1
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Jahan J, Joshi S, Oca IMD, Toelle A, Lopez-Yang C, Chacon CV, Beyer AM, Garcia CA, Jarajapu YP. The role of telomerase reverse transcriptase in the mitochondrial protective functions of Angiotensin-(1-7) in diabetic CD34 + cells. Biochem Pharmacol 2024; 222:116109. [PMID: 38458330 PMCID: PMC11007670 DOI: 10.1016/j.bcp.2024.116109] [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: 10/09/2023] [Revised: 01/08/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Angiotensin (Ang)-(1-7) stimulates vasoprotective functions of diabetic (DB) CD34+ hematopoietic stem/progenitor cells partly by decreasing reactive oxygen species (ROS), increasing nitric oxide (NO) levels and decreasing TGFβ1 secretion. Telomerase reverse transcriptase (TERT) translocates to mitochondria and regulates ROS generation. Alternative splicing of TERT results in variants α-, β- and α-β-TERT, which may oppose functions of full-length (FL) TERT. This study tested if the protective functions of Ang-(1-7) or TGFβ1-silencing are mediated by mitoTERT and that diabetes decreases FL-TERT expression by inducing splicing. CD34+ cells were isolated from the peripheral blood mononuclear cells of nondiabetic (ND, n = 68) or DB (n = 74) subjects. NO and mitoROS levels were evaluated by flow cytometry. TERT splice variants and mitoDNA-lesions were characterized by qPCR. TRAP assay was used for telomerase activity. Decoy peptide was used to block mitochondrial translocation (mitoXTERT). TERT inhibitor or mitoXTERT prevented the effects of Ang-(1-7) on NO or mitoROS levels in DB-CD34+ cells. FL-TERT expression and telomerase activity were lower and mitoDNA-lesions were higher in DB cells compared to ND and were reversed by Ang-(1-7) or TGFβ1-silencing. The prevalence of TERT splice variants, with predominant β-TERT expression, was higher and the expression of FL-TERT was lower in DB cells (n = 25) compared to ND (n = 30). Ang-(1-7) or TGFβ1-silencing decreased TERT-splicing and increased FL-TERT. Blocking of β-splicing increased FL-TERT and protected mitoDNA in DB-cells. The findings suggest that diabetes induces TERT-splicing in CD34+ cells and that β-TERT splice variant largely contributes to the mitoDNA oxidative damage.
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Affiliation(s)
- Jesmin Jahan
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | - Shrinidh Joshi
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | | | - Andrew Toelle
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | | | | | - Andreas M Beyer
- Department of Medicine and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Yagna Pr Jarajapu
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA.
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2
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Mekler AA, Schwartz DR, Savelieva OE. Genetic Discrimination of Grade 3 and Grade 4 Gliomas by Artificial Neural Network. Cell Mol Neurobiol 2023; 44:13. [PMID: 38150033 DOI: 10.1007/s10571-023-01448-z] [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: 10/08/2023] [Accepted: 12/16/2023] [Indexed: 12/28/2023]
Abstract
Gliomas, including anaplastic gliomas (AG; grade 3) and glioblastomas (GBM; grade 4), are malignant brain tumors associated with poor prognosis and low survival rates. Current classification systems based on histopathology have limitations due to intratumoral heterogeneity. The treatment and prognosis are distinctly different between grade 3 and grade 4 gliomas patients. Therefore, there is a need for molecular markers to differentiate these tumors accurately. In this study, we aimed to identify a gene expression signature using an artificial neural network (ANN) in application to microarray and serial analysis of gene expression (SAGE) data for grade 3 (AG) and grade 4 (GBM) gliomas discrimination. We acquired gene expression data from publicly available datasets on glial tumors of grades 3 and 4-a total of 93 grade 3 gliomas and 224 grade 4 gliomas. To select genes for classification, we implemented an artificial neural network-based method using a combination of self-organized maps (SOM) and perceptron. In general, we implemented a multi-stage procedure that involved multiple runs of a genetic algorithm to identify genes that provided optimal clusterization on the SOM. We performed this procedure multiple times, resulting in different sets of genes each time. Eventually, we selected several genes that appeared most frequently in the reduced sets and performed classification using them. Our analysis identified a set of seven genes (BCAS4, GLUD2, KCNJ10, KCND2, AKR7A2, FOLR1, and KIAA0319). The classification accuracy using this gene set was 87.5%. These findings suggest the potential of this gene set as a molecular marker for distinguishing grade 3 (AG) from grade 4 (GBM) gliomas.
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Affiliation(s)
- Aleksei A Mekler
- Department for Innovations and Analytics, St. Petersburg State Pediatric Medical University, Saint Petersburg, 194100, Russia.
| | - Dmitry R Schwartz
- Institute of Computer Science and Technologies, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Olga E Savelieva
- Research Center and Department of Biological Chemistry, St. Petersburg State Pediatric Medical University, Saint Petersburg, 194100, Russia
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3
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Liu B, Zhao S, Ma L, Zang T, Huang C, Tang X. Bioinformatics Analysis of Hub Genes Involved in Smoke-Induced Hemifacial Microsomia Pathogenesis. J Craniofac Surg 2023; 34:2551-2555. [PMID: 37665067 DOI: 10.1097/scs.0000000000009616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/20/2023] [Indexed: 09/05/2023] Open
Abstract
OBJECTIVE Tobacco smoke is a recognized teratogen, which increases the risk for hemifacial microsomia (HFM) of the fetus during maternal pregnancy. The present study aimed to explore potential mechanisms and verify hub genes of HFM associated with smoke and tobacco smoke pollution (TSP) via bioinformatics methods. METHODS Hemifacial microsomia and smoke and TSP pathogenic genes were obtained. A protein-protein interactional (PPI) network was constructed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and molecular complex detection were performed by Metascape. Finally, we used the cytoHubba plug-in to screen the hub genes. RESULTS A total of 43 HFM genes and 50 optimal smoke candidate genes were selected. Functional enrichment analysis largely focused on tissue morphogenesis and development. Two modules were identified from the PPI network, and 10 hub genes were screened out. The genes most relevant to smoke-induced HFM pathogenesis included TP53 , ESR1 , ESR2 , and HNRNPL. CONCLUSIONS This study identified some significant hub genes, pathways, and modules of HFM related to smoke by bioinformatics analyses. Our results suggest that the TP53 , ESR1 , ESR2 , and HNRNPL gene subfamilies may have played a major role in HFM induced by smoke and TSP.
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Affiliation(s)
- Bingyang Liu
- Department of Maxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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4
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Dar MS, Mensah IK, He M, McGovern S, Sohal IS, Whitlock HC, Bippus NE, Ceminsky M, Emerson ML, Tan HJ, Hall MC, Gowher H. Dnmt3bas coordinates transcriptional induction and alternative exon inclusion to promote catalytically active Dnmt3b expression. Cell Rep 2023; 42:112587. [PMID: 37294637 PMCID: PMC10592478 DOI: 10.1016/j.celrep.2023.112587] [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: 06/03/2022] [Revised: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/11/2023] Open
Abstract
Embryonic expression of DNMT3B is critical for establishing de novo DNA methylation. This study uncovers the mechanism through which the promoter-associated long non-coding RNA (lncRNA) Dnmt3bas controls the induction and alternative splicing of Dnmt3b during embryonic stem cell (ESC) differentiation. Dnmt3bas recruits the PRC2 (polycomb repressive complex 2) at cis-regulatory elements of the Dnmt3b gene expressed at a basal level. Correspondingly, Dnmt3bas knockdown enhances Dnmt3b transcriptional induction, whereas overexpression of Dnmt3bas dampens it. Dnmt3b induction coincides with exon inclusion, switching the predominant isoform from the inactive Dnmt3b6 to the active Dnmt3b1. Intriguingly, overexpressing Dnmt3bas further enhances the Dnmt3b1:Dnmt3b6 ratio, attributed to its interaction with hnRNPL (heterogeneous nuclear ribonucleoprotein L), a splicing factor that promotes exon inclusion. Our data suggest that Dnmt3bas coordinates alternative splicing and transcriptional induction of Dnmt3b by facilitating the hnRNPL and RNA polymerase II (RNA Pol II) interaction at the Dnmt3b promoter. This dual mechanism precisely regulates the expression of catalytically active DNMT3B, ensuring fidelity and specificity of de novo DNA methylation.
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Affiliation(s)
- Mohd Saleem Dar
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ikjot Singh Sohal
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Nina Elise Bippus
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Madison Ceminsky
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Martin L Emerson
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Hern J Tan
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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5
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Jiang X, Gatt A, Lashley T. HnRNP Pathologies in Frontotemporal Lobar Degeneration. Cells 2023; 12:1633. [PMID: 37371103 DOI: 10.3390/cells12121633] [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: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Frontotemporal dementia (FTD) is the second most common form of young-onset (<65 years) dementia. Clinically, it primarily manifests as a disorder of behavioural, executive, and/or language functions. Pathologically, frontotemporal lobar degeneration (FTLD) is the predominant cause of FTD. FTLD is a proteinopathy, and the main pathological proteins identified so far are tau, TAR DNA-binding protein 43 (TDP-43), and fused in sarcoma (FUS). As TDP-43 and FUS are members of the heterogeneous ribonucleic acid protein (hnRNP) family, many studies in recent years have expanded the research on the relationship between other hnRNPs and FTLD pathology. Indeed, these studies provide evidence for an association between hnRNP abnormalities and FTLD. In particular, several studies have shown that multiple hnRNPs may exhibit nuclear depletion and cytoplasmic mislocalisation within neurons in FTLD cases. However, due to the diversity and complex association of hnRNPs, most studies are still at the stage of histological discovery of different hnRNP abnormalities in FTLD. We herein review the latest studies relating hnRNPs to FTLD. Together, these studies outline an important role of multiple hnRNPs in the pathogenesis of FTLD and suggest that future research into FTLD should include the whole spectrum of this protein family.
