1
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Lee S, Lee S, Choi N, Kim J, Kweon J, Miller K, Kim J. PCAF promotes R-loop resolution via histone acetylation. Nucleic Acids Res 2024; 52:8643-8660. [PMID: 38936834 PMCID: PMC11347145 DOI: 10.1093/nar/gkae558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
R-loops cause genome instability, disrupting normal cellular functions. Histone acetylation, particularly by p300/CBP-associated factor (PCAF), is essential for maintaining genome stability and regulating cellular processes. Understanding how R-loop formation and resolution are regulated is important because dysregulation of these processes can lead to multiple diseases, including cancer. This study explores the role of PCAF in maintaining genome stability, specifically for R-loop resolution. We found that PCAF depletion promotes the generation of R-loop structures, especially during ongoing transcription, thereby compromising genome stability. Mechanistically, we found that PCAF facilitates histone H4K8 acetylation, leading to recruitment of the a double-strand break repair protein (MRE11) and exonuclease 1 (EXO1) to R-loop sites. These in turn recruit Fanconi anemia (FA) proteins, including FANCM and BLM, to resolve the R-loop structure. Our findings suggest that PCAF, histone acetylation, and FA proteins collaborate to resolve R-loops and ensure genome stability. This study therefore provides novel mechanistic insights into the dynamics of R-loops as well as the role of PCAF in preserving genome stability. These results may help develop therapeutic strategies to target diseases associated with genome instability.
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Affiliation(s)
- Seo Yun Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Soo Hyeon Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Nak Hun Choi
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Ja Young Kim
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Jun Hee Kweon
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jae Jin Kim
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
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2
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Chiang HC, Qi L, Mitra P, Huang Y, Hu Y, Li R. R-loop functions in Brca1-associated mammary tumorigenesis. Proc Natl Acad Sci U S A 2024; 121:e2403600121. [PMID: 39116124 PMCID: PMC11331088 DOI: 10.1073/pnas.2403600121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Deleterious accumulation of R-loops, a DNA-RNA hybrid structure, contributes to genome instability. They are associated with BRCA1 mutation-related breast cancer, an estrogen receptor α negative (ERα-) tumor type originating from luminal progenitor cells. However, a presumed causality of R-loops in tumorigenesis has not been established in vivo. Here, we overexpress mouse Rnaseh1 (Rh1-OE) in vivo to remove accumulated R-loops in Brca1-deficient mouse mammary epithelium (BKO). R-loop removal exacerbates DNA replication stress in proliferating BKO mammary epithelial cells, with little effect on homology-directed repair of double-strand breaks following ionizing radiation. Compared to their BKO counterparts, BKO-Rh1-OE mammary glands contain fewer luminal progenitor cells but more mature luminal cells. Despite a similar incidence of spontaneous mammary tumors in BKO and BKO-Rh1-OE mice, a significant percentage of BKO-Rh1-OE tumors express ERα and progesterone receptor. Our results suggest that rather than directly elevating the overall tumor incidence, R-loops influence the mammary tumor subtype by shaping the cell of origin for Brca1 tumors.
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Affiliation(s)
- Huai-Chin Chiang
- Department of Biochemistry and Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Leilei Qi
- Department of Anatomy and Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Payal Mitra
- Department of Biochemistry and Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Yimeng Huang
- Department of Biochemistry and Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Yanfen Hu
- Department of Anatomy and Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
| | - Rong Li
- Department of Biochemistry and Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC20037
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3
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Xu W, Liu X, Li J, Sun C, Chen L, Zhou J, Li K, Li Q, Meng A, Sun Q. ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis. CELL INSIGHT 2024; 3:100179. [PMID: 38974143 PMCID: PMC11225018 DOI: 10.1016/j.cellin.2024.100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
R-loop, a chromatin structure containing one RNA:DNA hybrid and one unpaired single-stranded DNA, plays multiple biological roles. However, due to technical limitations, the landscapes and potential functions of R-loops during embryogenesis remain elusive. Here, we developed a quantitative and high-resolution ultra-low input R-loop profiling method, named ULI-ssDRIP-seq, which can map global R-loops with as few as 1000 cells. By using ULI-ssDRIP-seq, we reveal the R-loop dynamics in the zebrafish from gametes to early embryos. In oocytes, the R-loop level is relatively low in most regions of the nuclear genome, except maternal-inherited rDNA and mitochondrial genome. The correlation between R-loop and CG methylation dynamics during early development is relatively weak. Furthermore, either up- or down-regulation of global R-loops by knockdown or overexpression of RNase H1 causes a delay of embryonic development with dramatic expression changes in zygotic and maternal genes. This study provides comprehensive R-loop landscapes during early vertebrate embryogenesis and demonstrates the implication of R-loops in embryonic development.
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Affiliation(s)
- Wei Xu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xin Liu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jinjin Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Changbin Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Luxi Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jincong Zhou
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qin Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qianwen Sun
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
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4
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Yang BZ, Liu MY, Chiu KL, Chien YL, Cheng CA, Chen YL, Tsui LY, Lin KR, Chu HPC, Wu CSP. DHX9 SUMOylation is required for the suppression of R-loop-associated genome instability. Nat Commun 2024; 15:6009. [PMID: 39019926 PMCID: PMC11255299 DOI: 10.1038/s41467-024-50428-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
RNA helicase DHX9 is essential for genome stability by resolving aberrant R-loops. However, its regulatory mechanisms remain unclear. Here we show that SUMOylation at lysine 120 (K120) is crucial for DHX9 function. Preventing SUMOylation at K120 leads to R-loop dysregulation, increased DNA damage, and cell death. Cells expressing DHX9 K120R mutant which cannot be SUMOylated are more sensitive to genotoxic agents and this sensitivity is mitigated by RNase H overexpression. Unlike the mutant, wild-type DHX9 interacts with R-loop-associated proteins such as PARP1 and DDX21 via SUMO-interacting motifs. Fusion of SUMO2 to the DHX9 K120R mutant enhances its association with these proteins, reduces R-loop accumulation, and alleviates survival defects of DHX9 K120R. Our findings highlight the critical role of DHX9 SUMOylation in maintaining genome stability by regulating protein interactions necessary for R-loop balance.
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Affiliation(s)
- Bing-Ze Yang
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Mei-Yin Liu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Kuan-Lin Chiu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106319, Taiwan
| | - Yuh-Ling Chien
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Ching-An Cheng
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Yu-Lin Chen
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Li-Yu Tsui
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Keng-Ru Lin
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | | | - Ching-Shyi Peter Wu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan.
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5
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Westover KR, Jin P, Yao B. Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. Epigenomics 2024; 16:589-608. [PMID: 38530068 PMCID: PMC11160457 DOI: 10.2217/epi-2023-0379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
R-loops, intricate three-stranded structures formed by RNA-DNA hybrids and an exposed non-template DNA strand, are fundamental to various biological phenomena. They carry out essential and contrasting functions within cellular mechanisms, underlining their critical role in maintaining cellular homeostasis. The specific cellular context that dictates R-loop formation determines their function, particularly emphasizing the necessity for their meticulous genomic regulation. Notably, the aberrant formation or misregulation of R-loops is implicated in numerous neurological disorders. This review focuses on the complex interactions between R-loops and double-strand DNA breaks, exploring how R-loop dysregulation potentially contributes to the pathogenesis of various brain disorders, which could provide novel insights into the molecular mechanisms underpinning neurological disease progression and identify potential therapeutic targets by highlighting these aspects.
