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Guo T, Wang Y, Sun X, Hou S, Lan Y, Yuan S, Yang S, Zhao F, Chu Y, Ma Y, Cheng T, Yu J, Liu B, Yuan W, Wang X. Loss of RNA-binding protein CELF2 promotes acute leukemia development via FAT10-mTORC1. Oncogene 2024; 43:1476-1487. [PMID: 38514854 PMCID: PMC11068570 DOI: 10.1038/s41388-024-03006-3] [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: 08/12/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024]
Abstract
RNA-binding proteins (RBPs) are critical regulators for RNA transcription and translation. As a key member of RBPs, ELAV-like family protein 2 (CELF2) has been shown to regulate RNA splicing and embryonic hematopoietic development and was frequently seen dysregulated in acute myeloid leukemia (AML). However, the functional role(s) of CELF2 in hematopoiesis and leukemogenesis has not been fully elucidated. In the current study, we showed that Celf2 deficiency in hematopoietic system led to enhanced HSCs self-renewal and differentiation toward myeloid cells in mice. Loss of Celf2 accelerated myeloid cell transformation and AML development in MLL-AF9-induced AML murine models. Gene expression profiling integrated with RNA immunoprecipitation sequencing (RIP-Seq), together with biochemical experiments revealed that CELF2 deficiency stabilizes FAT10 mRNA, promotes FAT10 translation, thereby increases AKT phosphorylation and mTORC1 signaling pathway activation. Notably, combination therapy with a mTORC1 inhibitor (Rapamycin) and a MA9/DOTL1 inhibitor (EPZ-5676) reduced the leukemia burden in MLL-AF9 mice lacking Celf2 in vivo. Our study elucidated a novel mechanism by which the CELF2/FAT10-AKT/mTORC1 axis regulates the proliferation of normal blood cells and the development of AML, thus providing potential therapeutic targets for myeloid leukemia suppression.
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Affiliation(s)
- Tengxiao Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Biomedical Center of Qingdao University, Qingdao, 266000, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yuxia Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xiaolu Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Shuaibing Hou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yanjie Lan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Shengnan Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Shuang Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Fei Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yajing Chu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yuanwu Ma
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medicine College, Chinese Academy of Medical Sciences, Beijing, 100021, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Jia Yu
- Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Bing Liu
- State Key Laboratory of Proteomics, Translational Medicine Center of Stem Cells, 307-Ivy Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Xiaomin Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- State Key Laboratory of Experimental Hematology, Department of Stem Cell and Regenerative Medicine, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
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Wang Q, Liu L, Gou X, Zhang T, Zhao Y, Xie Y, Zhou J, Liu Y, Song K. The 3'‑untranslated region of XB130 regulates its mRNA stability and translational efficiency in non‑small cell lung cancer cells. Oncol Lett 2023; 26:427. [PMID: 37720672 PMCID: PMC10502931 DOI: 10.3892/ol.2023.14013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023] Open
Abstract
Silencing XB130 inhibits cell proliferation and epithelial-mesenchymal transition in non-small cell lung cancer (NSCLC), suggesting that downregulating XB130 expression may impede NSCLC progression. However, the molecular mechanism underlying the regulation of XB130 expression remains unclear. In the present study, the role of the 3'-untranslated region (3'-UTR) in the regulation of XB130 expression was investigated. Recombinant psiCHECK-2 vectors with wild-type, truncated, or mutant XB130 3'-UTR were constructed, and the effects of these insertions on reporter gene expression were examined using a dual-luciferase reporter assay and reverse transcription-quantitative PCR. Additionally, candidate proteins that regulated XB130 expression by binding to critical regions of the XB130 3'-UTR were screened for using an RNA pull-down assay, followed by mass spectrometry and western blotting. The results revealed that insertion of the entire XB130 3'-UTR (1,218 bp) enhanced reporter gene expression. Positive regulatory elements were primarily found in nucleotides 113-989 of the 3'-UTR, while negative regulatory elements were found in the 1-112 and 990-1,218 regions of the 3'-UTR. Deletion analyses identified nucleotides 113-230 and 503-660 of the 3'-UTR as two major fragments that likely promote XB130 expression by increasing mRNA stability and translation rate. Additionally, a U-rich element in the 970-1,053 region of the 3'-UTR was identified as a negative regulatory element that inhibited XB130 expression by suppressing translation. Furthermore, seven candidate proteins that potentially regulated XB130 expression by binding to the 113-230, 503-660, and 970-1,053 regions of the 3'-UTR were identified, shedding light on the regulatory mechanism of XB130 expression. Collectively, these results suggested that complex sequence integrations in the mRNA 3'-UTR variably affected XB130 expression in NSCLC cells.
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Affiliation(s)
- Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Lingling Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Xuanjing Gou
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Ting Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yan Zhao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yuan Xie
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Jianjiang Zhou
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Ying Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Kewei Song
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Department of Sport and Health, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
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Epigenetic Alterations in Sports-Related Injuries. Genes (Basel) 2022; 13:genes13081471. [PMID: 36011382 PMCID: PMC9408207 DOI: 10.3390/genes13081471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
It is a well-known fact that physical activity benefits people of all age groups. However, highly intensive training, maladaptation, improper equipment, and lack of sufficient rest lead to contusions and sports-related injuries. From the perspectives of sports professionals and those performing regular–amateur sports activities, it is important to maintain proper levels of training, without encountering frequent injuries. The bodily responses to physical stress and intensive physical activity are detected on many levels. Epigenetic modifications, including DNA methylation, histone protein methylation, acetylation, and miRNA expression occur in response to environmental changes and play fundamental roles in the regulation of cellular activities. In the current review, we summarise the available knowledge on epigenetic alterations present in tissues and organs (e.g., muscles, the brain, tendons, and bones) as a consequence of sports-related injuries. Epigenetic mechanism observations have the potential to become useful tools in sports medicine, as predictors of approaching pathophysiological alterations and injury biomarkers that have already taken place.
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Fan HN, Zhao XY, Liang R, Chen XY, Zhang J, Chen NW, Zhu JS. CircPTK2 inhibits the tumorigenesis and metastasis of gastric cancer by sponging miR-134-5p and activating CELF2/PTEN signaling. Pathol Res Pract 2021; 227:153615. [PMID: 34562827 DOI: 10.1016/j.prp.2021.153615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND CircRNAs are a new subset of noncoding RNAs formed by covalent closed loops and play crucial roles in the regulation of cancer gene expression. However, the roles and underlying mechanisms of circRNAs in gastric cancer (GC) remain indistinct. This study aimed to explore the role and mechanism of hsa_circ_0006421 (circPTK2) in GC. METHODS The differential expression of circRNAs between GC tissues and adjacent normal tissues were identified by a circRNA expression profiling. Associations of circPTK2 or miR-134-5p expression with clinicopathological characteristics and prognosis of GC patients were analyzed by chi-square of Fisher's exact tests and Kaplan-Meier analysis. CCK8, colony formation, EdU assays and animal models were performed to assess the effects of circPTK2 on proliferation and invasion of GC cells. CircPTK2-specific probes were used to purify the RNA pulled down from the circPTK2, and enrichment of circPTK2 and miR-134-5p was detected by qRT-PCR. The effects of circPTK2 on miR-134-5p expression and CELF2/PTEN signaling were examined by qRT-PCR and Western blotting analysis. RESULTS Low expression of circPTK2 and high expression of miR-134-5p were related to the poor survival, and high expression of miR-134-5p was related to the tumor recurrence in GC patients. Overexpressing circPTK2 suppressed the proliferation, colony formation, DNA synthesis and cell invasion as well as xenograft tumor growth and lung metastasis in vitro and in vivo, whereas silencing circPTK2 had the opposite effects. Moreover, circPTK2 was negatively correlated and co-localized with miR-134-5p in the cytoplasm of GC tissue cells. circPTK2 bound to and sponged miR-134-5p in GC cells, and miR-134-5p facilitated cell growth and invasion but attenuated circPTK2 induced tumor suppressive effects and CELF2/PTEN signaling activation in GC cells. CONCLUSIONS circPTK2 functions as a tumor suppressor in GC by sponging miR-134-5p and activating the CELF2/PTEN axis.
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Affiliation(s)
- Hui-Ning Fan
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth people's Hospital, Shanghai 200233, PR China.
| | - Xiang-Yun Zhao
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth people's Hospital, Shanghai 200233, PR China.
| | - Rui Liang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth people's Hospital, Shanghai 200233, PR China.
| | - Xiao-Yu Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth people's Hospital, Shanghai 200233, PR China.
| | - Jing Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth people's Hospital, Shanghai 200233, PR China.
| | - Ni-Wei Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth people's Hospital, Shanghai 200233, PR China.
| | - Jin-Shui Zhu
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth people's Hospital, Shanghai 200233, PR China.
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5
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Ge L, Zhou F, Nie J, Wang X, Zhao Q. Hypoxic colorectal cancer-secreted exosomes deliver miR-210-3p to normoxic tumor cells to elicit a protumoral effect. Exp Biol Med (Maywood) 2021; 246:1895-1906. [PMID: 33969722 DOI: 10.1177/15353702211011576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Hypoxia, the most common feature in the tumor microenvironment, is closely related to tumor malignant progression and poor patient's prognosis. Exosomes, initially recognized as cellular "garbage dumpsters", are now known to be important mediums for mediating cellular communication in tumor microenvironment. However, the mechanisms of hypoxic tumor cell-derived exosomes facilitate colorectal cancer progression still need further exploration. In the present study, we found that exosomes from hypoxic colorectal cancer cells (H-Exos) promoted G1-S cycle transition and proliferation while preventing the apoptosis of colorectal cancer cells by transmitting miR-210-3p to normoxic tumor cells. Mechanistic investigation indicated that miR-210-3p from H-Exos elicited its protumoral effect via suppressing CELF2 expression. A preclinical study further confirmed that H-Exos could promote tumorigenesis in vivo. Clinically, the expression of miR-210-3p in circulating plasma exosomes was markedly upregulated in colorectal cancer patients, which were closely associated with multiple unfavorable clinicopathological features. Taken together, these results suggest that hypoxia may stimulate colorectal cancer cells to secrete miR-210-3p-enriched exosomes in tumor microenvironment, which elicit protumoral effects by inhibiting CELF2 expression. These findings provide new insights on the mechanism of colorectal cancer progression and potential therapeutic targets for colorectal cancer.
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Affiliation(s)
- Liuqing Ge
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University & Hubei Clinical Center and Key Laboratory for Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Feng Zhou
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University & Hubei Clinical Center and Key Laboratory for Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Jiayan Nie
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University & Hubei Clinical Center and Key Laboratory for Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Xiaobing Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University & Hubei Clinical Center and Key Laboratory for Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University & Hubei Clinical Center and Key Laboratory for Intestinal and Colorectal Diseases, Wuhan 430071, China
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Guo Q, Wu Y, Guo X, Cao L, Xu F, Zhao H, Zhu J, Wen H, Ju X, Wu X. The RNA-Binding Protein CELF2 Inhibits Ovarian Cancer Progression by Stabilizing FAM198B. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:169-184. [PMID: 33335801 PMCID: PMC7734233 DOI: 10.1016/j.omtn.2020.10.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023]
Abstract
An increasing number of studies have clarified the functional roles of RNA-binding proteins (RBPs) in driving post-transcriptional mechanisms of cancer progression. In this study, we integrated data from the RBP database and Gene Expression Omnibus (GEO) data with RNA sequencing (RNA-seq) data from 10 ovarian cancer tissues and 8 normal ovarian tissues and identified an RBP, CUGBP- and ETR-3-like family 2 (CELF2). We found that CELF2 expression was downregulated in ovarian cancer and positively correlated with the overall survival (OS) and progression-free survival (PFS) of patients with ovarian cancer. Altered CELF2 expression led to changes in the proliferation, migration, and invasion of ovarian cancer cells in vitro and in vivo. CELF2 expression increased the stability of its target, FAM198B, by binding to AU/U-rich elements (AREs) in the 3' untranslated region (3' UTR). FAM198B knockdown restored the CELF2-mediated suppression of proliferation and migration. We also found that CELF2/FAM198B may repress ovarian cancer progression by inhibiting the mitogen-activated protein kinase/extracellular-regulated protein kinase (MAPK/ERK) signaling pathway. Finally, a curcumin-induced increase in CELF2 expression resulted in increased ovarian cancer cell sensitivity to cisplatin. Our study elucidated a novel mechanism by which the CELF2/FAM198B axis regulates proliferation and metastasis in ovarian cancer, providing novel, potential therapeutic targets for ovarian cancer.