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Affiliation(s)
- Xinwa Jiang
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ariana Gatt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
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6
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Nuthalapati SS, Ulshöfer CJ, Bindereif A. CircRNP complexes: from nature to design. J Mol Cell Biol 2023; 15:mjad006. [PMID: 36722152 PMCID: PMC10234438 DOI: 10.1093/jmcb/mjad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/18/2022] [Accepted: 01/30/2023] [Indexed: 02/02/2023] Open
Affiliation(s)
| | | | - Albrecht Bindereif
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
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7
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Mathew V, Mei A, Giwa H, Cheong A, Chander A, Zou A, Blanton RM, Kashpur O, Cui W, Slonim D, Mahmoud T, O'Tierney-Ginn P, Mager J, Draper I, Wallingford MC. hnRNPL expression dynamics in the embryo and placenta. Gene Expr Patterns 2023; 48:119319. [PMID: 37148985 PMCID: PMC10330435 DOI: 10.1016/j.gep.2023.119319] [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: 03/07/2022] [Revised: 03/13/2023] [Accepted: 04/04/2023] [Indexed: 05/08/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein L (hnRNPL) is a conserved RNA binding protein (RBP) that plays an important role in the alternative splicing of gene transcripts, and thus in the generation of specific protein isoforms. Global deficiency in hnRNPL in mice results in preimplantation embryonic lethality at embryonic day (E) 3.5. To begin to understand the contribution of hnRNPL-regulated pathways in the normal development of the embryo and placenta, we determined hnRNPL expression profile and subcellular localization throughout development. Proteome and Western blot analyses were employed to determine hnRNPL abundance between E3.5 and E17.5. Histological analyses supported that the embryo and implantation site display distinct hnRNPL localization patterns. In the fully developed mouse placenta, nuclear hnRNPL was observed broadly in trophoblasts, whereas within the implantation site a discrete subset of cells showed hnRNPL outside the nucleus. In the first-trimester human placenta, hnRNPL was detected in the undifferentiated cytotrophoblasts, suggesting a role for this factor in trophoblast progenitors. Parallel in vitro studies utilizing Htr8 and Jeg3 cell lines confirmed expression of hnRNPL in cellular models of human trophoblasts. These studies [support] coordinated regulation of hnRNPL during the normal developmental program in the mammalian embryo and placenta.
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Affiliation(s)
- Vineetha Mathew
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Ariel Mei
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Hamida Giwa
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Agnes Cheong
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ashmita Chander
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Aaron Zou
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Robert M Blanton
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Olga Kashpur
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Donna Slonim
- Department of Computer Science, Tufts University, 177 College Avenue, Medford, MA, 02155, USA
| | - Taysir Mahmoud
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Perrie O'Tierney-Ginn
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Isabelle Draper
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA.
| | - Mary C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA; Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA.
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8
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Ellis JA, Hale MA, Cleary JD, Wang E, Andrew Berglund J. Alternative splicing outcomes across an RNA-binding protein concentration gradient. J Mol Biol 2023:168156. [PMID: 37230319 DOI: 10.1016/j.jmb.2023.168156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/18/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
Alternative splicing (AS) is a dynamic RNA processing step that produces multiple RNA isoforms from a single pre-mRNA transcript and contributes to the complexity of the cellular transcriptome and proteome. This process is regulated through a network of cis-regulatory sequence elements and trans-acting factors, most-notably RNA binding proteins (RBPs). The muscleblind-like (MBNL) and RNA binding fox-1 homolog (RBFOX) are two well characterized families of RBPs that regulate fetal to adult AS transitions critical for proper muscle, heart, and central nervous system development. To better understand how the concentration of these RBPs influences AS transcriptome wide, we engineered a MBNL1 and RBFOX1 inducible HEK-293 cell line. Modest induction of exogenous RBFOX1 in this cell line modulated MBNL1-dependent AS outcomes in 3 skipped exon events, despite significant levels of endogenous RBFOX1 and RBFOX2. Due to background RBFOX levels, we conducted a focused analysis of dose-dependent MBNL1 skipped exon AS outcomes and generated transcriptome wide dose-response curves. Analysis of this data demonstrates that MBNL1-regulated exclusion events may require higher concentrations of MBNL1 protein to properly regulate AS outcomes compared to inclusion events and that multiple arrangements of YGCY motifs can produce similar splicing outcomes. These results suggest that rather than a simple relationship between the organization of RBP binding sites and a specific splicing outcome, that complex interaction networks govern both AS inclusion and exclusion events across a RBP gradient.
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Affiliation(s)
- Joseph A Ellis
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Melissa A Hale
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; Department of Neurology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - John D Cleary
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Eric Wang
- Department of Microbiology and Molecular Genetics & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - J Andrew Berglund
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; Department of Biological Sciences, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; RNA Institute, State University of New York at Albany, LSRB-2033, 1400 Washington Avenue, Albany, New York, 12222.
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9
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Qazi S, Uckun FM. CD22 Exon 12 Deletion as an Independent Predictor of Poor Treatment Outcomes in B-ALL. Cancers (Basel) 2023; 15:1599. [PMID: 36900389 PMCID: PMC10000517 DOI: 10.3390/cancers15051599] [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: 01/15/2023] [Revised: 02/21/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
We previously reported a splicing defect (CD22ΔE12) associated with the deletion of exon 12 of the inhibitory co-receptor CD22 (Siglec-2) in leukemia cells from patients with CD19+ B-precursor acute lymphoblastic leukemia (B-ALL). CD22ΔE12 causes a truncating frameshift mutation and yields a dysfunctional CD22 protein that lacks most of the cytoplasmic domain required for its inhibitory function, and it is associated with aggressive in vivo growth of human B-ALL cells in mouse xenograft models. Although CD22ΔE12 with selective reduction of CD22 exon 12 (CD22E12) levels was detected in a high percentage of newly diagnosed as well as relapsed B-ALL patients, its clinical significance remains unknown. We hypothesized that B-ALL patients with very low levels of wildtype CD22 would exhibit a more aggressive disease with a worse prognosis because the missing inhibitory function of the truncated CD22 molecules could not be adequately compensated by competing wildtype CD22. Here, we demonstrate that newly diagnosed B-ALL patients with very low levels of residual wildtype CD22 ("CD22E12low"), as measured by RNAseq-based CD22E12 mRNA levels, have significantly worse leukemia-free survival (LFS) as well as overall survival (OS) than other B-ALL patients. CD22E12low status was identified as a poor prognostic indicator in both univariate and multivariate Cox proportional hazards models. CD22E12low status at presentation shows clinical potential as a poor prognostic biomarker that may guide the early allocation of risk-adjusted, patient-tailored treatment regimens and refine risk classification in high-risk B-ALL.
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Affiliation(s)
- Sanjive Qazi
- Ares Pharmaceuticals, Saint Paul, MN 55110, USA
- Division of Hematology-Oncology, Department of Pediatrics and Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine (USC KSOM), Los Angeles, CA 90027, USA
| | - Fatih M. Uckun
- Ares Pharmaceuticals, Saint Paul, MN 55110, USA
- Division of Hematology-Oncology, Department of Pediatrics and Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine (USC KSOM), Los Angeles, CA 90027, USA
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10
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Pinch M, Bendzus-Mendoza H, Hansen IA. Transcriptomics analysis of ethanol treatment of male Aedes aegypti reveals a small set of putative radioprotective genes. Front Physiol 2023; 14:1120408. [PMID: 36793417 PMCID: PMC9922702 DOI: 10.3389/fphys.2023.1120408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023] Open
Abstract
Introduction: Sterile Insect Technique (SIT) is based on releasing sterilized male insects into wild insect populations to compete for mating with wild females. Wild females mated with sterile males will produce inviable eggs, leading to a decline in population of that insect species. Sterilization with ionizing radiation (x-rays) is a commonly used mechanism for sterilization of males. Since irradiation can cause damage to both, somatic and germ cells, and can severely reduce the competitiveness of sterilized males relative to wild males, means to minimize the detrimental effects of radiation are required to produce sterile, competitive males for release. In an earlier study, we identified ethanol as a functional radioprotector in mosquitoes. Methods: Here, we used Illumina RNA-seq to profile changes in gene expression of male Aedes aegypti mosquitoes fed on 5% ethanol for 48 hours prior to receiving a sterilizing x-ray dose, compared to males fed on water prior to sterilization. Results: RNA-seq revealed a robust activation of DNA repair genes in both ethanol-fed and water-fed males after irradiation, but surprisingly few differences in gene expression between ethanol-fed and water-fed males regardless of radiation treatment. Discussion: While differences in gene expression due to ethanol exposure were minimal, we identified a small group of genes that may prime ethanol-fed mosquitoes for improved survivability in response to sterilizing radiation.
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Affiliation(s)
- Matthew Pinch
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | - Harley Bendzus-Mendoza
- Department of Computer Science, New Mexico State University, Las Cruces, NM, United States
| | - Immo A. Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
- Institute of Applied Biosciences, New Mexico State University, Las Cruces, NM, United States
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11
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Fouani Y, Kirchhof L, Stanicek L, Luxán G, Heumüller AW, Knau A, Fischer A, Devraj K, John D, Neumann P, Bindereif A, Boon RA, Liebner S, Wittig I, Mogler C, Karimova M, Dimmeler S, Jaé N. The splicing-regulatory lncRNA NTRAS sustains vascular integrity. EMBO Rep 2022; 23:e54157. [PMID: 35527520 PMCID: PMC9171682 DOI: 10.15252/embr.202154157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/17/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Vascular integrity is essential for organ homeostasis to prevent edema formation and infiltration of inflammatory cells. Long non‐coding RNAs (lncRNAs) are important regulators of gene expression and often expressed in a cell type‐specific manner. By screening for endothelial‐enriched lncRNAs, we identified the undescribed lncRNA NTRAS to control endothelial cell functions. Silencing of NTRAS induces endothelial cell dysfunction in vitro and increases vascular permeability and lethality in mice. Biochemical analysis revealed that NTRAS, through its CA‐dinucleotide repeat motif, sequesters the splicing regulator hnRNPL to control alternative splicing of tight junction protein 1 (TJP1; also named zona occludens 1, ZO‐1) pre‐mRNA. Deletion of the hnRNPL binding motif in mice (Ntras∆CA/∆CA) significantly repressed TJP1 exon 20 usage, favoring expression of the TJP1α‐ isoform, which augments permeability of the endothelial monolayer. Ntras∆CA/∆CA mice further showed reduced retinal vessel growth and increased vascular permeability and myocarditis. In summary, this study demonstrates that NTRAS is an essential gatekeeper of vascular integrity.
