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Odaka T, Sakamoto R, Kumagai K, Okuma K, Nishizawa M, Kimura T. Ephrin type-A receptor 2-antisense RNA1/2 promote proliferation and migration of MDA-MB-231 cells through EPHA2-dependent Ras signaling pathway mediated by MAPK8/JNK1, MAPK9/JNK2-NFATC2/NFAT1 and JUND. Front Mol Biosci 2024; 11:1402354. [PMID: 38855323 PMCID: PMC11157115 DOI: 10.3389/fmolb.2024.1402354] [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: 03/17/2024] [Accepted: 05/03/2024] [Indexed: 06/11/2024] Open
Abstract
Ephrin type-A receptor 2 (EPHA2) is a receptor tyrosine kinase that is overexpressed in a variety of cancers, including breast cancer. EPHA2 expression may be causally related to tumorigenesis; therefore, it is important to understand how EPHA2 expression is regulated. We previously reported that EPHA2 antisense RNA (EPHA2-AS), a natural antisense transcript, is an important modulator of EPHA2 mRNA levels and hence production of EPHA2 protein. EPHA2-AS encodes two splice variants, EPHA2-AS1 and EPHA2-AS2. The two variants are constitutively expressed in a concordant manner with EPHA2 mRNA in human breast adenocarcinoma cell lines and in patient samples, with the highest levels detected in the basal-like/triple-negative molecular subtype of breast cancer cells. In this study, we investigated the mechanism of EPHA2-AS1/2 in triple-negative breast cancer using MDA-MB-231 cells. We performed RNA-seq transcriptome analyses of MDA-MB-231 cells treated with AHCC®, which suppressed expression of EPHA2-AS1/2 and EPHA2 mRNA, and EPHA2-AS1/2-silenced MDA-MB-231 cells. Bioinformatics analyses identified 545 overlapping differentially expressed genes that were significantly up- or down-regulated by these treatments. Subsequent functional enrichment analyses of the overlapping genes in combination with in vitro assays indicated that EPHA2-AS1/2 may promote the proliferation and migration of MDA-MB-231 cells through the EPHA2-dependent Ras signaling pathways mediated by MAPK8/JNK1, MAPK9/JNK2-NFATC2/NFAT1 (proliferation and migration) and JUND (migration). These results thus suggest that EPHA2-AS1/2 may represent a potential molecular target for triple-negative breast cancer treatment.
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Affiliation(s)
- Tokifumi Odaka
- Laboratory of Microbiology and Cell Biology, Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
- Department of Microbiology, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Ryou Sakamoto
- Laboratory of Microbiology and Cell Biology, Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Kazuhiro Kumagai
- Laboratory of Microbiology and Cell Biology, Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Kazu Okuma
- Department of Microbiology, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Mikio Nishizawa
- Medical Chemistry Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Tominori Kimura
- Laboratory of Microbiology and Cell Biology, Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
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Li L, Qin C, Chen Y, Zhao W, Zhu Q, Dai D, Zhan S, Guo J, Zhong T, Wang L, Cao J, Zhang H. The novel RNA-RNA activation of H19 on MyoD transcripts promoting myogenic differentiation of goat muscle satellite cells. Int J Biol Macromol 2023; 253:127341. [PMID: 37852400 DOI: 10.1016/j.ijbiomac.2023.127341] [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: 01/31/2023] [Revised: 10/01/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
The elaborate interplay of coding and noncoding factors governs muscle growth and development. Here, we reported a mutual activation between long noncoding RNA (lncRNA) H19 and MyoD (myogenic determination gene number 1) in the muscle process. We successfully cloned the two isoforms of goat H19, which were significantly enriched and positively correlated with MyoD transcripts in skeletal muscles or differentiating muscle satellite cells (MuSCs). To systematically screen genes altered by H19, we performed RNA-seq using cDNA libraries of differentiating H19-deficiency MuSCs and consequently anchored MyoD as the critical genes in mediating H19 function. Intriguingly, some transcripts of MyoD and H19 overlapped in the cytoplasm, which was dramatically damaged when the core complementary nucleotides were mutated. Meanwhile, MyoD RNA successfully pulled down H19 in MS2-RIP experiments. Furthermore, HuR could bind both H19 and MyoD transcripts, while H19 or its truncated mutants successfully stabilized MyoD mRNA, with or without HuR deficiency. In turn, novel functional MyoD protein-binding sites were identified in the promoter and exons of the H19 gene. Our results suggest that MyoD activates H19 transcriptionally, and RNA-RNA hybridization is critical for H19-promoted MyoD expression, which extends our knowledge of the hierarchy of regulatory networks in muscle growth.
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Affiliation(s)
- Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Chenyu Qin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Yuan Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Wei Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Qi Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Dinghui Dai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China.
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Ali A, Salem M. Genome-wide identification of antisense lncRNAs and their association with susceptibility to Flavobacterium psychrophilum in rainbow trout. Front Immunol 2022; 13:1050722. [PMID: 36561762 PMCID: PMC9763276 DOI: 10.3389/fimmu.2022.1050722] [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: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes encode long noncoding natural antisense transcripts (lncNATs) that have been increasingly recognized as regulatory members of gene expression. Recently, we identified a few antisense transcripts correlating in expression with immune-related genes. However, a systematic genome-wide analysis of lncNATs in rainbow trout is lacking. This study used 134 RNA-Seq datasets from five different projects to identify antisense transcripts. A total of 13,503 lncNATs were identified genome-wide. About 75% of lncNATs showed multiple exons compared to 36.5% of the intergenic lncRNAs. RNA-Seq datasets from resistant, control, and susceptible rainbow trout genetic lines with significant differences in survival rate following Flavobacterium psychrophilum (Fp) infection were analyzed to investigate the potential role of the lncNATs during infection. Twenty-four pairwise comparisons between the different genetic lines, infectious status, and time points revealed 581 differentially expressed (DE) lncNATs and 179 differentially used exons (DUEs). Most of the DE lncNATs strongly and positively correlated in expression with their corresponding sense transcripts across 24 RNA-Seq datasets. LncNATs complementary to genes related to immunity, muscle contraction, proteolysis, and iron/heme metabolism were DE following infection. LncNATs complementary to hemolysis-related genes were DE in the resistant fish compared to susceptible fish on day 5 post-infection, suggesting enhanced clearance of free hemoglobin (Hb) and heme and increased erythropoiesis. LncNATs complementary to hepcidin, a master negative regulator of the plasma iron concentration, were the most downregulated lncNATs on day 5 of bacterial infection in the resistant fish. Ninety-four DE lncNAT, including five complementary to hepcidin, are located within 26 QTL regions previously identified in association with bacterial cold water disease (BCWD) in rainbow trout. Collectively, lncNATs are involved in the molecular architecture of fish immunity and should be further investigated for potential applications in genomic selection and genetic manipulation in aquaculture.
