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Fan J, Li Z, Pei L, Hou Y. Post-transcriptional regulation of DEAD-box RNA helicases in hematopoietic malignancies. Genes Dis 2024; 11:101252. [PMID: 38993792 PMCID: PMC11237855 DOI: 10.1016/j.gendis.2024.101252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 07/13/2024] Open
Abstract
Hematopoiesis represents a meticulously regulated and dynamic biological process. Genetic aberrations affecting blood cells, induced by various factors, frequently give rise to hematological tumors. These instances are often accompanied by a multitude of abnormal post-transcriptional regulatory events, including RNA alternative splicing, RNA localization, RNA degradation, and storage. Notably, post-transcriptional regulation plays a pivotal role in preserving hematopoietic homeostasis. The DEAD-Box RNA helicase genes emerge as crucial post-transcriptional regulatory factors, intricately involved in sustaining normal hematopoiesis through diverse mechanisms such as RNA alternative splicing, RNA modification, and ribosome assembly. This review consolidates the existing knowledge on the role of DEAD-box RNA helicases in regulating normal hematopoiesis and underscores the pathogenicity of mutant DEAD-Box RNA helicases in malignant hematopoiesis. Emphasis is placed on elucidating both the positive and negative contributions of DEAD-box RNA helicases within the hematopoietic system.
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Affiliation(s)
- Jiankun Fan
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zhigang Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Li Pei
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yu Hou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
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2
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Wu S, Sun X, Hua R, Hu C, Qin L. DDX21 functions as a potential novel oncopromoter in pancreatic ductal adenocarcinoma: a comprehensive analysis of the DExD box family. Discov Oncol 2024; 15:333. [PMID: 39095628 PMCID: PMC11297014 DOI: 10.1007/s12672-024-01204-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal tumor with an ill-defined pathogenesis. DExD box (DDX) family genes are widely distributed and involved in various RNA metabolism and cellular biogenesis; their dysregulation is associated with aberrant cellular processes and malignancies. However, the prognostic significance and expression patterns of the DDX family in PDAC are not fully understood. The present study aimed to explore the clinical value of DDX genes in PDAC. METHODS Differentially expressed DDX genes were identified. DDX genes related to prognostic signatures were further investigated using LASSO Cox regression analysis. DDX21 protein expression was analyzed using the UALCAN and human protein atlas (HPA) online tools and confirmed in 40 paired PDAC and normal tissues through Tissue Microarrays (TMA). The independent prognostic significance of DDX21 in PDAC was determined through the construction of nomogram models and calibration curves. The functional roles of DDX21 were investigated using gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). Cell proliferation, invasion, and migration were assessed using Cell Counting Kit-8, colony formation, Transwell, and wound healing assays. RESULTS Upregulation of genes related to prognostic signatures (DDX10, DDX21, DDX60, and DDX60L) was significantly associated with poor prognosis of patients with PDAC based on survival and recurrence time. Considering the expression profile and prognostic values of the signature-related genes, DDX21 was finally selected for further exploration. DDX21 was overexpressed significantly at both the mRNA and protein levels in PDAC compared to normal pancreatic tissues. DDX21 expression, pathological stage, and residual tumor were significant independent prognostic indicators in PDAC. Moreover, functional enrichment analysis revealed that Genes co-expressed with DDX21 are predominantly involved in RNA metabolism, helicase activity, ribosome biogenesis, cell cycle, and various cancer-related pathways, such as PI3K/Akt signaling pathway and TGF-β signaling pathway. Furthermore, in vitro experiments confirmed that the knockdown of DDX21 significantly reduced MIA PaCa-2 cell viability, proliferation, migration, and invasion. CONCLUSIONS Four signature-related genes could relatively precisely predict the prognosis of patients with PDAC. Specifically, DDX21 upregulation may signal an unfavorable prognosis by negatively affecting the biological properties of PDAC cells. DDX21 may be considered as a candidate therapeutic target in PDAC.
