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Alemi F, Poornajaf Y, Hosseini F, Vahedian V, Gharekhani M, Shoorei H, Taheri M. Interaction between lncRNAs and RNA-binding proteins (RBPs) influences DNA damage response in cancer chemoresistance. Mol Biol Rep 2024; 51:308. [PMID: 38366290 DOI: 10.1007/s11033-024-09288-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024]
Abstract
The DNA damage response (DDR) is a crucial cellular signaling pathway activated in response to DNA damage, including damage caused by chemotherapy. Chemoresistance, which refers to the resistance of cancer cells to the effects of chemotherapy, poses a significant challenge in cancer treatment. Understanding the relationship between DDR and chemoresistance is vital for devising strategies to overcome this resistance and improve treatment outcomes. Long non-coding RNAs (lncRNAs) are a class of RNA molecules that do not code for proteins but play important roles in various biological processes, including cancer development and chemoresistance. RNA-binding proteins (RBPs) are a group of proteins that bind to RNA molecules and regulate their functions. The interaction between lncRNAs and RBPs has been found to regulate gene expression at the post-transcriptional level, thereby influencing various cellular processes, including DDR signaling pathways. Multiple studies have demonstrated that lncRNAs can interact with RBPs to modulate the expression of genes involved in cancer chemoresistance by impacting DDR signaling pathways. Conversely, RBPs can regulate the expression and function of lncRNAs involved in DDR. Exploring these interactions can provide valuable insights for the development of innovative therapeutic approaches to overcome chemoresistance in cancer patients. This review article aims to summarize recent research on the interaction between lncRNAs and RBPs during cancer chemotherapy, with a specific focus on DDR pathways.
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Affiliation(s)
- Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Poornajaf
- Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Foroogh Hosseini
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Vahid Vahedian
- Department of Medical Clinic, Division of Hematology/Oncology and Cellular Therapy, Faculty of Medicine, University of Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Mahdi Gharekhani
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Shoorei
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.
- Rooyesh Infertility Center, Birjand University of Medical Sciences, Birjand, Iran.
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Baralle M, Romano M. Age-Related Alternative Splicing: Driver or Passenger in the Aging Process? Cells 2023; 12:2819. [PMID: 38132139 PMCID: PMC10742131 DOI: 10.3390/cells12242819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy;
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
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Ben-Oz BM, Machour FE, Nicola M, Argoetti A, Polyak G, Hanna R, Kleifeld O, Mandel-Gutfreund Y, Ayoub N. A dual role of RBM42 in modulating splicing and translation of CDKN1A/p21 during DNA damage response. Nat Commun 2023; 14:7628. [PMID: 37993446 PMCID: PMC10665399 DOI: 10.1038/s41467-023-43495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
p53-mediated cell cycle arrest during DNA damage is dependent on the induction of p21 protein, encoded by the CDKN1A gene. p21 inhibits cyclin-dependent kinases required for cell cycle progression to guarantee accurate repair of DNA lesions. Hence, fine-tuning of p21 levels is crucial to preserve genomic stability. Currently, the multilayered regulation of p21 levels during DNA damage is not fully understood. Herein, we identify the human RNA binding motif protein 42 (RBM42) as a regulator of p21 levels during DNA damage. Genome-wide transcriptome and interactome analysis reveals that RBM42 alters the expression of p53-regulated genes during DNA damage. Specifically, we demonstrate that RBM42 facilitates CDKN1A splicing by counteracting the splicing inhibitory effect of RBM4 protein. Unexpectedly, we also show that RBM42, underpins translation of various splicing targets, including CDKN1A. Concordantly, transcriptome-wide mapping of RBM42-RNA interactions using eCLIP further substantiates the dual function of RBM42 in regulating splicing and translation of its target genes, including CDKN1A. Collectively, our data show that RBM42 couples splicing and translation machineries to fine-tune gene expression during DNA damage response.
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Affiliation(s)
- Bella M Ben-Oz
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Feras E Machour
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Marian Nicola
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Amir Argoetti
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Galia Polyak
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Rawad Hanna
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Oded Kleifeld
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Yael Mandel-Gutfreund
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel.
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4
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Harries LW. Dysregulated RNA processing and metabolism: a new hallmark of ageing and provocation for cellular senescence. FEBS J 2023; 290:1221-1234. [PMID: 35460337 DOI: 10.1111/febs.16462] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022]
Abstract
The human genome is capable of producing hundreds of thousands of different proteins and non-coding RNAs from <20 000 genes, in a co-ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence-associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
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Awwad SW, Darawshe MM, Machour FE, Arman I, Ayoub N. Recruitment of RBM6 to DNA Double-Strand Breaks Fosters Homologous Recombination Repair. Mol Cell Biol 2023; 43:130-142. [PMID: 36941773 PMCID: PMC10038030 DOI: 10.1080/10985549.2023.2187105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/20/2022] [Accepted: 02/01/2023] [Indexed: 03/23/2023] Open
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that threaten genome integrity and cell survival. To avoid harmful repercussions of DSBs, a wide variety of DNA repair factors are recruited to execute DSB repair. Previously, we demonstrated that RBM6 splicing factor facilitates homologous recombination (HR) of DSB by regulating alternative splicing-coupled nonstop-decay of the HR protein APBB1/Fe65. Here, we describe a splicing-independent function of RBM6 in promoting HR repair of DSBs. We show that RBM6 is recruited to DSB sites and PARP1 activity indirectly regulates RBM6 recruitment to DNA breakage sites. Deletion mapping analysis revealed a region containing five glycine residues within the G-patch domain that regulates RBM6 accumulation at DNA damage sites. We further ascertain that RBM6 interacts with Rad51, and this interaction is attenuated in RBM6 mutant lacking the G-patch domain (RBM6del(G-patch)). Consequently, RBM6del(G-patch) cells exhibit reduced levels of Rad51 foci after ionizing radiation. In addition, while RBM6 deletion mutant lacking the G-patch domain has no detectable effect on the expression levels of its splicing targets Fe65 and Eya2, it fails to restore the integrity of HR. Altogether, our results suggest that RBM6 recruitment to DSB promotes HR repair, irrespective of its splicing activity.HIGHLIGHTSPARP1 activity indirectly regulates RBM6 recruitment to DNA damage sites.Five glycine residues within the G-patch domain of RBM6 are critical for its recruitment to DNA damage sites, but dispensable for its splicing activity.RBM6 G-patch domain fosters its interaction with Rad51 and promotes Rad51 foci formation following irradiation.RBM6 recruitment to DSB sites underpins HR repair.
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Affiliation(s)
- Samah W. Awwad
- Department of Biology, Technion – Israel Institute of Technology, Haifa, Israel
| | - Malak M. Darawshe
- Department of Biology, Technion – Israel Institute of Technology, Haifa, Israel
| | - Feras E. Machour
- Department of Biology, Technion – Israel Institute of Technology, Haifa, Israel
| | - Inbar Arman
- Department of Biology, Technion – Israel Institute of Technology, Haifa, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion – Israel Institute of Technology, Haifa, Israel
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Simon M, Yang J, Gigas J, Earley EJ, Hillpot E, Zhang L, Zagorulya M, Tombline G, Gilbert M, Yuen SL, Pope A, Van Meter M, Emmrich S, Firsanov D, Athreya A, Biashad SA, Han J, Ryu S, Tare A, Zhu Y, Hudgins A, Atzmon G, Barzilai N, Wolfe A, Moody K, Garcia BA, Thomas DD, Robbins PD, Vijg J, Seluanov A, Suh Y, Gorbunova V. A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A. EMBO J 2022; 41:e110393. [PMID: 36215696 PMCID: PMC9627671 DOI: 10.15252/embj.2021110393] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 02/02/2023] Open
Abstract
Sirtuin 6 (SIRT6) is a deacylase and mono-ADP ribosyl transferase (mADPr) enzyme involved in multiple cellular pathways implicated in aging and metabolism regulation. Targeted sequencing of SIRT6 locus in a population of 450 Ashkenazi Jewish (AJ) centenarians and 550 AJ individuals without a family history of exceptional longevity identified enrichment of a SIRT6 allele containing two linked substitutions (N308K/A313S) in centenarians compared with AJ control individuals. Characterization of this SIRT6 allele (centSIRT6) demonstrated it to be a stronger suppressor of LINE1 retrotransposons, confer enhanced stimulation of DNA double-strand break repair, and more robustly kill cancer cells compared with wild-type SIRT6. Surprisingly, centSIRT6 displayed weaker deacetylase activity, but stronger mADPr activity, over a range of NAD+ concentrations and substrates. Additionally, centSIRT6 displayed a stronger interaction with Lamin A/C (LMNA), which was correlated with enhanced ribosylation of LMNA. Our results suggest that enhanced SIRT6 function contributes to human longevity by improving genome maintenance via increased mADPr activity and enhanced interaction with LMNA.
