1
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Fan J, Li Z, Pei L, Hou Y. Post-transcriptional regulation of DEAD-box RNA helicases in hematopoietic malignancies. Genes Dis 2024; 11:101252. [PMID: 38993792 PMCID: PMC11237855 DOI: 10.1016/j.gendis.2024.101252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 07/13/2024] Open
Abstract
Hematopoiesis represents a meticulously regulated and dynamic biological process. Genetic aberrations affecting blood cells, induced by various factors, frequently give rise to hematological tumors. These instances are often accompanied by a multitude of abnormal post-transcriptional regulatory events, including RNA alternative splicing, RNA localization, RNA degradation, and storage. Notably, post-transcriptional regulation plays a pivotal role in preserving hematopoietic homeostasis. The DEAD-Box RNA helicase genes emerge as crucial post-transcriptional regulatory factors, intricately involved in sustaining normal hematopoiesis through diverse mechanisms such as RNA alternative splicing, RNA modification, and ribosome assembly. This review consolidates the existing knowledge on the role of DEAD-box RNA helicases in regulating normal hematopoiesis and underscores the pathogenicity of mutant DEAD-Box RNA helicases in malignant hematopoiesis. Emphasis is placed on elucidating both the positive and negative contributions of DEAD-box RNA helicases within the hematopoietic system.
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Affiliation(s)
- Jiankun Fan
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zhigang Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Li Pei
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yu Hou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
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2
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Matsui H. DDX41 and its unique contribution to myeloid leukemogenesis. Oncotarget 2024; 15:442-443. [PMID: 38953908 PMCID: PMC11218790 DOI: 10.18632/oncotarget.28603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Indexed: 07/04/2024] Open
Affiliation(s)
- Hirotaka Matsui
- Correspondence to:Hirotaka Matsui, Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan; Department of Medical Oncology and Translational Research, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan email
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3
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Wen C, Cao L, Wang S, Xu W, Yu Y, Zhao S, Yang F, Chen ZJ, Zhao S, Yang Y, Qin Y. MCM8 interacts with DDX5 to promote R-loop resolution. EMBO J 2024; 43:3044-3071. [PMID: 38858601 DOI: 10.1038/s44318-024-00134-0] [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: 08/12/2023] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
MCM8 has emerged as a core gene in reproductive aging and is crucial for meiotic homologous recombination repair. It also safeguards genome stability by coordinating the replication stress response during mitosis, but its function in mitotic germ cells remains elusive. Here we found that disabling MCM8 in mice resulted in proliferation defects of primordial germ cells (PGCs) and ultimately impaired fertility. We further demonstrated that MCM8 interacted with two known helicases DDX5 and DHX9, and loss of MCM8 led to R-loop accumulation by reducing the retention of these helicases at R-loops, thus inducing genome instability. Cells expressing premature ovarian insufficiency-causative mutants of MCM8 with decreased interaction with DDX5 displayed increased R-loop levels. These results show MCM8 interacts with R-loop-resolving factors to prevent R-loop-induced DNA damage, which may contribute to the maintenance of genome integrity of PGCs and reproductive reserve establishment. Our findings thus reveal an essential role for MCM8 in PGC development and improve our understanding of reproductive aging caused by genome instability in mitotic germ cells.
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Affiliation(s)
- Canxin Wen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Lili Cao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Shuhan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Weiwei Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Yongze Yu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Simin Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Fan Yang
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Zi-Jiang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- Department of Reproductive Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shidou Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
| | - Yajuan Yang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
| | - Yingying Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
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4
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Wang C, Huang Y, Yang Y, Li R, Li Y, Qiu H, Wu J, Shi G, Ma W, Songyang Z. ILF3 safeguards telomeres from aberrant homologous recombination as a telomeric R-loop reader. Protein Cell 2024; 15:493-511. [PMID: 37991243 PMCID: PMC11214836 DOI: 10.1093/procel/pwad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/09/2023] [Indexed: 11/23/2023] Open
Abstract
Telomeres are specialized structures at the ends of linear chromosomes that protect genome stability. The telomeric repeat-containing RNA (TERRA) that is transcribed from subtelomeric regions can invade into double-stranded DNA regions and form RNA:DNA hybrid-containing structure called R-loop. In tumor cells, R-loop formation is closely linked to gene expression and the alternative lengthening of telomeres (ALT) pathway. Dysregulated R-loops can cause stalled replication forks and telomere instability. However, how R-loops are recognized and regulated, particularly at telomeres, is not well understood. We discovered that ILF3 selectively associates with telomeric R-loops and safeguards telomeres from abnormal homologous recombination. Knocking out ILF3 results in excessive R-loops at telomeres and triggers telomeric DNA damage responses. In addition, ILF3 deficiency disrupts telomere homeostasis and causes abnormalities in the ALT pathway. Using the proximity-dependent biotin identification (BioID) technology, we mapped the ILF3 interactome and discovered that ILF3 could interact with several DNA/RNA helicases, including DHX9. Importantly, ILF3 may aid in the resolution of telomeric R-loops through its interaction with DHX9. Our findings suggest that ILF3 may function as a reader of telomeric R-loops, helping to prevent abnormal homologous recombination and maintain telomere homeostasis.
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Affiliation(s)
- Chuanle Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Yan Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Ruofei Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yingying Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hongxin Qiu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiali Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangzhou Key Laboratory of Healthy Aging, School of Lifesciences, Sun Yat-sen University, Guangzhou 510275, China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
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5
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Stepanchick E, Wilson A, Sulentic AM, Choi K, Hueneman K, Starczynowski DT, Chlon TM. DDX41 haploinsufficiency causes inefficient hematopoiesis under stress and cooperates with p53 mutations to cause hematologic malignancy. Leukemia 2024:10.1038/s41375-024-02304-9. [PMID: 38937548 DOI: 10.1038/s41375-024-02304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024]
Abstract
Germline heterozygous mutations in DDX41 predispose individuals to hematologic malignancies in adulthood. Most of these DDX41 mutations result in a truncated protein, leading to loss of protein function. To investigate the impact of these mutations on hematopoiesis, we generated mice with hematopoietic-specific knockout of one Ddx41 allele. Under normal steady-state conditions, there was minimal effect on lifelong hematopoiesis, resulting in a mild yet persistent reduction in red blood cell counts. However, stress induced by transplantation of the Ddx41+/- BM resulted in hematopoietic stem/progenitor cell (HSPC) defects and onset of hematopoietic failure upon aging. Transcriptomic analysis of HSPC subsets from the transplanted BM revealed activation of cellular stress responses, including upregulation of p53 target genes in erythroid progenitors. To understand how the loss of p53 affects the phenotype of Ddx41+/- HSPCs, we generated mice with combined Ddx41 and Trp53 heterozygous deletions. The reduction in p53 expression rescued the fitness defects in HSPC caused by Ddx41 heterozygosity. However, the combined Ddx41 and Trp53 mutant mice were prone to developing hematologic malignancies that resemble human myelodysplastic syndrome and acute myeloid leukemia. In conclusion, DDX41 heterozygosity causes dysregulation of the response to hematopoietic stress, which increases the risk of transformation with a p53 mutation.
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Affiliation(s)
- Emily Stepanchick
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Andrew Wilson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Analise M Sulentic
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kathleen Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
- University of Cincinnati Cancer Center, Cincinnati, OH, USA
| | - Timothy M Chlon
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.
- University of Cincinnati Cancer Center, Cincinnati, OH, USA.
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6
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Wulfridge P, Sarma K. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nat Cell Biol 2024:10.1038/s41556-024-01437-4. [PMID: 38914786 DOI: 10.1038/s41556-024-01437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
R-loops are three-stranded nucleic acid structures that are abundant and widespread across the genome and that have important physiological roles in many nuclear processes. Their accumulation is observed in cancers and neurodegenerative disorders. Recent studies have implicated a function for R-loops and G-quadruplex (G4) structures, which can form on the displaced single strand of R-loops, in three-dimensional genome organization in both physiological and pathological contexts. Here we discuss the interconnected functions of DNA:RNA hybrids and G4s within R-loops, their impact on DNA repair and gene regulatory networks, and their emerging roles in genome organization during development and disease.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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7
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Hidmi O, Oster S, Shatleh D, Monin J, Aqeilan RI. Protocol for mapping physiological DSBs using in-suspension break labeling in situ and sequencing. STAR Protoc 2024; 5:103059. [PMID: 38717906 PMCID: PMC11098942 DOI: 10.1016/j.xpro.2024.103059] [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: 03/02/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/20/2024] Open
Abstract
Physiological double-stranded breaks (DSBs) are a major source of genomic instability. Here, we present a protocol for mapping physiological DSBs by in-suspension break labeling in situ and sequencing (sBLISS) in a single-nucleotide resolution. We describe steps for cell fixation, labeling of DSBs, DNA isolation followed by in vitro transcription (IVT), reverse transcription, and library preparation. sBLISS provides a map of DSBs over the genome and can be used to study the role of different factors in DSB formation. For complete details on the use and execution of this protocol, please refer to Hidmi et al.1.
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Affiliation(s)
- Osama Hidmi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Sara Oster
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Diala Shatleh
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan Monin
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rami I Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel; Cyprus Cancer Research Institute (CCRI), Nicosia, Cyprus.
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8
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Leisegang MS, Warwick T, Stötzel J, Brandes RP. RNA-DNA triplexes: molecular mechanisms and functional relevance. Trends Biochem Sci 2024; 49:532-544. [PMID: 38582689 DOI: 10.1016/j.tibs.2024.03.009] [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: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024]
Abstract
Interactions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA-DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemical, and biophysical methods support in vivo functionality with relevance for gene expression control. Here, we review the central methodology and biology of triplexes, outline paradigms required for triplex function, and provide examples of physiologically important triplex-forming long non-coding RNAs.
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Affiliation(s)
- Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany.
| | - Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Julia Stötzel
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
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9
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Lee H, Han DW, Yoo S, Kwon O, La H, Park C, Lee H, Kang K, Uhm SJ, Song H, Do JT, Choi Y, Hong K. RNA helicase DEAD-box-5 is involved in R-loop dynamics of preimplantation embryos. Anim Biosci 2024; 37:1021-1030. [PMID: 38419548 PMCID: PMC11065950 DOI: 10.5713/ab.23.0401] [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: 10/06/2023] [Revised: 11/09/2023] [Accepted: 12/07/2023] [Indexed: 03/02/2024] Open
Abstract
OBJECTIVE R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. METHODS In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. RESULTS We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. CONCLUSION These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.
