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1.
Sci Rep ; 14(1): 10963, 2024 05 14.
Article in English | MEDLINE | ID: mdl-38745066

ABSTRACT

MicroRNAs (miRNAs) are sequence-specific inhibitors of post-transcriptional gene expression. However, the physiological functions of these non-coding RNAs in renal interstitial mesenchymal cells remain unclear. To conclusively evaluate the role of miRNAs, we generated conditional knockout (cKO) mice with platelet-derived growth factor receptor-ß (PDGFR-ß)-specific inactivation of the key miRNA pathway gene Dicer. The cKO mice were subjected to unilateral ureteral ligation, and renal interstitial fibrosis was quantitatively evaluated using real-time polymerase chain reaction and immunofluorescence staining. Compared with control mice, cKO mice had exacerbated interstitial fibrosis exhibited by immunofluorescence staining and mRNA expression of PDGFR-ß. A microarray analysis showed decreased expressions of miR-9-5p, miR-344g-3p, and miR-7074-3p in cKO mice compared with those in control mice, suggesting an association with the increased expression of PDGFR-ß. An analysis of the signaling pathways showed that the major transcriptional changes in cKO mice were related to smooth muscle cell differentiation, regulation of DNA metabolic processes and the actin cytoskeleton, positive regulation of fibroblast proliferation and Ras protein signal transduction, and focal adhesion-PI3K/Akt/mTOR signaling pathways. Depletion of Dicer in mesenchymal cells may downregulate the signaling pathway related to miR-9-5p, miR-344g-3p, and miR-7074-3p, which can lead to the progression of chronic kidney disease. These findings highlight the possibility for future diagnostic or therapeutic developments for renal fibrosis using miR-9-5p, miR-344g-3p, and miR-7074-3p.


Subject(s)
Fibrosis , Kidney , Mesenchymal Stem Cells , Mice, Knockout , MicroRNAs , Receptor, Platelet-Derived Growth Factor beta , Ribonuclease III , Animals , MicroRNAs/genetics , MicroRNAs/metabolism , Mice , Receptor, Platelet-Derived Growth Factor beta/genetics , Receptor, Platelet-Derived Growth Factor beta/metabolism , Kidney/pathology , Kidney/metabolism , Mesenchymal Stem Cells/metabolism , Ribonuclease III/genetics , Ribonuclease III/metabolism , Signal Transduction , Kidney Diseases/genetics , Kidney Diseases/pathology , Kidney Diseases/metabolism , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Male
2.
Hum Mol Genet ; 33(R1): R26-R33, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38779774

ABSTRACT

Mitochondria are vital organelles present in almost all eukaryotic cells. Although most of the mitochondrial proteins are nuclear-encoded, mitochondria contain their own genome, whose proper expression is necessary for mitochondrial function. Transcription of the human mitochondrial genome results in the synthesis of long polycistronic transcripts that are subsequently processed by endonucleases to release individual RNA molecules, including precursors of sense protein-encoding mRNA (mt-mRNA) and a vast amount of antisense noncoding RNAs. Because of mitochondrial DNA (mtDNA) organization, the regulation of individual gene expression at the transcriptional level is limited. Although transcription of most protein-coding mitochondrial genes occurs with the same frequency, steady-state levels of mature transcripts are different. Therefore, post-transcriptional processes are important for regulating mt-mRNA levels. The mitochondrial degradosome is a complex composed of the RNA helicase SUV3 (also known as SUPV3L1) and polynucleotide phosphorylase (PNPase, PNPT1). It is the best-characterized RNA-degrading machinery in human mitochondria, which is primarily responsible for the decay of mitochondrial antisense RNA. The mechanism of mitochondrial sense RNA decay is less understood. This review aims to provide a general picture of mitochondrial genome expression, with a particular focus on mitochondrial RNA (mtRNA) degradation.