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Affiliation(s)
- Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jiping Yang
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Jonathan Gigas
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Eric J Earley
- Biostatistics and Epidemiology, RTI International, Durham, NC, USA
| | - Eric Hillpot
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Lei Zhang
- Department of Biochemistry, Molecular Biology and Biophysics and Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Maria Zagorulya
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Greg Tombline
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Michael Gilbert
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samantha L Yuen
- Department of Biochemistry, Molecular Biology and Biophysics and Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Alexis Pope
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | | | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Denis Firsanov
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Advait Athreya
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Jeehae Han
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Seungjin Ryu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Archana Tare
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yizhou Zhu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Adam Hudgins
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | | | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics and Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Paul D Robbins
- Department of Biochemistry, Molecular Biology and Biophysics and Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA
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7
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DNA Damage Regulates the Functions of the RNA Binding Protein Sam68 through ATM-Dependent Phosphorylation. Cancers (Basel) 2022; 14:cancers14163847. [PMID: 36010841 PMCID: PMC9405969 DOI: 10.3390/cancers14163847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/26/2022] [Accepted: 08/05/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Alterations of the complex network of interactions between the DNA damage response pathway and RNA metabolism have been described in several tumors, and increasing efforts are devoted to the elucidation of the molecular mechanisms involved in this network. Previous large-scale proteomic studies identified the RNA binding protein Sam68 as a putative target of the ATM kinase. Herein, we demonstrate that ATM phosphorylates Sam68 upon DNA damage induction, and this post-translational modification regulates both the signaling function of Sam68 in the initial phase of the DNA damage response and its RNA processing activity. Thus, our study uncovers anew crosstalk between ATM and Sam68, which may represent a paradigm for the functional interaction between the DDR pathway and RNA binding proteins, and a possible actionabletarget in human cancers. Abstract Cancer cells frequently exhibit dysregulation of the DNA damage response (DDR), genomic instability, and altered RNA metabolism. Recent genome-wide studies have strongly suggested an interaction between the pathways involved in the cellular response to DDR and in the regulation of RNA metabolism, but the molecular mechanism(s) involved in this crosstalk are largely unknown. Herein, we found that activation of the DDR kinase ATM promotes its interaction with Sam68, leading to phosphorylation of this multifunctional RNA binding protein (RBP) on three residues: threonine 61, serine 388 and serine 390. Moreover, we demonstrate that ATM-dependent phosphorylation of threonine 61 promotes the function of Sam68 in the DDR pathway and enhances its RNA processing activity. Importantly, ATM-mediated phosphorylation of Sam68 in prostate cancer cells modulates alternative polyadenylation of transcripts that are targets of Sam68, supporting the notion that the ATM–Sam68 axis exerts a multifaceted role in the response to DNA damage. Thus, our work validates Sam68 as an ATM kinase substrate and uncovers an unexpected bidirectional interplay between ATM and Sam68, which couples the DDR pathway to modulation of RNA metabolism in response to genotoxic stress.
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Nikolakaki E, Sigala I, Giannakouros T. Good Cop, Bad Cop: The Different Roles of SRPKs. Front Genet 2022; 13:902718. [PMID: 35719374 PMCID: PMC9202992 DOI: 10.3389/fgene.2022.902718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/05/2022] [Indexed: 12/21/2022] Open
Abstract
SR Protein Kinases (SRPKs), discovered approximately 30 years ago, are widely known as splice factor kinases due to their decisive involvement in the regulation of various steps of mRNA splicing. However, they were also shown to regulate diverse cellular activities by phosphorylation of serine residues residing in serine-arginine/arginine-serine dipeptide motifs. Over the last decade, SRPK1 has been reported as both tumor suppressor and promoter, depending on the cellular context and has been implicated in both chemotherapy sensitivity and resistance. Moreover, SRPK2 has been reported to exhibit contradictory functions in different cell contexts promoting either apoptosis or tumor growth. The aim of the current review is to broaden and deepen our understanding of the SRPK function focusing on the subcellular localization of the kinases. There is ample evidence that the balance between cytoplasmic and nuclear SRPK levels is tightly regulated and determines cell response to external signals. Specific cell states coupled to kinase levels, spatial specific interactions with substrates but also changes in the extent of phosphorylation that allow SRPKs to exhibit a rheostat-like control on their substrates, could decide the proliferative or antiproliferative role of SRPKs.
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9
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Machour FE, Abu-Zhayia ER, Awwad SW, Bidany-Mizrahi T, Meinke S, Bishara LA, Heyd F, Aqeilan RI, Ayoub N. RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs. Nucleic Acids Res 2021; 49:11708-11727. [PMID: 34718714 PMCID: PMC8599755 DOI: 10.1093/nar/gkab976] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/26/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins regulate mRNA processing and translation and are often aberrantly expressed in cancer. The RNA-binding motif protein 6, RBM6, is a known alternative splicing factor that harbors tumor suppressor activity and is frequently mutated in human cancer. Here, we identify RBM6 as a novel regulator of homologous recombination (HR) repair of DNA double-strand breaks (DSBs). Mechanistically, we show that RBM6 regulates alternative splicing-coupled nonstop-decay of a positive HR regulator, Fe65/APBB1. RBM6 knockdown leads to a severe reduction in Fe65 protein levels and consequently impairs HR of DSBs. Accordingly, RBM6-deficient cancer cells are vulnerable to ATM and PARP inhibition and show remarkable sensitivity to cisplatin. Concordantly, cisplatin administration inhibits the growth of breast tumor devoid of RBM6 in mouse xenograft model. Furthermore, we observe that RBM6 protein is significantly lost in metastatic breast tumors compared with primary tumors, thus suggesting RBM6 as a potential therapeutic target of advanced breast cancer. Collectively, our results elucidate the link between the multifaceted roles of RBM6 in regulating alternative splicing and HR of DSBs that may contribute to tumorigenesis, and pave the way for new avenues of therapy for RBM6-deficient tumors.
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Affiliation(s)
- Feras E Machour
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Enas R Abu-Zhayia
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Samah W Awwad
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Tirza Bidany-Mizrahi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Stefan Meinke
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Laila A Bishara
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Rami I Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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10
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Cis-acting lnc-Cxcl2 restrains neutrophil-mediated lung inflammation by inhibiting epithelial cell CXCL2 expression in virus infection. Proc Natl Acad Sci U S A 2021; 118:2108276118. [PMID: 34607953 DOI: 10.1073/pnas.2108276118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 12/27/2022] Open
Abstract
Chemokine production by epithelial cells is important for neutrophil recruitment during viral infection, the appropriate regulation of which is critical for restraining inflammation and attenuating subsequent tissue damage. Epithelial cell expression of long noncoding RNAs (lncRNAs), RNA-binding proteins, and their functional interactions during viral infection and inflammation remain to be fully understood. Here, we identified an inducible lncRNA in the Cxcl2 gene locus, lnc-Cxcl2, which could selectively inhibit Cxcl2 expression in mouse lung epithelial cells but not in macrophages. lnc-Cxcl2-deficient mice exhibited increased Cxcl2 expression, enhanced neutrophils recruitment, and more severe inflammation in the lung after influenza virus infection. Mechanistically, nucleus-localized lnc-Cxcl2 bound to Cxcl2 promoter, recruited a ribonucleoprotein La, which inhibited the chromatin accessibility of chemokine promoters, and consequently inhibited Cxcl2 transcription in cis However, unlike mouse lnc-Cxcl2, human lnc-CXCL2-4-1 inhibited multiple immune cytokine expressions including chemokines in human lung epithelial cells. Together, our results demonstrate a self-protecting mechanism within epithelial cells to restrain chemokine and neutrophil-mediated inflammation, providing clues for better understanding chemokine regulation and epithelial cell function in lung viral infection.
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11
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The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing. Nat Commun 2021; 12:3153. [PMID: 34039990 PMCID: PMC8155215 DOI: 10.1038/s41467-021-23505-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
RNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csbm/m developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for transcription-coupled DNA repair disorders. XPA-binding protein (XAB)-2 is the human homologue of the yeast pre-mRNA splicing factor Syf1. Here the authors use an in vivo biotinylation tagging approach to show XAB2’s role in DNA repair, RNA splicing and transcription during mammalian development.
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12
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Mollaei M, Hassan ZM, Khorshidi F, Langroudi L. Chemotherapeutic drugs: Cell death- and resistance-related signaling pathways. Are they really as smart as the tumor cells? Transl Oncol 2021; 14:101056. [PMID: 33684837 PMCID: PMC7938256 DOI: 10.1016/j.tranon.2021.101056] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Chemotherapeutic drugs kill cancer cells or control their progression all over the patient's body, while radiation- and surgery-based treatments perform in a particular site. Based on their mechanisms of action, they are classified into different groups, including alkylating substrates, antimetabolite agents, anti-tumor antibiotics, inhibitors of topoisomerase I and II, mitotic inhibitors, and finally, corticosteroids. Although chemotherapeutic drugs have brought about more life expectancy, two major and severe complications during chemotherapy are chemoresistance and tumor relapse. Therefore, we aimed to review the underlying intracellular signaling pathways involved in cell death and resistance in different chemotherapeutic drug families to clarify the shortcomings in the conventional single chemotherapy applications. Moreover, we have summarized the current combination chemotherapy applications, including numerous combined-, and encapsulated-combined-chemotherapeutic drugs. We further discussed the possibilities and applications of precision medicine, machine learning, next-generation sequencing (NGS), and whole-exome sequencing (WES) in promoting cancer immunotherapies. Finally, some of the recent clinical trials concerning the application of immunotherapies and combination chemotherapies were included as well, in order to provide a practical perspective toward the future of therapies in cancer cases.
