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Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Mol Cell 2024; 84:1271-1289.e12. [PMID: 38387462 PMCID: PMC10997485 DOI: 10.1016/j.molcel.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ward G Walkup
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant Bonesteele
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carl R Urbinati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Parham Peyda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Enrique Amaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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2
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Zhu W, Zhu W, Wang S, Liu S, Zhang H. UCHL1 deficiency upon HCMV infection induces vascular endothelial inflammatory injury mediated by mitochondrial iron overload. Free Radic Biol Med 2024; 211:96-113. [PMID: 38081437 DOI: 10.1016/j.freeradbiomed.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023]
Abstract
Human cytomeglovirus (HCMV) infection predisposes blood vessels to atherosclerosis (AS) and post-transplantation restenosis, but the underlying molecular basis remains elusive. Here, we found that HCMV infection activates AIM2 inflammasome and pyroptosis in vascular endothelial cells by inducing mitochondrial iron overload. Mechanistically, under normal conditions, ubiquitin carboxyl terminal hydrolase-L1 (UCHL1) was identified as a DUB enzyme that interacts with, deubiquitylates, and stabilizes ferredoxin reductase (FDXR), an important mitochondrial protein that regulates mitochondral iron homeostasis. However, HCMV infection induces the aberrantly elevated m6A modification and R-loops, the three-stranded DNA-DNA:RNA hybrid structures. The expression of UCHL1 was remarkably reduced by m6A modification-mediated mRNA decay and R-loop-dependent transcriptional termination after HCMV infection. Deficiency of UCHL1 causes ubiquitination and degradation of FDXR. Loss of FDXR induces the mitochondrial iron overload, which consequently leads to AIM2 inflammasome activation and endothelial injury. Moreover, both downregulation expression of UCHL1 and related inflammatory injury in vascular endothelium was observed in MCMV-infected mice. Notably, STM2457, a METTL3 specific inhibitor, restores the expression of UCHL1 upon HCMV infection, thereby inhibiting the inflammatory injury of vascular endothelial cells. Our findings delineate a novel mechnism involved in HCMV-induced inflammatory injury to vascular endothelium and implicate the role of METTL3 inhibitor as a potential therapeutic approach.
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Affiliation(s)
- Wenbo Zhu
- The First Affiliated Hospital, Clinical Medical Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Wentong Zhu
- Unchained Labs (Shanghai) Trading Co., Ltd, Shanghai 201203, China
| | - Shao Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Science, Fuzhou 350013, China
| | - Shuangquan Liu
- The First Affiliated Hospital, Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Hongbo Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, United States.
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3
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Gan H, Zhou X, Lei Q, Wu L, Niu J, Zheng Q. RNA-dependent RNA polymerase of SARS-CoV-2 regulate host mRNA translation efficiency by hijacking eEF1A factors. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166871. [PMID: 37673357 DOI: 10.1016/j.bbadis.2023.166871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023]
Abstract
The RNA-dependent RNA polymerase (NSP12) of COVID-19 plays a significant role in the viral infection process, which promotes viral RNA replication by cooperating with NSP7 and NSP8, but little is known about its regulation on the function of host cells. We firstly found that overexpression of NSP12 had little effect on host mRNAs transcription. Using iCLIP technology, we found that NSP12 can bind a series of host RNAs with the conserved binding motif G(C/A/G)(U/G/A)UAG, especially ribosomal RNA. We found that NSP12 could directly bind to eEF1A factor via the NIRAN domain of NSP12 and N-terminal domain of eEF1A. NSP12 colocalized with eEF1A to inhibit type I interferon expression upon virus infection. In order to prove that NSP12 regulates the translation level of host cells, we found that NSP12 significantly affected the translation efficiency of many host mRNAs (such as ISG15, NF-κB2, ILK and SERPINI2) via ribosome profiling experiment, and the genes with significant upregulation in translation efficiency were mainly enriched in positive regulation of ubiquitin-dependent proteasomal process and NIK/NF-κB signaling pathway (such as NF-κB2, ILK), and negative regulation of type I interferon production, protein level of these genes were further confirmed in HEK293T and Calu3 cells upon NSP12 overexpression. These results indicate that NSP12 of SARS-CoV-2 can hijack the eEF1A factor to regulate translation efficiency of host mRNAs, which provides a new idea for us to evaluate the impact of SARS-CoV2 virus on the host and study the potential drug targets.
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Affiliation(s)
- Haili Gan
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China
| | - Xiaoguang Zhou
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025# Shennan Road, Shenzhen 518000, China
| | - Qiong Lei
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025# Shennan Road, Shenzhen 518000, China
| | - Linlin Wu
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025# Shennan Road, Shenzhen 518000, China
| | - Jianmin Niu
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025# Shennan Road, Shenzhen 518000, China
| | - Qingliang Zheng
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025# Shennan Road, Shenzhen 518000, China.
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4
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Li D, Huang C, Liu Z, Ai S, Wang HL. Decreased expression of Chrna4 by METTL3-mediated m6A modification participates in BPA-induced spatial memory deficit. ENVIRONMENTAL RESEARCH 2023; 236:116717. [PMID: 37495067 DOI: 10.1016/j.envres.2023.116717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
Bisphenol A (BPA), a widely used endocrine disruptor, has been implicated in cognitive impairment via epigenetic machinery. N6-methyl adenosine (m6A) has recently emerged as a new epigenetic factor that influences cognition, but the role of m6A in BPA induced cognitive deficits has not been explored yet. In this study, we found increased global m6A abundance accompanied with elevated expression of methyltransferase-like 3 (METTL3) in hippocampal neurons following BPA exposure. Inhibition of METTL3 activity by selective METTL3 inhibitor 2457 (STM) in cultured neurons abolished BPA induced m6A upregulation and abnormal synaptic transmission. Additionally, knockdown of METTL3 in hippocampus abrogated BPA induced learning and memory deficit in rats. Further study showed that m6A modification was enriched in mRNA of cholinergic receptor nicotinic alpha 4 subunit (Chrna4). Inhibition of METTL3 either by STM or shRNA restored BPA induced downregulation of Chrna4, suggesting that Chrna4 may be a potential target involved in BPA induced neurotoxicity that modified by m6A. Collectively, our findings demonstrated that METTL3 mediated m6A modification was involved in BPA induced cognitive deficit with Chrna4 as a potential target, which enriched our understanding of the role of epigenetics (RNA modifications) in BPA induced neurotoxicity and provided new insights into BPA or its substitutes induced damages in other organs.
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Affiliation(s)
- Danyang Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Chengqing Huang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Zhihua Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Shu Ai
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Hui-Li Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
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Feng Y, Zhu S, Liu T, Zhi G, Shao B, Liu J, Li B, Jiang C, Feng Q, Wu P, Wang D. Surmounting Cancer Drug Resistance: New Perspective on RNA-Binding Proteins. Pharmaceuticals (Basel) 2023; 16:1114. [PMID: 37631029 PMCID: PMC10458901 DOI: 10.3390/ph16081114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
RNA-binding proteins (RBPs), being pivotal elements in both physiological and pathological processes, possess the ability to directly impact RNA, thereby exerting a profound influence on cellular life. Furthermore, the dysregulation of RBPs not only induces alterations in the expression levels of genes associated with cancer but also impairs the occurrence of post-transcriptional regulatory mechanisms. Consequently, these circumstances can give rise to aberrations in cellular processes, ultimately resulting in alterations within the proteome. An aberrant proteome can disrupt the equilibrium between oncogenes and tumor suppressor genes, promoting cancer progression. Given their significant role in modulating gene expression and post-transcriptional regulation, directing therapeutic interventions towards RBPs represents a viable strategy for combating drug resistance in cancer treatment. RBPs possess significant potential as diagnostic and prognostic markers for diverse cancer types. Gaining comprehensive insights into the structure and functionality of RBPs, along with delving deeper into the molecular mechanisms underlying RBPs in tumor drug resistance, can enhance cancer treatment strategies and augment the prognostic outcomes for individuals afflicted with cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peijie Wu
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
| | - Dong Wang
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
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6
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Puri D, Sharma S, Samaddar S, Ravivarma S, Banerjee S, Ghosh-Roy A. Muscleblind-1 interacts with tubulin mRNAs to regulate the microtubule cytoskeleton in C. elegans mechanosensory neurons. PLoS Genet 2023; 19:e1010885. [PMID: 37603562 PMCID: PMC10470942 DOI: 10.1371/journal.pgen.1010885] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 08/31/2023] [Accepted: 07/26/2023] [Indexed: 08/23/2023] Open
Abstract
Regulation of the microtubule cytoskeleton is crucial for the development and maintenance of neuronal architecture, and recent studies have highlighted the significance of regulated RNA processing in the establishment and maintenance of neural circuits. In a genetic screen conducted using mechanosensory neurons of C. elegans, we identified a mutation in muscleblind-1/mbl-1 as a suppressor of loss of kinesin-13 family microtubule destabilizing factor klp-7. Muscleblind-1(MBL-1) is an RNA-binding protein that regulates the splicing, localization, and stability of RNA. Our findings demonstrate that mbl-1 is required cell-autonomously for axon growth and proper synapse positioning in the posterior lateral microtubule (PLM) neuron. Loss of mbl-1 leads to increased microtubule dynamics and mixed orientation of microtubules in the anterior neurite of PLM. These defects are also accompanied by abnormal axonal transport of the synaptic protein RAB-3 and reduction of gentle touch sensation in mbl-1 mutant. Our data also revealed that mbl-1 is genetically epistatic to mec-7 (β tubulin) and mec-12 (α tubulin) in regulating axon growth. Furthermore, mbl-1 is epistatic to sad-1, an ortholog of BRSK/Brain specific-serine/threonine kinase and a known regulator of synaptic machinery, for synapse formation at the correct location of the PLM neurite. Notably, the immunoprecipitation of MBL-1 resulted in the co-purification of mec-7, mec-12, and sad-1 mRNAs, suggesting a direct interaction between MBL-1 and these transcripts. Additionally, mbl-1 mutants exhibited reduced levels and stability of mec-7 and mec-12 transcripts. Our study establishes a previously unknown link between RNA-binding proteins and cytoskeletal machinery, highlighting their crucial roles in the development and maintenance of the nervous system.