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Affiliation(s)
- Shaohan Wu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, No. 899, Pinghai Road, Suzhou, 215006, Jiangsu, China
- Department of General Surgery, the Second Affiliated Hospital of Jiaxing University, No. 1518, Huancheng North Road, Jiaxing, 314000, Zhejiang, China
| | - Xiaofang Sun
- Department of General Surgery, the Second Affiliated Hospital of Jiaxing University, No. 1518, Huancheng North Road, Jiaxing, 314000, Zhejiang, China
| | - Ruheng Hua
- Department of General Surgery, The First Affiliated Hospital of Soochow University, No. 899, Pinghai Road, Suzhou, 215006, Jiangsu, China
| | - Chundong Hu
- Department of General Surgery, the Second Affiliated Hospital of Jiaxing University, No. 1518, Huancheng North Road, Jiaxing, 314000, Zhejiang, China
| | - Lei Qin
- Department of General Surgery, The First Affiliated Hospital of Soochow University, No. 899, Pinghai Road, Suzhou, 215006, Jiangsu, China.
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3
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Lederbauer J, Das S, Piton A, Lessel D, Kreienkamp HJ. The role of DEAD- and DExH-box RNA helicases in neurodevelopmental disorders. Front Mol Neurosci 2024; 17:1414949. [PMID: 39149612 PMCID: PMC11324592 DOI: 10.3389/fnmol.2024.1414949] [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: 04/09/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024] Open
Abstract
Neurodevelopmental disorders (NDDs) represent a large group of disorders with an onset in the neonatal or early childhood period; NDDs include intellectual disability (ID), autism spectrum disorders (ASD), attention deficit hyperactivity disorders (ADHD), seizures, various motor disabilities and abnormal muscle tone. Among the many underlying Mendelian genetic causes for these conditions, genes coding for proteins involved in all aspects of the gene expression pathway, ranging from transcription, splicing, translation to the eventual RNA decay, feature rather prominently. Here we focus on two large families of RNA helicases (DEAD- and DExH-box helicases). Genetic variants in the coding genes for several helicases have recently been shown to be associated with NDD. We address genetic constraints for helicases, types of pathological variants which have been discovered and discuss the biological pathways in which the affected helicase proteins are involved.
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Affiliation(s)
- Johannes Lederbauer
- Institute of Human Genetics, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarada Das
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amelie Piton
- Department of Translational Medicine and Neurogenetics, Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Davor Lessel
- Institute of Human Genetics, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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4
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Olotu O, Koskenniemi AR, Ma L, Paramonov V, Laasanen S, Louramo E, Bourgery M, Lehtiniemi T, Laasanen S, Rivero-Müller A, Löyttyniemi E, Sahlgren C, Westermarck J, Ventelä S, Visakorpi T, Poutanen M, Vainio P, Mäkelä JA, Kotaja N. Germline-specific RNA helicase DDX4 forms cytoplasmic granules in cancer cells and promotes tumor growth. Cell Rep 2024; 43:114430. [PMID: 38963760 DOI: 10.1016/j.celrep.2024.114430] [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: 11/12/2023] [Revised: 05/15/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
Cancer cells undergo major epigenetic alterations and transcriptomic changes, including ectopic expression of tissue- and cell-type-specific genes. Here, we show that the germline-specific RNA helicase DDX4 forms germ-granule-like cytoplasmic ribonucleoprotein granules in various human tumors, but not in cultured cancer cells. These cancerous DDX4 complexes contain RNA-binding proteins and splicing regulators, including many known germ granule components. The deletion of DDX4 in cancer cells induces transcriptomic changes and affects the alternative splicing landscape of a number of genes involved in cancer growth and invasiveness, leading to compromised capability of DDX4-null cancer cells to form xenograft tumors in immunocompromised mice. Importantly, the occurrence of DDX4 granules is associated with poor survival in patients with head and neck squamous cell carcinoma and higher histological grade of prostate cancer. Taken together, these results show that the germ-granule-resembling cancerous DDX4 granules control gene expression and promote malignant and invasive properties of cancer cells.
