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1.
Int J Cancer ; 154(11): 1999-2013, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38308587

ABSTRACT

The global pandemic of metabolic diseases has increased the incidence of hepatocellular carcinoma (HCC) in the context of non-alcoholic steatohepatitis (NASH). The downregulation of the E3 ubiquitin ligase TRIM21 has been linked to poor prognosis in different cancers including HCC. In order to investigate the role of TRIM21 in liver cancer progression on NASH, Trim21+/+ and Trim21-/- male mice were injected with streptozotocin at the neonatal stage. The hypoinsulinemic mice were then fed with a high-fat high-cholesterol diet (HFHCD) for 4, 8 or 12 weeks. All mice developed NASH which systematically resulted in HCC progression. Interestingly, compared to the Trim21+/+ control mice, liver damage was worsened in Trim21-/- mice, with more HCC nodules found after 12 weeks on HFHCD. Immune population analysis in the spleen and liver revealed a higher proportion of CD4+PD-1+ and CD8+PD-1+ T cells in Trim21-/- mice. The liver and HCC tumors of Trim21-/- mice also exhibited an increase in the number of PD-L1+ and CD68+ PD-L1+ cells. Thus, TRIM21 limits the emergence of HCC nodules in mice with NASH by potentially restricting the expression of PD-1 in lymphocytes and PD-L1 in tumors.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Non-alcoholic Fatty Liver Disease , Ribonucleoproteins , Animals , Male , Mice , B7-H1 Antigen/metabolism , Carcinogenesis , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/complications , Disease Models, Animal , Liver Neoplasms/genetics , Liver Neoplasms/complications , Non-alcoholic Fatty Liver Disease/complications , Programmed Cell Death 1 Receptor/metabolism , Up-Regulation , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics
2.
Immunology ; 159(3): 335-343, 2020 03.
Article in English | MEDLINE | ID: mdl-31755557

ABSTRACT

TRIM21 is an interferon-stimulated E3 ligase that controls the activity of pattern-recognition signaling via ubiquitination of interferon regulatory factors and DDX41. Previous studies on the role of TRIM21 in innate immune responses have yielded contradictory results, suggesting that the role of TRIM21 is cell specific. Here, we report that bone-marrow-derived macrophages (BMDMs) generated from Trim21-/- mice have reduced expression of mature macrophage markers. Reflecting their reduced differentiation in response to macrophage colony-stimulating factor (M-CSF), Trim21-/- BMDMs had decreased expression of M-CSF signature genes. Although Trim21-/- BMDMs responded normally to Toll-like receptor 9 (TLR9) activation, they produced lower levels of pro-inflammatory cytokines in response to the TLR2 agonist PAM3CSK4. In line with this, the response to infection with the Bacillus Calmette-Guérin strain of Mycobacterium bovis was also diminished in Trim21-/- BMDMs. Our results indicate that TRIM21 controls responses to TLR2 agonists.


Subject(s)
Cytokines/metabolism , Inflammation Mediators/metabolism , Macrophages/metabolism , Ribonucleoproteins/metabolism , Toll-Like Receptor 2/metabolism , Animals , Cell Differentiation , Cells, Cultured , Host-Pathogen Interactions , Lipopeptides/pharmacology , Macrophage Colony-Stimulating Factor/pharmacology , Macrophages/drug effects , Macrophages/immunology , Macrophages/microbiology , Mice, Inbred C57BL , Mice, Knockout , Mycobacterium bovis/immunology , Mycobacterium bovis/pathogenicity , Phenotype , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics , Signal Transduction , Toll-Like Receptor 2/agonists , Toll-Like Receptor 2/genetics
3.
Oncogene ; 39(2): 443-453, 2020 01.
Article in English | MEDLINE | ID: mdl-31488872

ABSTRACT

Chronic myeloid leukemia (CML) originates from normal hematopoietic stem cells acquiring BCR-ABL fusion gene, specific BCR-ABL inhibitors (e.g., imatinib mesylate, IM) have greatly improved patient management. However, some patients are still suffering from relapse and drug resistance, which urges better understanding of the growth/survival mechanisms of CML stem/progenitor cells. In the present study, the role and its underlying mechanism of heterogeneous nuclear ribonucleoprotein D-like (HNRPDL) in CML cells were investigated. Firstly, overexpression of HNRPDL promoted the growth of murine BaF3 cells in vitro and induced leukemia in vivo, which was enhanced by co-expression of BCR-ABL. Conversely, HNRPDL silencing inhibited colony-forming cell (CFC) production of CML CD34+ cells and attenuated BCR-ABL induced leukemia. In addition, HNRPDL modulated imatinib response of K562 cells and HNRPDL silencing sensitized CML CD34+ cells to imatinib treatment. Mechanistically, we found the stability of pre-B-cell leukemia homeobox 1 (PBX1) mRNA was sustained by HNRPDL through its binding to a specific motif (ACUAGC) in 3'-untranslated region (3'-UTR) of PBX1. The expression of PBX1 was significantly higher in CML CD34+ cells than that in control cells and PBX silencing inhibited the growth of CML cells and sensitized them to imatinib treatment. In contrast, overexpression of PBX1 elevated the CFC production of normal hematopoietic CD34+ cells and "rescued" HNRPDL silencing induced growth inhibition and imatinib sensitization. Taken together, our data have demonstrated that HNRPDL transforms hematopoietic cells and a novel HNRPDL/PBX1 axis plays an important role in human CML CD34+ cells.