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Affiliation(s)
- Youssef Fouani
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt, Germany
| | - Luisa Kirchhof
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt, Germany
| | - Laura Stanicek
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany.,Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Center, Amsterdam, The Netherlands
| | - Guillermo Luxán
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt, Germany
| | - Andreas W Heumüller
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt, Germany
| | - Andrea Knau
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany
| | - Ariane Fischer
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany
| | - Kavi Devraj
- Institute of Neurology (Edinger Institute), University Hospital, Goethe University, Frankfurt, Germany
| | - David John
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany
| | - Philipp Neumann
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany
| | | | - Reinier A Boon
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt, Germany.,Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Center, Amsterdam, The Netherlands
| | - Stefan Liebner
- Institute of Neurology (Edinger Institute), University Hospital, Goethe University, Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
| | - Carolin Mogler
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Madina Karimova
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt, Germany
| | - Nicolas Jaé
- Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University, Frankfurt, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt, Germany
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12
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Zhao H, Wu W, Li X, Chen W. Long noncoding RNA UCA1 promotes glutamine-driven anaplerosis of bladder cancer by interacting with hnRNP I/L to upregulate GPT2 expression. Transl Oncol 2022; 17:101340. [PMID: 35021150 PMCID: PMC8752948 DOI: 10.1016/j.tranon.2022.101340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/13/2021] [Accepted: 01/04/2022] [Indexed: 12/23/2022] Open
Abstract
Long noncoding RNA urothelial cancer associated 1 (UCA1), initially identified in bladder cancer, is associated with multiple cellular processes, including metabolic reprogramming. However, its characteristics in the anaplerosis context of bladder cancer (BLCA) remain elusive. We identified UCA1 as a binding partner of heterogeneous nuclear ribonucleoproteins (hnRNPs) I and L, RNA-binding proteins (RBPs) with no previously known role in metabolic reprogramming. UCA1 and hnRNP I/L profoundly affected glycolysis, TCA cycle, glutaminolysis, and proliferation of BLCA. Importantly, UCA1 specifically bound to and facilitated the combination of hnRNP I/L to the promoter of glutamic pyruvate transaminase 2 (GPT2), an enzyme transferring glutamate to α-ketoglutarate, resulting in upregulated expression of GPT2 and enhanced glutamine-derived carbons in the TCA cycle. We also systematically confirmed the influence of UCA1 and hnRNP I/L on metabolism and proliferation via glutamine-driven anaplerosis in BLCA. Our study revealed the critical role of UCA1-mediated mechanisms involved in glutamine-driven anaplerosis and provided novel evidence that lncRNA regulates metabolic reprogramming in tumor cells.
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Affiliation(s)
- Hua Zhao
- Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - Wenjing Wu
- Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China; Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - Wei Chen
- Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China.
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13
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Gañez-Zapater A, Mackowiak SD, Guo Y, Tarbier M, Jordán-Pla A, Friedländer MR, Visa N, Östlund Farrants AK. The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA. Mol Genet Genomics 2022; 297:463-484. [PMID: 35187582 PMCID: PMC8960663 DOI: 10.1007/s00438-022-01863-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes mainly associated with transcriptional initiation. They also have a role in alternative splicing, which has been shown for BRM-containing SWI/SNF complexes at a few genes. Here, we have identified a subset of genes which harbour alternative exons that are affected by SWI/SNF ATPases by expressing the ATPases BRG1 and BRM in C33A cells, a BRG1- and BRM-deficient cell line, and analysed the effect on splicing by RNA sequencing. BRG1- and BRM-affected sub-sets of genes favouring both exon inclusion and exon skipping, with only a minor overlap between the ATPase. Some of the changes in alternative splicing induced by BRG1 and BRM expression did not require the ATPase activity. The BRG1-ATPase independent included exons displayed an exon signature of a high GC content. By investigating three genes with exons affected by the BRG-ATPase-deficient variant, we show that these exons accumulated phosphorylated RNA pol II CTD, both serine 2 and serine 5 phosphorylation, without an enrichment of the RNA polymerase II. The ATPases were recruited to the alternative exons, together with both core and signature subunits of SWI/SNF complexes, and promoted the binding of RNA binding factors to chromatin and RNA at the alternative exons. The interaction with the nascent RNP, however, did not reflect the association to chromatin. The hnRNPL, hnRNPU and SAM68 proteins associated with chromatin in cells expressing BRG1 and BRM wild type, but the binding of hnRNPU to the nascent RNP was excluded. This suggests that SWI/SNF can regulate alternative splicing by interacting with splicing-RNA binding factor and influence their binding to the nascent pre-mRNA particle.
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Affiliation(s)
- Antoni Gañez-Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Center for Genomic Regulation, 08003, Barcelona, Spain
| | - Sebastian D Mackowiak
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencies Biológicas, Valencia University, C/Dr. Moliner, 50, 46100, Burjassot, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden.
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14
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Zhou X, Zou L, Liao H, Luo J, Yang T, Wu J, Chen W, Wu K, Cen S, Lv D, Shu F, Yang Y, Li C, Li B, Mao X. Abrogation of HnRNP L enhances anti-PD-1 therapy efficacy via diminishing PD-L1 and promoting CD8 + T cell-mediated ferroptosis in castration-resistant prostate cancer. Acta Pharm Sin B 2022; 12:692-707. [PMID: 35256940 PMCID: PMC8897216 DOI: 10.1016/j.apsb.2021.07.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/20/2021] [Accepted: 07/09/2021] [Indexed: 01/18/2023] Open
Abstract
Owing to incurable castration-resistant prostate cancer (CRPC) ultimately developing after treating with androgen deprivation therapy (ADT), it is vital to devise new therapeutic strategies to treat CRPC. Treatments that target programmed cell death protein 1 (PD-1) and programmed death ligand-1 (PD-L1) have been approved for human cancers with clinical benefit. However, many patients, especially prostate cancer, fail to respond to anti-PD-1/PD-L1 treatment, so it is an urgent need to seek a support strategy for improving the traditional PD-1/PD-L1 targeting immunotherapy. In the present study, analyzing the data from our prostate cancer tissue microarray, we found that PD-L1 expression was positively correlated with the expression of heterogeneous nuclear ribonucleoprotein L (HnRNP L). Hence, we further investigated the potential role of HnRNP L on the PD-L1 expression, the sensitivity of cancer cells to T-cell killing and the synergistic effect with anti-PD-1 therapy in CRPC. Indeed, HnRNP L knockdown effectively decreased PD-L1 expression and recovered the sensitivity of cancer cells to T-cell killing in vitro and in vivo, on the contrary, HnRNP L overexpression led to the opposite effect in CRPC cells. In addition, consistent with the previous study, we revealed that ferroptosis played a critical role in T-cell-induced cancer cell death, and HnRNP L promoted the cancer immune escape partly through targeting YY1/PD-L1 axis and inhibiting ferroptosis in CRPC cells. Furthermore, HnRNP L knockdown enhanced antitumor immunity by recruiting infiltrating CD8+ T cells and synergized with anti-PD-1 therapy in CRPC tumors. This study provided biological evidence that HnRNP L knockdown might be a novel therapeutic agent in PD-L1/PD-1 blockade strategy that enhanced anti-tumor immune response in CRPC.
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Key Words
- ADT, androgen deprivation therapy
- Anti-PD-1 therapy
- CRPC, castration-resistant prostate cancer
- Castration-resistant prostate cancer
- DMSO, dimethyl sulfoxide
- ELISA, enzyme-linked immunosorbent assay
- FBS, fetal bovine serum
- Fer-1, ferrostatin-1
- Ferroptosis
- GSH, glutathione
- HnRNP L
- HnRNP L, heterogeneous nuclear ribonucleoprotein L
- IL, interleukin
- INF-γ, interferon gamma
- Immune checkpoint blockade
- Immune escape
- PD-1, programmed cell death protein 1
- PD-L1
- PD-L1, programmed death ligand1
- ROS, reactive oxygen species
- STAT, signal transducer and activator of transcription
- YY1
- qRT-PCR, quantitative reverse transcription polymerase chain reaction
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Affiliation(s)
- Xumin Zhou
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Libin Zou
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Hangyu Liao
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Junqi Luo
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Taowei Yang
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Jun Wu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Wenbin Chen
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Kaihui Wu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Shengren Cen
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Daojun Lv
- Department of Urology, Minimally Invasive Surgery Center, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Fangpeng Shu
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yu Yang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Chun Li
- Nursing Department, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Corresponding authors. Tel.: +86 20 62782725; fax: +86 20 62782725.
| | - Bingkun Li
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
- Corresponding authors. Tel.: +86 20 62782725; fax: +86 20 62782725.
| | - Xiangming Mao
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
- Corresponding authors. Tel.: +86 20 62782725; fax: +86 20 62782725.
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15
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Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing. Nat Commun 2021; 12:6452. [PMID: 34750379 PMCID: PMC8575775 DOI: 10.1038/s41467-021-26799-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
The RNA recognition motif (RRM) binds to nucleic acids as well as proteins. More than one such domain is found in the pre-mRNA processing hnRNP proteins. While the mode of RNA recognition by RRMs is known, the molecular basis of their protein interaction remains obscure. Here we describe the mode of interaction between hnRNP L and LL with the methyltransferase SETD2. We demonstrate that for the interaction to occur, a leucine pair within a highly conserved stretch of SETD2 insert their side chains in hydrophobic pockets formed by hnRNP L RRM2. Notably, the structure also highlights that RRM2 can form a ternary complex with SETD2 and RNA. Remarkably, mutating the leucine pair in SETD2 also results in its reduced interaction with other hnRNPs. Importantly, the similarity that the mode of SETD2-hnRNP L interaction shares with other related protein-protein interactions reveals a conserved design by which splicing regulators interact with one another. Interaction between SETD2 and hnRNP L has previously been shown to be implicated in coupling gene transcription and mRNA processing. Here the authors elucidate the molecular basis of this functional interaction, showing that the RRM domain of hnRNP L possesses non-overlapping binding interfaces for engaging RNA and SETD2.
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16
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Yu X, Cao F, Yu Y, Li Y, Zhang J, Xu T, Di Q, Wu G, Zhang Z, Wang R, Li Y. HNRNPL Is Identified and Validated as a Prognostic Biomarker Associated with Microsatellite Instability in Human Gastric Cancer. DNA Cell Biol 2021; 40:1251-1260. [PMID: 34491823 DOI: 10.1089/dna.2021.0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microsatellite instability (MSI) is emerging as a promising subtype related to immunotherapy in gastric cancer (GC). However, the underlying mechanism between MSI and microsatellite stability (MSS) remains unclear. In this study, we conducted a weighted gene co-expression network analysis and found that the expression of heterogeneous nuclear ribonucleoprotein L (HNRNPL) was significantly increased in MSI GC compared with MSS GC. This finding was further validated in public GC cohorts and commercialized human GC tissue microarray. The significant negative correlation with the expression of mismatch repair protein mutL homolog 1 (MLH1) may be one of the potential mechanisms for the upregulation of HNRNPL expression in MSI GC (R = -0.689, p = 8.59e-11). In addition, HNRNPL expression was markedly upregulated in GC tissues compared with adjacent normal tissues. High HNRNPL expression also predicted a poor prognosis in GC patients. Finally, gene set enrichment analysis revealed that high HNRNPL MSI GC samples were highly positive associated with the biological functions of inflammation and cell proliferation, such as interferon gamma response, MYC targets, E2F targets, and G2/M checkpoints. In conclusion, HNRNPL could be a new MSI-associated prognostic biomarker in GC and could be a new target for the MSI GC treatment.
