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He L, Yang J, Hao Y, Yang X, Shi X, Zhang D, Zhao D, Yan W, Bie X, Chen L, Chen G, Zhao S, Liu X, Zheng H, Zhang K. DDX20: A Multifunctional Complex Protein. Molecules 2023; 28:7198. [PMID: 37894677 PMCID: PMC10608988 DOI: 10.3390/molecules28207198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/18/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
DEAD-box decapping enzyme 20 (DDX20) is a putative RNA-decapping enzyme that can be identified by the conserved motif Asp-Glu-Ala-Asp (DEAD). Cellular processes involve numerous RNA secondary structure alterations, including translation initiation, nuclear and mitochondrial splicing, and assembly of ribosomes and spliceosomes. DDX20 reportedly plays an important role in cellular transcription and post-transcriptional modifications. On the one hand, DDX20 can interact with various transcription factors and repress the transcriptional process. On the other hand, DDX20 forms the survival motor neuron complex and participates in the assembly of snRNP, ultimately affecting the RNA splicing process. Finally, DDX20 can potentially rely on its RNA-unwinding enzyme function to participate in microRNA (miRNA) maturation and act as a component of the RNA-induced silencing complex. In addition, although DDX20 is not a key component in the innate immune system signaling pathway, it can affect the nuclear factor kappa B (NF-κB) and p53 signaling pathways. In particular, DDX20 plays different roles in tumorigenesis development through the NF-κB signaling pathway. This process is regulated by various factors such as miRNA. DDX20 can influence processes such as viral replication in cells by interacting with two proteins in Epstein-Barr virus and can regulate the replication process of several viruses through the innate immune system, indicating that DDX20 plays an important role in the innate immune system. Herein, we review the effects of DDX20 on the innate immune system and its role in transcriptional and post-transcriptional modification processes, based on which we provide an outlook on the future of DDX20 research in innate immunity and viral infections.
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Affiliation(s)
- Lu He
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Jinke Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Yu Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Xing Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Xijuan Shi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Dajun Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Dengshuai Zhao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Wenqian Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Xintian Bie
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Lingling Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Guohui Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Siyue Zhao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Xiangtao Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Keshan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
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Pánek J, Roithová A, Radivojević N, Sýkora M, Prusty AB, Huston N, Wan H, Pyle AM, Fischer U, Staněk D. The SMN complex drives structural changes in human snRNAs to enable snRNP assembly. Nat Commun 2023; 14:6580. [PMID: 37852981 PMCID: PMC10584915 DOI: 10.1038/s41467-023-42324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Spliceosomal snRNPs are multicomponent particles that undergo a complex maturation pathway. Human Sm-class snRNAs are generated as 3'-end extended precursors, which are exported to the cytoplasm and assembled together with Sm proteins into core RNPs by the SMN complex. Here, we provide evidence that these pre-snRNA substrates contain compact, evolutionarily conserved secondary structures that overlap with the Sm binding site. These structural motifs in pre-snRNAs are predicted to interfere with Sm core assembly. We model structural rearrangements that lead to an open pre-snRNA conformation compatible with Sm protein interaction. The predicted rearrangement pathway is conserved in Metazoa and requires an external factor that initiates snRNA remodeling. We show that the essential helicase Gemin3, which is a component of the SMN complex, is crucial for snRNA structural rearrangements during snRNP maturation. The SMN complex thus facilitates ATP-driven structural changes in snRNAs that expose the Sm site and enable Sm protein binding.
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Affiliation(s)
- Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.
| | - Adriana Roithová
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Regulation of Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Nenad Radivojević
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sýkora
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Nicholas Huston
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
- Department of Chemistry, Yale University, New Haven, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic.
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Wang G, He X, Dai H, Lin L, Cao W, Fu Y, Diao W, Ding M, Zhang Q, Chen W, Guo H. WDR4 promotes the progression and lymphatic metastasis of bladder cancer via transcriptional down-regulation of ARRB2. Oncogenesis 2023; 12:47. [PMID: 37783676 PMCID: PMC10545698 DOI: 10.1038/s41389-023-00493-z] [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: 04/25/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
Lymph node (LN) metastasis is one of the key prognostic factors in bladder cancer, but its underlying mechanisms remain unclear. Here, we found that elevated expression of WD repeat domain 4 (WDR4) in bladder cancer correlated with worse prognosis. WDR4 can promote the LN metastasis and proliferation of bladder cancer cells. Mechanistic studies showed that WDR4 can promote the nuclear localization of DEAD-box helicase 20 (DDX20) and act as an adaptor to bind DDX20 and Early growth response 1 (Egr1), thereby inhibiting Egr1-promoted transcriptional expression of arrestin beta 2 (ARRB2) and ultimately contributing to the progression of bladder cancer. Immunohistochemical analysis confirmed that WDR4 expression is also an independent predictor of LN metastasis in bladder cancer. Our results reveal a novel mechanism of LN metastasis and progression in bladder cancer and identify WDR4 as a potential therapeutic target for metastatic bladder cancer.
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Affiliation(s)
- Guoli Wang
- Department of Urology, Nanjing Drum Tower Hospital, Clinical College of Nanjing University of Chinese Medicine, Nanjing, 210008, China
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Xin He
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Huiqi Dai
- Department of Urology, Nanjing Drum Tower Hospital, Clinical College of Nanjing University of Chinese Medicine, Nanjing, 210008, China
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Lingyi Lin
- Department of Urology, Nanjing Drum Tower Hospital, Clinical College of Nanjing University of Chinese Medicine, Nanjing, 210008, China
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Wenmin Cao
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Yao Fu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Wenli Diao
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Meng Ding
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Qing Zhang
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China.
| | - Wei Chen
- Department of Urology, Nanjing Drum Tower Hospital, Clinical College of Nanjing University of Chinese Medicine, Nanjing, 210008, China.
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China.
| | - Hongqian Guo
- Department of Urology, Nanjing Drum Tower Hospital, Clinical College of Nanjing University of Chinese Medicine, Nanjing, 210008, China.
