1
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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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2
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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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3
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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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4
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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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Mastrogiovanni M, Martínez-Navarro FJ, Bowman TV, Cayuela ML. Inflammation in Development and Aging: Insights from the Zebrafish Model. Int J Mol Sci 2024; 25:2145. [PMID: 38396822 PMCID: PMC10889087 DOI: 10.3390/ijms25042145] [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: 01/02/2024] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Zebrafish are an emergent animal model to study human diseases due to their significant genetic similarity to humans, swift development, and genetic manipulability. Their utility extends to the exploration of the involvement of inflammation in host defense, immune responses, and tissue regeneration. Additionally, the zebrafish model system facilitates prompt screening of chemical compounds that affect inflammation. This study explored the diverse roles of inflammatory pathways in zebrafish development and aging. Serving as a crucial model, zebrafish provides insights into the intricate interplay of inflammation in both developmental and aging contexts. The evidence presented suggests that the same inflammatory signaling pathways often play instructive or beneficial roles during embryogenesis and are associated with malignancies in adults.
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Affiliation(s)
- Marta Mastrogiovanni
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Francisco Juan Martínez-Navarro
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria-Arrixaca, 30120 Murcia, Spain
| | - Teresa V. Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - María L. Cayuela
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 30100 Murcia, Spain
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6
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Zhang S, Liu Y, Sun Y, Liu Q, Gu Y, Huang Y, Zeng Z, Tang F, Ouyang Y. Aberrant R-loop-mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis. Mol Cancer 2024; 23:11. [PMID: 38200551 PMCID: PMC10777569 DOI: 10.1186/s12943-023-01924-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Dysregulation of R-loop homeostasis is closely related to various human diseases, including cancer. However, the causality of aberrant R-loops in tumor progression remains unclear. In this study, using single-cell RNA-sequencing datasets from lung adenocarcinoma (LUAD), we constructed an R-loop scoring model to characterize the R-loop state according to the identified R-loop regulators related to EGFR mutations, tissue origins, and TNM stage. We then evaluated the relationships of the R-loop score with the tumor microenvironment (TME) and treatment response. Furthermore, the potential roles of FANCI-mediated R-loops in LUAD were explored using a series of in vitro experiments. Results showed that malignant cells with low R-loop scores displayed glycolysis and epithelial-mesenchymal transition pathway activation and immune escape promotion, thereby hampering the antitumor therapeutic effects. Cell communication analysis suggested that low R-loop scores contributed to T cell exhaustion. We subsequently validated the prognostic value of R-loop scores by using bulk transcriptome datasets across 33 tumor types. The R-loop scoring model well predicted patients' therapeutic response to targeted therapy, chemotherapy, or immunotherapy in 32 independent cohorts. Remarkably, changes in R-loop distribution mediated by FANCI deficiency blocked the activity of Ras signaling pathway, suppressing tumor-cell proliferation and dissemination. In conclusion, this study reveals the underlying molecular mechanism of metabolic reprogramming and T cell exhaustion under R-loop score patterns, and the changes in R-loops mediated by R-loop regulators resulting in tumor progression. Therefore, incorporating anticancer methods based on R-loop or R-loop regulators into the treatment schemes of precision medicine may be beneficial.
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Affiliation(s)
- Shichao Zhang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yang Liu
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yichi Sun
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Qin Liu
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yan Gu
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Ya Huang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Zhu Zeng
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China.
| | - Fuzhou Tang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China.
| | - Yan Ouyang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China.
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7
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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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Yang X, Li G, Lou P, Zhang M, Yao K, Xiao J, Chen Y, Xu J, Tian S, Deng M, Pan Y, Li M, Wu X, Liu R, Shi X, Tian Y, Yu L, Ke H, Jiao B, Cong Y, Plikus MV, Liu X, Yu Z, Lv C. Excessive nucleic acid R-loops induce mitochondria-dependent epithelial cell necroptosis and drive spontaneous intestinal inflammation. Proc Natl Acad Sci U S A 2024; 121:e2307395120. [PMID: 38157451 PMCID: PMC10769860 DOI: 10.1073/pnas.2307395120] [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: 05/04/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024] Open
Abstract
Oxidative stress, which can be activated by a variety of environmental risk factors, has been implicated as an important pathogenic factor for inflammatory bowel disease (IBD). However, how oxidative stress drives IBD onset remains elusive. Here, we found that oxidative stress was strongly activated in inflamed tissues from both ulcerative colitis patients and Crohn's disease patients, and it caused nuclear-to-cytosolic TDP-43 transport and a reduction in the TDP-43 protein level. To investigate the function of TDP-43 in IBD, we inducibly deleted exons 2 to 3 of Tardbp (encoding Tdp-43) in mouse intestinal epithelium, which disrupted its nuclear localization and RNA-processing function. The deletion gave rise to spontaneous intestinal inflammation by inducing epithelial cell necroptosis. Suppression of the necroptotic pathway with deletion of Mlkl or the RIP1 inhibitor Nec-1 rescued colitis phenotypes. Mechanistically, disruption of nuclear TDP-43 caused excessive R-loop accumulation, which triggered DNA damage and genome instability and thereby induced PARP1 hyperactivation, leading to subsequent NAD+ depletion and ATP loss, consequently activating mitochondrion-dependent necroptosis in intestinal epithelial cells. Importantly, restoration of cellular NAD+ levels with NAD+ or NMN supplementation, as well as suppression of ALKBH7, an α-ketoglutarate dioxygenase in mitochondria, rescued TDP-43 deficiency-induced cell death and intestinal inflammation. Furthermore, TDP-43 protein levels were significantly inversely correlated with γ-H2A.X and p-MLKL levels in clinical IBD samples, suggesting the clinical relevance of TDP-43 deficiency-induced mitochondrion-dependent necroptosis. Taken together, these findings identify a unique pathogenic mechanism that links oxidative stress to intestinal inflammation and provide a potent and valid strategy for IBD intervention.
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Affiliation(s)
- Xu Yang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
- College of Agriculture and Life Sciences, Ankang University, Ankang, Shaanxi725000, China
| | - Guilin Li
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Pengbo Lou
- China Astronaut Research and Training Center, Beijing100094, China
| | - Mingxin Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Kai Yao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Jintao Xiao
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha, Hunan410008, China
- Hunan International Scientific and Technological Cooperation Base of AI Computer Aided Diagnosis and Treatment for Digestive Disease, Changsha, Hunan, China
| | - Yiqian Chen
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha, Hunan410008, China
- Hunan International Scientific and Technological Cooperation Base of AI Computer Aided Diagnosis and Treatment for Digestive Disease, Changsha, Hunan, China
| | - Jiuzhi Xu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Shengyuan Tian
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Min Deng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Yuwei Pan
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Mengzhen Li
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Xi Wu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Ruiqi Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Xiaojing Shi
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Yuhua Tian
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
| | - Lu Yu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Hao Ke
- State Key Laboratory of Genetic Resources and Evolution of Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650223, China
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution of Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650223, China
| | - Yingzi Cong
- Division of Gastroenterology and Hepatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, IL60611
| | - Maksim V. Plikus
- Department of Developmental and Cell Biology, Sue and Bill Gross Stem Cell Research Center, Center for Complex Biological Systems, University of California, Irvine, Irvine, CA92697
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha, Hunan410008, China
- Hunan International Scientific and Technological Cooperation Base of AI Computer Aided Diagnosis and Treatment for Digestive Disease, Changsha, Hunan, China
| | - Zhengquan Yu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan450052, China
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing100193, China
| | - Cong Lv
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing100193, China
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9
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Wagner JN, Al-Bazaz M, Forstreuter A, Hammada MI, Hille J, Papingi D, Bokemeyer C, Fiedler W. Case Report of a DDX41 Germline Mutation in a Family with Multiple Relatives Suffering from Leukemia. Biomedicines 2023; 12:64. [PMID: 38255170 PMCID: PMC10813731 DOI: 10.3390/biomedicines12010064] [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: 12/07/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
INTRODUCTION Previously, it was assumed that genetic influence played a minor role in acute myeloid leukemia (AML). Increasing evidence of germline mutations has emerged, such as DDX41 germline mutation associated with familial AML. CASE PRESENTATION A 64-year-old male patient presented with reduced exercise tolerance and shortness of breath. Following confirmation of AML diagnosis, the patient was enrolled into the AMLSG-30-18 study with a requirement for allogenic stem cell transplantation. The sister was initially selected as a fully HLA-matched donor. However, the family history showed risks for familial AML. Due to the striking family history, further diagnostic steps were initiated to detect a germline mutation. METHODS Using NGS in the patients' bone marrow AML sample, a DDX41 mutation with a VAF of 49% was detected, raising the possibility of a germline mutation. DNA from cheek swabs and eyebrows were tested for the presence of the DDX41 mutation in all siblings. RESULTS DDX41 germline mutation was detected in 5 out of 6 siblings. The sister was excluded as a related donor and the search for an unrelated donor was initiated. CONCLUSION Obtaining family history of cancer patients plays a crucial role in oncology. If a germline mutation is suspected, further family work-up should be initiated.
