151
|
Long noncoding RNA related to periodontitis interacts with miR-182 to upregulate osteogenic differentiation in periodontal mesenchymal stem cells of periodontitis patients. Cell Death Dis 2016; 7:e2327. [PMID: 27512949 PMCID: PMC5108307 DOI: 10.1038/cddis.2016.125] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 03/15/2016] [Accepted: 03/29/2016] [Indexed: 12/23/2022]
Abstract
Periodontitis impairs the osteogenic differentiation of human periodontal mesenchymal stem cells (hPDLSCs), but the underlying molecular mechanisms are still poorly understood. Long noncoding RNAs (lncRNAs) have been demonstrated to have significant roles under both physiologic and pathological conditions. In this study, we performed comprehensive lncRNA profiling by lncRNA microarray analysis and identified a novel lncRNA, osteogenesis impairment-related lncRNA of PDLSCs from periodontitis patients (lncRNA-POIR), the expression of which was significantly decreased in PDLSCs from periodontitis patients (pPDLSCs) and was upregulated by osteogenic induction. To study the functions of lncRNA-POIR, we prepared cells with overexpression and knockdown of lncRNA-POIR and found that lncRNA-POIR positively regulated osteogenic differentiation of hPDLSCs and pPDLSCs both in vitro and in vivo. Using quantitative real-time PCRs (qPCRs) and luciferase reporter assays, we demonstrated that lncRNA-POIR may act as a competing endogenous RNA (ceRNA) for miR-182, leading to derepression of its target gene, FoxO1. In this process, lncRNA-POIR and miR-182 suppress each other and form a network to regulate FoxO1. FoxO1 increased bone formation of pPDLSCs by competing with TCF-4 for β-catenin and inhibiting the canonical Wnt pathway. Finally, inflammation increases miR-182 expression through the nuclear factor-κB pathway, and the miR-182 overexpression in the inflammatory microenvironment resulted in an imbalance in the lncRNA-POIR-miR-182 regulatory network. In conclusion, our results provide novel evidence that this lncRNA-miRNA (microRNA) regulatory network has a significant role in osteogenic differentiation of pPDLSCs and that it has potential as a therapeutic target in mesenchymal stem cells during inflammation.
Collapse
|
152
|
Guo C, Li C, Yang K, Kang H, Xu X, Xu X, Deng L. Increased EZH2 and decreased osteoblastogenesis during local irradiation-induced bone loss in rats. Sci Rep 2016; 6:31318. [PMID: 27499068 PMCID: PMC4976370 DOI: 10.1038/srep31318] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023] Open
Abstract
Radiation therapy is commonly used to treat cancer patients but exhibits adverse effects, including insufficiency fractures and bone loss. Epigenetic regulation plays an important role in osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). Here, we reported local bone changes after single-dose exposure to 137CS irradiation in rats. Femur bone mineral density (BMD) and trabecular bone volume in the tibia were significantly decreased at 12 weeks after irradiation. Micro-CT results showed that tBMD, Tb.h and Tb.N were also significantly reduced at 12 weeks after irradiation exposure. ALP-positive OB.S/BS was decreased by 42.3% at 2 weeks after irradiation and was decreased by 50.8% at 12 weeks after exposure. In contrast to the decreased expression of Runx2 and BMP2, we found EZH2 expression was significantly increased at 2 weeks after single-dose 137CS irradiation in BMSCs. Together, our results demonstrated that single-dose 137CS irradiation induces BMD loss and the deterioration of bone microarchitecture in the rat skeleton. Furthermore, EZH2 expression increased and osteoblastogenesis decreased after irradiation. The underlying mechanisms warrant further investigation.
Collapse
Affiliation(s)
- Changjun Guo
- Shanghai Key Laboratory for the Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine. Address: No. 197, Rui Jin Er Road, Shanghai 200025 China
| | - Changwei Li
- Shanghai Key Laboratory for the Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine. Address: No. 197, Rui Jin Er Road, Shanghai 200025 China
| | - Kai Yang
- Shanghai Key Laboratory for the Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine. Address: No. 197, Rui Jin Er Road, Shanghai 200025 China
| | - Hui Kang
- Shanghai Key Laboratory for the Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine. Address: No. 197, Rui Jin Er Road, Shanghai 200025 China
| | - Xiaoya Xu
- Department of Bone Metabolism, Institute of Radiation Medicine, Fudan University, Shanghai 200032, China. Address: No. 2094, Xietu Road, Shanghai 200032 China
| | - Xiangyang Xu
- Department of Orthopedics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine. Address: No. 197, Rui Jin Er Road, Shanghai 200025 China
| | - Lianfu Deng
- Shanghai Key Laboratory for the Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine. Address: No. 197, Rui Jin Er Road, Shanghai 200025 China
| |
Collapse
|
153
|
Jin C, Jia L, Huang Y, Zheng Y, Du N, Liu Y, Zhou Y. Inhibition of lncRNA MIR31HG Promotes Osteogenic Differentiation of Human Adipose-Derived Stem Cells. Stem Cells 2016; 34:2707-2720. [PMID: 27334046 DOI: 10.1002/stem.2439] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/30/2016] [Indexed: 01/04/2023]
Abstract
Osteogenic differentiation and bone formation is suppressed under condition of inflammation induced by proinflammation cytokines. A number of studies indicate miRNAs play a significant role in tumor necrosis factor-α-induced inhibition of bone formation, but whether long non-coding RNAs are also involved in this process remains unknown. In this study, we evaluated the role of MIR31HG in osteogenesis of human adipose-derived stem cells (hASCs) in vitro and in vivo. The results suggested that knockdown of MIR31HG not only significantly promoted osteogenic differentiation, but also dramatically overcame the inflammation-induced inhibition of osteogenesis in hASCs. Mechanistically, we found MIR31HG regulated bone formation and inflammation via interacting with NF-κB. The p65 subunit bound to the MIR31HG promoter and promoted MIR31HG expression. In turn, MIR31HG directly interacted with IκBα and participated in NF-κB activation, which builds a regulatory circuitry with NF-κB. Targeting this MIR31HG-NF-κB regulatory loop may be helpful to improve the osteogenic capacity of hASCs under inflammatory microenvironment in bone tissue engineering. Stem Cells 2016;34:2707-2720.
Collapse
Affiliation(s)
- Chanyuan Jin
- Department of Prosthodontics.,National Engineering Lab for Digital and Material Technology of Stomatology, Peking University School and Hospital of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing, China
| | - Lingfei Jia
- Department of Oral and Maxillofacial Surgery.,Central Laboratory
| | | | | | | | | | - Yongsheng Zhou
- Department of Prosthodontics.,National Engineering Lab for Digital and Material Technology of Stomatology, Peking University School and Hospital of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing, China
| |
Collapse
|
154
|
Schmitz SU, Grote P, Herrmann BG. Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci 2016; 73:2491-509. [PMID: 27007508 PMCID: PMC4894931 DOI: 10.1007/s00018-016-2174-5] [Citation(s) in RCA: 769] [Impact Index Per Article: 96.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 11/25/2022]
Abstract
Since decades it has been known that non-protein-coding RNAs have important cellular functions. Deep sequencing recently facilitated the discovery of thousands of novel transcripts, now classified as long noncoding RNAs (lncRNAs), in many vertebrate and invertebrate species. LncRNAs are involved in a wide range of cellular mechanisms, from almost all aspects of gene expression to protein translation and stability. Recent findings implicate lncRNAs as key players of cellular differentiation, cell lineage choice, organogenesis and tissue homeostasis. Moreover, lncRNAs are involved in pathological conditions such as cancer and cardiovascular disease, and therefore provide novel biomarkers and pharmaceutical targets. Here we discuss examples illustrating the versatility of lncRNAs in gene control, development and differentiation, as well as in human disease.