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Affiliation(s)
- Qinhao Guo
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Yong Wu
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Xueqi Guo
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Lijie Cao
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Fei Xu
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Haiyun Zhao
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Jun Zhu
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Hao Wen
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Xingzhu Ju
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
| | - Xiaohua Wu
- Department of Oncology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, China
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Wang D, Xu X, Pan J, Zhao S, Li Y, Wang Z, Yang J, Zhang X, Wang Y, Liu M. GAS5 knockdown alleviates spinal cord injury by reducing VAV1 expression via RNA binding protein CELF2. Sci Rep 2021; 11:3628. [PMID: 33574559 PMCID: PMC7878805 DOI: 10.1038/s41598-021-83145-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNA growth arrest specific transcript 5 (GAS5) has been found to be implicated in the pathogenesis of central nervous diseases and to be a contributor to hypoxic brain injury. However, the roles and molecular mechanisms of GAS5 in spinal cord injury (SCI) have not thoroughly investigated. Here, we reported that GAS5 knockdown improved rat locomotor function and alleviated pathological damage of spinal cord tissues by reducing oxidative stress, caspase-3 activity and vav guanine nucleotide exchange factor 1 (VAV1) expression in SCI rat models. GAS5 knockdown inhibited the increase of malondialdehyde (MDA) level and cell apoptotic rate induced by oxygen-glucose deprivation (OGD) and weakened the inhibitory effects of OGD on superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities and cell viability in RN-Sc cells, suggesting that GAS5 loss mitigated OGD-triggered oxidative stress and cell injury in RN-Sc cells. Molecular mechanism explorations revealed that GAS5 recruited CUGBP, Elav-like family member 2 (CELF2) to the coding region of VAV1 mRNA, resulting in the increase of VAV1 mRNA stability and expression levels. VAV1 knockdown weakened OGD-induced oxidative stress and cell injury in RN-Sc cells. VAV1 loss alleviated GAS5-induced oxidative stress and cell injury in OGD-treated RN-Sc cells. As a conclusion, our findings suggested that GAS5 aggravated SCI by increasing VAV1 expression via binding with CELF2, deepening our understanding on function and molecular basis of GAS5 in SCI.
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Affiliation(s)
- Dan Wang
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Xiaoxiao Xu
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Junwei Pan
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Shixin Zhao
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Yu Li
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Zhen Wang
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Jiahao Yang
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Xi Zhang
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Yisheng Wang
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China
| | - Ming Liu
- Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East road, Erqi District, Zhengzhou, 450052, China.
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LncRNA-SNHG16 promotes proliferation and migration of acute myeloid leukemia cells via PTEN/PI3K/AKT axis through suppressing CELF2 protein. J Biosci 2021. [DOI: 10.1007/s12038-020-00127-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure. BMC Genomics 2020; 21:866. [PMID: 33334313 PMCID: PMC7745412 DOI: 10.1186/s12864-020-07239-w] [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] [Indexed: 12/30/2022] Open
Abstract
Background RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. The identification of RBP binding sites is a crucial step in understanding the biological mechanism of post-transcriptional gene regulation. However, the determination of RBP binding sites on a large scale is a challenging task due to high cost of biochemical assays. Quite a number of studies have exploited machine learning methods to predict binding sites. Especially, deep learning is increasingly used in the bioinformatics field by virtue of its ability to learn generalized representations from DNA and protein sequences. Results In this paper, we implemented a novel deep neural network model, DeepRKE, which combines primary RNA sequence and secondary structure information to effectively predict RBP binding sites. Specifically, we used word embedding algorithm to extract features of RNA sequences and secondary structures, i.e., distributed representation of k-mers sequence rather than traditional one-hot encoding. The distributed representations are taken as input of convolutional neural networks (CNN) and bidirectional long-term short-term memory networks (BiLSTM) to identify RBP binding sites. Our results show that deepRKE outperforms existing counterpart methods on two large-scale benchmark datasets. Conclusions Our extensive experimental results show that DeepRKE is an efficacious tool for predicting RBP binding sites. The distributed representations of RNA sequences and secondary structures can effectively detect the latent relationship and similarity between k-mers, and thus improve the predictive performance. The source code of DeepRKE is available at https://github.com/youzhiliu/DeepRKE/. Supplementary Information The online version contains supplementary material available at (doi:10.1186/s12864-020-07239-w).
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10
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CELF2 regulates the species-specific alternative splicing of TREM2. Sci Rep 2020; 10:17995. [PMID: 33093587 PMCID: PMC7582162 DOI: 10.1038/s41598-020-75057-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/12/2020] [Indexed: 11/08/2022] Open
Abstract
Genetic variations of TREM2 have been implicated as a risk factor of Alzheimer’s disease (AD). Recent studies suggest that the loss of TREM2 function compromises microglial responses to the accumulation of amyloid beta. Previously, we found that exon 3 of TREM2 is an alternative exon whose skipping leads to a reduction in full-length TREM2 protein by inducing nonsense-mediated mRNA decay. Here, we aimed to identify factors regulating TREM2 splicing. Using a panel of RNA-binding proteins, we found that exon 3 skipping of TREM2 was promoted by two paralogous proteins, CELF1 and CELF2, which were both linked previously with risk loci of AD. Although the overexpression of both CELF1 and CELF2 enhanced exon 3 skipping, only CELF2 reduced the expression of full-length TREM2 protein. Notably, the TREM2 ortholog in the green monkey, but not in the mouse, showed alternative splicing of exon 3 like human TREM2. Similarly, splicing regulation of exon 3 by CELF1/2 was found to be common to humans and monkeys. Using chimeric minigenes of human and mouse TREM2, we mapped a CELF-responsive sequence within intron 3 of human TREM2. Collectively, our results revealed a novel regulatory factor of TREM2 expression and highlighted a species-dependent difference of its regulation.
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11
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Mallory MJ, McClory SP, Chatrikhi R, Gazzara MR, Ontiveros RJ, Lynch KW. Reciprocal regulation of hnRNP C and CELF2 through translation and transcription tunes splicing activity in T cells. Nucleic Acids Res 2020; 48:5710-5719. [PMID: 32338744 PMCID: PMC7261192 DOI: 10.1093/nar/gkaa295] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/23/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
RNA binding proteins (RBPs) frequently regulate the expression of other RBPs in mammalian cells. Such cross-regulation has been proposed to be important to control networks of coordinated gene expression; however, much remains to be understood about how such networks of cross-regulation are established and what the functional consequence is of coordinated or reciprocal expression of RBPs. Here we demonstrate that the RBPs CELF2 and hnRNP C regulate the expression of each other, such that depletion of one results in reduced expression of the other. Specifically, we show that loss of hnRNP C reduces the transcription of CELF2 mRNA, while loss of CELF2 results in decreased efficiency of hnRNP C translation. We further demonstrate that this reciprocal regulation serves to fine tune the splicing patterns of many downstream target genes. Together, this work reveals new activities of hnRNP C and CELF2, provides insight into a previously unrecognized gene regulatory network, and demonstrates how cross-regulation of RBPs functions to shape the cellular transcriptome.
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Affiliation(s)
- Michael J Mallory
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sean P McClory
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rakesh Chatrikhi
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert J Ontiveros
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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12
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Yeung YT, Fan S, Lu B, Yin S, Yang S, Nie W, Wang M, Zhou L, Li T, Li X, Bode AM, Dong Z. CELF2 suppresses non-small cell lung carcinoma growth by inhibiting the PREX2-PTEN interaction. Carcinogenesis 2020; 41:377-389. [PMID: 31241130 DOI: 10.1093/carcin/bgz113] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 06/03/2019] [Accepted: 06/20/2019] [Indexed: 12/31/2022] Open
Abstract
The phosphoinositide 3-kinase (PI3-K)/Akt signaling pathway is important in the regulation of cell proliferation through its production of phosphatidylinositol 3,4,5-triphosphate (PIP3). Activation of this pathway is frequently observed in human cancers, including non-small cell lung carcinoma. The PI3-K/Akt pathway is negatively regulated by the dual-specificity phosphatase and tensin homolog (PTEN) protein. PTEN acts as a direct antagonist of PI3-K by dephosphorylating PIP3. Studies have shown that PTEN phosphatase activity is inhibited by PREX2, a guanine nucleotide exchanger factor (GEF). Multiple studies revealed that CELF2, an RNA binding protein, cooperates synergistically with PTEN as a tumor suppressor in multiple cancers. However, the underlying mechanism as to how CELF2 enhances PTEN activity remains unclear. Here, we report that CELF2 interacts with PREX2 and reduces the association of PREX2 with PTEN. Consistent with this observation, PTEN phosphatase activity is upregulated with CELF2 overexpression. In addition, overexpression of CELF2 represses both Akt phosphorylation and cell proliferation only in the presence of PTEN. In an ex vivo study, CELF2 gene delivery could significantly inhibit patient-derived xenografts (PDX) tumor growth. To further investigate the clinical relevance of this finding, we analyzed 87 paired clinical lung adenocarcinoma samples and the results showed that CELF2 protein expression is downregulated in tumor tissues and associated with poor prognosis. The CELF2 gene is located on the chromosome 10p arm, a region frequently lost in human cancers, including breast invasive carcinoma, low-grade glioma and glioblastoma. Analysis of TCGA datasets showed that CELF2 expression is also associated with shorter patient survival time in all these cancers. Overall, our work suggests that CELF2 plays a novel role in PI3-K signaling by antagonizing the oncogenic effect of PREX2.
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Affiliation(s)
- Yiu To Yeung
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China.,The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Suyu Fan
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Bingbing Lu
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China.,Pathophysiology Department, Basic Medical College, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuying Yin
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China.,Pathophysiology Department, Basic Medical College, Zhengzhou University, Zhengzhou, Henan, China
| | - Sen Yang
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Wenna Nie
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Meixian Wang
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Liting Zhou
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Tiepeng Li
- Department of Immunotherapy, The Affiliated Cancer Hospital, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiang Li
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China.,Pathophysiology Department, Basic Medical College, Zhengzhou University, Zhengzhou, Henan, China.,Collaborative Innovation Center of Cancer Chemoprevention of Henan, Zhengzhou, Henan, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Zigang Dong
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China.,The Hormel Institute, University of Minnesota, Austin, MN, USA.,Pathophysiology Department, Basic Medical College, Zhengzhou University, Zhengzhou, Henan, China.,Department of Immunotherapy, The Affiliated Cancer Hospital, Zhengzhou University, Zhengzhou, Henan, China.,Collaborative Innovation Center of Cancer Chemoprevention of Henan, Zhengzhou, Henan, China
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13
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Yang X, Zhao L, Pei J, Wang Z, Zhang J, Wang B. CELF6 modulates triple-negative breast cancer progression by regulating the stability of FBP1 mRNA. Breast Cancer Res Treat 2020; 183:71-82. [PMID: 32601971 DOI: 10.1007/s10549-020-05753-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/13/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) remains a great challenge in clinical treatment due to a shortage of effective therapeutic targets and acquired chemoresistance. Here, we identified the role of an RNA-binding protein, CUG-BP Elav-like family member 6 (CELF6), in the TNBC development and paclitaxel (PTX) chemoresistance. METHODS Stable CELF6-overexpressing cell lines were established in BT549 and MDA-MB-231 cells. Cell proliferation was determined using cell counting, two-dimensional colony formation, and MTT assay. Meanwhile, cell migration and cell invasion were detected by Transwell assay. Furthermore, the downstream target gene of CELF6 was identified and the direct interaction was further determined by luciferase reporter assay, immunoprecipitation, and RNA pull-down. Additionally, the PTX resistant cell line was established to determine the role of CELF6 in PTX resistance. RESULTS CELF6 overexpression suppressed cell proliferation, cell migration, and cell invasion. Mechanistically, Fructose-Bisphosphatase 1 (FBP1) was identified as the target gene of CELF6 and stabilized by CELF6 via binding 3'UTR. CELF6 overexpression mediated inhibition in TNBC development was dependent on FBP1. Moreover, CELF6 overexpression increased the sensitivity to PTX treatment. CONCLUSION CELF6 functions as a tumor suppressor by upregulating FBP 1 expression via stabilizing its mRNA, and thereby inhibits TNBC progression.