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Singh S, Shyamal S, Panda AC. Detecting RNA-RNA interactome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1715. [PMID: 35132791 DOI: 10.1002/wrna.1715] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules, including protein, DNA, and RNA. It has been established that RNA-RNA interactions play a critical role in several biological processes by regulating the biogenesis and function of RNA molecules. Interestingly, RNA-RNA interactions regulate the biogenesis of diverse RNA molecules, including mRNAs, microRNAs, tRNAs, and circRNAs, through splicing or backsplicing. Structured RNAs like rRNA, tRNA, and snRNAs achieve their functional conformation by intramolecular RNA-RNA interactions. In addition, functional consequences of many intermolecular RNA-RNA interactions have been extensively studied in the regulation of gene expression. Hence, it is essential to understand the mechanism and functions of RNA-RNA interactions in eukaryotes. Conventionally, RNA-RNA interactions have been identified through diverse biochemical methods for decades. The advent of high-throughput RNA-sequencing technologies has revolutionized the identification of global RNA-RNA interactome in cells and their importance in RNA structure and function in gene expression regulation. Although these technologies revealed tens of thousands of intramolecular and intermolecular RNA-RNA interactions, we further look forward to future unbiased and quantitative high-throughput technologies for detecting transcriptome-wide RNA-RNA interactions. With the ability to detect RNA-RNA interactome, we expect that future studies will reveal the higher-order structures of RNA molecules and multi-RNA hybrids impacting human health and diseases. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Center for Biotechnology, Faridabad, India
| | | | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
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5
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Lai T, Qiu H, Si L, Zhen Y, Chu D, Guo R. Long noncoding RNA BMPR1B-AS1 facilitates endometrial cancer cell proliferation and metastasis by sponging miR-7-2-3p to modulate the DCLK1/Akt/NF-κB pathway. Cell Cycle 2022; 21:1599-1618. [PMID: 35404759 PMCID: PMC9291686 DOI: 10.1080/15384101.2022.2060003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Endometrial carcinoma (EC) originates from the endometrium and is one of the most common tumors in female patients, and its incidence has continued to increase in recent decades. LncRNAs are involved in the pathogenesis and metastasis of a variety of malignant tumors, which indicates that lncRNAs can be used as tumor diagnostic markers and potential therapeutic targets. In this study, we analyzed the RNA transcripts of EC cells from The Cancer Genome Atlas (TCGA) and first reported a novel lncRNA, BMPR1B-AS1, that was more highly expressed in endometrial cancer tissues than in adjacent tissues, and BMPR1B-AS1 could promote endometrial cancer cell proliferation and metastasis. Bioinformatics prediction and experimental results both suggested that BMPR1B-AS1 could modulate the malignant behaviors of endometrial cancer cell lines by sponging miR-7-2-3p to modulate DCLK1, and a DCLK1 inhibitor blocked the activation of the PI3K/Akt/NF-κB signaling pathway. Collectively, this study suggests that the BMPR1B-AS1/miR-7-2-3p/DCLK1 axis contributes to the proliferation and metastasis of endometrial cancer cells via the PI3K/Akt/NF-κB pathway.
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Affiliation(s)
- Tianjiao Lai
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou Henan, China.,Academy of Medical Science, Zhengzhou University, Henan, Zhengzhou China
| | - Haifeng Qiu
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou Henan, China
| | - Lulu Si
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou Henan, China
| | - Yu Zhen
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou Henan, China.,Academy of Medical Science, Zhengzhou University, Henan, Zhengzhou China
| | - Danxia Chu
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou Henan, China
| | - Ruixia Guo
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou Henan, China
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LncRNA-miRNA-mRNA regulatory axes in endometrial cancer: a comprehensive overview. Arch Gynecol Obstet 2022; 306:1431-1447. [PMID: 35182183 DOI: 10.1007/s00404-022-06423-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Recent research on tumorigenesis and progression has opened up an array of novel molecular mechanisms in the form of interactions between cellular non-coding RNAs (long non-coding RNA[lncRNA]/microRNA [miRNA]) and coding transcripts that regulate health and disease. Endometrial cancer (EC) is a prominent gynecological malignancy with a high incidence rate and poorly known etiology and prognostic factors that hinder the success of disease management. The emerging role of lncRNA-miRNA-mRNA interactions and their dysregulation in the pathophysiology of EC has been elucidated in many recent studies. METHODS A thorough literature review was conducted to explore information about lncRNA-miRNA-mRNA axes in EC. RESULTS Several lncRNAs act as molecular sponges that sequester various tumor suppressor miRNAs to inhibit their function, leading to the dysregulation of their target mRNA transcripts that contribute to the EC regulation. CONCLUSIONS This review summarizes these networks of molecular mechanisms and their contribution to different aspects of endometrial carcinogenesis, leading to a better conceptualization of the molecular pathways that underlie the disease and helping establish novel diagnostic biomarkers and therapeutic intervention points to aid the curative intent of EC.
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7
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Wittling MC, Cahalan SR, Levenson EA, Rabin RL. Shared and Unique Features of Human Interferon-Beta and Interferon-Alpha Subtypes. Front Immunol 2021; 11:605673. [PMID: 33542718 PMCID: PMC7850986 DOI: 10.3389/fimmu.2020.605673] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Type I interferons (IFN-I) were first discovered as an antiviral factor by Isaacs and Lindenmann in 1957, but they are now known to also modulate innate and adaptive immunity and suppress proliferation of cancer cells. While much has been revealed about IFN-I, it remains a mystery as to why there are 16 different IFN-I gene products, including IFNβ, IFNω, and 12 subtypes of IFNα. Here, we discuss shared and unique aspects of these IFN-I in the context of their evolution, expression patterns, and signaling through their shared heterodimeric receptor. We propose that rather than investigating responses to individual IFN-I, these contexts can serve as an alternative approach toward investigating roles for IFNα subtypes. Finally, we review uses of IFNα and IFNβ as therapeutic agents to suppress chronic viral infections or to treat multiple sclerosis.
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Affiliation(s)
- Megen C Wittling
- Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
| | - Shannon R Cahalan
- Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
| | - Eric A Levenson
- Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
| | - Ronald L Rabin
- Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
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8
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Byun Y, Choi YC, Jeong Y, Yoon J, Baek K. Long Noncoding RNA Expression Profiling Reveals Upregulation of Uroplakin 1A and Uroplakin 1A Antisense RNA 1 under Hypoxic Conditions in Lung Cancer Cells. Mol Cells 2020; 43:975-988. [PMID: 33273139 PMCID: PMC7772508 DOI: 10.14348/molcells.2020.0126] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/15/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Hypoxia plays important roles in cancer progression by inducing angiogenesis, metastasis, and drug resistance. However, the effects of hypoxia on long noncoding RNA (lncRNA) expression have not been clarified. Herein, we evaluated alterations in lncRNA expression in lung cancer cells under hypoxic conditions using lncRNA microarray analyses. Among 40,173 lncRNAs, 211 and 113 lncRNAs were up- and downregulated, respectively, in both A549 and NCI-H460 cells. Uroplakin 1A (UPK1A) and UPK1A-antisense RNA 1 (AS1), which showed the highest upregulation under hypoxic conditions, were selected to investigate the effects of UPK1AAS1 on the expression of UPK1A and the mechanisms of hypoxia-inducible expression. Following transfection of cells with small interfering RNA (siRNA) targeting hypoxiainducible factor 1α (HIF-1α), the hypoxia-induced expression of UPK1A and UPK1A-AS1 was significantly reduced, indicating that HIF-1α played important roles in the hypoxiainduced expression of these targets. After transfection of cells with UPK1A siRNA, UPK1A and UPK1A-AS1 levels were reduced. Moreover, transfection of cells with UPK1A-AS1 siRNA downregulated both UPK1A-AS1 and UPK1A. RNase protection assays demonstrated that UPK1A and UPK1A-AS1 formed a duplex; thus, transfection with UPK1A-AS1 siRNA decreased the RNA stability of UPK1A. Overall, these results indicated that UPK1A and UPK1A-AS1 expression increased under hypoxic conditions in a HIF-1α-dependent manner and that formation of a UPK1A/UPK1A-AS1 duplex affected RNA stability, enabling each molecule to regulate the expression of the other.