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, 210008, China.
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Miralles MP, Sansa A, Beltran M, Soler RM, Garcera A. Survival motor neuron protein and neurite degeneration are regulated by Gemin3 in spinal muscular atrophy motoneurons. Front Cell Neurosci 2022; 16:1054270. [PMID: 36619669 PMCID: PMC9813745 DOI: 10.3389/fncel.2022.1054270] [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: 09/26/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a genetic neuromuscular disorder caused by reduction of the ubiquitously expressed protein Survival Motor Neuron (SMN). Low levels of SMN impact on spinal cord motoneurons (MNs) causing their degeneration and progressive muscle weakness and atrophy. To study the molecular mechanisms leading to cell loss in SMN-reduced MNs, we analyzed the NF-κB intracellular pathway in SMA models. NF-κB pathway activation is required for survival and regulates SMN levels in cultured MNs. Here we describe that NF-κB members, inhibitor of kappa B kinase beta (IKKβ), and RelA, were reduced in SMA mouse and human MNs. In addition, we observed that Gemin3 protein level was decreased in SMA MNs, but not in non-neuronal SMA cells. Gemin3 is a core member of the SMN complex responsible for small nuclear ribonucleoprotein biogenesis, and it regulates NF-κB activation through the mitogen-activated protein kinase TAK1. Our experiments showed that Gemin3 knockdown reduced SMN, IKKβ, and RelA protein levels, and caused significant neurite degeneration. Overexpression of SMN increased Gemin3 protein in SMA MNs, but did not prevent neurite degeneration in Gemin3 knockdown cells. These data indicated that Gemin3 reduction may contribute to cell degeneration in SMA MNs.
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Yao C, Sun Y, Zhang Z, Jia X, Zou P, Wang Y. Integration of RNAi and RNA-seq uncovers the regulation mechanism of DDX20 on vitellogenin expression in Scylla paramamosain. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101028. [PMID: 36244220 DOI: 10.1016/j.cbd.2022.101028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022]
Abstract
Vitellogenesis in crustaceans is controlled by several steroid hormones. In humans, the expression of SF-1, a gene that regulates gonadal development and the synthesis of steroid hormones, is affected by DDX20. However, how the homologous gene FTZ-F1 is regulated by DDX20 and its association with vitellogenesis remains unknown in the mud crab Scylla paramamosain. In this study, SpDDX20 and SpFTZ-F1 were identified in the transcriptome of mature ovarian tissue from the mud crab. qRT-PCR results revealed that the expression levels of SpFTZ-F1 and SpVTG in the ovaries of crab in the experimental group injected with dsDDX20 (EO) were significantly higher (P < 0.05) than those in the negative control group injected with dsEGFP (NO) and the blank control group injected with SPSS (BO). The differentially expressed genes (DEGs) identified by comparative transcriptome analysis of the EO group and NO group were enriched into five pathways related to ovarian steroidogenesis. The expression of CYP17, CYP3A4, CYP1A1 and 3β-HSD were up-regulated in pathways related to steroid hormone production and biosynthesis. The expression of the INSR, IRS and PI3K genes in the insulin signaling pathway were significantly increased (P < 0.05). The expression level of the TGF-β gene was up-regulated (P < 0.05) in the transforming growth factor pathway, whereas the expression level of the Smad2 gene was down-regulated (P < 0.05). The expression of GnRHR, GS, AC and PKA genes in the gonadotropin-releasing hormone signaling pathway were up-regulated. Our data provide a foundation for investigating the relationship between DDX20 and FTZ-F1 in the regulation of vitellogenin expression in S. paramamosain.
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Affiliation(s)
- Chengjie Yao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Yulong Sun
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziping Zhang
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiwei Jia
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Pengfei Zou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China.
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Kowalczyk M, Kowalczyk E, Gogolewska M, Skrzypek M, Talarowska M, Majsterek I, Poplawski T, Kwiatkowski P, Sienkiewicz M. Association of polymorphic variants in GEMIN genes with the risk of depression in a Polish population. PeerJ 2022; 10:e14317. [PMID: 36405016 PMCID: PMC9673762 DOI: 10.7717/peerj.14317] [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: 05/23/2022] [Accepted: 10/09/2022] [Indexed: 11/16/2022] Open
Abstract
Background The role of miRNA in depression is widely described by many researchers. miRNA is a final product of many genes involved in its formation (maturation). One of the final steps in the formation of miRNAs is the formation of the RISC complex, called the RNA-induced silencing complex, which includes, among others, GEMIN proteins. Single-nucleotide polymorphisms (SNPs) may lead to disturbance of miRNA biogenesis and function. The objective of our research was to assess the relationship between the appearance of depression and single nucleotide polymorphisms in the GEMIN3 (rs197388) and GEMIN4 (rs7813; rs3744741) genes. Our research provides new knowledge on the genetic factors that influence the risk of depression. They can be used as an element of diagnostics helpful in identifying people at increased risk, as well as indicating people not at risk of depression. Methods A total of 218 participants were examined, including individuals with depressive disorders (n = 102; study group) and healthy people (n = 116, control group). All the patients in the study group and the people in the control group were non-related native Caucasian Poles from central Poland. Blood was collected from study and control groups in order to assess the SNPs of GEMIN genes. Results An analysis of the results obtained showed that in patient population, the risk of depression is almost doubled by polymorphic variants of the genes: rs197388/GEMIN3 genotype A/A in the recessive model and rs3744741/GEMIN4 genotype T/T, codominant and recessive model. The dual role of rs7813/GEMIN4 is noteworthy, where the G/A genotype in the codominant and over dominant model protects against depression.