Subject(s)
Antigens, CD34/metabolism , Carcinogenesis , Imatinib Mesylate/pharmacology , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology , Pre-B-Cell Leukemia Transcription Factor 1/metabolism , Ribonucleoproteins/metabolism , Cell Proliferation/drug effects , Gene Expression Regulation, Neoplastic/drug effects , Gene Silencing , Humans , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics
4.
Biochim Biophys Acta Gene Regul Mech ; 1861(4): 361-372, 2018 Apr.
Article in English | MEDLINE | ID: mdl-29397330

ABSTRACT

The conserved nuclear RNA-binding factor known as La protein arose in an ancient eukaryote, phylogenetically associated with another eukaryotic hallmark, synthesis of tRNA by RNA polymerase III (RNAP III). Because 3'-oligo(U) is the sequence-specific signal for transcription termination by RNAP III as well as the high affinity binding site for La, the latter is linked to the intranuclear posttranscriptional processing of eukaryotic precursor-tRNAs. The pre-tRNA processing pathway must accommodate a variety of substrates that are destined for both common steps as well as tRNA-specific events. The order of intranuclear pre-tRNA processing steps is mediated in part by three activities derived from interaction with La protein: 3'-end protection from untimely decay by 3' exonucleases, nuclear retention and chaperone activity that helps prevent pre-tRNA misfolding and mischanneling into offline pathways. A focus of this perspective will be on differences between yeast and mammals in the subcellular partitioning of pre-tRNA intermediates and differential interactions with La. We review how this is most relevant to pre-tRNA splicing which occurs in the cytoplasm of yeasts but in nuclei of higher eukaryotes. Also divergent is La architecture, comprised of three RNA-binding domains in organisms in all examined branches of the eukaryal tree except yeast, which have lost the C-terminal RNA recognition motif-2α (RRM2α) domain. We also review emerging data that suggest mammalian La interacts with nuclear pre-tRNA splicing intermediates and may impact this branch of the tRNA maturation pathway. Finally, because La is involved in intranuclear tRNA biogenesis we review relevant aspects of tRNA-associated neurodegenerative diseases. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.


Subject(s)
Autoantigens/genetics , Eukaryotic Cells/metabolism , RNA, Transfer/metabolism , Ribonucleoproteins/genetics , Yeasts/genetics , Amino Acid Sequence , Animals , Autoantigens/chemistry , Autoantigens/metabolism , Binding Sites , Fungal Proteins/genetics , Fungal Proteins/metabolism , Gene Expression Regulation, Fungal , Humans , Models, Molecular , Neurodegenerative Diseases/genetics , Neurodegenerative Diseases/metabolism , Oligoribonucleotides/genetics , Phosphoproteins/deficiency , Phosphoproteins/genetics , Phosphoproteins/metabolism , RNA/genetics , RNA/metabolism , RNA Polymerase III/metabolism , RNA Precursors/metabolism , RNA Processing, Post-Transcriptional/physiology , RNA Recognition Motif , RNA Splicing/physiology , RNA, Fungal/genetics , RNA, Fungal/metabolism , RNA, Transfer/genetics , Ribonucleoproteins/chemistry , Ribonucleoproteins/deficiency , Ribonucleoproteins/metabolism , Species Specificity , Subcellular Fractions/metabolism , Uracil Nucleotides/genetics , Yeasts/metabolism , SS-B Antigen
5.
Cardiovasc Res ; 114(1): 158-167, 2018 01 01.
Article in English | MEDLINE | ID: mdl-29016728