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MESH Headings
- Cell Hypoxia/genetics
- Cell Line, Tumor
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Lung Neoplasms/genetics
- Methylation
- RNA Stability/genetics
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Reproducibility of Results
- Ribonucleases/metabolism
- Up-Regulation/genetics
- Uroplakin Ia/genetics
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Affiliation(s)
- Yuree Byun
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Young-Chul Choi
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Yongsu Jeong
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Jaeseung Yoon
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Kwanghee Baek
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
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9
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EPHA2 antisense RNA modulates EPHA2 mRNA levels in basal-like/triple-negative breast cancer cells. Biochimie 2020; 179:169-180. [PMID: 33022313 DOI: 10.1016/j.biochi.2020.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 09/11/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022]
Abstract
Ephrin type-A receptor 2 (EPHA2) is a receptor tyrosine kinase (RTK), whose over-expression has been observed in a variety of cancers, including breast cancer. EPHA2 expression may be causally related to tumorigenesis; therefore, it is important to understand how EPHA2 gene (EPHA2) expression is regulated. Here, we report that EPHA2 antisense RNA (EPHA2-AS), a natural antisense transcript, is an important modulator of EPHA2 mRNA levels. EPHA2-AS is a ∼1.8 kb long non-coding RNA (lncRNA) with a poly(A) tail that encodes two splice variants, EPHA2-AS1/2. They are constitutively expressed in a concordant manner with EPHA2 mRNA in human breast adenocarcinoma cell lines and in patient samples, with the highest levels detected in the triple-negative breast cancer (TNBC) subtype. The silencing of EPHA2-AS1/2 by a sense oligonucleotide or over-expression of an antisense oligoribonucleotide, which were both designed from the EPHA2 mRNA region (nt 2955-2974) targeted by AS1/2, showed that EPHA2-AS1/2 modulated EPHA2 mRNA levels by interacting with the specific AS1/2-complementary region in the mRNA. The EPHA2-AS1/2 did not prevent microRNAs from acting on the relevant microRNA response elements shared by EPHA2-AS1/2 and EPHA2 mRNA. Our studies demonstrate a crucial role played by EPHA2-AS1/2 in modulating EPHA2 mRNA levels, and hence production of EPHA2 protein, a key oncogenic RTK that contributes to the tumorigenesis of TNBC cells.
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10
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Kimura T. [Non-coding Natural Antisense RNA: Mechanisms of Action in the Regulation of Target Gene Expression and Its Clinical Implications]. YAKUGAKU ZASSHI 2020; 140:687-700. [PMID: 32378673 DOI: 10.1248/yakushi.20-00002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent advances in high-throughput technologies have revealed that 75% of the human genome is transcribed to RNA, whereas only 3% of transcripts are translated into proteins. Consequently, many long non-coding RNAs (lncRNAs) have been identified, which has improved our understanding of the complexity of biological processes. LncRNAs comprise multiple classes of RNA transcripts that regulate the transcription, stability and translation of protein-coding genes in a genome. Natural antisense transcripts (NATs) form one such class, and the GENCODE v30 catalog contains 16193 lncRNA loci, of which 5611 are antisense loci. This review outlines our emerging understanding of lncRNAs, with a particular focus on how lncRNAs regulate gene expression using interferon-α1 (IFN-α1) mRNA and its antisense partner IFN-α1 antisense (as)RNA as an example. We have identified and characterized the asRNA that determines post-transcriptional IFN-α1 mRNA levels. IFN-α1 asRNA stabilizes IFN-α1 mRNA by cytoplasmic sense-antisense duplex formation, which may enhance the accessibility of an RNA stabilizer protein or decrease the affinity of an RNA decay factor for the RNA. IFN-α1 asRNA can also act as competing molecules in the competing endogenous (ce)RNA network with other members of the IFNA multigene family mRNAs/asRNAs, and other cellular mRNA transcripts. Furthermore, antisense oligoribonucleotides representing functional domains of IFN-α1 asRNA inhibit influenza virus proliferation in the respiratory tract of virus-infected animals. Thus, these findings support, at least in part, the rationale that dissecting the activity of NAT on gene expression regulation promises to reveal previously unanticipated biology, with potential to provide new therapeutic approaches to diseases.
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Affiliation(s)
- Tominori Kimura
- Laboratory of Microbiology and Cell Biology, Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University
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11
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Tingting Z, Xiaojing L, Xiaoyan T, Keqin H, Junjun Q. The Antisense long noncoding RNA AGAP2-AS1 regulates cell proliferation and metastasis in Epithelial Ovarian Cancer. J Cancer 2020; 11:5318-5328. [PMID: 32742478 PMCID: PMC7391213 DOI: 10.7150/jca.36636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/15/2020] [Indexed: 12/27/2022] Open
Abstract
Antisense long noncoding RNAs serve as important regulators of protein-coding genes and contribute to tumorigenesis and metastasis. AGAP2-AS1, an antisense lncRNA transcribed from AGAP2, is involved in various cancer types. However, the clinical significance, biological roles and regulatory mechanisms of AGAP2-AS1 in epithelial ovarian cancer (EOC) have not been thoroughly elucidated to date. In this study, we demonstrated the expression pattern and biological roles of AGAP2-AS1 in EOC. Clinically, AGAP2-AS1 expression was decreased in EOC tissues compared to that in the controls. Low expression of AGAP2-AS1 was associated with advanced FIGO stage, high histological grade, serous subtype and lymph node metastasis in patients with EOC. AGAP2-AS1 inhibited cell migration, invasion and proliferation in vitro. AGAP2-AS1 suppressed tumor growth in vivo. Mechanistically, AGAP2-AS1 inhibited cell metastasis and proliferation by downregulating KRAS, FGFR4, and CTSK and suppressing epithelial-mesenchymal transition. In conclusion, we provide the first evidence for the tumor-suppressing effect of AGAP2-AS1 in EOC and demonstrate that AGAP2-AS1 may represent a promising therapeutic target for EOC patients.