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Affiliation(s)
- Dharmendra Puri
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sunanda Sharma
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sarbani Samaddar
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sruthy Ravivarma
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sourav Banerjee
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
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7
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Gong H, Gong T, Liu Y, Wang Y, Wang X. Profiling of N6-methyladenosine methylation in porcine longissimus dorsi muscle and unravelling the hub gene ADIPOQ promotes adipogenesis in an m 6A-YTHDF1-dependent manner. J Anim Sci Biotechnol 2023; 14:50. [PMID: 37024992 PMCID: PMC10077699 DOI: 10.1186/s40104-023-00833-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/04/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Intramuscular fat (IMF) content is a critical indicator of pork quality, and abnormal IMF is also relevant to human disease as well as aging. Although N6-methyladenosine (m6A) RNA modification was recently found to regulate adipogenesis in porcine intramuscular fat, however, the underlying molecular mechanisms was still unclear. RESULTS In this work, we collected 20 longissimus dorsi muscle samples with high (average 3.95%) or low IMF content (average 1.22%) from a unique heterogenous swine population for m6A sequencing (m6A-seq). We discovered 70 genes show both differential RNA expression and m6A modification from high and low IMF group, including ADIPOQ and SFRP1, two hub genes inferred through gene co-expression analysis. Particularly, we observed ADIPOQ, which contains three m6A modification sites within 3' untranslated and protein coding region, could promote porcine intramuscular preadipocyte differentiation in an m6A-dependent manner. Furthermore, we found the YT521‑B homology domain family protein 1 (YTHDF1) could target and promote ADIPOQ mRNA translation. CONCLUSIONS Our study provided a comprehensive profiling of m6A methylation in porcine longissimus dorsi muscle and characterized the involvement of m6A epigenetic modification in the regulation of ADIPOQ mRNA on IMF deposition through an m6A-YTHDF1-dependent manner.
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Affiliation(s)
- Huanfa Gong
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Tao Gong
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Youhua Liu
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yizhen Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xinxia Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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8
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Tao X, Li S, Chen G, Wang J, Xu S. Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination. Int J Mol Sci 2023; 24:ijms24065562. [PMID: 36982636 PMCID: PMC10054671 DOI: 10.3390/ijms24065562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are not translated into known functional proteins. This broad definition covers a large collection of transcripts with diverse genomic origins, biogenesis, and modes of action. Thus, it is very important to choose appropriate research methodologies when investigating lncRNAs with biological significance. Multiple reviews to date have summarized the mechanisms of lncRNA biogenesis, their localization, their functions in gene regulation at multiple levels, and also their potential applications. However, little has been reviewed on the leading strategies for lncRNA research. Here, we generalize a basic and systemic mind map for lncRNA research and discuss the mechanisms and the application scenarios of ‘up-to-date’ techniques as applied to molecular function studies of lncRNAs. Taking advantage of documented lncRNA research paradigms as examples, we aim to provide an overview of the developing techniques for elucidating lncRNA interactions with genomic DNA, proteins, and other RNAs. In the end, we propose the future direction and potential technological challenges of lncRNA studies, focusing on techniques and applications.
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Affiliation(s)
- Xiaoyuan Tao
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sujuan Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wang
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shengchun Xu
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence:
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9
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Wu J, Xu J, Naguib M, Bie B. Blockade of Type 2A Protein Phosphatase Signaling Attenuates Complement C1q-Mediated Microglial Phagocytosis of Glutamatergic Synapses Induced by Amyloid Fibrils. Mol Neurobiol 2023; 60:1527-1536. [PMID: 36515857 PMCID: PMC9910161 DOI: 10.1007/s12035-022-03161-2] [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: 01/19/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022]
Abstract
We previously reported the critical involvement of metabotropic GluR1 (mGluR1) signaling in complement C1q-dependent microglial phagocytosis of glutamatergic synapses in a rat model of Alzheimer's disease (AD) injected with amyloid fibrils. Here, we explored the role of type 2A protein phosphatase (type 2A PPase), a key enzyme downstream of mGluR1 signaling, in the pathogenesis of AD in rats. Significant local upregulation of PP2A expression was observed in the hippocampal CA1 after bilateral microinjection of amyloid-beta (Aβ1-40) fibrils. Amyloid fibrils induced remarkable dephosphorylation of pFMRP (fragile X mental retardation protein) and C1q upregulation in hippocampal glutamatergic synapses, which was ameliorated by microinjection of type 2A PPase inhibitor okadaic acid (OA). Microinjection of OA further attenuated the microglial phagocytosis of glutamatergic synapses, recovered the hippocampal glutamatergic transmission, and improved the performance in Morris water maze test. These findings demonstrated that dysfunction of type 2A PPase signaling contributed to complement C1q-dependent microglial phagocytosis of glutamatergic synapses and the cognitive impairments in the rat model of AD.
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Affiliation(s)
- Jiang Wu
- Anesthesiology Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Jijun Xu
- Department of Pain Management, Anesthesiology Institute, 9500 Euclid Ave, Cleveland, OH, 44195, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Mohamed Naguib
- Anesthesiology Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Bihua Bie
- Anesthesiology Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA.
- Department of Biomedical Engineering, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA.
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Kirstein N, Dokaneheifard S, Cingaram PR, Valencia MG, Beckedorff F, Gomes Dos Santos H, Blumenthal E, Tayari MM, Gaidosh GS, Shiekhattar R. The Integrator complex regulates microRNA abundance through RISC loading. SCIENCE ADVANCES 2023; 9:eadf0597. [PMID: 36763664 PMCID: PMC9916992 DOI: 10.1126/sciadv.adf0597] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
MicroRNA (miRNA) homeostasis is crucial for the posttranscriptional regulation of their target genes during development and in disease states. miRNAs are derived from primary transcripts and are processed from a hairpin precursor intermediary to a mature 22-nucleotide duplex RNA. Loading of the duplex into the Argonaute (AGO) protein family is pivotal to miRNA abundance and its posttranscriptional function. The Integrator complex plays a key role in protein coding and noncoding RNA maturation, RNA polymerase II pause-release, and premature transcriptional termination. Here, we report that loss of Integrator results in global destabilization of mature miRNAs. Enhanced ultraviolet cross-linking and immunoprecipitation of Integrator uncovered an association with duplex miRNAs before their loading onto AGOs. Tracing miRNA fate from biogenesis to stabilization by incorporating 4-thiouridine in nascent transcripts pinpointed a critical role for Integrator in miRNA assembly into AGOs.
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Affiliation(s)
- Nina Kirstein
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Sadat Dokaneheifard
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Pradeep Reddy Cingaram
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Monica Guiselle Valencia
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Felipe Beckedorff
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Helena Gomes Dos Santos
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ezra Blumenthal
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
- Medical Scientist Training Program and Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mina Masoumeh Tayari
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Gabriel Stephen Gaidosh
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
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11
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Chen Y, Zhang R, Yang L, Zhang P, Wang F, Lin G, Zhang J, Zhu Y. Eltrombopag Inhibits Metastasis in Breast Carcinoma by Targeting HuR Protein. Int J Mol Sci 2023; 24:ijms24043164. [PMID: 36834574 PMCID: PMC9963984 DOI: 10.3390/ijms24043164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
Eltrombopag is a small molecule TPO-R agonist that has been shown in our previous studies to inhibit tumor growth by targeting Human antigen R (HuR) protein. HuR protein not only regulates the mRNA stability of tumor growth-related genes, but it also regulates the mRNA stability of a variety of cancer metastasis-related genes, such as Snail, Cox-2, and Vegf-c. However, the role and mechanisms of eltrombopag in breast cancer metastasis have not been fully investigated. The purpose of this study was to investigate whether eltrombopag can inhibit breast cancer metastasis by targeting HuR. Our study first found that eltrombopag can destroy HuR-AU-rich element (ARE) complexes at the molecular level. Secondly, eltrombopag was found to suppress 4T1 cell migration and invasion and inhibit macrophage-mediated lymphangiogenesis at the cellular level. In addition, eltrombopag exerted inhibitory effects on lung and lymph node metastasis in animal tumor metastasis models. Finally, it was verified that eltrombopag inhibited the expressions of Snail, Cox-2, and Vegf-c in 4T1 cells and Vegf-c in RAW264.7 cells by targeting HuR. In conclusion, eltrombopag displayed antimetastatic activity in breast cancer in an HuR dependent manner, which may provide a novel application for eltrombopag, hinting at the multiple effects of HuR inhibitors in cancer therapy.
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Affiliation(s)
- Yao Chen
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Rui Zhang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Liuqing Yang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Pei Zhang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Feiyun Wang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guoqiang Lin
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiange Zhang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Correspondence: (J.Z.); (Y.Z.); Tel./Fax: +86-21-51323104 (J.Z. & Y.Z.)
| | - Yuying Zhu
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Shanghai Institute of Traditional Chinese Medicine, Shanghai 201203, China
- Correspondence: (J.Z.); (Y.Z.); Tel./Fax: +86-21-51323104 (J.Z. & Y.Z.)
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12
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Wang X, Cooper S, Broxmeyer HE, Kapur R. Transient regulation of RNA methylation in human hematopoietic stem cells promotes their homing and engraftment. Leukemia 2023; 37:453-464. [PMID: 36460765 PMCID: PMC9898034 DOI: 10.1038/s41375-022-01761-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022]
Abstract
Enhancing the efficiency of hematopoietic stem cell (HSC) homing and engraftment is critical for cord blood (CB) hematopoietic cell transplantation (HCT). Recent studies indicate that N6-methyladenosine (m6A) modulates the expression of mRNAs that are critical for stem cell function by influencing their stability. Here, we demonstrate that inhibition of RNA decay by regulation of RNA methylation, enhances the expression of the homing receptor chemokine C-X-C receptor-4 (CXCR4) in HSCs. We show that YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), a m6A reader and FTO α-ketoglutarate dependent dioxygenase (FTO), a m6A eraser play an opposite role in this process. Through screening, we identified several FDA-approved compounds that regulate the expression of YTHDF2 and FTO in CB CD34+ cells. We show that transient downregulation of YTHDF2 or activation of FTO by using these compounds inhibits CXCR4 decay in CB HSCs and promotes their homing and engraftment. Our results demonstrate a novel regulation strategy to enhance the function of CB HSCs and provide a translational approach to enhance the clinical efficacy of HCT.
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Affiliation(s)
- Xuepeng Wang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Scott Cooper
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Reuben Kapur
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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13
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Zhang J, Li F, Sun P, Wang J, Li K, Zhao Z, Bai X, Cao Y, Bao H, Li D, Zhang J, Liu Z, Lu Z. Downregulation of miR-122 by porcine reproductive and respiratory syndrome virus promotes viral replication by targeting SOCS3. Vet Microbiol 2022; 275:109595. [DOI: 10.1016/j.vetmic.2022.109595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/23/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
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14
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Zhang J, Kong X, Sun W, Wang L, Shen T, Chen M, Chen X. The RNA-binding protein RBM24 regulates lipid metabolism and SLC7A11 mRNA stability to modulate ferroptosis and inflammatory response. Front Cell Dev Biol 2022; 10:1008576. [PMID: 36478739 PMCID: PMC9720322 DOI: 10.3389/fcell.2022.1008576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Lipids play a critical role in many cellular processes by serving as structural components of cell membranes or functioning as energy fuel and signaling molecules. The RNA-binding proteins RBM24 and RBM38 share an identical RNA-binding domain and thereby, regulate a group of same targets, such as p21. However, it is not certain whether RBM24 and RBM38 participates in lipid homeostasis. Here, lipidomic analysis showed that a deficiency in RBM24 or RBM38 leads to altered lipid metabolism, with more profound alteration by loss of RBM24 in MCF7 cells. We also showed that mice deficient in RBM24 were prone to chronic inflammation and liver steatosis, but not spontaneous tumors. These data let us speculate whether RBM24 regulates ferroptosis, a programmed cell death that links inflammation and liver steatosis via lipid peroxidation. Indeed, we found that over-expression of RBM24 protected, whereas knockout of RBM24 sensitized, cells to Erastin-induced ferroptosis by modulating the mRNA stability of SLC7A11, a ferroptosis inhibitor. Moreover, we showed that knockdown of SLC7A11 reversed the effect of RBM24 on ferroptosis. Together, our study revealed that RBM24 regulates lipid metabolism and SLC7A11 mRNA stability to modulate ferroptosis and inflammatory response.
