51
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Wang CC. Metabolic Stress Adaptations Underlie Mammary Gland Morphogenesis and Breast Cancer Progression. Cells 2021; 10:2641. [PMID: 34685621 PMCID: PMC8534177 DOI: 10.3390/cells10102641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
Breast cancers display dynamic reprogrammed metabolic activities as cancers develop from premalignant lesions to primary tumors, and then metastasize. Numerous advances focus on how tumors develop pro-proliferative metabolic signaling that differs them from adjacent, non-transformed epithelial tissues. This leads to targetable oncogene-driven liabilities among breast cancer subtypes. Other advances demonstrate how microenvironments trigger stress-response at single-cell resolution. Microenvironmental heterogeneities give rise to cell regulatory states in cancer cell spheroids in three-dimensional cultures and at stratified terminal end buds during mammary gland morphogenesis, where stress and survival signaling juxtapose. The cell-state specificity in stress signaling networks recapture metabolic evolution during cancer progression. Understanding lineage-specific metabolic phenotypes in experimental models is useful for gaining a deeper understanding of subtype-selective breast cancer metabolism.
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Affiliation(s)
- Chun-Chao Wang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan; ; Tel.: +886-3-516-2589
- Department of Medical Science, National Tsing Hua University, Hsinchu 30013, Taiwan
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52
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Castillo-Guzman D, Chédin F. Defining R-loop classes and their contributions to genome instability. DNA Repair (Amst) 2021; 106:103182. [PMID: 34303066 PMCID: PMC8691176 DOI: 10.1016/j.dnarep.2021.103182] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/20/2023]
Abstract
R-loops are non-B DNA structures that form during transcription when the nascent RNA anneals to the template DNA strand forming a RNA:DNA hybrid. Understanding the genomic distribution and function of R-loops is an important goal, since R-loops have been implicated in a number of adaptive and maladaptive processes under physiological and pathological conditions. Based on R-loop mapping datasets, we propose the existence of two main classes of R-loops, each associated with unique characteristics. Promoter-paused R-loops (Class I) are short R-loops that form at high frequency during promoter-proximal pausing by RNA polymerase II. Elongation-associated R-loops (Class II) are long structures that occur throughout gene bodies at modest frequencies. We further discuss the relationships between each R-loop class with instances of genome instability and suggest that increased class I R-loops, resulting from enhanced promoter-proximal pausing, represent the main culprits for R-loop mediated genome instability under pathological conditions.
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Affiliation(s)
- Daisy Castillo-Guzman
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA, 95616, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA, 95616, United States.
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53
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Racca C, Britton S, Hédouin S, Francastel C, Calsou P, Larminat F. BRCA1 prevents R-loop-associated centromeric instability. Cell Death Dis 2021; 12:896. [PMID: 34599155 PMCID: PMC8486751 DOI: 10.1038/s41419-021-04189-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/01/2021] [Accepted: 09/15/2021] [Indexed: 02/05/2023]
Abstract
Centromeres are defined by chromatin containing the histone H3 variant CENP-A assembled onto repetitive α-satellite sequences, which are actively transcribed throughout the cell cycle. Centromeres play an essential role in chromosome inheritance and genome stability through coordinating kinetochores assembly during mitosis. Structural and functional alterations of the centromeres cause aneuploidy and chromosome aberrations which can induce cell death. In human cells, the tumor suppressor BRCA1 associates with centromeric chromatin in the absence of exogenous damage. While we previously reported that BRCA1 contributes to proper centromere homeostasis, the mechanism underlying its centromeric function and recruitment was not fully understood. Here, we show that BRCA1 association with centromeric chromatin depends on the presence of R-loops, which are non-canonical three-stranded structures harboring a DNA:RNA hybrid and are frequently formed during transcription. Subsequently, BRCA1 counteracts the accumulation of R-loops at centromeric α-satellite repeats. Strikingly, BRCA1-deficient cells show impaired localization of CENP-A, higher transcription of centromeric RNA, increased breakage at centromeres and formation of acentric micronuclei, all these features being R-loop-dependent. Finally, BRCA1 depletion reveals a Rad52-dependent hyper-recombination process between centromeric satellite repeats, associated with centromere instability and missegregation. Altogether, our findings provide molecular insights into the key function of BRCA1 in maintaining centromere stability and identity.
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Affiliation(s)
- Carine Racca
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue contre le Cancer, 2018, Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue contre le Cancer, 2018, Toulouse, France
| | - Sabrine Hédouin
- Université de Paris, Epigénétique et Destin Cellulaire, CNRS, Paris, F-75013, France.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Claire Francastel
- Université de Paris, Epigénétique et Destin Cellulaire, CNRS, Paris, F-75013, France
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue contre le Cancer, 2018, Toulouse, France
| | - Florence Larminat
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France. .,Equipe Labellisée Ligue contre le Cancer, 2018, Toulouse, France.
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54
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Beyond the Double-Strand Breaks: The Role of DNA Repair Proteins in Cancer Stem-Cell Regulation. Cancers (Basel) 2021; 13:cancers13194818. [PMID: 34638302 PMCID: PMC8508278 DOI: 10.3390/cancers13194818] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cancer stem cells (CSCs) are a tumor cell population maintaining tumor growth and promoting tumor relapse if not wholly eradicated during treatment. CSCs are often equipped with molecular mechanisms making them resistant to conventional anti-cancer therapies whose curative potential depends on DNA damage-induced cell death. An elevated expression of some key DNA repair proteins is one of such defense mechanisms. However, new research reveals that the role of critical DNA repair proteins is extending far beyond the DNA repair mechanisms. This review discusses the diverse biological functions of DNA repair proteins in CSC maintenance and the adaptation to replication and oxidative stress, anti-cancer immune response, epigenetic reprogramming, and intracellular signaling mechanisms. It also provides an overview of their potential therapeutic targeting. Abstract Cancer stem cells (CSCs) are pluripotent and highly tumorigenic cells that can re-populate a tumor and cause relapses even after initially successful therapy. As with tissue stem cells, CSCs possess enhanced DNA repair mechanisms. An active DNA damage response alleviates the increased oxidative and replicative stress and leads to therapy resistance. On the other hand, mutations in DNA repair genes cause genomic instability, therefore driving tumor evolution and developing highly aggressive CSC phenotypes. However, the role of DNA repair proteins in CSCs extends beyond the level of DNA damage. In recent years, more and more studies have reported the unexpected role of DNA repair proteins in the regulation of transcription, CSC signaling pathways, intracellular levels of reactive oxygen species (ROS), and epithelial–mesenchymal transition (EMT). Moreover, DNA damage signaling plays an essential role in the immune response towards tumor cells. Due to its high importance for the CSC phenotype and treatment resistance, the DNA damage response is a promising target for individualized therapies. Furthermore, understanding the dependence of CSC on DNA repair pathways can be therapeutically exploited to induce synthetic lethality and sensitize CSCs to anti-cancer therapies. This review discusses the different roles of DNA repair proteins in CSC maintenance and their potential as therapeutic targets.
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55
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Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13153755. [PMID: 34359660 PMCID: PMC8345052 DOI: 10.3390/cancers13153755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Multiple myeloma is a hematologic cancer characterized by the accumulation of malignant plasma cells in the bone marrow. It remains a mostly incurable disease due to the inability to overcome refractory disease and drug-resistant relapse. Oncogenic transformation of PC in multiple myeloma is thought to occur within the secondary lymphoid organs. However, the precise molecular events leading to myelomagenesis remain obscure. Here, we identified genes involved in the prevention and the resolution of conflicts between the replication and transcription significantly overexpressed during the plasma cell differentiation process and in multiple myeloma cells. We discussed the potential role of these factors in myelomagenesis and myeloma biology. The specific targeting of these factors might constitute a new therapeutic strategy in multiple myeloma. Abstract Plasma cells (PCs) have an essential role in humoral immune response by secretion of antibodies, and represent the final stage of B lymphocytes differentiation. During this differentiation, the pre-plasmablastic stage is characterized by highly proliferative cells that start to secrete immunoglobulins (Igs). Thus, replication and transcription must be tightly regulated in these cells to avoid transcription/replication conflicts (TRCs), which could increase replication stress and lead to genomic instability. In this review, we analyzed expression of genes involved in TRCs resolution during B to PC differentiation and identified 41 genes significantly overexpressed in the pre-plasmablastic stage. This illustrates the importance of mechanisms required for adequate processing of TRCs during PCs differentiation. Furthermore, we identified that several of these factors were also found overexpressed in purified PCs from patients with multiple myeloma (MM) compared to normal PCs. Malignant PCs produce high levels of Igs concomitantly with cell cycle deregulation. Therefore, increasing the TRCs occurring in MM cells could represent a potent therapeutic strategy for MM patients. Here, we describe the potential roles of TRCs resolution factors in myelomagenesis and discuss the therapeutic interest of targeting the TRCs resolution machinery in MM.
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56
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Xiao K, Liu S, Xiao Y, Wang Y, Zhu Z, Wang Y, Tong D, Jiang J. Bioinformatics prediction of differential miRNAs in non-small cell lung cancer. PLoS One 2021; 16:e0254854. [PMID: 34288959 PMCID: PMC8294502 DOI: 10.1371/journal.pone.0254854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/03/2021] [Indexed: 12/26/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) accounts for 85% of all lung cancers. The drug resistance of NSCLC has clinically increased. This study aimed to screen miRNAs associated with NSCLC using bioinformatics analysis. We hope that the screened miRNA can provide a research direction for the subsequent treatment of NSCLC. Methods We screened out the common miRNAs after compared the NSCLC-related genes in the TCGA database and GEO database. Selected miRNA was performed ROC analysis, survival analysis, and enrichment analysis (GO term and KEGG pathway). Results A total of 21 miRNAs were screened in the two databases. And they were all highly expressed in normal and low in cancerous tissues. Hsa-mir-30a was selected by ROC analysis and survival analysis. Enrichment analysis showed that the function of hsa-mir-30a is mainly related to cell cycle regulation and drug metabolism. Conclusion Our study found that hsa-mir-30a was differentially expressed in NSCLC, and it mainly affected NSCLC by regulating the cell cycle and drug metabolism.
