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Della Bella E, Koch J, Baerenfaller K. Translation and emerging functions of non-coding RNAs in inflammation and immunity. Allergy 2022; 77:2025-2037. [PMID: 35094406 PMCID: PMC9302665 DOI: 10.1111/all.15234] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Regulatory non‐coding RNAs (ncRNAs) including small non‐coding RNAs (sRNAs), long non‐coding RNAs (lncRNAs), and circular RNAs (circRNAs) have gained considerable attention in the last few years. This is mainly due to their condition‐ and tissue‐specific expression and their various modes of action, which suggests them as promising biomarkers and therapeutic targets. One important mechanism of ncRNAs to regulate gene expression is through translation of short open reading frames (sORFs). These sORFs can be located in lncRNAs, in non‐translated regions of mRNAs where upstream ORFs (uORFs) represent the majority, or in circRNAs. Regulation of their translation can function as a quick way to adapt protein production to changing cellular or environmental cues, and can either depend solely on the initiation and elongation of translation, or on the roles of the produced functional peptides. Due to the experimental challenges to pinpoint translation events and to detect the produced peptides, translational regulation through regulatory RNAs is not well studied yet. In the case of circRNAs, they have only recently started to be recognized as regulatory molecules instead of mere artifacts of RNA biosynthesis. Of the many roles described for regulatory ncRNAs, we will focus here on their regulation during inflammation and in immunity.
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Affiliation(s)
| | - Jana Koch
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Swiss Institute of Bioinformatics (SIB) Davos Switzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Swiss Institute of Bioinformatics (SIB) Davos Switzerland
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2
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Wang M, Yang C, Liu X, Zheng J, Xue Y, Ruan X, Shen S, Wang D, Li Z, Cai H, Liu Y. An upstream open reading frame regulates vasculogenic mimicry of glioma via ZNRD1-AS1/miR-499a-5p/ELF1/EMI1 pathway. J Cell Mol Med 2020; 24:6120-6136. [PMID: 32368853 PMCID: PMC7294115 DOI: 10.1111/jcmm.15217] [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: 12/13/2019] [Revised: 02/20/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023] Open
Abstract
Increasing evidence has suggested that gliomas can supply blood through vasculogenic mimicry. In this study, the expression and function of ZNRD1‐AS1‐144aa‐uORF (144aa‐uORF) and some non‐coding RNAs in gliomas were assessed. Real‐time quantitative PCR or Western blot was used to discover the expression of 144aa‐uORF, ZNRD1‐AS1, miR‐499a‐5p, ELF1 and EMI1 in gliomas. In addition, RIP and RNA pull‐down assays were applied to explore the interrelationship between 144aa‐uORF and ZNRD1‐AS1. The role of the 144aa‐uORF\ZNRD1‐AS1\miR‐499a‐5p\ELF1\EMI1 axis in vasculogenic mimicry formation of gliomas was analysed. This study illustrates the reduced expression of the 144aa‐uORF in glioma tissues and cells. Up‐regulation of 144aa‐uORF inhibits proliferation, migration, invasion and vasculogenic mimicry formation within glioma cells. The up‐regulated 144aa‐uORF can increase the degradation of ZNRD1‐AS1 through the nonsense‐mediated RNA decay (NMD) pathway. Knockdown of ZNRD1‐AS1 inhibits vasculogenic mimicry in glioma cells by modulating miR‐499a‐5p. At the same time, miR‐499a‐5p is down‐regulated and has a tumour‐suppressive effect in gliomas. In addition, ZNRD1‐AS1 serves as a competitive endogenous RNA (ceRNA) and regulates the expression of ELF1 by binding to miR‐499a‐5p. Notably, ELF1 binds to the promoter region of EMI1 and up‐regulates EMI1 expression, while simultaneously promoting vasculogenic mimicry in glioma cells. This study suggests that the 144aa‐uORF\ZNRD1‐AS1\miR‐499a‐5p\ELF1\EMI1 axis takes key part in regulating the formation of vasculogenic mimicry in gliomas and may provide a potential target for glioma treatment.