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Affiliation(s)
- Katherine R Westover
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
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6
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Chiang HC, Qi L, Mitra P, Hu Y, Li R. R-Loop Functions in Brca1 -Associated Mammary Tumorigenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580374. [PMID: 38405919 PMCID: PMC10888925 DOI: 10.1101/2024.02.14.580374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Excessive R-loops, a DNA-RNA hybrid structure, are associated with genome instability and BRCA1 mutation-related breast cancer. Yet the causality of R-loops in tumorigenesis remains unclear. Here we show that R-loop removal by Rnaseh1 overexpression (Rh1-OE) in Brca1 -knockout (BKO) mouse mammary epithelium exacerbates DNA replication stress without affecting homology-directed DNA repair. R-loop removal also diminishes luminal progenitors, the cell of origin for estrogen receptor α (ERα)-negative BKO tumors. However, R-loop reduction does not dampen spontaneous BKO tumor incidence. Rather, it gives rise to a significant percentage of ERα-expressing BKO tumors. Thus, R-loops reshape mammary tumor subtype rather than promoting tumorigenesis.
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7
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Liu MY, Lin KR, Chien YL, Yang BZ, Tsui LY, Chu HP, Wu CSP. ATR phosphorylates DHX9 at serine 321 to suppress R-loop accumulation upon genotoxic stress. Nucleic Acids Res 2024; 52:204-222. [PMID: 37930853 PMCID: PMC10783509 DOI: 10.1093/nar/gkad973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
Aberrant DNA/RNA hybrids (R-loops) formed during transcription and replication disturbances pose threats to genome stability. DHX9 is an RNA helicase involved in R-loop resolution, but how DHX9 is regulated in response to genotoxic stress remains unclear. Here we report that DHX9 is phosphorylated at S321 and S688, with S321 phosphorylation primarily induced by ATR after DNA damage. Phosphorylation of DHX9 at S321 promotes its interaction with γH2AX, BRCA1 and RPA, and is required for its association with R-loops under genotoxic stress. Inhibition of ATR or expression of the non-phosphorylatable DHX9S321A prevents DHX9 from interacting with RPA and R-loops, leading to the accumulation of stress-induced R-loops. Furthermore, depletion of RPA reduces the association between DHX9 and γH2AX, and in vitro binding analysis confirms a direct interaction between DHX9 and RPA. Notably, cells with the non-phosphorylatable DHX9S321A variant exhibit hypersensitivity to genotoxic stress, while those expressing the phosphomimetic DHX9S321D variant prevent R-loop accumulation and display resistance to DNA damage agents. In summary, we uncover a new mechanism by which ATR directly regulates DHX9 through phosphorylation to eliminate stress-induced R-loops.
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Affiliation(s)
- Mei-Yin Liu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Keng-Ru Lin
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Yuh-Ling Chien
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Bing-Ze Yang
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Li-Yu Tsui
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | | | - Ching-Shyi Peter Wu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
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8
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Zhong AX, Chen Y, Chen PL. BRCA1 the Versatile Defender: Molecular to Environmental Perspectives. Int J Mol Sci 2023; 24:14276. [PMID: 37762577 PMCID: PMC10532398 DOI: 10.3390/ijms241814276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The evolving history of BRCA1 research demonstrates the profound interconnectedness of a single protein within the web of crucial functions in human cells. Mutations in BRCA1, a tumor suppressor gene, have been linked to heightened breast and ovarian cancer risks. However, despite decades of extensive research, the mechanisms underlying BRCA1's contribution to tissue-specific tumor development remain elusive. Nevertheless, much of the BRCA1 protein's structure, function, and interactions has been elucidated. Individual regions of BRCA1 interact with numerous proteins to play roles in ubiquitination, transcription, cell checkpoints, and DNA damage repair. At a cellular scale, these BRCA1 functions coordinate tumor suppression, R-loop prevention, and cellular differentiation, all of which may contribute to BRCA1's role in cancer tissue specificity. As research on BRCA1 and breast cancer continues to evolve, it will become increasingly evident that modern materials such as Bisphenol A should be examined for their relationship with DNA stability, cancer incidence, and chemotherapy. Overall, this review offers a comprehensive understanding of BRCA1's many roles at a molecular, cellular, organismal, and environmental scale. We hope that the knowledge gathered here highlights both the necessity of BRCA1 research and the potential for novel strategies to prevent and treat cancer in individuals carrying BRCA1 mutations.
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Affiliation(s)
- Amy X. Zhong
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Yumay Chen
- Department of Medicine, Division of Endocrinology, University of California, Irvine, CA 92697, USA;
| | - Phang-Lang Chen
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
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9
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Oubaddou Y, Ben Ali F, Oubaqui FE, Qmichou Z, Bakri Y, Rabii Ameziane RA. The Tumor Suppressor BRCA1/2, Cancer Susceptibility and Genome Instability in Gynecological and Mammary Cancers. Asian Pac J Cancer Prev 2023; 24:3139-3153. [PMID: 37774066 PMCID: PMC10762740 DOI: 10.31557/apjcp.2023.24.9.3139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/10/2023] [Indexed: 10/01/2023] Open
Abstract
BRCA1 and BRCA2 germline alterations highly predispose women to breast and ovarian cancers. They are mostly found within the TNBC (Triple-Negative Breast Cancer) and the HGSOC (High-Grade Serous Ovarian Carcinoma) subsets, known by an aggressive phenotype, the lack of therapeutic targets and poor prognosis. Importantly, there is an increased risk for cervical cancer in BRCA1 and BRCA2 mutation carriers that raises questions about the link between the HPV-driven genome instability and BRCA1 and BRCA2 germline mutations. Clinical, preclinical, and in vitro studies explained the increased risk for breast and ovarian cancers by genome instability resulting from the lack or loss of many functions related to BRCA1 or BRCA2 proteins such as DNA damage repair, stalled forks and R-loops resolution, transcription regulation, cell cycle control, and oxidative stress. In this review, we decipher the relationship between BRCA1/2 alterations and genomic instability leading to gynecomammary cancers through results from patients, mice, and cell lines. Understanding the early events of BRCA1/2-driven genomic instability in gynecomammary cancers would help to find new biomarkers for early diagnosis, improve the sensitivity of emerging therapies such as PARP inhibitors, and reveal new potential therapeutic targets.