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Affiliation(s)
- Xiongjie Yu
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Fengjun Cao
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Yuandong Yu
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Yong Li
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Jun Zhang
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Tao Xu
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Quanshu Di
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Guang Wu
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Zhe Zhang
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Ran Wang
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Yanli Li
- Department of Endocrinology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
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17
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Pereira-Castro I, Moreira A. On the function and relevance of alternative 3'-UTRs in gene expression regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1653. [PMID: 33843145 DOI: 10.1002/wrna.1653] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022]
Abstract
Messanger RNA (mRNA) isoforms with alternative 3'-untranslated regions (3'-UTRs) are produced by alternative polyadenylation (APA), which occurs during transcription in most eukaryotic genes. APA fine-tunes gene expression in a cell-type- and cellular state-dependent manner. Selection of an APA site entails the binding of core cleavage and polyadenylation factors to a particular polyadenylation site localized in the pre-mRNA and is controlled by multiple regulatory determinants, including transcription, pre-mRNA cis-regulatory sequences, and protein factors. Alternative 3'-UTRs serve as platforms for specific RNA binding proteins and microRNAs, which regulate gene expression in a coordinated manner by controlling mRNA fate and function in the cell. Genome-wide studies illustrated the full extent of APA prevalence and revealed that specific 3'-UTR profiles are associated with particular cellular states and diseases. Generally, short 3'-UTRs are associated with proliferative and cancer cells, and long 3'-UTRs are mostly found in polarized and differentiated cells. Fundamental new insights on the physiological consequences of this widespread event and the molecular mechanisms involved have been revealed through single-cell studies. Publicly available comprehensive databases that cover all APA mRNA isoforms identified in many cellular states and diseases reveal specific APA signatures. Therapies tackling APA mRNA isoforms or APA regulators may be regarded as innovative and attractive tools for diagnostics or treatment of several pathologies. We highlight the function of APA and alternative 3'-UTRs in gene expression regulation, the control of these mechanisms, their physiological consequences, and their potential use as new biomarkers and therapeutic tools. This article is categorized under: RNA Processing > 3' End Processing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Isabel Pereira-Castro
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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18
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Alexander MS, Hightower RM, Reid AL, Bennett AH, Iyer L, Slonim DK, Saha M, Kawahara G, Kunkel LM, Kopin AS, Gupta VA, Kang PB, Draper I. hnRNP L is essential for myogenic differentiation and modulates myotonic dystrophy pathologies. Muscle Nerve 2021; 63:928-940. [PMID: 33651408 DOI: 10.1002/mus.27216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION RNA-binding proteins (RBPs) play an important role in skeletal muscle development and disease by regulating RNA splicing. In myotonic dystrophy type 1 (DM1), the RBP MBNL1 (muscleblind-like) is sequestered by toxic CUG repeats, leading to missplicing of MBNL1 targets. Mounting evidence from the literature has implicated other factors in the pathogenesis of DM1. Herein we sought to evaluate the functional role of the splicing factor hnRNP L in normal and DM1 muscle cells. METHODS Co-immunoprecipitation assays using hnRNPL and MBNL1 expression constructs and splicing profiling in normal and DM1 muscle cell lines were performed. Zebrafish morpholinos targeting hnrpl and hnrnpl2 were injected into one-cell zebrafish for developmental and muscle analysis. In human myoblasts downregulation of hnRNP L was achieved with shRNAi. Ascochlorin administration to DM1 myoblasts was performed and expression of the CUG repeats, DM1 splicing biomarkers, and hnRNP L expression levels were evaluated. RESULTS Using DM1 patient myoblast cell lines we observed the formation of abnormal hnRNP L nuclear foci within and outside the expanded CUG repeats, suggesting a role for this factor in DM1 pathology. We showed that the antiviral and antitumorigenic isoprenoid compound ascochlorin increased MBNL1 and hnRNP L expression levels. Drug treatment of DM1 muscle cells with ascochlorin partially rescued missplicing of established early biomarkers of DM1 and improved the defective myotube formation displayed by DM1 muscle cells. DISCUSSION Together, these studies revealed that hnRNP L can modulate DM1 pathologies and is a potential therapeutic target.
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Affiliation(s)
- Matthew S Alexander
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, Alabama, USA.,Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rylie M Hightower
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, Alabama, USA.,Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Andrea L Reid
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, Alabama, USA
| | - Alexis H Bennett
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Lakshmanan Iyer
- Department of Neuroscience, Tufts University, Boston, Massachusetts, USA
| | - Donna K Slonim
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA
| | - Madhurima Saha
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Genri Kawahara
- Department of Pathophysiology, Tokyo Medical University, Tokyo, Japan
| | - Louis M Kunkel
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alan S Kopin
- Department of Medicine, Molecular Cardiology Research Institute, Tufts Medical Center, Boston, Massachusetts, USA
| | - Vandana A Gupta
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Peter B Kang
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Neurology, University of Florida College of Medicine, Gainesville, Florida, USA.,Genetics Institute and Myology Institute, University of Florida, Gainesville, Florida, USA.,Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, Minnesota, USA.,Neurology Department, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Isabelle Draper
- Department of Medicine, Molecular Cardiology Research Institute, Tufts Medical Center, Boston, Massachusetts, USA
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19
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Schreiner S, Didio A, Hung LH, Bindereif A. Design and application of circular RNAs with protein-sponge function. Nucleic Acids Res 2020; 48:12326-12335. [PMID: 33231682 PMCID: PMC7708053 DOI: 10.1093/nar/gkaa1085] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/06/2020] [Accepted: 11/02/2020] [Indexed: 12/23/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs, generated from pre-mRNAs by circular splicing of exons and functionally largely uncharacterized. Here we report on the design, expression, and characterization of artificial circRNAs that act as protein sponges, specifically binding and functionally inactivating hnRNP (heterogeneous nuclear ribonucleoprotein) L. HnRNP L regulates alternative splicing, depending on short CA-rich RNA elements. We demonstrate that designer hnRNP L-sponge circRNAs with CA-repeat or CA-rich sequence clusters can efficiently and specifically modulate splicing-regulatory networks in mammalian cells, including alternative splicing patterns and the cellular distribution of a splicing factor. This new strategy can in principle be applied to any RNA-binding protein, opening up new therapeutic strategies in molecular medicine.
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Affiliation(s)
- Silke Schreiner
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Anna Didio
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Lee-Hsueh Hung
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
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20
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García-Moreno JF, Romão L. Perspective in Alternative Splicing Coupled to Nonsense-Mediated mRNA Decay. Int J Mol Sci 2020; 21:ijms21249424. [PMID: 33321981 PMCID: PMC7764535 DOI: 10.3390/ijms21249424] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing (AS) of precursor mRNA (pre-mRNA) is a cellular post-transcriptional process that generates protein isoform diversity. Nonsense-mediated RNA decay (NMD) is an mRNA surveillance pathway that recognizes and selectively degrades transcripts containing premature translation-termination codons (PTCs), thereby preventing the production of truncated proteins. Nevertheless, NMD also fine-tunes the gene expression of physiological mRNAs encoding full-length proteins. Interestingly, around one third of all AS events results in PTC-containing transcripts that undergo NMD. Numerous studies have reported a coordinated action between AS and NMD, in order to regulate the expression of several genes, especially those coding for RNA-binding proteins (RBPs). This coupling of AS to NMD (AS-NMD) is considered a gene expression tool that controls the ratio of productive to unproductive mRNA isoforms, ultimately degrading PTC-containing non-functional mRNAs. In this review, we focus on the mechanisms underlying AS-NMD, and how this regulatory process is able to control the homeostatic expression of numerous RBPs, including splicing factors, through auto- and cross-regulatory feedback loops. Furthermore, we discuss the importance of AS-NMD in the regulation of biological processes, such as cell differentiation. Finally, we analyze interesting recent data on the relevance of AS-NMD to human health, covering its potential roles in cancer and other disorders.
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Affiliation(s)
- Juan F. García-Moreno
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal;
- Faculty of Science, BioISI—Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal;
- Faculty of Science, BioISI—Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217-508-155
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21
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Liu X, Xie F, Lai G, Wang J. Roles of heterogeneous nuclear ribonucleoprotein L in enamel organ development and the differentiation of ameloblasts. Arch Oral Biol 2020; 120:104933. [PMID: 33137652 DOI: 10.1016/j.archoralbio.2020.104933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVE We aimed to explore the role of Heterogeneous Nuclear Ribonucleoprotein L(hnRNP L) in enamel organ development through hnRNP L conditional knockout mice and knockdown of hnRNP L expression in mouse ameloblast-lineage cells (mALCs) METHODS: We created K14cre-mediated hnRNP L conditional knockout mice (hnRNP LK14/fl) and silenced the expression of hnRNP L in mALCs to investigate the role of hnRNP L in enamel organ development. RESULTS We found that hnRNP LK14/fl mice presented enamel organ development defects with reduced number of inner enamel epithelium (IEE) cells. The proliferation and differentiation of the IEE cells/ameloblasts were suppressed. The cell proliferation and mineralization ability were also decreased after hnRNP L knockdown. Further studies showed that Bone Morphogenetic Protein (BMP) signaling pathway was attenuated after the knockdown of hnRNP L expression both in vivo and in vitro. CONCLUSIONS These findings suggest that hnRNP L plays a critical role in enamel organ development by promoting the IEE cell/ameloblast proliferation and differentiation. BMP signaling pathway may be involved in the process.
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Affiliation(s)
- Xiao Liu
- Department of Pediatric Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, China; National Clinical Research Center for Oral Diseases, China; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Furong Xie
- Department of Pediatric Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, China; National Clinical Research Center for Oral Diseases, China; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Guangyun Lai
- Department of Pediatric Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, China; National Clinical Research Center for Oral Diseases, China; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, 200011, China.
| | - Jun Wang
- Department of Pediatric Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, China; National Clinical Research Center for Oral Diseases, China; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, 200011, China.