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Affiliation(s)
- Hyeonji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Dong Wook Han
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020,
China
| | - Seonho Yoo
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Ohbeom Kwon
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Heeji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Kiye Kang
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Sang Jun Uhm
- Department of Animal Science, Sangji University, Wonju 26339,
Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029,
Korea
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10
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Hwang WC, Park K, Park S, Cheon NY, Lee JY, Hwang T, Lee S, Lee JM, Ju MK, Lee JR, Kwon YR, Jo WL, Kim M, Kim YJ, Kim H. Impaired binding affinity of YTHDC1 with METTL3/METTL14 results in R-loop accumulation in myelodysplastic neoplasms with DDX41 mutation. Leukemia 2024; 38:1353-1364. [PMID: 38514771 PMCID: PMC11147762 DOI: 10.1038/s41375-024-02228-4] [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: 09/13/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024]
Abstract
DEAD box helicase 41 (DDX41) mutations are the most prevalent predisposition to familial myelodysplastic syndrome (MDS). However, the precise roles of these variants in the pathogenesis of MDS have yet to be elucidated. Here, we discovered a novel mechanism by which DDX41 contributes to R-loop-induced DNA damage responses (DDR) in cooperation with the m6A-METTL complex (MAC) and YTHDC1 using DDX41 knockout (KO) and DDX41 knock-in (KI, R525H, Y259C) cell lines as well as primary samples from MDS patients. Compared to wild type (WT), DDX41 KO and KI led to increased levels of m6A RNA methylated R-loop. Interestingly, we found that DDX41 regulates m6A/R-loop levels by interacting with MAC components. Further, DDX41 promoted the recruitment of YTHDC1 to R-loops by promoting the binding between METTL3 and YTHDC1, which was dysregulated in DDX41-deficient cells, contributing to genomic instability. Collectively, we demonstrated that DDX41 plays a key role in the physiological control of R-loops in cooperation with MAC and YTHDC1. These findings provide novel insights into how defects in DDX41 influence MDS pathogenesis and suggest potential therapeutic targets for the treatment of MDS.
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Affiliation(s)
- Won Chan Hwang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Kibeom Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Silvia Park
- Department of Hematology, Seoul St. Mary's Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Na Young Cheon
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Taejoo Hwang
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Semin Lee
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Jong-Mi Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Min Kyung Ju
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Joo Rak Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Yong-Rim Kwon
- Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woo-Lam Jo
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Orthopaedic Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Yoo-Jin Kim
- Department of Hematology, Seoul St. Mary's Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
- Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea.
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11
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Szelest M, Giannopoulos K. Biological relevance of alternative splicing in hematologic malignancies. Mol Med 2024; 30:62. [PMID: 38760666 PMCID: PMC11100220 DOI: 10.1186/s10020-024-00839-2] [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: 03/06/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024] Open
Abstract
Alternative splicing (AS) is a strictly regulated process that generates multiple mRNA variants from a single gene, thus contributing to proteome diversity. Transcriptome-wide sequencing studies revealed networks of functionally coordinated splicing events, which produce isoforms with distinct or even opposing functions. To date, several mechanisms of AS are deregulated in leukemic cells, mainly due to mutations in splicing and/or epigenetic regulators and altered expression of splicing factors (SFs). In this review, we discuss aberrant splicing events induced by mutations affecting SFs (SF3B1, U2AF1, SRSR2, and ZRSR2), spliceosome components (PRPF8, LUC7L2, DDX41, and HNRNPH1), and epigenetic modulators (IDH1 and IDH2). Finally, we provide an extensive overview of the biological relevance of aberrant isoforms of genes involved in the regulation of apoptosis (e. g. BCL-X, MCL-1, FAS, and c-FLIP), activation of key cellular signaling pathways (CASP8, MAP3K7, and NOTCH2), and cell metabolism (PKM).
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Affiliation(s)
- Monika Szelest
- Department of Experimental Hematooncology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland.
| | - Krzysztof Giannopoulos
- Department of Experimental Hematooncology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland
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12
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Matsui H, Hirata M. Evaluation of the pathogenic potential of germline DDX41 variants in hematopoietic neoplasms using the ACMG/AMP guidelines. Int J Hematol 2024; 119:552-563. [PMID: 38492200 DOI: 10.1007/s12185-024-03728-w] [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: 11/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/18/2024]
Abstract
Clinical use of gene panel testing for hematopoietic neoplasms in areas, such as diagnosis, prognosis prediction, and exploration of treatment options, has increased in recent years. The keys to interpreting gene variants detected in gene panel testing are to distinguish between germline and somatic variants and accurately determine whether the detected variants are pathogenic. If a variant is suspected to be a pathogenic germline variant, it is essential to confirm its consistency with the disease phenotype and gather a thorough family history. Donor eligibility must also be considered, especially if the patient's variant is also detected in the expected donor for hematopoietic stem cell transplantation. However, determining the pathogenicity of gene variants is often complicated, given the current limited availability of databases covering germline variants of hematopoietic neoplasms. This means that hematologists will frequently need to interpret gene variants themselves. Here, we outline how to assess the pathogenicity of germline variants according to criteria from the American College of Medical Genetics and Genomics/Association for Molecular Pathology standards and guidelines for the interpretation of variants using DDX41, a gene recently shown to be closely associated with myeloid neoplasms with a germline predisposition, as an example.
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Affiliation(s)
- Hirotaka Matsui
- Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
- Department of Medical Oncology and Translational Research, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
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13
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Xu Y, Jiao Y, Liu C, Miao R, Liu C, Wang Y, Ma C, Liu J. R-loop and diseases: the cell cycle matters. Mol Cancer 2024; 23:84. [PMID: 38678239 PMCID: PMC11055327 DOI: 10.1186/s12943-024-02000-3] [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: 02/11/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
The cell cycle is a crucial biological process that is involved in cell growth, development, and reproduction. It can be divided into G1, S, G2, and M phases, and each period is closely regulated to ensure the production of two similar daughter cells with the same genetic material. However, many obstacles influence the cell cycle, including the R-loop that is formed throughout this process. R-loop is a triple-stranded structure, composed of an RNA: DNA hybrid and a single DNA strand, which is ubiquitous in organisms from bacteria to mammals. The existence of the R-loop has important significance for the regulation of various physiological processes. However, aberrant accumulation of R-loop due to its limited resolving ability will be detrimental for cells. For example, DNA damage and genomic instability, caused by the R-loop, can activate checkpoints in the cell cycle, which in turn induce cell cycle arrest and cell death. At present, a growing number of factors have been proven to prevent or eliminate the accumulation of R-loop thereby avoiding DNA damage and mutations. Therefore, we need to gain detailed insight into the R-loop resolution factors at different stages of the cell cycle. In this review, we review the current knowledge of factors that play a role in resolving the R-loop at different stages of the cell cycle, as well as how mutations of these factors lead to the onset and progression of diseases.
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Affiliation(s)
- Yuqin Xu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yue Jiao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunming Ma
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China.
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14
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Cunningham ML, Schiewer MJ. PARP-ish: Gaps in Molecular Understanding and Clinical Trials Targeting PARP Exacerbate Racial Disparities in Prostate Cancer. Cancer Res 2024; 84:743102. [PMID: 38635890 PMCID: PMC11217733 DOI: 10.1158/0008-5472.can-23-3458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/25/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
PARP is a nuclear enzyme with a major function in the DNA damage response. PARP inhibitors (PARPi) have been developed for treating tumors harboring homologous recombination repair (HRR) defects that lead to a dependency on PARP. There are currently three PARPi approved for use in advanced prostate cancer (PCa), and several others are in clinical trials for this disease. Recent clinical trial results have reported differential efficacy based on the specific PARPi utilized as well as patient race. There is a racial disparity in PCa, where African American (AA) males are twice as likely to develop and die from the disease compared to European American (EA) males. Despite the disparity, there continues to be a lack of diversity in clinical trial cohorts for PCa. In this review, PARP nuclear functions, inhibition, and clinical relevance are explored through the lens of racial differences. This review will touch on the biological variations that have been explored thus far between AA and EA males with PCa to offer rationale for investigating PARPi response in the context of race at both the basic science and the clinical development levels.
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Affiliation(s)
- Moriah L. Cunningham
- Department of Urology, Thomas Jefferson University, Philadelphia, Pennsylvania.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
| | - Matthew J. Schiewer
- Department of Urology, Thomas Jefferson University, Philadelphia, Pennsylvania.
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
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15
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Ren X, Liu Q, Zhou P, Zhou T, Wang D, Mei Q, Flavell RA, Liu Z, Li M, Pan W, Zhu S. DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells. Nat Commun 2024; 15:3080. [PMID: 38594251 PMCID: PMC11004185 DOI: 10.1038/s41467-024-47235-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Epithelial barrier dysfunction and crypt destruction are hallmarks of inflammatory bowel disease (IBD). Intestinal stem cells (ISCs) residing in the crypts play a crucial role in the continuous self-renewal and rapid recovery of intestinal epithelial cells (IECs). However, how ISCs are dysregulated in IBD remains poorly understood. Here, we observe reduced DHX9 protein levels in IBD patients, and mice with conditional DHX9 depletion in the intestinal epithelium (Dhx9ΔIEC) exhibit an increased susceptibility to experimental colitis. Notably, Dhx9ΔIEC mice display a significant reduction in the numbers of ISCs and Paneth cells. Further investigation using ISC-specific or Paneth cell-specific Dhx9-deficient mice demonstrates the involvement of ISC-expressed DHX9 in maintaining epithelial homeostasis. Mechanistically, DHX9 deficiency leads to abnormal R-loop accumulation, resulting in genomic instability and the cGAS-STING-mediated inflammatory response, which together impair ISC function and contribute to the pathogenesis of IBD. Collectively, our findings highlight R-loop-mediated genomic instability in ISCs as a risk factor in IBD.
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Affiliation(s)
- Xingxing Ren
- Hefei National Research Center for Physical Sciences at the Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145, Guangzhou, China
| | - Qiuyuan Liu
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Peirong Zhou
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145, Guangzhou, China
| | - Tingyue Zhou
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Decai Wang
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qiao Mei
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Zhanju Liu
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
| | - Mingsong Li
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145, Guangzhou, China.
| | - Wen Pan
- Hefei National Research Center for Physical Sciences at the Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China.
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Shu Zhu
- Hefei National Research Center for Physical Sciences at the Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China.