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Affiliation(s)
| | - Edward Kowalczyk
- Department of Pharmacology and Toxicology, Medical University of Lodz, Lodz, Poland
| | - Monika Gogolewska
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Maciej Skrzypek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Monika Talarowska
- Department of Clinical Psychology and Psychopathology, University of Lodz, Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Tomasz Poplawski
- Department of Microbiology and Pharmaceutical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Paweł Kwiatkowski
- Department of Diagnostic Immunology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Monika Sienkiewicz
- Department of Pharmaceutical Microbiology and Microbiological Diagnostic, Medical University of Lodz, Lodz, Poland
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A Macrophage Differentiation-Mediated Gene: DDX20 as a Molecular Biomarker Encompassing the Tumor Microenvironment, Disease Staging, and Prognoses in Hepatocellular Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9971776. [PMID: 36246406 PMCID: PMC9556188 DOI: 10.1155/2022/9971776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/03/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022]
Abstract
Background DDX20 involves the mechanism of cell proliferate, mitogenic Ets transcriptional suppressor (METS), which can arrest the cell cycle of macrophages. However, little is known about DDX20 expression, clinical values, and the relationship with tumor microenvironment in HCC. Methods We mined the transcriptional, protein expression and survival data of DDX20 in HCC from online databases. The immunological effects of DDX20 were estimated by bioinformatic algorithms. The RNAi and CRISPR screening were used to assess the gene effect of DDX20 for the EGFR gene in liver tumor cell. Results We found that the DDX20 was highly expressed in HCC. The qRT-PCR result shows a significantly upregulated DDX20 expression in HCC samples from the West China Hospital. The high mRNA expression of DDX20 is associated with a poor survival. DDX20 expression is positively correlated with MDSCs in HCC tissues. Moreover, DDX20 has a high predicted ability for the response to immunotherapy. Furthermore, hsa-mir-324-5p could regulate the macrophage differentiation by interacting with DDX20. Meanwhile, the EGFR gene gets a high dependency score for DDX20. Conclusion In sum, DDX20 may serve as a prognostic marker for worse clinical outcomes with HCC and potentially enable more precise and personalized immunotherapeutic strategies in the future.
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Bizen N, Bepari AK, Zhou L, Abe M, Sakimura K, Ono K, Takebayashi H. Ddx20, an Olig2 binding factor, governs the survival of neural and oligodendrocyte progenitor cells via proper Mdm2 splicing and p53 suppression. Cell Death Differ 2022; 29:1028-1041. [PMID: 34974536 PMCID: PMC9090832 DOI: 10.1038/s41418-021-00915-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/05/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Olig2 is indispensable for motoneuron and oligodendrocyte fate-specification in the pMN domain of embryonic spinal cords, and also involved in the proliferation and differentiation of several cell types in the nervous system, including neural progenitor cells (NPCs) and oligodendrocytes. However, how Olig2 controls these diverse biological processes remains unclear. Here, we demonstrated that a novel Olig2-binding protein, DEAD-box helicase 20 (Ddx20), is indispensable for the survival of NPCs and oligodendrocyte progenitor cells (OPCs). A central nervous system (CNS)-specific Ddx20 conditional knockout (cKO) demonstrated apoptosis and cell cycle arrest in NPCs and OPCs, through the potentiation of the p53 pathway in DNA damage-dependent and independent manners, including SMN complex disruption and the abnormal splicing of Mdm2 mRNA. Analyzes of Olig2 null NPCs showed that Olig2 contributed to NPC proliferation through Ddx20 protein stabilization. Our findings provide novel mechanisms underlying the Olig2-mediated proliferation of NPCs, via the Ddx20-p53 axis, in the embryonic CNS.
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Affiliation(s)
- Norihisa Bizen
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Asim K Bepari
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Li Zhou
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan.,Center for Coordination of Research Facilities (CCRF), Niigata University, Niigata, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan.,Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan.,Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Katsuhiko Ono
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan. .,Center for Coordination of Research Facilities (CCRF), Niigata University, Niigata, Japan.
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Construction, Identification and Analysis of the Interaction Network of African Swine Fever Virus MGF360-9L with Host Proteins. Viruses 2021; 13:v13091804. [PMID: 34578385 PMCID: PMC8473002 DOI: 10.3390/v13091804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 12/24/2022] Open
Abstract
African swine fever virus (ASFV) is prevalent in many countries and is a contagious and lethal virus that infects pigs, posing a threat to the global pig industry and public health. The interaction between the virus and the host is key to unlocking the mystery behind viral pathogenesis. A comprehensive understanding of the viral and host protein interaction may provide clues for developing new antiviral strategies. Here, we show a network of ASFV MGF360-9L protein interactions in porcine kidney (PK-15) cells. Overall, 268 proteins that interact with MGF360-9L are identified using immunoprecipitation and liquid chromatography–mass spectrometry (LC-MS). Accordingly, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted, and the protein–protein interaction (PPI) network was created. It was speculated that the cellular proteins interacting with MGF360-9L are involved in protein binding, metabolism, and the innate immune response. Proteasome subunit alpha type (PSMA3), 26S protease regulatory subunit 4 (PSMC1), autophagy and beclin 1 regulator 1 (AMBRA1), and DEAD-box helicase 20 (DDX20) could interact with MGF360-9L in vitro. PSMA3 and PSMC1 overexpression significantly promoted ASFV replication, and MGF360-9L maintained the transcriptional level of PSMA3 and PSMC1. Here, we show the interaction between ASFV MGF360-9L and cellular proteins and elucidate the virus–host interaction network, which effectively provides useful protein-related information that can enable further study of the potential mechanism and pathogenesis of ASFV infection.