Collapse
Affiliation(s)
- Sandra U Schmitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
- Institute for Medical Genetics, Campus Benjamin Franklin, Charite-University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany.
| |
Collapse
|
155
|
Long noncoding RNAs in cell differentiation and pluripotency. Cell Tissue Res 2016; 366:509-521. [PMID: 27365087 DOI: 10.1007/s00441-016-2451-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/31/2016] [Indexed: 01/20/2023]
Abstract
Long noncoding RNAs (lncRNAs) were once regarded as nonfunctional by-products of transcription but their effects are now gradually being elucidated. Evidence suggests that lncRNAs play crucial roles in cell biology, especially in regulating gene expression. However, because of the diversity and complexity of their regulatory mechanisms, our knowledge of the function of lncRNAs represents only the tip of the iceberg. Recent studies have shown that lncRNAs are capable of regulating cell differentiation and pluripotency. Thus, we consider it to be an appropriate time to review the progress in understanding the role of lncRNAs in these two biological processes. In this review, the biological characteristics and regulatory mechanisms of lncRNAs at the chromatin remodeling level, transcriptional level and post-transcriptional level are described and recent advances in our comprehension of the role of lncRNAs in cell differentiation and pluripotency are discussed.
Collapse
|
156
|
Sun Y, Zheng ZP, Li H, Zhang HQ, Ma FQ. ANRIL is associated with the survival rate of patients with colorectal cancer, and affects cell migration and invasion in vitro. Mol Med Rep 2016; 14:1714-20. [PMID: 27314206 DOI: 10.3892/mmr.2016.5409] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 05/20/2016] [Indexed: 01/16/2023] Open
Abstract
Antisense noncoding RNA in the INK4 locus (ANRIL) has been reported to be upregulated in various types of human cancer, and is also highly expressed in normal human tissue. The aim of the present study was to identify whether ANRIL may be a possible target for colorectal cancer (CRC) therapy. Reverse transcription‑quantitative polymerase chain reaction was used to quantify the expression levels of the long noncoding RNA (lncRNA) ANRIL in 97 paired CRC and adjacent non‑neoplastic tissue samples. In addition, the HT29 and RKO human CRC cell lines underwent ANRIL RNA interference, and knockdown efficiency was evaluated by western blotting. Cell viability, and migratory and invasive ability were subsequently assessed. The CRC tissues were revealed to express higher levels of ANRIL lncRNA compared with the adjacent non‑neoplastic tissues (P<0.05). Furthermore, high ANRIL expression was significantly associated with reduced survival rate (P<0.05). ANRIL gene expression was successfully silenced in human CRC cells. ANRIL knockdown decreased proliferation, inhibited migration and invasion, and reduced the colony‑forming ability of the cells. These data indicated that the lncRNA ANRIL is upregulated in CRC tissues, and is associated with CRC cell pathogenesis. Furthermore, the underlying mechanisms of these effects may be exploited for therapeutic benefit.
Collapse
Affiliation(s)
- Yi Sun
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Zhao-Peng Zheng
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Hang Li
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Han-Qun Zhang
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Fa-Qiang Ma
- Department of Oncology, The Second Affiliated Hospital of Guizhou Medical University, Kaili, Guizhou 556000, P.R. China
| |
Collapse
|
157
|
Labott AT, Lopez-Pajares V. Epidermal differentiation gene regulatory networks controlled by MAF and MAFB. Cell Cycle 2016; 15:1405-9. [PMID: 27097296 DOI: 10.1080/15384101.2016.1172148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Numerous regulatory factors in epidermal differentiation and their role in regulating different cell states have been identified in recent years. However, the genetic interactions between these regulators over the dynamic course of differentiation have not been studied. In this Extra-View article, we review recent work by Lopez-Pajares et al. that explores a new regulatory network in epidermal differentiation. They analyze the changing transcriptome throughout epidermal regeneration to identify 3 separate gene sets enriched in the progenitor, early and late differentiation states. Using expression module mapping, MAF along with MAFB, are identified as transcription factors essential for epidermal differentiation. Through double knock-down of MAF:MAFB using siRNA and CRISPR/Cas9-mediated knockout, epidermal differentiation was shown to be impaired both in-vitro and in-vivo, confirming MAF:MAFB's role to activate genes that drive differentiation. Lopez-Pajares and collaborators integrated 42 published regulator gene sets and the MAF:MAFB gene set into the dynamic differentiation gene expression landscape and found that lncRNAs TINCR and ANCR act as upstream regulators of MAF:MAFB. Furthermore, ChIP-seq analysis of MAF:MAFB identified key transcription factor genes linked to epidermal differentiation as downstream effectors. Combined, these findings illustrate a dynamically regulated network with MAF:MAFB as a crucial link for progenitor gene repression and differentiation gene activation.
Collapse
Affiliation(s)
- Andrew T Labott
- a Program in Epithelial Biology, Stanford University , Stanford , CA , USA
| | | |
Collapse
|
158
|
Saus E, Brunet-Vega A, Iraola-Guzmán S, Pegueroles C, Gabaldón T, Pericay C. Long Non-Coding RNAs As Potential Novel Prognostic Biomarkers in Colorectal Cancer. Front Genet 2016; 7:54. [PMID: 27148353 PMCID: PMC4828582 DOI: 10.3389/fgene.2016.00054] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/21/2016] [Indexed: 01/27/2023] Open
Abstract
Colorectal cancer (CRC) is the fourth most common cause of death worldwide. Surgery is usually the first line of treatment for patients with CRC but many tumors with similar histopathological features show significantly different clinical outcomes. The discovery of robust prognostic biomarkers in patients with CRC is imperative to achieve more effective treatment strategies and improve patient's care. Recent progress in next generation sequencing methods and transcriptome analysis has revealed that a much larger part of the genome is transcribed into RNA than previously assumed. Collectively referred to as non-coding RNAs (ncRNAs), some of these RNA molecules such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been shown to be altered and to play critical roles in tumor biology. This discovery leads to exciting possibilities for personalized cancer diagnosis, and therapy. Many lncRNAs are tissue and cancer-type specific and have already revealed to be useful as prognostic markers. In this review, we focus on recent findings concerning aberrant expression of lncRNAs in CRC tumors and emphasize their prognostic potential in CRC. Further studies focused on the mechanisms of action of lncRNAs will contribute to the development of novel biomarkers for diagnosis and disease progression.
Collapse
Affiliation(s)
- Ester Saus
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Anna Brunet-Vega
- Department of Oncology Research, Parc Taulí Foundation, Corporació Sanitària Parc Taulí - University Institute - UAB Barcelona Sabadell, Spain
| | - Susana Iraola-Guzmán
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Cinta Pegueroles
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Institució Catalana de Recerca i Estudis AvançatsBarcelona, Spain
| | - Carles Pericay
- Department of Oncology Research, Parc Taulí Foundation, Corporació Sanitària Parc Taulí - University Institute - UAB BarcelonaSabadell, Spain; Oncology Service, Hospital de Sabadell, Corporació Sanitària Parc Taulí - University Institute - UAB BarcelonaSabadell, Spain
| |
Collapse
|
159
|
Lopez-Pajares V. Long non-coding RNA regulation of gene expression during differentiation. Pflugers Arch 2016; 468:971-81. [PMID: 26996975 DOI: 10.1007/s00424-016-1809-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 12/13/2022]
Abstract
Transcriptome analysis of mammalian genomes has revealed widespread transcription, much of which does not encode protein. Long non-coding RNAs (lncRNAs) are a subset of the non-coding transcriptome that are emerging as critical regulators of various cellular processes. Differentiation of stem and progenitor cells requires a careful execution of specific genetic programs, and recent studies have revealed that lncRNA expression contributes to specification of cell identity. LncRNAs participate in regulating differentiation at multiple levels of gene expression through various mechanisms of action. In this review, functional roles of lncRNAs in regulating cellular differentiation of blood, muscle, skin, cardiomyocytes, adipocytes, and neurons are discussed.
