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Sakurai K, Ito H. Multifaced roles of the long non-coding RNA DRAIC in cancer progression. Life Sci 2024; 343:122544. [PMID: 38458555 DOI: 10.1016/j.lfs.2024.122544] [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: 12/11/2023] [Revised: 02/15/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Long non-coding RNAs (lncRNA) are functional RNAs, with over 200 nucleotides in length and lacking protein-coding potential. Studies have indicated that lncRNAs are important gene regulators under physiological conditions. Aberrant lncRNA expression is associated with the initiation and progression of various diseases, including cancers. High-throughput transcriptome analyses have revealed thousands of lncRNAs as putative tumor suppressors or promoters in various cancers, but the detailed molecular mechanisms of each lncRNA remain unclear. Downregulated RNA In Cancer, inhibitor of cell invasion and migration (DRAIC) (also known as LOC145837 and RP11-279F6.1) is a lncRNA that inhibits or promotes cancer progression with several modes of action. DRAIC was originally identified as a tumor-suppressive lncRNA in prostate adenocarcinoma. Subsequent studies also revealed that it has an anti-tumor role in glioblastoma, triple-negative breast cancer, and stomach adenocarcinoma. However, DRAIC exhibits oncogenic functions in other malignancies, such as lung adenocarcinoma and esophageal carcinoma, indicating its highly context-dependent effects on cancer progression and clinical outcomes. DRAIC and its associated pathways regulate various biological processes, including proliferation, invasion, metastasis, autophagy, and neuroendocrine function. This review introduces the multifaceted roles of DRAIC, particularly in cancer progression, and discusses its biological significance and clinical implications.
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Affiliation(s)
- Kouhei Sakurai
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
| | - Hiroyasu Ito
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
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SAKURAI KOUHEI, NAGAI AKIRA, ANDO TATSUYA, SAKAI YASUHIRO, IDETA YUKA, HAYASHI YUICHIRO, BABA JUNICHI, MITSUDO KENJI, AKITA MASAHARU, YAMAMICHI NOBUTAKE, FUJIGAKI HIDETSUGU, KATO TAKU, ITO HIROYASU. Cytomorphology and Gene Expression Signatures of Anchorage-independent Aggregations of Oral Cancer Cells. Cancer Genomics Proteomics 2023; 20:64-74. [PMID: 36581338 PMCID: PMC9806669 DOI: 10.21873/cgp.20365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND/AIM Cancer cells with high anchorage independence can survive and proliferate in the absence of adhesion to the extracellular matrix. Under anchorage-independent conditions, cancer cells adhere to each other and form aggregates to overcome various stresses. In this study, we investigated the cytomorphology and gene expression signatures of oral cancer cell aggregates. MATERIALS AND METHODS Two oral cancer-derived cell lines, SAS and HSC-3 cells, were cultured in a low-attachment plate and their cytomorphologies were observed. The transcriptome between attached and detached SAS cells was examined using gene expression microarrays. Subsequently, gene enrichment analysis and Ingenuity Pathway Analysis were performed. Gene expression changes under attached, detached, and re-attached conditions were measured via RT-qPCR. RESULTS While SAS cells formed multiple round-shaped aggregates, HSC-3 cells, which had lower anchorage independence, did not form aggregates efficiently. Each SAS cell in the aggregate was linked by desmosomes and tight junctions. Comparative transcriptomic analysis revealed 1,698 differentially expressed genes (DEGs) between attached and detached SAS cells. The DEGs were associated with various functions and processes, including cell adhesion. Moreover, under the detached condition, the expression of some epithelial genes (DSC3, DSP, CLDN1 and OCLN) were up-regulated. The changes in both cytomorphology and epithelial gene expression under the detached condition overall returned to their original ones when cells re-attached. CONCLUSION The results suggest specific cytomorphological and gene expression changes in oral cancer cell aggregates. Our findings provide insights into the mechanisms underlying anchorage-independent oral cancer cell aggregation and reveal previously unknown potential diagnostic and therapeutic molecules.