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Affiliation(s)
- Yassire Oubaddou
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
| | - Fatima Ben Ali
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
| | - Fatima Ezzahrae Oubaqui
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat, Morocco.
| | - Zineb Qmichou
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat, Morocco.
| | - Youssef Bakri
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
| | - Rabii Ameziane Rabii Ameziane
- Laboratory of Biology of Human Pathologies (BioPatH), Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
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10
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Sharma AB, Ramlee MK, Kosmin J, Higgs MR, Wolstenholme A, Ronson GE, Jones D, Ebner D, Shamkhi N, Sims D, Wijnhoven PWG, Forment JV, Gibbs-Seymour I, Lakin ND. C16orf72/HAPSTR1/TAPR1 functions with BRCA1/Senataxin to modulate replication-associated R-loops and confer resistance to PARP disruption. Nat Commun 2023; 14:5003. [PMID: 37591890 PMCID: PMC10435583 DOI: 10.1038/s41467-023-40779-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023] Open
Abstract
While the toxicity of PARP inhibitors to cells with defects in homologous recombination (HR) is well established, other synthetic lethal interactions with PARP1/PARP2 disruption are poorly defined. To inform on these mechanisms we conducted a genome-wide screen for genes that are synthetic lethal with PARP1/2 gene disruption and identified C16orf72/HAPSTR1/TAPR1 as a novel modulator of replication-associated R-loops. C16orf72 is critical to facilitate replication fork restart, suppress DNA damage and maintain genome stability in response to replication stress. Importantly, C16orf72 and PARP1/2 function in parallel pathways to suppress DNA:RNA hybrids that accumulate at stalled replication forks. Mechanistically, this is achieved through an interaction of C16orf72 with BRCA1 and the RNA/DNA helicase Senataxin to facilitate their recruitment to RNA:DNA hybrids and confer resistance to PARP inhibitors. Together, this identifies a C16orf72/Senataxin/BRCA1-dependent pathway to suppress replication-associated R-loop accumulation, maintain genome stability and confer resistance to PARP inhibitors.
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Affiliation(s)
| | | | - Joel Kosmin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Amy Wolstenholme
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - George E Ronson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Dylan Jones
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Ebner
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Noor Shamkhi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - David Sims
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Paul W G Wijnhoven
- Early Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA, UK
| | - Josep V Forment
- Early Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA, UK
| | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK.
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11
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Santarosa M, Baldazzi D, Armellin M, Maestro R. In Silico Identification of a BRCA1:miR-29:DNMT3 Axis Involved in the Control of Hormone Receptors in BRCA1-Associated Breast Cancers. Int J Mol Sci 2023; 24:9916. [PMID: 37373065 DOI: 10.3390/ijms24129916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Germline inactivating mutations in the BRCA1 gene lead to an increased lifetime risk of ovarian and breast cancer (BC). Most BRCA1-associated BC are triple-negative tumors (TNBC), aggressive forms of BC characterized by a lack of expression of estrogen and progesterone hormone receptors (HR) and HER2. How BRCA1 inactivation may favor the development of such a specific BC phenotype remains to be elucidated. To address this question, we focused on the role of miRNAs and their networks in mediating BRCA1 functions. miRNA, mRNA, and methylation data were retrieved from the BRCA cohort of the TCGA project. The cohort was divided into a discovery set (Hi-TCGA) and a validation set (GA-TCGA) based on the platform used for miRNA analyses. The METABRIC, GSE81002, and GSE59248 studies were used as additional validation data sets. BCs were differentiated into BRCA1-like and non-BRCA1-like based on an established signature of BRCA1 pathway inactivation. Differential expression of miRNAs, gene enrichment analysis, functional annotation, and methylation correlation analyses were performed. The miRNAs downregulated in BRCA1-associated BC were identified by comparing the miRNome of BRCA1-like with non-BRCA1-like tumors from the Hi-TCGA discovery cohort. miRNAs:gene-target anticorrelation analyses were then performed. The target genes of miRNAs downregulated in the Hi-TCGA series were enriched in the BRCA1-like tumors from the GA-TCGA and METABRIC validation data sets. Functional annotation of these genes revealed an over-representation of several biological processes ascribable to BRCA1 activity. The enrichment of genes related to DNA methylation was particularly intriguing, as this is an aspect of BRCA1 functions that has been poorly explored. We then focused on the miR-29:DNA methyltransferase network and showed that the miR-29 family, which was downregulated in BRCA1-like tumors, was associated with poor prognosis in these BCs and inversely correlated with the expression of the DNA methyltransferases DNMT3A and DNMT3B. This, in turn, correlated with the methylation extent of the promoter of HR genes. These results suggest that BRCA1 may control the expression of HR via a miR-29:DNMT3:HR axis and that disruption of this network may contribute to the receptor negative phenotype of tumors with dysfunctional BRCA1.
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Affiliation(s)
- Manuela Santarosa
- Unit of Oncogenetics and Functional Oncogenomics, CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Davide Baldazzi
- Unit of Oncogenetics and Functional Oncogenomics, CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Michela Armellin
- Unit of Oncogenetics and Functional Oncogenomics, CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Roberta Maestro
- Unit of Oncogenetics and Functional Oncogenomics, CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
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12
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Elsakrmy N, Cui H. R-Loops and R-Loop-Binding Proteins in Cancer Progression and Drug Resistance. Int J Mol Sci 2023; 24:ijms24087064. [PMID: 37108225 PMCID: PMC10138518 DOI: 10.3390/ijms24087064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
R-loops are three-stranded DNA/RNA hybrids that form by the annealing of the mRNA transcript to its coding template while displacing the non-coding strand. While R-loop formation regulates physiological genomic and mitochondrial transcription and DNA damage response, imbalanced R-loop formation can be a threat to the genomic integrity of the cell. As such, R-loop formation is a double-edged sword in cancer progression, and perturbed R-loop homeostasis is observed across various malignancies. Here, we discuss the interplay between R-loops and tumor suppressors and oncogenes, with a focus on BRCA1/2 and ATR. R-loop imbalances contribute to cancer propagation and the development of chemotherapy drug resistance. We explore how R-loop formation can cause cancer cell death in response to chemotherapeutics and be used to circumvent drug resistance. As R-loop formation is tightly linked to mRNA transcription, their formation is unavoidable in cancer cells and can thus be explored in novel cancer therapeutics.
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Affiliation(s)
- Noha Elsakrmy
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
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13
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Gong Y, Liu Y. R-Loops at Chromosome Ends: From Formation, Regulation, and Cellular Consequence. Cancers (Basel) 2023; 15:cancers15072178. [PMID: 37046839 PMCID: PMC10093737 DOI: 10.3390/cancers15072178] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Telomeric repeat containing RNA (TERRA) is transcribed from subtelomeric regions to telomeres. TERRA RNA can invade telomeric dsDNA and form telomeric R-loop structures. A growing body of evidence suggests that TERRA-mediated R-loops are critical players in telomere length homeostasis. Here, we will review current knowledge on the regulation of R-loop levels at telomeres. In particular, we will discuss how the central player TERRA and its binding proteins modulate R-loop levels through various mechanisms. We will further provide an overview of the consequences of TERRA-mediated persistent or unscheduled R-loops at telomeres in human ALT cancers and other organisms, with a focus on telomere length regulation after replication interference-induced damage and DNA homologous recombination-mediated repair.