Subject(s)
Mitochondria , Polyribonucleotide Nucleotidyltransferase , RNA Stability , RNA, Mitochondrial , Humans , Mitochondria/metabolism , Mitochondria/genetics , RNA Stability/genetics , Polyribonucleotide Nucleotidyltransferase/metabolism , Polyribonucleotide Nucleotidyltransferase/genetics , RNA, Mitochondrial/metabolism , RNA, Mitochondrial/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Antisense/genetics , RNA, Antisense/metabolism , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , RNA Helicases/metabolism , RNA Helicases/genetics , RNA/metabolism , RNA/genetics , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Endoribonucleases , Exoribonucleases , Multienzyme Complexes
3.
Nat Aging ; 4(5): 664-680, 2024 May.
Article in English | MEDLINE | ID: mdl-38760576

ABSTRACT

Hyaline cartilage fibrosis is typically considered an end-stage pathology of osteoarthritis (OA), which results in changes to the extracellular matrix. However, the mechanism behind this is largely unclear. Here, we found that the RNA helicase DDX5 was dramatically downregulated during the progression of OA. DDX5 deficiency increased fibrosis phenotype by upregulating COL1 expression and downregulating COL2 expression. In addition, loss of DDX5 aggravated cartilage degradation by inducing the production of cartilage-degrading enzymes. Chondrocyte-specific deletion of Ddx5 led to more severe cartilage lesions in the mouse OA model. Mechanistically, weakened DDX5 resulted in abundance of the Fn1-AS-WT and Plod2-AS-WT transcripts, which promoted expression of fibrosis-related genes (Col1, Acta2) and extracellular matrix degradation genes (Mmp13, Nos2 and so on), respectively. Additionally, loss of DDX5 prevented the unfolding Col2 promoter G-quadruplex, thereby reducing COL2 production. Together, our data suggest that strategies aimed at the upregulation of DDX5 hold significant potential for the treatment of cartilage fibrosis and degradation in OA.


Subject(s)
Alternative Splicing , DEAD-box RNA Helicases , Fibrosis , G-Quadruplexes , Osteoarthritis , Animals , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Mice , Osteoarthritis/pathology , Osteoarthritis/genetics , Osteoarthritis/metabolism , Fibrosis/metabolism , Fibrosis/genetics , Fibrosis/pathology , Humans , Cartilage, Articular/pathology , Cartilage, Articular/metabolism , Chondrocytes/metabolism , Chondrocytes/pathology , Disease Models, Animal , Male
4.
Mol Cell ; 84(9): 1631-1632, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38701738

ABSTRACT

In this issue of Molecular Cell, Hao et al.1 demonstrate that the RNA helicase DDX21 recruits the m6A methyltransferase complex to R-loops, ensuring proper transcription termination and genome stability.


Subject(s)
DEAD-box RNA Helicases , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Humans , R-Loop Structures , Methyltransferases/metabolism , Methyltransferases/genetics , Genomic Instability , Adenosine/metabolism , Adenosine/analogs & derivatives , Transcription Termination, Genetic
5.
Nat Commun ; 15(1): 3747, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38702310

ABSTRACT

In malaria parasites, the regulation of mRNA translation, storage and degradation during development and life-stage transitions remains largely unknown. Here, we functionally characterized the DEAD-box RNA helicase PfDOZI in P. falciparum. Disruption of pfdozi enhanced asexual proliferation but reduced sexual commitment and impaired gametocyte development. By quantitative transcriptomics, we show that PfDOZI is involved in the regulation of invasion-related genes and sexual stage-specific genes during different developmental stages. PfDOZI predominantly participates in processing body-like mRNPs in schizonts but germ cell granule-like mRNPs in gametocytes to impose opposing actions of degradation and protection on different mRNA targets. We further show the formation of stress granule-like mRNPs during nutritional deprivation, highlighting an essential role of PfDOZI-associated mRNPs in stress response. We demonstrate that PfDOZI participates in distinct mRNPs to maintain mRNA homeostasis in response to life-stage transition and environmental changes by differentially executing post-transcriptional regulation on the target mRNAs.


Subject(s)
DEAD-box RNA Helicases , Plasmodium falciparum , Protozoan Proteins , RNA, Messenger , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Plasmodium falciparum/genetics , Plasmodium falciparum/metabolism , Plasmodium falciparum/growth & development , RNA, Messenger/metabolism , RNA, Messenger/genetics , Protozoan Proteins/metabolism , Protozoan Proteins/genetics , Ribonucleoproteins/metabolism , Ribonucleoproteins/genetics , Life Cycle Stages/genetics , RNA, Protozoan/metabolism , RNA, Protozoan/genetics , RNA Stability , Humans , Malaria, Falciparum/parasitology
6.
Mol Genet Genomic Med ; 12(5): e2453, 2024 May.
Article in English | MEDLINE | ID: mdl-38769888