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Affiliation(s)
- Zheng Tingting
- Department of Gynaecology, Obstetrics and Gynaecology Hospital, Fudan University, 419 Fangxie Road, Shanghai 200011, China Shanghai 200011, China.,Department of Obstetrics and Gynaecology of Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China.,Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai 200011, China.,Department of Gynaecology, The First affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jianshe Road, Zhengzhou 471000, Zhengzhou 471000, China
| | - Lin Xiaojing
- Department of Gynaecology, Obstetrics and Gynaecology Hospital, Fudan University, 419 Fangxie Road, Shanghai 200011, China Shanghai 200011, China.,Department of Obstetrics and Gynaecology of Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China.,Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai 200011, China
| | - Tang Xiaoyan
- Department of Gynaecology, Obstetrics and Gynaecology Hospital, Fudan University, 419 Fangxie Road, Shanghai 200011, China Shanghai 200011, China.,Department of Obstetrics and Gynaecology of Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China.,Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai 200011, China
| | - Hua Keqin
- Department of Gynaecology, Obstetrics and Gynaecology Hospital, Fudan University, 419 Fangxie Road, Shanghai 200011, China Shanghai 200011, China.,Department of Obstetrics and Gynaecology of Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China.,Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai 200011, China
| | - Qiu Junjun
- Department of Gynaecology, Obstetrics and Gynaecology Hospital, Fudan University, 419 Fangxie Road, Shanghai 200011, China Shanghai 200011, China.,Department of Obstetrics and Gynaecology of Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China.,Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai 200011, China
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12
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Zu W, Zhang H, Lan X, Tan X. Genome-wide evolution analysis reveals low CpG contents of fast-evolving genes and identifies antiviral microRNAs. J Genet Genomics 2020; 47:49-60. [DOI: 10.1016/j.jgg.2019.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/11/2019] [Accepted: 12/03/2019] [Indexed: 01/28/2023]
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13
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Sharma N, O'Neal AJ, Gonzalez C, Wittling M, Gjinaj E, Parsons LM, Panda D, Khalenkov A, Scott D, Misra S, Rabin RL. S27 of IFNα1 Contributes to Its Low Affinity for IFNAR2 and Weak Antiviral Activity. J Interferon Cytokine Res 2019; 39:283-292. [PMID: 30920934 DOI: 10.1089/jir.2018.0135] [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: 11/12/2022] Open
Abstract
Type I interferons (IFNs) signal by forming a high affinity IFN-IFNAR2 dimer, which subsequently recruits IFNAR1 to form a ternary complex that initiates JAK/STAT signaling. Among the 12 IFNα subtypes, IFNα1 has a uniquely low affinity for IFNAR2 (<100 × of the other IFNα subtypes) and commensurately weak antiviral activity, suggesting an undefined function distinct from suppression of viral infections. Also unique in IFNα1 is substitution of a serine for phenylalanine at position 27, a contact point that stabilizes the IFNα:IFNAR2 hydrophobic interface. To determine whether IFNα1-S27 contributes to the low affinity for IFNAR2, we created an IFNα1 mutein, IFNα1-S27F, and compared it to wild-type IFNα1 and IFNα2. Substitution of phenylalanine for serine increased affinity for IFNAR2 ∼4-fold and commensurately enhanced activation of STAT1, STAT3, and STAT5, transcription of a subset of interferon stimulated genes, and restriction of vesicular stomatitis virus infection in vitro. Structural modeling suggests that S27 of IFNα1 disrupts the IFNα:IFNAR2 hydrophobic interface that is otherwise stabilized by F27 and that replacing S27 with phenylalanine partially restores the hydrophobic surface. Disruption of the hydrophobic IFNα:IFNAR2 interface by the unique S27 of IFN α1 contributes to its low affinity and weak antiviral activity.
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Affiliation(s)
- Nikunj Sharma
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Anya J O'Neal
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Christian Gonzalez
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Megen Wittling
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Erisa Gjinaj
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Lisa M Parsons
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Debasis Panda
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Alexey Khalenkov
- 2 Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Dorothy Scott
- 2 Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Saurav Misra
- 3 Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
| | - Ronald L Rabin
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
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14
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Arias-Vásquez A, Groffen AJ, Spijker S, Ouwens KG, Klein M, Vojinovic D, Galesloot TE, Bralten J, Hottenga JJ, van der Most PJ, Kattenberg VM, Pool R, Nolte IM, Penninx BWJH, Fedko IO, Dolan CV, Nivard MG, den Braber A, van Duijn CM, Hoekstra PJ, Buitelaar JK, Kiemeney LA, Hoogman M, Middeldorp CM, Draisma HHM, Vermeulen SH, Sánchez-Mora C, Ramos-Quiroga JA, Ribasés M, Hartman CA, Kooij JJS, Amin N, Smit AB, Franke B, Boomsma DI. A Potential Role for the STXBP5-AS1 Gene in Adult ADHD Symptoms. Behav Genet 2019; 49:270-285. [PMID: 30659475 DOI: 10.1007/s10519-018-09947-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 12/26/2018] [Indexed: 12/15/2022]
Abstract
We aimed to detect Attention-deficit/hyperactivity (ADHD) risk-conferring genes in adults. In children, ADHD is characterized by age-inappropriate levels of inattention and/or hyperactivity-impulsivity and may persists into adulthood. Childhood and adulthood ADHD are heritable, and are thought to represent the clinical extreme of a continuous distribution of ADHD symptoms in the general population. We aimed to leverage the power of studies of quantitative ADHD symptoms in adults who were genotyped. Within the SAGA (Study of ADHD trait genetics in adults) consortium, we estimated the single nucleotide polymorphism (SNP)-based heritability of quantitative self-reported ADHD symptoms and carried out a genome-wide association meta-analysis in nine adult population-based and case-only cohorts of adults. A total of n = 14,689 individuals were included. In two of the SAGA cohorts we found a significant SNP-based heritability for self-rated ADHD symptom scores of respectively 15% (n = 3656) and 30% (n = 1841). The top hit of the genome-wide meta-analysis (SNP rs12661753; p-value = 3.02 × 10-7) was present in the long non-coding RNA gene STXBP5-AS1. This association was also observed in a meta-analysis of childhood ADHD symptom scores in eight population-based pediatric cohorts from the Early Genetics and Lifecourse Epidemiology (EAGLE) ADHD consortium (n = 14,776). Genome-wide meta-analysis of the SAGA and EAGLE data (n = 29,465) increased the strength of the association with the SNP rs12661753. In human HEK293 cells, expression of STXBP5-AS1 enhanced the expression of a reporter construct of STXBP5, a gene known to be involved in "SNAP" (Soluble NSF attachment protein) Receptor" (SNARE) complex formation. In mouse strains featuring different levels of impulsivity, transcript levels in the prefrontal cortex of the mouse ortholog Gm28905 strongly correlated negatively with motor impulsivity as measured in the five choice serial reaction time task (r2 = - 0.61; p = 0.004). Our results are consistent with an effect of the STXBP5-AS1 gene on ADHD symptom scores distribution and point to a possible biological mechanism, other than antisense RNA inhibition, involved in ADHD-related impulsivity levels.