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Affiliation(s)
- Mo Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Shuyuan Shen
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
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Scholz A, Rappl P, Böffinger N, Mota AC, Brüne B, Schmid T. Translation of TNFAIP2 is tightly controlled by upstream open reading frames. Cell Mol Life Sci 2020; 77:2017-2027. [PMID: 31392347 PMCID: PMC11104949 DOI: 10.1007/s00018-019-03265-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
Translation is a highly regulated process, both at the global as well as on a transcript-specific level. Regulatory upstream open reading frames (uORFs) represent a mode to alter cap-dependent translation efficiency in a transcript-specific manner and are found in numerous mRNAs. In the majority of cases, uORFs inhibit the translation of their associated main ORFs. Consequently, their inactivation results in enhanced translation of the main ORF, a phenomenon best characterized in the context of the integrated stress response. In the present study, we identified potent translation-inhibitory uORFs in the transcript leader sequence (TLS) of tumor necrosis factor alpha induced protein 2 (TNFAIP2). The initial description of the uORFs was based on the observation that despite a massive induction of TNFAIP2 mRNA expression in response to interleukin 1β (IL1β), TNFAIP2 protein levels remained low in MCF7 cells. While we were able to characterize the uORFs with respect to their exact size and sequential requirements in this cellular context, only TPA stimulation partially overcame the translation-inhibitory activity of the TNFAIP2 uORFs. Characterization of TNFAIP2 translation in the context of monocyte-to-macrophage differentiation suggested that, while the uORFs efficiently block TNFAIP2 protein synthesis in monocytes, they are inactivated in mature macrophages, thus allowing for a massive increase in TNFAIP2 protein expression. In summary, we establish TNFAIP2 as a novel target of uORF-mediated translational regulation. Furthermore, our findings suggest that during macrophage differentiation a major uORF-dependent translational switch occurs.
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Affiliation(s)
- Anica Scholz
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Peter Rappl
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Nicola Böffinger
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Ana Carolina Mota
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Bernhard Brüne
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
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4
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Weidle UH, Rohwedder I, Birzele F, Weiss EH, Schiller C. LST1: A multifunctional gene encoded in the MHC class III region. Immunobiology 2018; 223:699-708. [PMID: 30055863 DOI: 10.1016/j.imbio.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/14/2018] [Indexed: 12/11/2022]
Abstract
The LST1 gene is located in the MHC class III cluster between the MHC class I and II regions. While most genes in this cluster have been sufficiently characterised, a definitive function and expression pattern for LST1 still remains elusive. In the present review we describe its promotor, gene organisation, splice variants and expression in human tissues, cell lines and cancer. We focus on LST1 expression in inflammation and discuss known correlations with autoimmune diseases and cancer. Current data on LST1 polymorphisms and their known associations with pathologies are also discussed in detail. We summarize the potential functions that have been described for the full-length LST1 protein including its function as a transmembrane adaptor protein with inhibitory signal transduction and its role as a membrane scaffold facilitating the formation of tunnelling nanotubes. We also discuss further potential functions by compiling all known LST1-interacting proteins. Furthermore, we address knowledge gaps and conflictive issues regarding disease association, non-hematopoietic expression and the discrepancy between RNA and protein expression data.