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Affiliation(s)
- Kui Xiao
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China
- The Respiratory Disease Diagnosis and Treatment Center of Hunan Province, Changsha, Hunan, China
| | - Shenggang Liu
- Department of Pulmonary and Critical Care Medicine, University of South China Affiliated Changsha Central Hospital, Changsha City, Hunan Province, China
| | - Yijia Xiao
- Department of Pulmonary and Critical Care Medicine, University of South China Affiliated Changsha Central Hospital, Changsha City, Hunan Province, China
| | - Yang Wang
- Department of Pathology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiruo Zhu
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China
- The Respiratory Disease Diagnosis and Treatment Center of Hunan Province, Changsha, Hunan, China
| | - Yaohui Wang
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China
- The Respiratory Disease Diagnosis and Treatment Center of Hunan Province, Changsha, Hunan, China
| | - De Tong
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China
- The Respiratory Disease Diagnosis and Treatment Center of Hunan Province, Changsha, Hunan, China
| | - Jiehan Jiang
- Department of Pulmonary and Critical Care Medicine, University of South China Affiliated Changsha Central Hospital, Changsha City, Hunan Province, China
- * E-mail:
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57
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Crossley MP, Brickner JR, Song C, Zar SMT, Maw SS, Chédin F, Tsai MS, Cimprich KA. Catalytically inactive, purified RNase H1: A specific and sensitive probe for RNA-DNA hybrid imaging. J Cell Biol 2021; 220:212458. [PMID: 34232287 PMCID: PMC8266564 DOI: 10.1083/jcb.202101092] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures with both physiological and pathological roles in cells. R-loop imaging generally relies on detection of the RNA-DNA hybrid component of these structures using the S9.6 antibody. We show that the use of this antibody for imaging can be problematic because it readily binds to double-stranded RNA (dsRNA) in vitro and in vivo, giving rise to nonspecific signal. In contrast, purified, catalytically inactive human RNase H1 tagged with GFP (GFP-dRNH1) is a more specific reagent for imaging RNA-DNA hybrids. GFP-dRNH1 binds strongly to RNA-DNA hybrids but not to dsRNA oligonucleotides in fixed human cells and is not susceptible to binding endogenous RNA. Furthermore, we demonstrate that purified GFP-dRNH1 can be applied to fixed cells to detect hybrids after their induction, thereby bypassing the need for cell line engineering. GFP-dRNH1 therefore promises to be a versatile tool for imaging and quantifying RNA-DNA hybrids under a wide range of conditions.
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Affiliation(s)
- Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Chenlin Song
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Su Mon Thin Zar
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Su S Maw
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA
| | - Miaw-Sheue Tsai
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
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58
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Bossaert M, Pipier A, Riou JF, Noirot C, Nguyên LT, Serre RF, Bouchez O, Defrancq E, Calsou P, Britton S, Gomez D. Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands. eLife 2021; 10:65184. [PMID: 34180392 PMCID: PMC8279764 DOI: 10.7554/elife.65184] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/16/2021] [Indexed: 12/11/2022] Open
Abstract
G-quadruplexes (G4) are non-canonical DNA structures found in the genome of most species including human. Small molecules stabilizing these structures, called G4 ligands, have been identified and, for some of them, shown to induce cytotoxic DNA double-strand breaks. Through the use of an unbiased genetic approach, we identify here topoisomerase 2α (TOP2A) as a major effector of cytotoxicity induced by two clastogenic G4 ligands, pyridostatin and CX-5461, the latter molecule currently undergoing phase I/II clinical trials in oncology. We show that both TOP2 activity and transcription account for DNA break production following G4 ligand treatments. In contrast, clastogenic activity of these G4 ligands is countered by topoisomerase 1 (TOP1), which limits co-transcriptional G4 formation, and by factors promoting transcriptional elongation. Altogether our results support that clastogenic G4 ligands act as DNA structure-driven TOP2 poisons at transcribed regions bearing G4 structures.
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Affiliation(s)
- Madeleine Bossaert
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Angélique Pipier
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Jean-Francois Riou
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS, INSERM, Paris, France
| | - Céline Noirot
- INRAE, UR 875, Unité de Mathématique et Informatique Appliquées, Genotoul Bioinfo, Castanet-Tolosan, France
| | - Linh-Trang Nguyên
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Eric Defrancq
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, Grenoble, France
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Dennis Gomez
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
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59
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Vohhodina J, Goehring LJ, Liu B, Kong Q, Botchkarev VV, Huynh M, Liu Z, Abderazzaq FO, Clark AP, Ficarro SB, Marto JA, Hatchi E, Livingston DM. BRCA1 binds TERRA RNA and suppresses R-Loop-based telomeric DNA damage. Nat Commun 2021; 12:3542. [PMID: 34112789 PMCID: PMC8192922 DOI: 10.1038/s41467-021-23716-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
R-loop structures act as modulators of physiological processes such as transcription termination, gene regulation, and DNA repair. However, they can cause transcription-replication conflicts and give rise to genomic instability, particularly at telomeres, which are prone to forming DNA secondary structures. Here, we demonstrate that BRCA1 binds TERRA RNA, directly and physically via its N-terminal nuclear localization sequence, as well as telomere-specific shelterin proteins in an R-loop-, and a cell cycle-dependent manner. R-loop-driven BRCA1 binding to CpG-rich TERRA promoters represses TERRA transcription, prevents TERRA R-loop-associated damage, and promotes its repair, likely in association with SETX and XRN2. BRCA1 depletion upregulates TERRA expression, leading to overly abundant TERRA R-loops, telomeric replication stress, and signs of telomeric aberrancy. Moreover, BRCA1 mutations within the TERRA-binding region lead to an excess of TERRA-associated R-loops and telomeric abnormalities. Thus, normal BRCA1/TERRA binding suppresses telomere-centered genome instability. BRCA1-mediated resolution of R-loops has previously been described. Here the authors reveal a functional association of BRCA1 with TERRA RNA at telomeres, which develops in an R-loop-, and a cell cycle-dependent manner.
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Affiliation(s)
- Jekaterina Vohhodina
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Liana J Goehring
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ben Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Qing Kong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Vladimir V Botchkarev
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mai Huynh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zhiqi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fieda O Abderazzaq
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Allison P Clark
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elodie Hatchi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - David M Livingston
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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60
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Neiger HE, Siegler EL, Shi Y. Breast Cancer Predisposition Genes and Synthetic Lethality. Int J Mol Sci 2021; 22:5614. [PMID: 34070674 PMCID: PMC8198377 DOI: 10.3390/ijms22115614] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
BRCA1 and BRCA2 are tumor suppressor genes with pivotal roles in the development of breast and ovarian cancers. These genes are essential for DNA double-strand break repair via homologous recombination (HR), which is a virtually error-free DNA repair mechanism. Following BRCA1 or BRCA2 mutations, HR is compromised, forcing cells to adopt alternative error-prone repair pathways that often result in tumorigenesis. Synthetic lethality refers to cell death caused by simultaneous perturbations of two genes while change of any one of them alone is nonlethal. Therefore, synthetic lethality can be instrumental in identifying new therapeutic targets for BRCA1/2 mutations. PARP is an established synthetic lethal partner of the BRCA genes. Its role is imperative in the single-strand break DNA repair system. Recently, Olaparib (a PARP inhibitor) was approved for treatment of BRCA1/2 breast and ovarian cancer as the first successful synthetic lethality-based therapy, showing considerable success in the development of effective targeted cancer therapeutics. Nevertheless, the possibility of drug resistance to targeted cancer therapy based on synthetic lethality necessitates the development of additional therapeutic options. This literature review addresses cancer predisposition genes, including BRCA1, BRCA2, and PALB2, synthetic lethality in the context of DNA repair machinery, as well as available treatment options.
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Affiliation(s)
- Hannah E. Neiger
- College of Graduate Studies, California Northstate University, Elk Grove, CA 95757, USA;
| | - Emily L. Siegler
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA;
| | - Yihui Shi
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA;
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61
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San Martin Alonso M, Noordermeer S. Untangling the crosstalk between BRCA1 and R-loops during DNA repair. Nucleic Acids Res 2021; 49:4848-4863. [PMID: 33755171 PMCID: PMC8136775 DOI: 10.1093/nar/gkab178] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 01/13/2023] Open
Abstract
R-loops are RNA:DNA hybrids assembled during biological processes but are also linked to genetic instability when formed out of their natural context. Emerging evidence suggests that the repair of DNA double-strand breaks requires the formation of a transient R-loop, which eventually must be removed to guarantee a correct repair process. The multifaceted BRCA1 protein has been shown to be recruited at this specific break-induced R-loop, and it facilitates mechanisms in order to regulate R-loop removal. In this review, we discuss the different potential roles of BRCA1 in R-loop homeostasis during DNA repair and how these processes ensure faithful DSB repair.
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Affiliation(s)
- Marta San Martin Alonso
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
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62
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Ashour ME, Mosammaparast N. Mechanisms of damage tolerance and repair during DNA replication. Nucleic Acids Res 2021; 49:3033-3047. [PMID: 33693881 PMCID: PMC8034635 DOI: 10.1093/nar/gkab101] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/28/2021] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
Accurate duplication of chromosomal DNA is essential for the transmission of genetic information. The DNA replication fork encounters template lesions, physical barriers, transcriptional machinery, and topological barriers that challenge the faithful completion of the replication process. The flexibility of replisomes coupled with tolerance and repair mechanisms counteract these replication fork obstacles. The cell possesses several universal mechanisms that may be activated in response to various replication fork impediments, but it has also evolved ways to counter specific obstacles. In this review, we will discuss these general and specific strategies to counteract different forms of replication associated damage to maintain genomic stability.