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Affiliation(s)
- A Arias-Vásquez
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands. .,Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Route 855, Postbus 9101, 6500 HB, Nijmegen, The Netherlands. .,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - A J Groffen
- Department of Functional Genomics and Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam and VU Medical Center Amsterdam, Amsterdam, The Netherlands
| | - S Spijker
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - K G Ouwens
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health, Amsterdam, The Netherlands
| | - M Klein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Route 855, Postbus 9101, 6500 HB, Nijmegen, The Netherlands
| | - D Vojinovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - T E Galesloot
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J Bralten
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Route 855, Postbus 9101, 6500 HB, Nijmegen, The Netherlands
| | - J J Hottenga
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health, Amsterdam, The Netherlands
| | - P J van der Most
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - V M Kattenberg
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - R Pool
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health, Amsterdam, The Netherlands
| | - I M Nolte
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - B W J H Penninx
- Department of Psychiatry, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - I O Fedko
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health, Amsterdam, The Netherlands
| | - C V Dolan
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - M G Nivard
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health, Amsterdam, The Netherlands
| | - A den Braber
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - C M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - P J Hoekstra
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J K Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.,Karakter, Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - L A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M Hoogman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Route 855, Postbus 9101, 6500 HB, Nijmegen, The Netherlands
| | - C M Middeldorp
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Child Health Research Centre, University of Queensland, Brisbane, Australia.,Child and Youth Mental Health Service, Children's Health Queensland Hospital and Health Services, Brisbane, Australia
| | - H H M Draisma
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - S H Vermeulen
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C Sánchez-Mora
- Psychiatric Genetics Unit, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain
| | - J A Ramos-Quiroga
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain.,Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M Ribasés
- Psychiatric Genetics Unit, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain
| | | | - C A Hartman
- Department of Psychiatry, Interdisciplinary Center Psychopathology and Emotion Regulation, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J J S Kooij
- Psycho-Medical Programs, PsyQ, Program Adult ADHD, The Hague, The Netherlands
| | - N Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A B Smit
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - B Franke
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Route 855, Postbus 9101, 6500 HB, Nijmegen, The Netherlands
| | - D I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health, Amsterdam, The Netherlands
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15
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Increased levels of the long noncoding RNA, HOXA-AS3, promote proliferation of A549 cells. Cell Death Dis 2018; 9:707. [PMID: 29899328 PMCID: PMC5999602 DOI: 10.1038/s41419-018-0725-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 04/26/2018] [Accepted: 05/04/2018] [Indexed: 01/01/2023]
Abstract
Many long noncoding RNAs (lncRNAs) have been identified as powerful regulators of lung adenocarcinoma (LAD). However, the role of HOXA-AS3, a novel lncRNA, in LAD is largely unknown. In this study, we showed that HOXA-AS3 was significantly upregulated in LAD tissues and A549 cells. After knockdown of HOXA-AS3, cell proliferation, migration, and invasion were inhibited. Xenografts derived from A549 cells transfected with shRNA/HOXA-AS3 had significantly lower tumor weights and smaller tumor volumes. We also demonstrated that HOXA-AS3 increased HOXA6 mRNA stability by forming an RNA duplex. In addition, HOXA6 promoted cell proliferation, migration, and invasion in vitro. Using a RNA pull-down assay, we found that HOXA-AS3 bonded with NF110, which regulated the cell localization of HOXA-AS3. Moreover, histone acetylation was involved in upregulation of HOXA-AS3. These results demonstrate that HOXA-AS3 was activated in LAD and supported cancer cell progression. Therefore, inhibition of HOXA-AS3 could be an effective targeted therapy for patients with LAD.
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16
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Zhong L, Zheng C, Fang H, Xu M, Chen B, Li C. MicroRNA-1270 is associated with poor prognosis and its inhibition yielded anticancer mechanisms in human osteosarcoma. IUBMB Life 2018; 70:625-632. [PMID: 29774985 DOI: 10.1002/iub.1753] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/27/2018] [Accepted: 02/06/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Lei Zhong
- Department of Orthopedics; The Second Hospital of Jilin University; Changchun Jilin China
| | - Changjun Zheng
- Department of Orthopedics; The Second Hospital of Jilin University; Changchun Jilin China
| | - Hongjuan Fang
- Department of Electrical diagnose; The Fourth Hospital of Jilin University; Changchun Jilin China
| | - Meng Xu
- Department of Orthopedics; The Second Hospital of Jilin University; Changchun Jilin China
| | - Bingpeng Chen
- Department of Orthopedics; The Second Hospital of Jilin University; Changchun Jilin China
| | - Chen Li
- Department of Orthopedics; The Second Hospital of Jilin University; Changchun Jilin China
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17
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Antisense Long Non-Coding RNAs Are Deregulated in Skin Tissue of Patients with Systemic Sclerosis. J Invest Dermatol 2017; 138:826-835. [PMID: 29179949 DOI: 10.1016/j.jid.2017.09.053] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 08/31/2017] [Accepted: 09/23/2017] [Indexed: 01/02/2023]
Abstract
Systemic sclerosis is an autoimmune disease characterized by fibrosis of skin and multiple organs of which the pathogenesis is poorly understood. We studied differentially expressed coding and non-coding genes in relation to systemic sclerosis pathogenesis with a specific focus on antisense non-coding RNAs. Skin biopsy-derived RNAs from 14 early systemic sclerosis patients and six healthy individuals were sequenced with ion-torrent and analyzed using DEseq2. Overall, 4,901 genes with a fold change >1.5 and a false discovery rate <5% were detected in patients versus controls. Upregulated genes clustered in immunologic, cell adhesion, and keratin-related processes. Interestingly, 676 deregulated non-coding genes were detected, 257 of which were classified as antisense genes. Sense genes expressed opposite of these antisense genes were also deregulated in 42% of the observed sense-antisense gene pairs. The majority of the antisense genes had a similar effect sizes in an independent North American dataset with three genes (CTBP1-AS2, OTUD6B-AS1, and AGAP2-AS1) exceeding the study-wide Bonferroni-corrected P-value (PBonf < 0.0023, Pcombined = 1.1 × 10-9, 1.4 × 10-8, 1.7 × 10-6, respectively). In this study, we highlight that together with coding genes, (antisense) long non-coding RNAs are deregulated in skin tissue of systemic sclerosis patients suggesting a novel class of genes involved in pathogenesis of systemic sclerosis.
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18
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Huang B, Song JH, Cheng Y, Abraham JM, Ibrahim S, Sun Z, Ke X, Meltzer SJ. Long non-coding antisense RNA KRT7-AS is activated in gastric cancers and supports cancer cell progression by increasing KRT7 expression. Oncogene 2016; 35:4927-36. [PMID: 26876208 PMCID: PMC4985510 DOI: 10.1038/onc.2016.25] [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: 10/06/2015] [Revised: 12/10/2015] [Accepted: 12/11/2015] [Indexed: 12/21/2022]
Abstract
Alterations in long non-coding RNAs (lncRNAs) are associated with human carcinogenesis. One group of lncRNAs, which are antisense in orientation to coding mRNAs (ASs), have been recently described in cancers but are poorly understood. We sought to identify ASs involved in human gastric cancer (GC) and to elucidate their mechanisms of action in carcinogenesis. We performed massively parallel RNA sequencing in GCs and matched normal tissues, as well as in GC-derived and normal gastric epithelial cell lines. One AS, designated Homo sapiens keratin 7 (KRT7-AS), was selected due to its marked upregulation and concordant expression with its cognate sense counterpart, KRT7, in GC tissues and cell lines. KRT7-AS formed an RNA-RNA hybrid with KRT7 and controlled KRT7 expression at both the mRNA and the post-transcriptional levels. Moreover, forced overexpression of the KRT7-overlapping region (OL) of KRT7-AS (but not its non-KRT7-OL portions) increased keratin 7 protein levels in cells. Finally, forced overexpression of full-length KRT7-AS or OL KRT7-AS (but not its non-KRT7-OL regions) promoted GC cell proliferation and migration. We conclude that lncRNA KRT7-AS promotes GC, at least in part, by increasing KRT7 expression.