Collapse
Affiliation(s)
- Vanessa Lopez-Pajares
- Program in Epithelial Biology, Stanford University, 269 Campus Drive, Room 2150, Stanford, CA, 94305, USA.
| |
Collapse
|
160
|
Qu Q, Fang F, Wu B, Hu Y, Chen M, Deng Z, Ma D, Chen T, Hao Y, Ge Y. Potential Role of Long Non-Coding RNA in Osteogenic Differentiation of Human Periodontal Ligament Stem Cells. J Periodontol 2016; 87:e127-37. [PMID: 26991483 DOI: 10.1902/jop.2016.150592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are emerging as important regulators of eukaryotic gene expression and have been shown to regulate various modular components of development and differentiation. However, the roles of lncRNAs in the regulation of osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs) remain poorly understood. METHODS Expression patterns of lncRNA and messenger RNA (mRNA) during osteogenic differentiation were profiled using microarray analysis. Quantitative reverse transcription polymerase chain reaction was performed to validate the microarray data. Biologic functions of candidates were revealed by: 1) cluster analysis; 2) gene ontology (GO); and 3) pathway analysis. Coding-non-coding gene coexpression (CNC) networks were constructed to investigate potential regulatory roles of lncRNAs and osteogenesis-related mRNAs. RESULTS After osteoinduction, 3,557 mRNAs and 2,171 lncRNAs were differentially expressed, of which 994 lncRNAs were upregulated and 1,177 were downregulated (fold change >2.0 or <-2.0; P <0.05). Cluster analysis showed that lncRNAs and mRNAs from the experimental and control groups belonged to different clusters. GO analysis demonstrated that: 1) cellular process; 2) biologic regulation; and 3) regulation of biologic process were the most significant groups related to induction. Pathway analysis indicated that 83 pathways corresponded to differentially expressed mRNAs, including: 1) mitogen-activated protein kinase; 2) vascular endothelial growth factor; and 3) transforming growth factor-β signaling pathways. CNC network analysis indicated that 393 lncRNAs were closely related to osteogenesis-related mRNAs. CONCLUSIONS Expression profiles of lncRNAs and mRNAs were significantly altered during osteogenic differentiation of hPDLSCs. This result suggests that lncRNAs may play crucial roles in this process and could regulate mRNA expression.
Collapse
Affiliation(s)
- Qian Qu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fuchun Fang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Buling Wu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanwei Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University
| | - Ming Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zilong Deng
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dandan Ma
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yilin Hao
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yihong Ge
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
161
|
Dole NS, Delany AM. MicroRNA variants as genetic determinants of bone mass. Bone 2016; 84:57-68. [PMID: 26723575 PMCID: PMC4755870 DOI: 10.1016/j.bone.2015.12.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 02/07/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant genetic variants that contribute to the heritability of bone mass. MicroRNAs (miRNAs, miRs) are key post-transcriptional regulators that modulate the differentiation and function of skeletal cells by targeting multiple genes in the same or distinct signaling pathways. SNPs in miRNA genes and miRNA binding sites can alter miRNA abundance and mRNA targeting. This review describes the potential impact of miRNA-related SNPs on skeletal phenotype. Although many associations between SNPs and bone mass have been described, this review is limited to gene variants for which a function has been experimentally validated. SNPs in miRNA genes (miR-SNPs) that impair miRNA processing and alter the abundance of mature miRNA are discussed for miR-146a, miR-125a, miR-196a, miR-149 and miR-27a. SNPs in miRNA targeting sites (miR-TS-SNPs) that alter miRNA binding are described for the bone remodeling genes bone morphogenetic protein receptor 1 (Bmpr1), fibroblast growth factor 2 (Fgf2), osteonectin (Sparc) and histone deacetylase 5 (Hdac5). The review highlights two aspects of miRNA-associated SNPs: the mechanism for altering miRNA mediated gene regulation and the potential of miR-associated SNPs to alter osteoblast, osteoclast or chondrocyte differentiation and function. Given the polygenic nature of skeletal diseases like osteoporosis and osteoarthritis, validating the function of additional miRNA-associated SNPs has the potential to enhance our understanding of the genetic determinants of bone mass and predisposition to selected skeletal diseases.
Collapse
Affiliation(s)
- Neha S Dole
- Center for Molecular Medicine, UCONN Health, Farmington, CT, USA.
| | - Anne M Delany
- Center for Molecular Medicine, UCONN Health, Farmington, CT, USA.
| |
Collapse
|
162
|
McFadden EJ, Hargrove AE. Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin. Biochemistry 2016; 55:1615-30. [PMID: 26859437 DOI: 10.1021/acs.biochem.5b01141] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs), defined as nontranslated transcripts greater than 200 nucleotides in length, are often differentially expressed throughout developmental stages, tissue types, and disease states. The identification, visualization, and suppression/overexpression of these sequences have revealed impacts on a wide range of biological processes, including epigenetic regulation. Biochemical investigations on select systems have revealed striking insight into the biological roles of lncRNAs and lncRNA:protein complexes, which in turn prompt even more unanswered questions. To begin, multiple protein- and RNA-centric technologies have been employed to isolate lncRNA:protein and lncRNA:chromatin complexes. LncRNA interactions with the multi-subunit protein complex PRC2, which acts as a transcriptional silencer, represent some of the few cases where the binding affinity, selectivity, and activity of a lncRNA:protein complex have been investigated. At the same time, recent reports of full-length lncRNA secondary structures suggest the formation of complex structures with multiple independent folding domains and pave the way for more detailed structural investigations and predictions of lncRNA three-dimensional structure. This review will provide an overview of the methods and progress made to date as well as highlight new methods that promise to further inform the molecular recognition, specificity, and function of lncRNAs.
Collapse
Affiliation(s)
- Emily J McFadden
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Amanda E Hargrove
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University , 124 Science Drive, Durham, North Carolina 27708, United States
| |
Collapse
|
163
|
Liang WC, Fu WM, Wang YB, Sun YX, Xu LL, Wong CW, Chan KM, Li G, Waye MMY, Zhang JF. H19 activates Wnt signaling and promotes osteoblast differentiation by functioning as a competing endogenous RNA. Sci Rep 2016; 6:20121. [PMID: 26853553 PMCID: PMC4745008 DOI: 10.1038/srep20121] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/21/2015] [Indexed: 12/21/2022] Open
Abstract
Bone homeostasis is tightly orchestrated and maintained by the balance between osteoblasts and osteoclasts. Recent studies have greatly expanded our understanding of the molecular mechanisms of cellular differentiation. However, the functional roles of non-coding RNAs particularly lncRNAs in remodeling bone architecture remain elusive. In our study, lncRNA H19 was found to be upregulated during osteogenesis in hMSCs. Stable expression of H19 significantly accelerated in vivo and in vitro osteoblast differentiation. Meanwhile, by using bioinformatic investigations and RIP assays combined with luciferase reporter assays, we demonstrated that H19 functioned as an miRNA sponge for miR-141 and miR-22, both of which were negative regulators of osteogenesis and Wnt/β-catenin pathway. Further investigations revealed that H19 antagonized the functions of these two miRNAs and led to de-repression of their shared target gene β-catenin, which eventually activated Wnt/β-catenin pathway and hence potentiated osteogenesis. In addition, we also identified a novel regulatory feedback loop between H19 and its encoded miR-675-5p. And miR-675-5p was found to directly target H19 and counteracted osteoblast differentiation. To sum up, these observations indicate that the lncRNA H19 modulates Wnt/β-catenin pathway by acting as a competing endogenous RNA, which may shed light on the functional role of lncRNAs in coordinating osteogenesis.
Collapse
Affiliation(s)
- Wei-Cheng Liang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, P.R. China
| | - Wei-Ming Fu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R.China.,Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, 510000, P.R. China
| | - Yu-Bing Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, P.R. China
| | - Yu-Xin Sun
- Department of Orthopaedics &Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. China
| | - Liang-Liang Xu
- Department of Orthopaedics &Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, P.R. China
| | - Cheuk-Wa Wong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, P.R. China
| | - Kai-Ming Chan
- Department of Orthopaedics &Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. China.,Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. China
| | - Gang Li
- Department of Orthopaedics &Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, P.R. China.,Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. China
| | - Mary Miu-Yee Waye
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, P.R. China
| | - Jin-Fang Zhang
- Department of Orthopaedics &Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, P.R. China.,Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. China.,School of medicine, South China Unversity of Technlogy, Guangzhou, 510000, P.R. China
| |
Collapse
|
164
|
lncRNA DANCR suppresses odontoblast-like differentiation of human dental pulp cells by inhibiting wnt/β-catenin pathway. Cell Tissue Res 2015; 364:309-18. [DOI: 10.1007/s00441-015-2333-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022]
|
165
|
Gordon JAR, Stein JL, Westendorf JJ, van Wijnen AJ. Chromatin modifiers and histone modifications in bone formation, regeneration, and therapeutic intervention for bone-related disease. Bone 2015; 81:739-745. [PMID: 25836763 PMCID: PMC4591092 DOI: 10.1016/j.bone.2015.03.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/13/2015] [Indexed: 02/07/2023]
Abstract
Post-translational modifications of chromatin such as DNA methylation and different types of histone acetylation, methylation and phosphorylation are well-appreciated epigenetic mechanisms that confer information to progeny cells during lineage commitment. These distinct epigenetic modifications have defined roles in bone, development, tissue regeneration, cell commitment and differentiation, as well as disease etiologies. In this review, we discuss the role of these chromatin modifications and the enzymes regulating these marks (methyltransferases, demethylases, acetyltransferases, and deacetylases) in progenitor cells, osteoblasts and bone-related cells. In addition, the clinical relevance of deregulated histone modifications and enzymes as well as current and potential therapeutic interventions targeting chromatin modifiers are addressed.