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Motyl AAL, Faller KME, Groen EJN, Kline RA, Eaton SL, Ledahawsky LM, Chaytow H, Lamont DJ, Wishart TM, Huang YT, Gillingwater TH. Pre-natal manifestation of systemic developmental abnormalities in spinal muscular atrophy. Hum Mol Genet 2021; 29:2674-2683. [PMID: 32644120 PMCID: PMC7530529 DOI: 10.1093/hmg/ddaa146] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 02/02/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease caused by mutations in survival motor neuron 1 (SMN1). SMN-restoring therapies have recently emerged; however, preclinical and clinical studies revealed a limited therapeutic time window and systemic aspects of the disease. This raises a fundamental question of whether SMA has presymptomatic, developmental components to disease pathogenesis. We have addressed this by combining micro-computed tomography (μCT) and comparative proteomics to examine systemic pre-symptomatic changes in a prenatal mouse model of SMA. Quantitative μCT analyses revealed that SMA embryos were significantly smaller than littermate controls, indicative of general developmental delay. More specifically, cardiac ventricles were smaller in SMA hearts, whilst liver and brain remained unaffected. In order to explore the molecular consequences of SMN depletion during development, we generated comprehensive, high-resolution, proteomic profiles of neuronal and non-neuronal organs in SMA mouse embryos. Significant molecular perturbations were observed in all organs examined, highlighting tissue-specific prenatal molecular phenotypes in SMA. Together, our data demonstrate considerable systemic changes at an early, presymptomatic stage in SMA mice, revealing a significant developmental component to SMA pathogenesis.
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Affiliation(s)
- Anna A L Motyl
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Kiterie M E Faller
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Ewout J N Groen
- UMC Utrecht Brain Center, University Medical Center, Utrecht 3584 CG, The Netherlands
| | - Rachel A Kline
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH16 4SB, UK.,The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Samantha L Eaton
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH16 4SB, UK.,The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Leire M Ledahawsky
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Helena Chaytow
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Douglas J Lamont
- FingerPrints Proteomics Facility, University of Dundee, DD1 5EH, UK
| | - Thomas M Wishart
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH16 4SB, UK.,The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Yu-Ting Huang
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Thomas H Gillingwater
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH16 4SB, UK
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11
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Chong LC, Gandhi G, Lee JM, Yeo WWY, Choi SB. Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. Int J Mol Sci 2021; 22:8962. [PMID: 34445667 PMCID: PMC8396480 DOI: 10.3390/ijms22168962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/27/2021] [Indexed: 01/02/2023] Open
Abstract
Spinal muscular atrophy (SMA), one of the leading inherited causes of child mortality, is a rare neuromuscular disease arising from loss-of-function mutations of the survival motor neuron 1 (SMN1) gene, which encodes the SMN protein. When lacking the SMN protein in neurons, patients suffer from muscle weakness and atrophy, and in the severe cases, respiratory failure and death. Several therapeutic approaches show promise with human testing and three medications have been approved by the U.S. Food and Drug Administration (FDA) to date. Despite the shown promise of these approved therapies, there are some crucial limitations, one of the most important being the cost. The FDA-approved drugs are high-priced and are shortlisted among the most expensive treatments in the world. The price is still far beyond affordable and may serve as a burden for patients. The blooming of the biomedical data and advancement of computational approaches have opened new possibilities for SMA therapeutic development. This article highlights the present status of computationally aided approaches, including in silico drug repurposing, network driven drug discovery as well as artificial intelligence (AI)-assisted drug discovery, and discusses the future prospects.
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Affiliation(s)
- Li Chuin Chong
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Kuala Lumpur 50490, Malaysia; (L.C.C.); (J.M.L.)
| | - Gayatri Gandhi
- Perdana University Graduate School of Medicine, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Kuala Lumpur 50490, Malaysia; (G.G.); (W.W.Y.Y.)
| | - Jian Ming Lee
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Kuala Lumpur 50490, Malaysia; (L.C.C.); (J.M.L.)
| | - Wendy Wai Yeng Yeo
- Perdana University Graduate School of Medicine, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Kuala Lumpur 50490, Malaysia; (G.G.); (W.W.Y.Y.)
| | - Sy-Bing Choi
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Kuala Lumpur 50490, Malaysia; (L.C.C.); (J.M.L.)
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12
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Simankova A, Bizen N, Saitoh S, Shibata S, Ohno N, Abe M, Sakimura K, Takebayashi H. Ddx20, DEAD box helicase 20, is essential for the differentiation of oligodendrocyte and maintenance of myelin gene expression. Glia 2021; 69:2559-2574. [PMID: 34231259 DOI: 10.1002/glia.24058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022]
Abstract
Oligodendrocytes form myelin sheaths that surround axons, contributing to saltatory conduction and proper central nervous system (CNS) function. Oligodendrocyte progenitor cells (OPCs) are generated during the embryonic stage and differentiate into myelinating oligodendrocytes postnatally. Ddx20 is a multifunctional, DEAD-box helicase involved in multiple cellular processes, including transcription, splicing, microRNA biogenesis, and translation. Although defects in each of these processes result in abnormal oligodendrocyte differentiation and myelination, the involvement of Ddx20 in oligodendrocyte terminal differentiation remains unknown. To address this question, we used Mbp-Cre mice to generate Ddx20 conditional knockout (cKO) mice to allow for the deletion of Ddx20 from mature oligodendrocytes. Mbp-Cre;Ddx20 cKO mice demonstrated small body sizes, behavioral abnormalities, muscle weakness, and short lifespans, with mortality by the age of 2 months old. Histological analyses demonstrated significant reductions in the number of mature oligodendrocytes and drastic reductions in the expression levels of myelin-associated mRNAs, such as Mbp and Plp at postnatal day 42. The number of OPCs did not change. A thin myelin layer was observed for large-diameter axons in Ddx20 cKO mice, based on electron microscopic analysis. A bromodeoxyuridine (BrdU) labeling experiment demonstrated that terminal differentiation was perturbed from ages 2 weeks to 7 weeks in the CNS of Mbp-Cre;Ddx20 cKO mice. The activation of mitogen-activated protein (MAP) kinase, which promotes myelination, was downregulated in the Ddx20 cKO mice based on immunohistochemical detection. These results indicate that Ddx20 is an essential factor for terminal differentiation of oligodendrocytes and maintenance of myelin gene expression.