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Affiliation(s)
- B Huang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J H Song
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Y Cheng
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J M Abraham
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Ibrahim
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Z Sun
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - X Ke
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S J Meltzer
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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19
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Nalpas NC, Magee DA, Conlon KM, Browne JA, Healy C, McLoughlin KE, Rue-Albrecht K, McGettigan PA, Killick KE, Gormley E, Gordon SV, MacHugh DE. RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli. Sci Rep 2015; 5:13629. [PMID: 26346536 PMCID: PMC4642568 DOI: 10.1038/srep13629] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/31/2015] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium bovis, the agent of bovine tuberculosis, causes an estimated $3 billion annual losses to global agriculture due, in part, to the limitations of current diagnostics. Development of next-generation diagnostics requires a greater understanding of the interaction between the pathogen and the bovine host. Therefore, to explore the early response of the alveolar macrophage to infection, we report the first application of RNA-sequencing to define, in exquisite detail, the transcriptomes of M. bovis-infected and non-infected alveolar macrophages from ten calves at 2, 6, 24 and 48 hours post-infection. Differentially expressed sense genes were detected at these time points that revealed enrichment of innate immune signalling functions, and transcriptional suppression of host defence mechanisms (e.g., lysosome maturation). We also detected differentially expressed natural antisense transcripts, which may play a role in subverting innate immune mechanisms following infection. Furthermore, we report differential expression of novel bovine genes, some of which have immune-related functions based on orthology with human proteins. This is the first in-depth transcriptomics investigation of the alveolar macrophage response to the early stages of M. bovis infection and reveals complex patterns of gene expression and regulation that underlie the immunomodulatory mechanisms used by M. bovis to evade host defence mechanisms.
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Affiliation(s)
- Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin M Conlon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Claire Healy
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.,UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul A McGettigan
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kate E Killick
- Systems Biology Ireland, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Eamonn Gormley
- Tuberculosis Diagnostics and Immunology Research Centre, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
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20
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Panzeri I, Rossetti G, Abrignani S, Pagani M. Long Intergenic Non-Coding RNAs: Novel Drivers of Human Lymphocyte Differentiation. Front Immunol 2015; 6:175. [PMID: 25926836 PMCID: PMC4397839 DOI: 10.3389/fimmu.2015.00175] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/28/2015] [Indexed: 12/29/2022] Open
Abstract
Upon recognition of a foreign antigen, CD4(+) naïve T lymphocytes proliferate and differentiate into subsets with distinct functions. This process is fundamental for the effective immune system function, as CD4(+) T cells orchestrate both the innate and adaptive immune response. Traditionally, this differentiation event has been regarded as the acquisition of an irreversible cell fate so that memory and effector CD4(+) T subsets were considered terminally differentiated cells or lineages. Consequently, these lineages are conventionally defined thanks to their prototypical set of cytokines and transcription factors. However, recent findings suggest that CD4(+) T lymphocytes possess a remarkable phenotypic plasticity, as they can often re-direct their functional program depending on the milieu they encounter. Therefore, new questions are now compelling such as which are the molecular determinants underlying plasticity and stability and how the balance between these two opposite forces drives the cell fate. As already mentioned, in some cases, the mere expression of cytokines and master regulators could not fully explain lymphocytes plasticity. We should consider other layers of regulation, including epigenetic factors such as the modulation of chromatin state or the transcription of non-coding RNAs, whose high cell-specificity give a hint on their involvement in cell fate determination. In this review, we will focus on the recent advances in understanding CD4(+) T lymphocytes subsets specification from an epigenetic point of view. In particular, we will emphasize the emerging importance of non-coding RNAs as key players in these differentiation events. We will also present here new data from our laboratory highlighting the contribution of long non-coding RNAs in driving human CD4(+) T lymphocytes differentiation.
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Affiliation(s)
- Ilaria Panzeri
- Integrative Biology Unit, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", IRCCS Ospedale Maggiore Policlinico , Milano , Italy
| | - Grazisa Rossetti
- Integrative Biology Unit, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", IRCCS Ospedale Maggiore Policlinico , Milano , Italy
| | - Sergio Abrignani
- Integrative Biology Unit, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", IRCCS Ospedale Maggiore Policlinico , Milano , Italy
| | - Massimiliano Pagani
- Integrative Biology Unit, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", IRCCS Ospedale Maggiore Policlinico , Milano , Italy ; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano , Milano , Italy
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21
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Interferon-alpha competing endogenous RNA network antagonizes microRNA-1270. Cell Mol Life Sci 2015; 72:2749-61. [PMID: 25746225 PMCID: PMC4477080 DOI: 10.1007/s00018-015-1875-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 12/18/2022]
Abstract
A new form of circuitry for gene regulation has been identified in which RNAs can crosstalk by competing for shared microRNAs (miRNAs). Such competing endogenous RNAs (ceRNAs) form a network via shared miRNA response elements (MREs) to antagonize miRNA function. We previously reported natural antisense RNA (AS) as an important modulator of interferon-α1 (IFN-α1) mRNA levels by promoting IFN-α1 mRNA stability. We show that IFN-α1 AS forms a ceRNA network with specific IFN-α AS (IFN-α7/-α8/-α10/-α14) and mRNA (IFN-α8/-α10/-α14/-α17) subtypes from the IFN-α gene (IFNA) family to antagonize miRNA-1270 (miR-1270), thereby modulating IFN-α1 mRNA levels. Bioinformatic analysis demonstrated that IFN-α1 AS harbors multiple miR-1270 MREs (MRE-1270s), whose presence was substantiated by miR-1270 overexpression and transfection of antimiR-1270. The antimiR-1270, complementary to the miR-1270 seed region, revealed that IFN-α1 AS likely shares the MRE-1270 with IFN-α1 mRNA and specific IFN-α AS and mRNA subtypes. Subsequent bioinformatic analysis for MRE-1270s showed that IFN-α1 AS and other RNA subtypes shared the 6-mer MRE-1270 site. Further MRE-mapping demonstrated that the total number of MRE-1270s in IFN-α1 AS accounted for approximately 30 % of the miR-1270 population. AntimiR-1270 transfection also caused specific de-repression of five cellular mRNAs, including that of CAPRIN1. These results suggest that IFN-α1 AS, together with specific IFN-α AS and mRNA subtypes, as well as the five cellular mRNAs, participate as competing molecules in the ceRNA network against miR-1270. This coordinated regulatory architecture suggests a vital function for the innate immune system in maintaining precise physiological type I IFN levels via post-transcriptional regulatory mechanisms.