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Affiliation(s)
- Yi Gong
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Yie Liu
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
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14
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Su Y, Dang NM, Depypere H, Santucci-Pereira J, Gutiérrez-Díez PJ, Kanefsky J, Janssens JP, Russo J. Recombinant human chorionic gonadotropin induces signaling pathways towards cancer prevention in the breast of BRCA1/2 mutation carriers. Eur J Cancer Prev 2023; 32:126-138. [PMID: 35881946 PMCID: PMC9800649 DOI: 10.1097/cej.0000000000000763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Strategies for breast cancer prevention in women with germline BRCA1/2 mutations are limited. We previously showed that recombinant human chorionic gonadotropin (r-hCG) induces mammary gland differentiation and inhibits mammary tumorigenesis in rats. The present study investigated hCG-induced signaling pathways in the breast of young nulliparous women carrying germline BRCA1/2 mutations. METHODS We performed RNA-sequencing on breast tissues from 25 BRCA1/2 mutation carriers who received r-hCG treatment for 3 months in a phase II clinical trial, we analyzed the biological processes, reactome pathways, canonical pathways, and upstream regulators associated with genes differentially expressed after r-hCG treatment, and validated genes of interest. RESULTS We observed that r-hCG induces remarkable transcriptomic changes in the breast of BRCA1/2 carriers, especially in genes related to cell development, cell differentiation, cell cycle, apoptosis, DNA repair, chromatin remodeling, and G protein-coupled receptor signaling. We revealed that r-hCG inhibits Wnt/β-catenin signaling, MYC, HMGA1 , and HOTAIR , whereas activates TGFB/TGFBR-SMAD2/3/4, BRCA1, TP53, and upregulates BRCA1 protein. CONCLUSION Our data suggest that the use of r-hCG at young age may reduce the risk of breast cancer in BRCA1/2 carriers by inhibiting pathways associated with stem/progenitor cell maintenance and neoplastic transformation, whereas activating genes crucial for breast epithelial differentiation and lineage commitment, and DNA repair.
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Affiliation(s)
- Yanrong Su
- The Irma H Russo, MD, Breast Cancer Research Laboratory at the Fox Chase Cancer Center-Temple Health, 333 Cottman Avenue, Philadelphia, PA 19111, USA
- These authors contributed equally: Yanrong Su, Nhi M. Dang, and Herman Depypere
| | - Nhi M. Dang
- The Irma H Russo, MD, Breast Cancer Research Laboratory at the Fox Chase Cancer Center-Temple Health, 333 Cottman Avenue, Philadelphia, PA 19111, USA
- These authors contributed equally: Yanrong Su, Nhi M. Dang, and Herman Depypere
| | - Herman Depypere
- Department of Gynecology, Breast and Menopause clinic, University Hospital of Ghent, Corneel Heymanslaan 10, 9000 Ghent, Belgium
- These authors contributed equally: Yanrong Su, Nhi M. Dang, and Herman Depypere
| | - Julia Santucci-Pereira
- The Irma H Russo, MD, Breast Cancer Research Laboratory at the Fox Chase Cancer Center-Temple Health, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | | | - Joice Kanefsky
- The Irma H Russo, MD, Breast Cancer Research Laboratory at the Fox Chase Cancer Center-Temple Health, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Jaak Ph. Janssens
- European Cancer Prevention Organization, University of Hasselt, Klein Hilststraat 5, 3500 Hasselt, Belgium
| | - Jose Russo
- The Irma H Russo, MD, Breast Cancer Research Laboratory at the Fox Chase Cancer Center-Temple Health, 333 Cottman Avenue, Philadelphia, PA 19111, USA
- Dr. Russo conceived the study and supervised the work. Dr. Russo passed away on September 24, 2021
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15
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Saha S, Pommier Y. R-loops, type I topoisomerases and cancer. NAR Cancer 2023; 5:zcad013. [PMID: 37600974 PMCID: PMC9984992 DOI: 10.1093/narcan/zcad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
R-loops are abundant and dynamic structures ubiquitously present in human cells both in the nuclear and mitochondrial genomes. They form in cis in the wake of transcription complexes and in trans apart from transcription complexes. In this review, we focus on the relationship between R-loops and topoisomerases, and cancer genomics and therapies. We summarize the topological parameters associated with the formation and resolution of R-loops, which absorb and release high levels of genomic negative supercoiling (Sc-). We review the deleterious consequences of excessive R-loops and rationalize how human type IA (TOP3B) and type IB (TOP1) topoisomerases regulate and resolve R-loops in coordination with helicase and RNase H enzymes. We also review the drugs (topoisomerase inhibitors, splicing inhibitors, G4 stabilizing ligands) and cancer predisposing genes (BRCA1/2, transcription, and splicing genes) known to induce R-loops, and whether stabilizing R-loops and thereby inducing genomic damage can be viewed as a strategy for cancer treatment.
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Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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16
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Tang J, Wang X, Xiao D, Liu S, Tao Y. The chromatin-associated RNAs in gene regulation and cancer. Mol Cancer 2023; 22:27. [PMID: 36750826 PMCID: PMC9903551 DOI: 10.1186/s12943-023-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Eukaryotic genomes are prevalently transcribed into many types of RNAs that translate into proteins or execute gene regulatory functions. Many RNAs associate with chromatin directly or indirectly and are called chromatin-associated RNAs (caRNAs). To date, caRNAs have been found to be involved in gene and transcriptional regulation through multiple mechanisms and have important roles in different types of cancers. In this review, we first present different categories of caRNAs and the modes of interaction between caRNAs and chromatin. We then detail the mechanisms of chromatin-associated nascent RNAs, chromatin-associated noncoding RNAs and emerging m6A on caRNAs in transcription and gene regulation. Finally, we discuss the roles of caRNAs in cancer as well as epigenetic and epitranscriptomic mechanisms contributing to cancer, which could provide insights into the relationship between different caRNAs and cancer, as well as tumor treatment and intervention.
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Affiliation(s)
- Jun Tang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078 Hunan China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078 Hunan China
| | - Xiang Wang
- grid.216417.70000 0001 0379 7164Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China. .,Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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CPSF6-mediated XBP1 3'UTR shortening attenuates cisplatin-induced ER stress and elevates chemo-resistance in lung adenocarcinoma. Drug Resist Updat 2023; 68:100933. [PMID: 36821972 DOI: 10.1016/j.drup.2023.100933] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/28/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
Alternative polyadenylation (APA) is a widespread mechanism generating RNA molecules with alternative 3' ends. Herein, we discovered that TargetScan includes a novel XBP1 transcript with a longer 3' untranslated region (UTR) (XBP1-UL) than that included in NCBI. XBP1-UL exhibited a lowered level in blood samples from lung adenocarcinoma (LUAD) patients and in those after DDP treatment. Consistently, XBP1-UL was reduced in A549 cells compared to normal BEAS-2B cells, as well as in DDP-treated/resistant A549 cells relative to controls. Moreover, due to decreased usage of the distal polyadenylation site (PAS) in 3'UTR, XBP1-UL level was lowered in A549 cells and decreased further in DDP-resistant A549 (A549/DDP) cells. Importantly, use of the distal PAS (dPAS) and XBP1-UL level were gradually reduced in A549 cells under increasing concentrations of DDP, which was attributed to DDP-induced endoplasmic reticulum (ER) stress. Furthermore, XBP1 transcripts with shorter 3'UTR (XBP1-US) were more stable and presented stronger potentiation on DDP resistance. The choice of proximal PAS (pPAS) was attributed to CPSF6 elevation, which was caused by BRCA1-distrupted R-loop accumulation in CPSF6 5'end. DDP-induced nuclear LINC00221 also facilitated CPSF6-induced pPAS choice in the pre-XBP1 3'end. Finally, we found that unlike the unspliced XBP1 protein (XBP1-u), the spliced form XBP1-s retarded p53 degradation to facilitate DNA damage repair of LUAD cells. The current study provides new insights into tumor progression and DDP resistance in LUAD, which may contribute to improved LUAD treatment.