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- School of Data Science, University of Science and Technology of China, Hefei, 230026, China.
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16
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Rombaut D, Lefèvre C, Rached T, Bondu S, Letessier A, Mangione RM, Farhat B, Lesieur-Pasquier A, Castillo-Guzman D, Boussaid I, Friedrich C, Tourville A, De Carvalho M, Levavasseur F, Leduc M, Le Gall M, Battault S, Temple M, Houy A, Bouscary D, Willems L, Park S, Raynaud S, Cluzeau T, Clappier E, Fenaux P, Adès L, Margueron R, Wassef M, Alsafadi S, Chapuis N, Kosmider O, Solary E, Constantinou A, Stern MH, Droin N, Palancade B, Miotto B, Chédin F, Fontenay M. Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation. Nat Commun 2024; 15:3016. [PMID: 38589367 PMCID: PMC11001894 DOI: 10.1038/s41467-024-46547-7] [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: 12/07/2022] [Accepted: 02/29/2024] [Indexed: 04/10/2024] Open
Abstract
Myelodysplastic syndromes (MDS) with mutated SF3B1 gene present features including a favourable outcome distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we find that SF3B1-mutated MDS show reduced R-loop formation predominating in gene bodies associated with intron retention reduction, not found in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibit augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation. Importantly, histone deacetylase inhibition using vorinostat restores R-loop formation, slows down DNA replication forks and improves SF3B1-mutated erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress represents a hallmark of SF3B1-mutated MDS ineffective erythropoiesis, which could be used as a therapeutic target.
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Affiliation(s)
- David Rombaut
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Carine Lefèvre
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France
| | - Tony Rached
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Sabrina Bondu
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Anne Letessier
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
| | | | - Batoul Farhat
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Auriane Lesieur-Pasquier
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Daisy Castillo-Guzman
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Ismael Boussaid
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Chloé Friedrich
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Aurore Tourville
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Magali De Carvalho
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Françoise Levavasseur
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Marjorie Leduc
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Platform Proteom'IC, Université Paris Cité, Institut Cochin, Paris, France
| | - Morgane Le Gall
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Platform Proteom'IC, Université Paris Cité, Institut Cochin, Paris, France
| | - Sarah Battault
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Marie Temple
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Alexandre Houy
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Didier Bouscary
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Clinical Department of Hematology, Paris, France
| | - Lise Willems
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Clinical Department of Hematology, Paris, France
| | - Sophie Park
- Department of Hematology, Centre Hospitalier Universitaire, Université de Grenoble Alpes, Grenoble, France
| | - Sophie Raynaud
- Laboratory of Hematology, Université Côte d'Azur, Centre Hospitalier Universitaire, Nice, France
| | - Thomas Cluzeau
- Clinical Department of Hematology, Université Côte d'Azur, Centre Hospitalier Universitaire, Nice, France
| | - Emmanuelle Clappier
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Laboratory of Hematology, Paris, France
| | - Pierre Fenaux
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Service Hématologie Séniors, Paris, France
| | - Lionel Adès
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Service Hématologie Séniors, Paris, France
| | - Raphael Margueron
- Institut Curie, Paris Sciences Lettres Research University, Sorbonne University, INSERM U934, UMR3215, Paris, France
| | - Michel Wassef
- Institut Curie, Paris Sciences Lettres Research University, Sorbonne University, INSERM U934, UMR3215, Paris, France
| | - Samar Alsafadi
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Nicolas Chapuis
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Olivier Kosmider
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Eric Solary
- Institut Gustave Roussy, INSERM 1287, Université Paris Saclay, Villejuif, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Nathalie Droin
- Institut Gustave Roussy, INSERM 1287, Université Paris Saclay, Villejuif, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Miotto
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Michaela Fontenay
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France.
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France.
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France.
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France.
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17
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Zhao Y, Zhou Y, Qian Y, Wei W, Lin X, Mao S, Sun J, Jin J. m 6A-dependent upregulation of DDX21 by super-enhancer-driven IGF2BP2 and IGF2BP3 facilitates progression of acute myeloid leukaemia. Clin Transl Med 2024; 14:e1628. [PMID: 38572589 PMCID: PMC10993053 DOI: 10.1002/ctm2.1628] [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: 10/22/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is a haematological malignancy with unfavourable prognosis. Despite the effectiveness of chemotherapy and targeted therapy, relapse or drug resistance remains a major threat to AML patients. N6-methyladenosine (m6A) RNA methylation and super-enhancers (SEs) are extensively involved in the leukaemogenesis of AML. However, the potential relationship between m6A and SEs in AML has not been elaborated. METHODS Chromatin immunoprecipitation (ChIP) sequencing data from Gene Expression Omnibus (GEO) cohort were analysed to search SE-related genes. The mechanisms of m6 A-binding proteins IGF2BP2 and IGF2BP3 on DDX21 were explored via methylated RNA immunoprecipitation (MeRIP) assays, RNA immunoprecipitation (RIP) assays and luciferase reporter assays. Then we elucidated the roles of DDX21 in AML through functional assays in vitro and in vivo. Finally, co-immunoprecipitation (Co-IP) assays, RNA sequencing and ChIP assays were performed to investigate the downstream mechanisms of DDX21. RESULTS We identified two SE-associated transcripts IGF2BP2 and IGF2BP3 in AML. High enrichment of H3K27ac, H3K4me1 and BRD4 was observed in IGF2BP2 and IGF2BP3, whose expression were driven by SE machinery. Then IGF2BP2 and IGF2BP3 enhanced the stability of DDX21 mRNA in an m6A-dependent manner. DDX21 was highly expressed in AML patients, which indicated a poor survival. Functionally, knockdown of DDX21 inhibited cell proliferation, promoted cell apoptosis and led to cell cycle arrest. Mechanistically, DDX21 recruited transcription factor YBX1 to cooperatively trigger ULK1 expression. Moreover, silencing of ULK1 could reverse the promoting effects of DDX21 overexpression in AML cells. CONCLUSIONS Dysregulation of SE-IGF2BP2/IGF2BP3-DDX21 axis facilitated the progression of AML. Our findings provide new insights into the link between SEs and m6A modification, elucidate the regulatory mechanisms of IGF2BP2 and IGF2BP3 on DDX21, and reveal the underlying roles of DDX21 in AML.
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Affiliation(s)
- Yanchun Zhao
- Department of HematologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouZhejiangChina
- Zhejiang University Cancer CenterHangzhouZhejiangChina
| | - Yutong Zhou
- Department of HematologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouZhejiangChina
- Zhejiang University Cancer CenterHangzhouZhejiangChina
| | - Yu Qian
- Department of HematologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouZhejiangChina
- Zhejiang University Cancer CenterHangzhouZhejiangChina
| | - Wenwen Wei
- Department of HematologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouZhejiangChina
- Zhejiang University Cancer CenterHangzhouZhejiangChina
| | - Xiangjie Lin
- Department of HematologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouZhejiangChina
- Zhejiang University Cancer CenterHangzhouZhejiangChina
| | - Shihui Mao
- Department of HematologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouZhejiangChina
- Zhejiang University Cancer CenterHangzhouZhejiangChina
| | - Jie Sun
- Department of HematologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouZhejiangChina
- Zhejiang University Cancer CenterHangzhouZhejiangChina
| | - Jie Jin
- Department of HematologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Hematological DisordersHangzhouZhejiangChina
- Zhejiang University Cancer CenterHangzhouZhejiangChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanShandongChina
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18
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Xie J, Cheng J, Ko H, Tang Y. Cytosolic DNA sensors in neurodegenerative diseases: from physiological defenders to pathological culprits. EMBO Mol Med 2024; 16:678-699. [PMID: 38467840 PMCID: PMC11018843 DOI: 10.1038/s44321-024-00046-w] [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: 10/11/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Cytosolic DNA sensors are a group of pattern recognition receptors (PRRs) that vary in structures, molecular mechanisms, and origins but share a common function to detect intracellular microbial DNA and trigger the innate immune response like type 1 interferon production and autophagy. Cytosolic DNA sensors have been proven as indispensable defenders against the invasion of many pathogens; however, growing evidence shows that self-DNA misplacement to cytoplasm also frequently occurs in non-infectious circumstances. Accumulation of cytosolic DNA causes improper activation of cytosolic DNA sensors and triggers an abnormal autoimmune response, that significantly promotes pathological progression. Neurodegenerative diseases are a group of neurological disorders characterized by neuron loss and still lack effective treatments due to a limited understanding of pathogenesis. But current research has found a solid relationship between neurodegenerative diseases and cytosolic DNA sensing pathways. This review summarizes profiles of several major cytosolic DNA sensors and their common adaptor protein STING. It also discusses both the beneficial and detrimental roles of cytosolic DNA sensors in the genesis and progression of neurodegenerative diseases.
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Affiliation(s)
- Jiatian Xie
- Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat‑sen University, Guangzhou, 510120, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan, 528200, China
| | - Jinping Cheng
- Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat‑sen University, Guangzhou, 510120, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan, 528200, China
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics & Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yamei Tang
- Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
- Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat‑sen University, Guangzhou, 510120, China.
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan, 528200, China.
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19
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Kligfeld H, Han I, Abraham A, Shukla V. Alternative DNA structures in hematopoiesis and adaptive immunity. Adv Immunol 2024; 161:109-126. [PMID: 38763699 DOI: 10.1016/bs.ai.2024.03.002] [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: 05/21/2024]
Abstract
Besides the canonical B-form, DNA also adopts alternative non-B form conformations which are highly conserved in all domains of life. While extensive research over decades has centered on the genomic functions of B-form DNA, understanding how non-B-form conformations influence functional genomic states remains a fundamental and open question. Recent studies have ascribed alternative DNA conformations such as G-quadruplexes and R-loops as important functional features in eukaryotic genomes. This review delves into the biological importance of alternative DNA structures, with a specific focus on hematopoiesis and adaptive immunity. We discuss the emerging roles of G-quadruplex and R-loop structures, the two most well-studied alternative DNA conformations, in the hematopoietic compartment and present evidence for their functional roles in normal cellular physiology and associated pathologies.
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Affiliation(s)
- Heather Kligfeld
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Isabella Han
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States
| | - Ajay Abraham
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, United States.