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Affiliation(s)
- KOUHEI SAKURAI
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Aichi, Japan
| | - AKIRA NAGAI
- Student Researcher Program, School of Medicine, Fujita Health University, Aichi, Japan
| | - TATSUYA ANDO
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Aichi, Japan
| | - YASUHIRO SAKAI
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Aichi, Japan
| | - YUKA IDETA
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan
| | - YUICHIRO HAYASHI
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan,Department of Oral and Maxillofacial Surgery, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - JUNICHI BABA
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan,Department of Oral and Maxillofacial Surgery, Saiseikai Yokohamashi Nanbu Hospital, Kanagawa, Japan
| | - KENJI MITSUDO
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan
| | - MASAHARU AKITA
- Department of Nutrition and Dietetics, School of Family and Consumer Sciences, Kamakura Women’s University, Kanagawa, Japan
| | - NOBUTAKE YAMAMICHI
- Center for Epidemiology and Preventive Medicine, The University of Tokyo Hospital, Tokyo, Japan,Department of Gastroenterology, School of Medicine, The University of Tokyo, Tokyo, Japan
| | - HIDETSUGU FUJIGAKI
- Department of Advanced Diagnostic System Development, Graduate School of Health Sciences, Fujita Health University, Aichi, Japan
| | - TAKU KATO
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Aichi, Japan
| | - HIROYASU ITO
- Department of Joint Research Laboratory of Clinical Medicine, School of Medicine, Fujita Health University, Aichi, Japan
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3
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Ke X, He L, Wang R, Shen J, Wang Z, Shen Y, Fan L, Shao J, Qi H. miR-377-3p-Mediated EGR1 Downregulation Promotes B[a]P-Induced Lung Tumorigenesis by Wnt/Beta-Catenin Transduction. Front Oncol 2021; 11:699004. [PMID: 34497759 PMCID: PMC8419355 DOI: 10.3389/fonc.2021.699004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/26/2021] [Indexed: 12/24/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs), particularly benzo[a]pyrene (B[a]P), found in cigarette smoke and air pollution, is an important carcinogen. Nevertheless, early molecular events and related regulatory effects of B[a]P-mediated cell transformation and tumor initiation remain unclear. This study found that EGR1 was significantly downregulated during human bronchial epithelial cell transformation and mice lung carcinogenesis upon exposure to B[a]P and its active form BPDE, respectively. In contrast, overexpression of EGR1 inhibited the BPDE-induced cell malignant transformation. Moreover, miR-377-3p was strongly enhanced by BPDE/B[a]P exposure and crucial for the inhibition of EGR1 expression by targeting the 3'UTR of EGR1. MiR-377-3p antagomir reversed the effect of EGR1 downregulation in cell malignant transformation and tumor initiation models. Furthermore, the B[a]P-induced molecular changes were evaluated by IHC in clinical lung cancer tissues and examined with a clinic database. Mechanistically, EGR1 inhibition was also involved in the regulation of Wnt/β-catenin transduction, promoting lung tumorigenesis following B[a]P/BPDE exposure. Taken together, the results demonstrated that bBenzo[a]pyrene exposure might induce lung tumorigenesis through miR-377-3p-mediated reduction of EGR1 expression, suggesting an important role of EGR1 in PAHs-induced lung carcinogenesis.
