapeutic interventions.
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Affiliation(s)
- Callum Walker
- Krebs Institute, Department of Molecular biology and biotechnology, University of Sheffield, UK
- The Institute of Cancer Research, London, UK
| | - Sherif F El-Khamisy
- Krebs Institute, Department of Molecular biology and biotechnology, University of Sheffield, UK
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
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Palancade B. L’instabilité génétique associée aux R-loops. Med Sci (Paris) 2018; 34:300-302. [DOI: 10.1051/medsci/20183404007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Gavish-Izakson M, Velpula BB, Elkon R, Prados-Carvajal R, Barnabas GD, Ugalde AP, Agami R, Geiger T, Huertas P, Ziv Y, Shiloh Y. Nuclear poly(A)-binding protein 1 is an ATM target and essential for DNA double-strand break repair. Nucleic Acids Res 2018; 46:730-747. [PMID: 29253183 PMCID: PMC5778506 DOI: 10.1093/nar/gkx1240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 11/28/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022] Open
Abstract
The DNA damage response (DDR) is an extensive signaling network that is robustly mobilized by DNA double-strand breaks (DSBs). The primary transducer of the DSB response is the protein kinase, ataxia-telangiectasia, mutated (ATM). Here, we establish nuclear poly(A)-binding protein 1 (PABPN1) as a novel target of ATM and a crucial player in the DSB response. PABPN1 usually functions in regulation of RNA processing and stability. We establish that PABPN1 is recruited to the DDR as a critical regulator of DSB repair. A portion of PABPN1 relocalizes to DSB sites and is phosphorylated on Ser95 in an ATM-dependent manner. PABPN1 depletion sensitizes cells to DSB-inducing agents and prolongs the DSB-induced G2/M cell-cycle arrest, and DSB repair is hampered by PABPN1 depletion or elimination of its phosphorylation site. PABPN1 is required for optimal DSB repair via both nonhomologous end-joining (NHEJ) and homologous recombination repair (HRR), and specifically is essential for efficient DNA-end resection, an initial, key step in HRR. Using mass spectrometry analysis, we capture DNA damage-induced interactions of phospho-PABPN1, including well-established DDR players as well as other RNA metabolizing proteins. Our results uncover a novel ATM-dependent axis in the rapidly growing interface between RNA metabolism and the DDR.
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Affiliation(s)
- Michal Gavish-Izakson
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bhagya Bhavana Velpula
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rosario Prados-Carvajal
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, Spain
| | - Georgina D Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Pineiro Ugalde
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, Spain
| | - Yael Ziv
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yosef Shiloh
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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Cdc73 suppresses genome instability by mediating telomere homeostasis. PLoS Genet 2018; 14:e1007170. [PMID: 29320491 PMCID: PMC5779705 DOI: 10.1371/journal.pgen.1007170] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/23/2018] [Accepted: 12/25/2017] [Indexed: 12/18/2022] Open
Abstract
Defects in the genes encoding the Paf1 complex can cause increased genome instability. Loss of Paf1, Cdc73, and Ctr9, but not Rtf1 or Leo1, caused increased accumulation of gross chromosomal rearrangements (GCRs). Combining the cdc73Δ mutation with individual deletions of 43 other genes, including TEL1 and YKU80, which are involved in telomere maintenance, resulted in synergistic increases in GCR rates. Whole genome sequence analysis of GCRs indicated that there were reduced relative rates of GCRs mediated by de novo telomere additions and increased rates of translocations and inverted duplications in cdc73Δ single and double mutants. Analysis of telomere lengths and telomeric gene silencing in strains containing different combinations of cdc73Δ, tel1Δ and yku80Δ mutations suggested that combinations of these mutations caused increased defects in telomere maintenance. A deletion analysis of Cdc73 revealed that a central 105 amino acid region was necessary and sufficient for suppressing the defects observed in cdc73Δ strains; this region was required for the binding of Cdc73 to the Paf1 complex through Ctr9 and for nuclear localization of Cdc73. Taken together, these data suggest that the increased GCR rate of cdc73Δ single and double mutants is due to partial telomere dysfunction and that Ctr9 and Paf1 play a central role in the Paf1 complex potentially by scaffolding the Paf1 complex subunits or by mediating recruitment of the Paf1 complex to the different processes it functions in. Maintaining a stable genome is crucial for all organisms, and loss of genome stability has been linked to multiple human diseases, including many cancers. Previously we found that defects in Cdc73, a component of the Paf1 transcriptional elongation complex, give rise to increased genome instability. Here, we explored the mechanism underlying this instability and found that Cdc73 defects give rise to partial defects in maintaining telomeres, which are the specialized ends of chromosomes, and interact with other mutations causing telomere defects. Remarkably, Cdc73 function is mediated through a short central region of the protein that is not a part of previously identified protein domains but targets Cdc73 to the Paf1 complex through interaction with the Ctr9 subunit. Analysis of the other components of the Paf1 complex provides a model in which the Paf1 subunit mediates recruitment of the other subunits to different processes they function in. Together, these data suggest that the mutations in CDC73 and CTR9 found in patients with hyperparathyroidism-jaw tumor syndrome and some patients with Wilms tumors, respectively, may contribute to cancer progression by contributing to genome instability.