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Affiliation(s)
- Jan Nicolai Wagner
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.A.-B.); (A.F.); (M.I.H.); (J.H.); (C.B.)
| | - Maximilian Al-Bazaz
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.A.-B.); (A.F.); (M.I.H.); (J.H.); (C.B.)
| | - Anika Forstreuter
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.A.-B.); (A.F.); (M.I.H.); (J.H.); (C.B.)
| | - Mohammad Ibrahim Hammada
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.A.-B.); (A.F.); (M.I.H.); (J.H.); (C.B.)
| | - Jurek Hille
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.A.-B.); (A.F.); (M.I.H.); (J.H.); (C.B.)
| | - Dzhoy Papingi
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.A.-B.); (A.F.); (M.I.H.); (J.H.); (C.B.)
| | - Walter Fiedler
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.A.-B.); (A.F.); (M.I.H.); (J.H.); (C.B.)
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10
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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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11
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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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12
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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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13
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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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14
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Chlon TM, Patnaik MM. Germline DDX41 mutant predisposition syndromes: Slow driver states to hematological malignancies. Am J Hematol 2023; 98:1673-1676. [PMID: 37705260 DOI: 10.1002/ajh.27091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023]
Affiliation(s)
- Timothy M Chlon
- Division of Hematology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
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15
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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: 8] [Impact Index Per Article: 8.0] [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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16
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Reece AS, Hulse GK. Perturbation of 3D nuclear architecture, epigenomic aging and dysregulation, and cannabinoid synaptopathy reconfigures conceptualization of cannabinoid pathophysiology: part 2-Metabolome, immunome, synaptome. Front Psychiatry 2023; 14:1182536. [PMID: 37854446 PMCID: PMC10579598 DOI: 10.3389/fpsyt.2023.1182536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
The second part of this paper builds upon and expands the epigenomic-aging perspective presented in Part 1 to describe the metabolomic and immunomic bases of the epigenomic-aging changes and then considers in some detail the application of these insights to neurotoxicity, neuronal epigenotoxicity, and synaptopathy. Cannabinoids are well-known to have bidirectional immunomodulatory activities on numerous parts of the immune system. Immune perturbations are well-known to impact the aging process, the epigenome, and intermediate metabolism. Cannabinoids also impact metabolism via many pathways. Metabolism directly impacts immune, genetic, and epigenetic processes. Synaptic activity, synaptic pruning, and, thus, the sculpting of neural circuits are based upon metabolic, immune, and epigenomic networks at the synapse, around the synapse, and in the cell body. Many neuropsychiatric disorders including depression, anxiety, schizophrenia, bipolar affective disorder, and autistic spectrum disorder have been linked with cannabis. Therefore, it is important to consider these features and their complex interrelationships in reaching a comprehensive understanding of cannabinoid dependence. Together these findings indicate that cannabinoid perturbations of the immunome and metabolome are important to consider alongside the well-recognized genomic and epigenomic perturbations and it is important to understand their interdependence and interconnectedness in reaching a comprehensive appreciation of the true nature of cannabinoid pathophysiology. For these reasons, a comprehensive appreciation of cannabinoid pathophysiology necessitates a coordinated multiomics investigation of cannabinoid genome-epigenome-transcriptome-metabolome-immunome, chromatin conformation, and 3D nuclear architecture which therefore form the proper mechanistic underpinning for major new and concerning epidemiological findings relating to cannabis exposure.
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Affiliation(s)
- Albert Stuart Reece
- Division of Psychiatry, University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Gary Kenneth Hulse
- Division of Psychiatry, University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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17
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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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18
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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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19
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Xia J, Liu M, Zhu C, Liu S, Ai L, Ma D, Zhu P, Wang L, Liu F. Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity. Cell Res 2023; 33:448-463. [PMID: 37016019 PMCID: PMC10235423 DOI: 10.1038/s41422-023-00797-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/01/2023] [Indexed: 04/06/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are considered as a heterogeneous population, but precisely when, where and how HSPC heterogeneity arises remain largely unclear. Here, using a combination of single-cell multi-omics, lineage tracing and functional assays, we show that embryonic HSPCs originate from heterogeneous hemogenic endothelial cells (HECs) during zebrafish embryogenesis. Integrated single-cell transcriptome and chromatin accessibility analysis demonstrates transcriptional heterogeneity and regulatory programs that prime lymphoid/myeloid fates at the HEC level. Importantly, spi2+ HECs give rise to lymphoid/myeloid-primed HSPCs (L/M-HSPCs) and display a stress-responsive function under acute inflammation. Moreover, we uncover that Spi2 is required for the formation of L/M-HSPCs through tightly controlling the endothelial-to-hematopoietic transition program. Finally, single-cell transcriptional comparison of zebrafish and human HECs and human induced pluripotent stem cell-based hematopoietic differentiation results support the evolutionary conservation of L/M-HECs and a conserved role of SPI1 (spi2 homolog in mammals) in humans. These results unveil the lineage origin, biological function and molecular determinant of HSPC heterogeneity and lay the foundation for new strategies for induction of transplantable lineage-primed HSPCs in vitro.
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Affiliation(s)
- Jun Xia
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengyao Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Caiying Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Shicheng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lanlan Ai
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Dongyuan Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Sciences, Shandong University, Qingdao, Shandong, China.
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20
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Pezone A, Olivieri F, Napoli MV, Procopio A, Avvedimento EV, Gabrielli A. Inflammation and DNA damage: cause, effect or both. Nat Rev Rheumatol 2023; 19:200-211. [PMID: 36750681 DOI: 10.1038/s41584-022-00905-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Inflammation is a biological response involving immune cells, blood vessels and mediators induced by endogenous and exogenous stimuli, such as pathogens, damaged cells or chemicals. Unresolved (chronic) inflammation is characterized by the secretion of cytokines that maintain inflammation and redox stress. Mitochondrial or nuclear redox imbalance induces DNA damage, which triggers the DNA damage response (DDR) that is orchestrated by ATM and ATR kinases, which modify gene expression and metabolism and, eventually, establish the senescent phenotype. DDR-mediated senescence is induced by the signalling proteins p53, p16 and p21, which arrest the cell cycle in G1 or G2 and promote cytokine secretion, producing the senescence-associated secretory phenotype. Senescence and inflammation phenotypes are intimately associated, but highly heterogeneous because they vary according to the cell type that is involved. The vicious cycle of inflammation, DNA damage and DDR-mediated senescence, along with the constitutive activation of the immune system, is the core of an evolutionarily conserved circuitry, which arrests the cell cycle to reduce the accumulation of mutations generated by DNA replication during redox stress caused by infection or inflammation. Evidence suggests that specific organ dysfunctions in apparently unrelated diseases of autoimmune, rheumatic, degenerative and vascular origins are caused by inflammation resulting from DNA damage-induced senescence.