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Affiliation(s)
- Mohamed Elsaid Ashour
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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63
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Park K, Ryoo J, Jeong H, Kim M, Lee S, Hwang SY, Ahn J, Kim D, Moon HC, Baek D, Kim K, Park HY, Ahn K. Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription-replication conflict regions. PLoS Genet 2021; 17:e1009523. [PMID: 33857133 PMCID: PMC8078737 DOI: 10.1371/journal.pgen.1009523] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/27/2021] [Accepted: 03/29/2021] [Indexed: 12/25/2022] Open
Abstract
The comorbid association of autoimmune diseases with cancers has been a major obstacle to successful anti-cancer treatment. Cancer survival rate decreases significantly in patients with preexisting autoimmunity. However, to date, the molecular and cellular profiles of such comorbidities are poorly understood. We used Aicardi-Goutières syndrome (AGS) as a model autoimmune disease and explored the underlying mechanisms of genome instability in AGS-associated-gene-deficient patient cells. We found that R-loops are highly enriched at transcription-replication conflict regions of the genome in fibroblast of patients bearing SAMHD1 mutation, which is the AGS-associated-gene mutation most frequently reported with tumor and malignancies. In SAMHD1-depleted cells, R-loops accumulated with the concomitant activation of DNA damage responses. Removal of R-loops in SAMHD1 deficiency reduced cellular responses to genome instability. Furthermore, downregulation of SAMHD1 expression is associated with various types of cancer and poor survival rate. Our findings suggest that SAMHD1 functions as a tumor suppressor by resolving R-loops, and thus, SAMHD1 and R-loop may be novel diagnostic markers and targets for patient stratification in anti-cancer therapy. Mutations in SAMHD1 cause Aicardi-Goutières syndrome (AGS), a monogenic lupus-like autoimmune disease. Among AGS-associated genes, SAMHD1 is most frequently mutates in various types of tumors and malignancies, suggesting that it is biologically relevant to cancer development. Here, we show that SAMHD1 resolves R-loops induced by transcription-replication conflicts, thereby contributing to the maintenance of genome stability. Our findings provide insight into the molecular and mechanical understanding of the autoimmunity and cancer comorbidity, and suggest that SAMHD1 and R-loops are potential and reliable biomarkers in anti-cancer therapeutics.
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Affiliation(s)
- Kiwon Park
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jeongmin Ryoo
- Department of Hematology, Oncology and Stem Cell transplantation, Comprehensive Cancer center Freiburg, University of Freiburg, Freiburg, Germany
| | - Heena Jeong
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minsu Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sungwon Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sung-Yeon Hwang
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jiyoung Ahn
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Doyeon Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyungseok C. Moon
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Kwangseog Ahn
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail:
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64
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R-loops as Janus-faced modulators of DNA repair. Nat Cell Biol 2021; 23:305-313. [PMID: 33837288 DOI: 10.1038/s41556-021-00663-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 02/01/2023]
Abstract
R-loops are non-B DNA structures with intriguing dual consequences for gene expression and genome stability. In addition to their recognized roles in triggering DNA double-strand breaks (DSBs), R-loops have recently been demonstrated to accumulate in cis to DSBs, especially those induced in transcriptionally active loci. In this Review, we discuss whether R-loops actively participate in DSB repair or are detrimental by-products that must be removed to avoid genome instability.
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65
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Fu Y, Liu Q, Bao Q, Wen J, Liu Z, Hu Y, He G, Peng C, Xu Y, Zhang W. Development and analysis of long non-coding RNA-associated competing endogenous RNA network for osteosarcoma metastasis. Hereditas 2021; 158:9. [PMID: 33593435 PMCID: PMC7887822 DOI: 10.1186/s41065-021-00174-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
Background Osteosarcoma is the primary bone malignant neoplasm that often develops metastasis. Increasing evidences have shown that non-coding RNAs (ncRNAs) relate to the progression of osteosarcoma. However, the ncRNAs’ roles in osteosarcoma metastasis are still unknown. Methods Differentially expressed (DE) RNAs were identified from Gene Expression Omnibus (GEO) database. Protein-protein interaction (PPI) of DE messenger RNAs (DEmRNAs) was built through STRING database. The target mRNAs and long ncRNAs (lncRNAs) of microRNAs (miRNA) were predicted through miRDB, Targetscan and Genecode databases, which then cross-checked with previously obtained DERNAs to construct competing endogenous RNA (ceRNA) network. All networks were visualized via Cytoscape and the hub RNAs were screened out through Cytoscape plug-in Cytohubba. The gene functional and pathway analyses were performed through DAVID and MirPath databases. The survival analyses of hub RNAs were obtained through Kaplan-Meier (KM) survival curves. Results Five hundred sixty-four DEmRNAs, 16 DElncRNAs and 22 DEmiRNAs were screened out. GO functional and KEGG pathway analyses showed that DERNAs were significantly associated with tumor metastasis. The ceRNA network including 6 lncRNAs, 55 mRNAs and 20 miRNAs were constructed and the top 10 hub RNAs were obtained. Above all, PI3K/AKT signaling pathway was identified as the most important osteosarcoma metastasis-associated pathway and its hub ceRNA module was constructed. The survival analyses showed that the RNAs in hub ceRNA module closely related to osteosarcoma patients’ prognosis. Conclusions The current study provided a new perspective on osteosarcoma metastasis. More importantly, the RNAs in hub ceRNA module might act as the novel therapeutic targets and prognostic factors for osteosarcoma patients. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-021-00174-0.
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Affiliation(s)
- Yucheng Fu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Qi Liu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Qiyuan Bao
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Junxiang Wen
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Zhuochao Liu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Yuehao Hu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Guoyu He
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Cheng Peng
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Yiqi Xu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Weibin Zhang
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China.
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66
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Patel PS, Abraham KJ, Guturi KKN, Halaby MJ, Khan Z, Palomero L, Ho B, Duan S, St-Germain J, Algouneh A, Mateo F, El Ghamrasni S, Barbour H, Barnes DR, Beesley J, Sanchez O, Berman HK, Brown GW, El Bachir Affar, Chenevix-Trench G, Antoniou AC, Arrowsmith CH, Raught B, Pujana MA, Mekhail K, Hakem A, Hakem R. RNF168 regulates R-loop resolution and genomic stability in BRCA1/2-deficient tumors. J Clin Invest 2021; 131:140105. [PMID: 33529165 PMCID: PMC7843228 DOI: 10.1172/jci140105] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA1/2) genes considerably increase breast and ovarian cancer risk. Given that tumors with these mutations have elevated genomic instability, they exhibit relative vulnerability to certain chemotherapies and targeted treatments based on poly (ADP-ribose) polymerase (PARP) inhibition. However, the molecular mechanisms that influence cancer risk and therapeutic benefit or resistance remain only partially understood. BRCA1 and BRCA2 have also been implicated in the suppression of R-loops, triple-stranded nucleic acid structures composed of a DNA:RNA hybrid and a displaced ssDNA strand. Here, we report that loss of RNF168, an E3 ubiquitin ligase and DNA double-strand break (DSB) responder, remarkably protected Brca1-mutant mice against mammary tumorigenesis. We demonstrate that RNF168 deficiency resulted in accumulation of R-loops in BRCA1/2-mutant breast and ovarian cancer cells, leading to DSBs, senescence, and subsequent cell death. Using interactome assays, we identified RNF168 interaction with DHX9, a helicase involved in the resolution and removal of R-loops. Mechanistically, RNF168 directly ubiquitylated DHX9 to facilitate its recruitment to R-loop-prone genomic loci. Consequently, loss of RNF168 impaired DHX9 recruitment to R-loops, thereby abrogating its ability to resolve R-loops. The data presented in this study highlight a dependence of BRCA1/2-defective tumors on factors that suppress R-loops and reveal a fundamental RNF168-mediated molecular mechanism that governs cancer development and vulnerability.
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Affiliation(s)
- Parasvi S. Patel
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Karan Joshua Abraham
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Kiran Kumar Naidu Guturi
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Marie-Jo Halaby
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Zahra Khan
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Luis Palomero
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Brandon Ho
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Arash Algouneh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Francesca Mateo
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Haithem Barbour
- Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Daniel R. Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Beesley
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Otto Sanchez
- University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - Hal K. Berman
- Toronto General Research Institute, Toronto, Ontario, Canada
| | - Grant W. Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - El Bachir Affar
- Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | | | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Miquel Angel Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Anne Hakem
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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67
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Rinaldi C, Pizzul P, Longhese MP, Bonetti D. Sensing R-Loop-Associated DNA Damage to Safeguard Genome Stability. Front Cell Dev Biol 2021; 8:618157. [PMID: 33505970 PMCID: PMC7829580 DOI: 10.3389/fcell.2020.618157] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
DNA transcription and replication are two essential physiological processes that can turn into a threat for genome integrity when they compete for the same DNA substrate. During transcription, the nascent RNA strongly binds the template DNA strand, leading to the formation of a peculiar RNA-DNA hybrid structure that displaces the non-template single-stranded DNA. This three-stranded nucleic acid transition is called R-loop. Although a programed formation of R-loops plays important physiological functions, these structures can turn into sources of DNA damage and genome instability when their homeostasis is altered. Indeed, both R-loop level and distribution in the genome are tightly controlled, and the list of factors involved in these regulatory mechanisms is continuously growing. Over the last years, our knowledge of R-loop homeostasis regulation (formation, stabilization, and resolution) has definitely increased. However, how R-loops affect genome stability and how the cellular response to their unscheduled formation is orchestrated are still not fully understood. In this review, we will report and discuss recent findings about these questions and we will focus on the role of ATM- and Rad3-related (ATR) and Ataxia-telangiectasia-mutated (ATM) kinases in the activation of an R-loop-dependent DNA damage response.
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Affiliation(s)
- Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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68
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Dhar S, Datta A, Brosh RM. DNA helicases and their roles in cancer. DNA Repair (Amst) 2020; 96:102994. [PMID: 33137625 DOI: 10.1016/j.dnarep.2020.102994] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022]
Abstract
DNA helicases, known for their fundamentally important roles in genomic stability, are high profile players in cancer. Not only are there monogenic helicase disorders with a strong disposition to cancer, it is well appreciated that helicase variants are associated with specific cancers (e.g., breast cancer). Flipping the coin, DNA helicases are frequently overexpressed in cancerous tissues and reduction in helicase gene expression results in reduced proliferation and growth capacity, as well as DNA damage induction and apoptosis of cancer cells. The seminal roles of helicases in the DNA damage and replication stress responses, as well as DNA repair pathways, validate their vital importance in cancer biology and suggest their potential values as targets in anti-cancer therapy. In recent years, many laboratories have characterized the specialized roles of helicase to resolve transcription-replication conflicts, maintain telomeres, mediate cell cycle checkpoints, remodel stalled replication forks, and regulate transcription. In vivo models, particularly mice, have been used to interrogate helicase function and serve as a bridge for preclinical studies that may lead to novel therapeutic approaches. In this review, we will summarize our current knowledge of DNA helicases and their roles in cancer, emphasizing the latest developments.
