1
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Huang C, Aghaei-Zarch SM. From molecular pathogenesis to therapy: Unraveling non-coding RNAs/DNMT3A axis in human cancers. Biochem Pharmacol 2024; 222:116107. [PMID: 38438051 DOI: 10.1016/j.bcp.2024.116107] [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: 11/23/2023] [Revised: 02/03/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Cancer is a comprehensive classification encompassing more than 100 forms of malignancies that manifest in diverse tissues within the human body. Recent studies have provided evidence that aberrant epigenetic modifications are pivotal indicators of cancer. Epigenetics encapsulates DNA methyltransferases as a crucial class of modifiers. DNMTs, including DNMT3A, assume central roles in DNA methylation processes that orchestrate normal biological functions, such as gene transcription, predominantly in mammals. Typically, deviations in DNMT3A function engender distortions in factors that drive tumor growth and progression, thereby exacerbating the malignant phenotype of tumors. Consequently, such abnormalities pose significant challenges in cancer therapy because they impede treatment efficacy. Non-coding RNAs (ncRNAs) represent a group of RNA molecules that cannot encode functional proteins. Recent investigation attests to the crucial significance of regulatory ncRNAs in epigenetic regulation. Notably, recent reports have illuminated the complex interplay between ncRNA expression and epigenetic regulatory machinery, including DNMT3A, particularly in cancer. Recent findings have demonstrated that miRNAs, namely miR-770-5p, miR-101, and miR-145 exhibit the capability to target DNMT3A directly, and their aberration is implicated in diverse cellular abnormalities that predispose to cancer development. This review aims to articulate the interplay between DNMT3A and the ncRNAs, focusing on its impact on the development and progression of cancer, cancer therapy resistance, cancer stem cells, and prognosis. Importantly, the emergence of such reports that suggest a connection between DNMT3A and ncRNAs in several cancers indicates that this connecting axis offers a valuable target with significant therapeutic potential that might be exploited for cancer management.
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Affiliation(s)
- Chunjie Huang
- School of Medicine, Nantong University, Nantong 226001, China
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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2
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Mishra S, Stany B, Das A, Kanagavel D, Vijayan M. A Comprehensive Review of Membrane Transporters and MicroRNA Regulation in Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04135-2. [PMID: 38558361 DOI: 10.1007/s12035-024-04135-2] [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: 11/22/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Alzheimer's disease (AD) is a distressing neurodegenerative condition characterized by the accumulation of amyloid-beta (Aβ) plaques and tau tangles within the brain. The interconnectedness between membrane transporters (SLCs) and microRNAs (miRNAs) in AD pathogenesis has gained increasing attention. This review explores the localization, substrates, and functions of SLC transporters in the brain, emphasizing the roles of transporters for glutamate, glucose, nucleosides, and other essential compounds. The examination delves into the significance of SLCs in AD, their potential for drug development, and the intricate realm of miRNAs, encompassing their transcription, processing, functions, and regulation. MiRNAs have emerged as significant players in AD, including those associated with mitochondria and synapses. Furthermore, this review discusses the intriguing nexus of miRNAs targeting SLC transporters and their potential as therapeutic targets in AD. Finally, the review underscores the interaction between SLC transporters and miRNA regulation within the context of Alzheimer's disease, underscoring the need for further research in this area. This comprehensive review aims to shed light on the complex mechanisms underlying the causation of AD and provides insights into potential therapeutic approaches.
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Affiliation(s)
- Shatakshi Mishra
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - B Stany
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Anushka Das
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Deepankumar Kanagavel
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India.
| | - Murali Vijayan
- Department of Internal Medicine, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA.
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3
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Hynes C, Kakumani PK. Regulatory role of RNA-binding proteins in microRNA biogenesis. Front Mol Biosci 2024; 11:1374843. [PMID: 38567098 PMCID: PMC10985210 DOI: 10.3389/fmolb.2024.1374843] [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: 01/22/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that silence gene expression through their interaction with complementary sequences in the 3' untranslated regions (UTR) of target mRNAs. miRNAs undergo a series of steps during their processing and maturation, which are tightly regulated to fine-tune their abundance and ability to function in post-transcriptional gene silencing. miRNA biogenesis typically involves core catalytic proteins, namely, Drosha and Dicer, and several other RNA-binding proteins (RBPs) that recognize and interact with miRNA precursors and/or their intermediates, and mature miRNAs along with their interacting proteins. The series of RNA-protein and protein-protein interactions are critical to maintaining miRNA expression levels and their function, underlying a variety of cellular processes. Throughout this article, we review RBPs that play a role in miRNA biogenesis and focus on their association with components of the miRNA pathway with functional consequences in the processing and generation of mature miRNAs.
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Affiliation(s)
| | - Pavan Kumar Kakumani
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
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4
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Ishikawa T, Sugawara K, Zhang J, Funatsu T, Okabe K. Direct observation of cytoskeleton-dependent trafficking of miRNA visualized by the introduction of pre-miRNA. iScience 2024; 27:108811. [PMID: 38303695 PMCID: PMC10831896 DOI: 10.1016/j.isci.2024.108811] [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: 04/06/2023] [Revised: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
MicroRNA (miRNA) plays physiologically and pathologically important roles in post-transcriptional regulation. Although miRNA has been suggested to dynamically interact with cellular organelles, the dynamicity of intracellular miRNA behavior has remained unclear. Here, by introducing fluorescently labeled pre-miRNA into living cells, we improved the miRNA visualization method using exogenous miRNA precursors. Through the combination of our miRNA visualization method and single-molecule sensitive fluorescence microscopy, we quantitatively analyzed the process of miRNA maturation. Furthermore, single-particle tracking of fluorescent miRNA in cells revealed the directed movements of miRNA on cytoskeletal components (i.e., microtubules and actin filaments). Our results also suggest that cytoskeleton-dependent miRNA trafficking is associated with the interaction of miRNAs with the nucleus and the endoplasmic reticulum/Golgi apparatus. Our method should facilitate the elucidation of the mechanism and physiological significance of the subcellular localization and organelle interaction of miRNA.
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Affiliation(s)
- Toshinari Ishikawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Sugawara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junwei Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST, PRESTO, 4-8-1 Honcho, Kawaguchi, Saitama 332-0012, Japan
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5
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Gai C, Pomatto MAC, Deregibus MC, Dieci M, Piga A, Camussi G. Edible Plant-Derived Extracellular Vesicles for Oral mRNA Vaccine Delivery. Vaccines (Basel) 2024; 12:200. [PMID: 38400183 PMCID: PMC10893065 DOI: 10.3390/vaccines12020200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Nucleic acid delivery through extracellular vesicles (EVs) is a well-preserved evolutionary mechanism in all life kingdoms including eukaryotes, prokaryotes, and plants. EVs naturally allow horizontal transfer of native as well as exogenous functional mRNAs, which once incorporated in EVs are protected from enzymatic degradation. This observation has prompted researchers to investigate whether EVs from different sources, including plants, could be used for vaccine delivery. Several studies using human or bacterial EVs expressing mRNA or recombinant SARS-CoV-2 proteins showed induction of a humoral and cell mediated immune response. Moreover, EV-based vaccines presenting the natural configuration of viral antigens have demonstrated advantages in conferring long-lasting immunization and lower toxicity than synthetic nanoparticles. Edible plant-derived EVs were shown to be an alternative to human EVs for vaccine delivery, especially via oral administration. EVs obtained from orange juice (oEVs) loaded with SARS-CoV-2 mRNAs protected their cargo from enzymatic degradation, were stable at room temperature for one year, and were able to trigger a SARS-CoV-2 immune response in mice. Lyophilized oEVs containing the S1 mRNA administered to rats via gavage induced a specific humoral immune response with generation of blocking antibodies, including IgA and Th1 lymphocyte activation. In conclusion, mRNA-containing oEVs could be used for developing new oral vaccines due to optimal mucosal absorption, resistance to stress conditions, and ability to stimulate a humoral and cellular immune response.
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Affiliation(s)
- Chiara Gai
- EvoBiotech s.r.l., 10148 Torino, Italy; (C.G.); (M.A.C.P.); (M.D.); (A.P.)
- Department of Medical Sciences, University of Turin, 10126 Torino, Italy;
| | - Margherita Alba Carlotta Pomatto
- EvoBiotech s.r.l., 10148 Torino, Italy; (C.G.); (M.A.C.P.); (M.D.); (A.P.)
- Department of Medical Sciences, University of Turin, 10126 Torino, Italy;
| | | | - Marco Dieci
- EvoBiotech s.r.l., 10148 Torino, Italy; (C.G.); (M.A.C.P.); (M.D.); (A.P.)
| | - Alessandro Piga
- EvoBiotech s.r.l., 10148 Torino, Italy; (C.G.); (M.A.C.P.); (M.D.); (A.P.)
| | - Giovanni Camussi
- Department of Medical Sciences, University of Turin, 10126 Torino, Italy;
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Khan FA, Fang N, Zhang W, Ji S. The multifaceted role of Fragile X-Related Protein 1 (FXR1) in cellular processes: an updated review on cancer and clinical applications. Cell Death Dis 2024; 15:72. [PMID: 38238286 PMCID: PMC10796922 DOI: 10.1038/s41419-023-06413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
RNA-binding proteins (RBPs) modulate the expression level of several target RNAs (such as mRNAs) post-transcriptionally through interactions with unique binding sites in the 3'-untranslated region. There is mounting information that suggests RBP dysregulation plays a significant role in carcinogenesis. However, the function of FMR1 autosomal homolog 1(FXR1) in malignancies is just beginning to be unveiled. Due to the diversity of their RNA-binding domains and functional adaptability, FXR1 can regulate diverse transcript processing. Changes in FXR1 interaction with RNA networks have been linked to the emergence of cancer, although the theoretical framework defining these alterations in interaction is insufficient. Alteration in FXR1 expression or localization has been linked to the mRNAs of cancer suppressor genes, cancer-causing genes, and genes involved in genomic expression stability. In particular, FXR1-mediated gene regulation involves in several cellular phenomena related to cancer growth, metastasis, epithelial-mesenchymal transition, senescence, apoptosis, and angiogenesis. FXR1 dysregulation has been implicated in diverse cancer types, suggesting its diagnostic and therapeutic potential. However, the molecular mechanisms and biological effects of FXR1 regulation in cancer have yet to be understood. This review highlights the current knowledge of FXR1 expression and function in various cancer situations, emphasizing its functional variety and complexity. We further address the challenges and opportunities of targeting FXR1 for cancer diagnosis and treatment and propose future directions for FXR1 research in oncology. This work intends to provide an in-depth review of FXR1 as an emerging oncotarget with multiple roles and implications in cancer biology and therapy.
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Affiliation(s)
- Faiz Ali Khan
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Na Fang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Weijuan Zhang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Shaoping Ji
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Zhengzhou Shuqing Medical College, Zhengzhou, China.