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Affiliation(s)
- Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, UC, Davis, CA, United States,*Correspondence: Jin Zhang, ; Xinbin Chen,
| | - Xiangmudong Kong
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, UC, Davis, CA, United States
| | | | - Leyi Wang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, UC, Davis, CA, United States
| | - Tong Shen
- West Coast Metabolomics Center, UC, Davis, CA, United States
| | - Mingyi Chen
- Department of Pathology, Southwestern Medical Center, University of Texas, Austin, TX, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, UC, Davis, CA, United States,*Correspondence: Jin Zhang, ; Xinbin Chen,
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15
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Kim HI, Kim GN, Yu KL, Park SH, You JC. Identification of Novel Nucleocapsid Chimeric Proteins Inhibiting HIV-1 Replication. Int J Mol Sci 2022; 23:ijms232012340. [PMID: 36293198 PMCID: PMC9604505 DOI: 10.3390/ijms232012340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
The positive transcription elongation factor b (P-TEFb) is an essential factor that induces transcription elongation and is also negatively regulated by the cellular factor HEXIM1. Previously, the chimeric protein HEXIM1-Tat (HT) was demonstrated to inhibit human immunodeficiency virus-1 (HIV)-1 transcription. In this study, we attempted to develop an improved antiviral protein that specifically binds viral RNA (vRNA) by fusing HT to HIV-1 nucleocapsid (NC). Thus, we synthesized NC-HEXIM1-Tat (NHT) and HEXIM1-Tat-NC (HTN). NHT and HTN inhibited virus proliferation more effectively than HT, and they did not attenuate the function of HT. Notably, NHT and HTN inhibited the infectivity of the progeny virus, whereas HT had no such effect. NHT and HTN selectively and effectively interacted with vRNA and inhibited the proper packaging of the HIV-1 genome. Taken together, our results illustrated that the novel NC-fused chimeric proteins NHT and HTN display novel mechanisms of anti-HIV effects by inhibiting both HIV-1 transcription and packaging.
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Affiliation(s)
- Hae-In Kim
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Ga-Na Kim
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Kyung-Lee Yu
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Seong-Hyun Park
- Graduate Program in Bio-industrial Engineering, College of Life Science and Biotechnology, The Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Ji Chang You
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
- Correspondence:
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16
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Imp interacts with Lin28 to regulate adult stem cell proliferation in the Drosophila intestine. PLoS Genet 2022; 18:e1010385. [PMID: 36070313 PMCID: PMC9484684 DOI: 10.1371/journal.pgen.1010385] [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: 01/12/2022] [Revised: 09/19/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022] Open
Abstract
Stem cells are essential for the development and long-term maintenance of tissues and organisms. Preserving tissue homeostasis requires exquisite control of all aspects of stem cell function: cell potency, proliferation, fate decision and differentiation. RNA binding proteins (RBPs) are essential components of the regulatory network that control gene expression in stem cells to maintain self-renewal and long-term homeostasis in adult tissues. While the function of many RBPs may have been characterized in various stem cell populations, how these interact and are organized in genetic networks remains largely elusive. In this report, we show that the conserved RNA binding protein IGF2 mRNA binding protein (Imp) is expressed in intestinal stem cells (ISCs) and progenitors in the adult Drosophila midgut. We demonstrate that Imp is required cell autonomously to maintain stem cell proliferative activity under normal epithelial turnover and in response to tissue damage. Mechanistically, we show that Imp cooperates and directly interacts with Lin28, another highly conserved RBP, to regulate ISC proliferation. We found that both proteins bind to and control the InR mRNA, a critical regulator of ISC self-renewal. Altogether, our data suggests that Imp and Lin28 are part of a larger gene regulatory network controlling gene expression in ISCs and required to maintain epithelial homeostasis. Stem cells are essential to maintain healthy organs. However, dysregulation of their function is a potential major driver of diseases, including cancer and neurodegeneration, and significantly contributes to the aging process. For these reasons, numerous mechanisms control the ability of stem cells to divide and give rise to functional daughter cells. In this study, we used the Drosophila fruitfly as a genetically amenable experimental model to characterize the function of a conserved protein, the IGF2 mRNA binding protein, in the regulation of adult intestinal stem cells. We found that it is essential for stem cell proliferation under normal conditions and in response to tissue damage. We also report that it interacts with another known regulator, Lin28. Importantly, these two factors largely control stem cell biology and development in mammals, including humans, and are often dysregulated in cancer. This suggests that our work is shedding new light on the conserved mechanisms that maintain long-term stem cell function across organisms.
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17
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Bhattarai K, Richard T, Fatica T, Frangione B, Willmore WG, Holcik M. AMPK-related protein kinase ARK5 regulates subcellular localization of RNA-binding protein hnRNP A1 during hypertonic stress. J Biol Chem 2022; 298:102364. [PMID: 35963429 PMCID: PMC9478406 DOI: 10.1016/j.jbc.2022.102364] [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: 01/18/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 10/31/2022] Open
Abstract
The heterogeneous nuclear ribonucleoprotein hnRNP A1 is a nucleocytoplasmic-shuttling RNA-binding protein that plays an important role in nucleic acid metabolism and gene expression regulation. The function of hnRNP A1 is determined in part by its specific location within the cell. Although some work has been done to elucidate the signaling pathways that regulate the cellular localization of hnRNP A1, the precise mechanism(s), including physiological and pathophysiological conditions that alter hnRNP A1 localization, are not known. We previously conducted an unbiased RNAi-based kinome-wide screen to identify kinases that regulate hnRNP A1 localization during hypertonic stress. One of the hits from this screen is AMPK-related protein kinase 5 (ARK5). Here, we validate ARK5 as the kinase responsible for controlling hnRNP A1 subcellular localization in response to hypertonic stress. We find using immunoprecipitation and in vitro kinase assay methods that ARK5 directly interacts with and phosphorylates hnRNP A1 on serine residues within the F-peptide region. We further show that the M9 motif of hnRNP A1 is essential for the ARK5-hnRNP A1 interaction and subsequent phosphorylation. In addition, the silencing of ARK5 increases the expression of anti-apoptotic protein Bcl-xL and consequently delays caspase activation during hypertonic stress. Our results indicate that ARK5 phosphorylates hnRNP A1 and regulates its subcellular localization during hypertonic stress.
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Affiliation(s)
- Krishna Bhattarai
- Department of Health Sciences, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Travis Richard
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Thet Fatica
- Department of Health Sciences, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Brianna Frangione
- Department of Health Sciences, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | | | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, ON, K1S 5B6, Canada.
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18
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Mettl3-mediated mRNA m 6A modification controls postnatal liver development by modulating the transcription factor Hnf4a. Nat Commun 2022; 13:4555. [PMID: 35931692 PMCID: PMC9355946 DOI: 10.1038/s41467-022-32169-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Hepatic specification and functional maturation are tightly controlled throughout development. N6-methyladenosine (m6A) is the most abundant RNA modification of eukaryotic mRNAs and is involved in various physiological and pathological processes. However, the function of m6A in liver development remains elusive. Here we dissect the role of Mettl3-mediated m6A modification in postnatal liver development and homeostasis. Knocking out Mettl3 perinatally with Alb-Cre (Mettl3 cKO) induces apoptosis and steatosis of hepatocytes, results in severe liver injury, and finally leads to postnatal lethality within 7 weeks. m6A-RIP sequencing and RNA-sequencing reveal that mRNAs of a series of crucial liver-enriched transcription factors are modified by m6A, including Hnf4a, a master regulator for hepatic parenchymal formation. Deleting Mettl3 reduces m6A modification on Hnf4a, decreases its transcript stability in an Igf2bp1-dependent manner, and down-regulates Hnf4a expression, while overexpressing Hnf4a with AAV8 alleviates the liver injury and prolongs the lifespan of Mettl3 cKO mice. However, knocking out Mettl3 in adults using Alb-CreERT2 does not affect liver homeostasis. Our study identifies a dynamic role of Mettl3-mediated RNA m6A modification in liver development. m6A is the most abundant RNA modification of eukaryotic mRNAs and is involved in various physiological and pathological processes. Here the authors show a role for Mettl3-mediated RNA m6A modification in postnatal liver development by regulating the Hnf4a-centered transcriptional network
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19
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Kashikar R, Kotha AK, Shah S, Famta P, Singh SB, Srivastava S, Chougule MB. Advances in nanoparticle mediated targeting of RNA binding protein for cancer. Adv Drug Deliv Rev 2022; 185:114257. [PMID: 35381306 DOI: 10.1016/j.addr.2022.114257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022]
Abstract
RNA binding proteins (RBPs) enact a very crucial part in the RNA directive processes. Atypical expression of these RBPs affects many steps of RNA metabolism, majorly altering its expression. Altered expression and dysfunction of RNA binding proteins lead to cancer progression and other diseases. We enumerate various available interventions, and recent findings focused on targeting RBPs for cancer therapy and diagnosis. The treatment, sensitization, chemoprevention, gene-mediated, and virus mediated interventions were studied to treat and diagnose cancer. The application of passively and actively targeted lipidic nanoparticles, polymeric nanoparticles, virus-based particles, and vaccine-based immunotherapy for the delivery of therapeutic agent/s against cancer are discussed. We also discuss the formulation aspect of nanoparticles for achieving delivery at the site of action and ongoing clinical trials targeting RBPs.
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20
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CPEB1 directs muscle stem cell activation by reprogramming the translational landscape. Nat Commun 2022; 13:947. [PMID: 35177647 PMCID: PMC8854658 DOI: 10.1038/s41467-022-28612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/14/2022] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle stem cells, also called Satellite Cells (SCs), are actively maintained in quiescence but can activate quickly upon extrinsic stimuli. However, the mechanisms of how quiescent SCs (QSCs) activate swiftly remain elusive. Here, using a whole mouse perfusion fixation approach to obtain bona fide QSCs, we identify massive proteomic changes during the quiescence-to-activation transition in pathways such as chromatin maintenance, metabolism, transcription, and translation. Discordant correlation of transcriptomic and proteomic changes reveals potential translational regulation upon SC activation. Importantly, we show Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1), post-transcriptionally affects protein translation during SC activation by binding to the 3' UTRs of different transcripts. We demonstrate phosphorylation-dependent CPEB1 promoted Myod1 protein synthesis by binding to the cytoplasmic polyadenylation elements (CPEs) within its 3' UTRs to regulate SC activation and muscle regeneration. Our study characterizes CPEB1 as a key regulator to reprogram the translational landscape directing SC activation and subsequent proliferation.