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Affiliation(s)
- Xinxin Ke
- Department of Pathology and Pathophysiology, and Department of Radiation Oncology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lulu He
- Department of Pathology and Pathophysiology, and Department of Radiation Oncology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Runan Wang
- Department of Pathology and Pathophysiology, and Department of Radiation Oncology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Shen
- Department of Pathology and Pathophysiology, and Department of Medical Oncology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhengyang Wang
- Department of Pulmonary and Critical Care Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yifei Shen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Jimin Shao
- Department of Pathology and Pathophysiology, and Department of Radiation Oncology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, and Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hongyan Qi
- Department of Pathology and Pathophysiology, and Department of Radiation Oncology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. From Endogenous to Synthetic microRNA-Mediated Regulatory Circuits: An Overview. Cells 2019; 8:E1540. [PMID: 31795372 PMCID: PMC6952906 DOI: 10.3390/cells8121540] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation. Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular species involved and the type of interactions amongst them. Depending on their topology, these molecular circuits may carry out specific functions that years of studies have related to the processing of gene expression noise. In this review, we first present the different over-represented network motifs involving microRNAs and their specific role in implementing relevant biological functions, reviewing both theoretical and experimental studies. We then illustrate the recent advances in synthetic biology, such as the construction of artificially synthesised circuits, which provide a controlled tool to test experimentally the possible microRNA regulatory tasks and constitute a starting point for clinical applications.
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Affiliation(s)
- Elsi Ferro
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Chiara Enrico Bena
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Silvia Grigolon
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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5
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Jancewicz I, Siedlecki JA, Sarnowski TJ, Sarnowska E. BRM: the core ATPase subunit of SWI/SNF chromatin-remodelling complex-a tumour suppressor or tumour-promoting factor? Epigenetics Chromatin 2019; 12:68. [PMID: 31722744 PMCID: PMC6852734 DOI: 10.1186/s13072-019-0315-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023] Open
Abstract
BRM (BRAHMA) is a core, SWI2/SNF2-type ATPase subunit of SWI/SNF chromatin-remodelling complex (CRC) involved in various important regulatory processes including development. Mutations in SMARCA2, a BRM-encoding gene as well as overexpression or epigenetic silencing were found in various human diseases including cancer. Missense mutations in SMARCA2 gene were recently connected with occurrence of Nicolaides-Baraitser genetics syndrome. By contrast, SMARCA2 duplication rather than mutations is characteristic for Coffin-Siris syndrome. It is believed that BRM usually acts as a tumour suppressor or a tumour susceptibility gene. However, other studies provided evidence that BRM function may differ depending on the cancer type and the disease stage, where BRM may play a role in the disease progression. The existence of alternative splicing forms of SMARCA2 gene, leading to appearance of truncated functional, loss of function or gain-of-function forms of BRM protein suggest a far more complicated mode of BRM-containing SWI/SNF CRCs actions. Therefore, the summary of recent knowledge regarding BRM alteration in various types of cancer and highlighting of differences and commonalities between BRM and BRG1, another SWI2/SNF2 type ATPase, will lead to better understanding of SWI/SNF CRCs function in cancer development/progression. BRM has been recently proposed as an attractive target for various anticancer therapies including the use of small molecule inhibitors, synthetic lethality induction or proteolysis-targeting chimera (PROTAC). However, such attempts have some limitations and may lead to severe side effects given the homology of BRM ATPase domain to other ATPases, as well as due to the tissue-specific appearance of BRM- and BRG1-containing SWI/SNF CRC classes. Thus, a better insight into BRM-containing SWI/SNF CRCs function in human tissues and cancers is clearly required to provide a solid basis for establishment of new safe anticancer therapies.
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Affiliation(s)
- Iga Jancewicz
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
| | - Elzbieta Sarnowska
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland.