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Affiliation(s)
- Antonio Pezone
- Dipartimento di Biologia, Università Federico II, Napoli, Italy.
| | - Fabiola Olivieri
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Clinica di Medicina di Laboratorio e di Precisione, IRCCS INRCA, Ancona, Italy
| | - Maria Vittoria Napoli
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Antonio Procopio
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Clinica di Medicina di Laboratorio e di Precisione, IRCCS INRCA, Ancona, Italy
| | - Enrico Vittorio Avvedimento
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, Napoli, Italy.
| | - Armando Gabrielli
- Fondazione di Medicina Molecolare e Terapia Cellulare, Università Politecnica delle Marche, Ancona, Italy.
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21
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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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22
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Zhao Y, Simon M, Seluanov A, Gorbunova V. DNA damage and repair in age-related inflammation. Nat Rev Immunol 2023; 23:75-89. [PMID: 35831609 PMCID: PMC10106081 DOI: 10.1038/s41577-022-00751-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2022] [Indexed: 02/07/2023]
Abstract
Genomic instability is an important driver of ageing. The accumulation of DNA damage is believed to contribute to ageing by inducing cell death, senescence and tissue dysfunction. However, emerging evidence shows that inflammation is another major consequence of DNA damage. Inflammation is a hallmark of ageing and the driver of multiple age-related diseases. Here, we review the evidence linking DNA damage, inflammation and ageing, highlighting how premature ageing syndromes are associated with inflammation. We discuss the mechanisms by which DNA damage induces inflammation, such as through activation of the cGAS-STING axis and NF-κB activation by ATM. The triggers for activation of these signalling cascades are the age-related accumulation of DNA damage, activation of transposons, cellular senescence and the accumulation of persistent R-loops. We also discuss how epigenetic changes triggered by DNA damage can lead to inflammation and ageing via redistribution of heterochromatin factors. Finally, we discuss potential interventions against age-related inflammation.
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Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, USA.,Department of Physiology, Zhejiang University School of Medicine, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA. .,Department of Medicine, University of Rochester, Rochester, NY, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA. .,Department of Medicine, University of Rochester, Rochester, NY, USA.
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23
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De Novo Generation of Human Hematopoietic Stem Cells from Pluripotent Stem Cells for Cellular Therapy. Cells 2023; 12:cells12020321. [PMID: 36672255 PMCID: PMC9857267 DOI: 10.3390/cells12020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The ability to manufacture human hematopoietic stem cells (HSCs) in the laboratory holds enormous promise for cellular therapy of human blood diseases. Several differentiation protocols have been developed to facilitate the emergence of HSCs from human pluripotent stem cells (PSCs). Most approaches employ a stepwise addition of cytokines and morphogens to recapitulate the natural developmental process. However, these protocols globally lack clinical relevance and uniformly induce PSCs to produce hematopoietic progenitors with embryonic features and limited engraftment and differentiation capabilities. This review examines how key intrinsic cues and extrinsic environmental inputs have been integrated within human PSC differentiation protocols to enhance the emergence of definitive hematopoiesis and how advances in genomics set the stage for imminent breakthroughs in this field.
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24
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Kim K, Ong F, Sasaki K. Current Understanding of DDX41 Mutations in Myeloid Neoplasms. Cancers (Basel) 2023; 15:344. [PMID: 36672294 PMCID: PMC9857085 DOI: 10.3390/cancers15020344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
The DEAD-box RNA helicase 41 gene, DDX41, is frequently mutated in hereditary myeloid neoplasms, identified in 2% of entire patients with AML/MDS. The pathogenesis of DDX41 mutation is related to the defect in the gene's normal functions of RNA and innate immunity. About 80% of patients with germline DDX41 mutations have somatic mutations in another allele, resulting in the biallelic DDX41 mutation. Patients with the disease with DDX41 mutations reportedly often present with the higher-grade disease, but there are conflicting reports about its impact on survival outcomes. Recent studies using larger cohorts reported a favorable outcome with a better response to standard therapies in patients with DDX41 mutations to patients without DDX41 mutations. For stem-cell transplantation, it is important for patients with DDX41 germline mutations to identify family donors early to improve outcomes. Still, there is a gap in knowledge on whether germline DDX41 mutations and its pathology features can be targetable for treatment, and what constitutes an appropriate screening/surveillance strategy for identified carriers. This article reviews our current understanding of DDX41 mutations in myeloid neoplasms in pathologic and clinical features and their clinical implications.
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Affiliation(s)
| | | | - Koji Sasaki
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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25
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Kim JA, Shen S, Matson DR, Lovrien LN, Smith-Simmer KJ, Keles S, Churpek JE, Bresnick EH. Discriminating activities of DEAD-Box Helicase 41 from myeloid malignancy-associated germline variants by genetic rescue. Leukemia 2023; 37:235-239. [PMID: 36347925 PMCID: PMC9981304 DOI: 10.1038/s41375-022-01753-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jeong-Ah Kim
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Siqi Shen
- Department of Biostatistics and Biomedical Informatics, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Daniel R Matson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lauren N Lovrien
- Division of Hematology, Oncology, and Palliative Care, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kelcy J Smith-Simmer
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sunduz Keles
- Department of Biostatistics and Biomedical Informatics, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jane E Churpek
- Division of Hematology, Oncology, and Palliative Care, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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26
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Crossley MP, Song C, Bocek MJ, Choi JH, Kousouros JN, Sathirachinda A, Lin C, Brickner JR, Bai G, Lans H, Vermeulen W, Abu-Remaileh M, Cimprich KA. R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response. Nature 2023; 613:187-194. [PMID: 36544021 PMCID: PMC9949885 DOI: 10.1038/s41586-022-05545-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. However, the mechanisms and cellular consequences of such processing have remained unclear. Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. When nuclear R-loops were perturbed by depleting the RNA-DNA helicase senataxin (SETX) or the breast cancer gene BRCA1 (refs. 5-7), we observed XPG- and XPF-dependent cytoplasmic hybrid formation. We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. Cytoplasmic hybrids bind to the pattern recognition receptors cGAS and TLR3 (ref. 8), activating IRF3 and inducing apoptosis. Excised hybrids and an R-loop-induced innate immune response were also observed in SETX-mutated cells from patients with ataxia oculomotor apraxia type 2 (ref. 9) and in BRCA1-mutated cancer cells10. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer.
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Affiliation(s)
- Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Chenlin Song
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Michael J Bocek
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Jun-Hyuk Choi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon, South Korea
- Department of Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Joseph N Kousouros
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Ataya Sathirachinda
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Cindy Lin
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Gongshi Bai
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
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27
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Li Y, Gao Y, Jiang X, Cheng Y, Zhang J, Xu L, Liu X, Huang Z, Xie C, Gong Y. SAMHD1 silencing cooperates with radiotherapy to enhance anti-tumor immunity through IFI16-STING pathway in lung adenocarcinoma. J Transl Med 2022; 20:628. [PMID: 36578072 PMCID: PMC9798699 DOI: 10.1186/s12967-022-03844-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) is a DNA end resection factor, which is involved in DNA damage repair and innate immunity. However, the role of SAMHD1 in anti-tumor immunity is still unknown. This study investigated the effects of SAMHD1 on stimulator of interferon genes (STING)-type I interferon (IFN) pathway and radiation-induced immune responses. METHODS The roles of SAMHD1 in the activation of cytosolic DNA sensing STING pathway in lung adenocarcinoma (LUAD) cells were investigated with flow cytometry, immunofluorescence, immunoblotting and qPCR. The combined effects of SAMHD1 silencing and radiation on tumor cell growth and STING pathway activation were also evaluated with colony formation and CCK8 assay. The Lewis lung cancer mouse model was used to evaluate the combined efficiency of SAMHD1 silencing and radiotherapy in vivo. Macrophage M1 polarization and cytotoxic T cell infiltration were evaluated with flow cytometry. RESULTS The single-stranded DNA (ssDNA) accumulated in the cytosol of SAMHD1-deficient lung adenocarcinoma (LUAD) cells, accompanied by upregulated DNA sensor IFN-γ-inducible protein 16 (IFI16) and activated STING pathway. The translocation of IFI16 from nucleus to cytosol was detected in SAMHD1-deficient cells. IFI16 and STING were acquired in the activation of STING-IFN-I pathway in SAMHD1-deficient cells. SAMHD1 silencing in LUAD cells promoted macrophage M1 polarization in vitro. SAMHD1 silencing synergized with radiation to activate ssDNA-STING-IFN-I pathway, inhibit proliferation, promote apoptosis and regulate cell cycle. SAMHD1 silencing cooperated with radiotherapy to inhibit tumor growth and increase CD86+MHC-IIhigh M1 proportion and CD8+ T cell infiltration in vivo. CONCLUSIONS SAMHD1 deficiency induced IFN-I production through cytosolic IFI16-STING pathway in LUAD cells. Moreover, SAMHD1 downregulation and radiation cooperated to inhibit tumor growth and enhance anti-tumor immune responses through macrophage M1 polarization and CD8+ T cell infiltration. Combination of SAMHD1 inhibition and radiotherapy may be a potentially therapeutic strategy for LUAD patients.