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Affiliation(s)
- Opeyemi Olotu
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland
| | - Anna-Riina Koskenniemi
- Department of Pathology, Laboratory Division, Turku University Hospital and University of Turku, 20520 Turku, Finland
| | - Lin Ma
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland
| | - Valeriy Paramonov
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20500 Turku, Finland; Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Sini Laasanen
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland
| | - Elina Louramo
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland
| | - Matthieu Bourgery
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland; Centre for Population Health Research, Turku University Hospital and University of Turku, 20520 Turku, Finland
| | - Tiina Lehtiniemi
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland
| | - Samuli Laasanen
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Eliisa Löyttyniemi
- Department of Biostatistics, University of Turku and Turku University Hospital, 20520 Turku, Finland
| | - Cecilia Sahlgren
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20500 Turku, Finland; Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Jukka Westermarck
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland; Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Sami Ventelä
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department for Otorhinolaryngology, Head, and Neck Surgery, University of Turku and Turku University Hospital, 20520 Turku, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, 33520 Tampere, Finland; Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Matti Poutanen
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland; Turku Center for Disease Modeling, University of Turku, 20520 Turku, Finland; FICAN West Cancer Center, University of Turku, Turku University Hospital, 20500 Turku, Finland
| | - Paula Vainio
- Department of Pathology, Laboratory Division, Turku University Hospital and University of Turku, 20520 Turku, Finland
| | - Juho-Antti Mäkelä
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland
| | - Noora Kotaja
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, 20520 Turku, Finland.
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Yoshioka D, Nakamura T, Kubota Y, Takekawa M. Formation of the NLRP3 inflammasome inhibits stress granule assembly by multiple mechanisms. J Biochem 2024; 175:629-641. [PMID: 38299728 PMCID: PMC11155693 DOI: 10.1093/jb/mvae009] [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: 12/18/2023] [Revised: 01/21/2024] [Accepted: 01/30/2024] [Indexed: 02/02/2024] Open
Abstract
Proper regulation of cellular response to environmental stress is crucial for maintaining biological homeostasis and is achieved by the balance between cell death processes, such as the formation of the pyroptosis-inducing NLRP3 inflammasome, and pro-survival processes, such as stress granule (SG) assembly. However, the functional interplay between these two stress-responsive organelles remains elusive. Here, we identified DHX33, a viral RNA sensor for the NLRP3 inflammasome, as a SG component, and the SG-nucleating protein G3BP as an NLRP3 inflammasome component. We also found that a decrease in intracellular potassium (K+) concentration, a key 'common' step in NLRP3 inflammasome activation, markedly inhibited SG assembly. Therefore, when macrophages are exposed to stress stimuli with the potential to induce both SGs and the NLRP3 inflammasome, such as cytoplasmic poly(I:C) stimulation, they preferentially form the NLRP3 inflammasome but avoid SG assembly by sequestering G3BP into the inflammasome and by inducing a reduction in intracellular K+ levels. Thus, under such conditions, DHX33 is primarily utilized as a viral RNA sensor for the inflammasome. Our data reveal the functional crosstalk between NLRP3 inflammasome-mediated pyroptosis and SG-mediated cell survival pathways and delineate a molecular mechanism that regulates cell-fate decisions and anti-viral innate immunity under stress.
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Affiliation(s)
- Daisuke Yoshioka
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Takanori Nakamura
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuji Kubota
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Mutsuhiro Takekawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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6
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Sy VT, Boone EC, Xiao H, Vierling MM, Schmitz SF, Ung Q, Trawick SS, Hammond TM, Shiu PKT. A DEAD-box RNA helicase mediates meiotic silencing by unpaired DNA. G3 (BETHESDA, MD.) 2023; 13:jkad083. [PMID: 37052947 PMCID: PMC10411587 DOI: 10.1093/g3journal/jkad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023]
Abstract
During the sexual phase of Neurospora crassa, unpaired genes are subject to a silencing mechanism known as meiotic silencing by unpaired DNA (MSUD). MSUD targets the transcripts of an unpaired gene and utilizes typical RNA interference factors for its process. Using a reverse genetic screen, we have identified a meiotic silencing gene called sad-9, which encodes a DEAD-box RNA helicase. While not essential for vegetative growth, SAD-9 plays a crucial role in both sexual development and MSUD. Our results suggest that SAD-9, with the help of the SAD-2 scaffold protein, recruits the SMS-2 Argonaute to the perinuclear region, the center of MSUD activity.