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Affiliation(s)
- Srijita Dhar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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Abstract
Physiological and pathological roles for R-loop structures continue to be discovered, and studies suggest that R-loops could contribute to human disease. R-loops are nucleic acid structures characterized by a DNA:RNA hybrid and displaced single-stranded DNA that occur in connection with transcription. R-loops form naturally and have been shown to be important for a number of physiological processes such as mitochondrial replication initiation, class switch recombination, DNA repair, modulating DNA topology, and regulation of gene expression. However, subsets of R-loops or persistent R-loops lead to DNA breaks, chromosome rearrangement, and genome instability. In addition, R-loops have been linked to human diseases, specifically neurological disorders and cancer. Of the large amount of research produced recently on R-loops, this review covers evidence for R-loop involvement in normal cellular physiology and pathophysiology, as well as describing factors that contribute to R-loop regulation.
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Affiliation(s)
- Ryan Patrick Mackay
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Qinqin Xu
- Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Paul M Weinberger
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA.,Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
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70
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Crossley MP, Bocek MJ, Hamperl S, Swigut T, Cimprich KA. qDRIP: a method to quantitatively assess RNA-DNA hybrid formation genome-wide. Nucleic Acids Res 2020; 48:e84. [PMID: 32544226 PMCID: PMC7641308 DOI: 10.1093/nar/gkaa500] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022] Open
Abstract
R-loops are dynamic, co-transcriptional nucleic acid structures that facilitate physiological processes but can also cause DNA damage in certain contexts. Perturbations of transcription or R-loop resolution are expected to change their genomic distribution. Next-generation sequencing approaches to map RNA–DNA hybrids, a component of R-loops, have so far not allowed quantitative comparisons between such conditions. Here, we describe quantitative differential DNA–RNA immunoprecipitation (qDRIP), a method combining synthetic RNA–DNA-hybrid internal standards with high-resolution, strand-specific sequencing. We show that qDRIP avoids biases inherent to read-count normalization by accurately profiling signal in regions unaffected by transcription inhibition in human cells, and by facilitating accurate differential peak calling between conditions. We also use these quantitative comparisons to make the first estimates of the absolute count of RNA–DNA hybrids per cell and their half-lives genome-wide. Finally, we identify a subset of RNA–DNA hybrids with high GC skew which are partially resistant to RNase H. Overall, qDRIP allows for accurate normalization in conditions where R-loops are perturbed and for quantitative measurements that provide previously unattainable biological insights.
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Affiliation(s)
- Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bocek
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephan Hamperl
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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71
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Kim S, Kang N, Park SH, Wells J, Hwang T, Ryu E, Kim BG, Hwang S, Kim SJ, Kang S, Lee S, Stirling P, Myung K, Lee KY. ATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork. Nucleic Acids Res 2020; 48:7218-7238. [PMID: 32542338 PMCID: PMC7367208 DOI: 10.1093/nar/gkaa501] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/27/2022] Open
Abstract
R-loops are formed when replicative forks collide with the transcriptional machinery and can cause genomic instability. However, it is unclear how R-loops are regulated at transcription-replication conflict (TRC) sites and how replisome proteins are regulated to prevent R-loop formation or mediate R-loop tolerance. Here, we report that ATAD5, a PCNA unloader, plays dual functions to reduce R-loops both under normal and replication stress conditions. ATAD5 interacts with RNA helicases such as DDX1, DDX5, DDX21 and DHX9 and increases the abundance of these helicases at replication forks to facilitate R-loop resolution. Depletion of ATAD5 or ATAD5-interacting RNA helicases consistently increases R-loops during the S phase and reduces the replication rate, both of which are enhanced by replication stress. In addition to R-loop resolution, ATAD5 prevents the generation of new R-loops behind the replication forks by unloading PCNA which, otherwise, accumulates and persists on DNA, causing a collision with the transcription machinery. Depletion of ATAD5 reduces transcription rates due to PCNA accumulation. Consistent with the role of ATAD5 and RNA helicases in maintaining genomic integrity by regulating R-loops, the corresponding genes were mutated or downregulated in several human tumors.
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Affiliation(s)
- Sangin Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - James Wells
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada
| | - Taejoo Hwang
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Seong-Jung Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Semin Lee
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Peter Stirling
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
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Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
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Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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73
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New insight into the biology of R-loops. Mutat Res 2020; 821:111711. [PMID: 32516653 DOI: 10.1016/j.mrfmmm.2020.111711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 11/24/2022]
Abstract
R-loops form when RNA hybridizes with its template DNA generating a three-stranded structure leaving a displaced single strand non-template DNA. During transcription negative supercoiling of DNA behind the advancing RNA polymerase will facilitate the formation of R-loops by the nascent RNA as the DNA is under wound to facilitate transcription. In theory R-loops are classified into pathological and non-pathological depending on the context of its formation. R-loop which are formed normally in various physiological events like in gene regulation and at immunoglobulin class switch regions are considered non-pathological, whereas abnormally stable R-loop which leads to genomic instability are considered pathological. Although pathological R-loop formation is a rare event but once formed completely blocks transcription, mRNA export, elevates mutagenesis, and inhibits gene expression. Hence, R-loop either prevents or induces genomic instability indirectly and are potentially an endogenous source of DNA lesion. Although the existence of R-loop has been reported few decades ago, but only recently we have gained knowledge about its formation and resolution in cells due to the availability of reagents. R-loop biology has generated immense interest in past few years since it connects the important biological processes such as transcription, mRNA splicing, DNA replication, recombination and repair. In this review I will focus on the recent progress made about formation and resolution of R-loop, based on the methodologies that are currently available to study R-loop using biochemical, cell biology and molecular biology approaches.
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Singh AK, Yu X. Tissue-Specific Carcinogens as Soil to Seed BRCA1/2-Mutant Hereditary Cancers. Trends Cancer 2020; 6:559-568. [PMID: 32336659 DOI: 10.1016/j.trecan.2020.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 02/06/2023]
Abstract
Despite their ubiquitous expression, the inheritance of monoallelic germline mutations in breast cancer susceptibility gene type 1 or 2 (BRCA1/2) poses tissue-specific variations in cancer risks and primarily associate with familial breast and ovarian cancers. The molecular basis of this tissue-specific tumor incidence remains unknown and intriguing to cancer researchers. A plethora of recent reports support the idea that several nongenetic factors present in the tissue microenvironment could induce tumors in the mutant BRCA1/2 background. This Opinion article summarizes the recent advances on tissue-specific carcinogens and their complex crosstalk with the compromised DNA repair machinery of BRCA1/2-mutant cells. Finally, we present our perspective on the therapeutic and chemopreventive interpretations of these developments.
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Affiliation(s)
- Anup Kumar Singh
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
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Berthel E, Vincent A, Eberst L, Torres AG, Dacheux E, Rey C, Marcel V, Paraqindes H, Lachuer J, Catez F, de Pouplana LR, Treilleux I, Diaz JJ, Dalla Venezia N. Uncovering the Translational Regulatory Activity of the Tumor Suppressor BRCA1. Cells 2020; 9:cells9040941. [PMID: 32290274 PMCID: PMC7226996 DOI: 10.3390/cells9040941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/30/2020] [Accepted: 04/04/2020] [Indexed: 12/24/2022] Open
Abstract
BRCA1 inactivation is a hallmark of familial breast cancer, often associated with aggressive triple negative breast cancers. BRCA1 is a tumor suppressor with known functions in DNA repair, transcription regulation, cell cycle control, and apoptosis. In the present study, we demonstrate that BRCA1 is also a translational regulator. We previously showed that BRCA1 was implicated in translation regulation. Here, we asked whether translational control could be a novel function of BRCA1 that contributes to its tumor suppressive activity. A combination of RNA-binding protein immunoprecipitation, microarray analysis, and polysome profiling, was used to identify the mRNAs that were specifically deregulated under BRCA1 deficiency. Western blot analysis allowed us to confirm at the protein level the deregulated translation of a subset of mRNAs. A unique and dedicated cohort of patients with documented germ-line BRCA1 pathogenic variant statues was set up, and tissue microarrays with the biopsies of these patients were constructed and analyzed by immunohistochemistry for their content in each candidate protein. Here, we show that BRCA1 translationally regulates a subset of mRNAs with which it associates. These mRNAs code for proteins involved in major programs in cancer. Accordingly, the level of these key proteins is correlated with BRCA1 status in breast cancer cell lines and in patient breast tumors. ADAT2, one of these key proteins, is proposed as a predictive biomarker of efficacy of treatments recently recommended to patients with BRCA1 deficiency. This study proposes that translational control may represent a novel molecular mechanism with potential clinical impact through which BRCA1 is a tumor suppressor.
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Affiliation(s)
- Elise Berthel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Anne Vincent
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Lauriane Eberst
- Centre Léon Bérard, Medical Oncology Department, Université de Lyon 1, F-69008 Lyon, France;
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (A.G.T.); (L.R.d.P.)
| | - Estelle Dacheux
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Catherine Rey
- ProfileXpert, UNIV-US7 INSERM-UMS 3453 CNRS, F-69000 Lyon, France; (C.R.); (J.L.)
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Hermes Paraqindes
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Joël Lachuer
- ProfileXpert, UNIV-US7 INSERM-UMS 3453 CNRS, F-69000 Lyon, France; (C.R.); (J.L.)
| | - Frédéric Catez
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (A.G.T.); (L.R.d.P.)