ABSTRACT

Aims: Patients with hyperlipidemia are at risk of atherosclerosis, but not all develop cardiovascular disease, highlighting the importance of other risk factors such as inflammation. Both the innate and adaptive arms of the immune system have been suggested in the initiation and propagation of plaque formation. Tri-partite motif (TRIM) 21 is a regulator of tissue inflammation and pro-inflammatory cytokine production, and has been implicated in chronic inflammatory disease. Here, we investigate a potential role for TRIM21 in coronary artery disease. Methods and results: Trim21-deficient or wild-type bone marrow was transplanted into Ldlr-/- mice fed a hypercholesterolemic diet. The Trim21-/-->Ldlr-/- mice developed larger atherosclerotic plaques, with significantly higher collagen content compared to mice transplanted with wild-type cells. High collagen content of the atheroma is stabilizing, and has recently been linked to IL-17. Interestingly, Trim21-/-->Ldlr-/- mice had elevated CD4 and IL-17 mRNA expression in plaques, and increased numbers of activated CD4+ T cells in the periphery. An increased differentiation of naïve T cells lacking Trim21 into Th17 cells was confirmed in vitro, with transcriptomic analysis revealing upregulation of genes of a non-pathogenic Th17 phenotype. Also, decreased expression of matrix metalloproteinases (MMPs) was noted in aortic plaques. Analysis of human carotid plaques confirmed that TRIM21 expression negatively correlates with the expression of key Th17 genes and collagen, but positively to MMPs also in patients, linking our findings to a clinical setting. Conclusion: In this study, we demonstrate that TRIM21 influences atherosclerosis via regulation of Th17 responses, with TRIM21 deficiency promoting IL-17 expression and a more fibrous, stable, phenotype of the plaques.


Subject(s)
Aorta/metabolism , Aortic Diseases/metabolism , Atherosclerosis/metabolism , Cell Differentiation , Collagen/metabolism , Plaque, Atherosclerotic , Ribonucleoproteins/deficiency , Th17 Cells/metabolism , Animals , Aorta/immunology , Aorta/pathology , Aortic Diseases/genetics , Aortic Diseases/immunology , Aortic Diseases/pathology , Atherosclerosis/genetics , Atherosclerosis/immunology , Atherosclerosis/pathology , Carotid Stenosis/immunology , Carotid Stenosis/metabolism , Carotid Stenosis/pathology , Cells, Cultured , Disease Models, Animal , Female , Humans , Interleukin-17/metabolism , Mice, Inbred C57BL , Mice, Knockout , Phenotype , Receptors, LDL/deficiency , Receptors, LDL/genetics , Ribonucleoproteins/genetics , Th17 Cells/immunology , Th17 Cells/pathology
6.
Sci Rep ; 7: 46097, 2017 04 05.
Article in English | MEDLINE | ID: mdl-28378844

ABSTRACT

Activation of NF-κB transcription factor is strictly regulated to prevent excessive inflammatory responses leading to immunopathology. However, it still remains unclear how NF-κB activation is negatively controlled. The PDZ-LIM domain-containing protein PDLIM2 is a nuclear ubiquitin E3 ligase targeting the p65 subunit of NF-κB for degradation, thus terminating NF-κB-mediated inflammation. Using yeast two-hybrid screening, we sought to isolate PDLIM2-interacting proteins that are critical for suppressing NF-κB signaling. Here we identified MKRN2, a RING finger domain-containing protein that belongs to the makorin ring finger protein gene family, as a novel p65 ubiquitin E3 ligase. MKRN2 bound to p65 and promoted the polyubiquitination and proteasome-dependent degradation of p65 through the MKRN2 RING finger domain, thereby suppressing p65-mediated NF-κB transactivation. Notably, MKRN2 and PDLIM2 synergistically promote polyubiquitination and degradation of p65. Consistently, MKRN2 knockdown in dendritic cells resulted in larger amounts of nuclear p65 and augmented production of proinflammatory cytokines in responses to innate stimuli. These results delineate a novel role of MKRN2 in negatively regulating NF-κB-mediated inflammatory responses, cooperatively with PDLIM2.


Subject(s)
Inflammation/metabolism , Inflammation/pathology , Protein Subunits/metabolism , Ribonucleoproteins/metabolism , Transcription Factor RelA/metabolism , Adaptor Proteins, Signal Transducing/metabolism , Animals , Cell Line , Humans , LIM Domain Proteins/metabolism , Mice , Polyubiquitin/metabolism , Protein Binding , Proteolysis , RING Finger Domains , Ribonucleoproteins/chemistry , Ribonucleoproteins/deficiency , Signal Transduction , Ubiquitination
7.
Proc Natl Acad Sci U S A ; 114(3): 574-579, 2017 01 17.
Article in English | MEDLINE | ID: mdl-28049840

ABSTRACT

Alzheimer's disease (AD) and other neurodegenerative disorders are associated with the cytoplasmic aggregation of microtubule-associated protein tau. Recent evidence supports transcellular transfer of tau misfolding (seeding) as the mechanism of spread within an affected brain, a process reminiscent of viral infection. However, whereas microbial pathogens can be recognized as nonself by immune receptors, misfolded protein assemblies evade detection, as they are host-derived. Here, we show that when misfolded tau assemblies enter the cell, they can be detected and neutralized via a danger response mediated by tau-associated antibodies and the cytosolic Fc receptor tripartite motif protein 21 (TRIM21). We developed fluorescent, morphology-based seeding assays that allow the formation of pathological tau aggregates to be measured in situ within 24 h in the presence of picomolar concentrations of tau seeds. We found that anti-tau antibodies accompany tau seeds into the cell, where they recruit TRIM21 shortly after entry. After binding, TRIM21 neutralizes tau seeds through the activity of the proteasome and the AAA ATPase p97/VCP in a similar manner to infectious viruses. These results establish that intracellular antiviral immunity can be redirected against host-origin endopathogens involved in neurodegeneration.