Collapse
Affiliation(s)
| | - Janet L Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA.
| | | | | |
Collapse
|
166
|
Abstract
Non-coding RNAs (ncRNAs) have evolved in eukaryotes as epigenetic regulators of gene expression. The most abundant regulatory ncRNAs are the 20-24 nt small microRNAs (miRNAs) and long non-coding RNAs (lncRNAs, <200 nt). Each class of ncRNAs operates through distinct mechanisms, but their pathways to regulating gene expression are interrelated in ways that are just being recognized. While the importance of lncRNAs in epigenetic control of transcription, developmental processes and human traits is emerging, the identity of lncRNAs in skeletal biology is scarcely known. However, since the first profiling studies of miRNA at stages during osteoblast and osteoclast differentiation, over 1100 publications related to bone biology and pathologies can be found, as well as many recent comprehensive reviews summarizing miRNA in skeletal cells. Delineating the activities and targets of specific miRNAs regulating differentiation of osteogenic and resorptive bone cells, coupled with in vivo gain- and loss-of-function studies, discovered unique mechanisms that support bone development and bone homeostasis in adults. We present here "guiding principles" for addressing biological control of bone tissue formation by ncRNAs. This review emphasizes recent advances in understanding regulation of the process of miRNA biogenesis that impact on osteogenic lineage commitment, transcription factors and signaling pathways. Also discussed are the approaches to be pursued for an understanding of the role of lncRNAs in bone and the challenges in addressing their multiple and complex functions. Based on new knowledge of epigenetic control of gene expression to be gained for ncRNA regulation of the skeleton, new directions for translating the miRNAs and lncRNAs into therapeutic targets for skeletal disorders are possible. This article is part of a Special Issue entitled Epigenetics and Bone.
Collapse
Affiliation(s)
- Mohammad Q Hassan
- Department of Oral & Maxillofacial Surgery, School of Dentistry, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA.
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA.
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA.
| |
Collapse
|
167
|
Lennox KA, Behlke MA. Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Res 2015; 44:863-77. [PMID: 26578588 PMCID: PMC4737147 DOI: 10.1093/nar/gkv1206] [Citation(s) in RCA: 329] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/26/2015] [Indexed: 12/16/2022] Open
Abstract
Thousands of long non-coding RNAs (lncRNAs) have been identified in mammalian cells. Some have important functions and their dysregulation can contribute to a variety of disease states. However, most lncRNAs have not been functionally characterized. Complicating their study, lncRNAs have widely varying subcellular distributions: some reside predominantly in the nucleus, the cytoplasm or in both compartments. One method to query function is to suppress expression and examine the resulting phenotype. Methods to suppress expression of mRNAs include antisense oligonucleotides (ASOs) and RNA interference (RNAi). Antisense and RNAi-based gene-knockdown methods vary in efficacy between different cellular compartments. It is not known if this affects their ability to suppress lncRNAs. To address whether localization of the lncRNA influences susceptibility to degradation by either ASOs or RNAi, nuclear lncRNAs (MALAT1 and NEAT1), cytoplasmic lncRNAs (DANCR and OIP5-AS1) and dual-localized lncRNAs (TUG1, CasC7 and HOTAIR) were compared for knockdown efficiency. We found that nuclear lncRNAs were more effectively suppressed using ASOs, cytoplasmic lncRNAs were more effectively suppressed using RNAi and dual-localized lncRNAs were suppressed using both methods. A mixed-modality approach combining ASOs and RNAi reagents improved knockdown efficacy, particularly for those lncRNAs that localize to both nuclear and cytoplasmic compartments.
Collapse
Affiliation(s)
- Kim A Lennox
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| |
Collapse
|
168
|
Hart JR, Roberts TC, Weinberg MS, Morris KV, Vogt PK. MYC regulates the non-coding transcriptome. Oncotarget 2015; 5:12543-54. [PMID: 25587025 PMCID: PMC4350361 DOI: 10.18632/oncotarget.3033] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 01/17/2023] Open
Abstract
Using RNA-seq (RNA sequencing) of ribosome-depleted RNA, we have identified 1,273 lncRNAs (long non-coding RNAs) in P493-6 human B-cells. Of these, 534 are either up- or downregulated in response to MYC overexpression. An increase in MYC occupancy near their TSS (transcription start sites) was observed for MYC-responsive lncRNAs suggesting these are direct MYC targets. MYC binds to the same TSS across several cell lines, but the number of TSS bound depends on cellular MYC levels and increases with higher MYC concentrations. Despite this concordance in promoter binding, a majority of expressed lncRNAs are specific for one cell line, suggesting a determinant role of additional, possibly differentiation-specific factors in the activity of MYC-bound lncRNA promoters. A significant fraction of the lncRNA transcripts lack polyadenylation. The RNA-seq data were confirmed on eight selected lncRNAs by NRO (nuclear run-on) and RT-qPCR (quantitative reverse transcription PCR).
Collapse
Affiliation(s)
- Jonathan R Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas C Roberts
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS, South Africa
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW, Australia
| | - Peter K Vogt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| |
Collapse
|
169
|
Cho J, Yu NK, Choi JH, Sim SE, Kang SJ, Kwak C, Lee SW, Kim JI, Choi DI, Kim VN, Kaang BK. Multiple repressive mechanisms in the hippocampus during memory formation. Science 2015; 350:82-7. [PMID: 26430118 DOI: 10.1126/science.aac7368] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Memory stabilization after learning requires translational and transcriptional regulations in the brain, yet the temporal molecular changes that occur after learning have not been explored at the genomic scale. We used ribosome profiling and RNA sequencing to quantify the translational status and transcript levels in the mouse hippocampus after contextual fear conditioning. We revealed three types of repressive regulations: translational suppression of ribosomal protein-coding genes in the hippocampus, learning-induced early translational repression of specific genes, and late persistent suppression of a subset of genes via inhibition of estrogen receptor 1 (ESR1/ERα) signaling. In behavioral analyses, overexpressing Nrsn1, one of the newly identified genes undergoing rapid translational repression, or activating ESR1 in the hippocampus impaired memory formation. Collectively, this study unveils the yet-unappreciated importance of gene repression mechanisms for memory formation.
Collapse
Affiliation(s)
- Jun Cho
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea. Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - Nam-Kyung Yu
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - Jun-Hyeok Choi
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - Su-Eon Sim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - SukJae Joshua Kang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - Chuljung Kwak
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - Seung-Woo Lee
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - Ji-il Kim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - Dong Il Choi
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea. Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea.