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Affiliation(s)
- Anna Simankova
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Norihisa Bizen
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Sei Saitoh
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Biomedical Molecular Sciences (Anatomy II), Fujita Health University School of Medicine, Toyoake, Japan
| | - Shinsuke Shibata
- Division of Microscopic Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan.,Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Center for Coordination of Research Facilities, Niigata University, Niigata, Japan
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13
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Li Y, Shen QS, Peng Q, Ding W, Zhang J, Zhong X, An NA, Ji M, Zhou WZ, Li CY. Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. Brief Bioinform 2021; 22:6273384. [PMID: 33973996 PMCID: PMC8574621 DOI: 10.1093/bib/bbab157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/22/2021] [Accepted: 04/04/2021] [Indexed: 11/26/2022] Open
Abstract
Rhesus macaque is a unique nonhuman primate model for human evolutionary and translational study, but the error-prone gene models critically limit its applications. Here, we de novo defined full-length macaque gene models based on single molecule, long-read transcriptome sequencing in four macaque tissues (frontal cortex, cerebellum, heart and testis). Overall, 8 588 227 poly(A)-bearing complementary DNA reads with a mean length of 14 106 nt were generated to compile the backbone of macaque transcripts, with the fine-scale structures further refined by RNA sequencing and cap analysis gene expression sequencing data. In total, 51 605 macaque gene models were accurately defined, covering 89.7% of macaque or 75.7% of human orthologous genes. Based on the full-length gene models, we performed a human–macaque comparative analysis on polyadenylation (PA) regulation. Using macaque and mouse as outgroup species, we identified 79 distal PA events newly originated in humans and found that the strengthening of the distal PA sites, rather than the weakening of the proximal sites, predominantly contributes to the origination of these human-specific isoforms. Notably, these isoforms are selectively constrained in general and contribute to the temporospatially specific reduction of gene expression, through the tinkering of previously existed mechanisms of nuclear retention and microRNA (miRNA) regulation. Overall, the protocol and resource highlight the application of bioinformatics in integrating multilayer genomics data to provide an intact reference for model animal studies, and the isoform switching detected may constitute a hitherto underestimated regulatory layer in shaping the human-specific transcriptome and phenotypic changes.
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Affiliation(s)
- Yumei Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qi Peng
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Wanqiu Ding
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Xiaoming Zhong
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ni A An
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Mingjun Ji
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Beijing, China
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
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14
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The DEAD-box protein family of RNA helicases: sentinels for a myriad of cellular functions with emerging roles in tumorigenesis. Int J Clin Oncol 2021; 26:795-825. [PMID: 33656655 DOI: 10.1007/s10147-021-01892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/20/2021] [Indexed: 02/06/2023]
Abstract
DEAD-box RNA helicases comprise a family within helicase superfamily 2 and make up the largest group of RNA helicases. They are a profoundly conserved family of RNA-binding proteins, carrying a generic Asp-Glu-Ala-Asp (D-E-A-D) motif that gives the family its name. Members of the DEAD-box family of RNA helicases are engaged in all facets of RNA metabolism from biogenesis to decay. DEAD-box proteins ordinarily function as constituents of enormous multi-protein complexes and it is believed that interactions with other components in the complexes might be answerable for the various capacities ascribed to these proteins. Therefore, their exact function is probably impacted by their interacting partners and to be profoundly context dependent. This may give a clarification to the occasionally inconsistent reports proposing that DEAD-box proteins have both pro- and anti-proliferative functions in cancer. There is emerging evidence that DEAD-box family of RNA helicases play pivotal functions in various cellular processes and in numerous cases have been embroiled in cellular proliferation and/or neoplastic transformation. In various malignancy types, DEAD-box RNA helicases have been reported to possess pro-proliferation or even oncogenic roles as well as anti-proliferative or tumor suppressor functions. Clarifying the exact function of DEAD-box helicases in cancer is probably intricate, and relies upon the cellular milieu and interacting factors. This review aims to summarize the current data on the numerous capacities that have been ascribed to DEAD-box RNA helicases. It also highlights their diverse actions upon malignant transformation in the various tumor types.
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15
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Ronzio M, Bernardini A, Pavesi G, Mantovani R, Dolfini D. On the NF-Y regulome as in ENCODE (2019). PLoS Comput Biol 2020; 16:e1008488. [PMID: 33370256 PMCID: PMC7793273 DOI: 10.1371/journal.pcbi.1008488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 01/08/2021] [Accepted: 11/04/2020] [Indexed: 11/19/2022] Open
Abstract
NF-Y is a trimeric Transcription Factor -TF- which binds with high selectivity to the conserved CCAAT element. Individual ChIP-seq analysis as well as ENCODE have progressively identified locations shared by other TFs. Here, we have analyzed data introduced by ENCODE over the last five years in K562, HeLa-S3 and GM12878, including several chromatin features, as well RNA-seq profiling of HeLa cells after NF-Y inactivation. We double the number of sequence-specific TFs and co-factors reported. We catalogue them in 4 classes based on co-association criteria, infer target genes categorizations, identify positional bias of binding sites and gene expression changes. Larger and novel co-associations emerge, specifically concerning subunits of repressive complexes as well as RNA-binding proteins. On the one hand, these data better define NF-Y association with single members of major classes of TFs, on the other, they suggest that it might have a wider role in the control of mRNA production. The ongoing ENCODE consortium represents a useful compendium of locations of TFs, chromatin marks, gene expression data. In previous reports, we identified modules of CCAAT-binding NF-Y with individual TFs. Here, we analyzed all 363 factors currently present: 68 with enrichment of CCAAT in their locations, 38 with overlap of peaks. New sequence-specific TFs, co-activators and co-repressors are reported. Co-association patterns correspond to specific targeted genes categorizations and gene expression changes, as assessed by RNA-seq after NF-Y inactivation. These data widen and better define a coherent model of synergy of NF-Y with selected groups of TFs and co-factors.