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20
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Dowling JW, Smith JR, Forero A. Protocol for detection of in vitro R-loop formation using dot blots. STAR Protoc 2024; 5:102857. [PMID: 38285737 PMCID: PMC10839531 DOI: 10.1016/j.xpro.2024.102857] [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: 10/18/2023] [Revised: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Dot-blot analysis is a technique that allows for fast and convenient detection and identification of nucleic acids and proteins. Here, we provide a guide for nucleic acid isolation from eukaryotic cells and sample processing to detect RNA/DNA hybrids. We then provide detailed steps to quantify dot signal intensity. This protocol can be adapted for screening conditions that result in the accumulation of R-loops. For complete details on the use and execution of this protocol, please refer to Smith et al.1.
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Affiliation(s)
- Jack W Dowling
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Julian R Smith
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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21
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Huang TT, Chiang CY, Nair JR, Wilson KM, Cheng K, Lee JM. AKT1 interacts with DHX9 to Mitigate R Loop-Induced Replication Stress in Ovarian Cancer. Cancer Res 2024; 84:887-904. [PMID: 38241710 PMCID: PMC10947874 DOI: 10.1158/0008-5472.can-23-1908] [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: 06/26/2023] [Revised: 10/04/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
PARP inhibitor (PARPi)-resistant BRCA-mutant (BRCAm) high-grade serous ovarian cancer (HGSOC) represents a new clinical challenge with unmet therapeutic needs. Here, we performed a quantitative high-throughput drug combination screen that identified the combination of an ATR inhibitor (ATRi) and an AKT inhibitor (AKTi) as an effective treatment strategy for both PARPi-sensitive and PARPi-resistant BRCAm HGSOC. The ATRi and AKTi combination induced DNA damage and R loop-mediated replication stress (RS). Mechanistically, the kinase domain of AKT1 directly interacted with DHX9 and facilitated recruitment of DHX9 to R loops. AKTi increased ATRi-induced R loop-mediated RS by mitigating recruitment of DHX9 to R loops. Moreover, DHX9 was upregulated in tumors from patients with PARPi-resistant BRCAm HGSOC, and high coexpression of DHX9 and AKT1 correlated with worse survival. Together, this study reveals an interaction between AKT1 and DHX9 that facilitates R loop resolution and identifies combining ATRi and AKTi as a rational treatment strategy for BRCAm HGSOC irrespective of PARPi resistance status. SIGNIFICANCE Inhibition of the AKT and ATR pathways cooperatively induces R loop-associated replication stress in high-grade serous ovarian cancer, providing rationale to support the clinical development of AKT and ATR inhibitor combinations. See related commentary by Ramanarayanan and Oberdoerffer, p. 793.
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Affiliation(s)
- Tzu-Ting Huang
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chih-Yuan Chiang
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jayakumar R. Nair
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kelli M. Wilson
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ken Cheng
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jung-Min Lee
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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22
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Vu GT, Awad V, Norberto MF, Bowman TV, Trompouki E. Nucleic acid-induced inflammation on hematopoietic stem cells. Exp Hematol 2024; 131:104148. [PMID: 38151171 PMCID: PMC11061806 DOI: 10.1016/j.exphem.2023.104148] [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: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Hematopoiesis, the process of generating blood cells, starts during development with the primitive, pro-definitive, and definitive hematopoietic waves. The first two waves will generate erythrocytes and myeloid cells, although the definitive wave will give rise to hematopoietic stem cells (HSCs) that are multipotent and can produce most of the blood cells in an adult. Although HSCs are highly proliferative during development, during adulthood they remain quiescent in the bone marrow. Inflammatory signaling in the form of interferons, interleukins, tumor necrosis factors, and others is well-established to influence both developmental and adult hematopoiesis. Here we discuss the role of specific inflammatory pathways that are induced by sensing nucleic acids. We discuss the role of RNA-sensing members of the Toll-like, Rig-I-like, nucleotide-binding oligomerization domain (NOD)-like, and AIM2-like protein kinase receptors and the DNA-sensing receptors, DEAD-Box helicase 41 (DDX41) and cGAS. The main downstream pathways of these receptors are discussed, as well as their influence on developmental and adult hematopoiesis, including hematopoietic pathologies.
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Affiliation(s)
- Giang To Vu
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France
| | - Valerie Awad
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY
| | - Maria Feliz Norberto
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY.
| | - Eirini Trompouki
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France.
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23
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Wu W, Wu W, Zhou Y, Yang Q, Zhuang S, Zhong C, Li W, Li A, Zhao W, Yin X, Zu X, Chak-Lui Wong C, Yin D, Hu K, Cai M. The dePARylase NUDT16 promotes radiation resistance of cancer cells by blocking SETD3 for degradation via reversing its ADP-ribosylation. J Biol Chem 2024; 300:105671. [PMID: 38272222 PMCID: PMC10926213 DOI: 10.1016/j.jbc.2024.105671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a critical posttranslational modification that plays a vital role in maintaining genomic stability via a variety of molecular mechanisms, including activation of replication stress and the DNA damage response. The nudix hydrolase NUDT16 was recently identified as a phosphodiesterase that is responsible for removing ADP-ribose units and that plays an important role in DNA repair. However, the roles of NUDT16 in coordinating replication stress and cell cycle progression remain elusive. Here, we report that SETD3, which is a member of the SET-domain containing protein (SETD) family, is a novel substrate for NUDT16, that its protein levels fluctuate during cell cycle progression, and that its stability is strictly regulated by NUDT16-mediated dePARylation. Moreover, our data indicated that the E3 ligase CHFR is responsible for the recognition and degradation of endogenous SETD3 in a PARP1-mediated PARylation-dependent manner. Mechanistically, we revealed that SETD3 associates with BRCA2 and promotes its recruitment to stalled replication fork and DNA damage sites upon replication stress or DNA double-strand breaks, respectively. Importantly, depletion of SETD3 in NUDT16-deficient cells did not further exacerbate DNA breaks or enhance the sensitivity of cancer cells to IR exposure, suggesting that the NUDT16-SETD3 pathway may play critical roles in the induction of tolerance to radiotherapy. Collectively, these data showed that NUDT16 functions as a key upstream regulator of SETD3 protein stability by reversing the ADP-ribosylation of SETD3, and NUDT16 participates in the resolution of replication stress and facilitates HR repair.
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Affiliation(s)
- Weijun Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wenjing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Breast Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yingshi Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Ultrasound, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiao Yang
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Shuting Zhuang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Caixia Zhong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjia Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Aixin Li
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wanzhen Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaomin Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xuyu Zu
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Carmen Chak-Lui Wong
- Li Ka Shing Faculty of Medicine, Department of Pathology, The University of Hong Kong, Hong Kong, Guangdong, China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Manbo Cai
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
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24
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Winstone L, Jung Y, Wu Y. DDX41: exploring the roles of a versatile helicase. Biochem Soc Trans 2024; 52:395-405. [PMID: 38348889 PMCID: PMC10903454 DOI: 10.1042/bst20230725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/29/2024]
Abstract
DDX41 is a DEAD-box helicase and is conserved across species. Mutations in DDX41 have been associated with myeloid neoplasms, including myelodysplastic syndrome and acute myeloid leukemia. Though its pathogenesis is not completely known, DDX41 has been shown to have many cellular roles, including in pre-mRNA splicing, innate immune sensing, ribosome biogenesis, translational regulation, and R-loop metabolism. In this review, we will summarize the latest understandings regarding the various roles of DDX41, as well as highlight challenges associated with drug development to target DDX41. Overall, understanding the molecular and cellular mechanisms of DDX41 could help develop novel therapeutic options for DDX41 mutation-related hematologic malignancies.
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Affiliation(s)
- Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yohan Jung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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25
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Liu ZS, Sinha S, Bannister M, Song A, Arriaga-Gomez E, McKeeken AJ, Bonner EA, Hanson BK, Sarchi M, Takashima K, Zong D, Corral VM, Nguyen E, Yoo J, Chiraphapphaiboon W, Leibson C, McMahon MC, Rai S, Swisher EM, Sachs Z, Chatla S, Stirewalt DL, Deeg HJ, Skorski T, Papapetrou EP, Walter MJ, Graubert TA, Doulatov S, Lee SC, Nguyen HD. R-Loop Accumulation in Spliceosome Mutant Leukemias Confers Sensitivity to PARP1 Inhibition by Triggering Transcription-Replication Conflicts. Cancer Res 2024; 84:577-597. [PMID: 37967363 PMCID: PMC10922727 DOI: 10.1158/0008-5472.can-23-3239] [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: 10/16/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023]
Abstract
RNA splicing factor (SF) gene mutations are commonly observed in patients with myeloid malignancies. Here we showed that SRSF2- and U2AF1-mutant leukemias are preferentially sensitive to PARP inhibitors (PARPi), despite being proficient in homologous recombination repair. Instead, SF-mutant leukemias exhibited R-loop accumulation that elicited an R-loop-associated PARP1 response, rendering cells dependent on PARP1 activity for survival. Consequently, PARPi induced DNA damage and cell death in SF-mutant leukemias in an R-loop-dependent manner. PARPi further increased aberrant R-loop levels, causing higher transcription-replication collisions and triggering ATR activation in SF-mutant leukemias. Ultimately, PARPi-induced DNA damage and cell death in SF-mutant leukemias could be enhanced by ATR inhibition. Finally, the level of PARP1 activity at R-loops correlated with PARPi sensitivity, suggesting that R-loop-associated PARP1 activity could be predictive of PARPi sensitivity in patients harboring SF gene mutations. This study highlights the potential of targeting different R-loop response pathways caused by spliceosome gene mutations as a therapeutic strategy for treating cancer. SIGNIFICANCE Spliceosome-mutant leukemias accumulate R-loops and require PARP1 to resolve transcription-replication conflicts and genomic instability, providing rationale to repurpose FDA-approved PARP inhibitors for patients carrying spliceosome gene mutations.