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Affiliation(s)
- Xiaowei Yang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China.
| | - Lu Zhao
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, No. 1095, Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Jing Pei
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
| | - Zhaorui Wang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
| | - Jingjie Zhang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
| | - Benzhong Wang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
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14
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Yoon JSJ, Wu MK, Zhu TH, Zhao H, Cheung ST, Chamberlain TC, Mui ALF. Interleukin-10 control of pre-miR155 maturation involves CELF2. PLoS One 2020; 15:e0231639. [PMID: 32324763 PMCID: PMC7179890 DOI: 10.1371/journal.pone.0231639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/29/2020] [Indexed: 02/01/2023] Open
Abstract
The anti-inflammatory cytokine interleukin-10 (IL10) is essential for attenuating inflammatory responses, which includes reducing the expression of pro-inflammatory microRNA-155 (miR155) in lipopolysaccharide (LPS) activated macrophages. miR155 enhances the expression of pro-inflammatory cytokines such as TNFα and suppresses expression of anti-inflammatory molecules such as SHIP1 and SOCS1. We previously found that IL10 interfered with the maturation of pre-miR155 to miR155. To understand the mechanism by which IL10 interferes with pre-miR155 maturation we isolated proteins that associate with pre-miR155 in response to IL10 in macrophages. We identified CELF2, a member of the CUGBP, ELAV-Like Family (CELF) family of RNA binding proteins, as protein whose association with pre-miR155 increased in IL10 treated cells. CRISPR-Cas9 mediated knockdown of CELF2 impaired IL10’s ability to inhibit both miR155 expression and TNFα expression.
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Affiliation(s)
- Jeff S. J. Yoon
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, Canada
- Department of Surgery, University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Mike K. Wu
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, Canada
- Department of Surgery, University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Tian Hao Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Helen Zhao
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Sylvia T. Cheung
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, Canada
- Department of Surgery, University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Thomas C. Chamberlain
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, Canada
- Department of Surgery, University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Alice L-F. Mui
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, Canada
- Department of Surgery, University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
- * E-mail:
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15
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Gao C, Wang Y. mRNA Metabolism in Cardiac Development and Disease: Life After Transcription. Physiol Rev 2020; 100:673-694. [PMID: 31751167 PMCID: PMC7327233 DOI: 10.1152/physrev.00007.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 09/06/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
The central dogma of molecular biology illustrates the importance of mRNAs as critical mediators between genetic information encoded at the DNA level and proteomes/metabolomes that determine the diverse functional outcome at the cellular and organ levels. Although the total number of protein-producing (coding) genes in the mammalian genome is ~20,000, it is evident that the intricate processes of cardiac development and the highly regulated physiological regulation in the normal heart, as well as the complex manifestation of pathological remodeling in a diseased heart, would require a much higher degree of complexity at the transcriptome level and beyond. Indeed, in addition to an extensive regulatory scheme implemented at the level of transcription, the complexity of transcript processing following transcription is dramatically increased. RNA processing includes post-transcriptional modification, alternative splicing, editing and transportation, ribosomal loading, and degradation. While transcriptional control of cardiac genes has been a major focus of investigation in recent decades, a great deal of progress has recently been made in our understanding of how post-transcriptional regulation of mRNA contributes to transcriptome complexity. In this review, we highlight some of the key molecular processes and major players in RNA maturation and post-transcriptional regulation. In addition, we provide an update to the recent progress made in the discovery of RNA processing regulators implicated in cardiac development and disease. While post-transcriptional modulation is a complex and challenging problem to study, recent technological advancements are paving the way for a new era of exciting discoveries and potential clinical translation in the context of cardiac biology and heart disease.
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Affiliation(s)
- Chen Gao
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
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16
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Angiotensin II type 1 receptor-associated protein deficiency attenuates sirtuin1 expression in an immortalised human renal proximal tubule cell line. Sci Rep 2019; 9:16550. [PMID: 31719572 PMCID: PMC6851135 DOI: 10.1038/s41598-019-52566-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/17/2019] [Indexed: 11/08/2022] Open
Abstract
The proximal tubule is a particularly important site for ageing-related kidney damage. Sirtuin 1 (SIRT1), an NAD+ (nicotinamide adenine dinucleotide)-dependent deacetylase in the proximal tubule, may be involved in renal injury associated with ageing. However, the mechanisms of SIRT1 regulation remain to be elucidated. We recently reported that angiotensin II type 1 receptor (AT1R)-associated protein (ATRAP)-deficient mice displayed age-associated renal function decline and tubulointerstitial fibrosis. Our data showed that SIRT1 protein expression was reduced in ATRAP-deficient mice, although the relationship between ATRAP deficiency and age-associated renal fibrosis is still not fully understood. It is, therefore, necessary to investigate how ATRAP affects SIRT1 protein expression to resolve ageing-associated kidney dysfunction. Here, since ageing studies are inherently lengthy, we used an ex vivo model of the proximal tubule to determine the role of ATRAP in SIRT1 protein expression. We first generated a clonal immortalised human renal proximal tubule epithelial cell line (ciRPTEC) expressing AT1R and ATRAP. Using this cell line, we demonstrated that ATRAP knockdown reduced SIRT1 protein expression in the ciRPTEC but did not alter SIRT1 mRNA expression. Thus, ATRAP likely mediates SIRT1 protein abundance in ciRPTEC.
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17
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Li XC, Song MF, Sun F, Tian FJ, Wang YM, Wang BY, Chen JH. Fragile X-related protein 1 (FXR1) regulates cyclooxygenase-2 (COX-2) expression at the maternal-fetal interface. Reprod Fertil Dev 2019; 30:1566-1574. [PMID: 29852926 DOI: 10.1071/rd18037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/25/2018] [Indexed: 01/11/2023] Open
Abstract
Cyclooxygenase-2 (COX-2) is regulated post-transcriptionally by the AU-rich element (ARE) in the 3'-untranslated region (UTR) of its mRNA. However, the mechanism of COX-2 induction in infertility has not been thoroughly elucidated to date. The aim of this study was to examine the association between COX-2 and fragile X-related protein 1 (FXR1) in trophoblasts. Using quantitative reverse transcription polymerase chain reaction, our results showed that FXR1 mRNA expression levels were significantly decreased in trophoblasts from recurrent miscarriage patients compared with healthy controls; conversely, COX-2 mRNA expression levels were increased in patient samples. We also observed that FXR1 was highly expressed in human placental villi during early pregnancy. Furthermore, we used western blotting and immunofluorescence to analyse the expression levels of FXR1 and COX-2 in HTR-8 cells that were treated with tumour necrosis factor α; we observed that the expression of COX-2 was clearly increased in HTR-8 cells treated with FXR1 small interfering RNA, whereas the expression of COX-2 was effectively decreased in HTR-8 cells with FXR1 overexpressed via a plasmid. Importantly, bioinformatics analysis identified FXR1 binding sites in the 3'-UTR region of COX-2 and firefly luciferase reporter assay analysis verified that FXR1 binds directly to the 3'-UTR region of COX-2. ELISA assays showed that overexpression of FXR1 enhanced vascular endothelial growth factor-A and interleukin-8 expression in HTR-8 cells, whereas conversely, knockdown of FXR1 effectively repressed these effects. In conclusion, the results of this study indicate that FXR1 is a novel COX-2 regulatory factor.
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Affiliation(s)
- Xiao-Cui Li
- Department of Obstetrics and Gynaecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China
| | - Meng-Fan Song
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Feng Sun
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Fu-Ju Tian
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yu-Mei Wang
- Department of Obstetrics and Gynaecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China
| | - Bei-Ying Wang
- Department of Obstetrics and Gynaecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China
| | - Jin-Hong Chen
- Department of Obstetrics and Gynaecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China
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18
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Lin J, Zhang Y, Frankel WN, Ouyang Z. PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks. PLoS Comput Biol 2019; 15:e1007227. [PMID: 31425505 PMCID: PMC6716675 DOI: 10.1371/journal.pcbi.1007227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/30/2019] [Accepted: 06/28/2019] [Indexed: 11/19/2022] Open
Abstract
RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction. We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle. We also demonstrate the potential of PRAS for wide adoption by applying it to the enhanced CLIP-seq (eCLIP) datasets of 37 RNA decay related RBPs in two human cell lines. PRAS can be utilized to investigate any RBPs with available CLIP-seq peaks. PRAS is freely available at http://ouyanglab.jax.org/pras/.
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Affiliation(s)
- Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, United States of America
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, Connecticut, United States of America
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
- Center for Quantitative Medicine, University of Connecticut, Farmington, Connecticut, United States of America
| | - Wayne N. Frankel
- Department of Genetics and Development and Institute for Genomic Medicine, Columbia University Medical Center, New York City, New York, United States of America
| | - Zhengqing Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, United States of America
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, Connecticut, United States of America
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19
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Saul MJ, Emmerich AC, Steinhilber D, Suess B. Regulation of Eicosanoid Pathways by MicroRNAs. Front Pharmacol 2019; 10:824. [PMID: 31379585 PMCID: PMC6659501 DOI: 10.3389/fphar.2019.00824] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/26/2019] [Indexed: 01/07/2023] Open
Abstract
Over the last years, many microRNAs (miRNAs) have been identified that regulate the formation of bioactive lipid mediators such as prostanoids and leukotrienes. Many of these miRNAs are involved in complex regulatory circuits necessary for the fine-tuning of biological functions including inflammatory processes or cell growth. A better understanding of these networks will contribute to the development of novel therapeutic strategies for the treatment of inflammatory diseases and cancer. In this review, we provide an overview of the current knowledge of miRNA regulation in eicosanoid pathways with special focus on novel miRNA functions and regulatory circuits of leukotriene and prostaglandin biosynthesis.
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Affiliation(s)
- Meike J Saul
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Anne C Emmerich
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe Universität Frankfurt, Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe Universität Frankfurt, Frankfurt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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20
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New J, Subramaniam D, Ramalingam S, Enders J, Sayed AAA, Ponnurangam S, Standing D, Ramamoorthy P, O'Neil M, Dixon DA, Saha S, Umar S, Gunewardena S, Jensen RA, Thomas SM, Anant S. Pleotropic role of RNA binding protein CELF2 in autophagy induction. Mol Carcinog 2019; 58:1400-1409. [PMID: 31020708 DOI: 10.1002/mc.23023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/27/2019] [Accepted: 04/08/2019] [Indexed: 12/28/2022]
Abstract
We previously reported that ionizing radiation (IR) mediates cell death through the induction of CUGBP elav-like family member 2 (CELF2), a tumor suppressor. CELF2 is an RNA binding protein that modulates mRNA stability and translation. Since IR induces autophagy, we hypothesized that CELF2 regulates autophagy-mediated colorectal cancer (CRC) cell death. For clinical relevance, we determined CELF2 levels in The Cancer Genome Atlas (TCGA). Role of CELF2 in radiation response was carried out in CRC cell lines by immunoblotting, immunofluorescence, autophagic vacuole analyses, RNA stability assay, quantitative polymerase chain reaction and electron microscopy. In vivo studies were performed in a xenograft tumor model. TCGA analyses demonstrated that compared to normal tissue, CELF2 is expressed at significantly lower levels in CRC, and is associated with better overall 5-year survival in patients receiving radiation. Mechanistically, CELF2 increased levels of critical components of the autophagy cascade including Beclin-1, ATG5, and ATG12 by modulating mRNA stability. CELF2 also increased autophagic flux in CRC. IR significantly induced autophagy in CRC which correlates with increased levels of CELF2 and autophagy associated proteins. Silencing CELF2 with siRNA, mitigated IR induced autophagy. Moreover, knockdown of CELF2 in vivo conferred tumor resistance to IR. These studies elucidate an unrecognized role for CELF2 in inducing autophagy and potentiating the effects of radiotherapy in CRC.