Subject(s)
Receptors, Fc/metabolism , Ribonucleoproteins/metabolism , tau Proteins/metabolism , Animals , Antibodies, Neutralizing/metabolism , Cells, Cultured , Cytosol/metabolism , Humans , In Vitro Techniques , Mice , Mice, Inbred C57BL , Mice, Knockout , Nerve Degeneration/immunology , Nerve Degeneration/metabolism , Nerve Degeneration/prevention & control , Neurons/immunology , Neurons/metabolism , Proteasome Endopeptidase Complex/metabolism , Protein Aggregates , Protein Aggregation, Pathological/immunology , Protein Aggregation, Pathological/metabolism , Protein Aggregation, Pathological/prevention & control , Proteostasis Deficiencies/metabolism , Proteostasis Deficiencies/prevention & control , Receptors, Fc/deficiency , Receptors, Fc/genetics , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics , tau Proteins/chemistry , tau Proteins/immunology
8.
Clin Exp Immunol ; 188(1): 154-162, 2017 04.
Article in English | MEDLINE | ID: mdl-27936488

ABSTRACT

The presence of anti-Ro52/tripartite motif 21 (Trim21) autoantibodies has been associated with a distinctive clinical profile and has gained value as a prognostic marker in idiopathic inflammatory myopathies (IIM). The aim of the present work was to analyse Ro52/Trim21 expression in different subsets of peripheral blood mononuclear cells (PBMCs) of patients with IIM, as well as the ubiquitination profile and its association with proinflammatory cytokine production. We included 18 patients with recent-onset IIM and 18 age- and gender-matched healthy donors. PBMCs were isolated and different subsets (CD4+ , CD8+ , CD14+ ) were purified by magnetic selection. The expression of Ro52/Trim21 in different PBMC subsets of patients with IIM and healthy donors was analysed by Western blot. We assessed the presence of myositis-specific and associated autoantibodies by enzyme-linked immunosorbent assay (ELISA). Cytokine levels were measured by cytometric bead array. Patients with IIM showed decreased protein expression of Ro52/Trim21 in comparison to healthy controls in PBMC (0·97 ± 0·60 versus 1·84 ± 0·92, P = 0·016), CD4+ lymphocytes (0·79 ± 0·54 versus 2·41 ± 0·78, P = 0·017), and monocytes (0·87 ± 0·35 versus 1·89 ± 0·20, P < 0·001). There were no significant differences among IIM groups. Also, a lower K48-mediated ubiquitination profile was found, predominantly in CD4+ lymphocytes. Furthermore, after mitogenic stimulation, there was a higher synthesis of proinflammatory cytokines by T cells [interleukin (IL)-17A and tumour necrosis factor (TNF)-α] and monocytes [IL-6 and interferon (IFN)-α] from IIM patients compared with healthy controls. Our data suggest that patients with IIM, mainly DM, are characterized by a deficient expression of Ro52/TRIM21 in different PBMC subsets (CD4+ lymphocytes and monocytes), along with lower K48-mediated ubiquitination, which is associated with a proinflammatory cytokine response.


Subject(s)
Cytokines/metabolism , Gene Expression , Inflammation Mediators/metabolism , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/metabolism , Myositis/etiology , Myositis/metabolism , Ribonucleoproteins/deficiency , Adult , Aged , Autoantibodies/blood , Autoantibodies/immunology , Biomarkers , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , Case-Control Studies , Female , Humans , Lymphocyte Activation/immunology , Male , Middle Aged , Myositis/diagnosis , Ubiquitination
9.
Sci Rep ; 6: 39318, 2016 12 23.
Article in English | MEDLINE | ID: mdl-28008940

ABSTRACT

Although recent studies have shed insights on some of the potential causes of male infertility, new underlining molecular mechanisms still remain to be elucidated. Makorin-2 (Mkrn2) is an evolutionarily conserved gene whose biological functions are not fully known. We developed an Mrkn2 knockout mouse model to study the role of this gene, and found that deletion of Mkrn2 in mice led to male infertility. Mkrn2 knockout mice produced abnormal sperms characterized by low number, poor motility, and aberrant morphology. Disruption of Mkrn2 also caused failure of sperm release (spermiation failure) and misarrangement of ectoplasmic specialization (ES) in testes, thus impairing spermiogenesis and spermiation. To understand the molecular mechanism, we found that expression of Odf2, a vital protein in spermatogenesis, was significantly decreased. In addition, we found that expression levels of Odf2 were decreased in Mkrn2 knockout mice. We also found that MKRN2 was prominently expressed in the sperm of normal men, but was significantly reduced in infertile men. This result indicates that our finding is clinically relevant. The results of our study provided insights into a new mechanism of male infertility caused by the MKRN2 downregulation.