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea.
| |
Collapse
|
170
|
Huang Y, Zheng Y, Jia L, Li W. Long Noncoding RNA H19 Promotes Osteoblast Differentiation Via TGF-β1/Smad3/HDAC Signaling Pathway by Deriving miR-675. Stem Cells 2015; 33:3481-92. [PMID: 26417995 DOI: 10.1002/stem.2225] [Citation(s) in RCA: 240] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 08/01/2015] [Accepted: 08/24/2015] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as important regulatory molecules at the transcriptional and post-transcriptional levels and may play essential roles in the differentiation of human bone marrow mesenchymal stem cell (hMSC). However, their roles and functions remain unclear. Here, we showed that lncRNA H19 was significantly upregulated after the induction of osteoblast differentiation. Overexpression of H19 promoted osteogenic differentiation of hMSCs in vitro and enhanced heterotopic bone formation in vivo, whereas knockdown of H19 inhibited these effects. Subsequently, we found that miR-675, encoded by exon1 of H19, promoted osteoblast differentiation of hMSCs and was partially responsible for the pro-osteogenic effect of H19. Investigating the underlying mechanism, we demonstrated that H19/miR-675 inhibited mRNA and protein expression of transforming growth factor-β1 (TGF-β1). The downregulation of TGF-β1 subsequently inhibited phosphorylation of Smad3. Meanwhile, H19/miR-675 downregulated the mRNA and protein levels of histone deacetylase (HDAC) 4/5, and thus increased osteoblast marker gene expression. Taken together, our results demonstrated that the novel pathway H19/miR-675/TGF-β1/Smad3/HDAC regulates osteogenic differentiation of hMSCs and may serve as a potential target for enhancing bone formation in vivo.
Collapse
Affiliation(s)
- Yiping Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Yunfei Zheng
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Lingfei Jia
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China.,Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Weiran Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| |
Collapse
|
171
|
Sarkar D, Leung EY, Baguley BC, Finlay GJ, Askarian-Amiri ME. Epigenetic regulation in human melanoma: past and future. Epigenetics 2015; 10:103-21. [PMID: 25587943 PMCID: PMC4622872 DOI: 10.1080/15592294.2014.1003746] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The development and progression of melanoma have been attributed to independent or combined genetic and epigenetic events. There has been remarkable progress in understanding melanoma pathogenesis in terms of genetic alterations. However, recent studies have revealed a complex involvement of epigenetic mechanisms in the regulation of gene expression, including methylation, chromatin modification and remodeling, and the diverse activities of non-coding RNAs. The roles of gene methylation and miRNAs have been relatively well studied in melanoma, but other studies have shown that changes in chromatin status and in the differential expression of long non-coding RNAs can lead to altered regulation of key genes. Taken together, they affect the functioning of signaling pathways that influence each other, intersect, and form networks in which local perturbations disturb the activity of the whole system. Here, we focus on how epigenetic events intertwine with these pathways and contribute to the molecular pathogenesis of melanoma.
Collapse
Key Words
- 5hmC, 5-hydroxymethylcytosine
- 5mC, 5-methylcytosine
- ACE, angiotensin converting enzyme
- ANCR, anti-differentiation non-coding RNA
- ANRIL, antisense noncoding RNA in INK4 locus
- ASK1, apoptosis signal-regulating kinase 1
- ATRA, all-trans retinoic acid
- BANCR, BRAF-activated non-coding RNA
- BCL-2, B-cell lymphoma 2
- BRAF, B-Raf proto-oncogene, serine/threonine kinase
- BRG1, ATP-dependent helicase SMARCA4
- CAF-1, chromatin assembly factor-1
- CBX7, chromobox homolog 7
- CCND1, cyclin D1
- CD28, cluster of differentiation 28
- CDK, cyclin-dependent kinase
- CDKN2A/B, cyclin-dependent kinase inhibitor 2A/B
- CHD8, chromodomain-helicase DNA-binding protein 8
- CREB, cAMP response element-binding protein
- CUDR, cancer upregulated drug resistant
- Cdc6, cell division cycle 6
- DNA methylation/demethylation
- DNMT, DNA methyltransferase
- EMT, epithelial-mesenchymal transition
- ERK, extracellular signal-regulated kinase
- EZH2, enhancer of zeste homolog 2
- GPCRs, G-protein coupled receptors
- GSK3a, glycogen synthase kinase 3 α
- GWAS, genome-wide association study
- HDAC, histone deacetylase
- HOTAIR, HOX antisense intergenic RNA
- IAP, inhibitor of apoptosis
- IDH2, isocitrate dehydrogenase
- IFN, interferon, interleukin 23
- JNK, Jun N-terminal kinase
- Jak/STAT, Janus kinase/signal transducer and activator of transcription
- MAFG, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MAPK, mitogen-activated protein kinase
- MC1R, melanocortin-1 receptor
- MGMT, O6-methylguanine-DNA methyltransferase
- MIF, macrophage migration inhibitory factor
- MITF, microphthalmia-associated transcription factor
- MRE, miRNA recognition element
- MeCP2, methyl CpG binding protein 2
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOD, nucleotide-binding and oligomerization domain
- PBX, pre-B-cell leukemia homeobox
- PEDF, pigment epithelium derived factor
- PI3K, phosphatidylinositol-4, 5-bisphosphate 3-kinase
- PIB5PA, phosphatidylinositol-4, 5-biphosphate 5-phosphatase A
- PKA, protein kinase A
- PRC, polycomb repressor complex
- PSF, PTB associated splicing factor
- PTB, polypyrimidine tract-binding
- PTEN, phosphatase and tensin homolog
- RARB, retinoic acid receptor-β2
- RASSF1A, Ras association domain family 1A
- SETDB1, SET Domain, bifurcated 1
- SPRY4, Sprouty 4
- STAU1, Staufen1
- SWI/SNF, SWItch/Sucrose Non-Fermentable
- TCR, T-cell receptor
- TET, ten eleven translocase
- TGF β, transforming growth factor β
- TINCR, tissue differentiation-inducing non-protein coding RNA
- TOR, target of rapamycin
- TP53, tumor protein 53
- TRAF6, TNF receptor-associated factor 6
- UCA1, urothelial carcinoma-associated 1
- ceRNA, competitive endogenous RNAs
- chromatin modification
- chromatin remodeling
- epigenetics
- gene regulation
- lncRNA, long ncRNA
- melanoma
- miRNA, micro RNA
- ncRNA, non-coding RNA
- ncRNAs
- p14ARF, p14 alternative reading frame
- p16INK4a, p16 inhibitor of CDK4
- pRB, retinoblastoma protein
- snoRNA, small nucleolar RNA
- α-MSHm, α-melanocyte stimulating hormone
Collapse
Affiliation(s)
- Debina Sarkar
- a Auckland Cancer Society Research Center ; University of Auckland ; Auckland , New Zealand
| | | | | | | | | |
Collapse
|
172
|
Upregulation of long non-coding RNA HIF 1α-anti-sense 1 induced by transforming growth factor-β-mediated targeting of sirtuin 1 promotes osteoblastic differentiation of human bone marrow stromal cells. Mol Med Rep 2015; 12:7233-8. [PMID: 26460121 PMCID: PMC4626181 DOI: 10.3892/mmr.2015.4415] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 07/21/2015] [Indexed: 12/02/2022] Open
Abstract
The present study aimed to investigate the regulatory mechanism of long non-coding RNA hypoxia-inducible factor 1α-anti-sense 1 (lncRNA HIF1α-AS1) in osteoblast differentiation as well as its targeting by sirtuin 1 (SIRT1), which may be inhibited by transforming growth factor (TGF)-β in bone marrow stromal cells (BMSCs). Real-time polymerase chain reaction (PCR), western blot analysis, lncRNA PCR arrays and chromatin immunoprecipitation were performed in order to examine the interference of SIRT1 expression by TGF-β, the effects of SIRT1 overexpression on lncRNA HIF1α-AS1 and the regulation of the expression of homeobox (HOX)D10, which promotes BMSC differentiation, by lncRNA HIF1α-AS1. The results showed that TGF-β interfered with SIRT1 expression. Furthermore, lncRNA HIF1α-AS1 was significantly downregulated following overexpression of SIRT1. In addition, low expression of HIF1α-AS1 was sufficient to block the expression of HOXD10. The present study further demonstrated that downregulation of HOXD10 by HIF1α-AS1 interfered with acetylation, and subsequently resulted in the inhibition of osteoblast differentiation. These results suggested that HIF1α-AS1 is an essential mediator of osteoblast differentiation, and may thus represent a gene-therapeutic agent for the treatment of human bone diseases.