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Affiliation(s)
- Yangyi Li
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Yuke Gao
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Xueping Jiang
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Yajie Cheng
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Jianguo Zhang
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Liexi Xu
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Xinyu Liu
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Zhengrong Huang
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China ,grid.413247.70000 0004 1808 0969Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Conghua Xie
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China ,grid.413247.70000 0004 1808 0969Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China ,grid.413247.70000 0004 1808 0969Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Yan Gong
- grid.413247.70000 0004 1808 0969Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China ,grid.413247.70000 0004 1808 0969Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
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28
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Zhou J, Zhang W, Sun Q. R-loop: The new genome regulatory element in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2275-2289. [PMID: 36223078 DOI: 10.1111/jipb.13383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
An R-loop is a three-stranded chromatin structure that consists of a displaced single strand of DNA and an RNA:DNA hybrid duplex, which was thought to be a rare by-product of transcription. However, recent genome-wide data have shown that R-loops are widespread and pervasive in a variety of genomes, and a growing body of experimental evidence indicates that R-loops have both beneficial and harmful effects on an organism. To maximize benefit and avoid harm, organisms have evolved several means by which they tightly regulate R-loop levels. Here, we summarize our current understanding of the biogenesis and effects of R-loops, the mechanisms that regulate them, and methods of R-loop profiling, reviewing recent research advances on R-loops in plants. Furthermore, we provide perspectives on future research directions for R-loop biology in plants, which might lead to a more comprehensive understanding of R-loop functions in plant genome regulation and contribute to future agricultural improvements.
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Affiliation(s)
- Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
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29
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Weinreb JT, Bowman TV. Clinical and mechanistic insights into the roles of DDX41 in haematological malignancies. FEBS Lett 2022; 596:2736-2745. [PMID: 36036093 PMCID: PMC9669125 DOI: 10.1002/1873-3468.14487] [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: 06/17/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022]
Abstract
DEAD-box Helicase 41 (DDX41) is a member of the DExD/H-box helicase family that has a variety of cellular functions. Of note, germline and somatic mutations in the DDX41 gene are prevalently found in myeloid malignancies. Here, we present a comprehensive and analytic review covering relevant clinical, translational and basic science findings on DDX41. We first describe the initial characterisation of DDX41 mutations in patients affected by myelodysplastic syndromes, their associated clinical characteristics, and current treatment modalities. We then cover the known cellular functions of DDX41, spanning from its discovery in Drosophila as a neuroregulator through its more recently described roles in inflammatory signalling, R-loop metabolism and snoRNA processing. We end with a summary of the identified basic functions of DDX41 that when perturbed may contribute to the underlying pathology of haematologic neoplasms.
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Affiliation(s)
- Joshua T. Weinreb
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA
- Albert Einstein College of Medicine, Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Teresa V. Bowman
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA
- Albert Einstein College of Medicine, Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
- Albert Einstein College of Medicine and the Montefiore Medical Center, Department of Oncology, Bronx, NY, USA
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30
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Shinriki S, Matsui H. Unique role of DDX41, a DEAD-box type RNA helicase, in hematopoiesis and leukemogenesis. Front Oncol 2022; 12:992340. [PMID: 36119490 PMCID: PMC9478608 DOI: 10.3389/fonc.2022.992340] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
In myeloid malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), patient selection and therapeutic strategies are increasingly based on tumor-specific genetic mutations. Among these, mutations in DDX41, which encodes a DEAD-box type RNA helicase, are present in approximately 2–5% of AML and MDS patients; this disease subtype exhibits a distinctive disease phenotype characterized by late age of onset, tendency toward cytopenia in the peripheral blood and bone marrow, a relatively favorable prognosis, and a high frequency of normal karyotypes. Typically, individuals with a loss-of-function germline DDX41 variant in one allele later acquire the p.R525H mutation in the other allele before overt disease manifestation, suggesting that the progressive decrease in DDX41 expression and/or function is involved in myeloid leukemogenesis.RNA helicases play roles in many processes involving RNA metabolism by altering RNA structure and RNA-protein interactions through ATP-dependent helicase activity. A single RNA helicase can play multiple cellular roles, making it difficult to elucidate the mechanisms by which mutations in DDX41 are involved in leukemogenesis. Nevertheless, multiple DDX41 functions have been associated with disease development. The enzyme has been implicated in the regulation of RNA splicing, nucleic acid sensing in the cytoplasm, R-loop resolution, and snoRNA processing.Most of the mutated RNA splicing-related factors in MDS are involved in the recognition and determination of 3’ splice sites (SS), although their individual roles are distinct. On the other hand, DDX41 is likely incorporated into the C complex of the spliceosome, which may define a distinctive disease phenotype. This review summarizes the current understanding of how DDX41 is involved in this unique myeloid malignancy.
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31
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Tu J, Yu S, Li J, Ren M, Zhang Y, Luo J, Sun K, Lv Y, Han Y, Huang Y, Ren X, Jiang T, Tang Z, Williams MTS, Lu Q, Liu M. Dhx38 is required for the maintenance and differentiation of erythro-myeloid progenitors and hematopoietic stem cells by alternative splicing. Development 2022; 149:276218. [DOI: 10.1242/dev.200450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 07/21/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Mutations that occur in RNA-splicing machinery may contribute to hematopoiesis-related diseases. How splicing factor mutations perturb hematopoiesis, especially in the differentiation of erythro-myeloid progenitors (EMPs), remains elusive. Dhx38 is a pre-mRNA splicing-related DEAH box RNA helicase, for which the physiological functions and splicing mechanisms during hematopoiesis currently remain unclear. Here, we report that Dhx38 exerts a broad effect on definitive EMPs as well as the differentiation and maintenance of hematopoietic stem and progenitor cells (HSPCs). In dhx38 knockout zebrafish, EMPs and HSPCs were found to be arrested in mitotic prometaphase, accompanied by a ‘grape’ karyotype, owing to the defects in chromosome alignment. Abnormal alternatively spliced genes related to chromosome segregation, the microtubule cytoskeleton, cell cycle kinases and DNA damage were present in the dhx38 mutants. Subsequently, EMPs and HSPCs in dhx38 mutants underwent P53-dependent apoptosis. This study provides novel insights into alternative splicing regulated by Dhx38, a process that plays a crucial role in the proliferation and differentiation of fetal EMPs and HSPCs.