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Affiliation(s)
- Mojtaba Mollaei
- Department of Immunology, School of Medicine, Tarbiat Modares University, Tehran, Iran.
| | | | - Fatemeh Khorshidi
- Department of Immunology, School of Medicine, Tarbiat Modares University, Tehran, Iran; Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Langroudi
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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13
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Yuan M, Yu C, Chen X, Wu Y. Investigation on Potential Correlation Between Small Nuclear Ribonucleoprotein Polypeptide A and Lung Cancer. Front Genet 2021; 11:610704. [PMID: 33552128 PMCID: PMC7859448 DOI: 10.3389/fgene.2020.610704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/29/2020] [Indexed: 12/25/2022] Open
Abstract
SNRPA (small nuclear ribonucleoprotein polypeptide A) gene is essential for the pre-mRNA splicing process. Using the available datasets of TCGA or GEO, we aimed at exploring the potential association between the SNRPA gene and lung cancer by several online tools (such as GEIPA2, MEXPRESS, Oncomine) and bioinformatics analysis software (R or GSEA). SNRPA was highly expressed in the tissues of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma tissue (LUSC), compared with control tissues. The high SNRPA expression was associated with a poor survival prognosis of LUAD cases, while the genetic alteration within SNRPA was linked to the overall survival prognosis of LUSC cases. There was a potential correlation between promoter methylation and the expression of SNRPA for LUAD. Compared with normal tissues, we observed a higher phosphorylation level at the S115 site of SNRPA protein (NP_004587.1) (p = 0.002) in the primary LUAD tissues. The potential ATR kinase of the S115 site was predicted. Besides, SNRPA expression in lung cancer was negatively correlated with the infiltration level of M2 macrophage but positively correlated with that of Follicular B helper T cells, in both LUAD and LUSC. The enrichment analysis of SNRPA-correlated genes showed that cell cycle and ubiquitin mechanism-related issues were mainly observed for LUAD; however, RNA splicing-related cellular issues were mainly for LUSC. In summary, the SNRPA gene was identified as a potential prognosis biomarker of lung cancer, especially lung adenocarcinoma, which sheds new light on the association between the spliceosomal complex component and tumorigenesis.
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Affiliation(s)
- Maoxi Yuan
- Department of Thoracic Surgery, Linyi Central Hospital, Linyi, China
| | - Chunmei Yu
- Department of Thoracic Surgery, Linyi Central Hospital, Linyi, China
| | - Xin Chen
- Department of Thoracic Surgery, The People's Hospital of Feixian County, Linyi, China
| | - Yubing Wu
- Department of Thoracic Surgery, Linyi Central Hospital, Linyi, China
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14
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Kim A, Yoon D, Lim Y, Roh HJ, Kim S, Park CI, Kim HS, Cha HJ, Choi YH, Kim DH. Co-Expression Network Analysis of Spleen Transcriptome in Rock Bream ( Oplegnathus fasciatus) Naturally Infected with Rock Bream Iridovirus (RBIV). Int J Mol Sci 2020; 21:ijms21051707. [PMID: 32131541 PMCID: PMC7084886 DOI: 10.3390/ijms21051707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/12/2022] Open
Abstract
Rock bream iridovirus (RBIV) is a notorious agent that causes high mortality in aquaculture of rock bream (Oplegnathus fasciatus). Despite severity of this virus, no transcriptomic studies on RBIV-infected rock bream that can provide fundamental information on protective mechanism against the virus have been reported so far. This study aimed to investigate physiological mechanisms between host and RBIV through transcriptomic changes in the spleen based on RNA-seq. Depending on infection intensity and sampling time point, fish were divided into five groups: uninfected healthy fish at week 0 as control (0C), heavy infected fish at week 0 (0H), heavy mixed RBIV and bacterial infected fish at week 0 (0MH), uninfected healthy fish at week 3 (3C), and light infected fish at week 3 (3L). We explored clusters from 35,861 genes with Fragments Per Kilo-base of exon per Million mapped fragments (FPKM) values of 0.01 or more through signed co-expression network analysis using WGCNA package. Nine of 22 modules were highly correlated with viral infection (|gene significance (GS) vs. module membership (MM) |> 0.5, p-value < 0.05). Expression patterns in selected modules were divided into two: heavy infected (0H and 0MH) and control and light-infected groups (0C, 3C, and 3L). In functional analysis, genes in two positive modules (5448 unigenes) were enriched in cell cycle, DNA replication, transcription, and translation, and increased glycolysis activity. Seven negative modules (3517 unigenes) built in this study showed significant decreases in the expression of genes in lymphocyte-mediated immune system, antigen presentation, and platelet activation, whereas there was significant increased expression of endogenous apoptosis-related genes. These changes lead to RBIV proliferation and failure of host defense, and suggests the importance of blood cells such as thrombocytes and B cells in rock bream in RBIV infection. Interestingly, a hub gene, pre-mRNA processing factor 19 (PRPF19) showing high connectivity (kME), and expression of this gene using qRT-PCR was increased in rock bream blood cells shortly after RBIV was added. It might be a potential biomarker for diagnosis and vaccine studies in rock bream against RBIV. This transcriptome approach and our findings provide new insight into the understanding of global rock bream-RBIV interactions including immune and pathogenesis mechanisms.
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Affiliation(s)
- Ahran Kim
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
| | - Dahye Yoon
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong 27709, Korea
| | - Yunjin Lim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
- Hazardous Substances Analysis Division, Gwangju Regional Office of Food and Drug Safety, Gwangju 61012, Korea
| | - Heyong Jin Roh
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
| | - Suhkmann Kim
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
| | - Chan-Il Park
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, Tongyeong 53064, Korea;
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea;
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Korea;
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dongeui University, Busan 47227, Korea;
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
- Correspondence: ; Tel.: +82-51-629-5945
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15
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Katsogiannou M, Boyer JB, Valdeolivas A, Remy E, Calzone L, Audebert S, Rocchi P, Camoin L, Baudot A. Integrative proteomic and phosphoproteomic profiling of prostate cell lines. PLoS One 2019; 14:e0224148. [PMID: 31675377 PMCID: PMC6824562 DOI: 10.1371/journal.pone.0224148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/06/2019] [Indexed: 12/15/2022] Open
Abstract
Background Prostate cancer is a major public health issue, mainly because patients relapse after androgen deprivation therapy. Proteomic strategies, aiming to reflect the functional activity of cells, are nowadays among the leading approaches to tackle the challenges not only of better diagnosis, but also of unraveling mechanistic details related to disease etiology and progression. Methods We conducted here a large SILAC-based Mass Spectrometry experiment to map the proteomes and phosphoproteomes of four widely used prostate cell lines, namely PNT1A, LNCaP, DU145 and PC3, representative of different cancerous and hormonal status. Results We identified more than 3000 proteins and phosphosites, from which we quantified more than 1000 proteins and 500 phosphosites after stringent filtering. Extensive exploration of this proteomics and phosphoproteomics dataset allowed characterizing housekeeping as well as cell-line specific proteins, phosphosites and functional features of each cell line. In addition, by comparing the sensitive and resistant cell lines, we identified protein and phosphosites differentially expressed in the resistance context. Further data integration in a molecular network highlighted the differentially expressed pathways, in particular migration and invasion, RNA splicing, DNA damage repair response and transcription regulation. Conclusions Overall, this study proposes a valuable resource toward the characterization of proteome and phosphoproteome of four widely used prostate cell lines and reveals candidates to be involved in prostate cancer progression for further experimental validation.
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Affiliation(s)
- Maria Katsogiannou
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- Obstetrics and Gynecology department, Hôpital Saint Joseph, Marseille, France
| | - Jean-Baptiste Boyer
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Alberto Valdeolivas
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- ProGeLife, Marseille, France
| | - Elisabeth Remy
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Laurence Calzone
- Mines Paris Tech, Institut Curie, PSL Research University, Paris, France
| | - Stéphane Audebert
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Palma Rocchi
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail: (PR); (LC); (AB)
| | - Luc Camoin
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail: (PR); (LC); (AB)
| | - Anaïs Baudot
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- * E-mail: (PR); (LC); (AB)
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16
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1571. [PMID: 31657151 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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17
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Taverna E, De Bortoli M, Maffioli E, Corno C, Ciusani E, Trivulzio S, Pinelli A, Tedeschi G, Perego P, Bongarzone I. Alterations of RNA Metabolism by Proteomic Analysis of Breast Cancer Cells Exposed to Marycin: A New Optically Active Porphyrin. Curr Mol Pharmacol 2019; 12:147-159. [DOI: 10.2174/1874467212666190204102112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 01/31/2023]
Abstract
Objective:
Marycin is a porphyrin-type compound synthetically modified to spontaneously
release fluorescence. This study is aimed at understanding possible mechanisms that could account for
the antiproliferative effects observed in marycin. A proteomic approach was used to identify molecular
effects. The proteome of proliferating MDA-MB-231 breast cancer cells was compared with that of
marycin-treated cells.
Methods:
Label-free proteomic analysis by liquid chromatography coupled with tandem mass spectrometry
(LC-MS/MS) was used to reveal changes in protein expression and fluorescence microscopy
and flow cytometry were used to detect subcellular organelle dysfunctions.
Results:
The bioinformatic analysis indicated an enhancement of the expression of proteins remodeling
RNA splicing and more in general, of RNA metabolism. Marycin did not localize into the mitochondria
and did not produce a dramatic increase of ROS levels in MDA-MB-231 cells. Marycin stained organelles
probably peroxisomes.
Conclusions:
The results could support the possibility that the peroxisomes are involved in cell response
to marycin.