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Affiliation(s)
- Victor T Sy
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Erin C Boone
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Hua Xiao
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Michael M Vierling
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Shannon F Schmitz
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Quiny Ung
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Sterling S Trawick
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Patrick K T Shiu
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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7
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Therapeutic targeting of eukaryotic initiation factor (eIF) 4E. Biochem Soc Trans 2023; 51:113-124. [PMID: 36661272 DOI: 10.1042/bst20220285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/21/2023]
Abstract
Fundamental studies unraveled the role of eukaryotic initiation factor (eIF) 4E in mRNA translation and its control. Under physiological conditions, regulation of translation by eIF4E is essential to cellular homeostasis. Under stress, gene flow information is parsed by eIF4E to support adaptive mechanisms that favor cell survival. Dysregulated eIF4E activity fuels tumor formation and progression and modulates response to therapy. Thus, there has been heightened interest in understanding eIF4E function in controlling gene expression as well as developing strategies to block its activity to treat disease.
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8
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Helwer R, Charette JM. The SSU Processome Component Utp25p is a Pseudohelicase. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000606. [PMID: 36212518 PMCID: PMC9539457 DOI: 10.17912/micropub.biology.000606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/19/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022]
Abstract
RNA helicases are involved in nearly all aspects of RNA metabolism and factor prominently in ribosome assembly. The SSU processome includes 10 helicases and many helicase-cofactors. Together, they mediate the structural rearrangements that occur as part of ribosomal SSU assembly. During the identification of the SSU processome component Utp25/Def, it was noticed that the protein displays some sequence similarity to DEAD-box RNA helicases and is essential for growth. Interestingly, mutational ablation showed that Utp25's DEAD-box motifs are dispensable. Here, we show that the Utp25 AlphaFold prediction displays considerable structural similarity to DEAD-box helicases and is the first fully validated pseudohelicase.
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Affiliation(s)
- Rafe Helwer
- Department of Chemistry, Brandon University, Brandon, Manitoba, Canada.
,
Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
,
CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - J. Michael Charette
- Department of Chemistry, Brandon University, Brandon, Manitoba, Canada.
,
Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
,
CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada.
,
Correspondence to: J. Michael Charette (
)
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Secchi M, Lodola C, Garbelli A, Bione S, Maga G. DEAD-Box RNA Helicases DDX3X and DDX5 as Oncogenes or Oncosuppressors: A Network Perspective. Cancers (Basel) 2022; 14:cancers14153820. [PMID: 35954483 PMCID: PMC9367324 DOI: 10.3390/cancers14153820] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The transformation of a normal cell into a cancerous one is caused by the deregulation of different metabolic pathways, involving a complex network of protein–protein interactions. The cellular enzymes DDX3X and DDX5 play important roles in the maintenance of normal cell metabolism, but their deregulation can accelerate tumor transformation. Both DDX3X and DDX5 interact with hundreds of different cellular proteins, and depending on the specific pathways in which they are involved, both proteins can either act as suppressors of cancer or as oncogenes. In this review, we summarize the current knowledge about the roles of DDX3X and DDX5 in different tumors. In addition, we present a list of interacting proteins and discuss the possible contribution of some of these protein–protein interactions in determining the roles of DDX3X and DDX5 in the process of cancer proliferation, also suggesting novel hypotheses for future studies. Abstract RNA helicases of the DEAD-box family are involved in several metabolic pathways, from transcription and translation to cell proliferation, innate immunity and stress response. Given their multiple roles, it is not surprising that their deregulation or mutation is linked to different pathological conditions, including cancer. However, while in some cases the loss of function of a given DEAD-box helicase promotes tumor transformation, indicating an oncosuppressive role, in other contexts the overexpression of the same enzyme favors cancer progression, thus acting as a typical oncogene. The roles of two well-characterized members of this family, DDX3X and DDX5, as both oncogenes and oncosuppressors have been documented in several cancer types. Understanding the interplay of the different cellular contexts, as defined by the molecular interaction networks of DDX3X and DDX5 in different tumors, with the cancer-specific roles played by these proteins could help to explain their apparently conflicting roles as cancer drivers or suppressors.
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