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Affiliation(s)
- Jacob New
- Department of Anatomy & Cell Biology, University of Kansas Medical Center, Kansas, Kansas.,Department of Otolaryngology, University of Kansas Medical Center, Kansas, Kansas
| | | | - Satish Ramalingam
- Department of Cancer Biology, University of Kansas Medical Center, Kansas, Kansas
| | - Jonathan Enders
- Department of Anatomy & Cell Biology, University of Kansas Medical Center, Kansas, Kansas
| | | | | | - David Standing
- Department of Cancer Biology, University of Kansas Medical Center, Kansas, Kansas
| | - Prabhu Ramamoorthy
- Department of Cancer Biology, University of Kansas Medical Center, Kansas, Kansas
| | - Maura O'Neil
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas, Kansas
| | - Dan A Dixon
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Subhrajit Saha
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas, Kansas
| | - Shahid Umar
- Department of General Surgery, University of Kansas Medical Center, Kansas, Kansas
| | - Sumedha Gunewardena
- Department of Molecular Integrative Physiology, University of Kansas Medical Center, Kansas, Kansas
| | - Roy A Jensen
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas, Kansas
| | - Sufi Mary Thomas
- Department of Anatomy & Cell Biology, University of Kansas Medical Center, Kansas, Kansas.,Department of Otolaryngology, University of Kansas Medical Center, Kansas, Kansas.,Department of Cancer Biology, University of Kansas Medical Center, Kansas, Kansas
| | - Shrikant Anant
- Department of Cancer Biology, University of Kansas Medical Center, Kansas, Kansas
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Induction of the p53 Tumor Suppressor in Cancer Cells through Inhibition of Cap-Dependent Translation. Mol Cell Biol 2018; 38:MCB.00367-17. [PMID: 29483299 DOI: 10.1128/mcb.00367-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/18/2018] [Indexed: 12/17/2022] Open
Abstract
The p53 tumor suppressor plays a critical role in protecting normal cells from malignant transformation. Development of small molecules to reactivate p53 in cancer cells has been an area of intense research. We previously identified an internal ribosomal entry site (IRES) within the 5' untranslated region of p53 mRNA that mediates translation of the p53 mRNA independent of cap-dependent translation. Our results also show that in response to DNA damage, cells switch from cap-dependent translation to cap-independent translation of p53 mRNA. In the present study, we discovered a specific inhibitor of cap-dependent translation, 4EGI-1, that is capable of inducing the accumulation of p53 in cancer cells retaining wild-type p53. Our results show that 4EGI-1 causes an increase in p53 IRES activity, leading to increased translation of p53 mRNA. We also observed that 4EGI-1 induces cancer cell apoptosis in a p53-dependent manner. Furthermore, 4EGI-1 induces p53 in cancer cells without causing DNA double-strand breaks. In conclusion, we discovered a mechanistic link between inhibition of cap-dependent translation and enhanced p53 accumulation. This leads to apoptosis of cancer cells without causing collateral damage to normal cells, thus providing a novel and effective therapeutic strategy for cancer.
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Pasini A, Brand OJ, Jenkins G, Knox AJ, Pang L. Suberanilohydroxamic acid prevents TGF-β1-induced COX-2 repression in human lung fibroblasts post-transcriptionally by TIA-1 downregulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:463-472. [PMID: 29555582 PMCID: PMC5910054 DOI: 10.1016/j.bbagrm.2018.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/07/2018] [Accepted: 03/14/2018] [Indexed: 12/28/2022]
Abstract
Cyclooxygenase-2 (COX-2), with its main antifibrotic metabolite PGE2, is regarded as an antifibrotic gene. Repressed COX-2 expression and deficient PGE2 have been shown to contribute to the activation of lung fibroblasts and excessive deposition of collagen in pulmonary fibrosis. We have previously demonstrated that COX-2 expression in lung fibroblasts from patients with idiopathic pulmonary fibrosis (IPF) is epigenetically silenced and can be restored by epigenetic inhibitors. This study aimed to investigate whether COX-2 downregulation induced by the profibrotic cytokine transforming growth factor-β1 (TGF-β1) in normal lung fibroblasts could be prevented by epigenetic inhibitors. We found that COX-2 protein expression and PGE2 production were markedly reduced by TGF-β1 and this was prevented by the pan-histone deacetylase inhibitor suberanilohydroxamic acid (SAHA) and to a lesser extent by the DNA demethylating agent Decitabine (DAC), but not by the G9a histone methyltransferase (HMT) inhibitor BIX01294 or the EZH2 HMT inhibitor 3-deazaneplanocin A (DZNep). However, chromatin immunoprecipitation assay revealed that the effect of SAHA was unlikely mediated by histone modifications. Instead 3′-untranslated region (3′-UTR) luciferase reporter assay indicated the involvement of post-transcriptional mechanisms. This was supported by the downregulation by SAHA of the 3′-UTR mRNA binding protein TIA-1 (T-cell intracellular antigen-1), a negative regulator of COX-2 translation. Furthermore, TIA-1 knockdown by siRNA mimicked the effect of SAHA on COX-2 expression. These findings suggest SAHA can prevent TGF-β1-induced COX-2 repression in lung fibroblasts post-transcriptionally through a novel TIA-1-dependent mechanism and provide new insights into the mechanisms underlying its potential antifibrotic activity. Abbreviations Unlabelled TableSAHA | suberanilohydroxamic acid | TGF-β1 | transforming growth factor-β1 | COX-2 | cyclooxygenase-2 | TIA-1 | T-cell intracellular antigen-1 | PGE2 | prostaglandin E2 | IPF | idiopathic pulmonary fibrosis | DAC | Decitabine | HMT | histone methyltransferase | EZH2 | enhancer of zeste homolog 2 | DZNep | 3-deazaneplanocin A | 3′-UTR | 3′-untranslated region | α-SMA | α-smooth muscle actin | ECM | extracellular matrix | COL1 | collagen 1 | DNMT | DNA methyltransferase | HAT | histone acetyltransferase | HDAC | histone deacetylase | H3K9me3 | histone H3 lysine 9 trimethylation | ARE | AUUUA-rich element | HuR | human antigen R | ELAV1 | ELAV-like RNA binding protein 1 | TTP | Tristetraprolin | CUGBP2 | CUG triplet repeat, RNA binding protein 2 | F-NL | fibroblast from non-fibrotic lung | FCS | fetal calf serum |
The HDAC inhibitor SAHA upregulates the expression of the antifibrotic gene COX-2 post-transcriptionally. The mechanism relies on the downregulation of TIA-1, a negative regulator of COX-2 translation. SAHA has a therapeutic potential by preventing COX-2 repression induced by TGF-β1 in human lung fibroblasts.
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Affiliation(s)
- Alice Pasini
- Division of Respiratory Medicine, University of Nottingham School of Medicine, City Hospital, Nottingham NG5 1PB, United Kingdom; Department of Electrical, Electronic and Information Engineering "Guglielmo Marconi" (DEI), University of Bologna, Via Venezia 52, 47521 Cesena, FC, Italy
| | - Oliver J Brand
- Division of Respiratory Medicine, University of Nottingham School of Medicine, City Hospital, Nottingham NG5 1PB, United Kingdom
| | - Gisli Jenkins
- Division of Respiratory Medicine, University of Nottingham School of Medicine, City Hospital, Nottingham NG5 1PB, United Kingdom
| | - Alan J Knox
- Division of Respiratory Medicine, University of Nottingham School of Medicine, City Hospital, Nottingham NG5 1PB, United Kingdom
| | - Linhua Pang
- Division of Respiratory Medicine, University of Nottingham School of Medicine, City Hospital, Nottingham NG5 1PB, United Kingdom.
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Gong Y, Hewett JA. Maintenance of the Innate Seizure Threshold by Cyclooxygenase-2 is Not Influenced by the Translational Silencer, T-cell Intracellular Antigen-1. Neuroscience 2018; 373:37-51. [PMID: 29337236 DOI: 10.1016/j.neuroscience.2018.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/23/2017] [Accepted: 01/03/2018] [Indexed: 12/13/2022]
Abstract
Activity of neuronal cyclooxygenase-2 (COX-2), a primary source of PG synthesis in the normal brain, is enhanced by excitatory neurotransmission and this is thought to be involved in seizure suppression. Results herein showing that the incidence of pentylenetetrazole (PTZ)-induced convulsions is suppressed in transgenic mice overexpressing COX-2 in neurons support this notion. T-cell intracellular antigen-1 (TIA-1) is an mRNA binding protein that is known to bind to COX-2 mRNA and repress its translation in non-neuronal cell types. An examination of the expression profile of TIA-1 protein in the normal brain indicated that it is expressed broadly by neurons, including those that express COX-2. However, whether TIA-1 regulates COX-2 protein levels in neurons is not known. The purpose of this study was to test the possibility that deletion of TIA-1 increases basal COX-2 expression in neurons and consequently raises the seizure threshold. Results demonstrate that neither the basal nor seizure-induced expression profiles of COX-2 were altered in mice lacking a functional TIA-1 gene suggesting that TIA-1 does not contribute to regulation of COX-2 protein expression in neurons. The acute PTZ-induced seizure threshold was also unchanged in mice lacking TIA-1 protein, indicating that this RNA binding protein does not influence the innate seizure threshold. Nevertheless, the results raise the possibility that the level of neuronal COX-2 expression may be a determinant of the innate seizure threshold and suggest that a better understanding of the regulation of COX-2 expression in the brain could provide new insight into the molecular mechanisms that suppress seizure induction.
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Affiliation(s)
- Yifan Gong
- Program in Neuroscience, Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - James A Hewett
- Program in Neuroscience, Department of Biology, Syracuse University, Syracuse, NY 13244, USA.
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Diarra Dit Konté N, Krepl M, Damberger FF, Ripin N, Duss O, Šponer J, Allain FHT. Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination. Nat Commun 2017; 8:654. [PMID: 28935965 PMCID: PMC5608764 DOI: 10.1038/s41467-017-00631-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 07/16/2017] [Indexed: 11/13/2022] Open
Abstract
The cyclooxygenase-2 is a pro-inflammatory and cancer marker, whose mRNA stability and translation is regulated by the CUG-binding protein 2 interacting with AU-rich sequences in the 3' untranslated region. Here, we present the solution NMR structure of CUG-binding protein 2 RRM3 in complex with 5'-UUUAA-3' originating from the COX-2 3'-UTR. We show that RRM3 uses the same binding surface and protein moieties to interact with AU- and UG-rich RNA motifs, binding with low and high affinity, respectively. Using NMR spectroscopy, isothermal titration calorimetry and molecular dynamics simulations, we demonstrate that distinct sub-states characterized by different aromatic side-chain conformations at the RNA-binding surface allow for high- or low-affinity binding with functional implications. This study highlights a mechanism for RNA discrimination possibly common to multiple RRMs as several prominent members display a similar rearrangement of aromatic residues upon binding their targets.The RNA Recognition Motif (RRM) is the most ubiquitous RNA binding domain. Here the authors combined NMR and molecular dynamics simulations and show that the RRM RNA binding surface exists in different states and that a conformational switch of aromatic side-chains fine-tunes sequence specific binding affinities.
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Affiliation(s)
- Nana Diarra Dit Konté
- Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, HPP L 14.1 Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65, Brno, Czech Republic
- Department of Physical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University Olomouc, 17.listopadu 12, 771 46, Olomouc, Czech Republic
| | - Fred F Damberger
- Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, HPP L 14.1 Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Nina Ripin
- Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, HPP L 14.1 Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Olivier Duss
- Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, HPP L 14.1 Hönggerbergring 64, 8093, Zürich, Switzerland
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, MB-33 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65, Brno, Czech Republic
- Department of Physical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University Olomouc, 17.listopadu 12, 771 46, Olomouc, Czech Republic
| | - Frédéric H-T Allain
- Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, HPP L 14.1 Hönggerbergring 64, 8093, Zürich, Switzerland.