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Banaszak LG, Giudice V, Zhao X, Wu Z, Gao S, Hosokawa K, Keyvanfar K, Townsley DM, Gutierrez-Rodrigues F, Fernandez Ibanez MDP, Kajigaya S, Young NS. Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing. Blood Cells Mol Dis 2018; 69:10-22. [PMID: 29324392 DOI: 10.1016/j.bcmd.2017.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/31/2017] [Accepted: 12/31/2017] [Indexed: 12/20/2022]
Abstract
DNA methyltransferase 3A (DNMT3A) mediates de novo DNA methylation. Mutations in DNMT3A are associated with hematological malignancies, most frequently acute myeloid leukemia. DNMT3A mutations are hypothesized to establish a pre-leukemic state, rendering cells vulnerable to secondary oncogenic mutations and malignant transformation. However, the mechanisms by which DNMT3A mutations contribute to leukemogenesis are not well-defined. Here, we successfully created four DNMT3A-mutated K562 cell lines with frameshift mutations resulting in truncated DNMT3A proteins. DNMT3A-mutated cell lines exhibited significantly impaired growth and increased apoptotic activity compared to wild-type (WT) cells. Consistent with previous studies, DNMT3A-mutated cells displayed impaired differentiation capacity. RNA-seq was used to compare transcriptomes of DNMT3A-mutated and WT cells; DNMT3A ablation resulted in downregulation of genes involved in spliceosome function, causing dysfunction of RNA splicing. Unexpectedly, we observed DNMT3A-mutated cells to exhibit marked genomic instability and an impaired DNA damage response compared to WT. CRISPR/Cas9-mediated DNMT3A-mutated K562 cells may be used to model effects of DNMT3A mutations in human cells. Our findings implicate aberrant splicing and induction of genomic instability as potential mechanisms by which DNMT3A mutations might predispose to malignancy.
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Affiliation(s)
- Lauren G Banaszak
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA.
| | - Valentina Giudice
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Xin Zhao
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Zhijie Wu
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Shouguo Gao
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Kohei Hosokawa
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Keyvan Keyvanfar
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Danielle M Townsley
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Fernanda Gutierrez-Rodrigues
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Maria Del Pilar Fernandez Ibanez
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
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41
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Chang EYC, Novoa CA, Aristizabal MJ, Coulombe Y, Segovia R, Chaturvedi R, Shen Y, Keong C, Tam AS, Jones SJM, Masson JY, Kobor MS, Stirling PC. RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability. J Cell Biol 2017; 216:3991-4005. [PMID: 29042409 PMCID: PMC5716281 DOI: 10.1083/jcb.201703168] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 01/01/2023] Open
Abstract
Sgs1, the orthologue of human Bloom's syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription-replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1Δ reveals copy number changes flanked by repetitive regions with high R-loop-forming potential. Analysis of BLM in Bloom's syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop-associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop-mediated genome instability.
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Affiliation(s)
| | - Carolina A Novoa
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | | | - Yan Coulombe
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Romulo Segovia
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Richa Chaturvedi
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Yaoqing Shen
- Michael Smith Genome Sciences Centre, Vancouver, Canada
| | - Christelle Keong
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada .,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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42
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Hardiman O, Al-Chalabi A, Chio A, Corr EM, Logroscino G, Robberecht W, Shaw PJ, Simmons Z, van den Berg LH. Amyotrophic lateral sclerosis. Nat Rev Dis Primers 2017; 3:17071. [PMID: 28980624 DOI: 10.1038/nrdp.2017.71] [Citation(s) in RCA: 811] [Impact Index Per Article: 115.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, is characterized by the degeneration of both upper and lower motor neurons, which leads to muscle weakness and eventual paralysis. Until recently, ALS was classified primarily within the neuromuscular domain, although new imaging and neuropathological data have indicated the involvement of the non-motor neuraxis in disease pathology. In most patients, the mechanisms underlying the development of ALS are poorly understood, although a subset of patients have familial disease and harbour mutations in genes that have various roles in neuronal function. Two possible disease-modifying therapies that can slow disease progression are available for ALS, but patient management is largely mediated by symptomatic therapies, such as the use of muscle relaxants for spasticity and speech therapy for dysarthria.