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Affiliation(s)
- Zhiyan Silvia Liu
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- These authors contributed equally
| | - Sayantani Sinha
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Maxwell Bannister
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Axia Song
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Erica Arriaga-Gomez
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alexander J. McKeeken
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A. Bonner
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Benjamin K. Hanson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Martina Sarchi
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Molecular Medicine, University of Pavia, 27100 Pavia PV, Italy
| | - Kouhei Takashima
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Regenerative Medicine and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawei Zong
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Victor M. Corral
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Evan Nguyen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jennifer Yoo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | | | - Cassandra Leibson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Matthew C. McMahon
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Sumit Rai
- Massachusetts General Hospital Cancer Center, Charlestown, MA
| | - Elizabeth M. Swisher
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA 98195
| | - Zohar Sachs
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Srinivas Chatla
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Derek L. Stirewalt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - H. Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Regenerative Medicine and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J. Walter
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | - Sergei Doulatov
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Stanley C. Lee
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Hai Dang Nguyen
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
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Bhattacharjee R, Jolly LA, Corbett MA, Wee IC, Rao SR, Gardner AE, Ritchie T, van Hugte EJH, Ciptasari U, Piltz S, Noll JE, Nazri N, van Eyk CL, White M, Fornarino D, Poulton C, Baynam G, Collins-Praino LE, Snel MF, Nadif Kasri N, Hemsley KM, Thomas PQ, Kumar R, Gecz J. Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment. Nat Commun 2024; 15:1210. [PMID: 38331934 PMCID: PMC10853216 DOI: 10.1038/s41467-024-45121-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
We implicated the X-chromosome THOC2 gene, which encodes the largest subunit of the highly-conserved TREX (Transcription-Export) complex, in a clinically complex neurodevelopmental disorder with intellectual disability as the core phenotype. To study the molecular pathology of this essential eukaryotic gene, we generated a mouse model based on a hypomorphic Thoc2 exon 37-38 deletion variant of a patient with ID, speech delay, hypotonia, and microcephaly. The Thoc2 exon 37-38 deletion male (Thoc2Δ/Y) mice recapitulate the core phenotypes of THOC2 syndrome including smaller size and weight, and significant deficits in spatial learning, working memory and sensorimotor functions. The Thoc2Δ/Y mouse brain development is significantly impacted by compromised THOC2/TREX function resulting in R-loop accumulation, DNA damage and consequent cell death. Overall, we suggest that perturbed R-loop homeostasis, in stem cells and/or differentiated cells in mice and the patient, and DNA damage-associated functional alterations are at the root of THOC2 syndrome.
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Affiliation(s)
- Rudrarup Bhattacharjee
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lachlan A Jolly
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Mark A Corbett
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ing Chee Wee
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sushma R Rao
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alison E Gardner
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tarin Ritchie
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Eline J H van Hugte
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Ummi Ciptasari
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Sandra Piltz
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Jacqueline E Noll
- School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide and Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Nazzmer Nazri
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Clare L van Eyk
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Melissa White
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Dani Fornarino
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Rare Care Centre, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Lyndsey E Collins-Praino
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Marten F Snel
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Kim M Hemsley
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Paul Q Thomas
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Raman Kumar
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jozef Gecz
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia.
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Arai H, Matsui H, Chi S, Utsu Y, Masuda S, Aotsuka N, Minami Y. Germline Variants and Characteristic Features of Hereditary Hematological Malignancy Syndrome. Int J Mol Sci 2024; 25:652. [PMID: 38203823 PMCID: PMC10779750 DOI: 10.3390/ijms25010652] [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: 11/07/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Due to the proliferation of genetic testing, pathogenic germline variants predisposing to hereditary hematological malignancy syndrome (HHMS) have been identified in an increasing number of genes. Consequently, the field of HHMS is gaining recognition among clinicians and scientists worldwide. Patients with germline genetic abnormalities often have poor outcomes and are candidates for allogeneic hematopoietic stem cell transplantation (HSCT). However, HSCT using blood from a related donor should be carefully considered because of the risk that the patient may inherit a pathogenic variant. At present, we now face the challenge of incorporating these advances into clinical practice for patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) and optimizing the management and surveillance of patients and asymptomatic carriers, with the limitation that evidence-based guidelines are often inadequate. The 2016 revision of the WHO classification added a new section on myeloid malignant neoplasms, including MDS and AML with germline predisposition. The main syndromes can be classified into three groups. Those without pre-existing disease or organ dysfunction; DDX41, TP53, CEBPA, those with pre-existing platelet disorders; ANKRD26, ETV6, RUNX1, and those with other organ dysfunctions; SAMD9/SAMD9L, GATA2, and inherited bone marrow failure syndromes. In this review, we will outline the role of the genes involved in HHMS in order to clarify our understanding of HHMS.
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Affiliation(s)
- Hironori Arai
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Hirotaka Matsui
- Department of Laboratory Medicine, National Cancer Center Hospital, Tsukiji, Chuoku 104-0045, Japan;
- Department of Medical Oncology and Translational Research, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8665, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
| | - Yoshikazu Utsu
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Shinichi Masuda
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Nobuyuki Aotsuka
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
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28
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Haji-Seyed-Javadi R, Koyen AE, Rath SK, Madden MZ, Hou Y, Song BS, Kenney AM, Lan L, Yao B, Yu DS. HELZ promotes R loop resolution to facilitate DNA double-strand break repair by homologous recombination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571747. [PMID: 38168208 PMCID: PMC10760136 DOI: 10.1101/2023.12.14.571747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
R loops are RNA-DNA hybrid containing structures involved in diverse cellular processes, including DNA double-strand break (DSB) repair. R loop homeostasis involving the formation and resolution of R loops is critical for DSB repair, and its dysregulation leads to genome instability. Here we show that the HELZ helicase promotes R loop resolution to facilitate DSB repair by homologous recombination (HR). HELZ depletion causes hypersensitivity to DSB-inducing agents, and HELZ localizes and binds to DSBs. HELZ depletion further leads to genomic instability in a R loop dependent manner and the accumulation of R loops globally and at DSBs. HELZ binds to R loops in response to DSBs and promotes their resolution, thereby facilitating HR to promote genome integrity. Our findings thus define a role for HELZ in promoting the resolution of R loops critical for DSB repair by HR.
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Mikhalkevich N, Russ E, Iordanskiy S. Cellular RNA and DNA sensing pathways are essential for the dose-dependent response of human monocytes to ionizing radiation. Front Immunol 2023; 14:1235936. [PMID: 38152396 PMCID: PMC10751912 DOI: 10.3389/fimmu.2023.1235936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/30/2023] [Indexed: 12/29/2023] Open
Abstract
Circulating monocytes are important players of the inflammatory response to ionizing radiation (IR). These IR-resistant immune cells migrate to radiation-damaged tissues and differentiate into macrophages that phagocytize dying cells, but also facilitate inflammation. Besides the effect of damage-associated molecular patterns, released from irradiated tissues, the inflammatory activation of monocytes and macrophages is largely dependent on IR-induced DNA damage and aberrant transcriptional activity, which may facilitate expression of type I interferons (IFN-I) and numerous inflammation-related genes. We analyzed the accumulation of dsRNA, dsDNA fragments, and RNA:DNA hybrids in the context of induction of RNA-triggered MAVS-mediated and DNA-triggered STING-mediated signaling pathways, in primary human monocytes and a monocytic cell line, THP1, in response to various doses of gamma IR. We found that exposure to lower doses (<7.5 Gy) led to the accumulation of dsRNA, along with dsDNA and RNA:DNA hybrids and activated both MAVS and STING pathway-induced gene expression and signaling activity of IFN-I. Higher doses of IR resulted in the reduced dsRNA level, degradation of RNA-sensing mediators involved in MAVS signaling and coincided with an increased accumulation of dsDNA and RNA:DNA hybrids that correlated with elevated STING signaling and NF-κB-dependent gene expression. While both pathways activate IFN-I expression, using MAVS- and STING-knockout THP1 cells, we identified differences in the spectra of interferon-stimulated genes (ISGs) that are associated with each specific signaling pathway and outlined a large group of STING signaling-associated genes. Using the RNAi technique, we found that increasing the dose of IR activates STING signaling through the DNA sensor cGAS, along with suppression of the DDX41 helicase, which is known to reduce the accumulation of RNA:DNA hybrids and thereby limit cGAS/STING signaling activity. Together, these results indicate that depending on the applied dose, IR leads to the activation of either dsRNA-induced MAVS signaling, which predominantly leads to the expression of both pro- and anti-inflammatory markers, or dsDNA-induced STING signaling that contributes to pro-inflammatory activation of the cells. While RNA:DNA hybrids boost both MAVS- and STING-mediated signaling pathways, these structures being accumulated upon high IR doses promote type I interferon expression and appear to be potent enhancers of radiation dose-dependent pro-inflammatory activation of monocytes.
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Affiliation(s)
- Natallia Mikhalkevich
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Eric Russ
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Graduate Program of Cellular and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Sergey Iordanskiy
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Armed Forces Radiobiology Research Institute, Uniformed Services University of The Health Sciences, Bethesda, MD, United States
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30
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Abstract
Transcription and replication both require large macromolecular complexes to act on a DNA template, yet these machineries cannot simultaneously act on the same DNA sequence. Conflicts between the replication and transcription machineries (transcription-replication conflicts, or TRCs) are widespread in both prokaryotes and eukaryotes and have the capacity to both cause DNA damage and compromise complete, faithful replication of the genome. This review will highlight recent studies investigating the genomic locations of TRCs and the mechanisms by which they may be prevented, mitigated, or resolved. We address work from both model organisms and mammalian systems but predominantly focus on multicellular eukaryotes owing to the additional complexities inherent in the coordination of replication and transcription in the context of cell type-specific gene expression and higher-order chromatin organization.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA;
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31
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Girasol MJ, Briggs EM, Marques CA, Batista JM, Beraldi D, Burchmore R, Lemgruber L, McCulloch R. Immunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in the control of surface antigen expression needed for immune evasion by antigenic variation. Nucleic Acids Res 2023; 51:11123-11141. [PMID: 37843098 PMCID: PMC10639054 DOI: 10.1093/nar/gkad836] [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: 05/26/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of genomes that provide a diverse and growing range of activities. Understanding of these functions has been informed by characterising the proteins that interact with the hybrids, but all such analyses have so far focused on mammals, meaning it is unclear if a similar spectrum of RNA-DNA hybrid interactors is found in other eukaryotes. The African trypanosome is a single-cell eukaryotic parasite of the Discoba grouping and displays substantial divergence in several aspects of core biology from its mammalian host. Here, we show that DNA-RNA hybrid immunoprecipitation coupled with mass spectrometry recovers 602 putative interactors in T. brucei mammal- and insect-infective cells, some providing activities also found in mammals and some lineage-specific. We demonstrate that loss of three factors, two putative helicases and a RAD51 paralogue, alters T. brucei nuclear RNA-DNA hybrid and DNA damage levels. Moreover, loss of each factor affects the operation of the parasite immune survival mechanism of antigenic variation. Thus, our work reveals the broad range of activities contributed by RNA-DNA hybrids to T. brucei biology, including new functions in host immune evasion as well as activities likely fundamental to eukaryotic genome function.