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Isabelle Treilleux
- Department of Translational Research and Innovation, Centre Léon Bérard, F-69008 Lyon, France;
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Nicole Dalla Venezia
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
- Correspondence: ; Tel.: +33-426-556-745
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Trabert B, Sherman ME, Kannan N, Stanczyk FZ. Progesterone and Breast Cancer. Endocr Rev 2020; 41:5568276. [PMID: 31512725 PMCID: PMC7156851 DOI: 10.1210/endrev/bnz001] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 09/06/2019] [Indexed: 12/31/2022]
Abstract
Synthetic progestogens (progestins) have been linked to increased breast cancer risk; however, the role of endogenous progesterone in breast physiology and carcinogenesis is less clearly defined. Mechanistic studies using cell culture, tissue culture, and preclinical models implicate progesterone in breast carcinogenesis. In contrast, limited epidemiologic data generally do not show an association of circulating progesterone levels with risk, and it is unclear whether this reflects methodologic limitations or a truly null relationship. Challenges related to defining the role of progesterone in breast physiology and neoplasia include: complex interactions with estrogens and other hormones (eg, androgens, prolactin, etc.), accounting for timing of blood collections for hormone measurements among cycling women, and limitations of assays to measure progesterone metabolites in blood and progesterone receptor isotypes (PRs) in tissues. Separating the individual effects of estrogens and progesterone is further complicated by the partial dependence of PR transcription on estrogen receptor (ER)α-mediated transcriptional events; indeed, interpreting the integrated interaction of the hormones may be more essential than isolating independent effects. Further, many of the actions of both estrogens and progesterone, particularly in "normal" breast tissues, are driven by paracrine mechanisms in which ligand binding to receptor-positive cells evokes secretion of factors that influence cell division of neighboring receptor-negative cells. Accordingly, blood and tissue levels may differ, and the latter are challenging to measure. Given conflicting data related to the potential role of progesterone in breast cancer etiology and interest in blocking progesterone action to prevent or treat breast cancer, we provide a review of the evidence that links progesterone to breast cancer risk and suggest future directions for filling current gaps in our knowledge.
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Affiliation(s)
- Britton Trabert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Mark E Sherman
- Health Sciences Research, Mayo Clinic, Jacksonville, Florida
| | - Nagarajan Kannan
- Laboratory of Stem Cell and Cancer Biology, Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Frank Z Stanczyk
- Departments of Obstetrics and Gynecology, and Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California
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Zimmerman L, Zelichov O, Aizenmann A, Barbash Z, Vidne M, Tarcic G. A Novel System for Functional Determination of Variants of Uncertain Significance using Deep Convolutional Neural Networks. Sci Rep 2020; 10:4192. [PMID: 32144301 PMCID: PMC7060242 DOI: 10.1038/s41598-020-61173-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/24/2020] [Indexed: 11/08/2022] Open
Abstract
Many drugs are developed for commonly occurring, well studied cancer drivers such as vemurafenib for BRAF V600E and erlotinib for EGFR exon 19 mutations. However, most tumors also harbor mutations which have an uncertain role in disease formation, commonly called Variants of Uncertain Significance (VUS), which are not studied or characterized and could play a significant role in drug resistance and relapse. Therefore, the determination of the functional significance of VUS and their response to Molecularly Targeted Agents (MTA) is essential for developing new drugs and predicting response of patients. Here we present a multi-scale deep convolutional neural network (DCNN) architecture combined with an in-vitro functional assay to investigate the functional role of VUS and their response to MTA's. Our method achieved high accuracy and precision on a hold-out set of examples (0.98 mean AUC for all tested genes) and was used to predict the oncogenicity of 195 VUS in 6 genes. 63 (32%) of the assayed VUS's were classified as pathway activating, many of them to a similar extent as known driver mutations. Finally, we show that responses of various mutations to FDA approved MTAs are accurately predicted by our platform in a dose dependent manner. Taken together this novel system can uncover the treatable mutational landscape of a drug and be a useful tool in drug development.
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78
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Brambati A, Zardoni L, Nardini E, Pellicioli A, Liberi G. The dark side of RNA:DNA hybrids. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 784:108300. [PMID: 32430097 DOI: 10.1016/j.mrrev.2020.108300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/07/2020] [Accepted: 02/23/2020] [Indexed: 12/15/2022]
Abstract
RNA:DNA hybrids form when nascent transcripts anneal to the DNA template strand or any homologous DNA region. Co-transcriptional RNA:DNA hybrids, organized in R-loop structures together with the displaced non-transcribed strand, assist gene expression, DNA repair and other physiological cellular functions. A dark side of the matter is that RNA:DNA hybrids are also a cause of DNA damage and human diseases. In this review, we summarize recent advances in the understanding of the mechanisms by which the impairment of hybrid turnover promotes DNA damage and genome instability via the interference with DNA replication and DNA double-strand break repair. We also discuss how hybrids could contribute to cancer, neurodegeneration and susceptibility to viral infections, focusing on dysfunctions associated with the anti-R-loop helicase Senataxin.
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Affiliation(s)
- Alessandra Brambati
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy.
| | - Luca Zardoni
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy; Scuola Universitaria Superiore, IUSS, 27100, Pavia, Italy
| | - Eleonora Nardini
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Achille Pellicioli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy; IFOM Foundation, Via Adamello 16, 20139, Milan, Italy.
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79
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From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork. Int J Mol Sci 2020; 21:ijms21041506. [PMID: 32098397 PMCID: PMC7073102 DOI: 10.3390/ijms21041506] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Replicating the entire genome is one of the most complex tasks for all organisms. Research carried out in the last few years has provided us with a clearer picture on how cells preserve genomic information from the numerous insults that may endanger its stability. Different DNA repair pathways, coping with exogenous or endogenous threat, have been dissected at the molecular level. More recently, there has been an increasing interest towards intrinsic obstacles to genome replication, paving the way to a novel view on genomic stability. Indeed, in some cases, the movement of the replication fork can be hindered by the presence of stable DNA: RNA hybrids (R-loops), the folding of G-rich sequences into G-quadruplex structures (G4s) or repetitive elements present at Common Fragile Sites (CFS). Although differing in their nature and in the way they affect the replication fork, all of these obstacles are a source of replication stress. Replication stress is one of the main hallmarks of cancer and its prevention is becoming increasingly important as a target for future chemotherapeutics. Here we will try to summarize how these three obstacles are generated and how the cells handle replication stress upon their encounter. Finally, we will consider their role in cancer and their exploitation in current chemotherapeutic approaches.
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80
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Majhi PD, Sharma A, Roberts AL, Daniele E, Majewski AR, Chuong LM, Black AL, Vandenberg LN, Schneider SS, Dunphy KA, Jerry DJ. Effects of Benzophenone-3 and Propylparaben on Estrogen Receptor-Dependent R-Loops and DNA Damage in Breast Epithelial Cells and Mice. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:17002. [PMID: 31939680 PMCID: PMC7015622 DOI: 10.1289/ehp5221] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Endocrine-disrupting chemicals have been shown to have broad effects on development, but their mutagenic actions that can lead to cancer have been less clearly demonstrated. Physiological levels of estrogen have been shown to stimulate DNA damage in breast epithelial cells through mechanisms mediated by estrogen-receptor alpha (ERα). Benzophenone-3 (BP-3) and propylparaben (PP) are xenoestrogens found in the urine of >96% of U.S. OBJECTIVES We investigated the effect of BP-3 and PP on estrogen receptor-dependent transactivation and DNA damage at concentrations relevant to exposures in humans. METHODS In human breast epithelial cells, DNA damage following treatment with 17β-estradiol (E2), BP-3, and PP was determined by immunostaining with antibodies against γ-H2AX and 53BP1. Estrogenic responses were determined using luciferase reporter assays and gene expression. Formation of R-loops was determined with DNA: RNA hybrid-specific S9.6 antibody. Short-term exposure to the chemicals was also studied in ovariectomized mice. Immunostaining of mouse mammary epithelium was performed to quantify R-loops and DNA damage in vivo. RESULTS Concentrations of 1μM and 5μM BP-3 or PP increased DNA damage similar to that of E2 treatment in a ERα-dependent manner. However, BP-3 and PP had limited transactivation of target genes at 1μM and 5μM concentrations. BP-3 and PP exposure caused R-loop formation in a normal human breast epithelial cell line when ERα was introduced. R-loops and DNA damage were also detected in mammary epithelial cells of mice treated with BP-3 and PP. CONCLUSIONS Acute exposure to xenoestrogens (PP and BP-3) in mice induce DNA damage mediated by formation of ERα-dependent R-loops at concentrations 10-fold lower than those required for transactivation. Exposure to these xenoestrogens may cause deleterious estrogenic responses, such as DNA damage, in susceptible individuals. https://doi.org/10.1289/EHP5221.