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Wei N, Wang Y, Xu RX, Wang GQ, Xiong Y, Yu TY, Yang GS, Pang WJ. PU.1antisense lncRNA against its mRNA translation promotes adipogenesis in porcine preadipocytes. Anim Genet 2015; 46:133-40. [DOI: 10.1111/age.12275] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2014] [Indexed: 01/31/2023]
Affiliation(s)
- N. Wei
- Laboratory of Animal Fat Deposition & Muscle Development; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - Y. Wang
- Laboratory of Animal Fat Deposition & Muscle Development; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - R.-X. Xu
- Laboratory of Animal Fat Deposition & Muscle Development; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - G.-Q. Wang
- Laboratory of Animal Fat Deposition & Muscle Development; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - Y. Xiong
- Laboratory of Animal Fat Deposition & Muscle Development; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - T.-Y. Yu
- Laboratory of Animal Fat Deposition & Muscle Development; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - G.-S. Yang
- Laboratory of Animal Fat Deposition & Muscle Development; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - W.-J. Pang
- Laboratory of Animal Fat Deposition & Muscle Development; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
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Widespread genome transcription: new possibilities for RNA therapies. Biochem Biophys Res Commun 2014; 452:294-301. [PMID: 25193698 DOI: 10.1016/j.bbrc.2014.08.139] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 08/25/2014] [Indexed: 12/15/2022]
Abstract
Comprehensive analysis of mammalian transcriptomes has surprisingly revealed that a major fraction of the RNAs produced by mammalian cells and tissues is comprised of long non-coding RNAs (lncRNAs). Such RNAs were previously disregarded as useless, but recent functional studies have revealed that they have multiple regulatory functions. A large subset of these lncRNAs are antisense to protein-coding genes; such RNAs are particularly attractive to researchers because their functions are better understood than other lncRNAs and their action can be easily modulated and engineered by modifying the antisense region. We discuss various aspects of regulation by antisense RNAs and other small nucleic acids and the challenges to bring these technologies to gene therapy. Despite several remaining issues related to delivery, RNA stability, side effects, and toxicity, the field is moving quickly towards future biotechnological and health applications. Therapies based on lncRNAs may be the key to increased cell-specificity of future gene therapies.
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Wei N, Pang W, Wang Y, Xiong Y, Xu R, Wu W, Zhao C, Yang G. Knockdown of PU.1 mRNA and AS lncRNA regulates expression of immune-related genes in zebrafish Danio rerio. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 44:315-319. [PMID: 24463314 DOI: 10.1016/j.dci.2014.01.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
The transcription factor PU.1 plays a key role in the development of immune system. Recent evidence demonstrated bidirectional transcription and a sense/antisense transcriptional regulatory manner in PU.1 locus. However, the effect of PU.1 mRNA and its antisense long non-coding RNA (AS lncRNA) on adaptive immunity in vivo is still not clear. In this study, we first confirmed the expression of PU.1 AS lncRNA by strand-specific RT-PCR in zebrafish. Additionally, we found that GFP was detected in zebrafish kidney using tissue smears after zebrafish was intraperitoneally injected with pLentiHI-PU.1 shRNA or pLentiHI-PU.1 AS shRNA for 2 days. Moreover, on day 0, 2 and 4, the levels of PU.1 and immune-related genes including TCRAC, Rag2, AID, IgLC-1, mIg, and sIg mRNAs were detected using real-time qPCR. The results showed that the levels of PU.1 and above 6 immune-related gene mRNAs were significantly downregulated on day 2 (P<0.05) and day 4 (P<0.01) by the treatment with the pLentiHI-PU.1 shRNA, whereas these genes were markedly upregulated by the treatment with the pLentiHI-PU.1 AS shRNA. Based on our results, we suggested that the effects of PU.1 transcripts including mRNA and AS lncRNA on immune-related gene expression in zebrafish were opposite. To our knowledge, this was the first report that a novel functional AS lncRNA in adaptive immunity was transcribed from the zebrafish PU.1 locus. Our findings provided novel insight into further exploration on modulating adaptive immunity by regulating PU.1 mRNA and AS lncRNA.
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Affiliation(s)
- Ning Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Weijun Pang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Yu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yan Xiong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruxiang Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenjing Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Cunzhen Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Gongshe Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Yamanishi R, Yoshigai E, Okuyama T, Mori M, Murase H, Machida T, Okumura T, Nishizawa M. The anti-inflammatory effects of flavanol-rich lychee fruit extract in rat hepatocytes. PLoS One 2014; 9:e93818. [PMID: 24705335 PMCID: PMC3976307 DOI: 10.1371/journal.pone.0093818] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 03/07/2014] [Indexed: 12/23/2022] Open
Abstract
Flavanol (flavan-3-ol)-rich lychee fruit extract (FRLFE) is a mixture of oligomerized polyphenols primarily derived from lychee fruit and is rich in flavanol monomers, dimers, and trimers. Supplementation with this functional food has been shown to suppress inflammation and tissue damage caused by high-intensity exercise training. However, it is unclear whether FRLFE has in vitro anti-inflammatory effects, such as suppressing the production of the proinflammatory cytokine tumor necrosis factor α (TNF-α) and the proinflammatory mediator nitric oxide (NO), which is synthesized by inducible nitric oxide synthase (iNOS). Here, we analyzed the effects of FRLFE and its constituents on the expression of inflammatory genes in interleukin 1β (IL-1β)-treated rat hepatocytes. FRLFE decreased the mRNA and protein expression of the iNOS gene, leading to the suppression of IL-1β-induced NO production. FRLFE also decreased the levels of the iNOS antisense transcript, which stabilizes iNOS mRNA. By contrast, unprocessed lychee fruit extract, which is rich in flavanol polymers, and flavanol monomers had little effect on NO production. When a construct harboring the iNOS promoter fused to the firefly luciferase gene was used, FRLFE decreased the luciferase activity in the presence of IL-1β, suggesting that FRLFE suppresses the promoter activity of the iNOS gene at the transcriptional level. Electrophoretic mobility shift assays indicated that FRLFE reduced the nuclear transport of a key regulator, nuclear factor κB (NF-κB). Furthermore, FRLFE inhibited the phosphorylation of NF-κB inhibitor α (IκB-α). FRLFE also reduced the mRNA levels of NF-κB target genes encoding cytokines and chemokines, such as TNF-α. Therefore, FRLFE inhibited NF-κB activation and nuclear translocation to suppress the expression of these inflammatory genes. Our results suggest that flavanols may be responsible for the anti-inflammatory and hepatoprotective effects of FRLFE and may be used to treat inflammatory diseases.