Collapse
|
173
|
Dudakovic A, Camilleri ET, Xu F, Riester SM, McGee-Lawrence ME, Bradley EW, Paradise CR, Lewallen EA, Thaler R, Deyle DR, Larson AN, Lewallen DG, Dietz AB, Stein GS, Montecino MA, Westendorf JJ, van Wijnen AJ. Epigenetic Control of Skeletal Development by the Histone Methyltransferase Ezh2. J Biol Chem 2015; 290:27604-17. [PMID: 26424790 DOI: 10.1074/jbc.m115.672345] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 11/06/2022] Open
Abstract
Epigenetic control of gene expression is critical for normal fetal development. However, chromatin-related mechanisms that activate bone-specific programs during osteogenesis have remained underexplored. Therefore, we investigated the expression profiles of a large cohort of epigenetic regulators (>300) during osteogenic differentiation of human mesenchymal cells derived from the stromal vascular fraction of adipose tissue (AMSCs). Molecular analyses establish that the polycomb group protein EZH2 (enhancer of zeste homolog 2) is down-regulated during osteoblastic differentiation of AMSCs. Chemical inhibitor and siRNA knockdown studies show that EZH2, a histone methyltransferase that catalyzes trimethylation of histone 3 lysine 27 (H3K27me3), suppresses osteogenic differentiation. Blocking EZH2 activity promotes osteoblast differentiation and suppresses adipogenic differentiation of AMSCs. High throughput RNA sequence (mRNASeq) analysis reveals that EZH2 inhibition stimulates cell cycle inhibitory proteins and enhances the production of extracellular matrix proteins. Conditional genetic loss of Ezh2 in uncommitted mesenchymal cells (Prrx1-Cre) results in multiple defects in skeletal patterning and bone formation, including shortened forelimbs, craniosynostosis, and clinodactyly. Histological analysis and mRNASeq profiling suggest that these effects are attributable to growth plate abnormalities and premature cranial suture closure because of precocious maturation of osteoblasts. We conclude that the epigenetic activity of EZH2 is required for skeletal patterning and development, but EZH2 expression declines during terminal osteoblast differentiation and matrix production.
Collapse
Affiliation(s)
| | | | - Fuhua Xu
- From the Departments of Orthopedic Surgery
| | | | - Meghan E McGee-Lawrence
- the Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, Georgia 30912
| | | | | | | | | | | | | | | | - Allan B Dietz
- the Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905
| | - Gary S Stein
- the Department of Biochemistry, University of Vermont Medical School, Burlington, Vermont 05405, and
| | - Martin A Montecino
- the Centro de Investigaciones Biomedicas and Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias Center for Genome Regulation, Universidad Andres Bello, Santiago 837-0146, Chile
| | | | - Andre J van Wijnen
- From the Departments of Orthopedic Surgery, Biochemistry & Molecular Biology,
| |
Collapse
|
174
|
Li H, Zhang Z, Chen Z, Zhang D. Osteogenic growth peptide promotes osteogenic differentiation of mesenchymal stem cells mediated by LncRNA AK141205-induced upregulation of CXCL13. Biochem Biophys Res Commun 2015; 466:82-8. [PMID: 26321662 DOI: 10.1016/j.bbrc.2015.08.112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 08/25/2015] [Indexed: 02/06/2023]
Abstract
The aim of present study was to characterize long non-coding RNA (lncRNA) AK141205 as a cellular regulator of osteogenic differentiation of mice mesenchymal stem cells (MSCs) towards osteogenic growth peptide (OGP) stimulation. Mice MSCs cells were isolated, transfected with si-AK141205, pcDNA-AK141205 or control, and stimulated with OGP. The AK141205, CXC chemokine ligand-13 (CXCL13), and osteogenic differentiation-associated parameters were determined by western blotting or quantitative RT-PCR. To determine the role of AK141205/CXCL13 in SMCs osteogenic differentiation, SMCs subjected to co-transfection of pcDNA-AK141205 and si-CXCL13 or si-AK141205 and pcDNA-CXCL13, and were submitted for osteogenic differentiation-associated parameters analyses. The results showed that stimulation of SMCs with OGP induced upregulation of both AK141205 and CXCL13, and osteogenic differentiation of MSCs. Transfection of si-AK141205 partly suppressed OGP-induced formation of calcium salt nodules, alkaline phosphatase (ALP) activity and osteogenic differentiation-associated gene expression, suggesting key regulatory role of AK141205. Analysis of CXCL13 expression in SMCs(pcDNA-AK141205) revealed that AK141205 positively promoted CXCL13 expression via acetylation of H4 histone in the promoter region. This signal transduction was demonstrated to be essential for OGP-induced osteogenic differentiation of MSCs through osteogenic differentiation analysis in simultaneously AK141205/CXCL13 controlled SMCs. In summary, we report a completely novel role of AK141205/CXCL13 as a regulator of OGP-induced osteogenic differentiation of SMCs. Our finding provides a potential therapeutic targeting of AK141205 for enhancing disease-treatment effect of SMCs.
Collapse
Affiliation(s)
- Haiqing Li
- Department of Orthopedic Surgery, Liaocheng People's Hospital, 67 Dongchang West Road, Liaocheng 252000, China
| | - Zhonghe Zhang
- Department of Orthopedic Surgery, Liaocheng Hospital of Traditional Chinese Medicine, Liaocheng 252000, China
| | - Zhiqiang Chen
- Department of Orthopedic Surgery, Liaocheng People's Hospital, 67 Dongchang West Road, Liaocheng 252000, China.
| | - Dongdong Zhang
- Department of Ultrasound, Liaocheng People's Hospital, 67 Dongchang West Road, Liaocheng 252000, China.
| |
Collapse
|
175
|
A pathophysiological view of the long non-coding RNA world. Oncotarget 2015; 5:10976-96. [PMID: 25428918 PMCID: PMC4294373 DOI: 10.18632/oncotarget.2770] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/14/2014] [Indexed: 12/13/2022] Open
Abstract
Because cells are constantly exposed to micro-environmental changes, they require the ability to adapt to maintain a dynamic equilibrium. Proteins are considered critical for the regulation of gene expression, which is a fundamental process in determining the cellular responses to stimuli. Recently, revolutionary findings in RNA research and the advent of high-throughput genomic technologies have revealed a pervasive transcription of the human genome, which generates many long non-coding RNAs (lncRNAs) whose roles are largely undefined. However, there is evidence that lncRNAs are involved in several cellular physiological processes such as adaptation to stresses, cell differentiation, maintenance of pluripotency and apoptosis. The correct balance of lncRNA levels is crucial for the maintenance of cellular equilibrium, and the dysregulation of lncRNA expression is linked to many disorders; certain transcripts are useful prognostic markers for some of these pathologies. This review revisits the classic concept of cellular homeostasis from the perspective of lncRNAs specifically to understand how this novel class of molecules contributes to cellular balance and how its dysregulated expression can lead to the onset of pathologies such as cancer.
Collapse
|
176
|
Lopez-Pajares V, Qu K, Zhang J, Webster DE, Barajas BC, Siprashvili Z, Zarnegar BJ, Boxer LD, Rios EJ, Tao S, Kretz M, Khavari PA. A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Dev Cell 2015; 32:693-706. [PMID: 25805135 DOI: 10.1016/j.devcel.2015.01.028] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 12/11/2014] [Accepted: 01/21/2015] [Indexed: 02/02/2023]
Abstract
Progenitor differentiation requires remodeling of genomic expression; however, in many tissues, such as epidermis, the spectrum of remodeled genes and the transcription factors (TFs) that control them are not fully defined. We performed kinetic transcriptome analysis during regeneration of differentiated epidermis and identified gene sets enriched in progenitors (594 genes), in early (159 genes), and in late differentiation (387 genes). Module mapping of 1,046 TFs identified MAF and MAFB as necessary and sufficient for progenitor differentiation. MAF:MAFB regulated 393 genes altered in this setting. Integrative analysis identified ANCR and TINCR lncRNAs as essential upstream MAF:MAFB regulators. ChIP-seq analysis demonstrated MAF:MAFB binding to known epidermal differentiation TF genes whose expression they controlled, including GRHL3, ZNF750, KLF4, and PRDM1. Each of these TFs rescued expression of specific MAF:MAFB target gene subsets in the setting of MAF:MAFB loss, indicating they act downstream of MAF:MAFB. A lncRNA-TF network is thus essential for epidermal differentiation.