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7
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Zhang X, Zhao Q, Wang T, Long Q, Sun Y, Jiao L, Gullerova M. DNA damage response, a double-edged sword for vascular aging. Ageing Res Rev 2023; 92:102137. [PMID: 38007046 DOI: 10.1016/j.arr.2023.102137] [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: 04/14/2023] [Revised: 10/03/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Vascular aging is a major risk factor for age-related cardiovascular diseases, which have high rates of morbidity and mortality. It is characterized by changes in the blood vessels, such as macroscopically increased vascular diameter and intima-medial thickness, chronic inflammation, vascular calcification, arterial stiffening, and atherosclerosis. DNA damage and the subsequent various DNA damage response (DDR) pathways are important causative factors of vascular aging. Deficient DDR, which may result in the accumulation of unrepaired damaged DNA or mutations, can lead to vascular aging. On the other hand, over-activation of some DDR proteins, such as poly (ADP ribose) polymerase (PARP) and ataxia telangiectasia mutated (ATM), also can enhance the process of vascular aging, suggesting that DDR can have both positive and negative effects on vascular aging. Despite the evidence reviewed in this paper, the role of DDR in vascular aging and potential therapeutic targets remain poorly understood and require further investigation.
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Affiliation(s)
- Xiao Zhang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qing Zhao
- M.D. Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Tao Wang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qilin Long
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Yixin Sun
- First Hospital, Peking University, Beijing, China
| | - Liqun Jiao
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China; Department of Interventional Neuroradiology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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Hussen BM, Saleem SJ, Abdullah SR, Mohamadtahr S, Hidayat HJ, Rasul MF, Taheri M, Kiani A. Current landscape of miRNAs and TGF-β signaling in lung cancer progression and therapeutic targets. Mol Cell Probes 2023; 72:101929. [PMID: 37683829 DOI: 10.1016/j.mcp.2023.101929] [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: 08/11/2023] [Revised: 08/27/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Lung cancer (LC) is the primary reason for cancer-associated fatalities globally. Due to both tumor-suppressing and tumor-promoting activities, the TGF-β family of growth factors is extremely essential to tumorigenesis. A non-coding single-stranded short RNA called microRNA (miRNA), which is made up of about 22 nt and is encoded by endogenous genes, can control normal and pathological pathways in various kinds of cancer, including LC. Recent research demonstrated that the TGF-β signaling directly can affect the synthesis of miRNAs through suppressor of mothers against decapentaplegic (SMAD)-dependent activity or other unidentified pathways, which could generate allostatic feedback as a result of TGF-β signaling stimulation and ultimately affect the destiny of cancer tissues. In this review, we emphasize the critical functions of miRNAs in lung cancer progression and, more critically, how they affect the TGF-β signaling pathway, and explore the role of both the TGF-β signaling pathway and miRNAs as potential therapeutic targets for improving the treatments of LC patients.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Department of Biomedical Sciences, Cihan University-Erbil, Erbil, Kurdistan Region, 44001, Iraq
| | - Safeen Jasim Saleem
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Snur Rasool Abdullah
- Medical Laboratory Science, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sayran Mohamadtahr
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Arda Kiani
- Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Lung Research and Developmental Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Goswami B, Nag S, Ray PS. Fates and functions of RNA-binding proteins under stress. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1825. [PMID: 38014833 DOI: 10.1002/wrna.1825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/03/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Exposure to stress activates a well-orchestrated set of changes in gene expression programs that allow the cell to cope with and adapt to the stress, or undergo programmed cell death. RNA-protein interactions, mediating all aspects of post-transcriptional regulation of gene expression, play crucial roles in cellular stress responses. RNA-binding proteins (RBPs), which interact with sequence/structural elements in RNAs to control the steps of RNA metabolism, have therefore emerged as central regulators of post-transcriptional responses to stress. Following exposure to a variety of stresses, the dynamic alterations in the RNA-protein interactome enable cells to respond to intracellular or extracellular perturbations by causing changes in mRNA splicing, polyadenylation, stability, translation, and localization. As RBPs play a central role in determining the cellular proteome both qualitatively and quantitatively, it has become increasingly evident that their abundance, availability, and functions are also highly regulated in response to stress. Exposure to stress initiates a series of signaling cascades that converge on post-translational modifications (PTMs) of RBPs, resulting in changes in their subcellular localization, association with stress granules, extracellular export, proteasomal degradation, and RNA-binding activities. These alterations in the fate and function of RBPs directly impact their post-transcriptional regulatory roles in cells under stress. Adopting the ubiquitous RBP HuR as a prototype, three scenarios illustrating the changes in nuclear-cytoplasmic localization, RNA-binding activity, export and degradation of HuR in response to inflammation, genotoxic stress, and heat shock depict the complex and interlinked regulatory mechanisms that control the fate and functions of RBPs under stress. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Binita Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
| | - Sharanya Nag
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
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Tan GZL, Leong SM, Jin Y, Kuick CH, Chee JJK, Low SZ, Ding LW, Cheng H, Lim D, Hue SSS. MicroRNA Landscape in Endometrial Carcinomas in an Asian population: Unraveling Subtype-Specific Signatures. Cancers (Basel) 2023; 15:5260. [PMID: 37958433 PMCID: PMC10648581 DOI: 10.3390/cancers15215260] [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: 09/23/2023] [Revised: 10/24/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
MicroRNAs (MiRNAs) are small, non-coding RNA molecules that function in RNA silencing and post-transcriptional regulation of gene expression. We analyzed the differential expression of miRNAs in 119 endometrial carcinomas, measuring their expression in histological subtypes, molecular subtypes, and tumors with CTNNB1 mutations. Tumors were subdivided into histological and molecular subtypes as defined by The Cancer Genome Atlas. The expression levels of 352 miRNAs were quantified using the PanoramiR panel. Mir-449a, mir-449b-5p, and mir-449c-5p were the top three miRNAs showing increased expression in both endometrioid and de-differentiated carcinomas but were not significantly increased in serous and clear cell carcinomas. The miRNAs with the most increased expression in serous and clear cell carcinomas were miR-9-3p and miR-375, respectively. We also identified 62 differentially expressed miRNAs among different molecular subtypes. Using sequential forward selection, we built subtype classification models for some molecular subtypes of endometrial carcinoma, comprising 5 miRNAs for MMR-deficient tumors, 10 miRNAs for p53-mutated tumors, and 3 miRNAs for CTNNB1-mutated tumors, with areas under curves of 0.75, 0.85, and 0.78, respectively. Our findings confirm the differential expression of miRNAs between various endometrial carcinoma subtypes and may have implications for the development of diagnostic and prognostic tools.
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Affiliation(s)
- Gideon Ze Lin Tan
- Department of Pathology, National University Hospital, Singapore 118177, Singapore; (G.Z.L.T.); (S.Z.L.); (D.L.)
| | - Sai Mun Leong
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (S.M.L.)
| | - Yu Jin
- MiRXES Pte Ltd., Singapore 618305, Singapore (H.C.)
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women’s and Children’s Hospital, Singapore 229899, Singapore
| | - Jeremy Joon Keat Chee
- Department of Pathology, National University Hospital, Singapore 118177, Singapore; (G.Z.L.T.); (S.Z.L.); (D.L.)
| | - San Zeng Low
- Department of Pathology, National University Hospital, Singapore 118177, Singapore; (G.Z.L.T.); (S.Z.L.); (D.L.)
| | - Ling-Wen Ding
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (S.M.L.)
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - He Cheng
- MiRXES Pte Ltd., Singapore 618305, Singapore (H.C.)
| | - Diana Lim
- Department of Pathology, National University Hospital, Singapore 118177, Singapore; (G.Z.L.T.); (S.Z.L.); (D.L.)
| | - Susan Swee-Shan Hue
- Department of Pathology, National University Hospital, Singapore 118177, Singapore; (G.Z.L.T.); (S.Z.L.); (D.L.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (S.M.L.)
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11
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Zhang L, Song W, Shi J, Chen Y. Circ_0084188 Regulates the progression of colorectal cancer through the miR-769-5p/KIF20A axis. Biochem Genet 2023; 61:1727-1744. [PMID: 36763221 DOI: 10.1007/s10528-023-10339-3] [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: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the major gastrointestinal malignancies threatening human health. More and more studies indicate that circular RNAs (circRNAs) are important regulatory factors of CRC, but the mechanism is still indistinct. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were used to detect the expression of circ_0084188, microRNA-769-5p (miR-769-5p), and kinesin family member 20A (KIF20A) in CRC tissues. Kaplan-Meier curve was used to analyze the relationship between circ_0084188 expression and the survival rate of CRC patients. Cell proliferation, viability, apoptosis, migration, and invasion were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, wound-healing, and transwell assays, respectively. The relationship between miR-769-5p and circ_0084188 or KIF20A was detected by a dual-luciferase reporter and RNA pull-down. The effect of circ_0084188 on tumor growth was verified by xenograft studies in vivo. RESULTS Circ_0084188 and KIF20A were upregulated and miR-769-5p was downregulated in CRC. Circ_0084188 knockdown repressed the proliferation, migration, and invasion of CRC cells, as well as enhanced apoptosis in vitro. Mechanistically, circ_0084188 targeted miR-769-5p, and the reduction of miR-769-5p reversed the effects of circ_0084188 knockdown on cell functional behaviors. KLF20A was a direct miR-769-5p target, and circ_0084188 acted as a sponge for miR-769-5p to regulate the KIF20A level. Moreover, miR-769-5p regulated the functional behaviors of CRC cells by targeting KIF20A. In addition, circ_0084188 knockdown confined the growth of xenograft tumors in vivo. CONCLUSION Circ_0084188 upregulated the expression of KIF20A to promote the tumorigenesis of CRC through miR-769-5p, providing a new therapeutic target for CRC.
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Affiliation(s)
- Licheng Zhang
- Department of Gastrointestinal and Anorectal Surgery, Tianjin Third Central Hospital, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
| | - Weiliang Song
- Department of Gastrointestinal and Anorectal Surgery, Tianjin Third Central Hospital, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China.
| | - Junzhong Shi
- Department of Gastrointestinal and Anorectal Surgery, Tianjin Third Central Hospital, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
| | - Yuzhuo Chen
- Department of Gastrointestinal and Anorectal Surgery, Tianjin Third Central Hospital, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
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12
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Xu J, Jiang Y, Sherrard R, Ikegami K, Conradt B. PUF-8, a C. elegans ortholog of the RNA-binding proteins PUM1 and PUM2, is required for robustness of the cell death fate. Development 2023; 150:dev201167. [PMID: 37747106 PMCID: PMC10565243 DOI: 10.1242/dev.201167] [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: 07/29/2022] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
During C. elegans development, 1090 somatic cells are generated, of which 959 survive and 131 die, many through apoptosis. We present evidence that PUF-8, a C. elegans ortholog of the mammalian RNA-binding proteins PUM1 and PUM2, is required for the robustness of this 'survival and death' pattern. We found that PUF-8 prevents the inappropriate death of cells that normally survive, and we present evidence that this anti-apoptotic activity of PUF-8 is dependent on the ability of PUF-8 to interact with ced-3 (a C. elegans ortholog of caspase) mRNA, thereby repressing the activity of the pro-apoptotic ced-3 gene. PUF-8 also promotes the death of cells that are programmed to die, and we propose that this pro-apoptotic activity of PUF-8 may depend on the ability of PUF-8 to repress the expression of the anti-apoptotic ced-9 gene (a C. elegans ortholog of Bcl2). Our results suggest that stochastic differences in the expression of genes within the apoptosis pathway can disrupt the highly reproducible and robust survival and death pattern during C. elegans development, and that PUF-8 acts at the post-transcriptional level to level out these differences, thereby ensuring proper cell number homeostasis.