Subject(s)
Heat-Shock Proteins/biosynthesis , Infertility, Male , Ribonucleoproteins/deficiency , Spermatogenesis , Animals , Gene Expression Profiling , Male , Mice, Knockout , Spermatozoa/cytology , Spermatozoa/physiology
10.
BMC Genomics ; 17(Suppl 9): 749, 2016 10 17.
Article in English | MEDLINE | ID: mdl-27766953

ABSTRACT

BACKGROUND: Loss of function in genes required for telomere maintenance result in disorders known as telomeropathies, which are characterized by a pattern of symptoms including generalized and specific lymphocytopenias as well as very short telomere length and disease anticipation. METHODS: Because human LARP7 is the most likely ortholog of the Tetrahymena p65 protein, which is required for telomerase activity in that organism, we investigated the effects of LARP7 silencing in human cells as well as in two distinct families with Alazami syndrome (loss of function of LARP7). RESULTS: Depletion of LARP7 caused a reduction in telomerase enzymatic activity and progressively shorter telomeres in human cancer cell lines. Alazami syndrome patients from two separate cohorts exhibited very short lymphocyte telomeres. Further, wild-type offspring of LARP7 mutant individuals also had very short telomeres, comparable to what is observed in telomerase (hTERT) mutant cohorts. CONCLUSIONS: Together, these experiments demonstrate that in addition to the readily apparent developmental disorder associated with LARP7 deficiency, an underlying telomeropathy exists even in unaffected siblings of these individuals.


Subject(s)
Genetic Association Studies , Ribonucleoproteins/deficiency , Telomere/genetics , Adult , Cell Line , Child , Cohort Studies , Consanguinity , Female , Gene Knockdown Techniques , Humans , In Situ Hybridization, Fluorescence , Male , Models, Genetic , Mutation , Pedigree , Phenotype , Telomere Homeostasis/genetics
11.
Mol Cell ; 61(5): 720-733, 2016 Mar 03.
Article in English | MEDLINE | ID: mdl-26942676

ABSTRACT

TRIM21 is a RING finger domain-containing ubiquitin E3 ligase whose expression is elevated in autoimmune disease. While TRIM21 plays an important role in immune activation during pathogen infection, little is known about its inherent cellular function. Here we show that TRIM21 plays an essential role in redox regulation by directly interacting with SQSTM1/p62 and ubiquitylating p62 at lysine 7 (K7) via K63-linkage. As p62 oligomerizes and sequesters client proteins in inclusions, the TRIM21-mediated p62 ubiquitylation abrogates p62 oligomerization and sequestration of proteins including Keap1, a negative regulator of antioxidant response. TRIM21-deficient cells display an enhanced antioxidant response and reduced cell death in response to oxidative stress. Genetic ablation of TRIM21 in mice confers protection from oxidative damages caused by arsenic-induced liver insult and pressure overload heart injury. Therefore, TRIM21 plays an essential role in p62-regulated redox homeostasis and may be a viable target for treating pathological conditions resulting from oxidative damage.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Heat-Shock Proteins/metabolism , Oxidative Stress , Ribonucleoproteins/metabolism , Ubiquitination , Adaptor Proteins, Signal Transducing/genetics , Animals , Arsenic Trioxide , Arsenicals , Cell Death , Chemical and Drug Induced Liver Injury/enzymology , Chemical and Drug Induced Liver Injury/genetics , Chemical and Drug Induced Liver Injury/pathology , Chemical and Drug Induced Liver Injury/prevention & control , Cytoskeletal Proteins/metabolism , Disease Models, Animal , HEK293 Cells , Heart Failure/enzymology , Heart Failure/genetics , Heart Failure/pathology , Heart Failure/prevention & control , Heat-Shock Proteins/genetics , Homeostasis , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Kelch-Like ECH-Associated Protein 1 , Liver/enzymology , Liver/pathology , Lysine , Mice , Mice, Inbred C57BL , Mice, Knockout , Myocardium/enzymology , Myocardium/pathology , Oxidation-Reduction , Oxides , Protein Binding , Protein Interaction Domains and Motifs , Protein Multimerization , RNA Interference , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics , Sequestosome-1 Protein , Signal Transduction , Time Factors , Transfection
12.
Ophthalmic Res ; 54(1): 10-7, 2015.
Article in English | MEDLINE | ID: mdl-25997407