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Affiliation(s)
- Elena Taverna
- Molecular Mechanism Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maida De Bortoli
- Molecular Mechanism Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elisa Maffioli
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Cristina Corno
- Center for Nano Science and Technology at Polimi, Istituto Italiano di Tecnologia, Fondazione Filarete, Milan, Italy
| | - Emilio Ciusani
- Center for Nano Science and Technology at Polimi, Istituto Italiano di Tecnologia, Fondazione Filarete, Milan, Italy
| | - Silvio Trivulzio
- Laboratory of Clinical Pathology and Medical Genetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Arnaldo Pinelli
- Laboratory of Clinical Pathology and Medical Genetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Gabriella Tedeschi
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paola Perego
- Dipartimento di Medicina Veterinaria (DiMeVet), University of Milan, Milan, Italy
| | - Italia Bongarzone
- Molecular Mechanism Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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18
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Jimenez M, Arechederra M, Ávila MA, Berasain C. Splicing alterations contributing to cancer hallmarks in the liver: central role of dedifferentiation and genome instability. Transl Gastroenterol Hepatol 2018; 3:84. [PMID: 30505971 DOI: 10.21037/tgh.2018.10.11] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a major cause of cancer-related death worldwide. HCCs are molecularly heterogeneous tumors, and this complexity is to a great extent responsible for their poor response to conventional and targeted therapies. In this review we summarize recent evidence indicating that imbalanced expression of mRNA splicing factors can be a relevant source for this heterogeneity. We also discuss how these alterations may play a driver role in hepatocarcinogenesis by impinging on the general hallmarks of cancer. Considering the natural history of HCC, we focused on two pathogenic features that are characteristic of liver tumors: chromosomal instability and phenotypic de-differentiation. We highlight mechanisms connecting splicing derangement with these two processes and the enabling capacities acquired by liver cells along their neoplastic transformation. A thorough understanding of the alterations in the splicing machinery may also help to identify new HCC biomarkers and to design novel therapeutic strategies.
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Affiliation(s)
- Maddalen Jimenez
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
| | | | - Matías A Ávila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona, Spain
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19
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Biamonti G, Maita L, Montecucco A. The Krebs Cycle Connection: Reciprocal Influence Between Alternative Splicing Programs and Cell Metabolism. Front Oncol 2018; 8:408. [PMID: 30319972 PMCID: PMC6168629 DOI: 10.3389/fonc.2018.00408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a pervasive mechanism that molds the transcriptome to meet cell and organism needs. However, how this layer of gene expression regulation is coordinated with other aspects of the cell metabolism is still largely undefined. Glucose is the main energy and carbon source of the cell. Not surprisingly, its metabolism is finely tuned to satisfy growth requirements and in response to nutrient availability. A number of studies have begun to unveil the connections between glucose metabolism and splicing programs. Alternative splicing modulates the ratio between M1 and M2 isoforms of pyruvate kinase in this way determining the choice between aerobic glycolysis and complete glucose oxidation in the Krebs cycle. Reciprocally, intermediates in the Krebs cycle may impact splicing programs at different levels by modulating the activity of 2-oxoglutarate-dependent oxidases. In this review we discuss the molecular mechanisms that coordinate alternative splicing programs with glucose metabolism, two aspects with profound implications in human diseases.
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Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Lucia Maita
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
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20
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A multi-omics analysis of the regulatory changes induced by miR-223 in a monocyte/macrophage cell line. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2664-2678. [PMID: 29778662 DOI: 10.1016/j.bbadis.2018.05.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023]
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21
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Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-23046. [PMID: 29796170 PMCID: PMC5955416 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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22
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Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, d'Adda di Fagagna F. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev 2018; 118:4365-4403. [PMID: 29600857 DOI: 10.1021/acs.chemrev.7b00487] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.
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Affiliation(s)
- Flavia Michelini
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Sofia Francia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Chance Meers
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Zachary T Neeb
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | | | - Ubaldo Gioia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Julio Aguado
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | | | - Brian Luke
- Institute of Developmental Biology and Neurobiology , Johannes Gutenberg University , 55099 Mainz , Germany.,Institute of Molecular Biology (IMB) , 55128 Mainz , Germany
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Mariusz Nowacki
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | - Francesca Storici
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Piero Carninci
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku , Yokohama City , Kanagawa 230-0045 , Japan
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Fabrizio d'Adda di Fagagna
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
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23
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Coppin L, Leclerc J, Vincent A, Porchet N, Pigny P. Messenger RNA Life-Cycle in Cancer Cells: Emerging Role of Conventional and Non-Conventional RNA-Binding Proteins? Int J Mol Sci 2018; 19:ijms19030650. [PMID: 29495341 PMCID: PMC5877511 DOI: 10.3390/ijms19030650] [Citation(s) in RCA: 34] [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: 12/21/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 02/06/2023] Open
Abstract
Functional specialization of cells and tissues in metazoans require specific gene expression patterns. Biological processes, thus, need precise temporal and spatial coordination of gene activity. Regulation of the fate of messenger RNA plays a crucial role in this context. In the present review, the current knowledge related to the role of RNA-binding proteins in the whole mRNA life-cycle is summarized. This field opens up a new angle for understanding the importance of the post-transcriptional control of gene expression in cancer cells. The emerging role of non-classic RNA-binding proteins is highlighted. The goal of this review is to encourage readers to view, through the mRNA life-cycle, novel aspects of the molecular basis of cancer and the potential to develop RNA-based therapies.
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Affiliation(s)
- Lucie Coppin
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Julie Leclerc
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Audrey Vincent
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Nicole Porchet
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Pascal Pigny
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
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24
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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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25
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Scott DD, Trahan C, Zindy PJ, Aguilar LC, Delubac MY, Van Nostrand EL, Adivarahan S, Wei KE, Yeo GW, Zenklusen D, Oeffinger M. Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism. Nucleic Acids Res 2017; 45:12509-12528. [PMID: 29069457 PMCID: PMC5716212 DOI: 10.1093/nar/gkx963] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, we describe Nol12 as a multifunctional RBP with roles in RNA metabolism and genome maintenance. Nol12 is found in different subcellular compartments-nucleoli, where it associates with ribosomal RNA and is required for efficient separation of large and small subunit precursors at site 2; the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles; as well as GW/P-bodies in the cytoplasm. Loss of Nol12 results in the inability of cells to recover from DNA stress and a rapid p53-independent ATR-Chk1-mediated apoptotic response. Nol12 co-localizes with DNA repair proteins in vivo including Dhx9, as well as with TOPBP1 at sites of replication stalls, suggesting a role for Nol12 in the resolution of DNA stress and maintenance of genome integrity. Identification of a complex Nol12 interactome, which includes NONO, Dhx9, DNA-PK and Stau1, further supports the protein's diverse functions in RNA metabolism and DNA maintenance, establishing Nol12 as a multifunctional RBP essential for genome integrity.
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Affiliation(s)
- Daniel D. Scott
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Pierre J. Zindy
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Lisbeth C. Aguilar
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Marc Y. Delubac
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Eric L. Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Srivathsan Adivarahan
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Karen E. Wei
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Molecular Engineering Laboratory, A*STAR, Singapore
| | - Daniel Zenklusen
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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26
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Auboeuf D. Alternative mRNA processing sites decrease genetic variability while increasing functional diversity. Transcription 2017; 9:75-87. [PMID: 29099315 PMCID: PMC5834221 DOI: 10.1080/21541264.2017.1373891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Recent large-scale RNA sequencing efforts have revealed the extensive diversity of mRNA molecules produced from most eukaryotic coding genes, which arises from the usage of alternative, cryptic or non-canonical splicing and intronic polyadenylation sites. The prevailing view regarding the tremendous diversity of coding gene transcripts is that mRNA processing is a flexible and more-or-less noisy process leading to a diversity of proteins on which natural selection can act depending on protein-mediated cellular functions. However, this concept raises two main questions. First, do alternative mRNA processing pathways have a role other than generating mRNA and protein diversity? Second, is the cellular function of mRNA variants restricted to the biogenesis of functional protein isoforms? Here, I propose that the co-transcriptional use of alternative mRNA processing sites allows first, the resolution of co-transcriptional biophysical constraints that may otherwise result in DNA instability, and second, increases the diversity of cellular functions of mRNAs in a manner that is not restricted to protein synthesis.
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Affiliation(s)
- Didier Auboeuf
- a Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell , 46 Allée d'Italie Site Jacques Monod, Lyon , France
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27
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Lee MYWT, Wang X, Zhang S, Zhang Z, Lee EYC. Regulation and Modulation of Human DNA Polymerase δ Activity and Function. Genes (Basel) 2017; 8:genes8070190. [PMID: 28737709 PMCID: PMC5541323 DOI: 10.3390/genes8070190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 12/28/2022] Open
Abstract
This review focuses on the regulation and modulation of human DNA polymerase δ (Pol δ). The emphasis is on the mechanisms that regulate the activity and properties of Pol δ in DNA repair and replication. The areas covered are the degradation of the p12 subunit of Pol δ, which converts it from a heterotetramer (Pol δ4) to a heterotrimer (Pol δ3), in response to DNA damage and also during the cell cycle. The biochemical mechanisms that lead to degradation of p12 are reviewed, as well as the properties of Pol δ4 and Pol δ3 that provide insights into their functions in DNA replication and repair. The second focus of the review involves the functions of two Pol δ binding proteins, polymerase delta interaction protein 46 (PDIP46) and polymerase delta interaction protein 38 (PDIP38), both of which are multi-functional proteins. PDIP46 is a novel activator of Pol δ4, and the impact of this function is discussed in relation to its potential roles in DNA replication. Several new models for the roles of Pol δ3 and Pol δ4 in leading and lagging strand DNA synthesis that integrate a role for PDIP46 are presented. PDIP38 has multiple cellular localizations including the mitochondria, the spliceosomes and the nucleus. It has been implicated in a number of cellular functions, including the regulation of specialized DNA polymerases, mitosis, the DNA damage response, mouse double minute 2 homolog (Mdm2) alternative splicing and the regulation of the NADPH oxidase 4 (Nox4).