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Affiliation(s)
- Jimei Xu
- Faculty of Biology, Center for Integrative Protein Sciences Munich (CIPSM), Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Yanwen Jiang
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Ryan Sherrard
- Faculty of Biology, Center for Integrative Protein Sciences Munich (CIPSM), Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
| | - Kyoko Ikegami
- Faculty of Biology, Center for Integrative Protein Sciences Munich (CIPSM), Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
| | - Barbara Conradt
- Faculty of Biology, Center for Integrative Protein Sciences Munich (CIPSM), Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
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13
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Chen W, Hu L, Lu X, Wang X, Zhao C, Guo C, Li X, Ding Y, Zhao H, Tong D, Wang L, Huang C. The RNA binding protein MEX3A promotes tumor progression of breast cancer by post-transcriptional regulation of IGFBP4. Breast Cancer Res Treat 2023; 201:353-366. [PMID: 37433992 PMCID: PMC10460732 DOI: 10.1007/s10549-023-07028-5] [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: 02/17/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023]
Abstract
PURPOSE Breast cancer (BC) is the most frequent malignant tumor in women worldwide with exceptionally high morbidity. The RNA-binding protein MEX3A plays a crucial role in genesis and progression of multiple cancers. We attempted to explore its clinicopathological and functional significance in BC in which MEX3A is expressed. METHODS The expression of MEX3A detected by RT-qPCR and correlated the results with clinicopathological variables in 53 BC patients. MEX3A and IGFBP4 profile data of BC patients were downloaded from TCGA and GEO database. Kaplan-Meier (KM) analysis was used to estimate the survival rate of BC patients. Western Blot, CCK-8, EdU, colony formation and flow cytometry were performed to investigate the role of MEX3A and IGFBP4 in BC cell proliferation, invasion and cell cycle in vitro. A subcutaneous tumor mouse model was constructed to analyze in vivo growth of BC cells after MEX3A knockdown. The interactions among MEX3A and IGFBP4 were measured by RNA pull-down and RNA immunoprecipitation. RESULTS The expression of MEX3A was upregulated in BC tissues compared to adjacent tissues and high expression of MEX3A was associated with poor prognosis. Subsequent in vitro studies demonstrated that MEX3A knockdown inhibited BC cells proliferation and migration, as well as xenograft tumor growth in vivo. The expression of IGFBP4 was significantly negatively correlated with MEX3A in BC tissues. Mechanistic investigation showed that MEX3A binds to IGFBP4 mRNA in BC cells, decreasing IGFBP4 mRNA levels, which further activated the PI3K/AKT and other downstream signaling pathways implicated cell cycle progression and cell migration. CONCLUSION Our results indicate that MEX3A plays a prominent oncogenic role in BC tumorigenesis and progression by targeting IGFBP4 mRNA and activating PI3K/AKT signaling, which can be used as a novel therapeutic target for BC.
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Affiliation(s)
- Wenhu Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, 710061, Shanxi, China
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, 310053, China
| | - Liqiang Hu
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, 310012, China
| | - Xuemei Lu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xiaofei Wang
- Biomedical Experimental Center of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Changan Zhao
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Chen Guo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, 710061, Shanxi, China
| | - Xiaoyan Li
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, 310053, China
| | - Yuqin Ding
- Department of Breast Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310005, China
| | - Hongguang Zhao
- Department of Thoracic Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310005, China
| | - Dongdong Tong
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, 710061, Shanxi, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Lifang Wang
- College of Innovation & Entrepreneurship, Hangzhou Medical College, No. 548 Binwen Road, Hangzhou, 310053, Zhejiang, China.
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, 710061, Shanxi, China.
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China.
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710061, China.
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14
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Ma S, Kotar A, Hall I, Grote S, Rouskin S, Keane SC. Structure of pre-miR-31 reveals an active role in Dicer-TRBP complex processing. Proc Natl Acad Sci U S A 2023; 120:e2300527120. [PMID: 37725636 PMCID: PMC10523476 DOI: 10.1073/pnas.2300527120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/01/2023] [Indexed: 09/21/2023] Open
Abstract
As an essential posttranscriptional regulator of gene expression, microRNA (miRNA) levels must be strictly maintained. The biogenesis of many miRNAs is mediated by trans-acting protein partners through a variety of mechanisms, including remodeling of the RNA structure. miR-31 functions as an oncogene in numerous cancers, and interestingly, its biogenesis is not known to be regulated by protein-binding partners. Therefore, the intrinsic structural properties of the precursor element of miR-31 (pre-miR-31) can provide a mechanism by which its biogenesis is regulated. We determined the solution structure of pre-miR-31 to investigate the role of distinct structural elements in regulating processing by the Dicer-TRBP complex. We found that the presence or absence of mismatches within the helical stem does not strongly influence Dicer-TRBP processing of the pre-miRNAs. However, both the apical loop size and structure at the Dicing site are key elements for discrimination by the Dicer-TRBP complex. Interestingly, our NMR-derived structure reveals the presence of a triplet of base pairs that link the Dicer cleavage site and the apical loop. Mutational analysis in this region suggests that the stability of the junction region strongly influences processing by the Dicer-TRBP complex. Our results enrich our understanding of the active role that RNA structure plays in regulating miRNA biogenesis, which has direct implications for the control of gene expression.
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Affiliation(s)
- Sicong Ma
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
| | - Anita Kotar
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
| | - Ian Hall
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Scott Grote
- Department of Microbiology, Harvard Medical School,Boston, MA02115
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School,Boston, MA02115
| | - Sarah C. Keane
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
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15
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Yin S, Liu H, Zhou Z, Xu X, Wang P, Chen W, Deng G, Wang H, Yu H, Gu L, Huo M, Li M, Zeng L, He Y, Zhang C. PUM1 Promotes Tumor Progression by Activating DEPTOR-Meditated Glycolysis in Gastric Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301190. [PMID: 37469018 PMCID: PMC10520643 DOI: 10.1002/advs.202301190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/05/2023] [Indexed: 07/21/2023]
Abstract
RNA-binding proteins (RBPs) play essential roles in tumorigenesis and progression, but their functions in gastric cancer (GC) remain largely elusive. Here, it is reported that Pumilio 1 (PUM1), an RBP, induces metabolic reprogramming through post-transcriptional regulation of DEP domain-containing mammalian target of rapamycin (mTOR)-interacting protein (DEPTOR) in GC. In clinical samples, elevated expression of PUM1 is associated with recurrence, metastasis, and poor survival. In vitro and in vivo experiments demonstrate that knockdown of PUM1 inhibits the proliferation and metastasis of GC cells. In addition, RNA-sequencing and bioinformatics analyses show that PUM1 is enriched in the glycolysis gene signature. Metabolomics studies confirm that PUM1 deficiency suppresses glycolytic metabolism. Mechanistically, PUM1 binds directly to DEPTOR mRNA pumilio response element to maintain the stability of the transcript and prevent DEPTOR degradation through post-transcriptional pathway. PUM1-mediated DEPTOR upregulation inhibits mTORC1 and alleviates the inhibitory feedback signal transmitted from mTORC1 to PI3K under normal conditions, thus activating the PI3K-Akt signal and glycolysis continuously. Collectively, these results reveal the critical epigenetic role of PUM1 in modulating DEPTOR-dependent GC progression. These conclusions support further clinical investigation of PUM1 inhibitors as a metabolic-targeting treatment strategy for GC.
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Affiliation(s)
- Songcheng Yin
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Huifang Liu
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
- Department of RadiotherapyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenan450000China
| | - Zhijun Zhou
- Department of MedicineThe University of Oklahoma Health Sciences CenterOklahoma CityOK 73104USA
| | - Xiaoyu Xu
- Department of Gynecology and ObstetricsThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Pengliang Wang
- Department of Gastrointestinal SurgerySun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouGuangdong510120China
| | - Wei Chen
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Guofei Deng
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Han Wang
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Hong Yu
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Liang Gu
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Mingyu Huo
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Min Li
- Department of MedicineThe University of Oklahoma Health Sciences CenterOklahoma CityOK 73104USA
| | - Leli Zeng
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Yulong He
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
- Department of Gastrointestinal SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdong510062China
| | - Changhua Zhang
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
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16
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Navickas A, Asgharian H, Winkler J, Fish L, Garcia K, Markett D, Dodel M, Culbertson B, Miglani S, Joshi T, Yin K, Nguyen P, Zhang S, Stevers N, Hwang HW, Mardakheh F, Goga A, Goodarzi H. An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus. Nat Cell Biol 2023; 25:892-903. [PMID: 37156909 PMCID: PMC10264242 DOI: 10.1038/s41556-023-01141-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/27/2023] [Indexed: 05/10/2023]
Abstract
Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis; however, its effects on cancer progression remain poorly understood. Here, to address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed dedicated regression-based methods to analyse ribosome profiling and alternative polyadenylation data, and identified heterogeneous nuclear ribonucleoprotein C (HNRNPC) as a translational controller of a specific mRNA regulon. We found that HNRNPC is downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3' untranslated region lengthening and, subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. In addition, the reduced expression of HNRNPC and its regulon is associated with the worse prognosis in breast cancer patient cohorts.
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Affiliation(s)
- Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Institut Curie, CNRS UMR3348, INSERM U1278, Orsay, France
| | - Hosseinali Asgharian
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Lisa Fish
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Daniel Markett
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Bruce Culbertson
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Sohit Miglani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Tanvi Joshi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Keyi Yin
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Phi Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Steven Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Nicholas Stevers
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Hun-Way Hwang
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Faraz Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andrei Goga
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
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17
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Horii Y, Matsuda S, Toyota C, Morinaga T, Nakaya T, Tsuchiya S, Ohmuraya M, Hironaka T, Yoshiki R, Kasai K, Yamauchi Y, Takizawa N, Nagasaka A, Tanaka A, Kosako H, Nakaya M. VGLL3 is a mechanosensitive protein that promotes cardiac fibrosis through liquid-liquid phase separation. Nat Commun 2023; 14:550. [PMID: 36754961 PMCID: PMC9908974 DOI: 10.1038/s41467-023-36189-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Myofibroblasts cause tissue fibrosis by producing extracellular matrix proteins, such as collagens. Humoral factors like TGF-β, and matrix stiffness are important for collagen production by myofibroblasts. However, the molecular mechanisms regulating their ability to produce collagen remain poorly characterised. Here, we show that vestigial-like family member 3 (VGLL3) is specifically expressed in myofibroblasts from mouse and human fibrotic hearts and promotes collagen production. Further, substrate stiffness triggers VGLL3 translocation into the nucleus through the integrin β1-Rho-actin pathway. In the nucleus, VGLL3 undergoes liquid-liquid phase separation via its low-complexity domain and is incorporated into non-paraspeckle NONO condensates containing EWS RNA-binding protein 1 (EWSR1). VGLL3 binds EWSR1 and suppresses miR-29b, which targets collagen mRNA. Consistently, cardiac fibrosis after myocardial infarction is significantly attenuated in Vgll3-deficient mice, with increased miR-29b expression. Overall, our results reveal an unrecognised VGLL3-mediated pathway that controls myofibroblasts' collagen production, representing a novel therapeutic target for tissue fibrosis.
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Affiliation(s)
- Yuma Horii
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shoichi Matsuda
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikashi Toyota
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takumi Morinaga
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeo Nakaya
- Department of Pathology, Jichi Medical University, Tochigi, Japan
| | - Soken Tsuchiya
- Department of Pharmaceutical Biochemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Masaki Ohmuraya
- Department of Genetics, Hyogo College of Medicine, Hyogo, Japan
| | - Takanori Hironaka
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryo Yoshiki
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kotaro Kasai
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuto Yamauchi
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Noburo Takizawa
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akiomi Nagasaka
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akira Tanaka
- Department of Pathology, Jichi Medical University, Tochigi, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Michio Nakaya
- Department of Disease Control, Kyushu University, Fukuoka, Japan. .,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan. .,AMED-PRIME, Japan Agency for Medical Research and Development, Tokyo, Japan.