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22
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The role of hnRNPs in frontotemporal dementia and amyotrophic lateral sclerosis. Acta Neuropathol 2020; 140:599-623. [PMID: 32748079 PMCID: PMC7547044 DOI: 10.1007/s00401-020-02203-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022]
Abstract
Dysregulated RNA metabolism is emerging as a crucially important mechanism underpinning the pathogenesis of frontotemporal dementia (FTD) and the clinically, genetically and pathologically overlapping disorder of amyotrophic lateral sclerosis (ALS). Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins with diverse, multi-functional roles across all aspects of mRNA processing. The role of these proteins in neurodegeneration is far from understood. Here, we review some of the unifying mechanisms by which hnRNPs have been directly or indirectly linked with FTD/ALS pathogenesis, including their incorporation into pathological inclusions and their best-known roles in pre-mRNA splicing regulation. We also discuss the broader functionalities of hnRNPs including their roles in cryptic exon repression, stress granule assembly and in co-ordinating the DNA damage response, which are all emerging pathogenic themes in both diseases. We then present an integrated model that depicts how a broad-ranging network of pathogenic events can arise from declining levels of functional hnRNPs that are inadequately compensated for by autoregulatory means. Finally, we provide a comprehensive overview of the most functionally relevant cellular roles, in the context of FTD/ALS pathogenesis, for hnRNPs A1-U.
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23
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Yan P, Lu JY, Niu J, Gao J, Zhang MQ, Yin Y, Shen X. LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency. J Mol Cell Biol 2020; 13:295-313. [PMID: 33049031 PMCID: PMC8339366 DOI: 10.1093/jmcb/mjaa056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/17/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
Super-enhancers (SEs) comprise large clusters of enhancers, which are co-occupied by multiple lineage-specific and master transcription factors, and play pivotal roles in regulating gene expression and cell fate determination. However, it is still largely unknown whether and how SEs are regulated by the noncoding portion of the genome. Here, through genome-wide analysis, we found that long noncoding RNA (lncRNA) genes preferentially lie next to SEs. In mouse embryonic stem cells (mESCs), depletion of SE-associated lncRNA transcripts dysregulated the activity of their nearby SEs. Specifically, we revealed a critical regulatory role of the lncRNA gene Platr22 in modulating the activity of a nearby SE and the expression of the nearby pluripotency regulator ZFP281. Through these regulatory events, Platr22 contributes to pluripotency maintenance and proper differentiation of mESCs. Mechanistically, Platr22 transcripts coat chromatin near the SE region and interact with DDX5 and hnRNP-L. DDX5 further recruits p300 and other factors related to active transcription. We propose that these factors assemble into a transcription hub, thus promoting an open and active epigenetic chromatin state. Our study highlights an unanticipated role for a class of lncRNAs in epigenetically controlling the activity and vulnerability to perturbation of nearby SEs for cell fate determination.
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Affiliation(s)
- Pixi Yan
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - J Yuyang Lu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Niu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Juntao Gao
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Michael Q Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Yafei Yin
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohua Shen
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
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24
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Zhou Z, Gong Q, Lin Z, Wang Y, Li M, Wang L, Ding H, Li P. Emerging Roles of SRSF3 as a Therapeutic Target for Cancer. Front Oncol 2020; 10:577636. [PMID: 33072610 PMCID: PMC7544984 DOI: 10.3389/fonc.2020.577636] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022] Open
Abstract
Ser/Arg-rich (SR) proteins are RNA-binding proteins known as constitutive and alternative splicing (AS) regulators that regulate multiple aspects of the gene expression program. Ser/Arg-rich splicing factor 3 (SRSF3) is the smallest member of the SR protein family, and its level is controlled by multiple factors and involves complex mechanisms in eukaryote cells, whereas the aberrant expression of SRSF3 is associated with many human diseases, including cancer. Here, we review state-of-the-art research on SRSF3 in terms of its function, expression, and misregulation in human cancers. We emphasize the negative consequences of the overexpression of the SRSF3 oncogene in cancers, the pathways underlying SRSF3-mediated transformation, and implications of potential anticancer drugs by downregulation of SRSF3 expression for cancer therapy. Cumulative research on SRSF3 provides critical insight into its essential part in maintaining cellular processes, offering potential new targets for anti-cancer therapy.
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Affiliation(s)
- Zhixia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Qi Gong
- Departments of Pediatrics, Second Clinical Medical College of Qingdao University, Qingdao, China
| | - Zhijuan Lin
- Key Laboratory for Immunology in Universities of Shandong Province, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Mengkun Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lu Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Hongfei Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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25
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Cipponi A, Goode DL, Bedo J, McCabe MJ, Pajic M, Croucher DR, Rajal AG, Junankar SR, Saunders DN, Lobachevsky P, Papenfuss AT, Nessem D, Nobis M, Warren SC, Timpson P, Cowley M, Vargas AC, Qiu MR, Generali DG, Keerthikumar S, Nguyen U, Corcoran NM, Long GV, Blay JY, Thomas DM. MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer. Science 2020; 368:1127-1131. [PMID: 32499442 DOI: 10.1126/science.aau8768] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/09/2019] [Accepted: 04/10/2020] [Indexed: 12/12/2022]
Abstract
In microorganisms, evolutionarily conserved mechanisms facilitate adaptation to harsh conditions through stress-induced mutagenesis (SIM). Analogous processes may underpin progression and therapeutic failure in human cancer. We describe SIM in multiple in vitro and in vivo models of human cancers under nongenotoxic drug selection, paradoxically enhancing adaptation at a competing intrinsic fitness cost. A genome-wide approach identified the mechanistic target of rapamycin (MTOR) as a stress-sensing rheostat mediating SIM across multiple cancer types and conditions. These observations are consistent with a two-phase model for drug resistance, in which an initially rapid expansion of genetic diversity is counterbalanced by an intrinsic fitness penalty, subsequently normalizing to complete adaptation under the new conditions. This model suggests synthetic lethal strategies to minimize resistance to anticancer therapy.
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Affiliation(s)
- Arcadi Cipponi
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. .,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - David L Goode
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Justin Bedo
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Computing and Information Systems, the University of Melbourne, Parkville, VIC, Australia.,Peter MacCallum Cancer Centre, Parkville, VIC, Australia
| | - Mark J McCabe
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Alvaro Gonzalez Rajal
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Simon R Junankar
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Darren N Saunders
- School of Medical Sciences, University of New South Wales, NSW, Australia
| | | | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Computing and Information Systems, the University of Melbourne, Parkville, VIC, Australia.,Peter MacCallum Cancer Centre, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Danielle Nessem
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Max Nobis
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Sean C Warren
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Paul Timpson
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Mark Cowley
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ana C Vargas
- Douglass Hanly Moir Pathology, Turramurra, NSW, Australia
| | - Min R Qiu
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.,Anatomical and Molecular Oncology Pathology, SYDPATH, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Daniele G Generali
- Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Breast Cancer Unit and Translational Research Unit, ASST Cremona, Cremona, Italy
| | - Shivakumar Keerthikumar
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Uyen Nguyen
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Niall M Corcoran
- Division of Urology, Royal Melbourne Hospital, Parkville, VIC, Australia.,Department of Urology, Peninsula Health, Frankston, VIC, Australia.,Department of Surgery, University of Melbourne, VIC, Australia
| | - Georgina V Long
- Melanoma Institute Australia, Wollstonecraft, NSW, Australia.,The University of Sydney, Sydney, NSW, Australia.,Royal North Shore Hospital and Mater Hospital, Sydney, NSW, Australia.,Crown Princess Mary Cancer Centre Westmead Hospital, Sydney, NSW, Australia
| | - Jean-Yves Blay
- Centre Leon Berard and Université Claude Bernard Lyon, Lyon, France.,UNICANCER, Paris, France
| | - David M Thomas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. .,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
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26
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Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21103711. [PMID: 32466143 PMCID: PMC7279485 DOI: 10.3390/ijms21103711] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.
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27
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Heterogeneous Nuclear Ribonucleoprotein L Negatively Regulates Foot-and-Mouth Disease Virus Replication through Inhibition of Viral RNA Synthesis by Interacting with the Internal Ribosome Entry Site in the 5' Untranslated Region. J Virol 2020; 94:JVI.00282-20. [PMID: 32161169 DOI: 10.1128/jvi.00282-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 02/08/2023] Open
Abstract
Upon infection, the highly structured 5' untranslated region (5' UTR) of picornavirus is involved in viral protein translation and RNA synthesis. As a critical element in the 5' UTR, the internal ribosome entry site (IRES) binds to various cellular proteins to function in the processes of picornavirus replication. Foot-and-mouth disease virus (FMDV) is an important member in the family Picornaviridae, and its 5' UTR contains a functional IRES element. In this study, the cellular heterogeneous nuclear ribonucleoprotein L (hnRNP L) was identified as an IRES-binding protein for FMDV by biotinylated RNA pulldown assays, mass spectrometry (MS) analysis, and determination of hnRNP L-IRES interaction regions. Further, we found that hnRNP L inhibited the growth of FMDV through binding to the viral IRES and that the inhibitory effect of hnRNP L on FMDV growth was not due to FMDV IRES-mediated translation, but to influence on viral RNA synthesis. Finally, hnRNP L was demonstrated to coimmunoprecipitate with RNA-dependent RNA polymerase (3Dpol) in an FMDV RNA-dependent manner in the infected cells. Thus, our results suggest that hnRNP L, as a critical IRES-binding protein, negatively regulates FMDV replication by inhibiting viral RNA synthesis, possibly by remaining in the replication complex.IMPORTANCE Picornaviruses, as a large family of human and animal pathogens, cause a bewildering array of disease syndromes. Many host factors are implicated in the pathogenesis of these viruses, and some proteins interact with the viral IRES elements to affect function. Here, we report for the first time that cellular hnRNP L specifically interacts with the IRES of the picornavirus FMDV and negatively regulates FMDV replication through inhibiting viral RNA synthesis. Further, our results showed that hnRNP L coimmunoprecipitates with FMDV 3Dpol in a viral RNA-dependent manner, suggesting that it may remain in the replication complex to function. The data presented here would facilitate further understanding of virus-host interactions and the pathogenesis of picornavirus infections.
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28
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Gu J, Chen Z, Chen X, Wang Z. Heterogeneous nuclear ribonucleoprotein (hnRNPL) in cancer. Clin Chim Acta 2020; 507:286-294. [PMID: 32376323 DOI: 10.1016/j.cca.2020.04.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein L (hnRNPL) is a type of RNA binding protein that is mainly located in the nucleus. hnRNPL protein, encoded by the gene located at 19q13.2, is an important member of the hnRNP family. In recent years, studies have shown that hnRNPL is highly expressed in a variety of tumors and plays a vital role in tumor progression. hnRNPL promotes various biological processes of tumor cells, including proliferation, migration and invasion. In this review, we discuss the clinical significance of hnRNPL by reviewing the mechanism of hnRNPL in the tumorigenesis of various cancers.