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25
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Li B, Li X, Xiong H, Zhou P, Ni Z, Yang T, Zhang Y, Zeng Y, He J, Yang F, Zhang N, Wang Y, Zheng Y, He F. Inhibition of COX2 enhances the chemosensitivity of dichloroacetate in cervical cancer cells. Oncotarget 2017; 8:51748-51757. [PMID: 28881683 PMCID: PMC5584284 DOI: 10.18632/oncotarget.18518] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/06/2017] [Indexed: 12/14/2022] Open
Abstract
Dichloroacetate (DCA), a traditional mitochondria-targeting agent, has shown promising prospect as a sensitizer in fighting against malignancies including cervical cancer. But it is unclear about the effect of DCA alone on cervical tumor. Moreover, previous reports have demonstrated that the increased cyclooxygenase-2 (COX2) expression is associated with chemoresistance and poor prognosis of cervical cancer. However, it is still unknown whether COX2 can affect the sensitivity of DCA in cervical cancer cells. In this study, we found that cervical cancer cells were insensitive to DCA. Furthermore, we for the first time revealed that DCA could upregulate COX2 which impeded the chemosensitivity of DCA in cervical cancer cells. Mechanistic study showed that DCA reduced the level of RNA binding protein quaking (QKI), leading to the decay suppression of COX2 mRNA and the subsequent elevation of COX2 protein. Inhibition of COX2 using celecoxib could sensitize DCA in repressing the growth of cervical cancer cells both in vitro and in vivo. These results indicate that COX2 is a novel resistance factor of DCA, and combination of celecoxib with DCA may be beneficial to the treatment of cervical cancer.
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Affiliation(s)
- Bo Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Xinzhe Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Haojun Xiong
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Peng Zhou
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Zhenhong Ni
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Teng Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Yan Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Yijun Zeng
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Jintao He
- Battalion 17 of Students, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Fan Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Nan Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Yuting Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Yingru Zheng
- Department of Obstetrics and Gynecology, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, China
| | - Fengtian He
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
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Rumzhum NN, Ammit AJ. Cyclooxygenase 2: its regulation, role and impact in airway inflammation. Clin Exp Allergy 2016; 46:397-410. [PMID: 26685098 DOI: 10.1111/cea.12697] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Cyclooxygenase 2 (COX-2: official gene symbol - PTGS2) has long been regarded as playing a pivotal role in the pathogenesis of airway inflammation in respiratory diseases including asthma. COX-2 can be rapidly and robustly expressed in response to a diverse range of pro-inflammatory cytokines and mediators. Thus, increased levels of COX-2 protein and prostanoid metabolites serve as key contributors to pathobiology in respiratory diseases typified by dysregulated inflammation. But COX-2 products may not be all bad: prostanoids can exert anti-inflammatory/bronchoprotective functions in airways in addition to their pro-inflammatory actions. Herein, we outline COX-2 regulation and review the diverse stimuli known to induce COX-2 in the context of airway inflammation. We discuss some of the positive and negative effects that COX-2/prostanoids can exert in in vitro and in vivo models of airway inflammation, and suggest that inhibiting COX-2 expression to repress airway inflammation may be too blunt an approach; because although it might reduce the unwanted effects of COX-2 activation, it may also negate the positive effects. Evidence suggests that prostanoids produced via COX-2 upregulation show diverse actions (and herein we focus on prostaglandin E2 as a key example); these can be either beneficial or deleterious and their impact on respiratory disease can be dictated by local concentration and specific interaction with individual receptors. We propose that understanding the regulation of COX-2 expression and associated receptor-mediated functional outcomes may reveal number of critical steps amenable to pharmacological intervention. These may prove invaluable in our quest towards future development of novel anti-inflammatory pharmacotherapeutic strategies for the treatment of airway diseases.
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Affiliation(s)
- N N Rumzhum
- Faculty of Pharmacy, University of Sydney, Sydney, NSW, Australia
| | - A J Ammit
- Faculty of Pharmacy, University of Sydney, Sydney, NSW, Australia
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27
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Kato M, Wang M, Chen Z, Bhatt K, Oh HJ, Lanting L, Deshpande S, Jia Y, Lai JYC, O'Connor CL, Wu Y, Hodgin JB, Nelson RG, Bitzer M, Natarajan R. An endoplasmic reticulum stress-regulated lncRNA hosting a microRNA megacluster induces early features of diabetic nephropathy. Nat Commun 2016; 7:12864. [PMID: 27686049 PMCID: PMC5553130 DOI: 10.1038/ncomms12864] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 08/10/2016] [Indexed: 02/06/2023] Open
Abstract
It is important to find better treatments for diabetic nephropathy (DN), a debilitating renal complication. Targeting early features of DN, including renal extracellular matrix accumulation (ECM) and glomerular hypertrophy, can prevent disease progression. Here we show that a megacluster of nearly 40 microRNAs and their host long non-coding RNA transcript (lnc-MGC) are coordinately increased in the glomeruli of mouse models of DN, and mesangial cells treated with transforming growth factor-β1 (TGF- β1) or high glucose. Lnc-MGC is regulated by an endoplasmic reticulum (ER) stress-related transcription factor, CHOP. Cluster microRNAs and lnc-MGC are decreased in diabetic Chop-/- mice that showed protection from DN. Target genes of megacluster microRNAs have functions related to protein synthesis and ER stress. A chemically modified oligonucleotide targeting lnc-MGC inhibits cluster microRNAs, glomerular ECM and hypertrophy in diabetic mice. Relevance to human DN is also demonstrated. These results demonstrate the translational implications of targeting lnc-MGC for controlling DN progression.
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Affiliation(s)
- Mitsuo Kato
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Mei Wang
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Zhuo Chen
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Kirti Bhatt
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Hyung Jung Oh
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Supriya Deshpande
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Ye Jia
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Jennifer Y C Lai
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - YiFan Wu
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Robert G Nelson
- Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona 85014, USA
| | - Markus Bitzer
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
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28
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Liepelt A, Naarmann-de Vries IS, Simons N, Eichelbaum K, Föhr S, Archer SK, Castello A, Usadel B, Krijgsveld J, Preiss T, Marx G, Hentze MW, Ostareck DH, Ostareck-Lederer A. Identification of RNA-binding Proteins in Macrophages by Interactome Capture. Mol Cell Proteomics 2016; 15:2699-714. [PMID: 27281784 DOI: 10.1074/mcp.m115.056564] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 12/11/2022] Open
Abstract
Pathogen components, such as lipopolysaccharides of Gram-negative bacteria that activate Toll-like receptor 4, induce mitogen activated protein kinases and NFκB through different downstream pathways to stimulate pro- and anti-inflammatory cytokine expression. Importantly, post-transcriptional control of the expression of Toll-like receptor 4 downstream signaling molecules contributes to the tight regulation of inflammatory cytokine synthesis in macrophages. Emerging evidence highlights the role of RNA-binding proteins (RBPs) in the post-transcriptional control of the innate immune response. To systematically identify macrophage RBPs and their response to LPS stimulation, we employed RNA interactome capture in LPS-induced and untreated murine RAW 264.7 macrophages. This combines RBP-crosslinking to RNA, cell lysis, oligo(dT) capture of polyadenylated RNAs and mass spectrometry analysis of associated proteins. Our data revealed 402 proteins of the macrophage RNA interactome including 91 previously not annotated as RBPs. A comparison with published RNA interactomes classified 32 RBPs uniquely identified in RAW 264.7 macrophages. Of these, 19 proteins are linked to biochemical activities not directly related to RNA. From this group, we validated the HSP90 cochaperone P23 that was demonstrated to exhibit cytosolic prostaglandin E2 synthase 3 (PTGES3) activity, and the hematopoietic cell-specific LYN substrate 1 (HCLS1 or HS1), a hematopoietic cell-specific adapter molecule, as novel macrophage RBPs. Our study expands the mammalian RBP repertoire, and identifies macrophage RBPs that respond to LPS. These RBPs are prime candidates for the post-transcriptional regulation and execution of LPS-induced signaling pathways and the innate immune response. Macrophage RBP data have been deposited to ProteomeXchange with identifier PXD002890.
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Affiliation(s)
- Anke Liepelt
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Isabel S Naarmann-de Vries
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Nadine Simons
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Katrin Eichelbaum
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Sophia Föhr
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Stuart K Archer
- ¶EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Garran Rd, Acton (Canberra) ACT 2601, Australia
| | - Alfredo Castello
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Björn Usadel
- ‖Institute of Biology I, RWTH Aachen, Worringer Weg 2, 52074 Aachen, Germany
| | - Jeroen Krijgsveld
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Thomas Preiss
- ¶EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Garran Rd, Acton (Canberra) ACT 2601, Australia; **Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
| | - Gernot Marx
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Matthias W Hentze
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Dirk H Ostareck
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany;
| | - Antje Ostareck-Lederer
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany;
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29
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Chen L, Liu Z, Zhou B, Wei C, Zhou Y, Rosenfeld MG, Fu XD, Chisholm AD, Jin Y. CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of Syntaxins. eLife 2016; 5. [PMID: 27253061 PMCID: PMC4946901 DOI: 10.7554/elife.16072] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/01/2016] [Indexed: 01/08/2023] Open
Abstract
Axon injury triggers dramatic changes in gene expression. While transcriptional regulation of injury-induced gene expression is widely studied, less is known about the roles of RNA binding proteins (RBPs) in post-transcriptional regulation during axon regeneration. In C. elegans the CELF (CUGBP and Etr-3 Like Factor) family RBP UNC-75 is required for axon regeneration. Using crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq) we identify a set of genes involved in synaptic transmission as mRNA targets of UNC-75. In particular, we show that UNC-75 regulates alternative splicing of two mRNA isoforms of the SNARE Syntaxin/unc-64. In C. elegans mutants lacking unc-75 or its targets, regenerating axons form growth cones, yet are deficient in extension. Extending these findings to mammalian axon regeneration, we show that mouse Celf2 expression is upregulated after peripheral nerve injury and that Celf2 mutant mice are defective in axon regeneration. Further, mRNAs for several Syntaxins show CELF2 dependent regulation. Our data delineate a post-transcriptional regulatory pathway with a conserved role in regenerative axon extension. DOI:http://dx.doi.org/10.7554/eLife.16072.001 Nerve cells or neurons carry information around the body along projections known as axons. An injury or trauma, such as a stroke, can damage the axons and lead to permanent disability because the damaged axons fail to regenerate over long distances. Axon damage triggers large changes in the activity of many genes that promote regeneration. When a gene is active, its DNA is copied to make molecules of messenger RNA (mRNA), which are then used as templates to make proteins. Many mRNAs undergo a process called alternative splicing, in which different combinations of mRNA sections may be removed from the final molecule. This enables a single gene to produce more than one type of protein. Recent studies point to an important role for so-called RNA binding proteins in regulating the alternative splicing process. An RNA binding protein called UNC-75 in a worm known as Caenorhabditis elegans has previously been shown to be involved in axon regeneration, but it was not clear how UNC-75 acts on neurons. Here, Chen et al. combined a technique called CLIP-seq (Cross-linking ImmunoPrecipitation-deep sequencing) with genetic testing to identify the mRNAs that UNC-75 regulates during axon regeneration. The experiments found a set of C. elegans genes required for information to pass between neurons whose mRNAs are also targeted by UNC-75. Many of these genes are also required for axon regeneration. Chen et al. studied one of the mRNA targets – which encodes a protein called syntaxin – in more detail and found that the syntaxin mRNA is required for regenerating axons over long distances. UNC-75 alternatively splices this mRNA to produce a particular form of syntaxin that is mainly found in neurons. Mutant worms that lack either UNC-75 or syntaxin are unable to properly regenerate axons over long distances. Further experiments show that a mouse protein known as CELF2 that is equivalent to worm UNC-75 plays a similar role in regenerating axons. Moreover, mouse CELF2 restores the ability of worm neurons that lack UNC-75 to regenerate. Like worm UNC-75, the mouse protein is also involved in alternative splicing of syntaxin. The next step is to examine the other mRNA targets of UNC-75 to find out what role they play in axon regeneration and other processes in neurons. DOI:http://dx.doi.org/10.7554/eLife.16072.002
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Affiliation(s)
- Lizhen Chen
- Section of Neurobiology, University of California, San Diego, Division of Biological Sciences, San Diego, United States.,Howard Hughes Medical Institute, University of California, San Diego, United States
| | - Zhijie Liu
- Department of Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Chaoliang Wei
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, University of California, San Diego, United States.,Department of Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
| | - Andrew D Chisholm
- Section of Neurobiology, University of California, San Diego, Division of Biological Sciences, San Diego, United States
| | - Yishi Jin
- Section of Neurobiology, University of California, San Diego, Division of Biological Sciences, San Diego, United States.,Howard Hughes Medical Institute, University of California, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, San Diego, United States
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Developmental exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin may alter LH release patterns by abolishing sex differences in GABA/glutamate cell number and modifying the transcriptome of the male anteroventral periventricular nucleus. Neuroscience 2016; 329:239-53. [PMID: 27185484 DOI: 10.1016/j.neuroscience.2016.04.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/08/2016] [Accepted: 04/30/2016] [Indexed: 01/17/2023]
Abstract
Developmental exposure to arylhydrocarbon receptor (AhR) ligands abolishes sex differences in a wide range of neural structures and functions. A well-studied example is the anteroventral periventricular nucleus (AVPV), a structure that controls sex-specific luteinizing hormone (LH) release. In the male, testosterone (T) secreted by the developing testes defeminizes LH release mechanisms; conversely, perinatal AhR activation by 2,3,7,8,-tetrachlorodibenzo-p-dioxin (TCDD) blocks defeminization. To better understand developmental mechanisms altered by TCDD exposure, we first verified that neonatal TCDD exposure in male rats prevented the loss of AVPV GABA/glutamate neurons that are critical for female-typical LH surge release. We then used whole genome arrays and quantitative real-time polymerase chain reaction (QPCR) to compare AVPV transcriptomes of males treated neonatally with TCDD or vehicle. Our bioinformatics analyses showed that TCDD enriched gene sets important for neuron development, synaptic transmission, ion homeostasis, and cholesterol biosynthesis. In addition, upstream regulatory analysis suggests that both estrogen receptors (ER) and androgen receptors (AR) regulate genes targeted by TCDD. Of the 23 mRNAs found to be changed by TCDD at least 2-fold (p<0.05), most participate in the functions identified in our bioinformatics analyses. Several, including matrix metallopeptidase 9 and SRY-box 11 (Sox11), are known targets of E2. CUG triplet repeat, RNA binding protein 2 (cugbp2) is particularly interesting because it is sex-specific, oppositely regulated by estradiol (E2) and TCDD. Moreover, it regulates the post-transcriptional processing of molecules previously linked to sexual differentiation of the brain. These findings provide new insights into how TCDD may interfere with defeminization of LH release patterns.