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18
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Ma S, Kotar A, Grote S, Rouskin S, Keane SC. Structure of pre-miR-31 reveals an active role in Dicer processing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.519659. [PMID: 36711709 PMCID: PMC9881868 DOI: 10.1101/2023.01.03.519659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As an essential post-transcriptional regulator of gene expression, microRNA (miR) levels must be strictly maintained. The biogenesis of many, but not all, miRs is mediated by trans-acting protein partners through a variety of mechanisms, including remodeling of the RNA structure. miR-31 functions as an oncogene in numerous cancers and interestingly, its biogenesis is not known to be regulated by protein binding partners. Therefore, the intrinsic structural properties of pre-miR-31 can provide a mechanism by which its biogenesis is regulated. We determined the solution structure of the precursor element of miR-31 (pre-miR-31) to investigate the role of distinct structural elements in regulating Dicer processing. We found that the presence or absence of mismatches within the helical stem do not strongly influence Dicer processing of the pre-miR. However, both the apical loop size and structure at the Dicing site are key elements for discrimination by Dicer. Interestingly, our NMR-derived structure reveals the presence of a triplet of base pairs that link the Dicer cleavage site and the apical loop. Mutational analysis in this region suggests that the stability of the junction region strongly influence both Dicer binding and processing. Our results enrich our understanding of the active role that RNA structure plays in regulating Dicer processing which has direct implications for control of gene expression.
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Affiliation(s)
- Sicong Ma
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | - Anita Kotar
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | - Scott Grote
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah C. Keane
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
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19
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Circ_0044411 silencing protects infantile pneumonia from lipopolysaccharide-induced cell injury by sponging miR-141-3p to inhibit CCL16 expression. Int Immunopharmacol 2023; 114:109425. [PMID: 36700761 DOI: 10.1016/j.intimp.2022.109425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 10/21/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Circular RNA (circRNA) has been found to play an important role in the progression of many diseases, including infantile pneumonia. However, the role of circ_0044411 in infantile pneumonia progression is still unclear. METHODS MRC-5 cells were incubated with lipopolysaccharide (LPS) for 12 h to establish the in vitro cellular model for infantile pneumonia. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect the levels of circ_0044411, miR-141-3p (micoRNA-141-3p) and CCL16 (CC motif chemokine ligand 16). Cell viability and proliferation was assessed by 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT) assay and 5-ethynyl-2'-deoxyuridine (EdU) assay. The levels of inflammatory factors IL-1β, IL-6 and TNF-α were determined by enzyme-linked immunosorbent assay kits. Cell apoptosis and caspase-3 activity were detected by flow cytometry analysis and caspase-3 activity assay kit. The target interaction was confirmed by dual-luciferase reporter assay, RNA immunoprecipitation assay and RNA pull-down assay. RESULTS Circ_0044411 was highly repressed in the serum of infantile pneumonia patients and LPS-induced MRC-5 cells. Circ_0044411 could promote the cell viability and proliferation, inhibit inflammatory response and apoptosis in LPS-induced MRC-5 cells. Circ_0044411 could serve as a sponge of miR-141-3p, and miR-141-3p could reverse the function of circ_0044411 on LPS-induced MRC-5 cell injury. In addition, miR-141-3p could target CCL16, and miR-141-3p could protect MRC-5 cells from LPS-induced cell injury by targeting CCL16. Furthermore, circ_0044411 sponged miR-141-3p to positively regulate CCL16 expression. CONCLUSION Circ_0044411 knockdown promoted cell viability and proliferation, inhibited inflammatory response and apoptosis by regulating miR-141-3p/CCL16 axis, indicating that circ_0044411 might be a potential therapeutic target for IP.
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Cai X, Gao C, Lymbery AJ, Armstrong NJ, Ma L, Li C. The immune-related circRNA-miRNA-mRNA ceRNA regulatory network in the liver of turbot (Scophthalmus maximus L.) induced by Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108506. [PMID: 36574792 DOI: 10.1016/j.fsi.2022.108506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Recently, Vibrio anguillarum, a Gram-negative pathogenic bacterium, has been becoming a major constraint on the development of the turbot aquaculture industry because of its characteristics of worldwide distribution, broad host range and potentially devastating impacts. Although the functions of protein-coding mRNAs in the immune response against bacterial infection have been reported, as well as several non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs) and microRNAs (miRNAs), the relationships between mRNAs and ncRNAs in the immune system of turbot liver are still limited during bacterial infection. In present study, the comprehensive analyses of whole-transcriptome sequencing were conducted in turbot liver infected by V. anguillarum. The differential expression was analyzed in the data of circRNAs, miRNAs, and mRNAs. The interactions of miRNA-circRNA pairs and miRNA-mRNA pairs were predicted basing on the negative regulatory relationships between miRNAs and their target circRNAs\mRNAs. The circRNA-related ceRNA regulatory networks were constructed for the analyses of regulated mechanism in turbot immune system. Subsequently, the RT-qPCR was carried out to verify the results of sequencing. Finally, we identified 31 circRNAs, 53 miRNAs and 948 mRNAs with differential expression. Gene set enrichment analyses using Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that innate immunity was principally activated at the early stages of infection, while adaptive immunity was activated after 24 h. Finally, 65 circRNA-miRNA-mRNA pathways were constructed, based on the hypothesis of ceRNA regulatory networks. In conclusion, our findings provide new insights on the underlying immune response to bacterial infection and identify novel target genes for the prevention and control of disease in turbot.
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Affiliation(s)
- Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Alan J Lymbery
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| | - Le Ma
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Rosenblum SL, Garner AL. Optimization of RiPCA for the Live-Cell Detection of Pre-MicroRNA-Protein Interactions. Chembiochem 2022; 23:e202200508. [PMID: 36322053 PMCID: PMC9831681 DOI: 10.1002/cbic.202200508] [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: 08/31/2022] [Revised: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Advancements in methods for identifying RNA-protein interactions (RPIs) on a large scale has necessitated the development of assays for validation of these interactions, particularly in living cells. We previously reported the development of RiPCA (RNA interaction with protein-mediated complementation assay) to enable the cellular detection of the well-characterized interaction between the pre-microRNA, pre-let-7, and its RNA-binding protein (RBP) partner Lin28. In this study, the applicability of RiPCA for the detection of putative pre-miRNA-protein interactions was explored using an improved RiPCA protocol, termed RiPCA 2.0. RiPCA 2.0 was adapted to detect the sequence specificity of the RBPs hnRNP A1, Msi1, and Msi2 for reported pre-microRNA binding partners. Additionally, the ability of RiPCA 2.0 to detect site-specific binding was explored. Collectively, this work highlights the versatility of RiPCA 2.0 in detecting cellular RPIs.
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Affiliation(s)
- Sydney L. Rosenblum
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109 (USA)
| | - Amanda L. Garner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (USA)
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22
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2'-5' oligoadenylate synthetase‑like 1 (OASL1) protects against atherosclerosis by maintaining endothelial nitric oxide synthase mRNA stability. Nat Commun 2022; 13:6647. [PMID: 36333342 PMCID: PMC9636244 DOI: 10.1038/s41467-022-34433-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Endothelial nitric oxide synthase (eNOS) decreases following inflammatory stimulation. As a master regulator of endothelial homeostasis, maintaining optimal eNOS levels is important during cardiovascular events. However, little is known regarding the mechanism of eNOS protection. In this study, we demonstrate a regulatory role for endothelial expression of 2'-5' oligoadenylate synthetase-like 1 (OASL1) in maintaining eNOS mRNA stability during athero-prone conditions and consider its clinical implications. A lack of endothelial Oasl1 accelerated plaque progression, which was preceded by endothelial dysfunction, elevated vascular inflammation, and decreased NO bioavailability following impaired eNOS expression. Mechanistically, knockdown of PI3K/Akt signaling-dependent OASL expression increased Erk1/2 and NF-κB activation and decreased NOS3 (gene name for eNOS) mRNA expression through upregulation of the negative regulatory, miR-584, whereas a miR-584 inhibitor rescued the effects of OASL knockdown. These results suggest that OASL1/OASL regulates endothelial biology by protecting NOS3 mRNA and targeting miR-584 represents a rational therapeutic strategy for eNOS maintenance in vascular disease.
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Nag S, Goswami B, Das Mandal S, Ray PS. Cooperation and competition by RNA-binding proteins in cancer. Semin Cancer Biol 2022; 86:286-297. [PMID: 35248729 DOI: 10.1016/j.semcancer.2022.02.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023]
Abstract
Post-transcriptional regulation of gene expression plays a major role in determining the cellular proteome in health and disease. Post-transcriptional control mechanisms are disrupted in many cancers, contributing to multiple processes of tumorigenesis. RNA-binding proteins (RBPs), the main post-transcriptional regulators, often show altered expression and activity in cancer cells. Dysregulation of RBPs contributes to many cancer phenotypes, functioning in complex regulatory networks with other cellular players such as non-coding RNAs, signaling mediators and transcription factors to alter the expression of oncogenes and tumor suppressor genes. RBPs often function combinatorially, based on their binding to target sequences/structures on shared mRNA targets, to regulate the expression of cancer-related genes. This gives rise to cooperativity and competition between RBPs in mRNA binding and resultant functional outcomes in post-transcriptional processes such as mRNA splicing, stability, export and translation. Cooperation and competition is also observed in the case of interaction of RBPs and microRNAs with mRNA targets. RNA structural change is a common mechanism mediating the cooperative/competitive interplay between RBPs and between RBPs and microRNAs. RNA modifications, leading to changes in RNA structure, add a new dimension to cooperative/competitive binding of RBPs to mRNAs, further expanding the RBP regulatory landscape. Therefore, cooperative/competitive interplay between RBPs is a major determinant of the RBP interactome and post-transcriptional regulation of gene expression in cancer cells.
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Affiliation(s)
- Sharanya Nag
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Binita Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sukhen Das Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India.
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24
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Lu X, Zhong J, Liu L, Zhang W, Zhao S, Chen L, Wei Y, Zhang H, Wu J, Chen W, Ge F. The function and regulatory mechanism of RNA-binding proteins in breast cancer and their future clinical treatment prospects. Front Oncol 2022; 12:929037. [PMID: 36052258 PMCID: PMC9424610 DOI: 10.3389/fonc.2022.929037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/25/2022] [Indexed: 11/19/2022] Open
Abstract
Breast cancer is the most common female malignancy, but the mechanisms regulating gene expression leading to its development are complex. In recent years, as epigenetic research has intensified, RNA-binding proteins (RBPs) have been identified as a class of posttranscriptional regulators that can participate in regulating gene expression through the regulation of RNA stabilization and degradation, intracellular localization, alternative splicing and alternative polyadenylation, and translational control. RBPs play an important role in the development of normal mammary glands and breast cancer. Functional inactivation or abnormal expression of RBPs may be closely associated with breast cancer development. In this review, we focus on the function and regulatory mechanisms of RBPs in breast cancer, as well as the advantages and challenges of RBPs as potential diagnostic and therapeutic targets in breast cancer, and discuss the potential of RBPs in clinical treatment.