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Affiliation(s)
- Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Shanshan Yu
- Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology 2 , Wuhan, Hubei 430065 , P.R. China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mengmeng Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yangjun Zhang
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology 3 , Wuhan 430030 , P.R. China
| | - Jiong Luo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Tao Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mark Thomas Shaw Williams
- Charles Oakley Laboratories 4 , Department of Biological and Biomedical Sciences , , Glasgow G4 0BA , UK
- Glasgow Caledonian University 4 , Department of Biological and Biomedical Sciences , , Glasgow G4 0BA , UK
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
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Klein B, Kunz M. Current concepts of photosensitivity in cutaneous lupus erythematosus. Front Med (Lausanne) 2022; 9:939594. [PMID: 36091671 PMCID: PMC9452788 DOI: 10.3389/fmed.2022.939594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Cutaneous lupus erythematosus (CLE) represents a complex autoimmune disease with a broad phenotypic spectrum ranging from acute to chronic destructive cutaneous lesions. Patients with CLE exhibit high photosensitivity and ultraviolet (UV) irradiation can lead to systemic flares in systemic lupus erythematosus. However, the exact mechanisms how UV irradiation enhances cutaneous inflammation in lupus are not fully understood. Recently, new molecular mechanisms of UV-driven immune responses in CLE were identified, offering potential therapeutic approaches. Especially the induction of type I interferons, central cytokines in lupus pathogenesis which are released by various skin cells, have become the focus of current research. In this review, we describe current pathogenic concepts of photosensitivity in lupus erythematosus, including UV-driven activation of intracellular nucleic acid sensors, cellular cytokine production and immune cell activation. Furthermore, we discuss activated pathways contributing to enhanced apoptosis as well as intracellular translocation of autoantigens thereby promoting CLE upon UV light exposure.
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Duployez N, Largeaud L, Duchmann M, Kim R, Rieunier J, Lambert J, Bidet A, Larcher L, Lemoine J, Delhommeau F, Hirsch P, Fenwarth L, Kosmider O, Decroocq J, Bouvier A, Le Bris Y, Ochmann M, Santagostino A, Adès L, Fenaux P, Thomas X, Micol JB, Gardin C, Itzykson R, Soulier J, Clappier E, Recher C, Preudhomme C, Pigneux A, Dombret H, Delabesse E, Sébert M. Prognostic impact of DDX41 germline mutations in intensively treated acute myeloid leukemia patients: an ALFA-FILO study. Blood 2022; 140:756-768. [PMID: 35443031 PMCID: PMC9389637 DOI: 10.1182/blood.2021015328] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
DDX41 germline mutations (DDX41MutGL) are the most common genetic predisposition to myelodysplastic syndrome and acute myeloid leukemia (AML). Recent reports suggest that DDX41MutGL myeloid malignancies could be considered as a distinct entity, even if their specific presentation and outcome remain to be defined. We describe here the clinical and biological features of 191 patients with DDX41MutGL AML. Baseline characteristics and outcome of 86 of these patients, treated with intensive chemotherapy in 5 prospective Acute Leukemia French Association/French Innovative Leukemia Organization trials, were compared with those of 1604 patients with DDX41 wild-type (DDX41WT) AML, representing a prevalence of 5%. Patients with DDX41MutGL AML were mostly male (75%), in their seventh decade, and with low leukocyte count (median, 2 × 109/L), low bone marrow blast infiltration (median, 33%), normal cytogenetics (75%), and few additional somatic mutations (median, 2). A second somatic DDX41 mutation (DDX41MutSom) was found in 82% of patients, and clonal architecture inference suggested that it could be the main driver for AML progression. DDX41MutGL patients displayed higher complete remission rates (94% vs 69%; P < .0001) and longer restricted mean overall survival censored at hematopoietic stem cell transplantation (HSCT) than 2017 European LeukemiaNet intermediate/adverse (Int/Adv) DDX41WT patients (5-year difference in restricted mean survival times, 13.6 months; P < .001). Relapse rates censored at HSCT were lower at 1 year in DDX41MutGL patients (15% vs 44%) but later increased to be similar to Int/Adv DDX41WT patients at 3 years (82% vs 75%). HSCT in first complete remission was associated with prolonged relapse-free survival (hazard ratio, 0.43; 95% confidence interval, 0.21-0.88; P = .02) but not with longer overall survival (hazard ratio, 0.77; 95% confidence interval, 0.35-1.68; P = .5).
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Affiliation(s)
- Nicolas Duployez
- Hematology Laboratory, Unité 1277-Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), Centre Hospitalier Universitaire (CHU) de Lille, University of Lille, INSERM, Lille, France
| | - Laëtitia Largeaud
- Hematology Laboratory, CHU de Toulouse-Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Matthieu Duchmann
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Rathana Kim
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Julie Rieunier
- Hematology Laboratory, CHU de Toulouse-Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | | | - Audrey Bidet
- Hematology Laboratory, CHU de Bordeaux, Bordeaux, France
| | - Lise Larcher
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jean Lemoine
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - François Delhommeau
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Laboratoire d'hématologie biologique, Hôpital Saint-Antoine, Paris, France
| | - Pierre Hirsch
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Laboratoire d'hématologie biologique, Hôpital Saint-Antoine, Paris, France
| | - Laurène Fenwarth
- Hematology Laboratory, Unité 1277-Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), Centre Hospitalier Universitaire (CHU) de Lille, University of Lille, INSERM, Lille, France
| | | | | | - Anne Bouvier
- Hematology Laboratory, CHU Angers, Angers, France
| | - Yannick Le Bris
- Hematology Biology, Nantes University Hospital, Nantes, France
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France
| | | | | | - Lionel Adès
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Pierre Fenaux
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Xavier Thomas
- Hematology Department, Hospices Civils de Lyon, Lyon-Sud Hospital, Lyon, France
| | - Jean-Baptiste Micol
- Hematology Department, Gustave Roussy Institute, University of Paris-Saclay, Villejuif, France
| | - Claude Gardin
- Hematology Department, Avicenne Hospital, AP-HP, Bobigny, France
- Unité 3518, Saint-Louis Institute for Research, Université de Paris, Paris, France
| | - Raphael Itzykson
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Jean Soulier
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Emmanuelle Clappier
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Christian Recher
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Université Toulouse III Paul Sabatier, Toulouse, France; and
| | - Claude Preudhomme
- Hematology Laboratory, Unité 1277-Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), Centre Hospitalier Universitaire (CHU) de Lille, University of Lille, INSERM, Lille, France
| | - Arnaud Pigneux
- Hematology Department, CHU de Bordeaux, Bordeaux, France
| | - Hervé Dombret
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
- Unité 3518, Saint-Louis Institute for Research, Université de Paris, Paris, France
| | - Eric Delabesse
- Hematology Laboratory, CHU de Toulouse-Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Marie Sébert
- Université de Paris, Unité 944/7212-GenCellDi, INSERM and Centre National de la Recherche Scientifique (CNRS), Paris, France
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
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Ketharnathan S, Rajan V, Prykhozhij SV, Berman JN. Zebrafish models of inflammation in hematopoietic development and disease. Front Cell Dev Biol 2022; 10:955658. [PMID: 35923854 PMCID: PMC9340492 DOI: 10.3389/fcell.2022.955658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Zebrafish offer an excellent tool for studying the vertebrate hematopoietic system thanks to a highly conserved and rapidly developing hematopoietic program, genetic amenability, optical transparency, and experimental accessibility. Zebrafish studies have contributed to our understanding of hematopoiesis, a complex process regulated by signaling cues, inflammation being crucial among them. Hematopoietic stem cells (HSCs) are multipotent cells producing all the functional blood cells, including immune cells. HSCs respond to inflammation during infection and malignancy by proliferating and producing the blood cells in demand for a specific scenario. We first focus on how inflammation plays a crucial part in steady-state HSC development and describe the critical role of the inflammasome complex in regulating HSC expansion and balanced lineage production. Next, we review zebrafish studies of inflammatory innate immune mechanisms focusing on interferon signaling and the downstream JAK-STAT pathway. We also highlight insights gained from zebrafish models harbouring genetic perturbations in the role of inflammation in hematopoietic disorders such as bone marrow failure, myelodysplastic syndrome, and myeloid leukemia. Indeed, inflammation has been recently identified as a potential driver of clonal hematopoiesis and leukemogenesis, where cells acquire somatic mutations that provide a proliferative advantage in the presence of inflammation. Important insights in this area come from mutant zebrafish studies showing that hematopoietic differentiation can be compromised by epigenetic dysregulation and the aberrant induction of signaling pathways.