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Ladd AN. New Insights Into the Role of RNA-Binding Proteins in the Regulation of Heart Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:125-85. [PMID: 27017008 DOI: 10.1016/bs.ircmb.2015.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulation of gene expression during development takes place both at the transcriptional and posttranscriptional levels. RNA-binding proteins (RBPs) regulate pre-mRNA processing, mRNA localization, stability, and translation. Many RBPs are expressed in the heart and have been implicated in heart development, function, or disease. This chapter will review the current knowledge about RBPs in the developing heart, focusing on those that regulate posttranscriptional gene expression. The involvement of RBPs at each stage of heart development will be considered in turn, including the establishment of specific cardiac cell types and formation of the primitive heart tube, cardiac morphogenesis, and postnatal maturation and aging. The contributions of RBPs to cardiac birth defects and heart disease will also be considered in these contexts. Finally, the interplay between RBPs and other regulatory factors in the developing heart, such as transcription factors and miRNAs, will be discussed.
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Affiliation(s)
- A N Ladd
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America.
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Upregulation of cugbp2 increases response of pancreatic cancer cells to chemotherapy. Langenbecks Arch Surg 2015; 401:99-111. [PMID: 26691217 DOI: 10.1007/s00423-015-1364-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/07/2015] [Indexed: 02/06/2023]
Abstract
PURPOSE Altered expression and/or function of ribosomal RNA (rRNA)-binding proteins CUGBP2/CELF2 might influence post-transcriptional regulation of the HO-1- and COX-2-mediated cytoprotective pathways and represents an important therapeutic target. The aim of this study was to assess the effects of CUGBP2-mediated post-transcriptional regulation of COX-2 and HO-1 in pancreatic cancer cells in regard of response to gemcitabine (GEM) treatment. METHODS Expression of CUGBP2, COX-2, and HO-1 was evaluated using qRT-PCR and Western blot methods. Cell viability after treatment with GEM and/or curcumin and siCUGBP2 was evaluated using MTT and crystal violet tests. RNA immunoprecipitation analysis was used to confirm COX-2 and HO-1 post-transcriptional regulation by CUGBP2 protein. RESULTS CUGBP2 expression at the messenger RNA (mRNA) level was 2.2-fold lower (p = 0.007), but HO-1 and COX-2 expression was increased 6.9- (p = 0.023) and 2.3- (p = 0.046) fold in pancreatic cancer tissues. The median survival of patients with low CUGBP2 expression from the lowest tercile was 13.8 months. The median survival of patients in terciles of middle and high CUGBP2 expression levels was 21.9 month (p = 0.123). Induction of CUGBP2 expression by curcumin resulted in the downregulation of HO-1 and COX-2 and strongly sensitized tumor cells to GEM treatment. However, CUGBP2 silencing upregulated HO-1 and COX-2 protein expression and had a high effect on cells viability. CONCLUSION Decreased activity of CUGBP2 could be associated with high chemoresistance and early dissemination of pancreatic cancer through the HO-1- and COX-2-mediated cytoprotective and carcinogenesis pathways. Curcumin significantly increased the effectiveness of GEM treatment in vitro via the CUGBP2-mediated post-transcriptional regulation pathway.
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Abstract
Cytidine (C) to Uridine (U) RNA editing is a post-trancriptional modification that until recently was known to only affect Apolipoprotein b (Apob) RNA and minimally require 2 components of the C to U editosome, the deaminase APOBEC1 and the RNA-binding protein A1CF. Our latest work has identified a novel RNA-binding protein, RBM47, as a core component of the editosome, which can substitute A1CF for the editing of ApoB mRNA. In addition, new RNA species that are subjected to C to U editing have been identified. Here, we highlight these recent discoveries and discuss how they change our view of the composition of the C to U editing machinery and expand our knowledge of the functional attributes of C to U RNA editing.
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Affiliation(s)
- Nicolas Fossat
- a Embryology Unit; Children's Medical Research Institute ; Westmead , Australia
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Lamy S, Ben Saad A, Zgheib A, Annabi B. Olive oil compounds inhibit the paracrine regulation of TNF-α-induced endothelial cell migration through reduced glioblastoma cell cyclooxygenase-2 expression. J Nutr Biochem 2015; 27:136-45. [PMID: 26410343 DOI: 10.1016/j.jnutbio.2015.08.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 08/19/2015] [Accepted: 08/21/2015] [Indexed: 11/25/2022]
Abstract
The established causal relationship between the chronic inflammatory microenvironment, tumor development and cancer recurrence has provided leads for developing novel preventive strategies. Accumulating experimental, clinical and epidemiological data has provided support for the chemopreventive properties of olive oil compounds traditionally found within the Mediterranean diet. In this study, we investigated whether tyrosol (Tyr), hydroxytyrosol, oleuropein and oleic acid (OA), four compounds contained in extra virgin olive oil, can prevent tumor necrosis factor (TNF)-α-induced expression of cyclooxygenase (COX)-2 (an inflammation biomarker) in a human glioblastoma cell (U-87 MG) model. We found that Tyr and OA significantly inhibited TNF-α-induced COX-2 gene and protein expression, as well as PGE2 secretion. Both compounds also inhibited TNF-α-induced JNK and ERK phosphorylation, whereas only Tyr inhibited TNF-α-induced NF-κB phosphorylation. Paracrine-regulated migration of human brain microvascular endothelial cells (HBMECs) was assessed using growth factor-enriched conditioned media (CM) isolated from U-87 MG cells. We found that while PGE2 triggered HBMEC migration, the CM isolated from U-87 MG cells, where either COX-2 or NF-κB had been silenced or had been treated with Tyr or OA, exhibited decreased chemotactic properties. These observations demonstrate that olive oil compounds inhibit the effect of the chronic inflammatory microenvironment on glioblastoma progression through TNF-α actions and may be useful in cancer chemoprevention.
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Affiliation(s)
- Sylvie Lamy
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche BioMed, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, QC, Canada H3C 3P8.
| | - Aroua Ben Saad
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche BioMed, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, QC, Canada H3C 3P8.
| | - Alain Zgheib
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche BioMed, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, QC, Canada H3C 3P8.
| | - Borhane Annabi
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche BioMed, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, QC, Canada H3C 3P8.
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Del Pino Sans J, Krishnan S, Aggison LK, Adams HL, Shrikant MM, López-Giráldez F, Petersen SL. Microarray analysis of neonatal rat anteroventral periventricular transcriptomes identifies the proapoptotic Cugbp2 gene as sex-specific and regulated by estradiol. Neuroscience 2015; 303:312-22. [PMID: 26166732 DOI: 10.1016/j.neuroscience.2015.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/11/2015] [Accepted: 07/01/2015] [Indexed: 01/08/2023]
Abstract
Sexually dimorphic neural structures regulate numerous gender-specific functions including luteinizing hormone (LH) release patterns. The female cyclic surge pattern of release is controlled by the anteroventral periventricular nucleus (AVPV), a preoptic area (POA) region that is significantly smaller in males. The prevailing hypothesis used to explain these differences in structure and function is that a "default" feminine AVPV is defeminized by exposure to estradiol (E2), a metabolite of testosterone (T) produced by the perinatal testes. E2 exposure then culminates in apoptosis in the male AVPV, but the upstream pathways are poorly understood. To address this issue, we compared AVPV transcriptomes of postnatal day 2 (PND2) males and females with those of females treated with E2 or vehicle. Only six of 89 sex-specific genes were also regulated by E2 in the PND2 AVPV and E2 regulated over 280 genes not found to be sex-specific. Of targets that changed similarly in males and E2-treated females, the gene encoding CUG triplet repeat, RNA-binding protein 2 (Cugbp2), a proapoptotic protein, showed the highest fold-changes. Quantitative polymerase chain reaction (QPCR) studies confirmed higher mRNA levels in PND2 male and E2-treated female AVPVs wherein E2 induces apoptosis. POA mapping studies detected Cugbp2 mRNA in the AVPV and in the sexually dimorphic nucleus of the POA (SDN-POA); however, sex differences and E2 effects occurred only in the AVPV. Combined with evidence that Cugbp2 regulates splicing and translation of mRNAs linked to sexual differentiation, we propose that this gene mediates E2-dependent effects on AVPV defeminization.
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Affiliation(s)
- J Del Pino Sans
- Department of Veterinary and Animal Sciences, 661 North Pleasant Street, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - S Krishnan
- Department of Veterinary and Animal Sciences, 661 North Pleasant Street, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - L K Aggison
- Department of Veterinary and Animal Sciences, 661 North Pleasant Street, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - H L Adams
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - M M Shrikant
- Yale Center for Genome Analysis, Yale University, Orange, CT, United States
| | - F López-Giráldez
- Yale Center for Genome Analysis, Yale University, Orange, CT, United States
| | - S L Petersen
- Department of Veterinary and Animal Sciences, 661 North Pleasant Street, University of Massachusetts Amherst, Amherst, MA 01003, United States.
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Duss O, Diarra Dit Konté N, Allain FHT. Cut and paste RNA for nuclear magnetic resonance, paramagnetic resonance enhancement, and electron paramagnetic resonance structural studies. Methods Enzymol 2015; 565:537-62. [PMID: 26577744 DOI: 10.1016/bs.mie.2015.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA is a crucial regulator involved in most molecular processes of life. Understanding its function at the molecular level requires high-resolution structural information. However, the dynamic nature of RNA complicates structure determination because crystallization is often not possible or can result in crystal-packing artifacts resulting in nonnative structures. To study RNA and its complexes in solution, we described an approach in which large multi-domain RNA or protein-RNA complex structures can be determined at high resolution from isolated domains determined by nuclear magnetic resonance (NMR) spectroscopy, and then constructing the entire macromolecular structure using electron paramagnetic resonance (EPR) long-range distance constraints. Every step in this structure determination approach requires different types of isotope or spin-labeled RNAs. Here, we present a simple modular RNA cut and paste approach including protocols to generate (1) small isotopically labeled RNAs (<10 nucleotides) for NMR structural studies, which cannot be obtained by standard protocols, (2) large segmentally isotope and/or spin-labeled RNAs for diamagnetic NMR and paramagnetic relaxation enhancement NMR, and (3) large spin-labeled RNAs for pulse EPR spectroscopy.