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Affiliation(s)
- Xingjia Lu
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Jian Zhong
- Department of Reproductive Medicine, Affiliated Jinling Hospital, Nanjing Medical University, Nanjing, China
- Department of Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing, China
| | - Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Wenzhu Zhang
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Shengdi Zhao
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Liang Chen
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuxian Wei
- Department of Endocrine Breast Surgery, First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Zhang
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Jingxuan Wu
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Wenlin Chen
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Wenlin Chen, ; Fei Ge,
| | - Fei Ge
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Wenlin Chen, ; Fei Ge,
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Otsu H, Nambara S, Hu Q, Hisamatsu Y, Toshima T, Takeishi K, Yonemura Y, Masuda T, Oki E, Mimori K. Identification of serum microRNAs as potential diagnostic biomarkers for detecting precancerous lesions of gastric cancer. Ann Gastroenterol Surg 2022; 7:63-70. [PMID: 36643367 PMCID: PMC9831904 DOI: 10.1002/ags3.12610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/16/2022] [Indexed: 01/18/2023] Open
Abstract
Aim Gastric mucosal changes associated with chronic gastritis are known to be precancerous lesions of gastric cancer. We aimed to identify individuals with a high risk of gastric cancer by detection of microRNAs (miRNA) in the blood as biomarkers. Methods Of 1206 individuals screened, 144 who were positive for Helicobacter pylori (H. pylori) by the serum antibody test and who underwent endoscopy were the subjects of this study. For the gross assessment of mucosal inflammation, we applied the Kimura-Takemoto classification, in which normal mucosa was defined as grade 0, and atrophy was categorized as grade 1 (C-1 and C-2), grade 2 (C-3 and O-1), and grade 3 (O-2 and O-3). Serum samples were divided into two phases and used for miRNA microarray profiling. We compared the expression of miRNAs in grade 3 mucosa and other grades. Expression in gastric cancer was confirmed with TCGA data. Results miR-196b-3p was significantly upregulated, and miR-92a-2-5p was downregulated (P < .05 and q < 0.2). TCGA data showed a high expression of miR-196b-3p in gastric cancer cases (P < .001). Comparing grade 3 and the others, the area under the receiver operating characteristic curve using the detected miRNAs was as high as about 0.7. Furthermore, the combination of miRNAs resulted in higher accuracy. In terms of the significance of the combinatory mRNAs, the combination of three miRNAs (miR-196b-3p, miR-92a-2-5p, and miR-6791-3p) revealed high sensitivity and specificity, with the area under the curve exceeding 0.8. Conclusion The identified combinatory miRNAs may represent promising biomarkers of precancerous lesions in gastric cancer.
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Affiliation(s)
- Hajime Otsu
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Sho Nambara
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Qingjiang Hu
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | | | - Takeo Toshima
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Kazuki Takeishi
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yusuke Yonemura
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Takaaki Masuda
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Eiji Oki
- Department of Surgery and Science Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Koshi Mimori
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
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26
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Hai Y, Kawachi A, He X, Yoshimi A. Pathogenic Roles of RNA-Binding Proteins in Sarcomas. Cancers (Basel) 2022; 14:cancers14153812. [PMID: 35954475 PMCID: PMC9367343 DOI: 10.3390/cancers14153812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
RNA-binding proteins (RBPs) are proteins that physically and functionally bind to RNA to regulate the RNA metabolism such as alternative splicing, polyadenylation, transport, maintenance of stability, localization, and translation. There is accumulating evidence that dysregulated RBPs play an essential role in the pathogenesis of malignant tumors including a variety of types of sarcomas. On the other hand, prognosis of patients with sarcoma, especially with sarcoma in advanced stages, is very poor, and almost no effective standard treatment has been established for most of types of sarcomas so far, highlighting the urgent need for identifying novel therapeutic targets based on the deep understanding of pathogenesis. Therefore, defining the network of interactions between RBPs and disease-related RNA targets will contribute to a better understanding of sarcomagenesis and identification of a novel therapeutic target for sarcomas.
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Affiliation(s)
- Yu Hai
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Asuka Kawachi
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Xiaodong He
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Akihide Yoshimi
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Correspondence: ; Tel.: +81-3-3542-2511
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27
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Malhotra L, Singh A, Kaur P, Ethayathulla AS. Comprehensive omics studies of p53 mutants in human cancer. Brief Funct Genomics 2022; 22:97-108. [PMID: 35809339 DOI: 10.1093/bfgp/elac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/24/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
The p53 is the master regulator of the cell known for regulating a large array of cellular processes. Inactivation of p53 by missense mutations is one of the leading causes of cancer. Some of these mutations endow p53 with selective oncogenic functions to promote tumor progression. Due to the vast array of mutations found in p53, the experimental studies showing the role of different mutant p53 as an oncogene are also expanding. In this review, we discuss the oncogenic roles of different p53 mutants at the cellular level identified by multi-omics tools. We discuss some of the therapeutic studies to tackle p53 mutants and their downstream targets identified by omics. We also highlight the future prospective and scope of further studies of downstream p53 targets by omics.
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Affiliation(s)
- Lakshay Malhotra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Alankrita Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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28
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Kim YS, Tang PW, Welles JE, Pan W, Javed Z, Elhaw AT, Mythreye K, Kimball SR, Hempel N. HuR-dependent SOD2 protein synthesis is an early adaptation to anchorage-independence. Redox Biol 2022; 53:102329. [PMID: 35594792 PMCID: PMC9121325 DOI: 10.1016/j.redox.2022.102329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/18/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
During metastasis cancer cells must adapt to survive loss of anchorage and evade anoikis. An important pro-survival adaptation is the ability of metastatic tumor cells to increase their antioxidant capacity and restore cellular redox balance. Although much is known about the transcriptional regulation of antioxidant enzymes in response to stress, how cells acutely adapt to alter antioxidant enzyme levels is less well understood. Using ovarian cancer cells as a model, we demonstrate that an increase in mitochondrial superoxide dismutase SOD2 protein expression is a very early event initiated in response to detachment, an important step during metastasis that has been associated with increased oxidative stress. SOD2 protein synthesis is rapidly induced within 0.5-2 h of matrix detachment, and polyribosome profiling demonstrates an increase in the number of ribosomes bound to SOD2 mRNA, indicating an increase in SOD2 mRNA translation in response to anchorage-independence. Mechanistically, we find that anchorage-independence induces cytosolic accumulation of the RNA binding protein HuR/ELAVL1 and promotes HuR binding to SOD2 mRNA. Using HuR siRNA-mediated knockdown, we show that the presence of HuR is necessary for the increase in SOD2 mRNA association with the heavy polyribosome fraction and consequent nascent SOD2 protein synthesis in anchorage-independence. Cellular detachment also activates the stress-response mitogen-activated kinase p38, which is necessary for HuR-SOD2 mRNA interactions and induction of SOD2 protein output. These findings illustrate a novel translational regulatory mechanism of SOD2 by which ovarian cancer cells rapidly increase their mitochondrial antioxidant capacity as an acute stress response to anchorage-independence.
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Affiliation(s)
- Yeon Soo Kim
- Department of Pharmacology, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Priscilla W Tang
- Department of Pharmacology, College of Medicine, Pennsylvania State University, Hershey, PA, USA; Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh, PA, USA
| | - Jaclyn E Welles
- Department of Cellular and Molecular Physiology, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Weihua Pan
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh, PA, USA
| | - Zaineb Javed
- Department of Pharmacology, College of Medicine, Pennsylvania State University, Hershey, PA, USA; Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh, PA, USA
| | - Amal Taher Elhaw
- Department of Pharmacology, College of Medicine, Pennsylvania State University, Hershey, PA, USA; Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh, PA, USA
| | - Karthikeyan Mythreye
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Scot R Kimball
- Department of Cellular and Molecular Physiology, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Nadine Hempel
- Department of Pharmacology, College of Medicine, Pennsylvania State University, Hershey, PA, USA; Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh, PA, USA.
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29
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Dogan S, Spahiu E, Cilic A. Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs. Genes (Basel) 2022; 13:genes13071152. [PMID: 35885935 PMCID: PMC9316571 DOI: 10.3390/genes13071152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that function in post-transcriptional gene silencing and mRNA regulation. Although the number of nucleotides of miRNAs ranges from 17 to 27, they are mostly made up of 22 nucleotides. The expression of miRNAs changes significantly in cancer, causing protein alterations in cancer cells by preventing some genes from being translated into proteins. In this research, a structural analysis of 587 miRNAs that are differentially expressed in myeloid cancer was carried out. Length distribution studies revealed a mean and median of 22 nucleotides, with an average of 21.69 and a variance of 1.65. We performed nucleotide analysis for each position where Uracil was the most observed nucleotide and Adenine the least observed one with 27.8% and 22.6%, respectively. There was a higher frequency of Adenine at the beginning of the sequences when compared to Uracil, which was more frequent at the end of miRNA sequences. The purine content of each implicated miRNA was also assessed. A novel motif analysis script was written to detect the most frequent 3–7 nucleotide (3–7n) long motifs in the miRNA dataset. We detected CUG (42%) as the most frequent 3n motif, CUGC (15%) as a 4n motif, AGUGC (6%) as a 5n motif, AAGUGC (4%) as a 6n motif, and UUUAGAG (4%) as a 7n motif. Thus, in the second part of our study, we further characterized the motifs by analyzing whether these motifs align at certain consensus sequences in our miRNA dataset, whether certain motifs target the same genes, and whether these motifs are conserved within other species. This thorough structural study of miRNA sequences provides a novel strategy to study the implications of miRNAs in health and disease. A better understanding of miRNA structure is crucial to developing therapeutic settings.
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Affiliation(s)
- Senol Dogan
- Faculty of Physics and Earth Sciences, Peter Debye Institute, Leipzig University, 04103 Leipzig, Germany
- Correspondence:
| | - Emrulla Spahiu
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany;
| | - Anis Cilic
- Excellence Cluster Cardiopulmonary System, University of Giessen and Marburg Lung Center (UGMLC), Justus-Liebig-University, 35392 Giessen, Germany;
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Song J, Tian S, Yu L, Yang Q, Xing Y, Zhang C, Dai Q, Duan X. MD-MLI: Prediction of miRNA-lncRNA Interaction by Using Multiple Features and Hierarchical Deep Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1724-1733. [PMID: 33125334 DOI: 10.1109/tcbb.2020.3034922] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Long non-coding RNA(lncRNA) can interact with microRNA(miRNA) and play an important role in inhibiting or activating the expression of target genes and the occurrence and development of tumors. Accumulating studies focus on the prediction of miRNA-lncRNA interaction, and mostly are concerned with biological experiments and machine learning methods. These methods are found with long cycles, high costs, and requiring over much human intervention. In this paper, a data-driven hierarchical deep learning framework was proposed, which was composed of a capsule network, an independent recurrent neural network with attention mechanism and bi-directional long short-term memory network. This framework combines the advantages of different networks, uses multiple sequence-derived features of the original sequence and features of secondary structure to mine the dependency between features, and devotes to obtain better results. In the experiment, five-fold cross-validation was used to evaluate the performance of the model, and the zea mays data set was compared with the different model to obtain better classification effect. In addition, sorghum, brachypodium distachyon and bryophyte data sets were used to test the model, and the accuracy reached 0.9850, 0.9859 and 0.9777, respectively, which verified the model's good generalization ability.