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Affiliation(s)
- Jingyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Zhenyao Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China.
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29
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Sadek J, Omer A, Hall D, Ashour K, Gallouzi IE. Alternative polyadenylation and the stress response. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1540. [DOI: 10.1002/wrna.1540] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 03/18/2019] [Accepted: 04/02/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Jason Sadek
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Amr Omer
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Derek Hall
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Kholoud Ashour
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
| | - Imed Eddine Gallouzi
- Department of Biochemistry McGill University, Rosalind and Morris Goodman Cancer Centre Montreal Quebec Canada
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30
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Darnell JC, Mele A, Hung KYS, Darnell RB. Mapping of In Vivo RNA-Binding Sites by Ultraviolet (UV)-Cross-Linking Immunoprecipitation (CLIP). Cold Spring Harb Protoc 2018; 2018:2018/12/pdb.top097931. [PMID: 30510132 DOI: 10.1101/pdb.top097931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
RNA "CLIP" (cross-linking immunoprecipitation), the method by which RNA-protein complexes are covalently cross-linked and purified and the RNA sequenced, has attracted attention as a powerful means of developing genome-wide maps of direct, functional RNA-protein interaction sites. These maps have been used to identify points of regulation, and they hold promise for understanding the dynamics of RNA regulation in normal cell function and its dysregulation in disease.
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31
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McClory SP, Lynch KW, Ling JP. HnRNP L represses cryptic exons. RNA (NEW YORK, N.Y.) 2018; 24:761-768. [PMID: 29581412 PMCID: PMC5959245 DOI: 10.1261/rna.065508.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/21/2018] [Indexed: 05/14/2023]
Abstract
The fidelity of RNA splicing is regulated by a network of splicing enhancers and repressors, although the rules that govern this process are not yet fully understood. One mechanism that contributes to splicing fidelity is the repression of nonconserved cryptic exons by splicing factors that recognize dinucleotide repeats. We previously identified that TDP-43 and PTBP1/PTBP2 are capable of repressing cryptic exons utilizing UG and CU repeats, respectively. Here we demonstrate that hnRNP L (HNRNPL) also represses cryptic exons by utilizing exonic CA repeats, particularly near the 5'SS. We hypothesize that hnRNP L regulates CA repeat repression for both cryptic exon repression and developmental processes such as T cell differentiation.
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Affiliation(s)
- Sean P McClory
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | - Jonathan P Ling
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2196, USA
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32
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Multilevel Differential Control of Hormone Gene Expression Programs by hnRNP L and LL in Pituitary Cells. Mol Cell Biol 2018; 38:MCB.00651-17. [PMID: 29610151 PMCID: PMC5974433 DOI: 10.1128/mcb.00651-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
The pituitary-derived somatolactotrophe GH3 cells secrete both growth hormone (GH) and prolactin (PRL). We have found that the hnRNP L and L-like (LL) paralogs differentially regulate alternative splicing of genes in these cells. Here, we show that hnRNP L is essential for PRL only, but LL is essential for both PRL and GH production. Transcriptome-wide RNA sequencing (RNA-Seq) analysis indicates that they differentially control groups of hormone or hormone-related genes involved in hormone production/regulation at total transcript and alternative exon levels. Interestingly, hnRNP L also specifically binds and prevents the aberrant usage of a nonconserved CA-rich intron piece of Prl pre-mRNA transcripts, and many others involved in endocrine functions, to prevent mostly cryptic last exons and mRNA truncation. Essential for the full hnRNP L effect on specific exons is a proline-rich region that emerged during evolution in vertebrate hnRNP L only but not LL. Together, our data demonstrate that the hnRNP L and its paralog, LL, differentially control hormone gene expression programs at multiple levels, and hnRNP L in particular is critical for protecting the transcriptome from aberrant usage of intronic sequences. The multilevel differential control by hnRNPs likely tailors the transcriptome to help refine and safeguard the different gene expression programs for different hormones.
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33
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Dery KJ, Silver C, Yang L, Shively JE. Interferon regulatory factor 1 and a variant of heterogeneous nuclear ribonucleoprotein L coordinately silence the gene for adhesion protein CEACAM1. J Biol Chem 2018; 293:9277-9291. [PMID: 29720400 DOI: 10.1074/jbc.ra117.001507] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
The adhesion protein carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) is widely expressed in epithelial cells as a short cytoplasmic isoform (S-iso) and in leukocytes as a long cytoplasmic isoform (L-iso) and is frequently silenced in cancer by unknown mechanisms. Previously, we reported that interferon response factor 1 (IRF1) biases alternative splicing (AS) to include the variable exon 7 (E7) in CEACAM1, generating long cytoplasmic isoforms. We now show that IRF1 and a variant of heterogeneous nuclear ribonucleoprotein L (Lv1) coordinately silence the CEACAM1 gene. RNAi-mediated Lv1 depletion in IRF1-treated HeLa and melanoma cells induced significant CEACAM1 protein expression, reversed by ectopic Lv1 expression. The Lv1-mediated CEACAM1 repression resided in residues Gly71-Gly89 and Ala38-Gly89 in Lv1's N-terminal extension. ChIP analysis of IRF1- and FLAG-tagged Lv1-treated HeLa cells and global treatment with the global epigenetic modifiers 5-aza-2'-deoxycytidine and trichostatin A indicated that IRF1 and Lv1 together induce chromatin remodeling, restricting IRF1 access to the CEACAM1 promoter. In interferon γ-treated HeLa cells, the transcription factor SP1 did not associate with the CEACAM1 promoter, but binding by upstream transcription factor 1 (USF1), a known CEACAM1 regulator, was greatly enhanced. ChIP-sequencing revealed that Lv1 overexpression in IRF1-treated cells induces transcriptional silencing across many genes, including DCC (deleted in colorectal carcinoma), associated with CEACAM5 in colon cancer. Notably, IRF1, but not IRF3 and IRF7, affected CEACAM1 expression via translational repression. We conclude that IRF1 and Lv1 coordinately regulate CEACAM1 transcription, alternative splicing, and translation and may significantly contribute to CEACAM1 silencing in cancer.
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Affiliation(s)
- Kenneth J Dery
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Craig Silver
- Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, and
| | - Lu Yang
- The Integrative Genomics and Bioinformatics Core, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - John E Shively
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010,
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34
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Sen A, Gurdziel K, Liu J, Qu W, Nuga OO, Burl RB, Hüttemann M, Pique-Regi R, Ruden DM. Smooth, an hnRNP-L Homolog, Might Decrease Mitochondrial Metabolism by Post-Transcriptional Regulation of Isocitrate Dehydrogenase (Idh) and Other Metabolic Genes in the Sub-Acute Phase of Traumatic Brain Injury. Front Genet 2017; 8:175. [PMID: 29187863 PMCID: PMC5694756 DOI: 10.3389/fgene.2017.00175] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/24/2017] [Indexed: 12/28/2022] Open
Abstract
Traumatic brain injury (TBI) can cause persistent pathological alteration of neurons. This may lead to cognitive dysfunction, depression and increased susceptibility to life threatening diseases, such as epilepsy and Alzheimer's disease. To investigate the underlying genetic and molecular basis of TBI, we subjected w1118Drosophila melanogaster to mild closed head trauma and found that mitochondrial activity is reduced in the brains of these flies 24 h after inflicting trauma. To determine the transcriptomic changes after mild TBI, we collected fly heads 24 h after inflicting trauma, and performed RNA-seq analyses. Classification of alternative splicing changes showed selective retention (RI) of long introns (>81 bps), with a mean size of ~3,000 nucleotides. Some of the genes containing RI showed a significant reduction in transcript abundance and are involved in mitochondrial metabolism such as Isocitrate dehydrogenase (Idh), which makes α-KG, a co-factor needed for both DNA and histone demethylase enzymes. The long introns are enriched in CA-rich motifs known to bind to Smooth (Sm), a heterogeneous nuclear ribonucleoprotein L (hnRNP-L) class of splicing factor, which has been shown to interact with the H3K36 histone methyltransferase, SET2, and to be involved in intron retention in human cells. H3K36me3 is a histone mark that demarcates exons in genes by interacting with the mRNA splicing machinery. Mutating sm (sm4/Df) resulted in loss of both basal and induced levels of RI in many of the same long-intron containing genes. Reducing the levels of Kdm4A, the H3K36me3 histone demethylase, also resulted in loss of basal levels of RI in many of the same long-intron containing genes. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) for H3K36me3 revealed increased levels of this histone modification in retained introns post-trauma at CA-rich motifs. Based on these results, we propose a model in which TBI temporarily decreases mitochondrial activity in the brain 24 h after inflicting trauma, which decreases α-KG levels, and increases H3K36me3 levels and intron retention of long introns by decreasing Kdm4A activity. The consequent reduction in mature mRNA levels in metabolism genes, such as Idh, further reduces α-KG levels in a negative feedback loop. We further propose that decreasing metabolism after TBI in such a manner is a protective mechanism that gives the brain time to repair cellular damage induced by TBI.
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Affiliation(s)
- Arko Sen
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States.,Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Katherine Gurdziel
- C. S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Wen Qu
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Oluwademi O Nuga
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Rayanne B Burl
- C. S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
| | - Douglas M Ruden
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States.,C. S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
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35
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Kajitani N, Glahder J, Wu C, Yu H, Nilsson K, Schwartz S. hnRNP L controls HPV16 RNA polyadenylation and splicing in an Akt kinase-dependent manner. Nucleic Acids Res 2017; 45:9654-9678. [PMID: 28934469 PMCID: PMC5766200 DOI: 10.1093/nar/gkx606] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/04/2017] [Indexed: 11/14/2022] Open
Abstract
Inhibition of the Akt kinase activates HPV16 late gene expression by reducing HPV16 early polyadenylation and by activating HPV16 late L1 mRNA splicing. We identified ‘hot spots’ for RNA binding proteins at the early polyA signal and at splice sites on HPV16 late mRNAs. We observed that hnRNP L was associated with sequences at all HPV16 late splice sites and at the early polyA signal. Akt kinase inhibition resulted in hnRNP L dephosphorylation and reduced association of hnRNP L with HPV16 mRNAs. This was accompanied by an increased binding of U2AF65 and Sam68 to HPV16 mRNAs. Furthermore, siRNA knock-down of hnRNP L or Akt induced HPV16 gene expression. Treatment of HPV16 immortalized keratinocytes with Akt kinase inhibitor reduced hnRNP L binding to HPV16 mRNAs and induced HPV16 L1 mRNA production. Finally, deletion of the hnRNP L binding sites in HPV16 subgenomic expression plasmids resulted in activation of HPV16 late gene expression. In conclusion, the Akt kinase inhibits HPV16 late gene expression at the level of RNA processing by controlling the RNA-binding protein hnRNP L. We speculate that Akt kinase activity upholds an intracellular milieu that favours HPV16 early gene expression and suppresses HPV16 late gene expression.