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18
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The BRCA1 BRCT promotes antisense RNA production and double-stranded RNA formation to suppress ribosomal R-loops. Proc Natl Acad Sci U S A 2022; 119:e2217542119. [PMID: 36490315 PMCID: PMC9897471 DOI: 10.1073/pnas.2217542119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
R-loops, or RNA:DNA hybrids, can induce DNA damage, which requires DNA repair factors including breast cancer type 1 susceptibility protein (BRCA1) to restore genomic integrity. To date, several pathogenic mutations have been found within the tandem BRCA1 carboxyl-terminal (BRCT) domains that mediate BRCA1 interactions with proteins and DNA in response to DNA damage. Here, we describe a nonrepair role of BRCA1 BRCT in suppressing ribosomal R-loops via two mechanisms. Through its RNA binding and annealing activities, BRCA1 BRCT facilitates the formation of double-stranded RNA between ribosomal RNA (rRNA) and antisense-rRNA (as-rRNA), hereby minimizing rRNA hybridization to ribosomal DNA to form R-loops. BRCA1 BRCT also promotes RNA polymerase I-dependent transcription of as-rRNA to enhance double-stranded rRNA (ds-rRNA) formation. In addition, BRCA1 BRCT-mediated as-rRNA production restricts rRNA maturation in unperturbed cells. Hence, impairing as-rRNA transcription and ds-rRNA formation due to BRCA1 BRCT deficiency deregulates rRNA processing and increases ribosomal R-loops and DNA breaks. Our results link ribosomal biogenesis dysfunction to BRCA1-associated genomic instability.
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19
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Zhuang J, Chen P, Wu Y, Luo Q, Wang Q, Chen S, Chen X, Jiang Z, Qiu J, Li Y, Yuan Z, Zhuang J. Brca1 Is Regulated by the Transcription Factor Gata3, and Its Silencing Promotes Neural Differentiation in Retinal Neurons. Int J Mol Sci 2022; 23:ijms232213860. [PMID: 36430332 PMCID: PMC9694312 DOI: 10.3390/ijms232213860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Previous studies have indicated that Brca1 (Breast cancer suppressor gene 1) plays an important role in neural development and degenerative diseases. However, the bioactivity and regulatory mechanism of Brca1 expression in retinal neurocytes remain unclear. In the present study, our data indicated that Brca1 maintains the state of neuronal precursor cells. Brca1 silencing induces differentiation in 661W cells. Nestin, a marker of precursor cells, was significantly decreased in parallel with Brca1 silencing in 661W cells, whereas Map2 (Microtubule associated protein 2), a marker of differentiated neurons, was significantly increased. Neurite outgrowth was increased by ~4.0-fold in Brca1-silenced cells. Moreover, DNA affinity purification assays and ChIP assays demonstrated that Gata3 (GATA binding protein 3) regulates Brca1 transcription in 661W cells. Silencing or overexpressing Gata3 could significantly regulate the expression of Brca1 and affect its promoter inducibility. Furthermore, the expression of Gata3 generally occurred in parallel with that of Brca1 in developing mouse retinas. Both Gata3 and Brca1 are expressed in the neonatal mouse retina but are developmentally silenced with age. Exogenous Gata3 significantly inhibited neural activity by decreasing synaptophysin and neurite outgrowth. Thus, this study demonstrated that Brca1 is transcriptionally regulated by Gata3. Brca1/Gata3 silencing is involved in neuronal differentiation and maturation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhaohui Yuan
- Correspondence: (Z.Y.); (J.Z.); Tel.: +86-20-6667-8735 (J.Z.); Fax: +86-20-8733-3271 (J.Z.)
| | - Jing Zhuang
- Correspondence: (Z.Y.); (J.Z.); Tel.: +86-20-6667-8735 (J.Z.); Fax: +86-20-8733-3271 (J.Z.)
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20
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Petermann E, Lan L, Zou L. Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids. Nat Rev Mol Cell Biol 2022; 23:521-540. [PMID: 35459910 DOI: 10.1038/s41580-022-00474-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
RNA-DNA hybrids are generated during transcription, DNA replication and DNA repair and are crucial intermediates in these processes. When RNA-DNA hybrids are stably formed in double-stranded DNA, they displace one of the DNA strands and give rise to a three-stranded structure called an R-loop. R-loops are widespread in the genome and are enriched at active genes. R-loops have important roles in regulating gene expression and chromatin structure, but they also pose a threat to genomic stability, especially during DNA replication. To keep the genome stable, cells have evolved a slew of mechanisms to prevent aberrant R-loop accumulation. Although R-loops can cause DNA damage, they are also induced by DNA damage and act as key intermediates in DNA repair such as in transcription-coupled repair and RNA-templated DNA break repair. When the regulation of R-loops goes awry, pathological R-loops accumulate, which contributes to diseases such as neurodegeneration and cancer. In this Review, we discuss the current understanding of the sources of R-loops and RNA-DNA hybrids, mechanisms that suppress and resolve these structures, the impact of these structures on DNA repair and genome stability, and opportunities to therapeutically target pathological R-loops.
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Affiliation(s)
- Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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21
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Sou IF, Hamer G, Tee WW, Vader G, McClurg UL. Cancer and meiotic gene expression: Two sides of the same coin? Curr Top Dev Biol 2022; 151:43-68. [PMID: 36681477 DOI: 10.1016/bs.ctdb.2022.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Meiosis increases genetic diversity in offspring by generating genetically unique haploid gametes with reshuffled chromosomes. This process requires a specialized set of meiotic proteins, which facilitate chromosome recombination and segregation. However, re-expression of meiotic proteins in mitosis can have catastrophic oncogenic consequences and aberrant expression of meiotic proteins is a common occurrence in human tumors. Mechanistically, re-activation of meiotic genes in cancer promotes oncogenesis likely because cancers-conversely to healthy mitosis-are fueled by genetic instability which promotes tumor evolution, and evasion of immune response and treatment pressure. In this review, we explore similarities between meiotic and cancer cells with a particular focus on the oncogenic activation of meiotic genes in cancer. We emphasize the role of histones and their modifications, DNA methylation, genome organization, R-loops and the availability of distal enhancers.