ABSTRACT

BACKGROUND: 46,XY sex reversal 11 (SRXY11) [OMIM#273250] is characterized by genital ambiguity that may range from mild male genital defects to gonadal sex reversal in severe cases. DHX37 is an RNA helicase that has recently been reported as a cause of SRXY11. So far, a total of 21 variants in DHX37 have been reported in 58 cases with 46,XY disorders of sex development (DSD). METHODS: Whole exome sequencing (WES) was conducted to screen for variations in patients with 46,XY DSD. The subcellular localization of mutant DHX37 proteins was detected by immunofluorescence. And the levels of mutant DHX37 proteins were detected via Western blotting. RESULTS: A novel pathogenic variant of DHX37 was identified in a patient with 46,XY DSD c.2012G > C (p.Arg671Thr). Bioinformatics analysis showed that the protein function of the variant was impaired. Compared with the structure of the wild-type DHX37 protein, the number of hydrogen bonds and interacting amino acids of the variant protein were changed to varying degrees. In vitro assays revealed that the variant had no significant effect on the intracellular localization of the protein but significantly reduced the expression level of the protein. CONCLUSIONS: Our finding further expands the spectrum of the DHX37 variant and could assist in the molecular diagnosis of 46,XY DSD patients.


Subject(s)
DEAD-box RNA Helicases , Disorder of Sex Development, 46,XY , Humans , Disorder of Sex Development, 46,XY/genetics , Disorder of Sex Development, 46,XY/pathology , Male , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Female , HEK293 Cells
7.
Elife ; 132024 May 15.
Article in English | MEDLINE | ID: mdl-38747717

ABSTRACT

Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, Caenorhabditis elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1's helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.


Subject(s)
Caenorhabditis elegans Proteins , Caenorhabditis elegans , RNA, Double-Stranded , Ribonuclease III , Animals , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/chemistry , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , RNA, Double-Stranded/metabolism , Ribonuclease III/metabolism , Ribonuclease III/chemistry , Ribonuclease III/genetics , Cryoelectron Microscopy , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/chemistry , DEAD-box RNA Helicases/genetics , RNA Helicases/metabolism , RNA Helicases/genetics , RNA Helicases/chemistry , Protein Binding , Adenosine Triphosphate/metabolism , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , DEAD Box Protein 58/metabolism , DEAD Box Protein 58/genetics , DEAD Box Protein 58/chemistry
8.
Cell Death Dis ; 15(5): 342, 2024 May 17.
Article in English | MEDLINE | ID: mdl-38760378

ABSTRACT

U3 snoRNA is essential for ribosome biogenesis during interphase. Upon mitotic onset, the nucleolus disassembles and U3 snoRNA relocates to the perichromosomal region (PR) to be considered as a chromosome passenger. Whether U3 controls mitosis remains unknown. Here, we demonstrate that U3 snoRNA is required for mitotic progression. We identified DDX21 as the predominant U3-binding protein during mitosis and confirmed that U3 snoRNA colocalizes with DDX21 in the PR. DDX21 knockdown induces mitotic catastrophe and similar mitotic defects caused by U3 snoRNA depletion. Interestingly, the uniform PR distribution of U3 snoRNA and DDX21 is interdependent. DDX21 functions in mitosis depending on its PR localization. Mechanistically, U3 snoRNA regulates DDX21 PR localization through maintaining its mobility. Moreover, Cy5-U3 snoRNA downsizes the fibrous condensates of His-DDX21 at proper molecular ratios in vitro. This work highlights the importance of the equilibrium between U3 snoRNA and DDX21 in PR formation and reveals the potential relationship between the PR assembly and mitotic regulation.


Subject(s)
DEAD-box RNA Helicases , Mitosis , RNA, Small Nucleolar , Humans , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , RNA, Small Nucleolar/metabolism , RNA, Small Nucleolar/genetics , HeLa Cells
9.
Life Sci ; 349: 122716, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38762067