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Affiliation(s)
- Mirko Ronzio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
- * E-mail:
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16
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Cui Y, Hunt A, Li Z, Birkin E, Lane J, Ruge F, Jiang WG. Lead DEAD/H box helicase biomarkers with the therapeutic potential identified by integrated bioinformatic approaches in lung cancer. Comput Struct Biotechnol J 2020; 19:261-278. [PMID: 33425256 PMCID: PMC7779375 DOI: 10.1016/j.csbj.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
DEAD/H box helicases are implicated in lung cancer but have not been systematically investigated for their clinical significance and function. In this study, we aimed to evaluate the potential of DEAD/H box helicases as prognostic biomarkers and therapeutic targets in lung cancer by integrated bioinformatic analysis of multivariate large-scale databases. Survival and differential expression analysis of these helicases enabled us to identify four biomarkers with the most significant alterations. These were found to be the negative prognostic factors DDX11, DDX55 and DDX56, and positive prognostic factor DDX5. Pathway enrichment analysis indicates that MYC signalling is negatively associated with expression levels of the DDX5 gene while positively associated with that of DDX11, DDX55 and DDX56. High expression levels of the DDX5 gene is associated with low mutation levels of TP53 and MUC16, the two most frequently mutated genes in lung cancer. In contrast, high expression levels of DDX11, DDX55 and DDX56 genes are associated with high levels of TP53 and MUC16 mutation. The tumour-infiltrated CD8 + T and B cells positively correlate with levels of DDX5 gene expression, while negatively correlate with that of the other three DEAD box helicases, respectively. Moreover, the DDX5-associated miRNA profile is distinguished from the miRNA profiles of DDX11, DDX55 and DDX56, although each DDX has a different miRNA signature. The identification of these four DDX helicases as biomarkers will be valuable for prognostic prediction and targeted therapeutic development in lung cancer.
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Affiliation(s)
- Yuxin Cui
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Adam Hunt
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Zhilei Li
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, PR China
| | - Emily Birkin
- Cardiff & Vale University Health Board, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
| | - Jane Lane
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Fiona Ruge
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Wen G Jiang
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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17
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Lin Q, Jin HJ, Zhang D, Gao L. DDX46 silencing inhibits cell proliferation by activating apoptosis and autophagy in cutaneous squamous cell carcinoma. Mol Med Rep 2020; 22:4236-4242. [PMID: 33000271 PMCID: PMC7533510 DOI: 10.3892/mmr.2020.11509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/13/2020] [Indexed: 12/16/2022] Open
Abstract
DEAD-Box Helicase 46 (DDX46) is an ATP-dependent RNA helicase that plays a central role in transcription splicing and ribosome assembly. However, the role of DDX46 in cutaneous squamous cell carcinoma (CSCC) remains to be elucidated. The aim of the present study was to investigate the role of DDX46 in CSCC by assessing DDX46 expression levels in CSCC tissues and cell lines. The effect of DDX46 silencing on CSCC cell proliferation, apoptosis and autophagy were also analyzed. It was demonstrated that DDX46 was significantly overexpressed in CSCC tissues and cells (P<0.05). Furthermore, it was found that DDX46 silencing could dramatically inhibit cell proliferation (P<0.05). Moreover, cell apoptosis and autophagy were activated in DDX46 silencing groups (P<0.05). Therefore, the present results suggested that DDX46 was overexpressed in CSCC and that DDX46 silencing can inhibit cell proliferation by inducing apoptosis and activating autophagy. Thus, DDX46 may serve as a novel potential therapeutic target for CSCC.
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Affiliation(s)
- Quan Lin
- Department of Plastic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hong-Juan Jin
- Department of Plastic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Duo Zhang
- Department of Plastic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Ling Gao
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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18
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Wang Q, Ye Y, Lin R, Weng S, Cai F, Zou M, Niu H, Ge L, Lin Y. Analysis of the expression, function, prognosis and co-expression genes of DDX20 in gastric cancer. Comput Struct Biotechnol J 2020; 18:2453-2462. [PMID: 33005307 PMCID: PMC7509587 DOI: 10.1016/j.csbj.2020.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 01/04/2023] Open
Abstract
DDX20 (DEAD-box polypeptide 20) is implicated in many cellular processes involving alteration of RNA secondary structure. The role of DDX20 in gastric cancer is still unknown. In the research, the expression of DDX20 and the functional roles of DDX20 in gastric cancer were detected. The increased DDX20 expression in gastric cancer tissue compared with normal gastric tissue was observed. Functional experiments indicated that DDX20 promoted gastric cancer MGC-803 and AGS cells growth, migration, and invasion in vitro. Surprisingly, survival analysis showed that high expression of DDX20 is a favorable prognostic factor for patients with gastric cancer. In addition, enrichment analysis revealed that there is a positive correlation between DDX20 expression and T cell activation in gastric cancer. but not in normal gastric tissues. Furthermore, we found that DDX20 expression level has significant positive correlations with activated CD8 + T cells and activated CD4 + T cells in gastric cancer. Therefore, we hypothesize that the prognostic role of DDX20 in gastric cancer patients may be due to patients with high DDX20 expression contained better immune activation. Taken together, these findings suggest that DDX20 can promote the progression of gastric cancer in vitro and its prognostic value in gastric cancer may be related to many factors, including immune activation.