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Affiliation(s)
- Orla Hardiman
- Academic Unit of Neurology, Room 5.41 Trinity Biomedical Science Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Adriano Chio
- Rita Levi Montalcini Department of Neurosciences, University of Turin, Turin, Italy
| | - Emma M Corr
- Academic Unit of Neurology, Room 5.41 Trinity Biomedical Science Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland
| | | | - Wim Robberecht
- KU Leuven-University of Leuven, University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Zachary Simmons
- Department of Neurology, Milton S. Hershey Medical Center, Penn State Health, Hershey, Pennsylvania, USA
| | - Leonard H van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
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43
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Genome Instability and γH2AX. Int J Mol Sci 2017; 18:ijms18091979. [PMID: 28914798 PMCID: PMC5618628 DOI: 10.3390/ijms18091979] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/20/2022] Open
Abstract
γH2AX has emerged in the last 20 years as a central player in the DDR (DNA damage response), with specificity for DSBs (double-strand breaks). Upon the generation of DSBs, γ-phosphorylation extends along megabase-long domains in chromatin, both sides of the damage. The significance of this mechanism is of great importance; it depicts a biological amplification mechanism where one DSB induces the γ-phosphorylation of thousands of H2AX molecules along megabaselong domains of chromatin, that are adjusted to the sites of DSBs. A sequential recruitment of signal transduction factors that interact to each other and become activated to further amplify the signal that will travel to the cytoplasm take place on the γ-phosphorylated chromatin. γ-phosphorylation is an early event in the DSB damage response, induced in all phases of the cell cycle, and participates in both DSB repair pathways, the HR (homologous recombination) and NHEJ (non-homologous end joining). Today, numerous studies support the notion that γH2AX functions as a guardian of the genome by preventing misrepaired DSB that increase the mutation load of the cells and may further lead to genome instability and carcinogenesis.
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44
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Auboeuf D. Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic variation: A hypothesis. Bioessays 2017; 39. [DOI: 10.1002/bies.201700069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210; Laboratory of Biology and Modelling of the Cell; Site Jacques Monod; Lyon France
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45
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Bonnet A, Grosso AR, Elkaoutari A, Coleno E, Presle A, Sridhara SC, Janbon G, Géli V, de Almeida SF, Palancade B. Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability. Mol Cell 2017; 67:608-621.e6. [PMID: 28757210 DOI: 10.1016/j.molcel.2017.07.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 05/19/2017] [Accepted: 06/30/2017] [Indexed: 12/31/2022]
Abstract
Transcription is a source of genetic instability that can notably result from the formation of genotoxic DNA:RNA hybrids, or R-loops, between the nascent mRNA and its template. Here we report an unexpected function for introns in counteracting R-loop accumulation in eukaryotic genomes. Deletion of endogenous introns increases R-loop formation, while insertion of an intron into an intronless gene suppresses R-loop accumulation and its deleterious impact on transcription and recombination in yeast. Recruitment of the spliceosome onto the mRNA, but not splicing per se, is shown to be critical to attenuate R-loop formation and transcription-associated genetic instability. Genome-wide analyses in a number of distant species differing in their intron content, including human, further revealed that intron-containing genes and the intron-richest genomes are best protected against R-loop accumulation and subsequent genetic instability. Our results thereby provide a possible rationale for the conservation of introns throughout the eukaryotic lineage.
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Affiliation(s)
- Amandine Bonnet
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Ana R Grosso
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1600-276 Lisboa, Portugal
| | - Abdessamad Elkaoutari
- Cancer Research Center of Marseille (CRCM), Equipe Labellisée Ligue, U1068 INSERM, UMR7258 CNRS, Institut Paoli-Calmettes, Aix Marseille University, 13284 Marseille, France
| | - Emeline Coleno
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Adrien Presle
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Sreerama C Sridhara
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1600-276 Lisboa, Portugal
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, 75015 Paris, France
| | - Vincent Géli
- Cancer Research Center of Marseille (CRCM), Equipe Labellisée Ligue, U1068 INSERM, UMR7258 CNRS, Institut Paoli-Calmettes, Aix Marseille University, 13284 Marseille, France
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1600-276 Lisboa, Portugal
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
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46
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Nishida K, Kuwano Y, Nishikawa T, Masuda K, Rokutan K. RNA Binding Proteins and Genome Integrity. Int J Mol Sci 2017; 18:E1341. [PMID: 28644387 PMCID: PMC5535834 DOI: 10.3390/ijms18071341] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 01/10/2023] Open
Abstract
Genome integrity can be threatened by various endogenous or exogenous events. To counteract these stressors, the DNA damage response network contributes to the prevention and/or repair of genomic DNA damage and serves an essential function in cellular survival. DNA binding proteins are involved in this network. Recently, several RNA-binding proteins (RBPs) that are recruited to DNA damage sites have been shown to be direct players in the prevention or repair of DNA damage. In addition, non-coding RNAs, themselves, are involved in the RNA-mediated DNA repair system. Furthermore, RNA modification such as m6A methylation might also contribute to the ultraviolet-responsive DNA damage response. Accumulating evidence suggests that RNA metabolism is more deeply involved in diverse cellular functions than previously expected, and is also intricately associated with the maintenance of genome integrity. In this review, we highlight the roles of RBPs in the maintenance of genome integrity.