ABSTRACT

RNA helicases are involved in almost all biological events, and the DDXs family is one of the largest subfamilies of RNA helicases. Recently, studies have reported that RNA helicase DDX21 is involved in several biological events, specifically in orchestrating gene expression. Hence, in this review, we provide a comprehensive overview of the function of DDX21 in health and diseases. In the genome, DDX21 contributes to genome stability by promoting DNA damage repair and resolving R-loops. It also facilitates transcriptional regulation by directly binding to promoter regions, interacting with transcription factors, and enhancing transcription through non-coding RNA. Moreover, DDX21 is involved in various RNA metabolism such as RNA processing, translation, and decay. Interestingly, the activity and function of DDX21 are regulated by post-translational modifications, which affect the localization and degradation of DDX21. Except for its role of RNA helicase, DDX21 also acts as a non-enzymatic function in unwinding RNA, regulating transcriptional modifications and promoting transcription. Next, we discuss the potential application of DDX21 as a clinical predictor for diseases, which may facilitate providing novel pharmacological targets for molecular therapy.


Subject(s)
DEAD-box RNA Helicases , Gene Expression Regulation , Humans , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Animals , Genomic Instability , Protein Processing, Post-Translational/genetics
10.
Signal Transduct Target Ther ; 9(1): 127, 2024 May 24.
Article in English | MEDLINE | ID: mdl-38782919

ABSTRACT

DEAD-box helicase 17 (DDX17) is a typical member of the DEAD-box family with transcriptional cofactor activity. Although DDX17 is abundantly expressed in the myocardium, its role in heart is not fully understood. We generated cardiomyocyte-specific Ddx17-knockout mice (Ddx17-cKO), cardiomyocyte-specific Ddx17 transgenic mice (Ddx17-Tg), and various models of cardiomyocyte injury and heart failure (HF). DDX17 is downregulated in the myocardium of mouse models of heart failure and cardiomyocyte injury. Cardiomyocyte-specific knockout of Ddx17 promotes autophagic flux blockage and cardiomyocyte apoptosis, leading to progressive cardiac dysfunction, maladaptive remodeling and progression to heart failure. Restoration of DDX17 expression in cardiomyocytes protects cardiac function under pathological conditions. Further studies showed that DDX17 can bind to the transcriptional repressor B-cell lymphoma 6 (BCL6) and inhibit the expression of dynamin-related protein 1 (DRP1). When DDX17 expression is reduced, transcriptional repression of BCL6 is attenuated, leading to increased DRP1 expression and mitochondrial fission, which in turn leads to impaired mitochondrial homeostasis and heart failure. We also investigated the correlation of DDX17 expression with cardiac function and DRP1 expression in myocardial biopsy samples from patients with heart failure. These findings suggest that DDX17 protects cardiac function by promoting mitochondrial homeostasis through the BCL6-DRP1 pathway in heart failure.


Subject(s)
DEAD-box RNA Helicases , Heart Failure , Myocytes, Cardiac , Animals , Humans , Mice , Apoptosis/genetics , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Dynamins/genetics , Dynamins/metabolism , Heart Failure/genetics , Heart Failure/pathology , Heart Failure/metabolism , Homeostasis/genetics , Mice, Knockout , Mice, Transgenic , Mitochondria/genetics , Mitochondria/metabolism , Mitochondria/pathology , Mitochondrial Dynamics/genetics , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/pathology , Proto-Oncogene Proteins c-bcl-6/genetics , Proto-Oncogene Proteins c-bcl-6/metabolism
11.
Int J Mol Sci ; 25(9)2024 May 01.
Article in English | MEDLINE | ID: mdl-38732173

ABSTRACT

Lung adenocarcinoma (LUAD) is the most prevalent and aggressive subtype of lung cancer, exhibiting a dismal prognosis with a five-year survival rate below 5%. DEAD-box RNA helicase 18 (DDX18, gene symbol DDX18), a crucial regulator of RNA metabolism, has been implicated in various cellular processes, including cell cycle control and tumorigenesis. However, its role in LUAD pathogenesis remains elusive. This study demonstrates the significant upregulation of DDX18 in LUAD tissues and its association with poor patient survival (from public databases). Functional in vivo and in vitro assays revealed that DDX18 knockdown potently suppresses LUAD progression. RNA sequencing and chromatin immunoprecipitation experiments identified cyclin-dependent kinase 4 (CDK4), a cell cycle regulator, as a direct transcriptional target of DDX18. Notably, DDX18 depletion induced G1 cell cycle arrest, while its overexpression promoted cell cycle progression even in normal lung cells. Interestingly, while the oncogenic protein c-Myc bound to the DDX18 promoter, it did not influence its expression. Collectively, these findings establish DDX18 as a potential oncogene in LUAD, functioning through the CDK4-mediated cell cycle pathway. DDX18 may represent a promising therapeutic target for LUAD intervention.