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Affiliation(s)
- Prabin Dhangada Majhi
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Botany, Ravenshaw University, Cuttack, Odisha, India
| | - Aman Sharma
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Amy L. Roberts
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Elizabeth Daniele
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Aliza R. Majewski
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Lynn M. Chuong
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Amye L. Black
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Laura N. Vandenberg
- Department of Environmental Health Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Sallie S. Schneider
- University of Massachusetts Medical School, Baystate Campus, Springfield, Massachusetts, USA
- Pioneer Valley Life Sciences Institute, Springfield, Massachusetts, USA
| | - Karen A. Dunphy
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - D. Joseph Jerry
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
- Pioneer Valley Life Sciences Institute, Springfield, Massachusetts, USA
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81
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Hao H, Han T, Xuan B, Sun Y, Tang S, Yue N, Qian Z. Dissecting the Role of DDX21 in Regulating Human Cytomegalovirus Replication. J Virol 2019; 93:e01222-19. [PMID: 31554690 PMCID: PMC6880175 DOI: 10.1128/jvi.01222-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/09/2019] [Indexed: 12/20/2022] Open
Abstract
DDX21 regulates the biogenesis of rRNA and transcription of ribonucleoprotein genes. Recently, it has been reported that DDX21 regulates the growth of some RNA viruses through various mechanisms, such as inhibiting viral genome replication, suppressing virion assembly and release, and modulating antiviral immune responses (Chen et al., Cell Host Microbe 15:484-493, 2014, https://doi.org/10.1016/j.chom.2014.03.002; Dong et al., Biophys Res Commun, 473:648-653, 2016, https://doi.org/10.1016/j.bbrc.2016.03.120; and Watanabe et al., PLoS Pathog 5:e1000654, 2009, https://doi.org/10.1371/journal.ppat.1000654). The relationship between DDX21 and DNA viruses has not yet been explored. In this study, we used human cytomegalovirus (HCMV), a large human DNA virus, to investigate the potential role of DDX21 in DNA virus replication. We found that HCMV infection prevented the repression of DDX21 at protein and mRNA levels. Knockdown of DDX21 inhibited HCMV growth in human fibroblast cells (MRC5). Immunofluorescence and quantitative PCR (qPCR) results showed that knockdown of DDX21 did not affect viral DNA replication or the formation of the viral replication compartment but did significantly inhibit viral late gene transcription. Some studies have reported that DDX21 knockdown promotes the accumulation of R-loops that could restrain RNA polymerase II elongation and inhibit the transcription of certain genes. Thus, we used the DNA-RNA hybrid-specific S9.6 antibody to stain R-loops and observed that more R-loops formed in DDX21-knockdown cells than in control cells. Moreover, an DNA-RNA immunoprecipitation assay showed that more R-loops accumulated on a viral late gene in DDX21-knockdown cells. Altogether, these results suggest that DDX21 knockdown promotes the accumulation of R-loops, which prevents viral late gene transcription and consequently results in the suppression of HCMV growth. This finding provides new insight into the relationship between DDX21 and DNA virus replication.IMPORTANCE Previous studies have confirmed that DDX21 is vital for the regulation of various aspects of RNA virus replication. Our research is the first report on the role of DDX21 in HCMV DNA virus replication. We identified that DDX21 knockdown affected HCMV growth and viral late gene transcription. In order to elucidate how DDX21 regulated this transcription, we applied DNA-RNA immunoprecipitation by using the DNA-RNA hybrid-specific S9.6 antibody to test whether more R-loops accumulated on the viral late gene. Consistent with our expectation, more R-loops were detected on the viral late gene at late HCMV infection time points, which demonstrated that the accumulation of R-loops caused by DDX21 knockdown prevented viral late gene transcription and consequently impaired HCMV replication. These results reveal that DDX21 plays an important role in regulating HCMV replication and also provide a basis for investigating the role of DDX21 in regulating other DNA viruses.
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Affiliation(s)
- Hongyun Hao
- Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Tian Han
- Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Baoqin Xuan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yamei Sun
- Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Shubing Tang
- Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Nan Yue
- Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhikang Qian
- Unit of Herpesvirus and Molecular Virology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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82
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Goodman LD, Bonini NM. New Roles for Canonical Transcription Factors in Repeat Expansion Diseases. Trends Genet 2019; 36:81-92. [PMID: 31837826 DOI: 10.1016/j.tig.2019.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/05/2019] [Accepted: 11/08/2019] [Indexed: 12/11/2022]
Abstract
The presence of microsatellite repeat expansions within genes is associated with >30 neurological diseases. Of interest, (GGGGCC)>30-repeats within C9orf72 are associated with amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). These expansions can be 100s to 1000s of units long. Thus, it is perplexing how RNA-polymerase II (RNAPII) can successfully transcribe them. Recent investigations focusing on GGGGCC-transcription have identified specific, canonical complexes that may promote RNAPII-transcription at these GC-rich microsatellites: the DSIF complex and PAF1C. These complexes may be important for resolving the unique secondary structures formed by GGGGCC-DNA during transcription. Importantly, this process can produce potentially toxic repeat-containing RNA that can encode potentially toxic peptides, impacting neuron function and health. Understanding how transcription of these repeats occurs has implications for therapeutics in multiple diseases.
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Affiliation(s)
- Lindsey D Goodman
- Department of Molecular and Human Genetics, Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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83
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Chiang HC, Zhang X, Li J, Zhao X, Chen J, Wang HTH, Jatoi I, Brenner A, Hu Y, Li R. BRCA1-associated R-loop affects transcription and differentiation in breast luminal epithelial cells. Nucleic Acids Res 2019; 47:5086-5099. [PMID: 30982901 PMCID: PMC6547407 DOI: 10.1093/nar/gkz262] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/06/2019] [Accepted: 04/01/2019] [Indexed: 12/17/2022] Open
Abstract
BRCA1-associated basal-like breast cancer originates from luminal progenitor cells. Breast epithelial cells from cancer-free BRCA1 mutation carriers are defective in luminal differentiation. However, how BRCA1 deficiency leads to lineage-specific differentiation defect is not clear. BRCA1 is implicated in resolving R-loops, DNA-RNA hybrid structures associated with genome instability and transcriptional regulation. We recently showed that R-loops are preferentially accumulated in breast luminal epithelial cells of BRCA1 mutation carriers. Here, we interrogate the impact of a BRCA1 mutation-associated R-loop located in a putative transcriptional enhancer upstream of the ERα-encoding ESR1 gene. Genetic ablation confirms the relevance of this R-loop-containing region to enhancer-promoter interactions and transcriptional activation of the corresponding neighboring genes, including ESR1, CCDC170 and RMND1. BRCA1 knockdown in ERα+ luminal breast cancer cells increases intensity of this R-loop and reduces transcription of its neighboring genes. The deleterious effect of BRCA1 depletion on transcription is mitigated by ectopic expression of R-loop-removing RNase H1. Furthermore, RNase H1 overexpression in primary breast cells from BRCA1 mutation carriers results in a shift from luminal progenitor cells to mature luminal cells. Our findings suggest that BRCA1-dependent R-loop mitigation contributes to luminal cell-specific transcription and differentiation, which could in turn suppress BRCA1-associated tumorigenesis.
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Affiliation(s)
- Huai-Chin Chiang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA
| | - Xiaowen Zhang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA
| | - Jingwei Li
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xiayan Zhao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jerry Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Howard T-H Wang
- Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Ismail Jatoi
- Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Andrew Brenner
- Department of Medicine, The Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yanfen Hu
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA
| | - Rong Li
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA
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84
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Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM. Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. Genes Dev 2019; 33:1751-1774. [PMID: 31753913 PMCID: PMC6942044 DOI: 10.1101/gad.331231.119] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023]
Abstract
Bromodomain proteins (BRD) are key chromatin regulators of genome function and stability as well as therapeutic targets in cancer. Here, we systematically delineate the contribution of human BRD proteins for genome stability and DNA double-strand break (DSB) repair using several cell-based assays and proteomic interaction network analysis. Applying these approaches, we identify 24 of the 42 BRD proteins as promoters of DNA repair and/or genome integrity. We identified a BRD-reader function of PCAF that bound TIP60-mediated histone acetylations at DSBs to recruit a DUB complex to deubiquitylate histone H2BK120, to allowing direct acetylation by PCAF, and repair of DSBs by homologous recombination. We also discovered the bromo-and-extra-terminal (BET) BRD proteins, BRD2 and BRD4, as negative regulators of transcription-associated RNA-DNA hybrids (R-loops) as inhibition of BRD2 or BRD4 increased R-loop formation, which generated DSBs. These breaks were reliant on topoisomerase II, and BRD2 directly bound and activated topoisomerase I, a known restrainer of R-loops. Thus, comprehensive interactome and functional profiling of BRD proteins revealed new homologous recombination and genome stability pathways, providing a framework to understand genome maintenance by BRD proteins and the effects of their pharmacological inhibition.
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Affiliation(s)
- Jae Jin Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Seo Yun Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Fade Gong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Anna M Battenhouse
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Samantha T Refvik
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,The Howard Hughes Medical Institute
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Biochemistry, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Blerta Xhemalce
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,The Howard Hughes Medical Institute.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, USA
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85
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Matos DA, Zhang JM, Ouyang J, Nguyen HD, Genois MM, Zou L. ATR Protects the Genome against R Loops through a MUS81-Triggered Feedback Loop. Mol Cell 2019; 77:514-527.e4. [PMID: 31708417 DOI: 10.1016/j.molcel.2019.10.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/11/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022]
Abstract
R loops arising during transcription induce genomic instability, but how cells respond to the R loop-associated genomic stress is still poorly understood. Here, we show that cells harboring high levels of R loops rely on the ATR kinase for survival. In response to aberrant R loop accumulation, the ataxia telangiectasia and Rad3-related (ATR)-Chk1 pathway is activated by R loop-induced reversed replication forks. In contrast to the activation of ATR by replication inhibitors, R loop-induced ATR activation requires the MUS81 endonuclease. ATR protects the genome from R loops by suppressing transcription-replication collisions, promoting replication fork recovery, and enforcing a G2/M cell-cycle arrest. Furthermore, ATR prevents excessive cleavage of reversed forks by MUS81, revealing a MUS81-triggered and ATR-mediated feedback loop that fine-tunes MUS81 activity at replication forks. These results suggest that ATR is a key sensor and suppressor of R loop-induced genomic instability, uncovering a signaling circuitry that safeguards the genome against R loops.
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Affiliation(s)
- Dominick A Matos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jia-Min Zhang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Hai Dang Nguyen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Marie-Michelle Genois
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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86
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Type II DNA Topoisomerases Cause Spontaneous Double-Strand Breaks in Genomic DNA. Genes (Basel) 2019; 10:genes10110868. [PMID: 31671674 PMCID: PMC6895833 DOI: 10.3390/genes10110868] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/31/2022] Open
Abstract
Type II DNA topoisomerase enzymes (TOP2) catalyze topological changes by strand passage reactions. They involve passing one intact double stranded DNA duplex through a transient enzyme-bridged break in another (gated helix) followed by ligation of the break by TOP2. A TOP2 poison, etoposide blocks TOP2 catalysis at the ligation step of the enzyme-bridged break, increasing the number of stable TOP2 cleavage complexes (TOP2ccs). Remarkably, such pathological TOP2ccs are formed during the normal cell cycle as well as in postmitotic cells. Thus, this ‘abortive catalysis’ can be a major source of spontaneously arising DNA double-strand breaks (DSBs). TOP2-mediated DSBs are also formed upon stimulation with physiological concentrations of androgens and estrogens. The frequent occurrence of TOP2-mediated DSBs was previously not appreciated because they are efficiently repaired. This repair is performed in collaboration with BRCA1, BRCA2, MRE11 nuclease, and tyrosyl-DNA phosphodiesterase 2 (TDP2) with nonhomologous end joining (NHEJ) factors. This review first discusses spontaneously arising DSBs caused by the abortive catalysis of TOP2 and then summarizes proteins involved in repairing stalled TOP2ccs and discusses the genotoxicity of the sex hormones.