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Affiliation(s)
- Sarada Ketharnathan
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Vinothkumar Rajan
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | | | - Jason N. Berman
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Departments of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- *Correspondence: Jason N. Berman,
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McLemore AF, Hou HA, Meyer BS, Lam NB, Ward GA, Aldrich AL, Rodrigues MA, Vedder A, Zhang L, Padron E, Vincelette ND, Sallman DA, Abdel-Wahab O, List AF, McGraw KL. Somatic gene mutations expose cytoplasmic DNA to co-opt the cGAS-STING-NLRP3 axis in Myelodysplastic syndromes. JCI Insight 2022; 7:159430. [PMID: 35788117 PMCID: PMC9462508 DOI: 10.1172/jci.insight.159430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
NLRP3 inflammasome and IFN-stimulated gene (ISG) induction are key biological drivers of ineffective hematopoiesis and inflammation in myelodysplastic syndromes (MDSs). Gene mutations involving mRNA splicing and epigenetic regulatory pathways induce inflammasome activation and myeloid lineage skewing in MDSs through undefined mechanisms. Using immortalized murine hematopoietic stem and progenitor cells harboring these somatic gene mutations and primary MDS BM specimens, we showed accumulation of unresolved R-loops and micronuclei with concurrent activation of the cytosolic sensor cyclic GMP-AMP synthase. Cyclic GMP-AMP synthase/stimulator of IFN genes (cGAS/STING) signaling caused ISG induction, NLRP3 inflammasome activation, and maturation of the effector protease caspase-1. Deregulation of RNA polymerase III drove cytosolic R-loop generation, which upon inhibition, extinguished ISG and inflammasome response. Mechanistically, caspase-1 degraded the master erythroid transcription factor, GATA binding protein 1, provoking anemia and myeloid lineage bias that was reversed by cGAS inhibition in vitro and in Tet2–/– hematopoietic stem and progenitor cell–transplanted mice. Together, these data identified a mechanism by which functionally distinct mutations converged upon the cGAS/STING/NLRP3 axis in MDS, directing ISG induction, pyroptosis, and myeloid lineage skewing.
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Affiliation(s)
- Amy F McLemore
- Department of Malignant Hematology, Moffitt Cancer Center & Research institute, Tampa, United States of America
| | - Hsin-An Hou
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Benjamin S Meyer
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States of America
| | - Nghi B Lam
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States of America
| | - Grace A Ward
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States of America
| | - Amy L Aldrich
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States of America
| | | | - Alexis Vedder
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States of America
| | - Ling Zhang
- Department of Hemapathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States of America
| | - Eric Padron
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States of America
| | - Nicole D Vincelette
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States of America
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, United States of America
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, United States of America
| | - Alan F List
- Precision Biosciences, Precision Biosciences, Durham, United States of America
| | - Kathy L McGraw
- Center for Cancer Research, National Cancer Institute, Bethesda, United States of America
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Badar T, Chlon T. Germline and Somatic Defects in DDX41 and its Impact on Myeloid Neoplasms. Curr Hematol Malig Rep 2022; 17:113-120. [PMID: 35781188 DOI: 10.1007/s11899-022-00667-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW While DDX41 mutation (m) is one of the most prevalent predisposition genes in adult myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML), most patients do not always present with a family history of MDS/AML. In this review, we will be highlighting epidemiological data on DDX41m, roles of DDX41 in oncogenesis, mechanisms of clonal evolution with somatic DDX41m, and clinical phenotypes and management of MDS/AML in patients harboring DDX41m. RECENT FINDINGS DDX41 encodes a DEAD-box helicase protein that is considered essential for cell growth and viability. High incidence of myeloid malignancies and other cancers in patients bearing DDX41m suggests that defects in DDX41 lead to loss of a tumor suppressor function, likely related to activities in RNA splicing and processing pathways. Seventy percent of cancer cases with DDX41m are associated with MDS/AML alone. More than 65% of familial cases harbor heterozygous germline frameshift mutations, of which p.D140Gfs*2 is the most common. A somatic DDX41m of the second allele is acquired in 70% of cases, leading to hematological malignancy. Myeloid neoplasms with DDX41m are typically characterized by long latency, high-risk disease at presentation with normal cytogenetics and without any additional molecular markers. Recent reports suggests that a subgroup of these patients have an indolent clinical course and have a better long-term survival compared to favorable or intermediate risk AML. Distinct clinical/pathologic features and favorable outcomes in MDS/AML highlight the need for standardized classification and gene specific guidelines that could assist in management decisions in patients with DDX41m.
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Affiliation(s)
- Talha Badar
- Division of Hematology & Medical Oncology, Mayo Clinic Cancer Center, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
| | - Timothy Chlon
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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Cristini A, Tellier M, Constantinescu F, Accalai C, Albulescu LO, Heiringhoff R, Bery N, Sordet O, Murphy S, Gromak N. RNase H2, mutated in Aicardi-Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation. Nat Commun 2022; 13:2961. [PMID: 35618715 PMCID: PMC9135716 DOI: 10.1038/s41467-022-30604-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
RNase H2 is a specialized enzyme that degrades RNA in RNA/DNA hybrids and deficiency of this enzyme causes a severe neuroinflammatory disease, Aicardi Goutières syndrome (AGS). However, the molecular mechanism underlying AGS is still unclear. Here, we show that RNase H2 is associated with a subset of genes, in a transcription-dependent manner where it interacts with RNA Polymerase II. RNase H2 depletion impairs transcription leading to accumulation of R-loops, structures that comprise RNA/DNA hybrids and a displaced DNA strand, mainly associated with short and intronless genes. Importantly, accumulated R-loops are processed by XPG and XPF endonucleases which leads to DNA damage and activation of the immune response, features associated with AGS. Consequently, we uncover a key role for RNase H2 in the transcription of human genes by maintaining R-loop homeostasis. Our results provide insight into the mechanistic contribution of R-loops to AGS pathogenesis.
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Affiliation(s)
- Agnese Cristini
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Flavia Constantinescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Clelia Accalai
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Laura Oana Albulescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Robin Heiringhoff
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Nicolas Bery
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Olivier Sordet
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037, Toulouse, France
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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Singh RS, Vidhyasagar V, Yang S, Arna AB, Yadav M, Aggarwal A, Aguilera AN, Shinriki S, Bhanumathy KK, Pandey K, Xu A, Rapin N, Bosch M, DeCoteau J, Xiang J, Vizeacoumar FJ, Zhou Y, Misra V, Matsui H, Ross SR, Wu Y. DDX41 is required for cGAS-STING activation against DNA virus infection. Cell Rep 2022; 39:110856. [PMID: 35613581 PMCID: PMC9205463 DOI: 10.1016/j.celrep.2022.110856] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 12/27/2022] Open
Abstract
Upon binding double-stranded DNA (dsDNA), cyclic GMP-AMP synthase (cGAS) is activated and initiates the cGAS-stimulator of IFN genes (STING)-type I interferon pathway. DEAD-box helicase 41 (DDX41) is a DEAD-box helicase, and mutations in DDX41 cause myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). Here, we show that DDX41-knockout (KO) cells have reduced type I interferon production after DNA virus infection. Unexpectedly, activations of cGAS and STING are affected in DDX41 KO cells, suggesting that DDX41 functions upstream of cGAS. The recombinant DDX41 protein exhibits ATP-dependent DNA-unwinding activity and ATP-independent strand-annealing activity. The MDS/AML-derived mutant R525H has reduced unwinding activity but retains normal strand-annealing activity and stimulates greater cGAS dinucleotide-synthesis activity than wild-type DDX41. Overexpression of R525H in either DDX41-deficient or -proficient cells results in higher type I interferon production. Our results have led to the hypothesis that DDX41 utilizes its unwinding and annealing activities to regulate the homeostasis of dsDNA and single-stranded DNA (ssDNA), which, in turn, regulates cGAS-STING activation. cGAS is activated by dsDNA. Singh et al. find DDX41 regulates cGAS activation through unwinding and annealing activities on dsDNA and ssDNA, respectively, and MDS/AML patient mutant R525H causes overactivation of innate immune response due to its unbalanced activities. This DDX41-cGAS-STING pathway may be related to molecular pathogenesis of MDS/AML.