Subject(s)
Adenocarcinoma of Lung , Cyclin-Dependent Kinase 4 , DEAD-box RNA Helicases , Gene Expression Regulation, Neoplastic , Lung Neoplasms , Animals , Humans , Mice , Adenocarcinoma of Lung/genetics , Adenocarcinoma of Lung/pathology , Adenocarcinoma of Lung/metabolism , Carcinogenesis/genetics , Carcinogenesis/metabolism , Cell Cycle/genetics , Cell Line, Tumor , Cell Proliferation , Cyclin-Dependent Kinase 4/metabolism , Cyclin-Dependent Kinase 4/genetics , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Mice, Nude , Up-Regulation
12.
Proc Natl Acad Sci U S A ; 121(21): e2322974121, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38743621

ABSTRACT

SRSF1 is the founding member of the SR protein family. It is required-interchangeably with other SR proteins-for pre-mRNA splicing in vitro, and it regulates various alternative splicing events. Dysregulation of SRSF1 expression contributes to cancer and other pathologies. Here, we characterized SRSF1's interactome using proximity labeling and mass spectrometry. This approach yielded 190 proteins enriched in the SRSF1 samples, independently of the N- or C-terminal location of the biotin-labeling domain. The detected proteins reflect established functions of SRSF1 in pre-mRNA splicing and reveal additional connections to spliceosome proteins, in addition to other recently identified functions. We validated a robust interaction with the spliceosomal RNA helicase DDX23/PRP28 using bimolecular fluorescence complementation and in vitro binding assays. The interaction is mediated by the N-terminal RS-like domain of DDX23 and both RRM1 and the RS domain of SRSF1. During pre-mRNA splicing, DDX23's ATPase activity is essential for the pre-B to B spliceosome complex transition and for release of U1 snRNP from the 5' splice site. We show that the RS-like region of DDX23's N-terminal domain is important for spliceosome incorporation, while larger deletions in this domain alter subnuclear localization. We discuss how the identified interaction of DDX23 with SRSF1 and other SR proteins may be involved in the regulation of these processes.


Subject(s)
DEAD-box RNA Helicases , RNA Splicing , Serine-Arginine Splicing Factors , Spliceosomes , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Humans , Spliceosomes/metabolism , Serine-Arginine Splicing Factors/metabolism , Serine-Arginine Splicing Factors/genetics , RNA Precursors/metabolism , RNA Precursors/genetics , Protein Binding , HeLa Cells
13.
Cell Death Dis ; 15(5): 354, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38773094

ABSTRACT

Cancer cells undergo metabolic reprogramming in response to hostile microenvironments, such as energy stress; however, the underlying mechanisms remain largely unclear. It is also unknown whether energy stress-responsive circular RNA (circRNA) is involved in the regulation of glucose metabolism. Here we report that circDDX21 is upregulated in response to glucose deprivation by the transcription factor c-Myc. Functionally, circDDX21 is shown to promote glycolysis by increasing PGAM1 expression. Mechanistically, circDDX21 interacts with the RNA binding protein PABPC1, disrupting its association with the ubiquitin E3 ligase MKRN3. This disassociation attenuates MKRN3-mediated PABPC1 ubiquitination and enhances the binding of PABPC1 to PGAM1 mRNA, thereby leading to PGAM1 mRNA stabilization. The ability of the circDDX21-PGAM1 axis to promote hepatocellular carcinogenesis is validated in a xenograft mouse model. Additionally, in clinical hepatocellular carcinoma tissues, there is a positive correlation between circDDX21 and PGAM1 expression. These findings establish circDDX21 as an important regulator of glycolysis and suggest circDDX21 as a potential therapeutic target for hepatocellular carcinoma.