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Affiliation(s)
- Kensei Nishida
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| | - Tatsuya Nishikawa
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| | - Kiyoshi Masuda
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| | - Kazuhito Rokutan
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
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47
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Shafiq S, Chen C, Yang J, Cheng L, Ma F, Widemann E, Sun Q. DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice. MOLECULAR PLANT 2017; 10:821-833. [PMID: 28412545 DOI: 10.1016/j.molp.2017.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/02/2017] [Accepted: 04/03/2017] [Indexed: 05/21/2023]
Abstract
R-loop structures (RNA:DNA hybrids) have important functions in many biological processes, including transcriptional regulation and genome instability among diverse organisms. DNA topoisomerase 1 (TOP1), an essential manipulator of DNA topology during RNA transcription and DNA replication processes, can prevent R-loop accumulation by removing the positive and negative DNA supercoiling that is made by RNA polymerases during transcription. TOP1 is required for plant development, but little is known about its function in preventing co-transcriptional R-loop accumulation in various biological processes in plants. Here we show that knockdown of OsTOP1 strongly affects rice development, causing defects in root architecture and gravitropism, which are the consequences of misregulation of auxin signaling and transporter genes. We found that R-loops are naturally formed at rice auxin-related gene loci, and overaccumulate when OsTOP1 is knocked down or OsTOP1 protein activity is inhibited. OsTOP1 therefore sets the accurate expression levels of auxin-related genes by preventing the overaccumulation of inherent R-loops. Our data reveal R-loops as important factors in polar auxin transport and plant root development, and highlight that OsTOP1 functions as a key to link transcriptional R-loops with plant hormone signaling, provide new insights into transcriptional regulation of hormone signaling in plants.
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Affiliation(s)
- Sarfraz Shafiq
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Permanent affiliation: Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Cheng
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fei Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Emilie Widemann
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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48
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Replication Fork Protection Factors Controlling R-Loop Bypass and Suppression. Genes (Basel) 2017; 8:genes8010033. [PMID: 28098815 PMCID: PMC5295027 DOI: 10.3390/genes8010033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/02/2017] [Accepted: 01/09/2017] [Indexed: 12/17/2022] Open
Abstract
Replication–transcription conflicts have been a well-studied source of genome instability for many years and have frequently been linked to defects in RNA processing. However, recent characterization of replication fork-associated proteins has revealed that defects in fork protection can directly or indirectly stabilize R-loop structures in the genome and promote transcription–replication conflicts that lead to genome instability. Defects in essential DNA replication-associated activities like topoisomerase, or the minichromosome maintenance (MCM) helicase complex, as well as fork-associated protection factors like the Fanconi anemia pathway, both appear to mitigate transcription–replication conflicts. Here, we will highlight recent advances that support the concept that normal and robust replisome function itself is a key component of mitigating R-loop coupled genome instability.
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49
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Lingering Questions about Enhancer RNA and Enhancer Transcription-Coupled Genomic Instability. Trends Genet 2017; 33:143-154. [PMID: 28087167 DOI: 10.1016/j.tig.2016.12.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/22/2016] [Accepted: 12/08/2016] [Indexed: 12/12/2022]
Abstract
Intergenic and intragenic enhancers found inside topologically associated regulatory domains (TADs) express noncoding RNAs, known as enhancer RNAs (eRNAs). Recent studies have indicated these eRNAs play a role in gene regulatory networks by controlling promoter and enhancer interactions and topology of higher-order chromatin structure. Misregulation of enhancer and promoter associated noncoding RNAs (ncRNAs) could stabilize deleterious secondary DNA structures, noncoding RNA associated DNA/RNA hybrid formation, and promote collisions of transcription complexes with replisomes. It is revealing that many chromosomal aberrations, some associated with malignancies, are present inside enhancer and/or promoter sequences. Here, we expand on current concepts to discuss enhancer RNAs and enhancer transcription, and how enhancer transcription influences genomic organization and integrity.
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Barzilai A, Schumacher B, Shiloh Y. Genome instability: Linking ageing and brain degeneration. Mech Ageing Dev 2017; 161:4-18. [DOI: 10.1016/j.mad.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/23/2016] [Accepted: 03/26/2016] [Indexed: 02/06/2023]
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