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Affiliation(s)
- Qingshui Wang
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210000, China.,Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian Province 350117, China.,The Engineering Technology Research Center of Characteristic Medicinal Plants of Fujian, Ningde Normal University, Ningde, Fujian Province 352100, China.,Fujian Provincial Key Laboratory of Hepatic Drug Research, Fuzhou, Fujian Province 350014, China
| | - Yan Ye
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian Province 350117, China
| | - Rongbo Lin
- Department of Gastrointestinal Medical Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province 350014, China
| | - Shuyun Weng
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian Province 350117, China
| | - Fan Cai
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian Province 350117, China
| | - Mei Zou
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian Province 350117, China
| | - Haitao Niu
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian Province 350117, China
| | - Lilin Ge
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210000, China
| | - Yao Lin
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian Province 350117, China.,Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian Province 350014, China
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19
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Huang Y, Wang C, Li K, Ye Y, Shen A, Guo L, Chen P, Meng C, Wang Q, Yang X, Huang Z, Xing X, Lin Y, Liu X, Peng J, Lin Y. Death-associated protein kinase 1 suppresses hepatocellular carcinoma cell migration and invasion by upregulation of DEAD-box helicase 20. Cancer Sci 2020; 111:2803-2813. [PMID: 32449268 PMCID: PMC7419049 DOI: 10.1111/cas.14499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 01/21/2023] Open
Abstract
Death‐associated protein kinase 1 (DAPK) is a calcium/calmodulin kinase that plays a vital role as a suppressor gene in various cancers. Yet its role and target gene independent of p53 is still unknown in hepatocellular carcinoma (HCC). In this study, we discovered that DAPK suppressed HCC cell migration and invasion instead of proliferation or colony formation. Using a proteomics approach, we identified DEAD‐box helicase 20 (DDX20) as an important downstream target of DAPK in HCC cells and critical for DAPK‐mediated inhibition of HCC cell migration and invasion. Using integrin inhibitor RGD and GTPase activity assays, we discovered that DDX20 suppressed HCC cell migration and invasion through the CDC42‐integrin pathway, which was previously reported as an important downstream pathway of DAPK in cancer. Further research using cycloheximide found that DAPK attenuates the proteasomal degradation of DDX20 protein, which is dependent on the kinase activity of DAPK. Our results shed light on new functions and regulation for both DAPK and DDX20 in carcinogenesis and identifies new potential therapeutic targets for HCC.
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Affiliation(s)
- Yide Huang
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Chenyi Wang
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ke Li
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yan Ye
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Aling Shen
- Fujian Key Laboratory of Integrative Medicine on Geriatric, Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Libin Guo
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Pengchen Chen
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Chen Meng
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qingshui Wang
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xinliu Yang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhen Huang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xiaohua Xing
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Youyu Lin
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Jun Peng
- Fujian Key Laboratory of Integrative Medicine on Geriatric, Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yao Lin
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
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20
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Pei W, Xu L, Chen Z, Slevin CC, Pettie KP, Wincovitch S, Burgess SM. A subset of SMN complex members have a specific role in tissue regeneration via ERBB pathway-mediated proliferation. NPJ Regen Med 2020; 5:6. [PMID: 32218991 PMCID: PMC7096462 DOI: 10.1038/s41536-020-0089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/27/2020] [Indexed: 12/24/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the most common genetic disease in children. SMA is generally caused by mutations in the gene SMN1. The survival of motor neurons (SMN) complex consists of SMN1, Gemins (2-8), and Strap/Unrip. We previously demonstrated smn1 and gemin5 inhibited tissue regeneration in zebrafish. Here we investigated each individual SMN complex member and identified gemin3 as another regeneration-essential gene. These three genes are likely pan-regenerative, since they affect the regeneration of hair cells, liver, and caudal fin. RNA-Seq analysis reveals that smn1, gemin3, and gemin5 are linked to a common set of genetic pathways, including the tp53 and ErbB pathways. Additional studies indicated all three genes facilitate regeneration by inhibiting the ErbB pathway, thereby allowing cell proliferation in the injured neuromasts. This study provides a new understanding of the SMN complex and a potential etiology for SMA and potentially other rare unidentified genetic diseases with similar symptoms.
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Affiliation(s)
- Wuhong Pei
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Lisha Xu
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Claire C. Slevin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Kade P. Pettie
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Stephen Wincovitch
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
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21
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Neuromuscular Diseases Due to Chaperone Mutations: A Review and Some New Results. Int J Mol Sci 2020; 21:ijms21041409. [PMID: 32093037 PMCID: PMC7073051 DOI: 10.3390/ijms21041409] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Skeletal muscle and the nervous system depend on efficient protein quality control, and they express chaperones and cochaperones at high levels to maintain protein homeostasis. Mutations in many of these proteins cause neuromuscular diseases, myopathies, and hereditary motor and sensorimotor neuropathies. In this review, we cover mutations in DNAJB6, DNAJB2, αB-crystallin (CRYAB, HSPB5), HSPB1, HSPB3, HSPB8, and BAG3, and discuss the molecular mechanisms by which they cause neuromuscular disease. In addition, previously unpublished results are presented, showing downstream effects of BAG3 p.P209L on DNAJB6 turnover and localization.
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22
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Cacciottolo R, Ciantar J, Lanfranco M, Borg RM, Vassallo N, Bordonné R, Cauchi RJ. SMN complex member Gemin3 self-interacts and has a functional relationship with ALS-linked proteins TDP-43, FUS and Sod1. Sci Rep 2019; 9:18666. [PMID: 31822699 PMCID: PMC6904755 DOI: 10.1038/s41598-019-53508-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
The predominant motor neuron disease in infants and adults is spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS), respectively. SMA is caused by insufficient levels of the Survival Motor Neuron (SMN) protein, which operates as part of the multiprotein SMN complex that includes the DEAD-box RNA helicase Gemin3/DDX20/DP103. C9orf72, SOD1, TDP-43 and FUS are ranked as the four major genes causing familial ALS. Accumulating evidence has revealed a surprising molecular overlap between SMA and ALS. Here, we ask the question of whether Drosophila can also be exploited to study shared pathogenic pathways. Focusing on motor behaviour, muscle mass and survival, we show that disruption of either TBPH/TDP-43 or Caz/FUS enhance defects associated with Gemin3 loss-of-function. Gemin3-associated neuromuscular junction overgrowth was however suppressed. Sod1 depletion had a modifying effect in late adulthood. We also show that Gemin3 self-interacts and Gem3ΔN, a helicase domain deletion mutant, retains the ability to interact with its wild-type counterpart. Importantly, mutant:wild-type dimers are favoured more than wild-type:wild-type dimers. In addition to reinforcing the link between SMA and ALS, further exploration of mechanistic overlaps is now possible in a genetically tractable model organism. Notably, Gemin3 can be elevated to a candidate for modifying motor neuron degeneration.