Subject(s)
Carcinogenesis , Carcinoma, Hepatocellular , Glycolysis , Liver Neoplasms , RNA, Circular , Humans , Glycolysis/genetics , Liver Neoplasms/genetics , Liver Neoplasms/metabolism , Liver Neoplasms/pathology , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/pathology , Animals , RNA, Circular/genetics , RNA, Circular/metabolism , Mice , Carcinogenesis/genetics , Carcinogenesis/metabolism , Carcinogenesis/pathology , Mice, Nude , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Energy Metabolism/genetics , Ubiquitination , Male , Mice, Inbred BALB C
14.
Oncotarget ; 15: 313-325, 2024 May 16.
Article in English | MEDLINE | ID: mdl-38753413

ABSTRACT

The diheteroarylamide-based compound 1C8 and the aminothiazole carboxamide-related compound GPS167 inhibit the CLK kinases, and affect the proliferation of a broad range of cancer cell lines. A chemogenomic screen previously performed with GPS167 revealed that the depletion of components associated with mitotic spindle assembly altered sensitivity to GPS167. Here, a similar screen performed with 1C8 also established the impact of components involved in mitotic spindle assembly. Accordingly, transcriptome analyses of cells treated with 1C8 and GPS167 indicated that the expression and RNA splicing of transcripts encoding mitotic spindle assembly components were affected. The functional relevance of the microtubule connection was confirmed by showing that subtoxic concentrations of drugs affecting mitotic spindle assembly increased sensitivity to GPS167. 1C8 and GPS167 impacted the expression and splicing of transcripts in pathways relevant to tumor progression, including MYC targets and the epithelial mesenchymal transition (EMT). Finally, 1C8 and GPS167 altered the expression and alternative splicing of transcripts involved in the antiviral immune response. Consistent with this observation, depleting the double-stranded RNA sensor DHX33 suppressed GPS167-mediated cytotoxicity on HCT116 cells. Our study uncovered molecular mechanisms through which 1C8 and GPS167 affect cancer cell proliferation as well as processes critical for metastasis.


Subject(s)
Cell Proliferation , Epithelial-Mesenchymal Transition , Protein Kinase Inhibitors , Protein-Tyrosine Kinases , Humans , Epithelial-Mesenchymal Transition/drug effects , Protein-Tyrosine Kinases/metabolism , Protein-Tyrosine Kinases/antagonists & inhibitors , Protein-Tyrosine Kinases/genetics , Protein Kinase Inhibitors/pharmacology , Cell Proliferation/drug effects , Cell Line, Tumor , Antineoplastic Agents/pharmacology , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/antagonists & inhibitors , Thiazoles/pharmacology , Antiviral Agents/pharmacology , HCT116 Cells , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Gene Expression Profiling
15.
Nat Commun ; 15(1): 3080, 2024 Apr 09.
Article in English | MEDLINE | ID: mdl-38594251

ABSTRACT

Epithelial barrier dysfunction and crypt destruction are hallmarks of inflammatory bowel disease (IBD). Intestinal stem cells (ISCs) residing in the crypts play a crucial role in the continuous self-renewal and rapid recovery of intestinal epithelial cells (IECs). However, how ISCs are dysregulated in IBD remains poorly understood. Here, we observe reduced DHX9 protein levels in IBD patients, and mice with conditional DHX9 depletion in the intestinal epithelium (Dhx9ΔIEC) exhibit an increased susceptibility to experimental colitis. Notably, Dhx9ΔIEC mice display a significant reduction in the numbers of ISCs and Paneth cells. Further investigation using ISC-specific or Paneth cell-specific Dhx9-deficient mice demonstrates the involvement of ISC-expressed DHX9 in maintaining epithelial homeostasis. Mechanistically, DHX9 deficiency leads to abnormal R-loop accumulation, resulting in genomic instability and the cGAS-STING-mediated inflammatory response, which together impair ISC function and contribute to the pathogenesis of IBD. Collectively, our findings highlight R-loop-mediated genomic instability in ISCs as a risk factor in IBD.


Subject(s)
Inflammatory Bowel Diseases , R-Loop Structures , Animals , Humans , Mice , DEAD-box RNA Helicases/metabolism , Epithelial Cells/metabolism , Homeostasis , Inflammatory Bowel Diseases/pathology , Intestinal Mucosa/metabolism , Neoplasm Proteins/metabolism , Paneth Cells/metabolism , Stem Cells/metabolism
16.
Nat Commun ; 15(1): 3303, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38664397