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Affiliation(s)
- Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | | | - Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Manisha Yadav
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Aanchal Aggarwal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Alexya N Aguilera
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Satoru Shinriki
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Kannupriya Pandey
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Aizhang Xu
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - Noreen Rapin
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Mark Bosch
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - John DeCoteau
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Jim Xiang
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - Franco J Vizeacoumar
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada; Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Vikram Misra
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Susan R Ross
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada.
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RNPS1 inhibits excessive tumor necrosis factor/tumor necrosis factor receptor signaling to support hematopoiesis in mice. Proc Natl Acad Sci U S A 2022; 119:e2200128119. [PMID: 35482923 DOI: 10.1073/pnas.2200128119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceMessenger RNA (mRNA) splicing is fundamental to protein expression in mammals. Homozygous deletion of single protein components of the splicing machinery or its regulatory factors is embryonic lethal. However, through forward genetic screening in mice, we identified a viable hypomorphic missense mutation of the splicing regulator RNPS1. Homozygous mutant mice displayed altered immune cell development due to excessive tumor necrosis factor (TNF)-dependent immune cell apoptosis. Splicing was impaired in CD8+ T cells and hematopoietic stem cells from RNPS1 mutant mice. TNF knockout rescued hematopoiesis and dramatically reduced splicing defects in RNPS1 hematopoietic cells, demonstrating a surprising link between elevated TNF and defects in splicing caused by RNPS1 deficiency.
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40
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Brickner JR, Garzon JL, Cimprich KA. Walking a tightrope: The complex balancing act of R-loops in genome stability. Mol Cell 2022; 82:2267-2297. [PMID: 35508167 DOI: 10.1016/j.molcel.2022.04.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 12/14/2022]
Abstract
Although transcription is an essential cellular process, it is paradoxically also a well-recognized cause of genomic instability. R-loops, non-B DNA structures formed when nascent RNA hybridizes to DNA to displace the non-template strand as single-stranded DNA (ssDNA), are partially responsible for this instability. Yet, recent work has begun to elucidate regulatory roles for R-loops in maintaining the genome. In this review, we discuss the cellular contexts in which R-loops contribute to genomic instability, particularly during DNA replication and double-strand break (DSB) repair. We also summarize the evidence that R-loops participate as an intermediate during repair and may influence pathway choice to preserve genomic integrity. Finally, we discuss the immunogenic potential of R-loops and highlight their links to disease should they become pathogenic.
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Affiliation(s)
- Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jada L Garzon
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Ma J, Mahmud N, Bosland MC, Ross SR. DDX41 is needed for pre- and postnatal hematopoietic stem cell differentiation in mice. Stem Cell Reports 2022; 17:879-893. [PMID: 35303436 PMCID: PMC9023775 DOI: 10.1016/j.stemcr.2022.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
DDX41 is a tumor suppressor frequently mutated in human myeloid neoplasms, but whether it affects hematopoiesis is unknown. Using a knockout mouse, we demonstrate that DDX41 is required for mouse hematopoietic stem and progenitor cell (HSPC) survival and differentiation, particularly of myeloid lineage cells. Transplantation of Ddx41 knockout fetal liver and adult bone marrow (BM) cells was unable to rescue mice from lethal irradiation, and knockout stem cells were also defective in colony formation assays. RNA-seq analysis of Lin-/cKit+/Sca1+Ddx41 knockout cells from fetal liver demonstrated that the expression of many genes associated with hematopoietic differentiation were altered. Furthermore, differential splicing of genes involved in key biological processes was observed. Our data reveal a critical role for DDX41 in HSPC differentiation and myeloid progenitor development, likely through regulating gene expression programs and splicing.
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Affiliation(s)
- Jing Ma
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, 835 South Wolcott Avenue, E705 MSB (MC 790), Chicago, IL 60612, USA
| | - Nadim Mahmud
- Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Maarten C Bosland
- Department of Pathology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Susan R Ross
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, 835 South Wolcott Avenue, E705 MSB (MC 790), Chicago, IL 60612, USA.
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42
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Alecki C, Vera M. Role of Nuclear Non-Canonical Nucleic Acid Structures in Organismal Development and Adaptation to Stress Conditions. Front Genet 2022; 13:823241. [PMID: 35281835 PMCID: PMC8906566 DOI: 10.3389/fgene.2022.823241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
Over the last decades, numerous examples have involved nuclear non-coding RNAs (ncRNAs) in the regulation of gene expression. ncRNAs can interact with the genome by forming non-canonical nucleic acid structures such as R-loops or DNA:RNA triplexes. They bind chromatin and DNA modifiers and transcription factors and favor or prevent their targeting to specific DNA sequences and regulate gene expression of diverse genes. We review the function of these non-canonical nucleic acid structures in regulating gene expression of multicellular organisms during development and in response to different stress conditions and DNA damage using examples described in several organisms, from plants to humans. We also overview recent techniques developed to study where R-loops or DNA:RNA triplexes are formed in the genome and their interaction with proteins.
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Affiliation(s)
- Célia Alecki
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, QC, Canada
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43
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Shinriki S, Hirayama M, Nagamachi A, Yokoyama A, Kawamura T, Kanai A, Kawai H, Iwakiri J, Liu R, Maeshiro M, Tungalag S, Tasaki M, Ueda M, Tomizawa K, Kataoka N, Ideue T, Suzuki Y, Asai K, Tani T, Inaba T, Matsui H. DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells. Leukemia 2022; 36:2605-2620. [PMID: 36229594 PMCID: PMC9613458 DOI: 10.1038/s41375-022-01708-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
Abstract
Myeloid malignancies with DDX41 mutations are often associated with bone marrow failure and cytopenia before overt disease manifestation. However, the mechanisms underlying these specific conditions remain elusive. Here, we demonstrate that loss of DDX41 function impairs efficient RNA splicing, resulting in DNA replication stress with excess R-loop formation. Mechanistically, DDX41 binds to the 5' splice site (5'SS) of coding RNA and coordinates RNA splicing and transcriptional elongation; loss of DDX41 prevents splicing-coupled transient pausing of RNA polymerase II at 5'SS, causing aberrant R-loop formation and transcription-replication collisions. Although the degree of DNA replication stress acquired in S phase is small, cells undergo mitosis with under-replicated DNA being remained, resulting in micronuclei formation and significant DNA damage, thus leading to impaired cell proliferation and genomic instability. These processes may be responsible for disease phenotypes associated with DDX41 mutations.