ABSTRACT

AIMS: The aim of this study was to identify potential candidates and explore the possible mechanism in congenital cataract induced by tudor domain-containing 7 (TDRD7) deficiency. METHODS: The gene expression profile GSE25812 generated from 18 samples was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between disease and normal groups were identified. Then, gene ontology and pathway enrichment analysis of DEGs were performed. The protein-protein interaction (PPI) network and transcription factor (TF) regulatory network were constructed. The modules in the PPI network were identified. Significant target genes were selected from the TF regulatory network. RESULTS: A total of 329 DEGs were obtained, and downregulated DEGs were significantly enriched in biological processes including defense response and immune response. In the PPI network, high-degree genes of complement component 1, q subcomponent, A/B/C chain (C1QA/C1QB/C1QC), lymphocyte antigen 86 (LY86) and neuroblastoma RAS viral oncogene homolog (NRAS) were identified. From the TF regulatory network, the heat shock 27 kDa protein 1 (HSPB1) was the target of the estrogen receptor 1, and LY86 was the target of the v-myc avian myelocytomatosis viral oncogene homolog. CONCLUSION: HSPB1, NRAS, immune response, defense response and the related genes LY86, C1QA/C1QB/C1QC may play an important role in the development of congenital cataract induced by TDRD7 deficiency. However, further experiments are still needed.


Subject(s)
Cataract/congenital , Cataract/genetics , Ribonucleoproteins/deficiency , Animals , Cataract/metabolism , Computational Biology , Eye Proteins/genetics , Eye Proteins/metabolism , Gene Expression Profiling , Gene Knockdown Techniques , Gene Regulatory Networks , Mice , Microarray Analysis , Ribonucleoproteins/genetics , Signal Transduction/physiology , Transcription Factors/metabolism
13.
Nature ; 521(7552): 376-9, 2015 May 21.
Article in English | MEDLINE | ID: mdl-25970244

ABSTRACT

Recursive splicing is a process in which large introns are removed in multiple steps by re-splicing at ratchet points--5' splice sites recreated after splicing. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing. Here we identify 197 zero nucleotide exon ratchet points in 130 introns of 115 Drosophila genes from total RNA sequencing data generated from developmental time points, dissected tissues and cultured cells. The sequential nature of recursive splicing was confirmed by identification of lariat introns generated by splicing to and from the ratchet points. We also show that recursive splicing is a constitutive process, that depletion of U2AF inhibits recursive splicing, and that the sequence and function of ratchet points are evolutionarily conserved in Drosophila. Finally, we identify four recursively spliced human genes, one of which is also recursively spliced in Drosophila. Together, these results indicate that recursive splicing is commonly used in Drosophila, occurs in humans, and provides insight into the mechanisms by which some large introns are removed.


Subject(s)
Drosophila melanogaster/genetics , Genome, Insect/genetics , Nucleotides/genetics , RNA Splicing/genetics , Animals , Base Sequence , Cells, Cultured , Exons/genetics , Female , Genes, Insect/genetics , Humans , Introns/genetics , Male , Nuclear Proteins/deficiency , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , RNA Splice Sites/genetics , Reproducibility of Results , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics , Ribonucleoproteins/metabolism , Splicing Factor U2AF
14.
PLoS One ; 9(7): e101993, 2014.
Article in English | MEDLINE | ID: mdl-24999657

ABSTRACT

BACKGROUND: Despite the development and availability of hepatitis A virus (HAV) vaccine, HAV infection is still a major cause of acute hepatitis that occasionally leads to fatal liver disease. HAV internal ribosomal entry-site (IRES) is one of the attractive targets of antiviral agents against HAV. The aim of the present study is to evaluate the impact of La, one of the cellular proteins, on HAV IRES-mediated translation and HAV replication. METHODS AND FINDINGS: We investigated the therapeutic feasibility of siRNAs specific for cellular cofactors for HAV IRES-mediated translation in cell culture. It was revealed that siRNA against La could inhibit HAV IRES activities as well as HAV subgenomic replication. We also found that the Janus kinase (JAK) inhibitors SD-1029 and AG490, which reduce La expression, could inhibit HAV IRES activities as well as HAV replication. CONCLUSIONS: Inhibition of La by siRNAs and chemical agents could lead to the efficient inhibition of HAV IRES-mediated translation and HAV replication in cell culture models. La might play important roles in HAV replication and is being exploited as one of the therapeutic targets of host-targeting antivirals.