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21
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Chen W, Chen Y, Wu R, Guo G, Liu Y, Zeng B, Liao X, Wang Y, Wang X. DHA alleviates diet-induced skeletal muscle fiber remodeling via FTO/m 6A/DDIT4/PGC1α signaling. BMC Biol 2022; 20:39. [PMID: 35135551 PMCID: PMC8827147 DOI: 10.1186/s12915-022-01239-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 01/25/2022] [Indexed: 12/16/2022] Open
Abstract
Background Obesity leads to a decline in the exercise capacity of skeletal muscle, thereby reducing mobility and promoting obesity-associated health risks. Dietary intervention has been shown to be an important measure to regulate skeletal muscle function, and previous studies have demonstrated the beneficial effects of docosahexaenoic acid (DHA; 22:6 ω-3) on skeletal muscle function. At the molecular level, DHA and its metabolites were shown to be extensively involved in regulating epigenetic modifications, including DNA methylation, histone modifications, and small non-coding microRNAs. However, whether and how epigenetic modification of mRNA such as N6-methyladenosine (m6A) mediates DHA regulation of skeletal muscle function remains unknown. Here, we analyze the regulatory effect of DHA on skeletal muscle function and explore the involvement of m6A mRNA modifications in mediating such regulation. Results DHA supplement prevented HFD-induced decline in exercise capacity and conversion of muscle fiber types from slow to fast in mice. DHA-treated myoblasts display increased mitochondrial biogenesis, while slow muscle fiber formation was promoted through DHA-induced expression of PGC1α. Further analysis of the associated molecular mechanism revealed that DHA enhanced expression of the fat mass and obesity-associated gene (FTO), leading to reduced m6A levels of DNA damage-induced transcript 4 (Ddit4). Ddit4 mRNA with lower m6A marks could not be recognized and bound by the cytoplasmic m6A reader YTH domain family 2 (YTHDF2), thereby blocking the decay of Ddit4 mRNA. Accumulated Ddit4 mRNA levels accelerated its protein translation, and the consequential increased DDIT4 protein abundance promoted the expression of PGC1α, which finally elevated mitochondria biogenesis and slow muscle fiber formation. Conclusions DHA promotes mitochondrial biogenesis and skeletal muscle fiber remodeling via FTO/m6A/DDIT4/PGC1α signaling, protecting against obesity-induced decline in skeletal muscle function. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01239-w.
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Affiliation(s)
- Wei Chen
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China.,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China
| | - Yushi Chen
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China.,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China
| | - Ruifan Wu
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China.,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China
| | - Guanqun Guo
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China.,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China
| | - Youhua Liu
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China.,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China
| | - Botao Zeng
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China.,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China
| | - Xing Liao
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China.,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China.,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China.,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang province, China. .,Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, 310058, China. .,Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, 310058, China. .,Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, 310058, China.
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22
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Yi HC, You ZH, Guo ZH, Huang DS, Chan KCC. Learning Representation of Molecules in Association Network for Predicting Intermolecular Associations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2546-2554. [PMID: 32070992 DOI: 10.1109/tcbb.2020.2973091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A key aim of post-genomic biomedical research is to systematically understand molecules and their interactions in human cells. Multiple biomolecules coordinate to sustain life activities, and interactions between various biomolecules are interconnected. However, existing studies usually only focusing on associations between two or very limited types of molecules. In this study, we propose a network representation learning based computational framework MAN-SDNE to predict any intermolecular associations. More specifically, we constructed a large-scale molecular association network of multiple biomolecules in human by integrating associations among long non-coding RNA, microRNA, protein, drug, and disease, containing 6,528 molecular nodes, 9 kind of,105,546 associations. And then, the feature of each node is represented by its network proximity and attribute features. Furthermore, these features are used to train Random Forest classifier to predict intermolecular associations. MAN-SDNE achieves a remarkable performance with an AUC of 0.9552 and an AUPR of 0.9338 under five-fold cross-validation. To indicate the ability to predict specific types of interactions, a case study for predicting lncRNA-protein interactions using MAN-SDNE is also executed. Experimental results demonstrate this work offers a systematic insight for understanding the synergistic associations between molecules and complex diseases and provides a network-based computational tool to systematically explore intermolecular interactions.
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Srinivasan B, Samaddar S, Mylavarapu SVS, Clement JP, Banerjee S. Homeostatic scaling is driven by a translation-dependent degradation axis that recruits miRISC remodeling. PLoS Biol 2021; 19:e3001432. [PMID: 34813590 PMCID: PMC8610276 DOI: 10.1371/journal.pbio.3001432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/30/2021] [Indexed: 01/17/2023] Open
Abstract
Homeostatic scaling in neurons has been attributed to the individual contribution of either translation or degradation; however, there remains limited insight toward understanding how the interplay between the two processes effectuates synaptic homeostasis. Here, we report that a codependence between protein synthesis and degradation mechanisms drives synaptic homeostasis, whereas abrogation of either prevents it. Coordination between the two processes is achieved through the formation of a tripartite complex between translation regulators, the 26S proteasome, and the miRNA-induced silencing complex (miRISC) components such as Argonaute, MOV10, and Trim32 on actively translating transcripts or polysomes. The components of this ternary complex directly interact with each other in an RNA-dependent manner. Disruption of polysomes abolishes this ternary interaction, suggesting that translating RNAs facilitate the combinatorial action of the proteasome and the translational apparatus. We identify that synaptic downscaling involves miRISC remodeling, which entails the mTORC1-dependent translation of Trim32, an E3 ligase, and the subsequent degradation of its target, MOV10 via the phosphorylation of p70 S6 kinase. We find that the E3 ligase Trim32 specifically polyubiquitinates MOV10 for its degradation during synaptic downscaling. MOV10 degradation alone is sufficient to invoke downscaling by enhancing Arc translation through its 3' UTR and causing the subsequent removal of postsynaptic AMPA receptors. Synaptic scaling was occluded when we depleted Trim32 and overexpressed MOV10 in neurons, suggesting that the Trim32-MOV10 axis is necessary for synaptic downscaling. We propose a mechanism that exploits a translation-driven protein degradation paradigm to invoke miRISC remodeling and induce homeostatic scaling during chronic network activity.
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Affiliation(s)
| | | | | | - James P. Clement
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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24
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Liu W, Zhao Y, Liu X, Zhang X, Ding J, Li Y, Tian Y, Wang H, Liu W, Lu Z. A Novel Meiosis-Related lncRNA, Rbakdn, Contributes to Spermatogenesis by Stabilizing Ptbp2. Front Genet 2021; 12:752495. [PMID: 34707642 PMCID: PMC8542969 DOI: 10.3389/fgene.2021.752495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/23/2021] [Indexed: 01/18/2023] Open
Abstract
Spermatocyte meiosis is the cornerstone of mammalian production. Thousands of long noncoding RNAs (lncRNAs) have been reported to be functional in various cellular processes, but the function of lncRNAs in meiosis remains largely unknown. Here, we profiled lncRNAs in spermatocytes at stage I of meiosis and identified a testis-specific lncRNA, Rbakdn, as a vital regulator of meiosis. Rbakdn is dynamically expressed during meiosis I, and Rbakdn knockdown inhibits meiosis in vitro. Furthermore, Rbakdn knockdown in testes in mice by intratesticular injection disturbs meiosis, reduces testicular volume, and increases apoptosis of spermatocytes, resulting in vacuolation of the seminiferous tubules. Rbakdn can bind to Ptbp2, an RNA-binding protein that is important in the regulation of the alternative splicing of many genes in spermatogenesis. Rbakdn knockdown leads to a decrease in Ptbp2 through the ubiquitination degradation pathway, indicating that Rbakdn maintains the stability of Ptbp2. In conclusion, our study identified an lncRNA, Rbakdn, with a crucial role in meiosis.
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Affiliation(s)
- Wensheng Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yinan Zhao
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Xiaohua Liu
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China
| | - Xiaoya Zhang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Jiancheng Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yang Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yingpu Tian
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Zhongxian Lu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
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25
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Speckles and paraspeckles coordinate to regulate HSV-1 genes transcription. Commun Biol 2021; 4:1207. [PMID: 34675360 PMCID: PMC8531360 DOI: 10.1038/s42003-021-02742-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
Numbers of nuclear speckles and paraspeckles components have been demonstrated to regulate herpes simplex virus 1 (HSV-1) replication. However, how HSV-1 infection affects the two nuclear bodies, and whether this influence facilitates the expression of viral genes, remains elusive. In the current study, we found that HSV-1 infection leads to a redistribution of speckles and paraspeckles components. Serine/arginine-rich splicing factor 2 (SRSF2), the core component of speckles, was associated with multiple paraspeckles components, including nuclear paraspeckles assembly transcript 1 (NEAT1), PSPC1, and P54nrb, in HSV-1 infected cells. This association coordinates the transcription of viral genes by binding to the promoters of these genes. By association with the enhancer of zeste homolog 2 (EZH2) and P300/CBP complex, NEAT1 and SRSF2 influenced the histone modifications located near viral genes. This study elucidates the interplay between speckles and paraspeckles following HSV-1 infection and provides insight into the mechanisms by which HSV-1 utilizes host cellular nuclear bodies to facilitate its life cycle. Li & Wang report that components of nuclear speckles and paraspeckles are redistributed upon HSV-1 infection. They show that the association of Serine/arginine-rich splicing factor 2 (SRSF2) with nuclear paraspeckles assembly transcript 1 (NEAT1) coordinates the transcription of viral genes
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26
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Nair L, Zhang W, Laffleur B, Jha MK, Lim J, Lee H, Wu L, Alvarez NS, Liu ZP, Munteanu EL, Swayne T, Hanna JH, Ding L, Rothschild G, Basu U. Mechanism of noncoding RNA-associated N 6-methyladenosine recognition by an RNA processing complex during IgH DNA recombination. Mol Cell 2021; 81:3949-3964.e7. [PMID: 34450044 PMCID: PMC8571800 DOI: 10.1016/j.molcel.2021.07.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/04/2021] [Accepted: 07/28/2021] [Indexed: 01/13/2023]
Abstract
Immunoglobulin heavy chain (IgH) locus-associated G-rich long noncoding RNA (SμGLT) is important for physiological and pathological B cell DNA recombination. We demonstrate that the METTL3 enzyme-catalyzed N6-methyladenosine (m6A) RNA modification drives recognition and 3' end processing of SμGLT by the RNA exosome, promoting class switch recombination (CSR) and suppressing chromosomal translocations. The recognition is driven by interaction of the MPP6 adaptor protein with nuclear m6A reader YTHDC1. MPP6 and YTHDC1 promote CSR by recruiting AID and the RNA exosome to actively transcribe SμGLT. Direct suppression of m6A modification of SμGLT or of m6A reader YTHDC1 reduces CSR. Moreover, METTL3, an essential gene for B cell development in the bone marrow and germinal center, suppresses IgH-associated aberrant DNA breaks and prevents genomic instability. Taken together, we propose coordinated and central roles for MPP6, m6A modification, and m6A reader proteins in controlling long noncoding RNA processing, DNA recombination, and development in B cells.