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Affiliation(s)
- Mark J Girasol
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of the Philippines Manila, College of Medicine, Manila, Philippines
| | - Emma M Briggs
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of Edinburgh, Institute for Immunology and Infection Research, School of Biological Sciences, Edinburgh, UK
| | - Catarina A Marques
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - José M Batista
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Dario Beraldi
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard Burchmore
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Leandro Lemgruber
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard McCulloch
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
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32
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Bradley L, Savage KI. 'From R-lupus to cancer': Reviewing the role of R-loops in innate immune responses. DNA Repair (Amst) 2023; 131:103581. [PMID: 37832251 DOI: 10.1016/j.dnarep.2023.103581] [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: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
Cells possess an inherent and evolutionarily conserved ability to detect and respond to the presence of foreign and pathological 'self' nucleic acids. The result is the stimulation of innate immune responses, signalling to the host immune system that defence mechanisms are necessary to protect the organism. To date, there is a vast body of literature describing innate immune responses to various nucleic acid species, including dsDNA, ssDNA and ssRNA etc., however, there is limited information available on responses to R-loops. R-loops are 3-stranded nucleic acid structures that form during transcription, upon DNA damage and in various other settings. Emerging evidence suggests that innate immune responses may also exist for the detection of R-loop related nucleic acid structures, implicating R-loops as drivers of inflammatory states. In this review, we aim to summarise the evidence indicating that R-loops are immunogenic species that can trigger innate immune responses in physiological and pathological settings and discuss the implications of this in the study of various diseases and therapeutic development.
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Affiliation(s)
- Leanne Bradley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Rd, Belfast, United Kingdom
| | - Kienan I Savage
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Rd, Belfast, United Kingdom.
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33
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Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [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: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
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Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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34
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Bataller A, Loghavi S, Gerstein Y, Bazinet A, Sasaki K, Chien KS, Hammond D, Montalban-Bravo G, Borthakur G, Short N, Issa GC, Kadia TM, Daver N, Tang G, Quesada A, Patel KP, Ravandi F, Fiskus W, Mill CP, Kantarjian HM, Bhalla K, Garcia-Manero G, Oran B, DiNardo CD. Characteristics and clinical outcomes of patients with myeloid malignancies and DDX41 variants. Am J Hematol 2023; 98:1780-1790. [PMID: 37665752 DOI: 10.1002/ajh.27070] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023]
Abstract
DDX41 is the most frequently mutated gene in myeloid neoplasms associated with germline predisposition including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). We analyzed 3795 patients with myeloid neoplasms and identified 151 (4%) with DDX41 variants and a diagnosis of AML (n = 96), MDS (n = 52), and chronic myelomonocytic leukemia (n = 3). The most frequent DDX41 variants were the somatic variant p.R525H, followed by the germline variants p.M1I and p.D140fs. Most neoplasms had a normal karyotype (59%) and the most frequent co-mutations were TP53 (16%) and ASXL1 (15%). 30% of patients had no concomitant mutations besides DDX41 mutation. Patients with myeloid malignancies and DDX41 variants responded well to therapy, with an overall response rate for patients with treatment naïve AML and MDS of 87% and 84%, respectively. The median overall survival (mOS) of patients with treatment-naïve AML or MDS was 49 and 71 months, respectively. Patients with AML treated with low-intensity regimens including venetoclax had an improved survival (2-year OS 91% vs. 60%, p = .02) and lower cumulative incidence of relapse compared to those treated without venetoclax (10% vs. 56%, p = .03). In the 33% of patients receiving hematopoietic stem cell transplantation, the 2-year OS was 80% and 85% for AML and MDS, respectively.
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Affiliation(s)
- Alex Bataller
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sanam Loghavi
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yoheved Gerstein
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexandre Bazinet
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Koji Sasaki
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kelly S Chien
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Danielle Hammond
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Gautam Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nicholas Short
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ghayas C Issa
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tapan M Kadia
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guilin Tang
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Andres Quesada
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keyur P Patel
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Farhad Ravandi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Warren Fiskus
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cristopher P Mill
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hagop M Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kapil Bhalla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Betul Oran
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Courtney D DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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35
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Gu H, Li T, Beeraka NM, Zheng Y, Zhang X, Song R, Zhou R, Wang X, Sukocheva O, Fan R, Liu J. Molecular classification of human papilloma virus-negative head and neck squamous cell carcinomas: Cell cycle-based classifier and prognostic signature. PLoS One 2023; 18:e0286414. [PMID: 37903125 PMCID: PMC10615317 DOI: 10.1371/journal.pone.0286414] [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: 11/17/2022] [Accepted: 05/15/2023] [Indexed: 11/01/2023] Open
Abstract
The molecular classification of human papillomavirus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs) remains questionable. Differentially expressed genes were detected between tumor and normal tissues and GSEA showed they are associated with cell cycle pathways. This study aimed to classify HPV-negative HNSCCs based on cell cycle-related genes. The established gene pattern was correlated with tumor progression, clinical prognosis, and drug treatment efficacy. Biological analysis was performed using HNSCC patient sample data obtained from the Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Gene Expression Omnibus (GEO) databases. All samples included in this study contained survival information. RNA sequencing data from 740 samples were used for the analysis. Previously characterized cell cycle-related genes were included for unsupervised consensus clustering. Two subtypes of HPV-negative HNSCCs (C1, C2) were identified. Subtype C1 displayed low cell cycle activity, 'hot' tumor microenvironment (TME), earlier N stage, lower pathological grade, better prognosis, and higher response rate to the immunotherapy and targeted therapy. Subtype C2 was associated with higher cell cycle activity, 'cold' TME, later N stage, higher pathological grade, worse prognosis, and lower response rate to the treatment. According to the nearest template prediction method, classification rules were established and verified. Our work explored the molecular mechanism of HPV-negative HNSCCs in the view of cell cycle and might provide new sights for personalized anti-cancer treatment.
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Affiliation(s)
- Hao Gu
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tingxuan Li
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Narasimha M. Beeraka
- Raghavendra Institute of Pharmaceutical Education and Research (RIPER), Anantapuramu, Andhra Pradesh, India
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Yufei Zheng
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xintan Zhang
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruixia Song
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Runze Zhou
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoyan Wang
- Endocrinology Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Olga Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, Australia
- Department of Hepatology, Royal Adelaide Hospital, SA Health, Adelaide, SA, Australia
| | - Ruitai Fan
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junqi Liu
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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36
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Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
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Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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37
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Cameron DP, Grosser J, Ladigan S, Kuzin V, Iliopoulou E, Wiegard A, Benredjem H, Jackson K, Liffers ST, Lueong S, Cheung PF, Vangala D, Pohl M, Viebahn R, Teschendorf C, Wolters H, Usta S, Geng K, Kutter C, Arsenian-Henriksson M, Siveke JT, Tannapfel A, Schmiegel W, Hahn SA, Baranello L. Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription. SCIENCE ADVANCES 2023; 9:eadg5109. [PMID: 37831776 PMCID: PMC10575591 DOI: 10.1126/sciadv.adg5109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Pancreatic carcinoma lacks effective therapeutic strategies resulting in poor prognosis. Transcriptional dysregulation due to alterations in KRAS and MYC affects initiation, development, and survival of this tumor type. Using patient-derived xenografts of KRAS- and MYC-driven pancreatic carcinoma, we show that coinhibition of topoisomerase 1 (TOP1) and bromodomain-containing protein 4 (BRD4) synergistically induces tumor regression by targeting promoter pause release. Comparing the nascent transcriptome with the recruitment of elongation and termination factors, we found that coinhibition of TOP1 and BRD4 disrupts recruitment of transcription termination factors. Thus, RNA polymerases transcribe downstream of genes for hundreds of kilobases leading to readthrough transcription. This occurs during replication, perturbing replisome progression and inducing DNA damage. The synergistic effect of TOP1 + BRD4 inhibition is specific to cancer cells leaving normal cells unaffected, highlighting the tumor's vulnerability to transcriptional defects. This preclinical study provides a mechanistic understanding of the benefit of combining TOP1 and BRD4 inhibitors to treat pancreatic carcinomas addicted to oncogenic drivers of transcription and replication.
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Affiliation(s)
- Donald P. Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Grosser
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Swetlana Ladigan
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Evanthia Iliopoulou
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anika Wiegard
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hajar Benredjem
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kathryn Jackson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sven T. Liffers
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Smiths Lueong
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Phyllis F. Cheung
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Deepak Vangala
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Michael Pohl
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Richard Viebahn
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Surgery, Bochum, Germany
| | | | - Heiner Wolters
- Department of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Selami Usta
- Department of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Keyi Geng
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Jens T. Siveke
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Wolff Schmiegel
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Stephan A. Hahn
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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38
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He X, Yuan J, Gao Z, Wang Y. Promoter R-Loops Recruit U2AF1 to Modulate Its Phase Separation and RNA Splicing. J Am Chem Soc 2023; 145:21646-21660. [PMID: 37733759 PMCID: PMC10557143 DOI: 10.1021/jacs.3c08204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Indexed: 09/23/2023]
Abstract
R-loops and guanine quadruplexes (G4s) are secondary structures of nucleic acids that are ubiquitously present in cells and are enriched in promoter regions of genes. By employing a bioinformatic approach based on overlap analysis of transcription factor chromatin immunoprecipitation sequencing (ChIP-seq) data sets, we found that many splicing factors, including U2AF1 whose recognition of the 3' splicing site is crucial for pre-mRNA splicing, exhibit pronounced enrichment at endogenous R-loop- and DNA G4-structure loci in promoter regions of human genes. We also revealed that U2AF1 binds directly to R-loops and DNA G4 structures at a low-nM binding affinity. Additionally, we showed the ability of U2AF1 to undergo phase separation, which could be stimulated by binding with R-loops, but not duplex DNA, RNA/DNA hybrid, DNA G4, or single-stranded RNA. We also demonstrated that U2AF1 binds to promoter R-loops in human cells, and this binding competes with U2AF1's interaction with 3' splicing site and leads to augmented distribution of RNA polymerase II (RNAPII) to promoters over gene bodies, thereby modulating cotranscriptional pre-mRNA splicing. Together, we uncovered a group of candidate proteins that can bind to both R-loops and DNA G4s, revealed the direct and strong interactions of U2AF1 with these nucleic acid structures, and established a biochemical rationale for U2AF1's occupancy in gene promoters. We also unveiled that interaction with R-loops promotes U2AF1's phase separation, and our work suggests that U2AF1 modulates pre-mRNA splicing by regulating RNAPII's partition in transcription initiation versus elongation.