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AGO-RBP crosstalk on target mRNAs: Implications in miRNA-guided gene silencing and cancer. Transl Oncol 2022; 21:101434. [PMID: 35477066 PMCID: PMC9136600 DOI: 10.1016/j.tranon.2022.101434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) and RNA-binding proteins (RBPs) are important regulators of mRNA translation and stability in eukaryotes. While miRNAs can only bind their target mRNAs in association with Argonaute proteins (AGOs), RBPs directly bind their targets either as single entities or in complex with other RBPs to control mRNA metabolism. miRNA binding in 3' untranslated regions (3' UTRs) of mRNAs facilitates an intricate network of interactions between miRNA-AGO and RBPs, thus determining the fate of overlapping targets. Here, we review the current knowledge on the interplay between miRNA-AGO and multiple RBPs in different cellular contexts, the rules underlying their synergism and antagonism on target mRNAs, as well as highlight the implications of these regulatory modules in cancer initiation and progression.
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Taghavi A, Yildirim I. Computational Investigation of Bending Properties of RNA AUUCU, CCUG, CAG, and CUG Repeat Expansions Associated With Neuromuscular Disorders. Front Mol Biosci 2022; 9:830161. [PMID: 35480881 PMCID: PMC9037632 DOI: 10.3389/fmolb.2022.830161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/09/2022] [Indexed: 12/26/2022] Open
Abstract
Expansions of RNA AUUCU, CCUG, CAG, and CUG repeats cause spinocerebellar ataxia type 10, myotonic dystrophy type 2, Huntington’s disease, and myotonic dystrophy type 1, respectively. By performing extensive molecular dynamic simulations, we investigated the bending propensities and conformational landscapes adopted by 3×3, 2×2, and 1×1 internal loops observed in RNA AUUCU, CCUG, CAG, and CUG repeat expansions using model systems having biologically relevant repeat sizes. We show that the conformational variability experienced by these loops is more complex than previous reports where a variety of unconventional hydrogen bonds are formed. At the global scale, strong bending propensity was observed in r(AUUCU)10, r(CCUG)15, r(CAG)20, and r(CUG)20, and, to a lesser extent, in r(AUUCU)4, r(CCUG)10, r(CAG)10, and r(CUG)10. Furthermore, RNA CAG repeats exhibit a tendency toward bent states with more than 50% of observed conformations having bending angles greater than 50°, while RNA CUG repeats display relatively linear-like conformations with extremely bent conformations accounting for less than 25% of the observed structures. Conformations experienced by RNA AUUCU repeats are a combination of strongly bent and kinked structures. The bent states in RNA CCUG repeats mostly fall into the moderately bent category with a marginal ensemble experiencing extreme bending. The general pattern observed in all the bent structures indicates the collapse of the major groove width as the mechanical trigger for bending, which is caused by alteration of base pair step parameters at multiple locations along the RNA due to local distortions at the loop sites. Overextension is also observed in all the RNA repeats that is attributed to widening of the major groove width as well as undertwisting phenomenon. This information and the rich structural repository could be applied for structure based small molecule design targeting disease-causing RNAs. The bending propensities of these constructs, at the global level, could also have implications on how expanded RNA repeats interact with proteins.
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Affiliation(s)
- Amirhossein Taghavi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, United States
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, United States
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, United States
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, United States
- *Correspondence: Ilyas Yildirim,
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RBM24 in the Post-Transcriptional Regulation of Cancer Progression: Anti-Tumor or Pro-Tumor Activity? Cancers (Basel) 2022; 14:cancers14071843. [PMID: 35406615 PMCID: PMC8997389 DOI: 10.3390/cancers14071843] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary RBM24 is a highly conserved RNA-binding protein that plays critical roles in the post-transcriptional regulation of gene expression for initiating cell differentiation during embryonic development and for maintaining tissue homeostasis in adult life. Evidence is now accumulating that it is frequently dysregulated across human cancers. Importantly, RBM24 may act as a tumor suppressor or as an oncogene in a context- or background-dependent manner. Its activity can be regulated by protein–protein interactions and post-translational modifications, making it a potential therapeutic target for cancer treatment. However, molecular mechanisms underlying its function in tumor growth and metastasis remain elusive. Further investigation will be necessary to better understand how its post-transcriptional regulatory activity is controlled and how it is implicated in tumor progression. This review provides a comprehensive analysis of recent findings on the implication of RBM24 in cancer and proposes future research directions to delve more deeply into the mechanisms underlying its tumor-suppressive function or oncogenic activity. Abstract RNA-binding proteins are critical post-transcriptional regulators of gene expression. They are implicated in a wide range of physiological and pathological processes by modulating nearly every aspect of RNA metabolisms. Alterations in their expression and function disrupt tissue homeostasis and lead to the occurrence of various cancers. RBM24 is a highly conserved protein that binds to a large spectrum of target mRNAs and regulates many post-transcriptional events ranging from pre-mRNA splicing to mRNA stability, polyadenylation and translation. Studies using different animal models indicate that it plays an essential role in promoting cellular differentiation during organogenesis and tissue regeneration. Evidence is also accumulating that its dysregulation frequently occurs across human cancers. In several tissues, RBM24 clearly functions as a tumor suppressor, which is consistent with its inhibitory potential on cell proliferation. However, upregulation of RBM24 in other cancers appears to promote tumor growth. There is a possibility that RBM24 displays both anti-tumor and pro-tumor activities, which may be regulated in part through differential interactions with its protein partners and by its post-translational modifications. This makes it a potential biomarker for diagnosis and prognosis, as well as a therapeutic target for cancer treatment. The challenge remains to determine the post-transcriptional mechanisms by which RBM24 modulates gene expression and tumor progression in a context- or background-dependent manner. This review discusses recent findings on the potential function of RBM24 in tumorigenesis and provides future directions for better understanding its regulatory role in cancer cells.
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Silencing of Ago-2 Interacting Protein SERBP1 Relieves KCC2 Repression by miR-92 in Neurons. Cells 2022; 11:cells11061052. [PMID: 35326503 PMCID: PMC8947033 DOI: 10.3390/cells11061052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play important roles in modulating miRNA-mediated mRNA target repression. Argonaute2 (Ago2) is an essential component of the RNA-induced silencing complex (RISC) that plays a central role in silencing mechanisms via small non-coding RNA molecules known as siRNAs and miRNAs. Small RNAs loaded into Argonaute proteins catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and mRNA target destabilization. In previous studies we have shown that KCC2, a neuronal Cl (−) extruding K (+) Cl (−) co-transporter 2, is regulated by miR-92 in neuronal cells. Searching for Ago2 partners by immunoprecipitation and LC-MS/MS analysis, we isolated among other proteins the Serpine mRNA binding protein 1 (SERBP1) from SH-SY5Y neuroblastoma cells. Exploring the role of SERBP1 in miRNA-mediated gene silencing in SH-SY5Y cells and primary hippocampal neurons, we demonstrated that SERBP1 silencing regulates KCC2 expression through the 3′ untranslated region (UTR). In addition, we found that SERBP1 as well as Ago2/miR-92 complex bind to KCC2 3′UTR. Finally, we demonstrated the attenuation of miR-92-mediated repression of KCC2 3′UTR by SERBP1 silencing. These findings advance our knowledge regarding the miR-92-mediated modulation of KCC2 translation in neuronal cells and highlight SERBP1 as a key component of this gene regulation.
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Jungers CF, Djuranovic S. Modulation of miRISC-Mediated Gene Silencing in Eukaryotes. Front Mol Biosci 2022; 9:832916. [PMID: 35237661 PMCID: PMC8882679 DOI: 10.3389/fmolb.2022.832916] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression is regulated at multiple levels in eukaryotic cells. Regulation at the post-transcriptional level is modulated by various trans-acting factors that bind to specific sequences in the messenger RNA (mRNA). The binding of different trans factors influences various aspects of the mRNA such as degradation rate, translation efficiency, splicing, localization, etc. MicroRNAs (miRNAs) are short endogenous ncRNAs that combine with the Argonaute to form the microRNA-induced silencing complex (miRISC), which uses base-pair complementation to silence the target transcript. RNA-binding proteins (RBPs) contribute to post-transcriptional control by influencing the mRNA stability and translation upon binding to cis-elements within the mRNA transcript. RBPs have been shown to impact gene expression through influencing the miRISC biogenesis, composition, or miRISC-mRNA target interaction. While there is clear evidence that those interactions between RBPs, miRNAs, miRISC and target mRNAs influence the efficiency of miRISC-mediated gene silencing, the exact mechanism for most of them remains unclear. This review summarizes our current knowledge on gene expression regulation through interactions of miRNAs and RBPs.
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Cui F, Li S, Zhang Z, Sui M, Cao C, El-Latif Hesham A, Zou Q. DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins. Comput Struct Biotechnol J 2022; 20:2020-2028. [PMID: 35521556 PMCID: PMC9065708 DOI: 10.1016/j.csbj.2022.04.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022] Open
Abstract
Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play vital roles in gene expression. Accurate identification of these proteins is crucial. However, there are two existing challenges: one is the problem of ignoring DNA- and RNA-binding proteins (DRBPs), and the other is a cross-predicting problem referring to DBP predictors predicting DBPs as RBPs, and vice versa. In this study, we proposed a computational predictor, called DeepMC-iNABP, with the goal of solving these difficulties by utilizing a multiclass classification strategy and deep learning approaches. DBPs, RBPs, DRBPs and non-NABPs as separate classes of data were used for training the DeepMC-iNABP model. The results on test data collected in this study and two independent test datasets showed that DeepMC-iNABP has a strong advantage in identifying the DRBPs and has the ability to alleviate the cross-prediction problem to a certain extent. The web-server of DeepMC-iNABP is freely available at http://www.deepmc-inabp.net/. The datasets used in this research can also be downloaded from the website.
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Affiliation(s)
- Feifei Cui
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China
| | - Shuang Li
- Beidahuang Industry Group General Hospital, Harbin 150001, China
| | - Zilong Zhang
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China
| | - Miaomiao Sui
- Graduate School Agricultural and Life Science, The University of Tokyo, Tokyo 1138657, Japan
| | - Chen Cao
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Abd El-Latif Hesham
- Genetics Department, Faculty of Agriculture, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China
- Corresponding author at: Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China.
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Bioinformatic Analysis Identified Potentially Prognostic Long Noncoding RNAs and MicroRNAs for Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6683136. [PMID: 34926687 PMCID: PMC8683174 DOI: 10.1155/2021/6683136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 07/24/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022]
Abstract
Gastric cancer (GC) is the fifth most common malignant tumor in the world. The present study was performed to discover the potential diagnostic and therapeutic long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) of GC. Data used in this study to identify differentially expressed lncRNAs (DElncRNAs) and miRNAs (DEmiRNAs) were obtained from 187 GC tissues and 32 adjacent nontumor tissues. The total clinical data on GC included 187 cases. The above data were from the TCGA database. RStudio/Bioconductor software was used to conduct univariate analysis, the least absolute shrinkage and selection operator (LASSO) Cox, and multivariate Cox proportional risk regression for the DElncRNAs and DEmiRNAs. Clinical information was analyzed through univariate and multivariate Cox analysis. Results: five lncRNAs (AC007785.3, AC079385.3, LINC00392, LINC01729, and U95743.1) and two miRNAs (hsa-miR-3174, hsa-miR-605) were proven to be independent prognostic indicators of GC. Results of the Kaplan-Meier survival analysis showed that AC007785.3, AC079385.3, LINC01729, miR-3174, and miR-605 were significantly correlated with OS of GC. The target genes of AC079385.3, miR-3174, and miR-605 were obtained and clustered mainly on MAPK and cGMP-PKG signaling pathways. The clinical data showed that age and clinicopathologic stage were correlated with the prognosis of GC. Furthermore, AC007785.3 was associated with metastasis of GC, and miR-3174 was associated with the primary tumor condition of GC. We identified three lncRNAs (AC007785.3, AC079385.3, LINC01729), two miRNAs (miR-3174, miR-605), and clinical factors related to the pathogenesis and prognosis of GC. Our predicted results provide a possible entry point for the study of prognostic markers for GC.