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Affiliation(s)
- Marietta Y W T Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Xiaoxiao Wang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Zhongtao Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Ernest Y C Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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28
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Marchesini M, Ogoti Y, Fiorini E, Aktas Samur A, Nezi L, D'Anca M, Storti P, Samur MK, Ganan-Gomez I, Fulciniti MT, Mistry N, Jiang S, Bao N, Marchica V, Neri A, Bueso-Ramos C, Wu CJ, Zhang L, Liang H, Peng X, Giuliani N, Draetta G, Clise-Dwyer K, Kantarjian H, Munshi N, Orlowski R, Garcia-Manero G, DePinho RA, Colla S. ILF2 Is a Regulator of RNA Splicing and DNA Damage Response in 1q21-Amplified Multiple Myeloma. Cancer Cell 2017; 32:88-100.e6. [PMID: 28669490 PMCID: PMC5593798 DOI: 10.1016/j.ccell.2017.05.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 01/20/2017] [Accepted: 05/22/2017] [Indexed: 12/21/2022]
Abstract
Amplification of 1q21 occurs in approximately 30% of de novo and 70% of relapsed multiple myeloma (MM) and is correlated with disease progression and drug resistance. Here, we provide evidence that the 1q21 amplification-driven overexpression of ILF2 in MM promotes tolerance of genomic instability and drives resistance to DNA-damaging agents. Mechanistically, elevated ILF2 expression exerts resistance to genotoxic agents by modulating YB-1 nuclear localization and interaction with the splicing factor U2AF65, which promotes mRNA processing and the stabilization of transcripts involved in homologous recombination in response to DNA damage. The intimate link between 1q21-amplified ILF2 and the regulation of RNA splicing of DNA repair genes may be exploited to optimize the use of DNA-damaging agents in patients with high-risk MM.
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Affiliation(s)
- Matteo Marchesini
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yamini Ogoti
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elena Fiorini
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anil Aktas Samur
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Luigi Nezi
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marianna D'Anca
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paola Storti
- Department of Clinical and Experimental Medicine, University of Parma, Parma 43100, Italy
| | - Mehmet Kemal Samur
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Irene Ganan-Gomez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Teresa Fulciniti
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Nipun Mistry
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shan Jiang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Naran Bao
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Valentina Marchica
- Department of Clinical and Experimental Medicine, University of Parma, Parma 43100, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milano, Milan 20122, Italy
| | - Carlos Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Cancer Center, Houston, TX 77030, USA
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xinxin Peng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicola Giuliani
- Department of Clinical and Experimental Medicine, University of Parma, Parma 43100, Italy
| | - Giulio Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Karen Clise-Dwyer
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hagop Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nikhil Munshi
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Robert Orlowski
- Department of Lymphoma/Myeloma, The University of Texas MD Cancer Center, Houston, TX 77030, USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simona Colla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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29
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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: 34] [Impact Index Per Article: 4.9] [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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30
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Mec1/ATR, the Program Manager of Nucleic Acids Inc. Genes (Basel) 2016; 8:genes8010010. [PMID: 28036033 PMCID: PMC5295005 DOI: 10.3390/genes8010010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic cells are equipped with surveillance mechanisms called checkpoints to ensure proper execution of cell cycle events. Among these are the checkpoints that detect DNA damage or replication perturbations and coordinate cellular activities to maintain genome stability. At the forefront of damage sensing is an evolutionarily conserved molecule, known respectively in budding yeast and humans as Mec1 (Mitosis entry checkpoint 1) and ATR (Ataxia telangiectasia and Rad3-related protein). Through phosphorylation, Mec1/ATR activates downstream components of a signaling cascade to maintain nucleotide pool balance, protect replication fork integrity, regulate activation of origins of replication, coordinate DNA repair, and implement cell cycle delay. This list of functions continues to expand as studies have revealed that Mec1/ATR modularly interacts with various protein molecules in response to different cellular cues. Among these newly assigned functions is the regulation of RNA metabolism during checkpoint activation and the coordination of replication-transcription conflicts. In this review, I will highlight some of these new functions of Mec1/ATR with a focus on the yeast model organism.
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31
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The increasing diversity of functions attributed to the SAFB family of RNA-/DNA-binding proteins. Biochem J 2016; 473:4271-4288. [DOI: 10.1042/bcj20160649] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/28/2016] [Accepted: 09/02/2016] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins play a central role in cellular metabolism by orchestrating the complex interactions of coding, structural and regulatory RNA species. The SAFB (scaffold attachment factor B) proteins (SAFB1, SAFB2 and SAFB-like transcriptional modulator, SLTM), which are highly conserved evolutionarily, were first identified on the basis of their ability to bind scaffold attachment region DNA elements, but attention has subsequently shifted to their RNA-binding and protein–protein interactions. Initial studies identified the involvement of these proteins in the cellular stress response and other aspects of gene regulation. More recently, the multifunctional capabilities of SAFB proteins have shown that they play crucial roles in DNA repair, processing of mRNA and regulatory RNA, as well as in interaction with chromatin-modifying complexes. With the advent of new techniques for identifying RNA-binding sites, enumeration of individual RNA targets has now begun. This review aims to summarise what is currently known about the functions of SAFB proteins.
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32
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Onyango DO, Howard SM, Neherin K, Yanez DA, Stark JM. Tetratricopeptide repeat factor XAB2 mediates the end resection step of homologous recombination. Nucleic Acids Res 2016; 44:5702-16. [PMID: 27084940 PMCID: PMC4937314 DOI: 10.1093/nar/gkw275] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 04/05/2016] [Indexed: 12/15/2022] Open
Abstract
We examined the influence of the tetratricopeptide repeat factor XAB2 on chromosomal break repair, and found that XAB2 promotes end resection that generates the 3′ ssDNA intermediate for homologous recombination (HR). Namely, XAB2 is important for chromosomal double-strand break (DSB) repair via two pathways of HR that require end resection as an intermediate step, end resection of camptothecin (Cpt)-induced DNA damage, and RAD51 recruitment to ionizing radiation induced foci (IRIF), which requires end resection. Furthermore, XAB2 mediates specific aspects of the DNA damage response associated with end resection proficiency: CtIP hyperphosphorylation induced by Cpt and BRCA1 IRIF. XAB2 also promotes histone acetylation events linked to HR proficiency. From truncation mutation analysis, the capacity for XAB2 to promote HR correlates with its ability to form a complex with ISY1 and PRP19, which show a similar influence as XAB2 on HR. This XAB2 complex localizes to punctate structures consistent with interchromatin granules that show a striking adjacent-localization to the DSB marker γH2AX. In summary, we suggest that the XAB2 complex mediates DNA damage response events important for the end resection step of HR, and speculate that its adjacent-localization relative to DSBs marked by γH2AX is important for this function.
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Affiliation(s)
- David O Onyango
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Sean M Howard
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Kashfia Neherin
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Department of Biology, California State University, San Bernardino, CA 92407 USA; current address University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diana A Yanez
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, USA
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33
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Tresini M, Marteijn JA, Vermeulen W. Bidirectional coupling of splicing and ATM signaling in response to transcription-blocking DNA damage. RNA Biol 2016; 13:272-8. [PMID: 26913497 PMCID: PMC4829274 DOI: 10.1080/15476286.2016.1142039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/08/2016] [Accepted: 01/08/2016] [Indexed: 12/24/2022] Open
Abstract
In response to DNA damage cells activate intricate protein networks to ensure genomic fidelity and tissue homeostasis. DNA damage response signaling pathways coordinate these networks and determine cellular fates, in part, by modulating RNA metabolism. Here we discuss a replication-independent pathway activated by transcription-blocking DNA lesions, which utilizes the ATM signaling kinase to regulate spliceosome function in a reciprocal manner. We present a model according to which, displacement of co-transcriptional spliceosomes from lesion-arrested RNA polymerases, culminates in R-loop formation and non-canonical ATM activation. ATM signals in a feed-forward fashion to further impede spliceosome organization and regulates UV-induced gene expression and alternative splicing genome-wide. This reciprocal coupling between ATM and the spliceosome highlights the importance of ATM signaling in the cellular response to transcription-blocking lesions and supports a key role of the splicing machinery in this process.