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Affiliation(s)
- Xiaomei He
- Department
of Chemistry, University of California Riverside, Riverside, California 92521-0403, United
States
| | - Jun Yuan
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California 92521-0403, United States
| | - Zi Gao
- Department
of Chemistry, University of California Riverside, Riverside, California 92521-0403, United
States
| | - Yinsheng Wang
- Department
of Chemistry, University of California Riverside, Riverside, California 92521-0403, United
States
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California 92521-0403, United States
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39
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Wulfridge P, Yan Q, Rell N, Doherty J, Jacobson S, Offley S, Deliard S, Feng K, Phillips-Cremins JE, Gardini A, Sarma K. G-quadruplexes associated with R-loops promote CTCF binding. Mol Cell 2023; 83:3064-3079.e5. [PMID: 37552993 PMCID: PMC10529333 DOI: 10.1016/j.molcel.2023.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/24/2023] [Accepted: 07/07/2023] [Indexed: 08/10/2023]
Abstract
CTCF is a critical regulator of genome architecture and gene expression that binds thousands of sites on chromatin. CTCF genomic localization is controlled by the recognition of a DNA sequence motif and regulated by DNA modifications. However, CTCF does not bind to all its potential sites in all cell types, raising the question of whether the underlying chromatin structure can regulate CTCF occupancy. Here, we report that R-loops facilitate CTCF binding through the formation of associated G-quadruplex (G4) structures. R-loops and G4s co-localize with CTCF at many genomic regions in mouse embryonic stem cells and promote CTCF binding to its cognate DNA motif in vitro. R-loop attenuation reduces CTCF binding in vivo. Deletion of a specific G4-forming motif in a gene reduces CTCF binding and alters gene expression. Conversely, chemical stabilization of G4s results in CTCF gains and accompanying alterations in chromatin organization, suggesting a pivotal role for G4 structures in reinforcing long-range genome interactions through CTCF.
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Affiliation(s)
- Phillip Wulfridge
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qingqing Yan
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel Rell
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Doherty
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Skye Jacobson
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Offley
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra Deliard
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kelly Feng
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer E Phillips-Cremins
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kavitha Sarma
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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40
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Smith JR, Dowling JW, McFadden MI, Karp A, Schwerk J, Woodward JJ, Savan R, Forero A. MEF2A suppresses stress responses that trigger DDX41-dependent IFN production. Cell Rep 2023; 42:112805. [PMID: 37467105 PMCID: PMC10652867 DOI: 10.1016/j.celrep.2023.112805] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 05/17/2023] [Accepted: 06/27/2023] [Indexed: 07/21/2023] Open
Abstract
Cellular stress in the form of disrupted transcription, loss of organelle integrity, or damage to nucleic acids can elicit inflammatory responses by activating signaling cascades canonically tasked with controlling pathogen infections. These stressors must be kept in check to prevent unscheduled activation of interferon, which contributes to autoinflammation. This study examines the role of the transcription factor myocyte enhancing factor 2A (MEF2A) in setting the threshold of transcriptional stress responses to prevent R-loop accumulation. Increases in R-loops lead to the induction of interferon and inflammatory responses in a DEAD-box helicase 41 (DDX41)-, cyclic GMP-AMP synthase (cGAS)-, and stimulator of interferon genes (STING)-dependent manner. The loss of MEF2A results in the activation of ATM and RAD3-related (ATR) kinase, which is also necessary for the activation of STING. This study identifies the role of MEF2A in sustaining transcriptional homeostasis and highlights the role of ATR in positively regulating R-loop-associated inflammatory responses.
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Affiliation(s)
- Julian R Smith
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Jack W Dowling
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew I McFadden
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA; Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew Karp
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA; Discovery PREP, The Ohio State University, Columbus, OH 43210, USA
| | - Johannes Schwerk
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA; Cancer Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.
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41
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Suzuki MM, Iijima K, Ogami K, Shinjo K, Murofushi Y, Xie J, Wang X, Kitano Y, Mamiya A, Kibe Y, Nishimura T, Ohka F, Saito R, Sato S, Kobayashi J, Yao R, Miyata K, Kataoka K, Suzuki HI, Kondo Y. TUG1-mediated R-loop resolution at microsatellite loci as a prerequisite for cancer cell proliferation. Nat Commun 2023; 14:4521. [PMID: 37607907 PMCID: PMC10444773 DOI: 10.1038/s41467-023-40243-8] [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: 05/30/2022] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
Oncogene-induced DNA replication stress (RS) and consequent pathogenic R-loop formation are known to impede S phase progression. Nonetheless, cancer cells continuously proliferate under such high-stressed conditions through incompletely understood mechanisms. Here, we report taurine upregulated gene 1 (TUG1) long noncoding RNA (lncRNA), which is highly expressed in many types of cancers, as an important regulator of intrinsic R-loop in cancer cells. Under RS conditions, TUG1 is rapidly upregulated via activation of the ATR-CHK1 signaling pathway, interacts with RPA and DHX9, and engages in resolving R-loops at certain loci, particularly at the CA repeat microsatellite loci. Depletion of TUG1 leads to overabundant R-loops and enhanced RS, leading to substantial inhibition of tumor growth. Our data reveal a role of TUG1 as molecule important for resolving R-loop accumulation in cancer cells and suggest targeting TUG1 as a potent therapeutic approach for cancer treatment.
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Affiliation(s)
- Miho M Suzuki
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Kenta Iijima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Koichi Ogami
- Division of Molecular Oncology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yoshiteru Murofushi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Jingqi Xie
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Xuebing Wang
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yotaro Kitano
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Akira Mamiya
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yuji Kibe
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Tatsunori Nishimura
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Shinya Sato
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Asahi-ku, Yokohama, Kanagawa, 241-8515, Japan
| | - Junya Kobayashi
- School of Health Sciences at Narita, International University of Health and Welfare, 4-3 Kozunomori, Narita, Chiba, 286-8686, Japan
| | - Ryoji Yao
- Department of Cell Biology, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tono-machi, Kawasaki-ku, Kanagawa, 210-0821, Japan
- Institute for Future Initiatives, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroshi I Suzuki
- Division of Molecular Oncology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
- Institute for Glyco-core Research (iGCORE), Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan.
- Institute for Glyco-core Research (iGCORE), Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
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42
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Klapp V, Álvarez-Abril B, Leuzzi G, Kroemer G, Ciccia A, Galluzzi L. The DNA Damage Response and Inflammation in Cancer. Cancer Discov 2023; 13:1521-1545. [PMID: 37026695 DOI: 10.1158/2159-8290.cd-22-1220] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/27/2023] [Accepted: 02/23/2023] [Indexed: 04/08/2023]
Abstract
Genomic stability in normal cells is crucial to avoid oncogenesis. Accordingly, multiple components of the DNA damage response (DDR) operate as bona fide tumor suppressor proteins by preserving genomic stability, eliciting the demise of cells with unrepairable DNA lesions, and engaging cell-extrinsic oncosuppression via immunosurveillance. That said, DDR sig-naling can also favor tumor progression and resistance to therapy. Indeed, DDR signaling in cancer cells has been consistently linked to the inhibition of tumor-targeting immune responses. Here, we discuss the complex interactions between the DDR and inflammation in the context of oncogenesis, tumor progression, and response to therapy. SIGNIFICANCE Accumulating preclinical and clinical evidence indicates that DDR is intimately connected to the emission of immunomodulatory signals by normal and malignant cells, as part of a cell-extrinsic program to preserve organismal homeostasis. DDR-driven inflammation, however, can have diametrically opposed effects on tumor-targeting immunity. Understanding the links between the DDR and inflammation in normal and malignant cells may unlock novel immunotherapeutic paradigms to treat cancer.
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Affiliation(s)
- Vanessa Klapp
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Beatriz Álvarez-Abril
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
- Department of Hematology and Oncology, Hospital Universitario Morales Meseguer, Murcia, Spain
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, New York, New York
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, New York, New York
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
- Sandra and Edward Meyer Cancer Center, New York, New York
- Caryl and Israel Englander Institute for Precision Medicine, New York, New York
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43
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Zhang X, Duan J, Li Y, Jin X, Wu C, Yang X, Lu W, Ge W. NKAP acts with HDAC3 to prevent R-loop associated genome instability. Cell Death Differ 2023; 30:1811-1828. [PMID: 37322264 PMCID: PMC10307950 DOI: 10.1038/s41418-023-01182-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/09/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
Persistent R-loop accumulation can cause DNA damage and lead to genome instability, which contributes to various human diseases. Identification of molecules and signaling pathways in controlling R-loop homeostasis provide important clues about their physiological and pathological roles in cells. Here, we show that NKAP (NF-κB activating protein) is essential for preventing R-loop accumulation and maintaining genome integrity through forming a protein complex with HDAC3. NKAP depletion causes DNA damage and genome instability. Aberrant accumulation of R-loops is present in NKAP-deficient cells and leads to DNA damage and DNA replication fork progression defects. Moreover, NKAP depletion induced R-loops and DNA damage are dependent on transcription. Consistently, the NKAP interacting protein HDAC3 exhibits a similar role in suppressing R-loop associated DNA damage and replication stress. Further analysis uncovers that HDAC3 functions to stabilize NKAP protein, independent of its deacetylase activity. In addition, NKAP prevents R-loop formation by maintaining RNA polymerase II pausing. Importantly, R-loops induced by NKAP or HDAC3 depletion are processed into DNA double-strand breaks by XPF and XPG endonucleases. These findings indicate that both NKAP and HDAC3 are novel key regulators of R-loop homeostasis, and their dysregulation might drive tumorigenesis by causing R-loop associated genome instability.