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Affiliation(s)
- Lekha Nair
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Mukesh K Jha
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Heather Lee
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lijing Wu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Nehemiah S Alvarez
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan 250061, Shandong, China
| | - Emilia L Munteanu
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Theresa Swayne
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lei Ding
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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27
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Li L, Zhou M, Chen B, Wang Q, Pan S, Hou Y, Xia J, Zhou X. ALKBH5 promotes cadmium-induced transformation of human bronchial epithelial cells by regulating PTEN expression in an m6A-dependent manner. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112686. [PMID: 34438274 DOI: 10.1016/j.ecoenv.2021.112686] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Cadmium is a carcinogenic heavy metal that poses a severe threat to human beings. The underlying mechanism, however, remains elusive. N6-methyladenosine (m6A) is the most abundant post-transcriptional modification in mRNA that regulates RNA metabolism. Emerging evidence shows that m6A is involved in the pathogenesis of various cancers. In this study, human bronchial epithelial BEAS-2B cells were transformed by exposing to 2 μM of cadmium for 20 weeks to investigate the role of m6A in cadmium carcinogenesis. We found the level of m6A in mRNA was significantly decreased in cadmium-transformed BEAS-2B cells, and this change was regulated by m6A demethylase ALKBH5. ALKBH5 was significantly upregulated in the middle and late stages of cell transformation at week 8, 12, 16 and 20. Knockdown of ALKBH5 in cadmium-transformed cells alleviated cell proliferation, migration, invasion, and anchorage-independent growth, but co-transfection with ALKBH5 siRNA and PTEN siRNA restored the inhibitory effects of ALKBH5 knockdown on those transformation properties. ALKBH5 decreased the m6A level of PTEN mRNA, resulting in its instability and reduction of PTEN protein expression. These results indicate that ALKBH5-mediated demethylation m6A at PTEN mRNA is involved in cadmium-induced cell transformation. Our study provides a new perspective for the involvement of m6A modification in cadmium carcinogenesis.
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Affiliation(s)
- Luyao Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Mei Zhou
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Biyun Chen
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Qin Wang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Shuya Pan
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Yaxuan Hou
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Jiamin Xia
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Xue Zhou
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China.
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28
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METTL3-dependent N 6-methyladenosine RNA modification mediates the atherogenic inflammatory cascades in vascular endothelium. Proc Natl Acad Sci U S A 2021; 118:2025070118. [PMID: 33579825 DOI: 10.1073/pnas.2025070118] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Atherosclerosis is characterized by the plaque formation that restricts intraarterial blood flow. The disturbed blood flow with the associated oscillatory stress (OS) at the arterial curvatures and branch points can trigger endothelial activation and is one of the risk factors of atherosclerosis. Many studies reported the mechanotransduction related to OS and atherogenesis; however, the transcriptional and posttranscriptional regulatory mechanisms of atherosclerosis remain unclear. Herein, we investigated the role of N6-methyladenosine (m6A) RNA methylation in mechanotransduction in endothelial cells (ECs) because of its important role in epitranscriptome regulation. We have identified m6A methyltransferase METTL3 as a responsive hub to hemodynamic forces and atherogenic stimuli in ECs. OS led to an up-regulation of METTL3 expression, accompanied by m6A RNA hypermethylation, increased NF-κB p65 Ser536 phosphorylation, and enhanced monocyte adhesion. Knockdown of METTL3 abrogated this OS-induced m6A RNA hypermethylation and other manifestations, while METTL3 overexpression led to changes resembling the OS effects. RNA-sequencing and m6A-enhanced cross-linking and immunoprecipitation (eCLIP) experiments revealed NLRP1 and KLF4 as two hemodynamics-related downstream targets of METTL3-mediated hypermethylation. The METTL3-mediated RNA hypermethylation up-regulated NLRP1 transcript and down-regulated KLF4 transcript through YTHDF1 and YTHDF2 m6A reader proteins, respectively. In the in vivo atherosclerosis model, partial ligation of the carotid artery led to plaque formation and up-regulation of METTL3 and NLRP1, with down-regulation of KLF4; knockdown of METTL3 via repetitive shRNA administration prevented the atherogenic process, NLRP3 up-regulation, and KLF4 down-regulation. Collectively, we have demonstrated that METTL3 serves a central role in the atherogenesis induced by OS and disturbed blood flow.
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29
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Mohibi S, Zhang J, Chen M, Chen X. Mice Deficient in the RNA-Binding Protein Zfp871 Are Prone to Early Death and Steatohepatitis in Part through the p53-Mdm2 Axis. Mol Cancer Res 2021; 19:1751-1762. [PMID: 34257081 DOI: 10.1158/1541-7786.mcr-21-0239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/11/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
p53 transcription factor is activated upon exposure to various cellular stresses, leading to growth suppression. However, aberrant activation of p53 can lead to defects in embryonic development and other abnormalities. Here, we identified zinc finger protein Zfp871 as a p53 target gene. We showed that as an RNA-binding protein, Zfp871 binds to Mdm2 3'UTR and stabilizes Mdm2 mRNA, which in turn suppresses p53 expression through increased expression of Mdm2 E3 ubiquitin ligase. Consistently, Zfp871 deficiency increases p53 expression, leading to growth suppression in a p53-dependent manner. To determine the role of Zfp871 in the p53 pathway, we used Zfp871-deficient mouse model and found that Zfp871-null mice were prone to embryonic/pre-weaning lethality, which can be partially rescued by simultaneous deletion of Trp53. We also found that mice heterozygous for Zfp871 had a short lifespan and were susceptible to steatohepatitis but not to spontaneous tumors. To determine the underlying mechanism, RNA-seq analysis was performed and showed that an array of genes involved in development, lipid metabolism, and inflammation is regulated by Zfp871 in conjunction with p53. Taken together, we conclude that the Zfp871-Mdm2-p53 pathway plays a critical role in tumor-free survival and development. IMPLICATIONS: A fine equilibrium of p53 is required for preventing damaging effects of aberrant p53 expression. We identify the Zfp871-Mdm2-p53 pathway that plays a critical role in development of mice and steatohepatitis.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, California
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, California
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, California.
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30
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Cell-Penetrating Peptides and Transportan. Pharmaceutics 2021; 13:pharmaceutics13070987. [PMID: 34210007 PMCID: PMC8308968 DOI: 10.3390/pharmaceutics13070987] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
In the most recent 25–30 years, multiple novel mechanisms and applications of cell-penetrating peptides (CPP) have been demonstrated, leading to novel drug delivery systems. In this review, I present a brief introduction to the CPP area with selected recent achievements. This is followed by a nostalgic journey into the research in my own laboratories, which lead to multiple CPPs, starting from transportan and paving a way to CPP-based therapeutic developments in the delivery of bio-functional materials, such as peptides, proteins, vaccines, oligonucleotides and small molecules, etc.
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31
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Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein-RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing. Int J Mol Sci 2021; 22:ijms22105312. [PMID: 34070162 PMCID: PMC8158511 DOI: 10.3390/ijms22105312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/11/2022] Open
Abstract
During mRNA transcription, diverse RNA-binding proteins (RBPs) are recruited to RNA polymerase II (RNAP II) transcription machinery. These RBPs bind to distinct sites of nascent RNA to co-transcriptionally operate mRNA processing. Recent studies have revealed a close relationship between transcription and co-transcriptional RNA processing, where one affects the other’s activity, indicating an essential role of protein–RNA interactions for the fine-tuning of mRNA production. Owing to their limited amount in cells, the detection of protein–RNA interactions specifically assembled on the transcribing RNAP II machinery still remains challenging. Currently, cross-linking and immunoprecipitation (CLIP) has become a standard method to detect in vivo protein–RNA interactions, although it requires a large amount of input materials. Several improved methods, such as infrared-CLIP (irCLIP), enhanced CLIP (eCLIP), and target RNA immunoprecipitation (tRIP), have shown remarkable enhancements in the detection efficiency. Furthermore, the utilization of an RNA editing mechanism or proximity labeling strategy has achieved the detection of faint protein–RNA interactions in cells without depending on crosslinking. This review aims to explore various methods being developed to detect endogenous protein–RNA interaction sites and discusses how they may be applied to the analysis of co-transcriptional RNA processing.
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32
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Li N, Hui H, Bray B, Gonzalez GM, Zeller M, Anderson KG, Knight R, Smith D, Wang Y, Carlin AF, Rana TM. METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection. Cell Rep 2021; 35:109091. [PMID: 33961823 PMCID: PMC8090989 DOI: 10.1016/j.celrep.2021.109091] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/18/2021] [Accepted: 04/16/2021] [Indexed: 01/05/2023] Open
Abstract
It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlining molecular mechanism. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. Here, we investigate m6A modification of the SARS-CoV-2 gene in regulating the host cell innate immune response. Our data show that the SARS-CoV-2 virus has m6A modifications that are enriched in the 3' end of the viral genome. We find that depletion of the host cell m6A methyltransferase METTL3 decreases m6A levels in SARS-CoV-2 and host genes, and m6A reduction in viral RNA increases RIG-I binding and subsequently enhances the downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in patients with severe coronavirus disease 2019 (COVID-19). These findings will aid in the understanding of COVID-19 pathogenesis and the design of future studies regulating innate immunity for COVID-19 treatment.
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Affiliation(s)
- Na Li
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Hui Hui
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bill Bray
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Gwendolyn Michelle Gonzalez
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kristian G Anderson
- Department of Immunology and Microbiology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovations, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Tariq M Rana
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA.
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33
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Chen Y, Wu R, Chen W, Liu Y, Liao X, Zeng B, Guo G, Lou F, Xiang Y, Wang Y, Wang X. Curcumin prevents obesity by targeting TRAF4-induced ubiquitylation in m 6 A-dependent manner. EMBO Rep 2021; 22:e52146. [PMID: 33880847 PMCID: PMC8097347 DOI: 10.15252/embr.202052146] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022] Open
Abstract
Obesity has become a major health problem that has rapidly prevailed over the past several decades worldwide. Curcumin, a natural polyphenolic compound present in turmeric, has been shown to have a protective effect on against obesity and metabolic diseases. However, its underlying mechanism remains largely unknown. Here, we show that the administration of curcumin significantly prevents HFD-induced obesity and decreases the fat mass of the subcutaneous inguinal WAT (iWAT) and visceral epididymal WAT (eWAT) in mice. Mechanistically, curcumin inhibits adipogenesis by reducing the expression of AlkB homolog 5 (ALKHB5), an m6 A demethylase, which leads to higher m6 A-modified TNF receptor-associated factor 4 (TRAF4) mRNA. TRAF4 mRNA with higher m6 A level is recognized and bound by YTHDF1, leading to enhanced translation of TRAF4. TRAF4, acting as an E3 RING ubiquitin ligase, promotes degradation of adipocyte differentiation regulator PPARγ by a ubiquitin-proteasome pathway thereby inhibiting adipogenesis. Thus, m6 A-dependent TRAF4 expression upregulation by ALKBH5 and YTHDF1 contributes to curcumin-induced obesity prevention. Our findings provide mechanistic insights into how m6 A is involved in the anti-obesity effect of curcumin.