Collapse
Affiliation(s)
| | - Kun Qu
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Jiajing Zhang
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Dan E Webster
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Brook C Barajas
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Brian J Zarnegar
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Lisa D Boxer
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Eon J Rios
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Shiying Tao
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA.
| |
Collapse
|
177
|
Tye CE, Gordon JAR, Martin-Buley LA, Stein JL, Lian JB, Stein GS. Could lncRNAs be the missing links in control of mesenchymal stem cell differentiation? J Cell Physiol 2015; 230:526-34. [PMID: 25258250 DOI: 10.1002/jcp.24834] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/31/2022]
Abstract
Long suspected, recently recognized, and increasingly studied, non protein-coding RNAs (ncRNAs) are emerging as key drivers of biological control and pathology. Since their discovery in 1993, microRNAs (miRNAs) have been the subject of intense research focus and investigations have revealed striking findings, establishing that these molecules can exert a substantial level of biological control in numerous tissues. More recently, long ncRNAs (lncRNAs), the lesser-studied siblings of miRNA, have been suggested to have a similar robust role in developmental and adult tissue regulation. Mesenchymal stem cells (MSCs) are an important source of multipotent cells for normal and therapeutic tissue repair. Much is known about the critical role of miRNAs in biogenesis and differentiation of MSCs however; recent studies have suggested lncRNAs may play an equally important role in the regulation of these cells. Here we highlight the role of lncRNAs in the regulation of mesenchymal stem cell lineages including adipocytes, chondrocytes, myoblasts, and osteoblasts. In addition, the potential for these noncoding RNAs to be used as biomarkers for disease or therapeutic targets is also discussed.
Collapse
Affiliation(s)
- Coralee E Tye
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont
| | | | | | | | | | | |
Collapse
|
178
|
Tong X, Gu PC, Xu SZ, Lin XJ. Long non-coding RNA-DANCR in human circulating monocytes: a potential biomarker associated with postmenopausal osteoporosis. Biosci Biotechnol Biochem 2015; 79:732-7. [PMID: 25660720 DOI: 10.1080/09168451.2014.998617] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Osteoporosis is a common disease characterized by low bone mineral density (BMD) and low trauma fractures, mainly resulting from exceeding bone resorption by osteoclasts over bone formation by osteoblasts. Circulating monocytes are directly involved in osteoclastogenesis, and lncRNAs are believed to be involved in the osteoblast differentiation. However, no study has been conducted to identify the roles of lncRNA in circulating monocytes associated with human osteoporosis. In this study, we found significant upregulation of DANCR in the blood mononuclear cells (MNCs) from low-BMD patients with the qRT-PCR analyses. We further found that DANCR promoted the expression of IL6 and TNF-α at both mRNA level and protein level in MNCs. After deletion of DANCR with siRNAs, the levels of IL6 and TNF-α are decreased in the MNCs from low-BMD postmenopausal women. Moreover, DANCR level was correlated with IL6 and TNF-α in postmenopausal women with low BMD. Furthermore, we found that DANCR-induced IL6 and TNF-α in MNCs had bone-resorbing activity. These results indicate that DANCR is involved in the pathology of osteoporosis and may be as a biomarker for postmenopausal osteoporosis.
Collapse
Affiliation(s)
- Xiang Tong
- a Department of Orthopedic Surgery, The 1st Affiliated Hospital, College of Medicine , Zhejiang University , Hangzhou , China
| | | | | | | |
Collapse
|
179
|
Gordon JAR, Montecino MA, Aqeilan RI, Stein JL, Stein GS, Lian JB. Epigenetic pathways regulating bone homeostasis: potential targeting for intervention of skeletal disorders. Curr Osteoporos Rep 2014; 12:496-506. [PMID: 25260661 PMCID: PMC4216616 DOI: 10.1007/s11914-014-0240-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation utilizes different mechanisms to convey heritable traits to progeny cells that are independent of DNA sequence, including DNA silencing, post-translational modifications of histone proteins, and the post-transcriptional modulation of RNA transcript levels by non-coding RNAs. Although long non-coding RNAs have recently emerged as important regulators of gene imprinting, their functions during osteogenesis are as yet unexplored. In contrast, microRNAs (miRNAs) are well characterized for their control of osteogenic and osteoclastic pathways; thus, further defining how gene regulatory networks essential for skeleton functions are coordinated and finely tuned through the activities of miRNAs. Roles of miRNAs are constantly expanding as new studies uncover associations with skeletal disorders. The distinct functions of epigenetic regulators and evidence for integrating their activities to control normal bone gene expression and bone disease will be presented. In addition, potential for using "signature miRNAs" to identify, manage, and therapeutically treat osteosarcoma will be discussed in this review.
Collapse
Affiliation(s)
- Jonathan A. R. Gordon
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Martin A. Montecino
- Centro de Investigaciones Biomedicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile
| | - Rami I. Aqeilan
- Lautenberg Center for Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, PO Box 12272, Ein Karem Campus, Jerusalem 91120, Israel
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
- Corresponding Author: Jane B. Lian – P: 802-656-4872, F: 802-656-8216,
| |
Collapse
|
180
|
Jia Q, Jiang W, Ni L. Down-regulated non-coding RNA (lncRNA-ANCR) promotes osteogenic differentiation of periodontal ligament stem cells. Arch Oral Biol 2014; 60:234-41. [PMID: 25463901 DOI: 10.1016/j.archoralbio.2014.10.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Our studies aimed to figure out how anti-differentiation noncoding RNA (ANCR) regulates the proliferation and osteogenic differentiation of periodontal ligament stem cells (PDLSCs). DESIGN In this study, we used lentivirus infection to down-regulate the expression of ANCR in PDLSCs. Then we compared the proliferation of control cells and PDLSC/ANCR-RNAi cells by Cell Counting Kit-8. And the osteogenic differentiation of control cells and PDLSC/ANCR-RNAi cells were evaluated by Alkaline phosphatase (ALP) activity quantification and Alizarin red staining. WNT inhibitor was used to analyze the relationship between ANCR and canonical WNT signalling pathway. The expression of osteogenic differentiation marker mRNAs, DKK1, GSK3-β and β-catenin were evaluated by qRT-PCR. RESULTS The results showed that down-regulated ANCR promoted proliferation of PDLSCs. Down-regulated ANCR also promoted osteogenic differentiation of PDLSCs by up-regulating osteogenic differentiation marker genes. After the inhibition of canonical WNT signalling pathway, the osteogenic differentiation of PDLSC/ANCR-RNAi cells was inhibited too. qRT-PCR results also demonstrated that canonical WNT signalling pathway was activated for ANCR-RNAi on PDLSCs during the procedure of proliferation and osteogenic induction. CONCLUSIONS These results indicated that ANCR was a key regulator of the proliferation and osteogenic differentiation of PDLSCs, and its regulating effects was associated with the canonical WNT signalling pathway, thus offering a new target for oral stem cell differentiation studies that could also facilitate oral tissue engineering.