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6
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Yong YX, Yang H, Lian J, Xu XW, Han K, Hu MY, Wang HC, Zhou LM. Up-regulated microRNA-199b-3p represses the apoptosis of cerebral microvascular endothelial cells in ischemic stroke through down-regulation of MAPK/ERK/EGR1 axis. Cell Cycle 2019; 18:1868-1881. [PMID: 31204565 DOI: 10.1080/15384101.2019.1632133] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as key mediators of posttranscriptional gene silencing in both pathogenic and pathological aspects of ischemic stroke biology. Therefore, the purpose of present study was to explore the effect of microRNA-199b-3p (miR-199b-3p) on the cerebral microvascular endothelial cells (CMECs) in middle cerebral artery occlusion-reperfusion (MCAO-R) mice by regulating MAPK/ERK/EGR1 axis. Mice were used to establish MCAO-R models and to measure the expression of miR-199b-3p and the MAPK/ERK/EGR1 axis-related genes. CMECs were extracted from the MCAO-R mice. A series of mimic or inhibitor for miR-199b-3p, or U0126 (an inhibitor for the MAPK/ERK/EGR1 axis) were introduced to treat these CMECs. The levels of miR-199b-3p and MAPK/ERK/EGR1 axis-related genes in tissues and cells were detected. The effects miR-199b-3p on the process of CMECs, including cell viability, cell cycle and cell apoptosis were evaluated. miR-199b-3p expressed poorly in the brain tissues after MCAO-R, along with activated MAPK/ERK/EGR1 axis and increased CMECs apoptosis. CMECs transfected with miR-199b-3p mimics and U0126 manifested with increased cell viability, more cells arrested at the S stage, and inhibited apoptosis of CMECs. In conclusion, these key results demonstrated up-regulated miR-199b-3p could protect mice against ischemic stroke by inhibiting the apoptosis of CMECs through blockade of MAPK/ERK/EGR1 axis.
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Affiliation(s)
- Ya-Xiong Yong
- a Guizhou Medical University , Guiyang , P. R. China.,b Department of Neurology, the Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen , P. R. China
| | - Hua Yang
- a Guizhou Medical University , Guiyang , P. R. China.,c Institute of Medical Sciences, Guizhou Medical University , Guiyang , P.R. China.,d Department of Neurosurgery, the Affiliated Hospital of Guizhou Medical University , Guiyang , P. R. China
| | - Jia Lian
- e Department of Neurology, the Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen , P.R. China
| | - Xiao-Wei Xu
- b Department of Neurology, the Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen , P. R. China
| | - Ke Han
- b Department of Neurology, the Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen , P. R. China
| | - Ming-Yi Hu
- b Department of Neurology, the Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen , P. R. China
| | - Hua-Cheng Wang
- b Department of Neurology, the Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen , P. R. China
| | - Lie-Min Zhou
- b Department of Neurology, the Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen , P. R. China
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7
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Bocci F, Jolly MK, Levine H, Onuchic JN. Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks. Methods Mol Biol 2019; 1912:341-366. [PMID: 30635901 DOI: 10.1007/978-1-4939-8982-9_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RNA is mostly known for its role in protein synthesis, where it encodes information for protein sequence in its messenger RNA (mRNA) form (translation). Yet, RNA molecules regulate several cellular processes other than translation. Here, we present an overview of several mathematical models that help understanding and characterizing the role of noncoding RNA molecules (ncRNAs) in regulating gene expression and protein synthesis. First, we discuss relatively simple models where ncRNAs can modulate protein synthesis via targeting a mRNA. Then, we consider the case of feedback interactions between ncRNAs and their target proteins, and discuss several biological applications where these feedback architectures modulate a cellular phenotype and control the levels of intrinsic and extrinsic noise. Building from these simple circuit motifs, we examine feed-forward circuit motifs involving ncRNAs that generate precise spatial and temporal patterns of protein expression. Further, we investigate the competition between ncRNAs and other endogenous RNA molecules and show that the cross talk between coding and noncoding RNAs can form large genetic circuits that involve up to hundreds of chemical species. Finally, we discuss the role of ncRNAs in modulating cell-cell signaling pathways and therefore the dynamics of spatiotemporal pattern formation in a tissue.
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Affiliation(s)
- Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Chemistry, Rice University, Houston, TX, USA
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA. .,Department of Physics and Astronomy, Rice University, Houston, TX, USA.
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA. .,Department of Physics and Astronomy, Rice University, Houston, TX, USA. .,Department of Biosciences, Rice University, Houston, TX, USA.