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Affiliation(s)
- Yushi Chen
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Ruifan Wu
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Wei Chen
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Youhua Liu
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Xing Liao
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Botao Zeng
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Guanqun Guo
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Fangfang Lou
- Jinhua Academy of Agricultural SciencesJinhuaChina
| | - Yun Xiang
- Jinhua Academy of Agricultural SciencesJinhuaChina
| | - Yizhen Wang
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Xinxia Wang
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
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Sun W, Laubach K, Lucchessi C, Zhang Y, Chen M, Zhang J, Chen X. Fine-tuning p53 activity by modulating the interaction between eukaryotic translation initiation factor eIF4E and RNA-binding protein RBM38. Genes Dev 2021; 35:542-555. [PMID: 33664057 PMCID: PMC8015715 DOI: 10.1101/gad.346148.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/02/2021] [Indexed: 01/09/2023]
Abstract
p53 is critical for tumor suppression but also elicits detrimental effects when aberrantly overexpressed. Thus, multiple regulators, including RNA-binding protein RBM38, are found to tightly control p53 expression. Interestingly, RBM38 is unique in that it can either suppress or enhance p53 mRNA translation via altered interaction with eIF4E potentially mediated by serine-195 (S195) in RBM38. Thus, multiple RBM38/eIF4E knock-in (KI) cell lines were generated to investigate the significance of eIF4E-RBM38 interaction in controlling p53 activity. We showed that KI of RBM38-S195D or -Y192C enhances, whereas KI of RBM38-S195K/R/L weakens, the binding of eIF4E to p53 mRNA and subsequently p53 expression. We also showed that KI of eIF4E-D202K weakens the interaction of eIF4E with RBM38 and thereby enhances p53 expression, suggesting that D202 in eIF4E interacts with S195 in RBM38. Moreover, we generated an Rbm38 S193D KI mouse model in which human-equivalent serine-193 is substituted with aspartic acid. We showed that S193D KI enhances p53-dependent cellular senescence and that S193D KI mice have a shortened life span and are prone to spontaneous tumors, chronic inflammation, and liver steatosis. Together, we provide in vivo evidence that the RBM38-eIF4E loop can be explored to fine-tune p53 expression for therapeutic development.
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Affiliation(s)
- Wenqiang Sun
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Kyra Laubach
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Christopher Lucchessi
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Yanhong Zhang
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jin Zhang
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Xinbin Chen
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
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Shi R, Ying S, Li Y, Zhu L, Wang X, Jin H. Linking the YTH domain to cancer: the importance of YTH family proteins in epigenetics. Cell Death Dis 2021; 12:346. [PMID: 33795663 PMCID: PMC8016981 DOI: 10.1038/s41419-021-03625-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 02/06/2023]
Abstract
N6-methyladenosine (m6A), the most prevalent and reversible modification of mRNA in mammalian cells, has recently been extensively studied in epigenetic regulation. YTH family proteins, whose YTH domain can recognize and bind m6A-containing RNA, are the main "readers" of m6A modification. YTH family proteins perform different functions to determine the metabolic fate of m6A-modified RNA. The crystal structure of the YTH domain has been completely resolved, highlighting the important roles of several conserved residues of the YTH domain in the specific recognition of m6A-modified RNAs. Upstream and downstream targets have been successively revealed in different cancer types and the role of YTH family proteins has been emphasized in m6A research. This review describes the regulation of RNAs by YTH family proteins, the structural features of the YTH domain, and the connections of YTH family proteins with human cancers.
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Affiliation(s)
- Rongkai Shi
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Shilong Ying
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Yadan Li
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
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36
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Measuring Translation Efficiency by RNA Immunoprecipitation of Translation Initiation Factors. Methods Mol Biol 2021. [PMID: 33786785 DOI: 10.1007/978-1-0716-1217-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Eukaryotic mRNAs are bound by a multitude of RNA binding proteins (RBPs) that control their localization, transport, and translation. Measuring the rate of translation of mRNAs is critical for understanding the factors and pathways involved in gene expression. In this chapter, we present a method to compare the rate of translation of individual mRNA species based on the fraction of mRNA bound by a specific ribonucleoprotein involved in the general translation machinery. The ribonucleoprotein complex is immunoprecipitated using an antibody for the RBP, followed by RT-PCR to semi-quantitatively determine the amount of an individual mRNA fraction bound by a translation regulating protein such as eIF4E.
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Shim JS, Park SH, Lee DK, Kim YS, Park SC, Redillas MCFR, Seo JS, Kim JK. The Rice GLYCINE-RICH PROTEIN 3 Confers Drought Tolerance by Regulating mRNA Stability of ROS Scavenging-Related Genes. RICE (NEW YORK, N.Y.) 2021; 14:31. [PMID: 33742286 PMCID: PMC7979854 DOI: 10.1186/s12284-021-00473-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/10/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant glycine-rich proteins are categorized into several classes based on their protein structures. The glycine-rich RNA binding proteins (GRPs) are members of class IV subfamily possessing N-terminus RNA-recognition motifs (RRMs) and proposed to be involved in post-transcriptional regulation of its target transcripts. GRPs are involved in developmental process and cellular stress responses, but the molecular mechanisms underlying these regulations are still elusive. RESULTS Here, we report the functional characterization of rice GLYCINE-RICH PROTEIN 3 (OsGRP3) and its physiological roles in drought stress response. Both drought stress and ABA induce the expression of OsGRP3. Transgenic plants overexpressing OsGRP3 (OsGRP3OE) exhibited tolerance while knock-down plants (OsGRP3KD) were susceptible to drought compared to the non-transgenic control. In vivo, subcellular localization analysis revealed that OsGRP3-GFP was transported from cytoplasm/nucleus into cytoplasmic foci following exposure to ABA and mannitol treatments. Comparative transcriptomic analysis between OsGRP3OE and OsGRP3KD plants suggests that OsGRP3 is involved in the regulation of the ROS related genes. RNA-immunoprecipitation analysis revealed the associations of OsGRP3 with PATHOGENESIS RELATED GENE 5 (PR5), METALLOTHIONEIN 1d (MT1d), 4,5-DOPA-DIOXYGENASE (DOPA), and LIPOXYGENASE (LOX) transcripts. The half-life analysis showed that PR5 transcripts decayed slower in OsGRP3OE but faster in OsGRP3KD, while MT1d and LOX transcripts decayed faster in OsGRP3OE but slower in OsGRP3KD plants. H2O2 accumulation was reduced in OsGRP3OE and increased in OsGRP3KD plants compared to non-transgenic plants (NT) under drought stress. CONCLUSION OsGRP3 plays a positive regulator in rice drought tolerance and modulates the transcript level and mRNA stability of stress-responsive genes, including ROS-related genes. Moreover, OsGRP3 contributes to the reduction of ROS accumulation during drought stress. Our results suggested that OsGRP3 alleviates ROS accumulation by regulating ROS-related genes' mRNA stability under drought stress, which confers drought tolerance.
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Affiliation(s)
- Jae Sung Shim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Hyun Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Dong-Keun Lee
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- E GREEN GLOBAL, Gunpo, 15843, South Korea
| | - Youn Shic Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, 24341, South Korea
| | - Soo-Chul Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 54874, South Korea
| | | | - Jun Sung Seo
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
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OsCRP1, a Ribonucleoprotein Gene, Regulates Chloroplast mRNA Stability That Confers Drought and Cold Tolerance. Int J Mol Sci 2021; 22:ijms22041673. [PMID: 33562320 PMCID: PMC7915912 DOI: 10.3390/ijms22041673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 02/03/2023] Open
Abstract
Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded and highly abundant proteins that are proposed to function in chloroplast RNA metabolism. However, the molecular mechanisms underlying the regulation of chloroplast RNAs involved in stress tolerance are poorly understood. Here, we demonstrate that CHLOROPLAST RNA-BINDING PROTEIN 1 (OsCRP1), a rice (Oryza sativa) cpRNP gene, is essential for stabilization of RNAs from the NAD(P)H dehydrogenase (NDH) complex, which in turn enhances drought and cold stress tolerance. An RNA-immunoprecipitation assay revealed that OsCRP1 is associated with a set of chloroplast RNAs. Transcript profiling indicated that the mRNA levels of genes from the NDH complex significantly increased in the OsCRP1 overexpressing compared to non-transgenic plants, whereas the pattern in OsCRP1 RNAi plants were opposite. Importantly, the OsCRP1 overexpressing plants showed a higher cyclic electron transport (CET) activity, which is essential for elevated levels of ATP for photosynthesis. Additionally, overexpression of OsCRP1 resulted in significantly enhanced drought and cold stress tolerance with higher ATP levels compared to wild type. Thus, our findings suggest that overexpression of OsCRP1 stabilizes a set of mRNAs from genes of the NDH complex involved in increasing CET activity and production of ATP, which consequently confers enhanced drought and cold tolerance.
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Voss G, Haflidadóttir BS, Järemo H, Persson M, Catela Ivkovic T, Wikström P, Ceder Y. Regulation of cell-cell adhesion in prostate cancer cells by microRNA-96 through upregulation of E-Cadherin and EpCAM. Carcinogenesis 2021; 41:865-874. [PMID: 31738404 PMCID: PMC7359773 DOI: 10.1093/carcin/bgz191] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/24/2019] [Accepted: 11/15/2019] [Indexed: 11/15/2022] Open
Abstract
Prostate cancer is one of the most common cancers in men, yet the biology behind lethal disease progression and bone metastasis is poorly understood. In this study, we found elevated levels of microRNA-96 (miR-96) in prostate cancer bone metastasis samples. To determine the molecular mechanisms by which miR-96 deregulation contributes to metastatic progression, we performed an Argonaute2-immunoprecipitation assay, in which mRNAs associated with cell–cell interaction were enriched. The expression of two cell adhesion molecules, E-Cadherin and EpCAM, was upregulated by miR-96, and potential targets sites were identified in the coding sequences of their mRNAs. We further showed that miR-96 enhanced cell–cell adhesion between prostate cancer cells as well as their ability to bind to osteoblasts. Our findings suggest that increased levels of miR-96 give prostate cancer cells an advantage at forming metastases in the bone microenvironment due to increased cell–cell interaction. We propose that miR-96 promotes bone metastasis in prostate cancer patients by facilitating the outgrowth of macroscopic tumours in the bone.