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Affiliation(s)
- Naoko Kajitani
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Jacob Glahder
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Chengjun Wu
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Haoran Yu
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Kersti Nilsson
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Stefan Schwartz
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
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36
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HnRNP-L promotes prostate cancer progression by enhancing cell cycling and inhibiting apoptosis. Oncotarget 2017; 8:19342-19353. [PMID: 28038443 PMCID: PMC5386688 DOI: 10.18632/oncotarget.14258] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/01/2016] [Indexed: 01/23/2023] Open
Abstract
Expression of the RNA-binding protein HnRNP-L was previously shown to associate with tumorigenesis in liver and lung cancer. In this study, we examined the role of HnRNP-L in prostate cancer (Pca). We found that HnRNP-L is overexpressed in prostate tissue samples from 160 PC patients compared with tissue samples from 32 donors with cancers other than Pca. Moreover, HnRNP-L positively correlated with aggressive tumor characteristics. HnRNP-L knockdown inhibited cell proliferation and promoted cell apoptosis of Pca cell lines in vitro, and suppressed tumor growth when the cells were subcutaneously implanted in an athymic mouse model. Conversely, overexpression of HnRNP-L promoted cell proliferation and tumor growth while prohibiting cell apoptosis. HnRNP-L promoted cell proliferation and tumor growth in Pca in part by interacting with endogenous p53 mRNA, which was closely associated with cyclin p21. In addition, HnRNP-L affected cell apoptosis by directly binding the classical apoptosis protein BCL-2. These observations suggest HnRNP-L is an important regulatory factor that exerts pro-proliferation and anti-apoptosis effects in Pca through actions affecting the cell cycle and intrinsic apoptotic signaling. Thus HnRNP-L could potentially serve as a valuable molecular biomarker or therapeutic target in the treatment of Pca.
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37
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Lv D, Wu H, Xing R, Shu F, Lei B, Lei C, Zhou X, Wan B, Yang Y, Zhong L, Mao X, Zou Y. HnRNP-L mediates bladder cancer progression by inhibiting apoptotic signaling and enhancing MAPK signaling pathways. Oncotarget 2017; 8:13586-13599. [PMID: 28088793 PMCID: PMC5355122 DOI: 10.18632/oncotarget.14600] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/03/2017] [Indexed: 12/28/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein L (hnRNP-L) is a promoter of various kinds of cancers, but its actions in bladder cancer (BC) are unclear. In this study, we investigated the function and the underlying mechanism of hnRNP-L in bladder carcinogenesis. Our results demonstrated that enhanced hnRNP-L expression in BC tissues was associated with poor overall survival of BC patients. Depletion of hnRNP-L significantly suppressed cell proliferation in vitro and inhibited xenograft tumor growth in vivo. Furthermore, downregulation of hnRNP-L resulted in G1-phase cell cycle arrest and enhanced apoptosis accompanied by inhibition of EMT and cell migration. All these cellular changes were reversed by ectopic expression of hnRNP-L. Deletion of hnRNP-L resulted in decreased expression of Bcl-2, enhanced expression of caspases-3, -6 and -9 and inhibition of the MAPK signaling pathway. These findings demonstrate that hnRNP-L contributes to poor prognosis and tumor progression of BC by inhibiting the intrinsic apoptotic signaling and enhancing MAPK signaling pathways.
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Affiliation(s)
- Daojun Lv
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Huayan Wu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Rongwei Xing
- Department of Urology, Affiliated Weihai Second Municipal Hospital of Qingdao University, Weihai 264200, P. R. China
| | - Fangpeng Shu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Bin Lei
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Chengyong Lei
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Xumin Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Bo Wan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Yu Yang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, Guangdong Province, 518036, China
| | - Liren Zhong
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Xiangming Mao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China.,Department of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, Guangdong Province, 518036, China
| | - Yaguang Zou
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
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38
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Neve J, Patel R, Wang Z, Louey A, Furger AM. Cleavage and polyadenylation: Ending the message expands gene regulation. RNA Biol 2017; 14:865-890. [PMID: 28453393 PMCID: PMC5546720 DOI: 10.1080/15476286.2017.1306171] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/02/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022] Open
Abstract
Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease.
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Affiliation(s)
- Jonathan Neve
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Radhika Patel
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Zhiqiao Wang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Alastair Louey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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39
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Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proc Natl Acad Sci U S A 2017; 114:E5207-E5215. [PMID: 28611215 DOI: 10.1073/pnas.1617467114] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Alternative RNA splicing plays an important role in cancer. To determine which factors involved in RNA processing are essential in prostate cancer, we performed a genome-wide CRISPR/Cas9 knockout screen to identify the genes that are required for prostate cancer growth. Functional annotation defined a set of essential spliceosome and RNA binding protein (RBP) genes, including most notably heterogeneous nuclear ribonucleoprotein L (HNRNPL). We defined the HNRNPL-bound RNA landscape by RNA immunoprecipitation coupled with next-generation sequencing and linked these RBP-RNA interactions to changes in RNA processing. HNRNPL directly regulates the alternative splicing of a set of RNAs, including those encoding the androgen receptor, the key lineage-specific prostate cancer oncogene. HNRNPL also regulates circular RNA formation via back splicing. Importantly, both HNRNPL and its RNA targets are aberrantly expressed in human prostate tumors, supporting their clinical relevance. Collectively, our data reveal HNRNPL and its RNA clients as players in prostate cancer growth and potential therapeutic targets.
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40
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Mannen T, Yamashita S, Tomita K, Goshima N, Hirose T. The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL. J Cell Biol 2017; 214:45-59. [PMID: 27377249 PMCID: PMC4932371 DOI: 10.1083/jcb.201601024] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/14/2016] [Indexed: 01/21/2023] Open
Abstract
The mammalian cell nucleus contains membraneless suborganelles referred to as nuclear bodies (NBs). Some NBs are formed with an architectural RNA (arcRNA) as the structural core. Here, we searched for new NBs that are built on unidentified arcRNAs by screening for ribonuclease (RNase)-sensitive NBs using 32,651 fluorescently tagged human cDNA clones. We identified 32 tagged proteins that required RNA for their localization in distinct nuclear foci. Among them, seven RNA-binding proteins commonly localized in the Sam68 nuclear body (SNB), which was disrupted by RNase treatment. Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures.
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Affiliation(s)
- Taro Mannen
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Seisuke Yamashita
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Kozo Tomita
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koutou 135-0064, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
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41
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Loh TJ, Choi N, Moon H, Jang HN, Liu Y, Zhou J, Zheng X, Shen H. Suppression of 5' splice-sites through multiple exonic motifs by hnRNP L. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:363-373. [PMID: 28119102 DOI: 10.1016/j.bbagrm.2017.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
Abstract
Selection of 5' splice-sites (5'SS) in alternative splicing plays an important role in gene regulation. Although regulatory mechanisms of heterogeneous nuclear ribonucleoprotein L (hnRNP L), a well-known splicing regulatory protein, have been studied in a substantial level, its role in 5'SS selection is not thoroughly defined. By using a KLF6 pre-mRNA alternative splicing model, we demonstrate in this report that hnRNP L inhibits proximal 5'SS but promotes two consecutive distal 5'SS splicing, antagonizing SRSF1 roles in KLF6 pre-mRNA splicing. In addition, three consecutive CA-rich sequences in a CA cassette immediately upstream of the proximal 5'SS are all required for hnRNP L functions. Importantly, the CA-cassette locations on the proximal exon do not affect hnRNP L roles. We further show that the proximal 5'SS but not the two distal 5'SSs are essential for hnRNP L activities. Notably, in a Bcl-x pre-mRNA model that contains two alternative 5'SS but includes CA-rich elements at distal exon, we demonstrate that hnRNP L also suppresses nearby 5'SS activation. Taken together, we conclude that hnRNP L suppresses 5'SS selection through multiple exonic motifs.
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Affiliation(s)
- Tiing Jen Loh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Namjeong Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Heegyum Moon
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Ha Na Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Yongchao Liu
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Jianhua Zhou
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.
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42
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HnRNP L is important for the expression of oncogene SRSF3 and oncogenic potential of oral squamous cell carcinoma cells. Sci Rep 2016; 6:35976. [PMID: 27808105 PMCID: PMC5093901 DOI: 10.1038/srep35976] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/07/2016] [Indexed: 01/02/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the leading cause of death related to oral diseases. The mechanisms of OSCC development remain largely unknown. Heterogeneous nuclear ribonucleoprotein L (HnRNP L) is a multi-functional splicing factor. It has been reported to be an important regulator of apoptosis. However, the functions of hnRNP L in cancer need to be further explored. In the present study, we found that OSCC tissues expressed significantly higher levels of hnRNP L than normal tissues. Depletion of hnRNP L retarded cell growth, cell migration, and tumorigenesis of OSCC cells. HnRNP L regulates both the expression of oncogenic splicing factor SRSF3 and the alternative splicing of SRSF3 exon 4. Expression of hnRNP L is correlated with SRSF3 expression in OSCC tissues. These findings suggest that hnRNP L is important for the pathogenesis of OSCC and may be a novel potential therapeutic target of OSCC.
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43
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The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression. Nat Commun 2016; 7:12791. [PMID: 27666543 PMCID: PMC5052669 DOI: 10.1038/ncomms12791] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022] Open
Abstract
Molecular classification of cancers into subtypes has resulted in an advance in our understanding of tumour biology and treatment response across multiple tumour types. However, to date, cancer profiling has largely focused on protein-coding genes, which comprise <1% of the genome. Here we leverage a compendium of 58,648 long noncoding RNAs (lncRNAs) to subtype 947 breast cancer samples. We show that lncRNA-based profiling categorizes breast tumours by their known molecular subtypes in breast cancer. We identify a cohort of breast cancer-associated and oestrogen-regulated lncRNAs, and investigate the role of the top prioritized oestrogen receptor (ER)-regulated lncRNA, DSCAM-AS1. We demonstrate that DSCAM-AS1 mediates tumour progression and tamoxifen resistance and identify hnRNPL as an interacting protein involved in the mechanism of DSCAM-AS1 action. By highlighting the role of DSCAM-AS1 in breast cancer biology and treatment resistance, this study provides insight into the potential clinical implications of lncRNAs in breast cancer. LncRNAs have been associated with cancer. Here, the authors carry out a systematic review of lncRNAs in breast cancer and show that DSCAM-AS1 is highly expressed in oestrogen receptor positive tumours and enhances cancer through an interaction with hnRNPL; and is also associated with tamoxifen resistance.