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Affiliation(s)
- Maria Tresini
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A. Marteijn
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
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34
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Rubio-Peña K, Fontrodona L, Aristizábal-Corrales D, Torres S, Cornes E, García-Rodríguez FJ, Serrat X, González-Knowles D, Foissac S, Porta-De-La-Riva M, Cerón J. Modeling of autosomal-dominant retinitis pigmentosa in Caenorhabditis elegans uncovers a nexus between global impaired functioning of certain splicing factors and cell type-specific apoptosis. RNA (NEW YORK, N.Y.) 2015; 21:2119-31. [PMID: 26490224 PMCID: PMC4647465 DOI: 10.1261/rna.053397.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/19/2015] [Indexed: 06/05/2023]
Abstract
Retinitis pigmentosa (RP) is a rare genetic disease that causes gradual blindness through retinal degeneration. Intriguingly, seven of the 24 genes identified as responsible for the autosomal-dominant form (adRP) are ubiquitous spliceosome components whose impairment causes disease only in the retina. The fact that these proteins are essential in all organisms hampers genetic, genomic, and physiological studies, but we addressed these difficulties by using RNAi in Caenorhabditis elegans. Our study of worm phenotypes produced by RNAi of splicing-related adRP (s-adRP) genes functionally distinguishes between components of U4 and U5 snRNP complexes, because knockdown of U5 proteins produces a stronger phenotype. RNA-seq analyses of worms where s-adRP genes were partially inactivated by RNAi, revealed mild intron retention in developing animals but not in adults, suggesting a positive correlation between intron retention and transcriptional activity. Interestingly, RNAi of s-adRP genes produces an increase in the expression of atl-1 (homolog of human ATR), which is normally activated in response to replicative stress and certain DNA-damaging agents. The up-regulation of atl-1 correlates with the ectopic expression of the pro-apoptotic gene egl-1 and apoptosis in hypodermal cells, which produce the cuticle, but not in other cell types. Our model in C. elegans resembles s-adRP in two aspects: The phenotype caused by global knockdown of s-adRP genes is cell type-specific and associated with high transcriptional activity. Finally, along with a reduced production of mature transcripts, we propose a model in which the retina-specific cell death in s-adRP patients can be induced through genomic instability.
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Affiliation(s)
- Karinna Rubio-Peña
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Laura Fontrodona
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - David Aristizábal-Corrales
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Silvia Torres
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Eric Cornes
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Francisco J García-Rodríguez
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Xènia Serrat
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - David González-Knowles
- Integromics, Integromics SL, Parque Científico de Madrid, 28760, Tres Cantos, Madrid, Spain
| | | | - Montserrat Porta-De-La-Riva
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain C. elegans Core Facility, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Julián Cerón
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
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Francia S. Non-Coding RNA: Sequence-Specific Guide for Chromatin Modification and DNA Damage Signaling. Front Genet 2015; 6:320. [PMID: 26617633 PMCID: PMC4643122 DOI: 10.3389/fgene.2015.00320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/09/2015] [Indexed: 12/19/2022] Open
Abstract
Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as promote the activation of the DNA damage response (DDR) and DNA repair. Therefore, transcription paradoxically functions to both threaten and safeguard genome integrity. On the other hand, DNA damage signaling is known to modulate chromatin to suppress transcription of the surrounding genetic unit. It is thus intriguing to understand how transcription can modulate DDR signaling while, in turn, DDR signaling represses transcription of chromatin around the DNA lesion. An unexpected player in this field is the RNA interference (RNAi) machinery, which play roles in transcription, splicing and chromatin modulation in several organisms. Non-coding RNAs (ncRNAs) and several protein factors involved in the RNAi pathway are well known master regulators of chromatin while only recent reports show their involvement in DDR. Here, we discuss the experimental evidence supporting the idea that ncRNAs act at the genomic loci from which they are transcribed to modulate chromatin, DDR signaling and DNA repair.
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Affiliation(s)
- Sofia Francia
- IFOM - FIRC Institute of Molecular Oncology Milan, Italy ; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche Pavia, Italy
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Manova V, Gruszka D. DNA damage and repair in plants - from models to crops. FRONTIERS IN PLANT SCIENCE 2015; 6:885. [PMID: 26557130 PMCID: PMC4617055 DOI: 10.3389/fpls.2015.00885] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 10/05/2015] [Indexed: 05/17/2023]
Abstract
The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction. It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity. DNA repair processes have been characterized in bacterial, fungal, and mammalian model systems. The description of these processes in plants, in contrast, was initiated relatively recently and has been focused largely on the model plant Arabidopsis thaliana. Consequently, our knowledge about DNA repair in plant genomes - particularly in the genomes of crop plants - is by far more limited. However, the relatively small size of the Arabidopsis genome, its rapid life cycle and availability of various transformation methods make this species an attractive model for the study of eukaryotic DNA repair mechanisms and mutagenesis. Moreover, abnormalities in DNA repair which proved to be lethal for animal models are tolerated in plant genomes, although sensitivity to DNA damaging agents is retained. Due to the high conservation of DNA repair processes and factors mediating them among eukaryotes, genes and proteins that have been identified in model species may serve to identify homologous sequences in other species, including crop plants, in which these mechanisms are poorly understood. Crop breeding programs have provided remarkable advances in food quality and yield over the last century. Although the human population is predicted to "peak" by 2050, further advances in yield will be required to feed this population. Breeding requires genetic diversity. The biological impact of any mutagenic agent used for the creation of genetic diversity depends on the chemical nature of the induced lesions and on the efficiency and accuracy of their repair. More recent targeted mutagenesis procedures also depend on host repair processes, with different pathways yielding different products. Enhanced understanding of DNA repair processes in plants will inform and accelerate the engineering of crop genomes via both traditional and targeted approaches.
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Affiliation(s)
- Vasilissa Manova
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of SciencesSofia
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, University of SilesiaKatowice, Poland
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Komeno Y, Huang YJ, Qiu J, Lin L, Xu Y, Zhou Y, Chen L, Monterroza DD, Li H, DeKelver RC, Yan M, Fu XD, Zhang DE. SRSF2 Is Essential for Hematopoiesis, and Its Myelodysplastic Syndrome-Related Mutations Dysregulate Alternative Pre-mRNA Splicing. Mol Cell Biol 2015; 35:3071-82. [PMID: 26124281 PMCID: PMC4525309 DOI: 10.1128/mcb.00202-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 06/19/2015] [Indexed: 01/06/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of neoplasms characterized by ineffective myeloid hematopoiesis and various risks for leukemia. SRSF2, a member of the serine/arginine-rich (SR) family of splicing factors, is one of the mutation targets associated with poor survival in patients suffering from myelodysplastic syndromes. Here we report the biological function of SRSF2 in hematopoiesis by using conditional knockout mouse models. Ablation of SRSF2 in the hematopoietic lineage caused embryonic lethality, and Srsf2-deficient fetal liver cells showed significantly enhanced apoptosis and decreased levels of hematopoietic stem/progenitor cells. Induced ablation of SRSF2 in adult Mx1-Cre Srsf2(flox/flox) mice upon poly(I):poly(C) injection demonstrated a significant decrease in lineage(-) Sca(+) c-Kit(+) cells in bone marrow. To reveal the functional impact of myelodysplastic syndromes-associated mutations in SRSF2, we analyzed splicing responses on the MSD-L cell line and found that the missense mutation of proline 95 to histidine (P95H) and a P95-to-R102 in-frame 8-amino-acid deletion caused significant changes in alternative splicing. The affected genes were enriched in cancer development and apoptosis. These findings suggest that intact SRSF2 is essential for the functional integrity of the hematopoietic system and that its mutations likely contribute to development of myelodysplastic syndromes.
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Affiliation(s)
- Yukiko Komeno
- Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Yi-Jou Huang
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Leo Lin
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - YiJun Xu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Liang Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Dora D Monterroza
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Russell C DeKelver
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Ming Yan
- Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Xiang-Dong Fu
- Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Dong-Er Zhang
- Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA Department of Pathology, University of California, San Diego, La Jolla, California, USA
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Cremaschi P, Oliverio M, Leva V, Bione S, Carriero R, Mazzucco G, Palamidessi A, Scita G, Biamonti G, Montecucco A. Chronic Replication Problems Impact Cell Morphology and Adhesion of DNA Ligase I Defective Cells. PLoS One 2015; 10:e0130561. [PMID: 26151554 PMCID: PMC4495043 DOI: 10.1371/journal.pone.0130561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022] Open
Abstract
Moderate DNA damage resulting from metabolic activities or sub-lethal doses of exogenous insults may eventually lead to cancer onset. Human 46BR.1G1 cells bear a mutation in replicative DNA ligase I (LigI) which results in low levels of replication-dependent DNA damage. This replication stress elicits a constitutive phosphorylation of the ataxia telangiectasia mutated (ATM) checkpoint kinase that fails to arrest cell cycle progression or to activate apoptosis or cell senescence. Stable transfection of wild type LigI, as in 7A3 cells, prevents DNA damage and ATM activation. Here we show that parental 46BR.1G1 and 7A3 cells differ in important features such as cell morphology, adhesion and migration. Comparison of gene expression profiles in the two cell lines detects Bio-Functional categories consistent with the morphological and migration properties of LigI deficient cells. Interestingly, ATM inhibition makes 46BR.1G1 more similar to 7A3 cells for what concerns morphology, adhesion and expression of cell-cell adhesion receptors. These observations extend the influence of the DNA damage response checkpoint pathways and unveil a role for ATM kinase activity in modulating cell biology parameters relevant to cancer progression.