ABSTRACT

The DEAD-box RNA helicase (DDX) plays a central role in many aspects of RNA metabolism by remodeling the defined structure of RNA molecules. While a number of structural studies have revealed the atomistic details of the interaction between DDX and RNA ligands, the molecular mechanism of how this molecule unwinds a structured RNA into an unstructured single-stranded RNA (ssRNA) has largely remained elusive. This is due to challenges in structurally characterizing the unwinding intermediate state and the lack of thermodynamic details underlying this process. In this study, we use solution nuclear magnetic resonance (NMR) spectroscopy to characterize the interaction of human DDX3X, a member of the DDX family, with various RNA ligands. Our results show that the inherent binding affinity of DDX3X for ssRNA is significantly higher than that for structured RNA elements. This preferential binding, accompanied by the formation of a domain-closed conformation in complex with ssRNA, effectively stabilizes the denatured ssRNA state and thus underlies the unwinding activity of DDX3X. Our results provide a thermodynamic and structural basis for the DDX function, whereby DDX can recognize and remodel a distinct set of structured RNAs to participate in a wide range of physiological processes.


Subject(s)
DEAD-box RNA Helicases , Protein Binding , RNA , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/chemistry , Humans , RNA/metabolism , RNA/chemistry , Thermodynamics , Magnetic Resonance Spectroscopy , Models, Molecular , Nucleic Acid Conformation
17.
Theriogenology ; 222: 22-30, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38615433

ABSTRACT

Primordial germ cells (PGCs) are the precursors of germ cells and play a crucial role in germline transmission. In chickens, PGCs can be cultured in vitro while maintaining their germline stem cell characteristics. The Deleted in Azoospermia-Like (DAZL) gene, which is highly expressed in PGCs, is essential for germ cell development. Here, through gene knockout experiments, we discovered that the loss of DAZL expression in chicken PGCs led to decreased proliferation and survival. By next employed techniques such as RIP-seq (RNA Binding Protein Immunoprecipitation) and Co-IP-MS/MS (Co-immunoprecipitation Mass Spectrometry), we identified genes directly regulated by DAZL or cooperating with DAZL at the transcriptomic and proteomic levels. DAZL was found to control genes related to germline development, pluripotency, and cell proliferation in PGCs. Additionally, we observed a significant overlap between RNAs and proteins that interact with both DAZL and DDX4, indicating their cooperation in the gene regulation network in chicken PGCs. Our research provides valuable insights into the function of the DAZL gene in germline cells.


Subject(s)
Cell Proliferation , Chickens , DEAD-box RNA Helicases , Germ Cells , RNA-Binding Proteins , Animals , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Chickens/genetics , Germ Cells/metabolism , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Gene Expression Regulation , Gene Expression Regulation, Developmental
18.
Cell Mol Biol (Noisy-le-grand) ; 70(4): 40-44, 2024 Apr 28.
Article in English | MEDLINE | ID: mdl-38678629

ABSTRACT

This study aimed to investigate the expression of long non-coding ribonucleic acid (lncRNA) DDX11 antisense RNA 1 (DDX11-AS1) in breast cancer (BC) tissues and cells and investigate its biological function and potential molecular mechanism through in vitro experiments. Tissue specimens were obtained from 44 BC patients. TRIzol method was used to extract RNAs from the tissues. The relative expression of DDX11-AS1 in BC tissues and the expression of DDX11-AS1 in BC cells were detected via quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The effect of DDX11-AS1 on the proliferation ability of BC cells was detected via cell counting kit-8 (CCK-8) assay. Flow cytometry was adopted to study the effect of DDX11-AS1 on the distribution of BC cell cycle. Transwell assays were performed to analyze the effects of DDX11-AS1 on the migration and invasion abilities of BC cells. Finally, after interfering with the expression of DDX11-AS1 in BC cells, changes in the expressions of molecular markers for epithelial-mesenchymal transition (EMT) were detected via Western blotting. According to the results of qRT-PCR, the expression of DDX11-AS1 was up-regulated in 38 out of 44 cases of BC tissues compared with that in the para-carcinoma tissues, and the expression of DDX11-AS1 in BC cells was up-regulated as well. After interference with the expression of DDX11-AS1 in BC cells, it was found via CCK-8 assay that the proliferation ability of BC cells was restrained, flow cytometry results showed that the BC cell cycle was arrested at G1/G0 phase, and the results of transwell assays revealed that the cell invasion and migration abilities were suppressed in experimental group compared with those in control group. According to the results of Western blotting, after interfering with the expression of DDX11-AS1 in BC cells, there were changes in the expressions of molecular markers for EMT. In BC, the expression of lncRNA DDX11-AS1 is up-regulated, which promotes the proliferation, migration and invasion of BC cells by regulating EMT.