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Affiliation(s)
- Xing Zhang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Jingwei Duan
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Yang Li
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Xiaoye Jin
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Cheng Wu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Xiaohang Yang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Weiguo Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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44
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Huang N, Song Y, Shi W, Guo J, Zhang Z, He Q, Wu L, Li X, Xu F. DHX9-mediated pathway contributes to the malignant phenotype of myelodysplastic syndromes. iScience 2023; 26:106962. [PMID: 37305700 PMCID: PMC10250162 DOI: 10.1016/j.isci.2023.106962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/06/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
DHX9 is a member of the DEAH (Asp-Glu-Ala-His) helicase family and regulates DNA replication and RNA processing. DHX9 dysfunction promotes tumorigenesis in several solid cancers. However, the role of DHX9 in MDS is still unknown. Here, we analyzed the expression of DHX9 and its clinical significance in 120 MDS patients and 42 non-MDS controls. Lentivirus-mediated DHX9-knockdown experiments were performed to investigate its biological function. We also performed cell functional assays, gene microarray, and pharmacological intervention to investigate the mechanistic involvement of DHX9. We found that overexpression of DHX9 is frequent in MDS and associated with poor survival and high risk of acute myeloid leukemia (AML) transformation. DHX9 is essential for the maintenance of malignant proliferation of leukemia cells, and DHX9 suppression increases cell apoptosis and causes hypersensitivity to chemotherapeutic agents. Besides, knockdown of DHX9 inactivates the PI3K-AKT and ATR-Chk1 signaling, promotes R-loop accumulation, and R-loop-mediated DNA damage.
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Affiliation(s)
- Nanfang Huang
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Yang Song
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Wenhui Shi
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Juan Guo
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Zheng Zhang
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Qi He
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Lingyun Wu
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Xiao Li
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Feng Xu
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
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45
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Chen X, Huang C. Chromatin-interacting RNA-binding proteins regulate transcription. Trends Cell Biol 2023:S0962-8924(23)00089-2. [PMID: 37270323 DOI: 10.1016/j.tcb.2023.05.006] [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: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/05/2023]
Abstract
RNA-binding proteins (RBPs) are essential regulators involved in the fate determination of diverse RNA species; however, emerging evidence indicates that a subset of RBPs may physically interact with chromatin and function at the transcriptional level. Here, we highlight the recently discovered mechanisms of chromatin-interacting RBPs (ChRBPs) in the regulation of chromatin/transcriptional activities.
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Affiliation(s)
- Xiaolan Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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46
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Marchena-Cruz E, Camino LP, Bhandari J, Silva S, Marqueta-Gracia JJ, Amdeen SA, Guillén-Mendoza C, García-Rubio ML, Calderón-Montaño JM, Xue X, Luna R, Aguilera A. DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops. Cell Rep 2023; 42:112148. [PMID: 36827184 PMCID: PMC10066596 DOI: 10.1016/j.celrep.2023.112148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/20/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Unscheduled R loops can be a source of genome instability, a hallmark of cancer cells. Although targeted proteomic approaches and cellular analysis of specific mutants have uncovered factors potentially involved in R-loop homeostasis, we report a more open screening of factors whose depletion causes R loops based on the ability of activation-induced cytidine deaminase (AID) to target R loops. Immunofluorescence analysis of γH2AX caused by small interfering RNAs (siRNAs) covering 3,205 protein-coding genes identifies 59 potential candidates, from which 13 are analyzed further and show a significant increase of R loops. Such candidates are enriched in factors involved in chromatin, transcription, and RNA biogenesis and other processes. A more focused study shows that the DDX47 helicase is an R-loop resolvase, whereas the MeCP2 methyl-CpG-binding protein uncovers a link between DNA methylation and R loops. Thus, our results suggest that a plethora of gene dysfunctions can alter cell physiology via affecting R-loop homeostasis by different mechanisms.
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Affiliation(s)
- Esther Marchena-Cruz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Lola P Camino
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Jay Bhandari
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Sónia Silva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - José Javier Marqueta-Gracia
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Shahad A Amdeen
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Cristina Guillén-Mendoza
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - José M Calderón-Montaño
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Xiaoyu Xue
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
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47
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Lee SY, Miller KM, Kim JJ. Clinical and Mechanistic Implications of R-Loops in Human Leukemias. Int J Mol Sci 2023; 24:ijms24065966. [PMID: 36983041 PMCID: PMC10052022 DOI: 10.3390/ijms24065966] [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: 03/04/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic mutations or environmental agents are major contributors to leukemia and are associated with genomic instability. R-loops are three-stranded nucleic acid structures consisting of an RNA-DNA hybrid and a non-template single-stranded DNA. These structures regulate various cellular processes, including transcription, replication, and DSB repair. However, unregulated R-loop formation can cause DNA damage and genomic instability, which are potential drivers of cancer including leukemia. In this review, we discuss the current understanding of aberrant R-loop formation and how it influences genomic instability and leukemia development. We also consider the possibility of R-loops as therapeutic targets for cancer treatment.
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Affiliation(s)
- Seo-Yun Lee
- 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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48
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Laspata N, Kaur P, Mersaoui S, Muoio D, Liu Z, Bannister MH, Nguyen H, Curry C, Pascal J, Poirier G, Wang H, Masson JY, Fouquerel E. PARP1 associates with R-loops to promote their resolution and genome stability. Nucleic Acids Res 2023; 51:2215-2237. [PMID: 36794853 PMCID: PMC10018367 DOI: 10.1093/nar/gkad066] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
PARP1 is a DNA-dependent ADP-Ribose transferase with ADP-ribosylation activity that is triggered by DNA breaks and non-B DNA structures to mediate their resolution. PARP1 was also recently identified as a component of the R-loop-associated protein-protein interaction network, suggesting a potential role for PARP1 in resolving this structure. R-loops are three-stranded nucleic acid structures that consist of a RNA-DNA hybrid and a displaced non-template DNA strand. R-loops are involved in crucial physiological processes but can also be a source of genome instability if persistently unresolved. In this study, we demonstrate that PARP1 binds R-loops in vitro and associates with R-loop formation sites in cells which activates its ADP-ribosylation activity. Conversely, PARP1 inhibition or genetic depletion causes an accumulation of unresolved R-loops which promotes genomic instability. Our study reveals that PARP1 is a novel sensor for R-loops and highlights that PARP1 is a suppressor of R-loop-associated genomic instability.
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Affiliation(s)
- Natalie Laspata
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15213, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Parminder Kaur
- Physics Department, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, Raleigh, NC 27695, USA
| | - Sofiane Yacine Mersaoui
- CHU de Québec Research Centre, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, McMahon, Québec City, Québec G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, Canada
| | - Daniela Muoio
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15213, USA
| | - Zhiyan Silvia Liu
- Department of Pharmacology, The Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maxwell Henry Bannister
- Department of Pharmacology, The Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hai Dang Nguyen
- Department of Pharmacology, The Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caroline Curry
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, Canada
- CHU de Québec Research Centre, CHUL Pavilion, Oncology Division, Quebec, Canada
| | - Hong Wang
- Physics Department, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Jean-Yves Masson
- CHU de Québec Research Centre, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, McMahon, Québec City, Québec G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, Canada
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15213, USA
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49
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Yu Z, Richard S. DDX47 untangles R-loops with only certain other helicases. Trends Cell Biol 2023; 33:359-360. [PMID: 36914533 DOI: 10.1016/j.tcb.2023.03.001] [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: 03/01/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/13/2023]
Abstract
R-loops, formed transiently during gene transcription, are tightly controlled to avoid conflict with ongoing processes. Marchena-Cruz et al. identified DExD/H box RNA helicase DDX47 using a new R-loop resolving screen and defined a unique role for this helicase in nucleolar R-loops and its interplay with senataxin (SETX) and DDX39B.
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Affiliation(s)
- Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec H3T 1E2, Canada; Gerald Bronfman Department of Oncology McGill University, Montréal, Québec H3T 1E2, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3T 1E2, Canada; Department of Human Genetics McGill University, Montréal, Québec H3T 1E2, Canada; Department of Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec H3T 1E2, Canada; Gerald Bronfman Department of Oncology McGill University, Montréal, Québec H3T 1E2, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3T 1E2, Canada; Department of Human Genetics McGill University, Montréal, Québec H3T 1E2, Canada; Department of Medicine, McGill University, Montréal, Québec H3T 1E2, Canada.
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Yun J, Song H, Kim SM, Kim S, Kwon SR, Lee YE, Jeong D, Park JH, Kwon S, Yun H, Lee DS. Analysis of clinical and genomic profiles of therapy-related myeloid neoplasm in Korea. Hum Genomics 2023; 17:13. [PMID: 36814285 PMCID: PMC9948421 DOI: 10.1186/s40246-023-00458-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Therapy-related myeloid neoplasm (T-MN) rarely occurs among cancer survivors, and was characterized by poor prognosis. T-MN has germline predisposition in a considerable proportion. Here, clinical characteristics and germline/somatic variant profiles in T-MN patients were investigated, and the findings were compared with those of previous studies. METHODS A review of medical records, cytogenetic study, targeted sequencing by next-generation sequencing, and survival analysis were performed on 53 patients with T-MN at a single institution in Korea. RESULTS The patients were relatively younger compared to T-MN patients in other studies. Our T-MN patients showed a high frequency of complex karyotypes, -5/del(5q), and -7/del(7q), which was similar to the Japanese study group but higher than the Australian study group. The most common primary disease was non-Hodgkin lymphoma, followed by breast cancer. The detailed distributions of primary diseases were different across study groups. Seven patients (13.2%) harbored deleterious presumed/potential germline variants in cancer predisposition genes (CPG) such as BRIP1, CEBPA, DDX41, FANCM, NBN, NF1, and RUNX1. In the somatic variant profile, TP53 was the most frequently mutated gene, which was consistent with the previous studies about T-MN. However, the somatic variant frequency in our study group was lower than in other studies. Adverse factors for overall survival were male sex, older age, history of previous radiotherapy, previous longer cytotoxic therapy, and -5/del(5q). CONCLUSION The findings of our study corroborate important information about T-MN patients. As well as a considerable predisposition to CPG, the clinical characteristics and somatic variant profile showed distinctive patterns. Germline variant testing should be recommended for T-MN patients. If the T-MN patients harbor pathogenic germline variants, the family members for stem cell donation should be screened for carrier status through germline variant testing to avoid donor-derived myeloid neoplasm. For the prediction of the prognosis in T-MN patients, sex, age, past treatment history, and cytogenetic findings can be considered.
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Affiliation(s)
- Jiwon Yun
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Laboratory Medicine, Chung-Ang University Hospital, Seoul, Republic of Korea
| | - Hyojin Song
- Department of Genomic Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sung-Min Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soonok Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seok Ryun Kwon
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Young Eun Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Dajeong Jeong
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Dong Soon Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Genomic Medicine Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea.
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