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Affiliation(s)
- Ieng Fong Sou
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom; Chromatin Dynamics and Disease Epigenetics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Geert Hamer
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gerben Vader
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Urszula Lucja McClurg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
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22
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Functions of Breast Cancer Predisposition Genes: Implications for Clinical Management. Int J Mol Sci 2022; 23:ijms23137481. [PMID: 35806485 PMCID: PMC9267387 DOI: 10.3390/ijms23137481] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Approximately 5–10% of all breast cancer (BC) cases are caused by germline pathogenic variants (GPVs) in various cancer predisposition genes (CPGs). The most common contributors to hereditary BC are BRCA1 and BRCA2, which are associated with hereditary breast and ovarian cancer (HBOC). ATM, BARD1, CHEK2, PALB2, RAD51C, and RAD51D have also been recognized as CPGs with a high to moderate risk of BC. Primary and secondary cancer prevention strategies have been established for HBOC patients; however, optimal preventive strategies for most hereditary BCs have not yet been established. Most BC-associated CPGs participate in DNA damage repair pathways and cell cycle checkpoint mechanisms, and function jointly in such cascades; therefore, a fundamental understanding of the disease drivers in such cascades can facilitate the accurate estimation of the genetic risk of developing BC and the selection of appropriate preventive and therapeutic strategies to manage hereditary BCs. Herein, we review the functions of key BC-associated CPGs and strategies for the clinical management in individuals harboring the GPVs of such genes.
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23
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Brickner JR, Garzon JL, Cimprich KA. Walking a tightrope: The complex balancing act of R-loops in genome stability. Mol Cell 2022; 82:2267-2297. [PMID: 35508167 DOI: 10.1016/j.molcel.2022.04.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 12/14/2022]
Abstract
Although transcription is an essential cellular process, it is paradoxically also a well-recognized cause of genomic instability. R-loops, non-B DNA structures formed when nascent RNA hybridizes to DNA to displace the non-template strand as single-stranded DNA (ssDNA), are partially responsible for this instability. Yet, recent work has begun to elucidate regulatory roles for R-loops in maintaining the genome. In this review, we discuss the cellular contexts in which R-loops contribute to genomic instability, particularly during DNA replication and double-strand break (DSB) repair. We also summarize the evidence that R-loops participate as an intermediate during repair and may influence pathway choice to preserve genomic integrity. Finally, we discuss the immunogenic potential of R-loops and highlight their links to disease should they become pathogenic.
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Affiliation(s)
- Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jada L Garzon
- 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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24
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Abstract
DNA repair and DNA damage signaling pathways are critical for the maintenance of genomic stability. Defects of DNA repair and damage signaling contribute to tumorigenesis, but also render cancer cells vulnerable to DNA damage and reliant on remaining repair and signaling activities. Here, we review the major classes of DNA repair and damage signaling defects in cancer, the genomic instability that they give rise to, and therapeutic strategies to exploit the resulting vulnerabilities. Furthermore, we discuss the impacts of DNA repair defects on both targeted therapy and immunotherapy, and highlight emerging principles for targeting DNA repair defects in cancer therapy.
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Affiliation(s)
- Jessica L Hopkins
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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25
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Circulating Tumor Cells in Breast Cancer Patients: A Balancing Act between Stemness, EMT Features and DNA Damage Responses. Cancers (Basel) 2022; 14:cancers14040997. [PMID: 35205744 PMCID: PMC8869884 DOI: 10.3390/cancers14040997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 02/04/2023] Open
Abstract
Circulating tumor cells (CTCs) traverse vessels to travel from the primary tumor to distant organs where they adhere, transmigrate, and seed metastases. To cope with these challenges, CTCs have reached maximal flexibility to change their differentiation status, morphology, migratory capacity, and their responses to genotoxic stress caused by metabolic changes, hormones, the inflammatory environment, or cytostatic treatment. A significant percentage of breast cancer cells are defective in homologous recombination repair and other mechanisms that protect the integrity of the replication fork. To prevent cell death caused by broken forks, alternative, mutagenic repair, and bypass pathways are engaged but these increase genomic instability. CTCs, arising from such breast tumors, are endowed with an even larger toolbox of escape mechanisms that can be switched on and off at different stages during their journey according to the stress stimulus. Accumulating evidence suggests that DNA damage responses, DNA repair, and replication are integral parts of a regulatory network orchestrating the plasticity of stemness features and transitions between epithelial and mesenchymal states in CTCs. This review summarizes the published information on these regulatory circuits of relevance for the design of biomarkers reflecting CTC functions in real-time to monitor therapeutic responses and detect evolving chemoresistance mechanisms.
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26
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Bunch H, Jeong J, Kang K, Jo DS, Cong ATQ, Kim D, Kim D, Cho DH, Lee YM, Chen BPC, Schellenberg MJ, Calderwood SK. BRCA1-BARD1 regulates transcription through modulating topoisomerase IIβ. Open Biol 2021; 11:210221. [PMID: 34610268 PMCID: PMC8492178 DOI: 10.1098/rsob.210221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
RNA polymerase II (Pol II)-dependent transcription in stimulus-inducible genes requires topoisomerase IIβ (TOP2B)-mediated DNA strand break and the activation of DNA damage response signalling in humans. Here, we report a novel function of the breast cancer 1 (BRCA1)-BRCA1-associated ring domain 1 (BARD1) complex in this process. We found that BRCA1 is phosphorylated at S1524 by the kinases ataxia-telangiectasia mutated and ATR during gene activation, and that this event is important for productive transcription. Our biochemical and genomic analyses showed that the BRCA1-BARD1 complex interacts with TOP2B in the EGR1 transcription start site and in a large number of protein-coding genes. Intriguingly, the BRCA1-BARD1 complex ubiquitinates TOP2B, which stabilizes TOP2B binding to DNA while BRCA1 phosphorylation at S1524 controls the TOP2B ubiquitination by the complex. Together, these findings suggest the novel function of the BRCA1-BARD1 complex in the regulation of TOP2B and Pol II-mediated gene expression.
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Affiliation(s)
- Heeyoun Bunch
- Department of Applied Biosciences, College of Agriculture and Life Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea,School of Applied Biosciences, College of Agriculture and Life Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jaehyeon Jeong
- Department of Applied Biosciences, College of Agriculture and Life Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Doo Sin Jo
- School of Life Sciences, BK21 Four KNU Creative Bioresearch Group, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Anh T. Q. Cong
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Deukyeong Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Donguk Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dong-Hyung Cho
- School of Life Sciences, BK21 Four KNU Creative Bioresearch Group, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - You Mie Lee
- Vessel-Organ Interaction Research Center, VOICE (MRC), Department of Molecular Pathophysiology, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Benjamin P. C. Chen
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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27
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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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28
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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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29
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Uribe ML, Dahlhoff M, Batra RN, Nataraj NB, Haga Y, Drago-Garcia D, Marrocco I, Sekar A, Ghosh S, Vaknin I, Lebon S, Kramarski L, Tsutsumi Y, Choi I, Rueda OM, Caldas C, Yarden Y. TSHZ2 is an EGF-regulated tumor suppressor that binds to the cytokinesis regulator PRC1 and inhibits metastasis. Sci Signal 2021; 14:eabe6156. [PMID: 34158398 PMCID: PMC7614343 DOI: 10.1126/scisignal.abe6156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Unlike early transcriptional responses to mitogens, later events are less well-characterized. Here, we identified delayed down-regulated genes (DDGs) in mammary cells after prolonged treatment with epidermal growth factor (EGF). The expression of these DDGs was low in mammary tumors and correlated with prognosis. The proteins encoded by several DDGs directly bind to and inactivate oncoproteins and might therefore act as tumor suppressors. The transcription factor teashirt zinc finger homeobox 2 (TSHZ2) is encoded by a DDG, and we found that overexpression of TSHZ2 inhibited tumor growth and metastasis and accelerated mammary gland development in mice. Although the gene TSHZ2 localizes to a locus (20q13.2) that is frequently amplified in breast cancer, we found that hypermethylation of its promoter correlated with down-regulation of TSHZ2 expression in patients. Yeast two-hybrid screens and protein-fragment complementation assays in mammalian cells indicated that TSHZ2 nucleated a multiprotein complex containing PRC1/Ase1, cyclin B1, and additional proteins that regulate cytokinesis. TSHZ2 increased the inhibitory phosphorylation of PRC1, a key driver of mitosis, mediated by cyclin-dependent kinases. Furthermore, similar to the tumor suppressive transcription factor p53, TSHZ2 inhibited transcription from the PRC1 promoter. By recognizing DDGs as a distinct group in the transcriptional response to EGF, our findings uncover a group of tumor suppressors and reveal a role for TSHZ2 in cell cycle regulation.