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Affiliation(s)
- Gjendine Voss
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Helena Järemo
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Tina Catela Ivkovic
- Department of Laboratory Medicine, Lund University, Lund, Sweden.,Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | | | - Yvonne Ceder
- Department of Laboratory Medicine, Lund University, Lund, Sweden
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Muscone derivative ZM-32 inhibits breast tumor angiogenesis by suppressing HuR-mediated VEGF and MMP9 expression. Biomed Pharmacother 2021; 136:111265. [PMID: 33450490 DOI: 10.1016/j.biopha.2021.111265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Inhibition of tumor angiogenesis is a highly effective strategy for cancer treatment. Human antigen R (HuR), an RNA-binding protein, is overexpressed in many cancers and regulates the mRNAs of multiple angiogenic factors by binding to the adenylate-uridylate-rich element in their 3' untranslated region. HuR protein has been demonstrated to be an important regulatory factor in macrophage-mediated angiogenesis, a process in which macrophages are critical for tumor progression. Muscone is a synthetic equivalent of musk, and recent studies have shown that it has a regulatory effect on angiogenesis. In this study, we synthesized five series of muscone derivatives and discovered that compound ZM-32 was effective in preventing HuR RRM1/2-Vegf-a mRNA complex formation. ZM-32 bound to HuR RRM1/2 protein with a KD value of 521.7 nmol/L. Furthermore, ZM-32 inhibited endothelial cell proliferation, migration, and tubule formation, and suppressed the VEGF/VEGFR2/ERK1/2 signaling axis mediated by macrophages in vitro. We also demonstrated that ZM-32 effectively prevented the proliferation and migration of breast cancer cells and inhibited the growth and angiogenesis of MDA-MB-231 xenograft tumors without any obvious toxicity in vivo. Mechanistically, exposure to ZM-32 influenced the mRNA stability of Vegf-a and Mmp9 in a HuR-dependent manner in both macrophages and MDA-MB-231 cells. Thus, in this study we identified a new muscone derivative, ZM-32, with anti-angiogenesis effects mediated via targeting HuR in breast cancer, that may become a potentially valuable lead compound for anti-cancer angiogenesis.
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Chiefari E, Arcidiacono B, Mirabelli M, Brunetti FS, Greco E, Foti DP, Brunetti A. Methods to Study Protein-Binding to Pseudogene Transcripts. Methods Mol Biol 2021; 2324:187-202. [PMID: 34165716 DOI: 10.1007/978-1-0716-1503-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
One of the most commonly described biological feature of processed pseudogenes is the ability to influence the expression of their parental coding genes. As evidenced in several studies, the high sequence similarity between these RNA pairs sets up a certain level of competition for posttranscriptional regulators, including, among others, RNA-binding proteins (RBPs). RBPs may affect, positively or negatively, the stability of bound mRNAs, so that, if an overexpressed pseudogene competes with its homologous coding gene, the downstream protein synthesis would change, with potential pathological consequences. Given these premises, a rigorous and comprehensive understanding of interactions between pseudogene-parental gene RNA pairs and RBPs could provide further insights into the biological bases of complex diseases, such as cancer, cardiovascular disease, and type 2 diabetes, identifying novel predictive and/or prognostic biomarkers.Herein, we detail easily adaptable protocols of plasmid-based molecular cloning and RNA-electrophoretic mobility shift assay (EMSA) used in our laboratory for determining the interaction between a cytoplasmatic stabilizing protein (αCP1) and the pseudogene-parental gene RNA pair HMGA1-p /HMGA1. We also offer a general overview of RNA immunoprecipitation procedures and present novel bioinformatic tools for predicting RBPs binding sites on pseudogene transcripts.
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Affiliation(s)
- Eusebio Chiefari
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Biagio Arcidiacono
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Maria Mirabelli
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | | | - Emanuela Greco
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Daniela Patrizia Foti
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Antonio Brunetti
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy.
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Liao HQ, Zhou J, Cao Y, Nie YL, Li MQ, Zhou J. Vigilin interacts with ER-β to protect against palmitic acid-induced granulosa cells apoptosis via inhibiting calcineurin-mediated Drp1 signaling pathway. Steroids 2020; 163:108699. [PMID: 32687845 DOI: 10.1016/j.steroids.2020.108699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/12/2020] [Accepted: 07/11/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Hypercholesterolemia is one of the causes of female infertility, and as a common fatty acid in follicular fluid, palmitic acid (PA) level plays a vital role in granule cell which is closely related to the developmental potential of follicle. METHODS The ovarian granulosa cell-like human granulosa (KGN) cell line and the immortalized normal ovarian surface epithelial cell line (IOSE80) were used to verify the effect of PA on cell viability and apoptosis by MTT and flow cytometry assay, respectively. Then mitochondria damage was confirmed by mitochondrial membrane potential, mitochondrial ROS detection assay and western blot in KGN cells. Thorough luciferase reporter assay and RIP-qPCR, the relationship between vigilin and ER-β was investigated. RESULTS In our study, PA induced mitochondrial damage-mediated cell apoptosis of KGN cells was dose-dependently, while PA shown no effects on in IOSE80 cells. Then the role of calcineurin (CnA)-mediated Drp1 signaling pathway on KGN cells was confirmed by treating with Mdivi-1 or FK506T. In addition, the changed level of vigilin and ER-β was observed in cell apoptosis of KGN cells induced by PA. By transfecting vigilin vector or ER-β vector into KGN cells, respectively, vigilin and ER-β were demonstrated to regulate the apoptosis of KGN cells. And vigilin was a binding protein of ER-β mRNA. CONCLUSION Vigilin could interact with ER-β mRNA to promote ER-β expression. And Vigilin/ ER-β relieve the mitochondrial damage and cell apoptosis induced by PA through regulating CnA-mediated Drp1 signaling pathway, which revealed the mechanism and strategy of hypercholesterolemia in female infertility.
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Affiliation(s)
- Hong-Qing Liao
- The Second Affiliated Hospital of South China University, Hengyang 421001, PR China; Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China
| | - Jun Zhou
- The Second Affiliated Hospital of South China University, Hengyang 421001, PR China; Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China
| | - Yang Cao
- Hunan University of Technology and Business, Changsha 410205, PR China
| | - Yu-Lin Nie
- Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China
| | - Mei-Qing Li
- The Second Affiliated Hospital of South China University, Hengyang 421001, PR China; Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China
| | - Jing Zhou
- The Second Affiliated Hospital of South China University, Hengyang 421001, PR China; Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China.
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43
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Boots JL, von Pelchrzim F, Weiss A, Zimmermann B, Friesacher T, Radtke M, Żywicki M, Chen D, Matylla-Kulińska K, Zagrovic B, Schroeder R. RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription in cis. Transcription 2020; 11:217-229. [PMID: 32663063 PMCID: PMC7714431 DOI: 10.1080/21541264.2020.1790990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Transcription elongation is a highly regulated process affected by many proteins, RNAs and the underlying DNA. Here we show that the nascent RNA can interfere with transcription in human cells, extending our previous findings from bacteria and yeast. We identified a variety of Pol II-binding aptamers (RAPs), prominent in repeat elements such as ACRO1 satellites, LINE1 retrotransposons and CA simple repeats, and also in several protein-coding genes. ACRO1 repeat, when translated in silico, exhibits ~50% identity with the Pol II CTD sequence. Taken together with a recent proposal that proteins in general tend to interact with RNAs similar to their cognate mRNAs, this suggests a mechanism for RAP binding. Using a reporter construct, we show that ACRO1 potently inhibits Pol II elongation in cis. We propose a novel mode of transcriptional regulation in humans, in which the nascent RNA binds Pol II to silence its own expression.
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Affiliation(s)
- Jennifer L. Boots
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Frederike von Pelchrzim
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Adam Weiss
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Bob Zimmermann
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Theres Friesacher
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Maximilian Radtke
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Marek Żywicki
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Doris Chen
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Katarzyna Matylla-Kulińska
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Renée Schroeder
- Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria,CONTACT Renée Schroeder Department of Biochemistry and Molecular Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
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Discovery of the anti-angiogenesis effect of eltrombopag in breast cancer through targeting of HuR protein. Acta Pharm Sin B 2020; 10:1414-1425. [PMID: 32963940 PMCID: PMC7488360 DOI: 10.1016/j.apsb.2020.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/04/2020] [Accepted: 01/07/2020] [Indexed: 01/26/2023] Open
Abstract
HuR (human antigen R), an mRNA-binding protein responsible for poor prognosis in nearly all kinds of malignancies, is a potential anti-tumor target for drug development. While screening HuR inhibitors with a fluorescence polarization (FP) based high-throughput screening (HTS) system, the clinically used drug eltrombopag was identified. Activity of eltrombopag on molecular level was verified with FP, electrophoretic mobility shift assay (EMSA), simulation docking and surface plasmon resonance (SPR). Further, we showed that eltrombopag inhibited in vitro cell proliferation of multiple cancer cell lines and macrophages, and the in vivo anti-tumor activity was also demonstrated in a 4T1 tumor-bearing mouse model. The in vivo data showed that eltrombopag was efficient in reducing microvessels in tumor tissues. We then confirmed the HuR-dependent anti-angiogenesis effect of eltrombopag in 4T1 cells and RAW264.7 macrophages with qRT-PCR, HuR-overexpression and HuR-silencing assays, RNA stability assays, RNA immunoprecipitation and luciferase assays. Finally, we analyzed the in vitro anti-angiogenesis effect of eltrombopag on human umbilical vein endothelial cells (HUVECs) mediated by macrophages with cell scratch assay and in vitro Matrigel angiogenesis assay. With these data, we revealed the HuR-dependent anti-angiogenesis effect of eltrombopag in breast tumor, suggesting that the existing drug eltrombopag may be used as an anti-cancer drug.
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Key Words
- ARE, AU-rich element
- Angiogenesis
- Anti-tumor
- ELB, eltrombopag
- ELISA, enzyme linked immune sorbent assay
- EMSA, electrophoretic mobility shift assay
- Eltrombopag
- FP, fluorescence polarization
- HTS, high-throughput screening
- HUVEC, human umbilical vein endothelial cell
- HuR
- HuR, human antigen R
- IHC, immunohistochemistry
- RIP, RNA immunoprecipitation
- SPR, surface plasmon resonance
- mRNAs stability
- qRT-PCR, quantitative real-time PCR
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Degradation of MicroRNA miR-466d-3p by Japanese Encephalitis Virus NS3 Facilitates Viral Replication and Interleukin-1β Expression. J Virol 2020; 94:JVI.00294-20. [PMID: 32461319 DOI: 10.1128/jvi.00294-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/13/2020] [Indexed: 11/20/2022] Open
Abstract
Japanese encephalitis virus (JEV) infection alters microRNA (miRNA) expression in the central nervous system (CNS). However, the mechanism contributing to miRNA regulation in the CNS is not known. We discovered global degradation of mature miRNA in mouse brains and neuroblastoma (NA) cells after JEV infection. Integrative analysis of miRNAs and mRNAs suggested that several significantly downregulated miRNAs and their targeted mRNAs were clustered into an inflammation pathway. Transfection with miRNA 466d-3p (miR-466d-3p) decreased interleukin-1β (IL-1β) expression and inhibited JEV replication in NA cells. However, miR-466d-3p expression increased after JEV infection in the presence of cycloheximide, indicating that viral protein expression reduced miR-466d-3p expression. We generated all the JEV coding proteins and demonstrated NS3 helicase protein to be a potent miRNA suppressor. The NS3 proteins of Zika virus, West Nile virus, and dengue virus serotype 1 (DENV-1) and DENV-2 also decreased miR-466d-3p expression. Results from helicase-blocking assays and in vitro unwinding assays demonstrated that NS3 could unwind pre-miR-466d and induce miRNA dysfunction. Computational models and an RNA immunoprecipitation assay revealed arginine-rich domains of NS3 to be crucial for pre-miRNA binding and degradation of host miRNAs. Importantly, site-directed mutagenesis of conserved residues in NS3 revealed that R226G and R202W reduced the binding affinity and degradation of pre-miR-466d. These results expand the function of flavivirus helicases beyond unwinding duplex RNA to degrade pre-miRNAs. Hence, we revealed a new mechanism for NS3 in regulating miRNA pathways and promoting neuroinflammation.IMPORTANCE Host miRNAs have been reported to regulate JEV-induced inflammation in the CNS. We found that JEV infection could reduce expression of host miRNA. The helicase region of the NS3 protein bound specifically to miRNA precursors and could lead to incorrect unwinding of miRNA precursors, thereby reducing the expression of mature miRNAs. This observation led to two major findings. First, our results suggested that JEV NS3 protein induced miR-466d-3p degradation, which promoted IL-1β expression and JEV replication. Second, arginine molecules on NS3 were the main miRNA-binding sites, because we demonstrated that miRNA degradation was abolished if arginines at R226 and R202 were mutated. Our study provides new insights into the molecular mechanism of JEV and reveals several amino acid sites that could be mutated for a JEV vaccine.