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87
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Abstract
The repair of DNA double-strand breaks occurs through a series of defined steps that are evolutionarily conserved and well-understood in most experimental organisms. However, it is becoming increasingly clear that repair does not occur in isolation from other DNA transactions. Transcription of DNA produces topological changes, RNA species, and RNA-dependent protein complexes that can dramatically influence the efficiency and outcomes of DNA double-strand break repair. The transcription-associated history of several double-strand break repair factors is reviewed here, with an emphasis on their roles in regulating R-loops and the emerging role of R-loops in coordination of repair events. Evidence for nucleolytic processing of R-loops is also discussed, as well as the molecular tools commonly used to measure RNA-DNA hybrids in cells.
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Affiliation(s)
- Tanya T Paull
- The Department of Molecular Biosciences and the Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
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88
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Wells JP, White J, Stirling PC. R Loops and Their Composite Cancer Connections. Trends Cancer 2019; 5:619-631. [DOI: 10.1016/j.trecan.2019.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022]
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89
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Chang EYC, Tsai S, Aristizabal MJ, Wells JP, Coulombe Y, Busatto FF, Chan YA, Kumar A, Dan Zhu Y, Wang AYH, Fournier LA, Hieter P, Kobor MS, Masson JY, Stirling PC. MRE11-RAD50-NBS1 promotes Fanconi Anemia R-loop suppression at transcription-replication conflicts. Nat Commun 2019; 10:4265. [PMID: 31537797 PMCID: PMC6753070 DOI: 10.1038/s41467-019-12271-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
Ectopic R-loop accumulation causes DNA replication stress and genome instability. To avoid these outcomes, cells possess a range of anti-R-loop mechanisms, including RNaseH that degrades the RNA moiety in R-loops. To comprehensively identify anti-R-loop mechanisms, we performed a genome-wide trigenic interaction screen in yeast lacking RNH1 and RNH201. We identified >100 genes critical for fitness in the absence of RNaseH, which were enriched for DNA replication fork maintenance factors including the MRE11-RAD50-NBS1 (MRN) complex. While MRN has been shown to promote R-loops at DNA double-strand breaks, we show that it suppresses R-loops and associated DNA damage at transcription-replication conflicts. This occurs through a non-nucleolytic function of MRE11 that is important for R-loop suppression by the Fanconi Anemia pathway. This work establishes a novel role for MRE11-RAD50-NBS1 in directing tolerance mechanisms at transcription-replication conflicts.
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Affiliation(s)
| | - Shuhe Tsai
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, V5Z 4H4, Canada
| | - James P Wells
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Yan Coulombe
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Franciele F Busatto
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Yujia A Chan
- The Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Arun Kumar
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Yi Dan Zhu
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | | | | | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, V5Z 4H4, Canada
| | - Jean-Yves Masson
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada.
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90
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Meghani K, Fuchs W, Detappe A, Drané P, Gogola E, Rottenberg S, Jonkers J, Matulonis U, Swisher EM, Konstantinopoulos PA, Chowdhury D. Multifaceted Impact of MicroRNA 493-5p on Genome-Stabilizing Pathways Induces Platinum and PARP Inhibitor Resistance in BRCA2-Mutated Carcinomas. Cell Rep 2019; 23:100-111. [PMID: 29617652 DOI: 10.1016/j.celrep.2018.03.038] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/05/2018] [Accepted: 03/10/2018] [Indexed: 10/17/2022] Open
Abstract
BRCA1/2-mutated ovarian cancers (OCs) are defective in homologous recombination repair (HRR) of double-strand breaks (DSBs) and thereby sensitive to platinum and PARP inhibitors (PARPis). Multiple PARPis have recently received US Food and Drug Administration (FDA) approval for treatment of OCs, and resistance to PARPis is a major clinical problem. Utilizing primary and recurrent BRCA1/2-mutated carcinomas from OC patients, patient-derived lines, and an in vivo BRCA2-mutated mouse model, we identified a microRNA, miR-493-5p, that induced platinum/PARPi resistance exclusively in BRCA2-mutated carcinomas. However, in contrast to the most prevalent resistance mechanisms in BRCA mutant carcinomas, miR-493-5p did not restore HRR. Expression of miR-493-5p in BRCA2-mutated/depleted cells reduced levels of nucleases and other factors involved in maintaining genomic stability. This resulted in relatively stable replication forks, diminished single-strand annealing of DSBs, and increased R-loop formation. We conclude that impact of miR-493-5p on multiple pathways pertinent to genome stability cumulatively causes PARPi/platinum resistance in BRCA2 mutant carcinomas.
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Affiliation(s)
- Khyati Meghani
- Department of Radiation Oncology, Division of Radiation and Genome Stability, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Walker Fuchs
- Department of Radiation Oncology, Division of Radiation and Genome Stability, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alexandre Detappe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pascal Drané
- Department of Radiation Oncology, Division of Radiation and Genome Stability, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ewa Gogola
- Division of Molecular Pathology and Cancer Genomics Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology and Cancer Genomics Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laenggassstr. 122, 3012 Bern, Switzerland
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ursula Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth M Swisher
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | | | - Dipanjan Chowdhury
- Department of Radiation Oncology, Division of Radiation and Genome Stability, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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91
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Venkitaraman AR. How do mutations affecting the breast cancer genes BRCA1 and BRCA2 cause cancer susceptibility? DNA Repair (Amst) 2019; 81:102668. [PMID: 31337537 PMCID: PMC6765401 DOI: 10.1016/j.dnarep.2019.102668] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The inheritance of monoallelic germline mutations affecting BRCA1 or BRCA2 predisposes with a high penetrance to several forms of epithelial malignancy. The large, nuclear-localized BRCA proteins act as custodians of chromosome integrity through distinct functions in the assembly and activity of macromolecular complexes that mediate DNA repair, replication reactivation and mitotic progression. The loss of these tumour suppressive functions following biallelic BRCA gene inactivation has long been thought to provoke genomic instability and carcinogenesis. However, recent studies not only identify new functions for BRCA1 and BRCA2 in the regulation of transcription and RNA processing potentially relevant to their tumour suppressive activity, but also suggest that monoallelic BRCA2 gene mutations suffice for carcinogenesis. This emerging evidence opens fresh lines of enquiry concerning tissue-specific cancer evolution in BRCA mutation carriers. Collectively, these insights engender new models to explain how BRCA gene mutations cause cancer susceptibility in specific tissues.
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Affiliation(s)
- Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Box 197, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XZ, United Kingdom.
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92
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Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2019; 19:464-478. [PMID: 29740129 DOI: 10.1038/s41580-018-0010-5] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dynamic regulation of transcription elongation by RNA polymerase II (Pol II) is an integral part of the implementation of gene expression programmes during development. In most metazoans, the majority of transcribed genes exhibit transient pausing of Pol II at promoter-proximal regions, and the release of Pol II into gene bodies is controlled by many regulatory factors that respond to environmental and developmental cues. Misregulation of the elongation stage of transcription is implicated in cancer and other human diseases, suggesting that mechanistic understanding of transcription elongation control is therapeutically relevant. In this Review, we discuss the features, establishment and maintenance of Pol II pausing, the transition into productive elongation, the control of transcription elongation by enhancers and by factors of other cellular processes, such as topoisomerases and poly(ADP-ribose) polymerases (PARPs), and the potential of therapeutic targeting of the elongation stage of transcription by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Edwin R Smith
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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93
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Kuznetsov VA, Bondarenko V, Wongsurawat T, Yenamandra SP, Jenjaroenpun P. Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers. Nucleic Acids Res 2019; 46:7566-7585. [PMID: 29945198 PMCID: PMC6125637 DOI: 10.1093/nar/gky554] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/08/2018] [Indexed: 12/31/2022] Open
Abstract
R-loops are three-stranded RNA:DNA hybrid structures essential for many normal and pathobiological processes. Previously, we generated a quantitative R-loop forming sequence (RLFS) model, quantitative model of R-loop-forming sequences (QmRLFS) and predicted ∼660 000 RLFSs; most of them located in genes and gene-flanking regions, G-rich regions and disease-associated genomic loci in the human genome. Here, we conducted a comprehensive comparative analysis of these RLFSs using experimental data and demonstrated the high performance of QmRLFS predictions on the nucleotide and genome scales. The preferential co-localization of RLFS with promoters, U1 splice sites, gene ends, enhancers and non-B DNA structures, such as G-quadruplexes, provides evidence for the mechanical linkage between DNA tertiary structures, transcription initiation and R-loops in critical regulatory genome regions. We introduced and characterized an abundant class of reverse-forward RLFS clusters highly enriched in non-B DNA structures, which localized to promoters, gene ends and enhancers. The RLFS co-localization with promoters and transcriptionally active enhancers suggested new models for in cis and in trans regulation by RNA:DNA hybrids of transcription initiation and formation of 3D-chromatin loops. Overall, this study provides a rationale for the discovery and characterization of the non-B DNA regulatory structures involved in the formation of the RNA:DNA interactome as the basis for an emerging quantitative R-loop biology and pathobiology.
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Affiliation(s)
- Vladimir A Kuznetsov
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Vladyslav Bondarenko
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Thidathip Wongsurawat
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Surya P Yenamandra
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Piroon Jenjaroenpun
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.,Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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94
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Tharmapalan P, Mahendralingam M, Berman HK, Khokha R. Mammary stem cells and progenitors: targeting the roots of breast cancer for prevention. EMBO J 2019; 38:e100852. [PMID: 31267556 PMCID: PMC6627238 DOI: 10.15252/embj.2018100852] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/11/2019] [Accepted: 04/11/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer prevention is daunting, yet not an unsurmountable goal. Mammary stem and progenitors have been proposed as the cells-of-origin in breast cancer. Here, we present the concept of limiting these breast cancer precursors as a risk reduction approach in high-risk women. A wealth of information now exists for phenotypic and functional characterization of mammary stem and progenitor cells in mouse and human. Recent work has also revealed the hormonal regulation of stem/progenitor dynamics as well as intrinsic lineage distinctions between mammary epithelial populations. Leveraging these insights, molecular marker-guided chemoprevention is an achievable reality.