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Affiliation(s)
- Mary L Uribe
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maik Dahlhoff
- Institute of in vivo and in vitro Models, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Rajbir N Batra
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nishanth B Nataraj
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuya Haga
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Diana Drago-Garcia
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilaria Marrocco
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Arunachalam Sekar
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Soma Ghosh
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Itay Vaknin
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sacha Lebon
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lior Kramarski
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan
| | - Inpyo Choi
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 306-809, South Korea
| | - Oscar M Rueda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
- MRC Biostatistics Unit, University of Cambridge, Forvie Site, Robinson Way, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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30
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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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31
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Zheng J, Mao Z, Zhang J, Jiang L, Wang N. Paeonol Pretreatment Attenuates Anoxia-Reoxygenation Induced Injury in Cardiac Myocytes via a BRCA1 Dependent Pathway. Chem Pharm Bull (Tokyo) 2021; 68:1163-1169. [PMID: 33268648 DOI: 10.1248/cpb.c20-00524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Breast cancer type 1 sensitive protein (BRCA1) is a well-known tumor suppressor and its role in oxidative stress has been confirmed. The purpose of this study is to evaluate whether paeonol has a protective effect on myocardial hypoxia-reoxygenation (A/R) injury, and to explore H9C2 cells through a mechanism-dependent pathway mediated by BRCA1. H9C2 cells were pretreated with paeonol (10 µM) for 18 h before hypoxia was induced to establish a cell model of myocardial ischemia/reperfusion (I/R) injury. Use commercial kits to detect antioxidant indicators, including relative oxygen content (ROS) levels, total antioxidant capacity (T-AOC), superoxide dismutase (SOD), lactate dehydrogenase (LDH) activity, and creatine kinase (CK-MB) and nuclear factor-kappaB (NF-κB) activity. The cell viability was analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction method. Real-time fluorescent quantitative PCR was used to detect BRCA1 mRNA and protein levels. The expression levels of BRCA1, NLRP3 and ACS were determined by Western blotting. In addition, the release of interleukin (IL)-1β (IL-1β), IL-6 and tumor necrosis factor-α (TNF-α) was also evaluated by an enzyme-linked immunosorbent assay (ELISA) kit. The results showed that paeonol (10 µM) can significantly improve the hypoxic A/R damage of H9C2 cells, and the BRCA1 expression of H9C2 cells pretreated with paeonol was significantly increased before A/R damage was induced. BRCA1 is widely known in breast and ovarian cancer. Our data proves that the down-regulation of BRCA1 participates in the decrease of cell viability and the decrease of CK-MB and LDH activities, and protects cells by inhibiting the production of ROS and the activation of Nod-like receptor protein 3 (NLRP3) inflammasomes and NF-κB. In conclusion, paeonol significantly improved the A/R damage of H9C2 cells induced by hypoxia through the BRCA1/ROS-regulated NLRP3 inflammasome/IL-1β and NF-κB/TNF-α/IL-6 pathways. It may be a potential drug against myocardial I/R injury.
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Affiliation(s)
- Jifeng Zheng
- Department of Cardiology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital.,Department of Cardiology, The Affiliated Second Hospital of Jiaxing Medical University
| | - Zhiyao Mao
- Department of Cardiology, The Affiliated Second Hospital of Jiaxing Medical University
| | - Jianqin Zhang
- Department of Cardiology, The Affiliated Second Hospital of Jiaxing Medical University
| | - Liqing Jiang
- Department of Cardiology, The Affiliated Second Hospital of Jiaxing Medical University
| | - Ningfu Wang
- Department of Cardiology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital
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32
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Hu L, Su L, Cheng H, Mo C, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, Zhang J, Xie Y. Single-Cell RNA Sequencing Reveals the Cellular Origin and Evolution of Breast Cancer in BRCA1 Mutation Carriers. Cancer Res 2021; 81:2600-2611. [PMID: 33727227 DOI: 10.1158/0008-5472.can-20-2123] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/29/2020] [Accepted: 03/11/2021] [Indexed: 11/16/2022]
Abstract
The cell of origin and the development of breast cancer are not fully elucidated in BRCA1 mutation carriers, especially for estrogen receptor (ER)-positive breast cancers. Here, we performed single-cell RNA sequencing (RNA-seq) on 82,122 cells isolated from the breast cancer tissues and adjacent or prophylactic normal breast tissues from four BRCA1 mutation carriers and three noncarriers. Whole-exome sequencing was performed on breast tumors from the four BRCA1 mutation carriers; for validation, bulk RNA-seq was performed on adjacent normal breast tissues from eight additional BRCA1 mutation carriers and 14 noncarriers. Correlation analyses suggested that breast cancers in BRCA1 mutation carriers might originate from luminal cells. The aberrant luminal progenitor cells with impaired differentiation were significantly increased in normal breast tissues in BRCA1 mutation carriers compared with noncarriers. These observations were further validated by the bulk RNA-seq data from additional BRCA1 mutation carriers. These data suggest that the cell of origin of basal-like breast tumors (ERneg) in BRCA1 mutation carriers might be luminal progenitor cells. The expression of TP53 and BRCA1 was decreased in luminal progenitor cells from normal breast tissue in BRCA1 mutation carriers, which might trigger the basal/mesenchymal transition of luminal progenitors and might result in basal-like tumor development. Furthermore, ERhigh luminal tumors might originate from mature luminal cells. Our study provides in-depth evidence regarding the cells of origin of different breast cancer subtypes in BRCA1 mutation carriers. SIGNIFICANCE: Single-cell RNA-seq data indicate that basal-like breast cancer (ERneg) might originate from luminal progenitors, and ERhigh luminal breast cancer might originate from mature luminal cells in BRCA1 mutation carriers.
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Affiliation(s)
- Li Hu
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Liming Su
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Hainan Cheng
- Berry Oncology Co., Ltd. (Berry Genomics Group), Beijing, P.R. China
| | - Chunling Mo
- Berry Oncology Co., Ltd. (Berry Genomics Group), Beijing, P.R. China
| | - Tao Ouyang
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Jinfeng Li
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Tianfeng Wang
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Zhaoqing Fan
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Tie Fan
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Benyao Lin
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Jianguang Zhang
- Berry Oncology Co., Ltd. (Berry Genomics Group), Beijing, P.R. China.
| | - Yuntao Xie
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, P.R. China.