Subject(s)
Autoantigens/metabolism , Hepatitis A virus/physiology , Ribonucleoproteins/metabolism , Animals , Autoantigens/genetics , Cell Line, Tumor , Feasibility Studies , Gene Silencing , Genome, Viral/drug effects , Genome, Viral/genetics , Hepatitis A virus/genetics , Humans , Janus Kinases/antagonists & inhibitors , Protein Biosynthesis/drug effects , Protein Biosynthesis/genetics , Protein Kinase Inhibitors/pharmacology , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Small Interfering/genetics , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics , Tyrphostins/pharmacology , Virus Replication/drug effects , Virus Replication/genetics , Xanthenes/pharmacology , SS-B Antigen
15.
N Engl J Med ; 368(26): 2467-75, 2013 Jun 27.
Article in English | MEDLINE | ID: mdl-23738509

ABSTRACT

BACKGROUND: The onset of puberty is first detected as an increase in pulsatile secretion of gonadotropin-releasing hormone (GnRH). Early activation of the hypothalamic-pituitary-gonadal axis results in central precocious puberty. The timing of pubertal development is driven in part by genetic factors, but only a few, rare molecular defects associated with central precocious puberty have been identified. METHODS: We performed whole-exome sequencing in 40 members of 15 families with central precocious puberty. Candidate variants were confirmed with Sanger sequencing. We also performed quantitative real-time polymerase-chain-reaction assays to determine levels of messenger RNA (mRNA) in the hypothalami of mice at different ages. RESULTS: We identified four novel heterozygous mutations in MKRN3, the gene encoding makorin RING-finger protein 3, in 5 of the 15 families; both sexes were affected. The mutations included three frameshift mutations, predicted to encode truncated proteins, and one missense mutation, predicted to disrupt protein function. MKRN3 is a paternally expressed, imprinted gene located in the Prader-Willi syndrome critical region (chromosome 15q11-q13). All affected persons inherited the mutations from their fathers, a finding that indicates perfect segregation with the mode of inheritance expected for an imprinted gene. Levels of Mkrn3 mRNA were high in the arcuate nucleus of prepubertal mice, decreased immediately before puberty, and remained low after puberty. CONCLUSIONS: Deficiency of MKRN3 causes central precocious puberty in humans. (Funded by the National Institutes of Health and others.).


Subject(s)
Frameshift Mutation , Mutation, Missense , Puberty, Precocious/genetics , Ribonucleoproteins/genetics , Animals , Arcuate Nucleus of Hypothalamus/chemistry , Child , Child, Preschool , Exome , Female , Genetic Association Studies , Heterozygote , Humans , Hypothalamus/metabolism , Male , Mice , Pedigree , RNA, Messenger/analysis , Ribonucleoproteins/deficiency , Sequence Analysis, DNA , Ubiquitin-Protein Ligases
16.
Eukaryot Cell ; 12(6): 864-74, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23563484

ABSTRACT

The Saccharomyces cerevisiae Pbp1 [poly(A)-binding protein (Pab1)-binding protein] is believed to be involved in RNA metabolism and regulation of translation, since Pbp1 regulates a length of poly(A) tail and is involved in stress granule (SG) formation. However, a physiological function of Pbp1 remains unclear, since the pbp1Δ mutation has no obvious effect on cell growth. In this study, we showed that PBP1 genetically interacts with CCR4 and KHD1, which encode a cytoplasmic deadenylase and an RNA-binding protein, respectively. Ccr4 and Khd1 modulate a signal from Rho1 in the cell wall integrity pathway by regulating the expression of RhoGEF and RhoGAP, and the double deletion of CCR4 and KHD1 confers a severe growth defect displaying cell lysis. We found that the pbp1Δ mutation suppressed the growth defect caused by the ccr4Δ khd1Δ mutation. The pbp1Δ mutation also suppressed the growth defect caused by double deletion of POP2, encoding another cytoplasmic deadenylase, and KHD1. Deletion of the gene encoding previously known Pbp1-interacting factor Lsm12, Pbp4, or Mkt1 did not suppress the growth defect of the ccr4Δ khd1Δ mutant, suggesting that Pbp1 acts independently of these factors in this process. We then screened novel Pbp1-interacting factors and found that Pbp1 interacts with ribosomal proteins Rpl12a and Rpl12b. Similarly to the pbp1Δ mutation, the rpl12aΔ and rpl12bΔ mutations also suppressed the growth defect caused by the ccr4Δ khd1Δ mutation. Our results suggest that Pbp1 is involved in the Ccr4- and Khd1-mediated regulation of cell growth through the association with Rpl12a and Rpl12b.


Subject(s)
Carrier Proteins/genetics , Gene Expression Regulation, Fungal , Ribonucleases/genetics , Ribonucleoproteins/genetics , Ribosomal Proteins/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Carrier Proteins/metabolism , Escherichia coli/genetics , Gene Deletion , Gene Expression Regulation, Developmental , Ribonucleases/deficiency , Ribonucleoproteins/deficiency , Ribosomal Proteins/deficiency , Saccharomyces cerevisiae/growth & development , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Signal Transduction
17.
Nat Immunol ; 14(2): 172-8, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23222971

ABSTRACT

DDX41 is a sensor of intracellular double-stranded DNA (dsDNA) in myeloid dendritic cells (mDCs) that triggers a type I interferon response via the signaling adaptor STING. We identified the E3 ligase TRIM21 as a DDX41-interacting protein and found that knockdown of or deficiency in TRIM21 resulted in enhanced type I interferon responses to intracellular dsDNA and DNA viruses. Overexpression of TRIM21 resulted in more degradation of DDX41 and less production of interferon-ß (IFN-ß) in response to intracellular dsDNA. The SPRY-PRY domain of TRIM21 interacted with the DEADc domain of DDX41. Lys9 and Lys115 of DDX41 were the targets of TRIM21-mediated ubiquitination. TRIM21 is therefore an interferon-inducible E3 ligase that induces the Lys48 (K48)-linked ubiquitination and degradation of DDX41 and negatively regulates the innate immune response to intracellular dsDNA.