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Yi HC, You ZH, Huang DS, Guo ZH, Chan KCC, Li Y. Learning Representations to Predict Intermolecular Interactions on Large-Scale Heterogeneous Molecular Association Network. iScience 2020; 23:101261. [PMID: 32580123 PMCID: PMC7317230 DOI: 10.1016/j.isci.2020.101261] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/29/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Molecular components that are functionally interdependent in human cells constitute molecular association networks. Disease can be caused by disturbance of multiple molecular interactions. New biomolecular regulatory mechanisms can be revealed by discovering new biomolecular interactions. To this end, a heterogeneous molecular association network is formed by systematically integrating comprehensive associations between miRNAs, lncRNAs, circRNAs, mRNAs, proteins, drugs, microbes, and complex diseases. We propose a machine learning method for predicting intermolecular interactions, named MMI-Pred. More specifically, a network embedding model is developed to fully exploit the network behavior of biomolecules, and attribute features are also calculated. Then, these discriminative features are combined to train a random forest classifier to predict intermolecular interactions. MMI-Pred achieves an outstanding performance of 93.50% accuracy in hybrid associations prediction under 5-fold cross-validation. This work provides systematic landscape and machine learning method to model and infer complex associations between various biological components.
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Affiliation(s)
- Hai-Cheng Yi
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhu-Hong You
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China
| | - Zhen-Hao Guo
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Keith C C Chan
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
| | - Yangming Li
- College of Engineering Technology, Rochester Institute of Technology, Rochester, NY 14623, USA
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Zhang J, Kong X, Zhang Y, Sun W, Wang J, Chen M, Chen X. FDXR regulates TP73 tumor suppressor via IRP2 to modulate aging and tumor suppression. J Pathol 2020; 251:284-296. [PMID: 32304229 DOI: 10.1002/path.5451] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/27/2020] [Accepted: 04/03/2020] [Indexed: 11/10/2022]
Abstract
Ferredoxin reductase (FDXR) is a mitochondrial flavoprotein that initiates electron transport from NADPH to several cytochromes P450 via two electron carriers, ferredoxin 1 (FDX1) and FDX2. FDXR is the sole ferredoxin reductase in humans and plays a critical role in steroidogenesis and biosynthesis of heme and iron-sulfur clusters. However, much less is known about the role of FDXR in cancer. Here, we show that FDXR plays a role in tumorigenesis by modulating expression of the tumor suppressor p73. By using genetically modified mouse models, we recently showed that mice deficient in either Fdxr or Trp73 had a shorter lifespan and were prone to spontaneous tumors as compared with wild-type (WT) mice. Interestingly, compound Trp73 +/- ;Fdxr +/- mice lived longer and developed fewer tumors when compared with Fdxr +/- or Trp73 +/- mice. Moreover, we found that cellular senescence was increased in Trp73 +/- and Fdxr +/- mouse embryonic fibroblasts (MEFs), which was further increased in Trp73 +/- ;Fdxr +/- MEFs, as compared with that in WT MEFs. As FDXR is regulated by p73, we examined whether there was a feedback regulation between p73 and FDXR. Indeed, we found that Trp73 expression was decreased by loss of Fdxr in MEFs and that FDXR is required for p73 expression in multiple human cancer cell lines independent of p53. Mechanistically, we found that loss of FDXR, via FDX2, increased expression of iron-binding protein 2 (IRP2), which subsequently repressed TP73 mRNA stability. We also showed that TP73 transcript contained an iron response element in its 3'UTR, which was required for IRP2 to destabilize TP73 mRNA. Together, these data reveal a novel regulation of p73 by FDXR via IRP2 and that the FDXR-p73 axis plays a critical role in aging and tumor suppression. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, CA, USA
| | - Xiangmudong Kong
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, CA, USA
| | - Yanhong Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, CA, USA
| | - Wenqiang Sun
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, CA, USA
| | - Jian Wang
- School of Medicine, Wayne State University, Detroit, MI, USA
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, CA, USA
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Zhang Y, Feng X, Zhang J, Chen X. Iron Regulatory Protein 2 Exerts its Oncogenic Activities by Suppressing TAp63 Expression. Mol Cancer Res 2020; 18:1039-1049. [PMID: 32276991 DOI: 10.1158/1541-7786.mcr-19-1104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/19/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022]
Abstract
Iron regulatory protein 2 (IRP2) is a key regulator of iron homeostasis and is found to be altered in several types of human cancer. However, how IRP2 contributes to tumorigenesis remains to be elucidated. In this study, we sought to investigate the role of IRP2 in tumorigenesis and found that IRP2 promotes cell growth by repressing TAp63, a member of p53 tumor suppressor family. Specifically, we found that IRP2 overexpression decreased, whereas IRP2 deficiency increased, TAp63 expression. We also showed that the repression of TAp63 by IRP2 was independent of tumor suppressor p53. To uncover the molecular basis, we found that IRP2 stabilized TAp63 mRNA by binding to an iron response element in the 3'UTR of p63 mRNA. To determine the biological significance of this regulation, we showed that IRP2 facilitates cell proliferation, at least in part, via repressing TAp63 expression. Moreover, we found that IRP2 deficiency markedly alleviated cellular senescence in TAp63-deficient mouse embryo fibroblasts. Together, we have uncovered a novel regulation of TAp63 by IRP2 and our data suggest that IRP2 exerts its oncogenic activities at least in part by repressing TAp63 expression. IMPLICATIONS: We have revealed a novel regulation of TAp63 by IRP2 and our data suggest that IRP2 exerts its oncogenic activities, at least in part, by repressing TAp63 expression.
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Affiliation(s)
- Yanhong Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Xiuli Feng
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California.
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PABPN1, a Target of p63, Modulates Keratinocyte Differentiation through Regulation of p63α mRNA Translation. J Invest Dermatol 2020; 140:2166-2177.e6. [PMID: 32243883 DOI: 10.1016/j.jid.2020.03.942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 01/25/2023]
Abstract
p63 is expressed from two promoters and produces two N-terminal isoforms, TAp63 and ΔNp63. Alternative splicing creates three C-terminal isoforms p63α, p63β, and p63δ, whereas alternative polyadenylation (APA) in coding sequence creates two more C-terminal isoforms p63γ and p63ε. Although several transcription factors have been identified to differentially regulate the N-terminal p63 isoforms, it is unclear how the C-terminal p63 isoforms are regulated. Thus, we determined whether PABPN1, a key regulator of APA, may differentially regulate the C-terminal p63 isoforms. We found that PABPN1 deficiency increases p63γ mRNA through APA in coding sequence. We also found that PABPN1 is necessary for p63α translation by modulating the binding of translation initiation factors eIF4E and eIF4G to p63α mRNA. Moreover, we found that the p53 family, especially p63α, regulates PABPN1 transcription, suggesting that the mutual regulation between p63 and PABPN1 forms a feedback loop. Furthermore, we found that PABPN1 deficiency inhibits keratinocyte cell growth, which can be rescued by ectopic ΔNp63α. Finally, we found that PABPN1 controls the terminal differentiation of HaCaT keratinocytes by modulating ΔNp63α expression. Taken together, our findings suggest that PABPN1 is a key regulator of the C-terminal p63 isoforms through APA in coding sequence and mRNA translation and that the p63-PABPN1 loop modulates p63 activity and the APA landscape.
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Franchini DM, Lanvin O, Tosolini M, Patras de Campaigno E, Cammas A, Péricart S, Scarlata CM, Lebras M, Rossi C, Ligat L, Pont F, Arimondo PB, Laurent C, Ayyoub M, Despas F, Lapeyre-Mestre M, Millevoi S, Fournié JJ. Microtubule-Driven Stress Granule Dynamics Regulate Inhibitory Immune Checkpoint Expression in T Cells. Cell Rep 2020; 26:94-107.e7. [PMID: 30605689 DOI: 10.1016/j.celrep.2018.12.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/02/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022] Open
Abstract
Despite the clinical success of blocking inhibitory immune checkpoint receptors such as programmed cell death-1 (PD-1) in cancer, the mechanisms controlling the expression of these receptors have not been fully elucidated. Here, we identify a post-transcriptional mechanism regulating PD-1 expression in T cells. Upon activation, the PDCD1 mRNA and ribonucleoprotein complexes coalesce into stress granules that require microtubules and the kinesin 1 molecular motor to proceed to translation. Hence, PD-1 expression is highly sensitive to microtubule or stress granule inhibitors targeting this pathway. Evidence from healthy donors and cancer patients reveals a common regulation for the translation of CTLA4, LAG3, TIM3, TIGIT, and BTLA but not of the stimulatory co-receptors OX40, GITR, and 4-1BB mRNAs. In patients, disproportionality analysis of immune-related adverse events for currently used microtubule drugs unveils a significantly higher risk of autoimmunity. Our findings reveal a fundamental mechanism of immunoregulation with great importance in cancer immunotherapy.
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Affiliation(s)
- Don-Marc Franchini
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France.
| | - Olivia Lanvin
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Marie Tosolini
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Emilie Patras de Campaigno
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Anne Cammas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France
| | - Sarah Péricart
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Clara-Maria Scarlata
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Morgane Lebras
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France
| | - Cédric Rossi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Laetitia Ligat
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France
| | - Fréderic Pont
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France
| | - Paola B Arimondo
- Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Epigenetic Targeting of Cancer, FRE3600 CNRS, 31035 Toulouse, France
| | - Camille Laurent
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Maha Ayyoub
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Fabien Despas
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Maryse Lapeyre-Mestre
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Stefania Millevoi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France.
| | - Jean-Jacques Fournié
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France.
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