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Affiliation(s)
- Ulrich H Weidle
- Zentrum Seniorenstudium, Ludwig-Maximilians-Universität München, Hohenstaufenstrasse 1, 80801 München, Germany
| | - Ina Rohwedder
- Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Fabian Birzele
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Grenzacherstrasse 124, 4052 Basel, Switzerland
| | - Elisabeth H Weiss
- Zentrum Seniorenstudium, Ludwig-Maximilians-Universität München, Hohenstaufenstrasse 1, 80801 München, Germany; Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Christian Schiller
- Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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5
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Yuan FF, Ye XP, Liu W, Xue LQ, Ma YR, Zhang LL, Zhang MM, Sun F, Wan YY, Zhang QY, Zhao SX, Song HD. Genetic study of early-onset Graves' disease in the Chinese Han population. Clin Genet 2017; 93:103-110. [PMID: 28598035 DOI: 10.1111/cge.13072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/31/2017] [Indexed: 01/19/2023]
Abstract
Graves' disease (GD) is a complex autoimmune disorder in which genetic and environmental factors are both involved in the pathogenesis. Early-onset patients have a shorter exposure time to environmental factors and are, therefore, good models to help understand the genetic architecture of GD. Based on previous studies of early-onset GD, 11 single nucleotide polymorphisms (SNPs) and their related SNPs (R2 > .6), SNPs located within a ±1-Mb region of the FOXP3 gene, and 20 validated GD-risk SNPs were selected and screened for genotyping in 3735 GD and 4893 control patients to investigate whether early-onset GD is a subtype of GD with distinct susceptibility genes. Ultimately, we did not confirm the reported genetic markers of early-onset GD in our Chinese Han population but found that a GD-risk SNP located in the human leukocyte antigen class I region-rs4947296-was more strongly correlated with early-onset GD than non-early-onset GD. In addition, heterogeneity analysis of GD patients suggests that it may be more reasonable to define early-onset GD as an onset age ≤20 years.
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Affiliation(s)
- F-F Yuan
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China.,Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - X-P Ye
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - W Liu
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China.,Department of Endocrinology, The Ninth People's Hospital (the north branch) Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - L-Q Xue
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Y-R Ma
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - L-L Zhang
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - M-M Zhang
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - F Sun
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Y-Y Wan
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Q-Y Zhang
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - S-X Zhao
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - H-D Song
- The Core Laboratory in Medicine Center of Clinical Research, Department of Endocrinology, The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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Leist SR, Kollmus H, Hatesuer B, Lambertz RLO, Schughart K. Lst1 deficiency has a minor impact on course and outcome of the host response to influenza A H1N1 infections in mice. Virol J 2016; 13:17. [PMID: 26817701 PMCID: PMC4729168 DOI: 10.1186/s12985-016-0471-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previously, we performed a quantitative trait locus (QTL) mapping study in BXD recombinant inbred mice to identify host genetic factors that confer resistance to influenza A virus infection. We found Lst1 (leukocyte specific transcript 1) as one of the most promising candidate genes in the Qivr17-2 locus because it is non-functional in DBA/2 J mice. Several studies have proposed that LST1 plays a role in the immune response to inflammatory diseases in humans and has additional immune-regulatory functions. Here, we evaluated the relevance of LST1 for the host response to influenza A infection in B6-Lst1 (-/-) mutant mice. FINDINGS To investigate the role of LST1, we infected B6-Lst1 (-/-) mutant and C57BL/6 N wild-type mice with a low-virulent influenza A virus (PR8M; H1N1). Lst1 deficient mice exhibited significantly increased body weight loss at days 5 and 6 after infection and slightly increased lethality compared to infected wild-type mice. Determination of viral loads, histopathological examination and analysis of immune cell composition in bronchoalveolar lavage of infected lungs did not reveal any obvious differences between KO and wild-type mice. CONCLUSIONS The absence of Lst1 leads to a slightly more susceptible phenotype. However, deletion of Lst1 in DBA/2 J mice alone does not explain the high susceptibility of this strain to PR8M influenza infections.
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Affiliation(s)
- Sarah R Leist
- Department of Infection Genetics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany. .,University of Veterinary Medicine Hannover, Hannover, Germany.
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany. .,University of Veterinary Medicine Hannover, Hannover, Germany.
| | - Bastian Hatesuer
- Department of Infection Genetics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany. .,University of Veterinary Medicine Hannover, Hannover, Germany.
| | - Ruth L O Lambertz
- Department of Infection Genetics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany. .,University of Veterinary Medicine Hannover, Hannover, Germany.
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany. .,University of Veterinary Medicine Hannover, Hannover, Germany. .,University of Tennessee Health Science Center, Memphis, Tennessee, United States of America.
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