Subject(s)
DNA, Viral/immunology , DNA/immunology , Dendritic Cells/immunology , Immunity, Innate , Ribonucleoproteins/immunology , Animals , DNA/genetics , DNA, Viral/genetics , Dendritic Cells/pathology , Dendritic Cells/virology , Gene Expression Regulation , Interferon-beta/biosynthesis , Interferon-beta/immunology , Lysine/metabolism , Membrane Proteins/genetics , Membrane Proteins/immunology , Mice , Mice, Transgenic , Orthoreovirus, Mammalian/physiology , Protein Structure, Tertiary , Proteolysis , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics , Signal Transduction/immunology , Ubiquitination , Vesiculovirus/physiology
18.
Am J Physiol Cell Physiol ; 298(1): C46-55, 2010 Jan.
Article in English | MEDLINE | ID: mdl-19889961

ABSTRACT

Acheron (Achn) was originally identified as novel gene that is induced when insect muscles become committed to die at the end of metamorphosis. In separate studies, we have demonstrated that Achn acts upstream of MyoD and is required by mammalian myoblasts to either differentiate or undergo apoptosis following loss of growth factors. In the present study we examined the role of Achn in regulating integrin-extracellular matrix interactions that are required for myogenesis. Both control C2C12 myoblasts and those engineered to express ectopic Achn expressed the fibronectin receptor integrin alpha(5)beta(1) in the presence of growth factors and the laminin receptor alpha(7)beta(1) following growth factor withdrawal. Expression of the laminin receptor was blocked in cells expressing either Achn antisense or an Achn deletion mutant that blocks differentiation. Control cells and those expressing ectopic Achn undergo sequential and transient increases in both substrate adhesion and migration before cell fusion. Blockade of Achn expression reduced these effects on laminin but not on fibronectin. Taken together, these data suggest that Achn may influence differentiation in part via its control of cell adhesion dynamics.


Subject(s)
Autoantigens/physiology , Integrins/genetics , Myoblasts/physiology , Ribonucleoproteins/physiology , Autoantigens/genetics , Blotting, Western , Cell Differentiation/genetics , Cell Differentiation/physiology , Cell Movement , Cytoskeleton/physiology , DNA Primers , Genetic Engineering/methods , Homeostasis , Humans , Microscopy, Fluorescence , Myoblasts/cytology , Polymerase Chain Reaction , RNA, Messenger/genetics , Reverse Transcriptase Polymerase Chain Reaction , Ribonucleoproteins/deficiency , Ribonucleoproteins/genetics , Transfection , SS-B Antigen
20.
J Virol ; 83(23): 12526-34, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19776129

ABSTRACT

Moloney murine leukemia virus (MLV) selectively encapsidates host mY1 and mY3 RNAs. These noncoding RNA polymerase III transcripts are normally complexed with the Ro60 and La proteins, which are autoantigens associated with rheumatic disease that function in RNA biogenesis and quality control. Here, MLV replication and mY RNA packaging were analyzed using Ro60 knockout embryonic fibroblasts, which contain only approximately 3% as much mY RNA as wild-type cells. Virus spread at the same rate in wild-type and Ro knockout cells. Surprisingly, MLV virions shed by Ro60 knockout cells continued to package high levels of mY1 and mY3 (about two copies of each) like those from wild-type cells, even though mY RNAs were barely detectable within producer cells. As a result, for MLV produced in Ro60 knockout cells, encapsidation selectivity from among all cell RNAs was even higher for mY RNAs than for the viral genome. Whereas mY RNAs are largely cytoplasmic in wild-type cells, fractionation of knockout cells revealed that the residual mY RNAs were relatively abundant in nuclei, likely reflecting the fact that most mY RNAs were degraded shortly after transcription in the absence of Ro60. Together, these data suggest that these small, labile host RNAs may be recruited at a very early stage of their biogenesis and may indicate an intersection of retroviral assembly and RNA quality control pathways.


Subject(s)
Moloney murine leukemia virus/physiology , RNA, Small Cytoplasmic/metabolism , Virus Assembly , Animals , Autoantigens , Cell Line , Fibroblasts/virology , Mice , Mice, Knockout , Ribonucleoproteins/deficiency
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