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Affiliation(s)
- Satoru Shinriki
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
| | - Mayumi Hirayama
- grid.274841.c0000 0001 0660 6749Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Akiko Nagamachi
- grid.257022.00000 0000 8711 3200Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Akihiko Yokoyama
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Yamagata, Japan
| | - Takeshi Kawamura
- grid.26999.3d0000 0001 2151 536XIsotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Akinori Kanai
- grid.26999.3d0000 0001 2151 536XLaboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hidehiko Kawai
- grid.257022.00000 0000 8711 3200Department of Nucleic Acids Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Junichi Iwakiri
- grid.26999.3d0000 0001 2151 536XLaboratory of Genome Informatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Rin Liu
- grid.274841.c0000 0001 0660 6749Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Manabu Maeshiro
- grid.274841.c0000 0001 0660 6749Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Saruul Tungalag
- grid.274841.c0000 0001 0660 6749Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masayoshi Tasaki
- grid.274841.c0000 0001 0660 6749Department of Biomedical Laboratory Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Mitsuharu Ueda
- grid.274841.c0000 0001 0660 6749Department of Neurology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuhito Tomizawa
- grid.274841.c0000 0001 0660 6749Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Naoyuki Kataoka
- grid.26999.3d0000 0001 2151 536XLaboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Ideue
- grid.274841.c0000 0001 0660 6749Department of Biological Sciences, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Yutaka Suzuki
- grid.26999.3d0000 0001 2151 536XLaboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kiyoshi Asai
- grid.26999.3d0000 0001 2151 536XLaboratory of Genome Informatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tokio Tani
- grid.274841.c0000 0001 0660 6749Department of Biological Sciences, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Toshiya Inaba
- grid.257022.00000 0000 8711 3200Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
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R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun 2021; 12:7314. [PMID: 34916496 PMCID: PMC8677849 DOI: 10.1038/s41467-021-27530-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription poses a threat to genomic stability through the formation of R-loops that can obstruct progression of replication forks. R-loops are three-stranded nucleic acid structures formed by an RNA-DNA hybrid with a displaced non-template DNA strand. We developed RNA-DNA Proximity Proteomics to map the R-loop proximal proteome of human cells using quantitative mass spectrometry. We implicate different cellular proteins in R-loop regulation and identify a role of the tumor suppressor DDX41 in opposing R-loop and double strand DNA break accumulation in promoters. DDX41 is enriched in promoter regions in vivo, and can unwind RNA-DNA hybrids in vitro. R-loop accumulation upon loss of DDX41 is accompanied with replication stress, an increase in the formation of double strand DNA breaks and transcriptome changes associated with the inflammatory response. Germline loss-of-function mutations in DDX41 lead to predisposition to acute myeloid leukemia in adulthood. We propose that R-loop accumulation and genomic instability-associated inflammatory response may contribute to the development of familial AML with mutated DDX41.
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46
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Chlon TM, Stepanchick E, Hershberger CE, Daniels NJ, Hueneman KM, Kuenzi Davis A, Choi K, Zheng Y, Gurnari C, Haferlach T, Padgett RA, Maciejewski JP, Starczynowski DT. Germline DDX41 mutations cause ineffective hematopoiesis and myelodysplasia. Cell Stem Cell 2021; 28:1966-1981.e6. [PMID: 34473945 DOI: 10.1016/j.stem.2021.08.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/10/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022]
Abstract
DDX41 mutations are the most common germline alterations in adult myelodysplastic syndromes (MDSs). The majority of affected individuals harbor germline monoallelic frameshift DDX41 mutations and subsequently acquire somatic mutations in their other DDX41 allele, typically missense R525H. Hematopoietic progenitor cells (HPCs) with biallelic frameshift and R525H mutations undergo cell cycle arrest and apoptosis, causing bone marrow failure in mice. Mechanistically, DDX41 is essential for small nucleolar RNA (snoRNA) processing, ribosome assembly, and protein synthesis. Although monoallelic DDX41 mutations do not affect hematopoiesis in young mice, a subset of aged mice develops features of MDS. Biallelic mutations in DDX41 are observed at a low frequency in non-dominant hematopoietic stem cell clones in bone marrow (BM) from individuals with MDS. Mice chimeric for monoallelic DDX41 mutant BM cells and a minor population of biallelic mutant BM cells develop hematopoietic defects at a younger age, suggesting that biallelic DDX41 mutant cells are disease modifying in the context of monoallelic DDX41 mutant BM.
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Affiliation(s)
- Timothy M Chlon
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Emily Stepanchick
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Courtney E Hershberger
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Noah J Daniels
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Kathleen M Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ashley Kuenzi Davis
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44106, USA; Department of Biomedicine and Prevention & PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome, Tor Vergata, Rome, Italy
| | | | - Richard A Padgett
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45229, USA.
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Sugden WW, North TE. Making Blood from the Vessel: Extrinsic and Environmental Cues Guiding the Endothelial-to-Hematopoietic Transition. Life (Basel) 2021; 11:life11101027. [PMID: 34685398 PMCID: PMC8539454 DOI: 10.3390/life11101027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023] Open
Abstract
It is increasingly recognized that specialized subsets of endothelial cells carry out unique functions in specific organs and regions of the vascular tree. Perhaps the most striking example of this specialization is the ability to contribute to the generation of the blood system, in which a distinct population of “hemogenic” endothelial cells in the embryo transforms irreversibly into hematopoietic stem and progenitor cells that produce circulating erythroid, myeloid and lymphoid cells for the lifetime of an animal. This review will focus on recent advances made in the zebrafish model organism uncovering the extrinsic and environmental factors that facilitate hemogenic commitment and the process of endothelial-to-hematopoietic transition that produces blood stem cells. We highlight in particular biomechanical influences of hemodynamic forces and the extracellular matrix, metabolic and sterile inflammatory cues present during this developmental stage, and outline new avenues opened by transcriptomic-based approaches to decipher cell–cell communication mechanisms as examples of key signals in the embryonic niche that regulate hematopoiesis.
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Affiliation(s)
- Wade W. Sugden
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E. North
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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48
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Cargill M, Venkataraman R, Lee S. DEAD-Box RNA Helicases and Genome Stability. Genes (Basel) 2021; 12:1471. [PMID: 34680866 PMCID: PMC8535883 DOI: 10.3390/genes12101471] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 02/06/2023] Open
Abstract
DEAD-box RNA helicases are important regulators of RNA metabolism and have been implicated in the development of cancer. Interestingly, these helicases constitute a major recurring family of RNA-binding proteins important for protecting the genome. Current studies have provided insight into the connection between genomic stability and several DEAD-box RNA helicase family proteins including DDX1, DDX3X, DDX5, DDX19, DDX21, DDX39B, and DDX41. For each helicase, we have reviewed evidence supporting their role in protecting the genome and their suggested mechanisms. Such helicases regulate the expression of factors promoting genomic stability, prevent DNA damage, and can participate directly in the response and repair of DNA damage. Finally, we summarized the pathological and therapeutic relationship between DEAD-box RNA helicases and cancer with respect to their novel role in genome stability.
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Affiliation(s)
- Michael Cargill
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
| | - Rasika Venkataraman
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Stanley Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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50
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Wan Z, Han B. Clinical features of DDX41 mutation-related diseases: a systematic review with individual patient data. Ther Adv Hematol 2021; 12:20406207211032433. [PMID: 34349893 PMCID: PMC8287267 DOI: 10.1177/20406207211032433] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/25/2021] [Indexed: 01/19/2023] Open
Abstract
Background: DDX41 serves as a DNA sensor in innate immunity and mutated DDX41 is pathogenic, mainly for myeloid neoplasms. Methods: In this study, “DDX41” was searched in PubMed and Web of Science between 1 January 2015 and 29 April 2021 with individual-patient data seeking. A meta-analysis was not valid here due to the absence of a large dataset. Thirty articles were finally included in the qualitative analysis and 277 patients from 20 studies without overlap were involved in the quantitative summary. Results: Pooled incidence was 3.3% (95% confidence interval 2.4–4.2%) of unselected myeloid neoplasms. Patients with hematologic disorders harboring mutated DDX41 were featured as 80% males, median 66 (20–88) years old at diagnosis, 75% acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS), 64% with normal karyotype. Eighty-five percent of patients had germline variants which were nationally diverse and more of frameshift type, whereas 64% of patients had somatic DDX41 variants where p.R525H and missense dominated. ASXL1 and TP53 were the top frequent concomitant somatic mutations. Therapeutically, 70% overall response rate was obtained of hypomethylating agents in MDS, 96% complete remission of chemotherapy in AML, and 8% of relapse in hematopoietic stem cell transplant. Neither overall survival nor progression-free survival could be summed. Conclusions: Several significant clinical differences were observed in different diagnosis groups, familial and sporadic cases, and p.R525H compared with other somatic variants. In conclusion, myeloid neoplasms carrying DDX41 mutations were mainly older, male, MDS, and AML patients who had promising responses to treatment. Both germline and somatic DDX41 variants possessed unique characteristics and groups of interest presented certain differences worth further research. (CRD42021228886)
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Affiliation(s)
- Ziqi Wan
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Bing Han
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, 1#Shuaifuyuan, Dongcheng District, Beijing, 100730, China
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