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Affiliation(s)
| | - Mathepan Mahendralingam
- Princess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoONCanada
| | - Hal K Berman
- Princess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoONCanada
| | - Rama Khokha
- Princess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoONCanada
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95
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Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates? DNA Repair (Amst) 2019; 81:102661. [PMID: 31331819 DOI: 10.1016/j.dnarep.2019.102661] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Although long overlooked, it is now well understood that DNA does not systematically assemble into a canonical double helix, known as B-DNA, throughout the entire genome but can also accommodate other structures including DNA hairpins, G-quadruplexes and RNA:DNA hybrids. Notably, these non-canonical DNA structures form preferentially at transcriptionally active loci. Acting as replication roadblocks and being targeted by multiple machineries, these structures weaken the genome and render it prone to damage, including DNA double-strand breaks (DSB). In addition, secondary structures also further accumulate upon DSB formation. Here we discuss the potential functions of pre-existing or de novo formed nucleic acid structures, as bona fide repair intermediates or repair roadblocks, especially during Transcription-Coupled DNA Double-Strand Break repair (TC-DSBR), and provide an update on the specialized protein complexes displaying the ability to remove these structures to safeguard genome integrity.
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96
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Abstract
Genome replication involves dealing with obstacles that can result from DNA damage but also from chromatin alterations, topological stress, tightly bound proteins or non-B DNA structures such as R loops. Experimental evidence reveals that an engaged transcription machinery at the DNA can either enhance such obstacles or be an obstacle itself. Thus, transcription can become a potentially hazardous process promoting localized replication fork hindrance and stress, which would ultimately cause genome instability, a hallmark of cancer cells. Understanding the causes behind transcription-replication conflicts as well as how the cell resolves them to sustain genome integrity is the aim of this review.
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97
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Zhang X, Wang Y, Chiang HC, Hsieh YP, Lu C, Park BH, Jatoi I, Jin VX, Hu Y, Li R. BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells. Breast Cancer Res 2019; 21:51. [PMID: 30995943 PMCID: PMC6472090 DOI: 10.1186/s13058-019-1132-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/27/2019] [Indexed: 01/07/2023] Open
Abstract
Background BRCA1-associated breast cancer originates from luminal progenitor cells. BRCA1 functions in multiple biological processes, including double-strand break repair, replication stress suppression, transcriptional regulation, and chromatin reorganization. While non-malignant cells carrying cancer-predisposing BRCA1 mutations exhibit increased genomic instability, it remains unclear whether BRCA1 haploinsufficiency affects transcription and chromatin dynamics in breast epithelial cells. Methods H3K27ac-associated super-enhancers were compared in primary breast epithelial cells from BRCA1 mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+). Non-tumorigenic MCF10A breast epithelial cells with engineered BRCA1 haploinsufficiency were used to confirm the H3K27ac changes. The impact of BRCA1 mutations on enhancer function and enhancer-promoter looping was assessed in MCF10A cells. Results Here, we show that primary mammary epithelial cells from women with BRCA1 mutations display significant loss of H3K27ac-associated super-enhancers. These BRCA1-dependent super-enhancers are enriched with binding motifs for the GATA family. Non-tumorigenic BRCA1mut/+ MCF10A cells recapitulate the H3K27ac loss. Attenuated histone mark and enhancer activity in these BRCA1mut/+ MCF10A cells can be partially restored with wild-type BRCA1. Furthermore, chromatin conformation analysis demonstrates impaired enhancer-promoter looping in BRCA1mut/+ MCF10A cells. Conclusions H3K27ac-associated super-enhancer loss is a previously unappreciated functional deficiency in ostensibly normal BRCA1 mutation-carrying breast epithelium. Our findings offer new mechanistic insights into BRCA1 mutation-associated transcriptional and epigenetic abnormality in breast epithelial cells and tissue/cell lineage-specific tumorigenesis. Electronic supplementary material The online version of this article (10.1186/s13058-019-1132-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaowen Zhang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Yao Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Huai-Chin Chiang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ben Ho Park
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Ismail Jatoi
- Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Yanfen Hu
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC, 20037, USA.
| | - Rong Li
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, 20037, USA.
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98
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Herold S, Kalb J, Büchel G, Ade CP, Baluapuri A, Xu J, Koster J, Solvie D, Carstensen A, Klotz C, Rodewald S, Schülein-Völk C, Dobbelstein M, Wolf E, Molenaar J, Versteeg R, Walz S, Eilers M. Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase. Nature 2019; 567:545-549. [PMID: 30894746 DOI: 10.1038/s41586-019-1030-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 02/18/2019] [Indexed: 01/17/2023]
Abstract
MYC is an oncogenic transcription factor that binds globally to active promoters and promotes transcriptional elongation by RNA polymerase II (RNAPII)1,2. Deregulated expression of the paralogous protein MYCN drives the development of neuronal and neuroendocrine tumours and is often associated with a particularly poor prognosis3. Here we show that, similar to MYC, activation of MYCN in human neuroblastoma cells induces escape of RNAPII from promoters. If the release of RNAPII from transcriptional pause sites (pause release) fails, MYCN recruits BRCA1 to promoter-proximal regions. Recruitment of BRCA1 prevents MYCN-dependent accumulation of stalled RNAPII and enhances transcriptional activation by MYCN. Mechanistically, BRCA1 stabilizes mRNA decapping complexes and enables MYCN to suppress R-loop formation in promoter-proximal regions. Recruitment of BRCA1 requires the ubiquitin-specific protease USP11, which binds specifically to MYCN when MYCN is dephosphorylated at Thr58. USP11, BRCA1 and MYCN stabilize each other on chromatin, preventing proteasomal turnover of MYCN. Because BRCA1 is highly expressed in neuronal progenitor cells during early development4 and MYC is less efficient than MYCN in recruiting BRCA1, our findings indicate that a cell-lineage-specific stress response enables MYCN-driven tumours to cope with deregulated RNAPII function.
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Affiliation(s)
- Steffi Herold
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany.
| | - Jacqueline Kalb
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Gabriele Büchel
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Carsten P Ade
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jiajia Xu
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel Solvie
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Anne Carstensen
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christina Klotz
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sabrina Rodewald
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Christina Schülein-Völk
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jan Molenaar
- Department of Translational Research, Prinses Máxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne Walz
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany.
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99
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Abstract
MYC is an oncogenic transcription factor that binds globally to active promoters and promotes transcriptional elongation by RNA polymerase II (RNAPII)1,2. Deregulated expression of the paralogous protein MYCN drives the development of neuronal and neuroendocrine tumours and is often associated with a particularly poor prognosis3. Here we show that, similar to MYC, activation of MYCN in human neuroblastoma cells induces escape of RNAPII from promoters. If the release of RNAPII from transcriptional pause sites (pause release) fails, MYCN recruits BRCA1 to promoter-proximal regions. Recruitment of BRCA1 prevents MYCN-dependent accumulation of stalled RNAPII and enhances transcriptional activation by MYCN. Mechanistically, BRCA1 stabilizes mRNA decapping complexes and enables MYCN to suppress R-loop formation in promoter-proximal regions. Recruitment of BRCA1 requires the ubiquitin-specific protease USP11, which binds specifically to MYCN when MYCN is dephosphorylated at Thr58. USP11, BRCA1 and MYCN stabilize each other on chromatin, preventing proteasomal turnover of MYCN. Because BRCA1 is highly expressed in neuronal progenitor cells during early development4 and MYC is less efficient than MYCN in recruiting BRCA1, our findings indicate that a cell-lineage-specific stress response enables MYCN-driven tumours to cope with deregulated RNAPII function.
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100
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Padeken J, Zeller P, Towbin B, Katic I, Kalck V, Methot SP, Gasser SM. Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression. Genes Dev 2019; 33:436-451. [PMID: 30804228 PMCID: PMC6446544 DOI: 10.1101/gad.322495.118] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/14/2019] [Indexed: 01/11/2023]
Abstract
Padeken et al. performed a genome-wide synthetic lethality screen and show that the BRCA1/BARD1 complex is necessary for germline viability in worms lacking MET-2 but not SET-25. The synthetic sterility upon BRCA1/BARD1 and H3K9me2 loss is directly linked to the DNA damage provoked by unscheduled satellite repeat transcription. Caenorhabditis elegans has two histone H3 Lys9 methyltransferases, MET-2 (SETDB1 homolog) and SET-25 (G9a/SUV39H1 related). In worms, we found simple repeat sequences primarily marked by H3K9me2, while transposable elements and silent tissue-specific genes bear H3K9me3. RNA sequencing (RNA-seq) in histone methyltransferase (HMT) mutants shows that MET-2-mediated H3K9me2 is necessary for satellite repeat repression, while SET-25 silences a subset of transposable elements and tissue-specific genes through H3K9me3. A genome-wide synthetic lethality screen showed that RNA processing, nuclear RNA degradation, the BRCA1/BARD1 complex, and factors mediating replication stress survival are necessary for germline viability in worms lacking MET-2 but not SET-25. Unlike set-25 mutants, met-2-null worms accumulated satellite repeat transcripts, which form RNA:DNA hybrids on repetitive sequences, additively with the loss of BRCA1 or BARD1. BRCA1/BARD1-mediated H2A ubiquitination and MET-2 deposited H3K9me2 on satellite repeats are partially interdependent, suggesting both that the loss of silencing generates BRCA-recruiting DNA damage and that BRCA1 recruitment by damage helps silence repeats. The artificial induction of MSAT1 transcripts can itself trigger damage-induced germline lethality in a wild-type background, arguing that the synthetic sterility upon BRCA1/BARD1 and H3K9me2 loss is directly linked to the DNA damage provoked by unscheduled satellite repeat transcription.
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Affiliation(s)
- Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Peter Zeller
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Benjamin Towbin
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Iskra Katic
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Veronique Kalck
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Stephen P Methot
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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