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44
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RNA-seq analysis for detecting quantitative trait-associated genes. Sci Rep 2016; 6:24375. [PMID: 27071914 PMCID: PMC4829873 DOI: 10.1038/srep24375] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/22/2016] [Indexed: 02/06/2023] Open
Abstract
Many recent RNA-seq studies were focused mainly on detecting the differentially expressed genes (DEGs) between two or more conditions. In contrast, only a few attempts have been made to detect genes associated with quantitative traits, such as obesity index and milk yield, on RNA-seq experiment with large number of biological replicates. This study illustrates the linear model application on trait associated genes (TAGs) detection in two real RNA-seq datasets: 89 replicated human obesity related data and 21 replicated Holsteins’ milk production related RNA-seq data. Based on these two datasets, the performance between suggesting methods, such as ordinary regression and robust regression, and existing methods: DESeq2 and Voom, were compared. The results indicate that suggesting methods have much lower false discoveries compared to the precedent two group comparisons based approaches in our simulation study and qRT-PCR experiment. In particular, the robust regression outperforms existing DEG finding method as well as ordinary regression in terms of precision. Given the current trend in RNA-seq pricing, we expect our methods to be successfully applied in various RNA-seq studies with numerous biological replicates that handle continuous response traits.
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45
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Immunoprecipitation and mass spectrometry defines an extensive RBM45 protein-protein interaction network. Brain Res 2016; 1647:79-93. [PMID: 26979993 DOI: 10.1016/j.brainres.2016.02.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 02/25/2016] [Accepted: 02/28/2016] [Indexed: 12/12/2022]
Abstract
The pathological accumulation of RNA-binding proteins (RBPs) within inclusion bodies is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RBP aggregation results in both toxic gain and loss of normal function. Determining the protein binding partners and normal functions of disease-associated RBPs is necessary to fully understand molecular mechanisms of RBPs in disease. Herein, we characterized the protein-protein interactions (PPIs) of RBM45, a RBP that localizes to inclusions in ALS/FTLD. Using immunoprecipitation coupled to mass spectrometry (IP-MS), we identified 132 proteins that specifically interact with RBM45 within HEK293 cells. Select PPIs were validated by immunoblot and immunocytochemistry, demonstrating that RBM45 associates with a number of other RBPs primarily via RNA-dependent interactions in the nucleus. Analysis of the biological processes and pathways associated with RBM45-interacting proteins indicates enrichment for nuclear RNA processing/splicing via association with hnRNP proteins and cytoplasmic RNA translation via eiF2 and eiF4 pathways. Moreover, several other ALS-linked RBPs, including TDP-43, FUS, Matrin-3, and hnRNP-A1, interact with RBM45, consistent with prior observations of these proteins within intracellular inclusions in ALS/FTLD. Taken together, our results define a PPI network for RBM45, suggest novel functions for this protein, and provide new insights into the contributions of RBM45 to neurodegeneration in ALS/FTLD. This article is part of a Special Issue entitled SI:RNA Metabolism in Disease.
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46
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The Role of Alternative Splicing in the Control of Immune Homeostasis and Cellular Differentiation. Int J Mol Sci 2015; 17:ijms17010003. [PMID: 26703587 PMCID: PMC4730250 DOI: 10.3390/ijms17010003] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing of pre-mRNA helps to enhance the genetic diversity within mammalian cells by increasing the number of protein isoforms that can be generated from one gene product. This provides a great deal of flexibility to the host cell to alter protein function, but when dysregulation in splicing occurs this can have important impact on health and disease. Alternative splicing is widely used in the mammalian immune system to control the development and function of antigen specific lymphocytes. In this review we will examine the splicing of pre-mRNAs yielding key proteins in the immune system that regulate apoptosis, lymphocyte differentiation, activation and homeostasis, and discuss how defects in splicing can contribute to diseases. We will describe how disruption to trans-acting factors, such as heterogeneous nuclear ribonucleoproteins (hnRNPs), can impact on cell survival and differentiation in the immune system.
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47
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Cole BS, Tapescu I, Allon SJ, Mallory MJ, Qiu J, Lake RJ, Fan HY, Fu XD, Lynch KW. Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons. RNA (NEW YORK, N.Y.) 2015; 21:2053-66. [PMID: 26437669 PMCID: PMC4647460 DOI: 10.1261/rna.052969.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/24/2015] [Indexed: 05/27/2023]
Abstract
HnRNP L is a ubiquitous splicing-regulatory protein that is critical for the development and function of mammalian T cells. Previous work has identified a few targets of hnRNP L-dependent alternative splicing in T cells and has described transcriptome-wide association of hnRNP L with RNA. However, a comprehensive analysis of the impact of hnRNP L on mRNA expression remains lacking. Here we use next-generation sequencing to identify transcriptome changes upon depletion of hnRNP L in a model T-cell line. We demonstrate that hnRNP L primarily regulates cassette-type alternative splicing, with minimal impact of hnRNP L depletion on transcript abundance, intron retention, or other modes of alternative splicing. Strikingly, we find that binding of hnRNP L within or flanking an exon largely correlates with exon repression by hnRNP L. In contrast, exons that are enhanced by hnRNP L generally lack proximal hnRNP L binding. Notably, these hnRNP L-enhanced exons share sequence and context features that correlate with poor nucleosome positioning, suggesting that hnRNP may enhance inclusion of a subset of exons via a cotranscriptional or epigenetic mechanism. Our data demonstrate that hnRNP L controls inclusion of a broad spectrum of alternative cassette exons in T cells and suggest both direct RNA regulation as well as indirect mechanisms sensitive to the epigenetic landscape.
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Affiliation(s)
- Brian S Cole
- Department of Biochemistry and Biophysics Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Iulia Tapescu
- Department of Biochemistry and Biophysics Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Samuel J Allon
- Department of Biochemistry and Biophysics Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael J Mallory
- Department of Biochemistry and Biophysics Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jinsong Qiu
- Department of Cell and Molecular Medicine, University of California San Diego, San Diego, California 92093, USA
| | - Robert J Lake
- Department of Biochemistry and Biophysics Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hua-Ying Fan
- Department of Biochemistry and Biophysics Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xiang-Dong Fu
- Department of Cell and Molecular Medicine, University of California San Diego, San Diego, California 92093, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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48
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Vakilian H, Mirzaei M, Sharifi Tabar M, Pooyan P, Habibi Rezaee L, Parker L, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH. DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation. J Proteome Res 2015; 14:3474-83. [PMID: 26144214 DOI: 10.1021/acs.jproteome.5b00512] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although it is apparent that chromosome complement mediates sexually dimorphic expression patterns of some proteins that lead to functional differences, there has been insufficient evidence following the manipulation of the male-specific region of the Y chromosome (MSY) gene expression during neural development. In this study, we profiled the expression of 23 MSY genes and 15 of their X-linked homologues during neural cell differentiation of NTERA-2 human embryonal carcinoma cell line (NT2) cells in three different developmental stages using qRT-PCR, Western blotting, and immunofluorescence. The expression level of 12 Y-linked genes significantly increased over neural differentiation, including RBMY1, EIF1AY, DDX3Y, HSFY1, BPY2, PCDH11Y, UTY, RPS4Y1, USP9Y, SRY, PRY, and ZFY. We showed that siRNA-mediated knockdown of DDX3Y, a DEAD box RNA helicase enzyme, in neural progenitor cells impaired cell cycle progression and increased apoptosis, consequently interrupting differentiation. Label-free quantitative shotgun proteomics based on a spectral counting approach was then used to characterize the proteomic profile of the cells after DDX3Y knockdown. Among 917 reproducibly identified proteins detected, 71 proteins were differentially expressed following DDX3Y siRNA treatment compared with mock treated cells. Functional grouping indicated that these proteins were involved in cell cycle, RNA splicing, and apoptosis, among other biological functions. Our results suggest that MSY genes may play an important role in neural differentiation and demonstrate that DDX3Y could play a multifunctional role in neural cell development, probably in a sexually dimorphic manner.
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Affiliation(s)
- Haghighat Vakilian
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Mehdi Sharifi Tabar
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Paria Pooyan
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Lida Habibi Rezaee
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Lindsay Parker
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Hamid Gourabi
- Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture , Sharif Esfahani Blvd, Park Street, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran.,Seed and Plant Improvement Institute's Campus, Agricultural Biotechnology Research Institute of Iran , Mahdasht Road, Karaj, Iran
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49
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Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FHT. The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein. J Mol Biol 2015; 427:3001-22. [PMID: 26051023 DOI: 10.1016/j.jmb.2015.05.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 12/23/2022]
Abstract
The RNA recognition motif (RRM) is the far most abundant RNA binding domain. In addition to the typical β1α1β2β3α2β4 fold, various sub-structural elements have been described and reportedly contribute to the high functional versatility of RRMs. The heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a highly abundant protein of 64 kDa comprising four RRM domains. Involved in many aspects of RNA metabolism, hnRNP L specifically binds to RNAs containing CA repeats or CA-rich clusters. However, a comprehensive structural description of hnRNP L including its sub-structural elements is missing. Here, we present the structural characterization of the RRM domains of hnRNP L and demonstrate their function in repressing exon 4 of SLC2A2. By comparison of the sub-structural elements between the two highly similar paralog families of hnRNP L and PTB, we defined signatures underlying interacting C-terminal coils (ICCs), the RRM34 domain interaction and RRMs with a C-terminal fifth β-strand, a variation we denoted vRRMs. Furthermore, computational analysis revealed new putative ICC-containing RRM families and allowed us to propose an evolutionary scenario explaining the origins of the ICC and fifth β-strand sub-structural extensions. Our studies provide insights of domain requirements in alternative splicing mediated by hnRNP L and molecular descriptions for the sub-structural elements. In addition, the analysis presented may help to classify other abundant RRM extensions and to predict structure-function relationships.
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Affiliation(s)
- Markus Blatter
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Inna Grishina
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Christophe Maris
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Stephane Thore
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Timm Maier
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
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50
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Loh TJ, Cho S, Moon H, Jang HN, Williams DR, Jung DW, Kim IC, Ghigna C, Biamonti G, Zheng X, Shen H. hnRNP L inhibits CD44 V10 exon splicing through interacting with its upstream intron. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:743-50. [DOI: 10.1016/j.bbagrm.2015.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 12/27/2022]
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