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Sun W, Sun L, Sun X, Ma S. Long non-coding RNA SNHG7 upregulates FGF9 to alleviate oxygen and glucose deprivation-induced neuron cell injury in a miR-134-5p-dependent manner. Metab Brain Dis 2021; 36:2483-2494. [PMID: 34661812 DOI: 10.1007/s11011-021-00852-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/28/2021] [Indexed: 11/28/2022]
Abstract
Long non-coding RNA small nucleolar RNA host gene 7 (SNHG7) was reported to regulate the pathogenesis of ischemic stroke. The study aimed to disclose SNHG7 role in oxygen and glucose deprivation (OGD)-induced Neuro-2a (N2a) cell disorders. An OGD injury cell model was established using N2a cells. The expression of SNHG7, microRNA-134-5p (miR-134-5p) and fibroblast growth factor 9 (FGF9) was determined by quantitative real-time polymerase chain reaction. Protein expression was detected by western blot. Cell viability and Lactate Dehydrogenase (LDH) leakage were determined by cell counting kit-8 and LDH activity detection assays. Oxidative stress was investigated by Superoxide Dismutase and Catalase activity assays as well as Malondialdehyde and Reactive Oxygen Species detection kits. Cell apoptosis and caspase-3 activity were severally demonstrated by flow cytometry and caspase-3 activity assays. The interaction between miR-134-5p and SNHG7 or FGF9 was predicted by online databases, and identified by mechanism assays. OGD treatment decreased SNHG7 and FGF9 expression, but increased miR-134-5p expression. OGD treatment repressed cell viability, promoted LDH leakage and induced oxidative stress and apoptosis in N2a cells, which was rescued by SNHG7 overexpression. SNHG7 acted as a sponge for miR-134-5p, and regulated OGD-triggered cell damage by associating with miR-134-5p. Additionally, miR-134-5p depletion protected N2a cells from OGD-induced injury by targeting FGF9. Ectopic SNHG7 expression protected against OGD-induced neuronal cell injury by inducing FGF9 through sponging miR-134-5p, providing a novel therapeutic target for ischemic stroke.
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Affiliation(s)
- Wei Sun
- Department of Internal Medicine-Neurology, Dalian Third People's Hospital Affiliated to Dalian Medical University, Dalian City, Liaoning Province, China
| | - Lu Sun
- Department of Cardiac Function Examination, Dalian Third People's Hospital Affiliated to Dalian Medical University, Dalian City, Liaoning Province, China
| | - Xiaopeng Sun
- Department of Internal Medicine-Neurology, Dalian Municipal Central Hospital Affiliated to Dalian Medical University, No.826 Southwest Road, Shahekou District, Dalian City, 116021, Liaoning Province, China
| | - Shubei Ma
- Department of Internal Medicine-Neurology, Dalian Municipal Central Hospital Affiliated to Dalian Medical University, No.826 Southwest Road, Shahekou District, Dalian City, 116021, Liaoning Province, China.
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Li D, Zhang Z, Xia C, Niu C, Zhou W. Non-Coding RNAs in Glioma Microenvironment and Angiogenesis. Front Mol Neurosci 2021; 14:763610. [PMID: 34803608 PMCID: PMC8595242 DOI: 10.3389/fnmol.2021.763610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
Glioma, especially glioblastoma, is the most common and lethal brain tumor. In line with the complicated vascularization processes and the strong intratumoral heterogeneity, tumor-associated blood vessels in glioma are regulated by multiple types of cells through a variety of molecular mechanisms. Components of the tumor microenvironment, including tumor cells and tumor-associated stromata, produce various types of molecular mediators to regulate glioma angiogenesis. As critical regulatory molecules, non-coding RNAs (ncRNAs) inside cells or secreted to the tumor microenvironment play essential roles in glioma angiogenesis. In this review, we briefly summarize recent studies about the production, delivery, and functions of ncRNAs in the tumor microenvironment, as well as the molecular mechanisms underlying the regulation of angiogenesis by ncRNAs. We also discuss the ncRNA-based therapeutic strategies in the anti-angiogenic therapy for glioma treatment.
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Affiliation(s)
- Dongxue Li
- Intelligent Pathology Institute, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhe Zhang
- Basic Medical College, Qingdao University, Qingdao, China
| | - Chengyu Xia
- Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chaoshi Niu
- Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wenchao Zhou
- Intelligent Pathology Institute, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Pathology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Liu S, Medina-Perez P, Ha-Thi MC, Wieland A, Stecklum M, Hoffmann J, Tchernitsa O, Sers C, Schäfer R. Rapid testing of candidate oncogenes and tumour suppressor genes in signal transduction and neoplastic transformation. Adv Biol Regul 2021; 83:100841. [PMID: 34866037 DOI: 10.1016/j.jbior.2021.100841] [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: 11/05/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/18/2022]
Abstract
The COSMIC database (version 94) lists 576 genes in the Cancer Gene Census which have a defined function as drivers of malignancy (oncogenes) or as tumour suppressors (Tier 1). In addition, there are 147 genes with similar functions, but which are less well characterised (Tier 2). Furthermore, next-generation sequencing projects in the context of precision oncology activities are constantly discovering new ones. Since cancer genes differ from their wild-type precursors in numerous molecular and biochemical properties and exert significant differential effects on downstream processes, simple assays that can uncover oncogenic or anti-oncogenic functionality are desirable and may precede more sophisticated analyses. We describe simple functional assays for PTPN11 (protein-tyrosine phosphatase, non-receptor-type 11)/SHP2 mutants, which are typically found in RASopathies and exhibit potential oncogenic activity. We have also designed a functional test for lysyl oxidase (LOX), a prototypical class II tumour suppressor gene whose loss of function may contribute to neoplastic transformation by RAS oncogenes. Moreover, we applied this test to analyse three co-regulated, RAS-responsive genes for transformation-suppressive activity. The integration of these tests into systems biology studies will contribute to a better understanding of cellular networks in cancer.
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Affiliation(s)
- Sha Liu
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Paula Medina-Perez
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Minh-Cam Ha-Thi
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Anja Wieland
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Maria Stecklum
- Experimental Pharmacology and Oncology GmbH, Robert-Rössle-Str. 10, D-13125, Berlin-Buch, Germany
| | - Jens Hoffmann
- Experimental Pharmacology and Oncology GmbH, Robert-Rössle-Str. 10, D-13125, Berlin-Buch, Germany
| | - Oleg Tchernitsa
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Christine Sers
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Reinhold Schäfer
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany; Charité Comprehensive Cancer Center Berlin, Germany.
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41
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Huang H, Li L, Wen K. Interactions between long non‑coding RNAs and RNA‑binding proteins in cancer (Review). Oncol Rep 2021; 46:256. [PMID: 34676873 PMCID: PMC8548813 DOI: 10.3892/or.2021.8207] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) fulfill important roles in the majority of cellular processes. Previous studies have demonstrated that lncRNAs are involved in the pathogenesis of various diseases, including cancer. However, to date, the functions of only a small number of the known lncRNAs have been well-documented. lncRNAs comprise a class of multifunctional non-coding transcripts that are able to interact with different types of biomolecules. Interactions between lncRNAs and RNA-binding proteins (RBPs) provide an important mechanism through which lncRNAs exert their regulatory functions, mainly through findings on ‘generalized RBPs’. Regulatory effects on lncRNAs mediated by RBPs have also been explored. Taking account of the research that has been completed to date, the continued and in-depth study of the bidirectional interactions between lncRNAs and RBPs will prove to be of major importance for understanding the pathogenesis of cancer and for developing effective therapies. The present review aims to explore the interactions between lncRNAs and RBPs that have been investigated in cancer, taking into consideration several different aspects, including the regulation of expression, subcellular localization and the mediation of diverse functions.
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Affiliation(s)
- Handong Huang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Lu Li
- Department of Ophthalmology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Kunming Wen
- Department of Gastrointestinal Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
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Li S, Zhang L, Li S, Zhao H, Chen Y. Curcumin suppresses the progression of gastric cancer by regulating circ_0056618/miR-194-5p axis. Open Life Sci 2021; 16:937-949. [PMID: 34553074 PMCID: PMC8422978 DOI: 10.1515/biol-2021-0092] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 07/06/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Curcumin has been demonstrated to be an anti-tumor agent in many types of cancers, including gastric cancer (GC). However, the molecular mechanisms by which curcumin performs its anti-tumor effects remain elusive. circ_0056618 and miR-194-5p are reported to be involved in GC progression, but their relationships with curcumin are unclear. In this study, circ_0056618 was elevated, and miR-194-5p was reduced in GC tissues and cells. Curcumin treatment led to a decrease in circ_0056618 level in GC cells. Overexpression of circ_0056618 promoted cell proliferation, migration, and invasion and suppressed cell cycle arrest and apoptosis in curcumin-treated GC cells. Moreover, miR-194-5p was identified as the target of circ_0056618, and its expression in GC cells increased after curcumin treatment. Overexpression of miR-194-5p reversed the promotional effect of circ_0056618 on cell progression in curcumin-treated GC cells. Additionally, curcumin treatment repressed the tumorigenesis of GC in vivo through regulating circ_0056618. Curcumin treatment delayed the development of GC partly through decreasing circ_0056618 and increasing miR-194-5p.
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Affiliation(s)
- Shan Li
- Department of Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Lihai Zhang
- Department of General Surgery, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Shuhua Li
- Department of Drug, Medical Apparatus Supply, Zhongyuan Oilfield General Hospital, Puyang, China
| | - Hengyi Zhao
- Department of Clinical Pharmacy, Xuzhou Central Hospital, No. 199, Jiefang South Road, Xuzhou 221009, China
| | - Yonggang Chen
- Department of Clinical Pharmacy, Xuzhou Central Hospital, No. 199, Jiefang South Road, Xuzhou 221009, China
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Ma Y, Shen N, Wicha MS, Luo M. The Roles of the Let-7 Family of MicroRNAs in the Regulation of Cancer Stemness. Cells 2021; 10:cells10092415. [PMID: 34572067 PMCID: PMC8469079 DOI: 10.3390/cells10092415] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 12/17/2022] Open
Abstract
Cancer has long been viewed as a disease of normal development gone awry. Cancer stem-like cells (CSCs), also termed as tumor-initiating cells (TICs), are increasingly recognized as a critical tumor cell population that drives not only tumorigenesis but also cancer progression, treatment resistance and metastatic relapse. The let-7 family of microRNAs (miRNAs), first identified in C. elegans but functionally conserved from worms to human, constitutes an important class of regulators for diverse cellular functions ranging from cell proliferation, differentiation and pluripotency to cancer development and progression. Here, we review the current state of knowledge regarding the roles of let-7 miRNAs in regulating cancer stemness. We outline several key RNA-binding proteins, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) involved in the regulation of let-7 biogenesis, maturation and function. We then highlight key gene targets and signaling pathways that are regulated or mutually regulated by the let-7 family of miRNAs to modulate CSC characteristics in various types of cancer. We also summarize the existing evidence indicating distinct metabolic pathways regulated by the let-7 miRNAs to impact CSC self-renewal, differentiation and treatment resistance. Lastly, we review current preclinical studies and discuss the clinical implications for developing let-7-based replacement strategies as potential cancer therapeutics that can be delivered through different platforms to target CSCs and reduce/overcome treatment resistance when applied alone or in combination with current chemo/radiation or molecularly targeted therapies. By specifically targeting CSCs, these strategies have the potential to significantly improve the efficacy of cancer therapies.