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8
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Kobayashi K, Hiramatsu H, Nakamura S, Kobayashi K, Haraguchi T, Iba H. Tumor suppression via inhibition of SWI/SNF complex-dependent NF-κB activation. Sci Rep 2017; 7:11772. [PMID: 28924147 PMCID: PMC5603518 DOI: 10.1038/s41598-017-11806-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/30/2017] [Indexed: 02/07/2023] Open
Abstract
The transcription factor NF-κB is constitutively activated in many epithelial tumors but few NF-κB inhibitors are suitable for cancer therapy because of its broad biological effects. We previously reported that the d4-family proteins (DPF1, DPF2, DPF3a/b) function as adaptor proteins linking NF-κB with the SWI/SNF complex. Here, using epithelial tumor cell lines, A549 and HeLaS3, we demonstrate that exogenous expression of the highly-conserved N-terminal 84-amino acid region (designated "CT1") of either DPF2 or DPF3a/b has stronger inhibitory effects on anchorage-independent growth than the single knockdown of any d4-family protein. This indicates that CT1 can function as an efficient dominant-negative mutant of the entire d4-family proteins. By in situ proximity ligation assay, CT1 was found to retain full adaptor function, indicating that the C-terminal region of d4-family proteins lacking in CT1 would include essential domains for SWI/SNF-dependent NF-κB activation. Microarray analysis revealed that CT1 suppresses only a portion of the NF-κB target genes, including representative SWI/SNF-dependent genes. Among these genes, IL6 was shown to strongly contribute to anchorage-independent growth. Finally, exogenous CT1 expression efficiently suppressed tumor formation in a mouse xenograft model, suggesting that the d4-family proteins are promising cancer therapy targets.
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Affiliation(s)
- Kazuyoshi Kobayashi
- Division of Host-Parasite Interaction, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.,Division of RNA Therapy, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Hiroaki Hiramatsu
- Division of Host-Parasite Interaction, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.,Division of RNA Therapy, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Shinya Nakamura
- Division of Host-Parasite Interaction, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Kyousuke Kobayashi
- Division of Host-Parasite Interaction, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Takeshi Haraguchi
- Division of Host-Parasite Interaction, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.,Division of RNA Therapy, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Hideo Iba
- Division of Host-Parasite Interaction, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan. .,Division of RNA Therapy, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan.
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9
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MiR-199a Inhibits Secondary Envelopment of Herpes Simplex Virus-1 Through the Downregulation of Cdc42-specific GTPase Activating Protein Localized in Golgi Apparatus. Sci Rep 2017; 7:6650. [PMID: 28751779 PMCID: PMC5532371 DOI: 10.1038/s41598-017-06754-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/16/2017] [Indexed: 02/06/2023] Open
Abstract
Because several studies have shown that exogenous miR-199a has antiviral effects against various viruses, including herpesviruses, we examined how miR-199a exerts its antiviral effects using epithelial tumour cell lines infected with herpes simplex virus-1 (HSV-1). We found that both miR-199a-5p and -3p impair the secondary envelopment of HSV-1 by suppressing their common target, ARHGAP21, a Golgi-localized GTPase-activating protein for Cdc42. We further found that the trans-cisternae of the Golgi apparatus are a potential membrane compartment for secondary envelopment. Exogenous expression of either pre-miR-199a or sh-ARHGAP21 exhibited shared phenotypes i.e. alteration of Golgi function in uninfected cells, inhibition of HSV-1 secondary envelopment, and reduction of trans-Golgi proteins upon HSV-1 infection. A constitutively active form of Cdc42 also inhibited HSV-1 secondary envelopment. Endogenous levels of miR-199a in epithelial tumour cell lines were negatively correlated with the efficiency of HSV-1 secondary envelopment within these cells. These results suggest that miR-199a is a crucial regulator of Cdc42 activity on Golgi membranes, which is important for the maintenance of Golgi function and for the secondary envelopment of HSV-1 upon its infection.