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Affiliation(s)
- Ryota Yamanishi
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Emi Yoshigai
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Tetsuya Okuyama
- Graduate School of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Masatoshi Mori
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Hiromitsu Murase
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Toru Machida
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Tadayoshi Okumura
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Shiga, Japan
- Department of Surgery, Kansai Medical University, Hirakata, Osaka, Japan
| | - Mikio Nishizawa
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
- * E-mail:
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Wang Y, Pang WJ, Wei N, Xiong Y, Wu WJ, Zhao CZ, Shen QW, Yang GS. Identification, stability and expression of Sirt1 antisense long non-coding RNA. Gene 2014; 539:117-24. [PMID: 24480449 DOI: 10.1016/j.gene.2014.01.037] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/31/2013] [Accepted: 01/10/2014] [Indexed: 01/23/2023]
Abstract
Natural antisense transcripts (NATs) exist ubiquitously as pivotal molecules to regulate coding gene expression. Sirtuin 1 (Sirt1) is a NAD-dependent deacetylase which is involved in myogenesis. However, whether Sirt1 transcribes NAT during C2C12 differentiation is still unknown. In this study, we identified a Sirt1 NAT which was designated as Sirt1 antisense long non-coding RNA (AS lncRNA) by sequencing and bioinformatic analysis. The level of Sirt1 AS lncRNA was greater in spleen but less in muscle tissue. The expression of both Sirt1 mRNA and Sirt1 AS lncRNA decreased during C2C12 myogenic differentiation, whereas the levels of miR-34a, which targets Sirt1, increased gradually. We further found that the half-life of Sirt1 AS lncRNA was 10h, but that of Sirt1 mRNA was 6h in C2C12 cells treated with 2 μg/ml Actinomycin D. Therefore, compared with Sirt1 mRNA, Sirt1 AS lncRNA was more stable. Overexpression of Sirt1 AS lncRNA increased the levels of Sirt1 protein, whereas overexpression of Sirt1 AS lncRNA mutant did not affect the level of Sirt1 protein in C2C12 cells. Moreover, downregulation of Sirt1 mRNA caused by miR-34a was counteracted by Sirt1 AS lncRNA in C2C12 cells. Taken together, we identified a novel NAT of Sirt1 which implicated in myogenesis through regulating Sirt1 expression.
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Affiliation(s)
- Yu Wang
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China.
| | - Wei-Jun Pang
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China.
| | - Ning Wei
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Yan Xiong
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Wen-Jing Wu
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Cun-Zhen Zhao
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Qing-Wu Shen
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Gong-She Yang
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
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Batagov AO, Yarmishyn AA, Jenjaroenpun P, Tan JZ, Nishida Y, Kurochkin IV. Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 3:S11. [PMID: 24555823 PMCID: PMC3852107 DOI: 10.1186/1752-0509-7-s3-s11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Mammalian genomes are extensively transcribed producing thousands of long non-protein-coding RNAs (lncRNAs). The biological significance and function of the vast majority of lncRNAs remain unclear. Recent studies have implicated several lncRNAs as playing important roles in embryonic development and cancer progression. LncRNAs are characterized with different genomic architectures in relationship with their associated protein-coding genes. Our study aimed at bridging lncRNA architecture with dynamical patterns of their expression using differentiating human neuroblastoma cells model. RESULTS LncRNA expression was studied in a 120-hours timecourse of differentiation of human neuroblastoma SH-SY5Y cells into neurons upon treatment with retinoic acid (RA), the compound used for the treatment of neuroblastoma. A custom microarray chip was utilized to interrogate expression levels of 9,267 lncRNAs in the course of differentiation. We categorized lncRNAs into 19 architecture classes according to their position relatively to protein-coding genes. For each architecture class, dynamics of expression of lncRNAs was studied in association with their protein-coding partners. It allowed us to demonstrate positive correlation of lncRNAs with their associated protein-coding genes at bidirectional promoters and for sense-antisense transcript pairs. In contrast, lncRNAs located in the introns and downstream of the protein-coding genes were characterized with negative correlation modes. We further classified the lncRNAs by the temporal patterns of their expression dynamics. We found that intronic and bidirectional promoter architectures are associated with rapid RA-dependent induction or repression of the corresponding lncRNAs, followed by their constant expression. At the same time, lncRNAs expressed downstream of protein-coding genes are characterized by rapid induction, followed by transcriptional repression. Quantitative RT-PCR analysis confirmed the discovered functional modes for several selected lncRNAs associated with proteins involved in cancer and embryonic development. CONCLUSIONS This is the first report detailing dynamical changes of multiple lncRNAs during RA-induced neuroblastoma differentiation. Integration of genomic and transcriptomic levels of information allowed us to demonstrate specific behavior of lncRNAs organized in different genomic architectures. This study also provides a list of lncRNAs with possible roles in neuroblastoma.
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Wright CM, Kirschner MB, Cheng YY, O'Byrne KJ, Gray SG, Schelch K, Hoda MA, Klebe S, McCaughan B, van Zandwijk N, Reid G. Long non coding RNAs (lncRNAs) are dysregulated in Malignant Pleural Mesothelioma (MPM). PLoS One 2013; 8:e70940. [PMID: 23976967 PMCID: PMC3747266 DOI: 10.1371/journal.pone.0070940] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 06/24/2013] [Indexed: 12/29/2022] Open
Abstract
Malignant Pleural Mesothelioma (MPM) is an aggressive cancer that is often diagnosed at an advanced stage and is characterized by a long latency period (20–40 years between initial exposure and diagnosis) and prior exposure to asbestos. Currently accurate diagnosis of MPM is difficult due to the lack of sensitive biomarkers and despite minor improvements in treatment, median survival rates do not exceed 12 months. Accumulating evidence suggests that aberrant expression of long non-coding RNAs (lncRNAs) play an important functional role in cancer biology. LncRNAs are a class of recently discovered non-protein coding RNAs >200 nucleotides in length with a role in regulating transcription. Here we used NCode long noncoding microarrays to identify differentially expressed lncRNAs potentially involved in MPM pathogenesis. High priority candidate lncRNAs were selected on the basis of statistical (P<0.05) and biological significance (>3-fold difference). Expression levels of 9 candidate lncRNAs were technically validated using RT-qPCR, and biologically validated in three independent test sets: (1) 57 archived MPM tissues obtained from extrapleural pneumonectomy patients, (2) 15 cryopreserved MPM and 3 benign pleura, and (3) an extended panel of 10 MPM cell lines. RT-qPCR analysis demonstrated consistent up-regulation of these lncRNAs in independent datasets. ROC curve analysis showed that two candidates were able to separate benign pleura and MPM with high sensitivity and specificity, and were associated with nodal metastases and survival following induction chemotherapy. These results suggest that lncRNAs have potential to serve as biomarkers in MPM.
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Affiliation(s)
- Casey M. Wright
- Asbestos Diseases Research Institute, The University of Sydney, Concord New South Wales, Australia
- * E-mail:
| | - Michaela B. Kirschner
- Asbestos Diseases Research Institute, The University of Sydney, Concord New South Wales, Australia
| | - Yuen Yee Cheng
- Asbestos Diseases Research Institute, The University of Sydney, Concord New South Wales, Australia
| | | | | | - Karin Schelch
- Institute of Cancer Research and Division of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Mir Alireza Hoda
- Institute of Cancer Research and Division of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sonja Klebe
- Flinders Medical Centre, Adelaide, Australia
| | - Brian McCaughan
- Department of Cardiothoracic Surgery, Royal Prince Alfred Hospital, and Department of Medical Oncology, Royal North Shore Hospital, Sydney, Australia
| | - Nico van Zandwijk
- Asbestos Diseases Research Institute, The University of Sydney, Concord New South Wales, Australia
| | - Glen Reid
- Asbestos Diseases Research Institute, The University of Sydney, Concord New South Wales, Australia
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Natural antisense transcript-targeted regulation of inducible nitric oxide synthase mRNA levels. Nitric Oxide 2013; 30:9-16. [DOI: 10.1016/j.niox.2013.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/26/2012] [Accepted: 01/14/2013] [Indexed: 12/27/2022]
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