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Affiliation(s)
- Paolo Cremaschi
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | - Matteo Oliverio
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Valentina Leva
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Silvia Bione
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Roberta Carriero
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Istituto Universitario di Studi Superiori (IUSS), Pavia, Italy
| | - Giulia Mazzucco
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | | | - Giorgio Scita
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Alessandra Montecucco
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- * E-mail:
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Boucas J, Fritz C, Schmitt A, Riabinska A, Thelen L, Peifer M, Leeser U, Nuernberg P, Altmueller J, Gaestel M, Dieterich C, Reinhardt HC. Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression. PLoS One 2015; 10:e0125745. [PMID: 25993413 PMCID: PMC4439058 DOI: 10.1371/journal.pone.0125745] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/26/2015] [Indexed: 12/11/2022] Open
Abstract
Growing evidence suggests a key role for RNA binding proteins (RBPs) in genome stability programs. Additionally, recent developments in RNA sequencing technologies, as well as mass-spectrometry techniques, have greatly expanded our knowledge on protein-RNA interactions. We here use full transcriptome sequencing and label-free LC/MS/MS to identify global changes in protein-RNA interactions in response to etoposide-induced genotoxic stress. We show that RBPs have distinct binding patterns in response to genotoxic stress and that inactivation of the RBP regulator module, p38/MK2, can affect the entire spectrum of protein-RNA interactions that take place in response to stress. In addition to validating the role of known RBPs like Srsf1, Srsf2, Elavl1 in the genotoxic stress response, we add a new collection of RBPs to the DNA damage response. We identify Khsrp as a highly regulated RBP in response to genotoxic stress and further validate its role as a driver of the G1/S transition through the suppression of Cdkn1aP21 transcripts. Finally, we identify KHSRP as an indicator of overall survival, as well as disease free survival in glioblastoma multiforme.
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Affiliation(s)
- Jorge Boucas
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
- * E-mail: (HCR); (JB)
| | - Christian Fritz
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Anna Schmitt
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Arina Riabinska
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Lisa Thelen
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Uschi Leeser
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Peter Nuernberg
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Janine Altmueller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Matthias Gaestel
- Institute of Biochemistry, Hannover Medical School, Hannover, Germany
| | - Christoph Dieterich
- Computational RNA Biology and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Straße 9b, 50913, Cologne, Germany
| | - H. Christian Reinhardt
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
- * E-mail: (HCR); (JB)
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40
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Henriksson S, Farnebo M. On the road with WRAP53β: guardian of Cajal bodies and genome integrity. Front Genet 2015; 6:91. [PMID: 25852739 PMCID: PMC4371746 DOI: 10.3389/fgene.2015.00091] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/19/2015] [Indexed: 12/16/2022] Open
Abstract
The WRAP53 gene encodes both an antisense transcript (WRAP53α) that stabilizes the tumor suppressor p53 and a protein (WRAP53β) involved in maintenance of Cajal bodies, telomere elongation and DNA repair. WRAP53β is one of many proteins containing WD40 domains, known to mediate a variety of cellular processes. These proteins lack enzymatic activity, acting instead as platforms for the assembly of large complexes of proteins and RNAs thus facilitating their interactions. WRAP53β mediates site-specific interactions between Cajal body factors and DNA repair proteins. Moreover, dysfunction of this protein has been linked to premature aging, cancer and neurodegeneration. Here we summarize the current state of knowledge concerning the multifaceted roles of WRAP53β in intracellular trafficking, formation of the Cajal body, DNA repair and maintenance of genomic integrity and discuss potential crosstalk between these processes.
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Affiliation(s)
- Sofia Henriksson
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm, Sweden
| | - Marianne Farnebo
- Department of Oncology-Pathology, Cancer Centrum Karolinska, Karolinska Institutet Stockholm, Sweden
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41
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Krajewska M, Fehrmann RSN, de Vries EGE, van Vugt MATM. Regulators of homologous recombination repair as novel targets for cancer treatment. Front Genet 2015; 6:96. [PMID: 25852742 PMCID: PMC4367534 DOI: 10.3389/fgene.2015.00096] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/23/2015] [Indexed: 12/20/2022] Open
Abstract
To cope with DNA damage, cells possess a complex signaling network called the ‘DNA damage response’, which coordinates cell cycle control with DNA repair. The importance of this network is underscored by the cancer predisposition that frequently goes along with hereditary mutations in DNA repair genes. One especially important DNA repair pathway in this respect is homologous recombination (HR) repair. Defects in HR repair are observed in various cancers, including hereditary breast, and ovarian cancer. Intriguingly, tumor cells with defective HR repair show increased sensitivity to chemotherapeutic reagents, including platinum-containing agents. These observations suggest that HR-proficient tumor cells might be sensitized to chemotherapeutics if HR repair could be therapeutically inactivated. HR repair is an extensively regulated process, which depends strongly on the activity of various other pathways, including cell cycle pathways, protein-control pathways, and growth factor-activated receptor signaling pathways. In this review, we discuss how the mechanistic wiring of HR is controlled by cell-intrinsic or extracellular pathways. Furthermore, we have performed a meta-analysis on available genome-wide RNA interference studies to identify additional pathways that control HR repair. Finally, we discuss how these HR-regulatory pathways may provide therapeutic targets in the context of radio/chemosensitization.
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Affiliation(s)
- Małgorzata Krajewska
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Elisabeth G E de Vries
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen Groningen, Netherlands
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42
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Sánchez-Jiménez C, Ludeña MD, Izquierdo JM. T-cell intracellular antigens function as tumor suppressor genes. Cell Death Dis 2015; 6:e1669. [PMID: 25741594 PMCID: PMC4385921 DOI: 10.1038/cddis.2015.43] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/16/2014] [Accepted: 01/19/2015] [Indexed: 12/12/2022]
Abstract
Knockdown of T-cell intracellular antigens TIA1 and TIAR in transformed cells triggers cell proliferation and tumor growth. Using a tetracycline-inducible system, we report here that an increased expression of TIA1 or TIAR in 293 cells results in reduced rates of cell proliferation. Ectopic expression of these proteins abolish endogenous TIA1 and TIAR levels via the regulation of splicing of their pre-mRNAs, and partially represses global translation in a phospho-eukaryotic initiation factor 2 alpha-dependent manner. This is accompanied by cell cycle arrest at G1/S and cell death through caspase-dependent apoptosis and autophagy. Genome-wide profiling illustrates a selective upregulation of p53 signaling pathway-related genes. Nude mice injected with doxycycline-inducible cells expressing TIA1 or TIAR retard, or even inhibit, growth of xenotumors. Remarkably, low expressions of TIA1 and TIAR correlate with poor prognosis in patients with lung squamous cell carcinoma. These findings strongly support the concept that TIA proteins act as tumor suppressor genes.
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Affiliation(s)
- C Sánchez-Jiménez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera 1, Madrid, Spain
| | - M D Ludeña
- Facultad de Medicina, Departamento de Biología Celular y Patología, Universidad de Salamanca-Hospital Universitario de Salamanca, C/ Paseo de San Vicente 58-182, Salamanca, Spain
| | - J M Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera 1, Madrid, Spain
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43
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Montecucco A, Zanetta F, Biamonti G. Molecular mechanisms of etoposide. EXCLI JOURNAL 2015; 14:95-108. [PMID: 26600742 PMCID: PMC4652635 DOI: 10.17179/excli2015-561] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/24/2014] [Indexed: 12/21/2022]
Abstract
Etoposide derives from podophyllotoxin, a toxin found in the American Mayapple. It was first synthesized in 1966 and approved for cancer therapy in 1983 by the U.S. Food and Drug Administration (Hande, 1998[25]). Starting from 1980s several studies demonstrated that etoposide targets DNA topoisomerase II activities thus leading to the production of DNA breaks and eliciting a response that affects several aspects of cell metabolisms. In this review we will focus on molecular mechanisms that account for the biological effect of etoposide.
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Affiliation(s)
| | - Francesca Zanetta
- Istituto di Genetica Molecolare, CNR, via Abbiategrasso 207, Pavia ; Dipartimento di Biologia e Biotecnologia, Università degli Studi di Pavia, via Ferrata 9, Pavia, Italy
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44
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End of the beginning: elongation and termination features of alternative modes of chromosomal replication initiation in bacteria. PLoS Genet 2015; 11:e1004909. [PMID: 25569209 PMCID: PMC4287441 DOI: 10.1371/journal.pgen.1004909] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In bacterial cells, bidirectional replication of the circular chromosome is initiated from a single origin (oriC) and terminates in an antipodal terminus region such that movement of the pair of replication forks is largely codirectional with transcription. The terminus region is flanked by discrete Ter sequences that act as polar, or direction-dependent, arrest sites for fork progression. Alternative oriC-independent modes of replication initiation are possible, one of which is constitutive stable DNA replication (cSDR) from transcription-associated RNA–DNA hybrids or R-loops. Here, I discuss the distinctive attributes of fork progression and termination associated with different modes of bacterial replication initiation. Two hypothetical models are proposed: that head-on collisions between pairs of replication forks, which are a feature of replication termination in all kingdoms of life, provoke bilateral fork reversal reactions; and that cSDR is characterized by existence of distinct subpopulations in bacterial cultures and a widespread distribution of origins in the genome, each with a small firing potential. Since R-loops are known to exist in eukaryotic cells and to inflict genome damage in G1 phase, it is possible that cSDR-like events promote aberrant replication initiation even in eukaryotes.