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33
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Du C, Peng Y, He Y, Chen G, Chen H. Low levels of BRCA1 protein expression predict a worse prognosis in stage I-II colon cancer. Int J Biol Markers 2021; 36:47-53. [PMID: 33583275 DOI: 10.1177/1724600820986572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND BRCA1 and BRCA2 have been well studied for their roles in tumorigeneis, plus cancer diagnosis and treatment, but their prognostic value in colon cancer, especially for early-stage cancer, has not been fully illuminated. This study examined the expression levels of BRCA1 and BRCA2 proteins in sporadic colon cancer cases and investigated their value in prognosis. METHODS The expression levels of BRCA1 and BRCA2 in 275 colon cancer patients who underwent radical surgeries were assayed by immunohistochemical staining in dissected tumor samples. Also, its correlation with clinicopathological characteristics, disease-free survival, and overall survival was investigated. RESULTS Tumors with low expression levels of BRCA1, BRCA2, and both were 19.6%, 17.8%, and 6.5%, respectively. The levels of BRCA1/2 expression were not associated with clinicopathological parameters (gender, age, histological differentiation, and tumor node metastasis stage). Patients with low-levels of BRCA1 protein in their tumors demonstrated a lower chance of 5-year disease-free survival (55.6% vs. 69.7%, P=0.046), which was more obvious in the patients with stage I-II tumors without chemotherapy (52.6% vs. 82.6%, P=0.006). Neither BRCA1 nor BRCA2 affected overall survival in this cohort. Multivariate analysis revealed that pathologic stage and the level of BRCA1 protein were independent factors of long-term disease-free survival. CONCLUSION This study highlights BRCA1 as an independent prognosticator of early-stage colon cancer.
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Affiliation(s)
- Changzheng Du
- School of Medicine, the Southern University of Science and Technology, Shenzhen, Guangdong, People's Republic of China.,Southern University of Science and Technology Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Yifan Peng
- Gastrointestinal Cancer Center, Beijing Cancer Hospital, Beijing, People's Republic of China
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA.,Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Guoan Chen
- School of Medicine, the Southern University of Science and Technology, Shenzhen, Guangdong, People's Republic of China
| | - Hao Chen
- School of Medicine, the Southern University of Science and Technology, Shenzhen, Guangdong, People's Republic of China
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34
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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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35
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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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36
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RNA-cDNA hybrids mediate transposition via different mechanisms. Sci Rep 2020; 10:16034. [PMID: 32994470 PMCID: PMC7524711 DOI: 10.1038/s41598-020-73018-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/04/2020] [Indexed: 11/21/2022] Open
Abstract
Retrotransposons can represent half of eukaryotic genomes. Retrotransposon dysregulation destabilizes genomes and has been linked to various human diseases. Emerging regulators of retromobility include RNA–DNA hybrid-containing structures known as R-loops. Accumulation of these structures at the transposons of yeast 1 (Ty1) elements has been shown to increase Ty1 retromobility through an unknown mechanism. Here, via a targeted genetic screen, we identified the rnh1Δ rad27Δ yeast mutant, which lacked both the Ty1 inhibitor Rad27 and the RNA–DNA hybrid suppressor Rnh1. The mutant exhibited elevated levels of Ty1 cDNA-associated RNA–DNA hybrids that promoted Ty1 mobility. Moreover, in this rnh1Δ rad27Δ mutant, but not in the double RNase H mutant rnh1Δ rnh201Δ, RNA–DNA hybrids preferentially existed as duplex nucleic acid structures and increased Ty1 mobility in a Rad52-dependent manner. The data indicate that in cells lacking RNA–DNA hybrid and Ty1 repressors, elevated levels of RNA-cDNA hybrids, which are associated with duplex nucleic acid structures, boost Ty1 mobility via a Rad52-dependent mechanism. In contrast, in cells lacking RNA–DNA hybrid repressors alone, elevated levels of RNA-cDNA hybrids, which are associated with triplex nucleic acid structures, boost Ty1 mobility via a Rad52-independent process. We propose that duplex and triplex RNA–DNA hybrids promote transposon mobility via Rad52-dependent or -independent mechanisms.
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Intrinsic and Extrinsic Factors Governing the Transcriptional Regulation of ESR1. Discov Oncol 2020; 11:129-147. [PMID: 32592004 DOI: 10.1007/s12672-020-00388-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/02/2020] [Indexed: 02/06/2023] Open
Abstract
Transcriptional regulation of ESR1, the gene that encodes for estrogen receptor α (ER), is critical for regulating the downstream effects of the estrogen signaling pathway in breast cancer such as cell growth. ESR1 is a large and complex gene that is regulated by multiple regulatory elements, which has complicated our understanding of how ESR1 expression is controlled in the context of breast cancer. Early studies characterized the genomic structure of ESR1 with subsequent studies focused on identifying intrinsic (chromatin environment, transcription factors, signaling pathways) and extrinsic (tumor microenvironment, secreted factors) mechanisms that impact ESR1 gene expression. Currently, the introduction of genomic sequencing platforms and additional genome-wide technologies has provided additional insight on how chromatin structures may coordinate with these intrinsic and extrinsic mechanisms to regulate ESR1 expression. Understanding these interactions will allow us to have a clearer understanding of how ESR1 expression is regulated and eventually provide clues on how to influence its regulation with potential treatments. In this review, we highlight key studies concerning the genomic structure of ESR1, mechanisms that affect the dynamics of ESR1 expression, and considerations towards affecting ESR1 expression and hormone responsiveness in breast cancer.
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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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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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40
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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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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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Fang Y, Chen L, Lin K, Feng Y, Zhang P, Pan X, Sanders J, Wu Y, Wang XE, Su Z, Chen C, Wei H, Zhang W. Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice. Genome Res 2019; 29:1287-1297. [PMID: 31262943 PMCID: PMC6673715 DOI: 10.1101/gr.246009.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 06/27/2019] [Indexed: 11/24/2022]
Abstract
We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expression and epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-loop peak levels was dependent on the positions of R-loops within gene structures (hereafter named “genic position”). Both antisense only (ASO)-R-loops and sense/antisense (S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peak levels corresponded positively with transcript levels of overlapping genes. In contrast, sense only (SO)-R-loops were generally spread over the coding regions, and their peak levels corresponded inversely to transcript levels of overlapping genes. In addition, integrative analyses of R-loop data with existing RNA-seq, chromatin immunoprecipitation sequencing (ChIP-seq), DNase I hypersensitive sites sequencing (DNase-seq), and whole-genome bisulfite sequencing (WGBS or BS-seq) data revealed interrelationships and intricate connections among R-loops, gene expression, and epigenetic signatures. Experimental validation provided evidence that the demethylation of both DNA and histone marks can influence R-loop peak levels on a genome-wide scale. This is the first study in plants that reveals novel functional aspects of R-loops, their interrelations with epigenetic methylation, and roles in transcriptional regulation.
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Affiliation(s)
- Yuan Fang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Lifen Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Kande Lin
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Pengyue Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Xiucai Pan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Jennifer Sanders
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan 49931, USA
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Xiu-E Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, P.R. China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, 410125, P.R. China
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan 49931, USA.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, P.R. China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
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