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Affiliation(s)
- Olivier Duss
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
| | | | - Frédéric H-T Allain
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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Moraes KCM, Diniz LF, Bahia MT. Role of cyclooxygenase-2 in Trypanosoma cruzi survival in the early stages of parasite host-cell interaction. Mem Inst Oswaldo Cruz 2015; 110:181-91. [PMID: 25946241 PMCID: PMC4489448 DOI: 10.1590/0074-02760140311] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 03/18/2015] [Indexed: 12/22/2022] Open
Abstract
Chagas disease, caused by the intracellular protozoan Trypanosoma cruzi, is a serious health problem in Latin America. During this parasitic infection, the heart is one of the major organs affected. The pathogenesis of tissue remodelling, particularly regarding cardiomyocyte behaviour after parasite infection and the molecular mechanisms that occur immediately following parasite entry into host cells are not yet completely understood. When cells are infected with T. cruzi, they develop an inflammatory response, in which cyclooxygenase-2 (COX-2) catalyses rate-limiting steps in the arachidonic acid pathway. However, how the parasite interaction modulates COX-2 activity is poorly understood. In this study, the H9c2 cell line was used as our model and we investigated cellular and biochemical aspects during the initial 48 h of parasitic infection. Oscillatory activity of COX-2 was observed, which correlated with the control of the pro-inflammatory environment in infected cells. Interestingly, subcellular trafficking was also verified, correlated with the control of Cox-2 mRNA or the activated COX-2 protein in cells, which is directly connected with the assemble of stress granules structures. Our collective findings suggest that in the very early stage of the T. cruzi-host cell interaction, the parasite is able to modulate the cellular metabolism in order to survives.
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Affiliation(s)
- Karen CM Moraes
- Laboratório de Biologia Molecular, Departamento de Biologia, Instituto
de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP,
Brasil
| | - Lívia F Diniz
- Laboratório de Doença de Chagas, Departamento de Ciências Biológicas,
Núcleo de Pesquisa em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro
Preto, MG, Brasil
| | - Maria Terezinha Bahia
- Laboratório de Doença de Chagas, Departamento de Ciências Biológicas,
Núcleo de Pesquisa em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro
Preto, MG, Brasil
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Klein-Cosson C, Chambrier P, Rogowsky PM, Vernoud V. Regulation of a maize HD-ZIP IV transcription factor by a non-conventional RDR2-dependent small RNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:747-758. [PMID: 25619590 DOI: 10.1111/tpj.12771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 12/22/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Small non-coding RNAs are versatile riboregulators that control gene expression at the transcriptional or post-transcriptional level, governing many facets of plant development. Here we present evidence for the existence of a 24 nt small RNA (named small1) that is complementary to the 3' UTR of OCL1 (Outer Cell Layer1), the founding member of the maize HD-ZIP IV gene family encoding plant-specific transcription factors that are mainly involved in epidermis differentiation and specialization. The biogenesis of small1 depends on DICER-like 3 (DCL3), RNA-dependent RNA polymerase 2 (RDR2) and RNA polymerase IV, components that are usually required for RNA-dependent DNA-methylation. Unexpectedly, GFP sensor experiments in transient and stable transformation systems revealed that small1 may regulate its target at the post-transcriptional level, mainly through translational repression. This translational repression is attenuated in an rdr2 mutant background in which small1 does not accumulate. Our experiments further showed the possible involvement of a secondary stem-loop structure present in the 3' UTR of OCL1 for efficient target repression, suggesting the existence of several regulatory mechanisms affecting OCL1 mRNA stability and translation.
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Affiliation(s)
- Catherine Klein-Cosson
- Unité Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, F-69364, Lyon, France; Institut National de la Recherche Agronomique, UMR879 Reproduction et Développement des Plantes, F-69364, Lyon, France; Centre National de la Recherche Scientifique, UMR5667 Reproduction et Développement des Plantes, F-69364, Lyon, France
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Dávila D, Jiménez-Mateos EM, Mooney CM, Velasco G, Henshall DC, Prehn JHM. Hsp27 binding to the 3'UTR of bim mRNA prevents neuronal death during oxidative stress-induced injury: a novel cytoprotective mechanism. Mol Biol Cell 2014; 25:3413-23. [PMID: 25187648 PMCID: PMC4214787 DOI: 10.1091/mbc.e13-08-0495] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neurons face a changeable microenvironment and therefore need mechanisms that allow rapid switch on/off of their cytoprotective and apoptosis-inducing signaling pathways. Cellular mechanisms that control apoptosis activation include the regulation of pro/antiapoptotic mRNAs through their 3'-untranslated region (UTR). This region holds binding elements for RNA-binding proteins, which can control mRNA translation. Here we demonstrate that heat shock protein 27 (Hsp27) prevents oxidative stress-induced cell death in cerebellar granule neurons by specific regulation of the mRNA for the proapoptotic BH3-only protein, Bim. Hsp27 depletion induced by oxidative stress using hydrogen peroxide (H2O2) correlated with bim gene activation and subsequent neuronal death, whereas enhanced Hsp27 expression prevented these. This effect could not be explained by proteasomal degradation of Bim or bim promoter inhibition; however, it was associated with a specific increase in the levels of bim mRNA and with its binding to Hsp27. Finally, we determined that enhanced Hsp27 expression in neurons exposed to H2O2 or glutamate prevented the translation of a reporter plasmid where bim-3'UTR mRNA sequence was cloned downstream of a luciferase gene. These results suggest that repression of bim mRNA translation through binding to the 3'UTR constitutes a novel cytoprotective mechanism of Hsp27 during stress in neurons.
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Affiliation(s)
- David Dávila
- Department of Physiology and Medical Physics and RCSI Centre for the Study of Neurological Disorders, Royal College of Surgeons in Ireland, Dublin 2, Ireland Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, 28040 Madrid, Spain
| | - Eva M Jiménez-Mateos
- Department of Physiology and Medical Physics and RCSI Centre for the Study of Neurological Disorders, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Claire M Mooney
- Department of Physiology and Medical Physics and RCSI Centre for the Study of Neurological Disorders, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Guillermo Velasco
- Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, 28040 Madrid, Spain
| | - David C Henshall
- Department of Physiology and Medical Physics and RCSI Centre for the Study of Neurological Disorders, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics and RCSI Centre for the Study of Neurological Disorders, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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Cornett AL, Lutz CS. Regulation of COX-2 expression by miR-146a in lung cancer cells. RNA (NEW YORK, N.Y.) 2014; 20:1419-30. [PMID: 25047043 PMCID: PMC4138325 DOI: 10.1261/rna.044149.113] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 05/24/2014] [Indexed: 06/03/2023]
Abstract
Prostaglandins are a class of molecules that mediate cellular inflammatory responses and control cell growth. The oxidative conversion of arachidonic acid to prostaglandin H2 is carried out by two isozymes of cyclooxygenase, COX-1 and COX-2. COX-1 is constitutively expressed, while COX-2 can be transiently induced by external stimuli, such as pro-inflammatory cytokines. Interestingly, COX-2 is overexpressed in numerous cancers, including lung cancer. MicroRNAs (miRNAs) are small RNA molecules that function to regulate gene expression. Previous studies have implicated an important role for miRNAs in human cancer. We demonstrate here that miR-146a expression levels are significantly lower in lung cancer cells as compared with normal lung cells. Conversely, lung cancer cells have higher levels of COX-2 protein and mRNA expression. Introduction of miR-146a can specifically ablate COX-2 protein and the biological activity of COX-2 as measured by prostaglandin production. The regulation of COX-2 by miR-146a is mediated through a single miRNA-binding site present in the 3' UTR. Therefore, we propose that decreased miR-146a expression contributes to the up-regulation and overexpression of COX-2 in lung cancer cells. Since potential miRNA-mediated regulation is a functional consequence of alternative polyadenylation site choice, understanding the molecular mechanisms that regulate COX-2 mRNA alternative polyadenylation and miRNA targeting will give us key insights into how COX-2 expression is involved in the development of a metastatic condition.
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Affiliation(s)
- Ashley L Cornett
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, New Jersey Medical School and the Graduate School of Biomedical Sciences, Newark, New Jersey 07103, USA
| | - Carol S Lutz
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, New Jersey Medical School and the Graduate School of Biomedical Sciences, Newark, New Jersey 07103, USA
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Tan SM, Altschuler G, Zhao TY, Ang HS, Yang H, Lim B, Vardy L, Hide W, Thomson AM, Lareu RR. Divergent LIN28-mRNA associations result in translational suppression upon the initiation of differentiation. Nucleic Acids Res 2014; 42:7997-8007. [PMID: 24860167 PMCID: PMC4081066 DOI: 10.1093/nar/gku430] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
LIN28 function is fundamental to the activity and behavior of human embryonic stem cells (hESCs) and induced pluripotent stem cells. Its main roles in these cell types are the regulation of translational efficiency and let-7 miRNA maturation. However, LIN28-associated mRNA cargo shifting and resultant regulation of translational efficiency upon the initiation of differentiation remain unknown. An RNA-immunoprecipitation and microarray analysis protocol, eRIP, that has high specificity and sensitivity was developed to test endogenous LIN28-associated mRNA cargo shifting. A combined eRIP and polysome analysis of early stage differentiation of hESCs with two distinct differentiation cues revealed close similarities between the dynamics of LIN28 association and translational modulation of genes involved in the Wnt signaling, cell cycle, RNA metabolism and proteasomal pathways. Our data demonstrate that change in translational efficiency is a major contributor to early stages of differentiation of hESCs, in which LIN28 plays a central role. This implies that eRIP analysis of LIN28-associated RNA cargoes may be used for rapid functional quality control of pluripotent stem cells under manufacture for therapeutic applications.
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Affiliation(s)
- Shen Mynn Tan
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), 138672, Singapore
| | - Gabriel Altschuler
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Tian Yun Zhao
- Institute of Medical Biology, A*STAR, 138648, Singapore
| | - Haw Siang Ang
- Cancer Science Institute, National University of Singapore (NUS), 117599, Singapore
| | - Henry Yang
- Cancer Science Institute, National University of Singapore (NUS), 117599, Singapore
| | - Bing Lim
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), 138672, Singapore
| | - Leah Vardy
- Institute of Medical Biology, A*STAR, 138648, Singapore
| | - Winston Hide
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Andrew M Thomson
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), 138672, Singapore
| | - Ricky R Lareu
- Department of Orthopedic Surgery, NUS Tissue Engineering Program, Yong Loo Lin School of Medicine, NUS, 119228, Singapore and School of Pharmacy, CHIRI Biosciences, Curtin University, Western Australia 6102, Australia
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Lutz CS, Cornett AL. Regulation of genes in the arachidonic acid metabolic pathway by RNA processing and RNA-mediated mechanisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:593-605. [PMID: 23956046 DOI: 10.1002/wrna.1183] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 01/22/2023]
Abstract
Arachidonic acid (AA) is converted by enzymes in an important metabolic pathway to produce molecules known collectively as eicosanoids, 20 carbon molecules with significant physiological and pathological functions in the human body. Cyclooxygenase (COX) enzymes work in one arm of the pathway to produce prostaglandins (PGs) and thromboxanes (TXs), while the actions of 5-lipoxygenase (ALOX5 or 5LO) and its associated protein (ALOX5AP or FLAP) work in the other arm of the metabolic pathway to produce leukotrienes (LTs). The expression of the COX and ALOX5 enzymes that convert AA to eicosanoids is highly regulated at the post- or co-transcriptional level by alternative mRNA splicing, alternative mRNA polyadenylation, mRNA stability, and microRNA (miRNA) regulation. This review article will highlight these mechanisms of mRNA modulation.
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Affiliation(s)
- Carol S Lutz
- Department of Biochemistry and Molecular Biology, New Jersey Medical School and the Graduate School of Biomedical Sciences, Rutgers, NJ, USA.