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Affiliation(s)
- Rebecca Cacciottolo
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR 5535, Université de Montpellier, Montpellier, France.,Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.,Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Joanna Ciantar
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.,Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Maia Lanfranco
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR 5535, Université de Montpellier, Montpellier, France.,Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.,Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Rebecca M Borg
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR 5535, Université de Montpellier, Montpellier, France.,Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.,Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Neville Vassallo
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.,Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR 5535, Université de Montpellier, Montpellier, France
| | - Ruben J Cauchi
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta. .,Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta.
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23
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Penrad-Mobayed M, Perrin C, Herman L, Todeschini AL, Nigon F, Cosson B, Caburet S, Veitia RA. Conventional and unconventional interactions of the transcription factor FOXL2 uncovered by a proteome-wide analysis. FASEB J 2019; 34:571-587. [PMID: 31914586 DOI: 10.1096/fj.201901573r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/11/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022]
Abstract
Beyond the study of its transcriptional target genes, the identification of the various interactors of a transcription factor (TF) is crucial to understand its diverse cellular roles. We focused on FOXL2, a winged-helix forkhead TF important for ovarian development and maintenance. FOXL2 has been implicated in diverse cellular processes, including apoptosis, the control of cell cycle or the regulation of steroid hormone synthesis. To reliably identify partners of endogenous FOXL2, we performed a proteome-wide analysis using co-immunoprecipitation in the murine granulosa cell-derived AT29c and the pituitary-derived alpha-T3 cell lines, using three antibodies targeting different parts of the protein. Following a stringent selection of mass spectrometry data on the basis of identification reliability and protein enrichment, we identified a core set of 255 partners common to both cell lines. Their analysis showed that we could co-precipitate several complexes involved in mRNA processing, chromatin remodeling and DNA replication and repair. We further validated (direct and/or indirect) interactions with selected partners, suggesting an unexpected role for FOXL2 in those processes. Overall, this comprehensive analysis of the endogenous FOXL2 interactome sheds light on its numerous and diverse interactors and unconventional cellular roles.
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Affiliation(s)
- May Penrad-Mobayed
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
| | - Caroline Perrin
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
| | - Laetitia Herman
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
| | | | - Fabienne Nigon
- Epigenetics and Cell Fate, CNRS UMR7216, Université de Paris, Paris, France
| | - Bertrand Cosson
- Epigenetics and Cell Fate, CNRS UMR7216, Université de Paris, Paris, France
| | - Sandrine Caburet
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
| | - Reiner A Veitia
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
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24
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Composition of the Survival Motor Neuron (SMN) Complex in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:491-503. [PMID: 30563832 PMCID: PMC6385987 DOI: 10.1534/g3.118.200874] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Spinal Muscular Atrophy (SMA) is caused by homozygous mutations in the human survival motor neuron 1 (SMN1) gene. SMN protein has a well-characterized role in the biogenesis of small nuclear ribonucleoproteins (snRNPs), core components of the spliceosome. SMN is part of an oligomeric complex with core binding partners, collectively called Gemins. Biochemical and cell biological studies demonstrate that certain Gemins are required for proper snRNP assembly and transport. However, the precise functions of most Gemins are unknown. To gain a deeper understanding of the SMN complex in the context of metazoan evolution, we investigated its composition in Drosophila melanogaster Using transgenic flies that exclusively express Flag-tagged SMN from its native promoter, we previously found that Gemin2, Gemin3, Gemin5, and all nine classical Sm proteins, including Lsm10 and Lsm11, co-purify with SMN. Here, we show that CG2941 is also highly enriched in the pulldown. Reciprocal co-immunoprecipitation reveals that epitope-tagged CG2941 interacts with endogenous SMN in Schneider2 cells. Bioinformatic comparisons show that CG2941 shares sequence and structural similarity with metazoan Gemin4. Additional analysis shows that three other genes (CG14164, CG31950 and CG2371) are not orthologous to Gemins 6-7-8, respectively, as previously suggested. In D.melanogaster, CG2941 is located within an evolutionarily recent genomic triplication with two other nearly identical paralogous genes (CG32783 and CG32786). RNAi-mediated knockdown of CG2941 and its two close paralogs reveals that Gemin4 is essential for organismal viability.
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25
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Aquilina B, Cauchi RJ. Modelling motor neuron disease in fruit flies: Lessons from spinal muscular atrophy. J Neurosci Methods 2018; 310:3-11. [DOI: 10.1016/j.jneumeth.2018.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 12/25/2022]
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26
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Genetic screen identifies a requirement for SMN in mRNA localisation within the Drosophila oocyte. BMC Res Notes 2018; 11:378. [PMID: 29895323 PMCID: PMC5998591 DOI: 10.1186/s13104-018-3496-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/06/2018] [Indexed: 01/07/2023] Open
Abstract
Objective Spinal muscular atrophy (SMA) results from insufficient levels of the survival motor neuron (SMN) protein. Drosophila is conducive to large-scale genetic-modifier screens which can reveal novel pathways underpinning the disease mechanism. We tested the ability of a large collection of genomic deletions to enhance SMN-dependent lethality. To test our design, we asked whether our study can identify loci containing genes identified in previous genetic screens. Our objective was to find a common link between genes flagged in independent screens, which would allow us to expose novel functions for SMN in vivo. Results Out of 128 chromosome deficiency lines, 12 (9.4%) were found to consistently depress adult viability when crossed to SMN loss-of-function heterozygotes. In their majority, the enhancing deletions harboured genes that were previously identified as genetic modifiers, hence, validating the design of the screen. Importantly, gene overlap allowed us to flag genes with a role in post-transcriptional regulation of mRNAs that are crucial for determining the axes of the oocyte and future embryo. We find that SMN is also required for the correct localisation of gurken and oskar mRNAs in oocytes. These findings extend the role of SMN in oogenesis by identifying a key requirement for mRNA trafficking. Electronic supplementary material The online version of this article (10.1186/s13104-018-3496-1) contains supplementary material, which is available to authorized users.
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