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Affiliation(s)
- Yuxi Ma
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.M.); (N.S.)
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Na Shen
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.M.); (N.S.)
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Max S. Wicha
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.M.); (N.S.)
- Correspondence: (M.S.W.); (M.L.)
| | - Ming Luo
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.M.); (N.S.)
- Correspondence: (M.S.W.); (M.L.)
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The regulatory impact of RNA-binding proteins on microRNA targeting. Nat Commun 2021; 12:5057. [PMID: 34417449 PMCID: PMC8379221 DOI: 10.1038/s41467-021-25078-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/20/2021] [Indexed: 12/31/2022] Open
Abstract
Argonaute is the primary mediator of metazoan miRNA targeting (MT). Among the currently identified >1,500 human RNA-binding proteins (RBPs), there are only a handful of RBPs known to enhance MT and several others reported to suppress MT, leaving the global impact of RBPs on MT elusive. In this study, we have systematically analyzed transcriptome-wide binding sites for 150 human RBPs and evaluated the quantitative effect of individual RBPs on MT efficacy. In contrast to previous studies, we show that most RBPs significantly affect MT and that all of those MT-regulating RBPs function as MT enhancers rather than suppressors, by making the local secondary structure of the target site accessible to Argonaute. Our findings illuminate the unappreciated regulatory impact of human RBPs on MT, and as these RBPs may play key roles in the gene regulatory network governed by metazoan miRNAs, MT should be understood in the context of co-regulating RBPs. miRNAs are loaded into Argonaute protein and repress complementary mRNA targets. Here the authors show the unappreciated role of RNA binding proteins for efficient miRNA targeting and expand the current understanding of miRNA targeting.
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Li G, Wang Q, Li Z, Shen Y. Serum miR-21 and miR-210 as promising non-invasive biomarkers for the diagnosis and prognosis of colorectal cancer. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2021; 112:832-837. [PMID: 33054296 DOI: 10.17235/reed.2020.6801/2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE this study aimed to investigate the expression and clinical significance of miR-21 and miR-210 in serum of patients with colorectal cancer (CRC). METHODS the expression levels of serum miR-21 and miR-210 in 40 CRC patients (CRC group) and 20 healthy patients (control group) were measured by qRT-PCR. Correlation analysis was performed of the relationship between serum miR-21 and miR-210 levels with clinical characteristics, including gender, age, tumor location, tumor size, tumor stage, local invasion and TNM staging. The expression levels of miR-21 and miR-210 in the CRC group were separately measured before and after surgery. ROC analysis was performed to evaluate the diagnostic value of miR-21 and miR-210. RESULTS serum miR-21 and miR-210 in the CRC group were much higher than those in the control group. Meanwhile, the levels of serum miR-21 and miR-210 were closely related to tumor size (p = 0.028, p = 0.047), lymphatic metastasis (p = 0.038, p = 0.028), TNM staging (p = 0.014, p = 0.047) and tumor stage (p = 0.014, p = 0.017), but independent of gender, age and tumor location. In addition, serum miR-21 and miR-210 in the CRC group (n = 18) after surgery were lower than those before surgery (p < 0.001). ROC curves showed that miR-21 (AUC = 0.863) and miR-210 (AUC = 0.818) both had diagnostic efficacy in CRC patients. CONCLUSION miR-21 and miR-210 can be used as novel non-invasive biomarkers for CRC diagnosis and prognosis.
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Affiliation(s)
- Gang Li
- Colorectal Surgery, Shaoxing People's Hospital
| | - Qi Wang
- Colorectal Surgery, Shaoxing People's Hospital
| | - Zhenjun Li
- Colorectal Surgery, Shaoxing People's Hospital
| | - Yi Shen
- Colorectal Surgery, Shaoxing People's Hospital,
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Arslan Ö, Soylu NK, Akillilar PT, Tazebay UH. Coiled-coil domain-containing protein-124 (Ccdc124) is a novel RNA binding factor up-regulated in endometrial, ovarian, and urinary bladder cancers. Cancer Biomark 2021; 31:149-164. [PMID: 33896821 DOI: 10.3233/cbm-200802] [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: 01/04/2023]
Abstract
BACKGROUND Coiled-coil domain containing protein-124 (Ccdc124) is a putative mRNA-binding factor associated with cell division, and ribosome biology. Previous reports mentioned an up-regulation of CCDC124 gene in cancer, and listed its mRNA in a molecular prognostic signature in breast cancer. OBJECTIVES Establishing RNA-binding characteristics of Ccdc124 for a better molecular functional characterization, and carrying-out retrospective studies in order to evaluate its aberrant expression in human cancer samples from various tissue origins. METHODS Bioinformatics calculations followed by RIP and RNA-seq experiments were performed to investigate mRNA targets of Ccdc124. Quantitative studies on arrays of cDNAs from different cancers and IHC assays on tissue arrays were used to assess CCDC124 expression levels in cancers. RESULTS Ccdc124 was characterized as an RNA-binding protein (RBP) interacting with various mRNAs. CCDC124 mRNA levels were high in tumors, with a particular up-regulation in cancers from esophagus, adrenal gland, endometrium, liver, ovary, thyroid, and urinary bladder. IHC assays indicated strong Ccdc124 positivity in endometrial (95.4%), urinary bladder (68.4%), and ovarian cancers (86.8%). CONCLUSION Ccdc124 is a cytokinesis related RBP interacting with various mRNAs. CCDC124 mRNA over-expression and an accompanied increase in Ccdc124 protein accumulation was reported in cancers, indicating this RBP as a novel cancer cell marker.
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Affiliation(s)
- Özge Arslan
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey.,GTU-MAR Center Research Laboratory, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Neşe Karadağ Soylu
- Department of Pathology, Inönü University Faculty of Medicine, Battalgazi, Malatya, Turkey
| | | | - Uygar H Tazebay
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey.,GTU-MAR Center Research Laboratory, Gebze Technical University, Gebze, Kocaeli, Turkey
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Kinoshita C, Kubota N, Aoyama K. Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22105292. [PMID: 34069857 PMCID: PMC8157344 DOI: 10.3390/ijms22105292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/07/2023] Open
Abstract
The number of patients with neurodegenerative diseases (NDs) is increasing, along with the growing number of older adults. This escalation threatens to create a medical and social crisis. NDs include a large spectrum of heterogeneous and multifactorial pathologies, such as amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and multiple system atrophy, and the formation of inclusion bodies resulting from protein misfolding and aggregation is a hallmark of these disorders. The proteinaceous components of the pathological inclusions include several RNA-binding proteins (RBPs), which play important roles in splicing, stability, transcription and translation. In addition, RBPs were shown to play a critical role in regulating miRNA biogenesis and metabolism. The dysfunction of both RBPs and miRNAs is often observed in several NDs. Thus, the data about the interplay among RBPs and miRNAs and their cooperation in brain functions would be important to know for better understanding NDs and the development of effective therapeutics. In this review, we focused on the connection between miRNAs, RBPs and neurodegenerative diseases.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
| | - Noriko Kubota
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
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CSDE1 attenuates microRNA-mediated silencing of PMEPA1 in melanoma. Oncogene 2021; 40:3231-3244. [PMID: 33833398 DOI: 10.1038/s41388-021-01767-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
MicroRNAs and RNA-binding proteins (RBPs) primarily target the 3' UTR of mRNAs to control their translation and stability. However, their co-regulatory effects on specific mRNAs in physiology and disease are yet to be fully explored. CSDE1 is an RBP that promotes metastasis in melanoma and mechanisms underlying its oncogenic activities need to be completely defined. Here we report that CSDE1 interacts with specific miRNA-induced silencing complexes (miRISC) in melanoma. We find an association of CSDE1 with AGO2, the essential component of miRISC, which is facilitated by target mRNAs and depends on the first cold shock domain of CSDE1. Both CSDE1 and AGO2 bind to 3' UTR of PMEPA1. CSDE1 counters AGO2 binding, leading to an increase of PMEPA1 expression. We also identify a miRNA, miR-129-5p, that represses PMEPA1 expression in melanoma. Collectively, our results show that PMEPA1 promotes tumorigenic traits and that CSDE1 along with miR-129-5p/AGO2 miRISC act antagonistically to fine-tune PMEPA1 expression toward the progression of melanoma.
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Kelaini S, Chan C, Cornelius VA, Margariti A. RNA-Binding Proteins Hold Key Roles in Function, Dysfunction, and Disease. BIOLOGY 2021; 10:biology10050366. [PMID: 33923168 PMCID: PMC8146904 DOI: 10.3390/biology10050366] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
RNA-binding proteins (RBPs) are multi-faceted proteins in the regulation of RNA or its RNA splicing, localisation, stability, and translation. Amassing proof from many recent and dedicated studies reinforces the perception of RBPs exerting control through differing expression levels, cellular localization and post-transcriptional alterations. However, since the regulation of RBPs is reliant on the micro-environment and events like stress response and metabolism, their binding affinities and the resulting RNA-RBP networks may be affected. Therefore, any misregulation and disruption in the features of RNA and its related homeostasis can lead to a number of diseases that include diabetes, cardiovascular disease, and other disorders such as cancer and neurodegenerative diseases. As such, correct regulation of RNA and RBPs is crucial to good health as the effect RBPs exert through loss of function can cause pathogenesis. In this review, we will discuss the significance of RBPs and their typical function and how this can be disrupted in disease.
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Long Q, Liu Z, Gullerova M. Sweet Melody or Jazz? Transcription Around DNA Double-Strand Breaks. Front Mol Biosci 2021; 8:655786. [PMID: 33959637 PMCID: PMC8096065 DOI: 10.3389/fmolb.2021.655786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/22/2021] [Indexed: 12/23/2022] Open
Abstract
Genomic integrity is continuously threatened by thousands of endogenous and exogenous damaging factors. To preserve genome stability, cells developed comprehensive DNA damage response (DDR) pathways that mediate the recognition of damaged DNA lesions, the activation of signaling cascades, and the execution of DNA repair. Transcription has been understood to pose a threat to genome stability in the presence of DNA breaks. Interestingly, accumulating evidence in recent years shows that the transient transcriptional activation at DNA double-strand break (DSB) sites is required for efficient repair, while the rest of the genome exhibits temporary transcription silencing. This genomic shut down is a result of multiple signaling cascades involved in the maintenance of DNA/RNA homeostasis, chromatin stability, and genome fidelity. The regulation of transcription of protein-coding genes and non-coding RNAs has been extensively studied; however, the exact regulatory mechanisms of transcription at DSBs remain enigmatic. These complex processes involve many players such as transcription-associated protein complexes, including kinases, transcription factors, chromatin remodeling complexes, and helicases. The damage-derived transcripts themselves also play an essential role in DDR regulation. In this review, we summarize the current findings on the regulation of transcription at DSBs and discussed the roles of various accessory proteins in these processes and consequently in DDR.
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Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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