Subject(s)
Breast Neoplasms , Cell Movement , Cell Proliferation , DNA Helicases , Epithelial-Mesenchymal Transition , Gene Expression Regulation, Neoplastic , Neoplasm Invasiveness , RNA, Long Noncoding , Humans , Epithelial-Mesenchymal Transition/genetics , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Breast Neoplasms/metabolism , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Female , Cell Movement/genetics , Cell Proliferation/genetics , Neoplasm Invasiveness/genetics , Cell Line, Tumor , Middle Aged , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Cell Cycle/genetics
19.
Mitochondrion ; 76: 101881, 2024 May.
Article in English | MEDLINE | ID: mdl-38604460

ABSTRACT

DEAD-box helicases are important players in mitochondrial gene expression, which is necessary for mitochondrial respiration. In this study, we characterized Schizosaccharomyces pombe Mss116 (spMss116), a member of the family of DEAD-box RNA helicases. Deletion of spmss116 in a mitochondrial intron-containing background significantly reduced the levels of mitochondrial DNA (mtDNA)-encoded cox1 and cob1 mRNAs and impaired mitochondrial translation, leading to a severe respiratory defect and a loss of cell viability during stationary phase. Deletion of mitochondrial introns restored the levels of cox1 and cob1 mRNAs to wide-type (WT) levels but could not restore mitochondrial translation and respiration in Δspmss116 cells. Furthermore, deletion of spmss116 in both mitochondrial intron-containing and intronless backgrounds impaired mitoribosome assembly and destabilization of mitoribosomal proteins. Our findings suggest that defective mitochondrial translation caused by deletion of spmss116 is most likely due to impaired mitoribosome assembly.


Subject(s)
DEAD-box RNA Helicases , Mitochondrial Ribosomes , Protein Biosynthesis , Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Mitochondrial Ribosomes/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces pombe Proteins/genetics , Mitochondria/metabolism , Mitochondria/genetics , Gene Deletion , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics
20.
Gene ; 917: 148443, 2024 Jul 30.
Article in English | MEDLINE | ID: mdl-38582263

ABSTRACT

Acute promyelocytic leukemia (APL) is a type of acute myeloid leukemia (AML) with a high mortality rate, and the production of PML-RARα fusion protein is the cause of its pathogenesis. Our group has synthesized a novel compound, 4-amino-2-trifluoromethyl-phenyl retinate (ATPR), by structural modification of All-trans retinoic acid (ATRA), which has strong cell differentiation-inducing effects and inhibits the expression of PML-RARα. In this study, acute promyelocytic leukemia NB4 cells before and after ATPR induction were analyzed by whole transcriptome microarray, and the expression of lncRNA CONCR was found to be significantly downregulated. The role of CONCR in ATPR-induced cell differentiation and cycle arrest was explored through overexpression and silencing of CONCR. And then the database was used to predict that CONCR may bind to DEAD/H-Box Helicase 11 (DDX11) protein to further explore the role of CONCR binding to DDX11. The results showed that ATPR could reduce the expression of CONCR, and overexpression of CONCR could reverse the ATPR-induced cell differentiation and cycle blocking effect, and conversely silencing of CONCR could promote this effect. RNA immunoprecipitation (RIP) experiments showed that CONCR could bind to DDX11, the protein expression levels of DDX11 and PML-RARα were elevated after overexpression of CONCR. These results suggest that ATPR can regulate the expression of DDX11 through CONCR to affect the expression of PML-RARα fusion protein, which in turn induces the differentiation and maturation of APL cells.


Subject(s)
Cell Cycle Checkpoints , Cell Differentiation , DEAD-box RNA Helicases , Leukemia, Promyelocytic, Acute , Oncogene Proteins, Fusion , RNA, Long Noncoding , Signal Transduction , Humans , Leukemia, Promyelocytic, Acute/genetics , Leukemia, Promyelocytic, Acute/metabolism , Leukemia, Promyelocytic, Acute/pathology , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Oncogene Proteins, Fusion/genetics , Oncogene Proteins, Fusion/metabolism , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Cell Line, Tumor , Cell Cycle Checkpoints/drug effects , Cell Cycle Checkpoints/genetics , Tretinoin/pharmacology , Gene Expression Regulation, Leukemic
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