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Basu A, Poddar D, Robinet P, Smith JD, Febbraio M, Baldwin WM, Mazumder B. Ribosomal protein L13a deficiency in macrophages promotes atherosclerosis by limiting translation control-dependent retardation of inflammation. Arterioscler Thromb Vasc Biol 2014; 34:533-42. [PMID: 24436370 DOI: 10.1161/atvbaha.113.302573] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Unresolved inflammatory response of macrophages plays a pivotal role in the pathogenesis of atherosclerosis. Previously we showed that ribosomal protein L13a-dependent translational silencing suppresses the synthesis of a cohort of inflammatory proteins in monocytes and macrophages. We also found that genetic abrogation of L13a expression in macrophages significantly compromised the resolution of inflammation in a mouse model of lipopolysaccharide-induced endotoxemia. However, its function in the pathogenesis of atherosclerosis is not known. Here, we examine whether L13a in macrophage has a protective role against high-fat diet-induced atherosclerosis. APPROACH AND RESULTS We bred the macrophage-specific L13a knockout mice L13a Flox(+/+) Cre(+/+) onto apolipoprotein E-deficient background and generated the experimental double knockout mice L13a Flox(+/+) Cre(+/+) apolipoprotein E deficient (apoE(-/-)). L13a Flox(+/+) Cre(-/-) mice on apolipoprotein E-deficient background were used as controls. Control and knockout mice were subjected to high-fat diet for 10 weeks. Evaluation of aortic sinus sections and entire aorta by en face showed significantly higher atherosclerosis in the knockout mice. Severity of atherosclerosis in knockout mice was accompanied by thinning of the smooth muscle cell layer in the media, larger macrophage area in the intimal plaque region and higher plasma levels of inflammatory cytokines. In addition, macrophages isolated from knockout mice had higher polyribosomal abundance of several target mRNAs, thus showing defect in translation control. CONCLUSIONS Our data demonstrate that loss of L13a in macrophages increases susceptibility to atherosclerosis in apolipoprotein E-deficient mice, revealing an important role of L13a-dependent translational control as an endogenous protection mechanism against atherosclerosis.
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Affiliation(s)
- Abhijit Basu
- From the Department of Biology, Geology, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH (A.B., D.P., B.M.); Department of Cellular and Molecular Medicine (P.R., J.D.S.), Department of Immunology (W.M.B.), and Department of Molecular Cardiology (M.F), Cleveland Clinic Lerner College of Medicine, Cleveland, OH
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Zago M, Sheridan JA, Nair P, Rico de Souza A, Gallouzi IE, Rousseau S, Di Marco S, Hamid Q, Eidelman DH, Baglole CJ. Aryl hydrocarbon receptor-dependent retention of nuclear HuR suppresses cigarette smoke-induced cyclooxygenase-2 expression independent of DNA-binding. PLoS One 2013; 8:e74953. [PMID: 24086407 PMCID: PMC3785509 DOI: 10.1371/journal.pone.0074953] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/07/2013] [Indexed: 12/02/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor that responds to man-made environmental toxicants, has emerged as an endogenous regulator of cyclooxygenase-2 (Cox-2) by a mechanism that is poorly understood. In this study, we first used AhR-deficient (AhR−/−) primary pulmonary cells, together with pharmacological tools to inhibit new RNA synthesis, to show that the AhR is a prominent factor in the destabilization of Cox-2 mRNA. The destabilization of Cox-2 mRNA and subsequent suppression of cigarette smoke-induced COX-2 protein expression by the AhR was independent of its ability to bind the dioxin response element (DRE), thereby differentiating the DRE-driven toxicological AhR pathway from its anti-inflammatory abilities. We further describe that the AhR destabilizes Cox-2 mRNA by sequestering HuR within the nucleus. The role of HuR in AhR stabilization of Cox-2 mRNA was confirmed by knockdown of HuR, which resulted in rapid Cox-2 mRNA degradation. Finally, in the lungs of AhR−/− mice exposed to cigarette smoke, there was little Cox-2 mRNA despite robust COX-2 protein expression, a finding that correlates with almost exclusive cytoplasmic HuR within the lungs of AhR−/− mice. Therefore, we propose that the AhR plays an important role in suppressing the expression of inflammatory proteins, a function that extends beyond the ability of the AhR to respond to man-made toxicants. These findings open the possibility that a DRE-independent AhR pathway may be exploited therapeutically as an anti-inflammatory target.
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MESH Headings
- Animals
- Azo Compounds/pharmacology
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- Cells, Cultured
- Cyclooxygenase 2/genetics
- Cyclooxygenase 2/metabolism
- DNA/metabolism
- ELAV Proteins/metabolism
- Fibroblasts/drug effects
- Fibroblasts/enzymology
- Fibroblasts/pathology
- Humans
- Lung/pathology
- Mice
- Models, Biological
- Prostaglandins/biosynthesis
- Protein Binding/drug effects
- Protein Structure, Tertiary
- Protein Transport/drug effects
- Pyrazoles/pharmacology
- RNA Stability/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Receptors, Aryl Hydrocarbon/antagonists & inhibitors
- Receptors, Aryl Hydrocarbon/chemistry
- Receptors, Aryl Hydrocarbon/deficiency
- Receptors, Aryl Hydrocarbon/metabolism
- Smoking/adverse effects
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Affiliation(s)
- Michela Zago
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | | | - Parameswaran Nair
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Angela Rico de Souza
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Imed-Eddine Gallouzi
- Department of Biochemistry and the Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Simon Rousseau
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Sergio Di Marco
- Department of Biochemistry and the Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Qutayba Hamid
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - David H. Eidelman
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Carolyn J. Baglole
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- * E-mail:
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45
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Abstract
Post-transcriptional mechanisms that modulate global and/or transcript-specific mRNA stability and translation contribute to the rapid and flexible control of gene expression in immune effector cells. These mechanisms rely on RNA-binding proteins (RBPs) that direct regulatory complexes (e.g. exosomes, deadenylases, decapping complexes, RNA-induced silencing complexes) to the 3'-untranslated regions of specific immune transcripts. Here, we review the surprising variety of post-transcriptional control mechanisms that contribute to gene expression in the immune system and discuss how defects in these pathways can contribute to autoimmune disease.
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Affiliation(s)
- Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA.
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46
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Ochs MJ, Steinhilber D, Suess B. MicroRNAs - Novel Therapeutic Targets of Eicosanoid Signalling. Basic Clin Pharmacol Toxicol 2013; 114:92-6. [DOI: 10.1111/bcpt.12116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/23/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Meike J. Ochs
- Department of Biology; Technical University Darmstadt; Darmstadt Germany
- Institute of Pharmaceutical Chemistry/ZAFES; Goethe University Frankfurt; Frankfurt/M. Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry/ZAFES; Goethe University Frankfurt; Frankfurt/M. Germany
| | - Beatrix Suess
- Department of Biology; Technical University Darmstadt; Darmstadt Germany
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47
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Potential targets for colorectal cancer prevention. Int J Mol Sci 2013; 14:17279-303. [PMID: 23975167 PMCID: PMC3794728 DOI: 10.3390/ijms140917279] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/09/2013] [Accepted: 08/14/2013] [Indexed: 12/18/2022] Open
Abstract
The step-wise development of colorectal neoplasia from adenoma to carcinoma suggests that specific interventions could delay or prevent the development of invasive cancer. Several key factors involved in colorectal cancer pathogenesis have already been identified including cyclooxygenase 2 (COX-2), nuclear factor kappa B (NF-κB), survivin and insulin-like growth factor-I (IGF-I). Clinical trials of COX-2 inhibitors have provided the “proof of principle” that inhibition of this enzyme can prevent the formation of colonic adenomas and potentially carcinomas, however concerns regarding the potential toxicity of these drugs have limited their use as a chemopreventative strategy. Curcumin, resveratrol and quercetin are chemopreventive agents that are able to suppress multiple signaling pathways involved in carcinogenesis and hence are attractive candidates for further research.
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Bronicki LM, Jasmin BJ. Emerging complexity of the HuD/ELAVl4 gene; implications for neuronal development, function, and dysfunction. RNA (NEW YORK, N.Y.) 2013; 19:1019-1037. [PMID: 23861535 PMCID: PMC3708524 DOI: 10.1261/rna.039164.113] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Precise control of messenger RNA (mRNA) processing and abundance are increasingly being recognized as critical for proper spatiotemporal gene expression, particularly in neurons. These regulatory events are governed by a large number of trans-acting factors found in neurons, most notably RNA-binding proteins (RBPs) and micro-RNAs (miRs), which bind to specific cis-acting elements or structures within mRNAs. Through this binding mechanism, trans-acting factors, particularly RBPs, control all aspects of mRNA metabolism, ranging from altering the transcription rate to mediating mRNA degradation. In this context the best-characterized neuronal RBP, the Hu/ELAVl family member HuD, is emerging as a key component in multiple regulatory processes--including pre-mRNA processing, mRNA stability, and translation--governing the fate of a substantial amount of neuronal mRNAs. Through its ability to regulate mRNA metabolism of diverse groups of functionally similar genes, HuD plays important roles in neuronal development and function. Furthermore, compelling evidence indicates supplementary roles for HuD in neuronal plasticity, in particular, recovery from axonal injury, learning and memory, and multiple neurological diseases. The purpose of this review is to provide a detailed overview of the current knowledge surrounding the expression and roles of HuD in the nervous system. Additionally, we outline the present understanding of the molecular mechanisms presiding over the localization, abundance, and function of HuD in neurons.
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Edwards JM, Long J, de Moor CH, Emsley J, Searle MS. Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1. Nucleic Acids Res 2013; 41:7153-66. [PMID: 23748565 PMCID: PMC3737555 DOI: 10.1093/nar/gkt470] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The CUG-BP, Elav-like family (CELF) of RNA-binding proteins control gene expression at a number of different levels by regulating pre-mRNA splicing, deadenylation and mRNA stability. We present structural insights into the binding selectivity of CELF member 1 (CELF1) for GU-rich mRNA target sequences of the general form 5'-UGUNxUGUNyUGU and identify a high affinity interaction (Kd ∼ 100 nM for x = 2 and y = 4) with simultaneous binding of all three RNA recognition motifs within a single 15-nt binding element. RNA substrates spin-labelled at either the 3' or 5' terminus result in differential nuclear magnetic resonance paramagnetic relaxation enhancement effects, which are consistent with a non-sequential 2-1-3 arrangement of the three RNA recognition motifs on UGU sites in a 5' to 3' orientation along the RNA target. We further demonstrate that CELF1 binds to dispersed single-stranded UGU sites at the base of an RNA hairpin providing a structural rationale for recognition of CUG expansion repeats and splice site junctions in the regulation of alternative splicing.
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Affiliation(s)
- John M Edwards
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
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50
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Moraes KCM, Monteiro CJ, Pacheco-Soares C. A novel function for CUGBP2 in controlling the pro-inflammatory stimulus in H9c2 cells: subcellular trafficking of messenger molecules. Cell Biol Int 2013; 37:1129-38. [PMID: 23661609 DOI: 10.1002/cbin.10127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/02/2013] [Indexed: 01/13/2023]
Abstract
Accumulating evidence demonstrates that chronic inflammation plays an important role in heart hypertrophy and cardiac diseases. However, the fine-tuning of cellular and molecular mechanisms that connect inflammatory process and cardiac diseases is still under investigation. Many reports have demonstrated that the overexpression of the cyclooxygenase-2 (COX-2), a key enzyme in the conversion of arachidonic acid to prostaglandins and other prostanoids, is correlated with inflammatory processes. Increased level of prostaglandin E2 was also found in animal model of left ventricle of hypertrophy. Based on previous observations that demonstrated a regulatory loop between COX-2 and the RNA-binding protein CUGBP2, we studied cellular and molecular mechanisms of a pro-inflammatory stimulus in a cardiac cell to verify if the above two molecules could be correlated with the inflammatory process in the heart. A cellular model of investigation was established and H9c2 was used. We also demonstrated a regulatory connection between COX-2 and CUGBP2 in the cardiac cells. Based on a set of different assays including gene silencing and fluorescence microscopy, we describe a novel function for the RNA-binding protein CUGBP2 in controlling the pro-inflammatory stimulus: subcellular trafficking of messenger molecules to specific cytoplasmic stress granules to maintain homeostasis.
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Affiliation(s)
- Karen C M Moraes
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil.
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