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Li S, Li Z, Shu FJ, Xiong H, Phillips AC, Dynan WS. Double-strand break repair deficiency in NONO knockout murine embryonic fibroblasts and compensation by spontaneous upregulation of the PSPC1 paralog. Nucleic Acids Res 2014; 42:9771-80. [PMID: 25100870 PMCID: PMC4150768 DOI: 10.1093/nar/gku650] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
NONO, SFPQ and PSPC1 make up a family of proteins with diverse roles in transcription, RNA processing and DNA double-strand break (DSB) repair. To understand long-term effects of loss of NONO, we characterized murine embryonic fibroblasts (MEFs) from knockout mice. In the absence of genotoxic stress, wild-type and mutant MEFs showed similar growth rates and cell cycle distributions, and the mutants were only mildly radiosensitive. Further investigation showed that NONO deficiency led to upregulation of PSPC1, which replaced NONO in a stable complex with SFPQ. Knockdown of PSPC1 in a NONO-deficient background led to severe radiosensitivity and delayed resolution of DSB repair foci. The DNA-dependent protein kinase (DNA-PK) inhibitor, NU7741, sensitized wild-type and singly deficient MEFs, but had no additional effect on doubly deficient cells, suggesting that NONO/PSPC1 and DNA-PK function in the same pathway. We tested whether NONO and PSPC1 might also affect repair indirectly by influencing mRNA levels for other DSB repair genes. Of 12 genes tested, none were downregulated, and several were upregulated. Thus, NONO or related proteins are critical for DSB repair, NONO and PSPC1 are functional homologs with partially interchangeable functions and a compensatory response involving PSPC1 blunts the effect of NONO deficiency.
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Affiliation(s)
- Shuyi Li
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA Department of Biochemistry, Emory University, Atlanta, GA 30322, USA Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, GA 30912, USA
| | - Zhentian Li
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA Department of Biochemistry, Emory University, Atlanta, GA 30322, USA Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, GA 30912, USA
| | - Feng-Jue Shu
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
| | - Hairong Xiong
- Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, GA 30912, USA State Key Laboratory of Virology/Institute of Medical Virology, Wuhan University, Wuhan 430071, China
| | - Andrew C Phillips
- Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, GA 30912, USA
| | - William S Dynan
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA Department of Biochemistry, Emory University, Atlanta, GA 30322, USA Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, GA 30912, USA
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Britton S, Dernoncourt E, Delteil C, Froment C, Schiltz O, Salles B, Frit P, Calsou P. DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal. Nucleic Acids Res 2014; 42:9047-62. [PMID: 25030905 PMCID: PMC4132723 DOI: 10.1093/nar/gku601] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We previously identified the heterogeneous ribonucleoprotein SAF-A/hnRNP U as a substrate for DNA-PK, a protein kinase involved in DNA damage response (DDR). Using laser micro-irradiation in human cells, we report here that SAF-A exhibits a two-phase dynamics at sites of DNA damage, with a rapid and transient recruitment followed by a prolonged exclusion. SAF-A recruitment corresponds to its binding to Poly(ADP-ribose) while its exclusion is dependent on the activity of ATM, ATR and DNA-PK and reflects the dissociation from chromatin of SAF-A associated with ongoing transcription. Having established that SAF-A RNA-binding domain recapitulates SAF-A dynamics, we show that this domain is part of a complex comprising several mRNA biogenesis proteins of which at least two, FUS/TLS and TAFII68/TAF15, exhibit similar biphasic dynamics at sites of damage. Using an original reporter for live imaging of DNA:RNA hybrids (R-loops), we show a transient transcription-dependent accumulation of R-loops at sites of DNA damage that is prolonged upon inhibition of RNA biogenesis factors exclusion. We propose that a new component of the DDR is an active anti-R-loop mechanism operating at damaged transcribed sites which includes the exclusion of mRNA biogenesis factors such as SAF-A, FUS and TAF15.
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Affiliation(s)
- Sébastien Britton
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Emma Dernoncourt
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Christine Delteil
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Carine Froment
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Odile Schiltz
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Bernard Salles
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
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Cau P, Navarro C, Harhouri K, Roll P, Sigaudy S, Kaspi E, Perrin S, De Sandre-Giovannoli A, Lévy N. WITHDRAWN: Nuclear matrix, nuclear envelope and premature aging syndromes in a translational research perspective. Semin Cell Dev Biol 2014:S1084-9521(14)00058-5. [PMID: 24685615 DOI: 10.1016/j.semcdb.2014.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/03/2014] [Accepted: 03/09/2014] [Indexed: 10/25/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.semcdb.2014.03.022. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Pierre Cau
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(2).
| | - Claire Navarro
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1)
| | - Karim Harhouri
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1)
| | - Patrice Roll
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(2)
| | - Sabine Sigaudy
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(3)
| | - Elise Kaspi
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(2)
| | - Sophie Perrin
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1)
| | - Annachiara De Sandre-Giovannoli
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(3)
| | - Nicolas Lévy
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France(1); AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France(3).
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Cau P, Navarro C, Harhouri K, Roll P, Sigaudy S, Kaspi E, Perrin S, De Sandre-Giovannoli A, Lévy N. Nuclear matrix, nuclear envelope and premature aging syndromes in a translational research perspective. Semin Cell Dev Biol 2014; 29:125-47. [PMID: 24662892 DOI: 10.1016/j.semcdb.2014.03.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lamin A-related progeroid syndromes are genetically determined, extremely rare and severe. In the past ten years, our knowledge and perspectives for these diseases has widely progressed, through the progressive dissection of their pathophysiological mechanisms leading to precocious and accelerated aging, from the genes mutations discovery until therapeutic trials in affected children. A-type lamins are major actors in several structural and functional activities at the nuclear periphery, as they are major components of the nuclear lamina. However, while this is usually poorly considered, they also play a key role within the rest of the nucleoplasm, whose defects are related to cell senescence. Although nuclear shape and nuclear envelope deformities are obvious and visible events, nuclear matrix disorganization and abnormal composition certainly represent the most important causes of cell defects with dramatic pathological consequences. Therefore, lamin-associated diseases should be better referred as laminopathies instead of envelopathies, this later being too restrictive, considering neither the key structural and functional roles of soluble lamins in the entire nucleoplasm, nor the nuclear matrix contribution to the pathophysiology of lamin-associated disorders and in particular in defective lamin A processing-associated aging diseases. Based on both our understanding of pathophysiological mechanisms and the biological and clinical consequences of progeria and related diseases, therapeutic trials have been conducted in patients and were terminated less than 10 years after the gene discovery, a quite fast issue for a genetic disease. Pharmacological drugs have been repurposed and used to decrease the toxicity of the accumulated, unprocessed and truncated prelaminA in progeria. To date, none of them may be considered as a cure for progeria and these clinical strategies were essentially designed toward reducing a subset of the most dramatic and morbid features associated to progeria. New therapeutic strategies under study, in particular targeting the protein expression pathway at the mRNA level, have shown a remarkable efficacy both in vitro in cells and in vivo in mice models. Strategies intending to clear the toxic accumulated proteins from the nucleus are also under evaluation. However, although exceedingly rare, improving our knowledge of genetic progeroid syndromes and searching for innovative and efficient therapies in these syndromes is of paramount importance as, even before they can be used to save lives, they may significantly (i) expand the affected childrens' lifespan and preserve their quality of life; (ii) improve our understanding of aging-related disorders and other more common diseases; and (iii) expand our fundamental knowledge of physiological aging and its links with major physiological processes such as those involved in oncogenesis.
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Affiliation(s)
- Pierre Cau
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France.
| | - Claire Navarro
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Karim Harhouri
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Patrice Roll
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France
| | - Sabine Sigaudy
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France
| | - Elise Kaspi
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Service de Biologie Cellulaire, Hôpital La Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France
| | - Sophie Perrin
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Annachiara De Sandre-Giovannoli
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France
| | - Nicolas Lévy
- Aix-Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; INSERM, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France; AP-HM, Département de Génétique Médicale, Hôpital d'enfants Timone, 264 Rue Saint Pierre, 13385 Marseille Cedex 5, France.
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Biamonti G, Catillo M, Pignataro D, Montecucco A, Ghigna C. The alternative splicing side of cancer. Semin Cell Dev Biol 2014; 32:30-6. [PMID: 24657195 DOI: 10.1016/j.semcdb.2014.03.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/11/2014] [Indexed: 12/22/2022]
Abstract
Alternative splicing emerges as a potent and pervasive mechanism of gene expression regulation that expands the coding capacity of the genome and forms an intermediate layer of regulation between transcriptional and post-translational networks. Indeed, alternative splicing occupies a pivotal position in developmental programs and in the cell response to external and internal stimuli. Not surprisingly, therefore, its deregulation frequently leads to human disease. In this review we provide an updated overview of the impact of alternative splicing on tumorigenesis. Moreover, we discuss the intricacy of the reciprocal interactions between alternative splicing programs and signal transduction pathways, which appear to be crucially linked to cancer progression in response to the tumor microenvironment. Finally, we focus on the recently described interplay between splicing and chromatin organization which is expected to shed new lights into gene expression regulation in normal and cancer cells.
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Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy.
| | - Morena Catillo
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
| | - Daniela Pignataro
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
| | | | - Claudia Ghigna
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
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Biagiotti S, Menotta M, Giacomini E, Radici L, Bianchi M, Bozzao C, Chessa L, Magnani M. Forward subtractive libraries containing genes transactivated by dexamethasone in ataxia-telangiectasia lymphoblastoid cells. Mol Cell Biochem 2014; 392:13-30. [DOI: 10.1007/s11010-014-2013-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/28/2014] [Indexed: 11/30/2022]
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