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10
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miR-2478 inhibits TGFβ1 expression by targeting the transcriptional activation region downstream of the TGFβ1 promoter in dairy goats. Sci Rep 2017; 7:42627. [PMID: 28198456 PMCID: PMC5309801 DOI: 10.1038/srep42627] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 01/13/2017] [Indexed: 02/08/2023] Open
Abstract
In a previous study, miR-2478 was demonstrated to be up-regulated in dairy goat mammary glands during peak lactation compared with the dry period. However, the detailed mechanisms by which miR-2478 regulates physiological lactation and mammary gland development in dairy goats remain unclear. In this study, we used bioinformatics analysis and homologous cloning to predict the target genes of miR-2478 and selected INSR, FBXO11, TGFβ1 and ING4 as candidate target genes of miR-2478. Subsequently, by targeting the 5′UTR of the TGFβ1 gene, we verified that miR-2478 significantly inhibited TGFβ1 transcription and the Pearson’s correlation coefficient between miR-2478 expression and TGFβ1 expression was −0.98. Furthermore, we identified the potential promoter and transcription factor binding regions of TGFβ1 and analyzed the potential mechanisms of interaction between miR-2478 and TGFβ1. Dual-luciferase reporter assays revealed that two regions, spanning from −904 to −690 bp and from −79 to +197 bp, were transcription factor binding regions of TGFβ1. Interesting, the miR-2478 binding sequence was determined to span from +123 to +142 bp in the TGFβ1 gene promoter. Thus, our results have demonstrated that miR-2478 binds to the core region of the TGFβ1 promoter and that it affects goat mammary gland development by inhibiting TGFβ1 transcription.
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11
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Lai X, Wolkenhauer O, Vera J. Understanding microRNA-mediated gene regulatory networks through mathematical modelling. Nucleic Acids Res 2016; 44:6019-35. [PMID: 27317695 PMCID: PMC5291278 DOI: 10.1093/nar/gkw550] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 06/06/2016] [Indexed: 12/19/2022] Open
Abstract
The discovery of microRNAs (miRNAs) has added a new player to the regulation of gene expression. With the increasing number of molecular species involved in gene regulatory networks, it is hard to obtain an intuitive understanding of network dynamics. Mathematical modelling can help dissecting the role of miRNAs in gene regulatory networks, and we shall here review the most recent developments that utilise different mathematical modelling approaches to provide quantitative insights into the function of miRNAs in the regulation of gene expression. Key miRNA regulation features that have been elucidated via modelling include: (i) the role of miRNA-mediated feedback and feedforward loops in fine-tuning of gene expression; (ii) the miRNA–target interaction properties determining the effectiveness of miRNA-mediated gene repression; and (iii) the competition for shared miRNAs leading to the cross-regulation of genes. However, there is still lack of mechanistic understanding of many other properties of miRNA regulation like unconventional miRNA–target interactions, miRNA regulation at different sub-cellular locations and functional miRNA variant, which will need future modelling efforts to deal with. This review provides an overview of recent developments and challenges in this field.
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Affiliation(s)
- Xin Lai
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, 91054, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, 18051, Germany Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, 7600, South Africa
| | - Julio Vera
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, 91054, Germany
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Wu Q, Qin H, Zhao Q, He XX. Emerging role of transcription factor-microRNA-target gene feed-forward loops in cancer. Biomed Rep 2015; 3:611-616. [PMID: 26405533 DOI: 10.3892/br.2015.477] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/28/2015] [Indexed: 12/28/2022] Open
Abstract
Transcriptional regulatory networks are biological network motifs that act in accordance with each other to play decisive roles in the pathological processes of cancer. One of the most common types, the feed-forward loop (FFL), has recently attracted interest. Three connected deregulated nodes, a transcription factor (TF), its downstream microRNA (miRNA) and their shared target gene can make up a class of cancer-involved FFLs as ≥1 of the 3 can act individually as a bona fide oncogene or a tumor suppressor. Numerous notable elements, such as p53, miR-17-92 cluster and cyclins, are proven members of their respective FFLs. Databases of interaction prediction, verification of experimental methods and confirmation of loops have been continually emerging during recent years. Development of TF-miRNA-target loops may help understand the mechanism of tumorgenesis at a higher level and explain the discovery and screening of the therapeutic target for drug exploitation.
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Affiliation(s)
- Qian Wu
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Hua Qin
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Qiu Zhao
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xing-Xing He
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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