Collapse
Affiliation(s)
- Qian Jia
- State Key Laboratory of Military Stomatology, Department of Operative Dentistry and Endodontics, School of Stomatology, 4th Military Medical University, 145 Changle West Road, Xi'an 710032, Shannxi, PR China
| | - Wenkai Jiang
- State Key Laboratory of Military Stomatology, Department of Operative Dentistry and Endodontics, School of Stomatology, 4th Military Medical University, 145 Changle West Road, Xi'an 710032, Shannxi, PR China
| | - Longxing Ni
- State Key Laboratory of Military Stomatology, Department of Operative Dentistry and Endodontics, School of Stomatology, 4th Military Medical University, 145 Changle West Road, Xi'an 710032, Shannxi, PR China.
| |
Collapse
|
181
|
Wang Y, Guo Q, Zhao Y, Chen J, Wang S, Hu J, Sun Y. BRAF-activated long non-coding RNA contributes to cell proliferation and activates autophagy in papillary thyroid carcinoma. Oncol Lett 2014; 8:1947-1952. [PMID: 25289082 PMCID: PMC4186573 DOI: 10.3892/ol.2014.2487] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/23/2014] [Indexed: 11/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are novel regulators in cancer biology. BRAF-activated lncRNA (BANCR) is overexpressed in melanoma and has a potential functional role in melanoma cell migration. However, little is known about the role of BANCR in the development of papillary thyroid carcinoma (PTC). In the present study, BANCR expression was examined in six pairs of PTC and matched adjacent normal tissues. The results revealed that BANCR levels were significantly higher in the PTC tissues and PTC IHH-4 cells compared with the normal controls. Knockdown of BANCR in the IHH-4 cells inhibited proliferation and increased apoptosis of the cells in vitro. Further investigation of the underlying mechanisms revealed that BANCR markedly activated autophagy. Overexpression of BANCR inhibited apoptosis in the IHH-4 cells, whereas inhibition of autophagy stimulated apoptosis in the BANCR-overexpressed cells. BANCR overexpression also increased cell proliferation and the inhibition of autophagy abrogated BANCR overexpression-induced cell proliferation. In addition, the overexpression of BANCR resulted in an increase in the ratio of LC3-II/LC3-I, a marker for autophagy, while the knockdown of BANCR decreased the ratio of LC3-II/LC3-I. These results revealed that BANCR expression levels are upregulated in PTC. Additionally, BANCR increases PTC cell proliferation, which could activate autophagy.
Collapse
Affiliation(s)
- Yong Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| | - Qinhao Guo
- Department of Obstetrics and Gynecology, Northern Jiangsu Province Hospital, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Yan Zhao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| | - Jiejing Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| | - Shuwei Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| | - Jun Hu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| | - Yueming Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210000, P.R. China
| |
Collapse
|
182
|
Lowe TC, A Reiss R. Understanding the biological responses of nanostructured metals and surfaces. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1757-899x/63/1/012172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
183
|
Herriges MJ, Swarr DT, Morley MP, Rathi KS, Peng T, Stewart KM, Morrisey EE. Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. Genes Dev 2014; 28:1363-79. [PMID: 24939938 PMCID: PMC4066405 DOI: 10.1101/gad.238782.114] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Long noncoding RNAs (lncRNAs) are thought to play important roles in regulating gene transcription, yet few have known biological functions. Using a conservative pipeline, Herriges et al. identify lncRNAs with key functions during mammalian development. Loss-of-function analyses show that two lncRNAs play distinct roles in endoderm development by controlling the expression of critical transcription factors and pathways, including retinoic acid signaling. The data demonstrate that lncRNAs regulate multiple aspects of gene transcription during foregut and lung endoderm development. Long noncoding RNAs (lncRNAs) are thought to play important roles in regulating gene transcription, but few have well-defined expression patterns or known biological functions during mammalian development. Using a conservative pipeline to identify lncRNAs that have important biological functions, we identified 363 lncRNAs in the lung and foregut endoderm. Importantly, we show that these lncRNAs are spatially correlated with transcription factors across the genome. In-depth expression analyses of lncRNAs with genomic loci adjacent to the critical transcription factors Nkx2.1, Gata6, Foxa2 (forkhead box a2), and Foxf1 mimic the expression patterns of their protein-coding neighbor. Loss-of-function analysis demonstrates that two lncRNAs, LL18/NANCI (Nkx2.1-associated noncoding intergenic RNA) and LL34, play distinct roles in endoderm development by controlling expression of critical developmental transcription factors and pathways, including retinoic acid signaling. In particular, we show that LL18/NANCI acts upstream of Nkx2.1 and downstream from Wnt signaling to regulate lung endoderm gene expression. These studies reveal that lncRNAs play an important role in foregut and lung endoderm development by regulating multiple aspects of gene transcription, often through regulation of transcription factor expression.
Collapse
Affiliation(s)
- Michael J Herriges
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daniel T Swarr
- Division of Neonatology, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | | - Edward E Morrisey
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Department of Medicine, Institute for Regenerative Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
184
|
Yamaguchi H, Hung MC. Regulation and Role of EZH2 in Cancer. Cancer Res Treat 2014; 46:209-22. [PMID: 25038756 PMCID: PMC4132442 DOI: 10.4143/crt.2014.46.3.209] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/05/2014] [Indexed: 12/11/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is the epigenetic regulator that induces histone H3 lysine 27 methylation (H3K27me3) and silences specific gene transcription. Enhancer of zeste homolog 2 (EZH2) is an enzymatic subunit of PRC2, and evidence shows that EZH2 plays an essential role in cancer initiation, development, progression, metastasis, and drug resistance. EZH2 expression is indeed regulated by various oncogenic transcription factors, tumor suppressor miRNAs, and cancer-associated non-coding RNA. EZH2 activity is also controlled by post-translational modifications, which are deregulated in cancer. The canonical role of EZH2 is gene silencing through H3K27me3, but accumulating evidence shows that EZH2 methlyates substrates other than histone and has methylase-independent functions. These non-canonical functions of EZH2 are shown to play a role in cancer progression. In this review, we summarize current information on the regulation and roles of EZH2 in cancer. We also discuss various therapeutic approaches to targeting EZH2.
Collapse
Affiliation(s)
- Hirohito Yamaguchi
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | |
Collapse
|
185
|
Backofen R, Vogel T. Biological and bioinformatical approaches to study crosstalk of long-non-coding RNAs and chromatin-modifying proteins. Cell Tissue Res 2014; 356:507-26. [PMID: 24820400 DOI: 10.1007/s00441-014-1885-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 03/27/2014] [Indexed: 02/04/2023]
Abstract
Long-non-coding RNA (lncRNA) regulates gene expression through transcriptional and epigenetic regulation as well as alternative splicing in the nucleus. In addition, regulation is achieved at the levels of mRNA translation, storage and degradation in the cytoplasm. During recent years, several studies have described the interaction of lncRNAs with enzymes that confer so-called epigenetic modifications, such as DNA methylation, histone modifications and chromatin structure or remodelling. LncRNA interaction with chromatin-modifying enzymes (CME) is an emerging field that confers another layer of complexity in transcriptional regulation. Given that CME-lncRNA interactions have been identified in many biological processes, ranging from development to disease, comprehensive understanding of underlying mechanisms is important to inspire basic and translational research in the future. In this review, we highlight recent findings to extend our understanding about the functional interdependencies between lncRNAs and CMEs that activate or repress gene expression. We focus on recent highlights of molecular and functional roles for CME-lncRNAs and provide an interdisciplinary overview of recent technical and methodological developments that have improved biological and bioinformatical approaches for detection and functional studies of CME-lncRNA interaction.
Collapse
Affiliation(s)
- Rolf Backofen
- Institute of Computer Science, Albert-Ludwigs-University, Freiburg, Germany
| | | |
Collapse
|
186
|
Abstract
Over the past few years, advances in genome analyses have identified an emerging class of noncoding RNAs that play critical roles in the regulation of gene expression and epigenetic reprogramming. Given their transcriptional pervasiveness, the potential for these intriguing macromolecules to integrate a myriad of external cellular cues with nuclear responses has become increasingly apparent. Recent studies have implicated noncoding RNAs in epidermal development and keratinocyte differentiation, but the complexity of multilevel regulation of transcriptional programs involved in these processes remains ill defined. In this review, we discuss the relevance of noncoding RNA in normal skin development, their involvement in cutaneous malignancies, and their role in the regulation of adult stem-cell maintenance in stratified epithelial tissues. Furthermore, we provide additional examples highlighting the ubiquity of noncoding RNAs in diverse human diseases.
Collapse
|
187
|
van Heesch S, van Iterson M, Jacobi J, Boymans S, Essers PB, de Bruijn E, Hao W, MacInnes AW, Cuppen E, Simonis M. Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. Genome Biol 2014; 15:R6. [PMID: 24393600 PMCID: PMC4053777 DOI: 10.1186/gb-2014-15-1-r6] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 01/07/2014] [Indexed: 02/04/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been convincingly demonstrated that these transcripts do not code for proteins. To obtain a comprehensive understanding of the extent to which lncRNAs bind ribosomes, we performed systematic RNA sequencing on ribosome-associated RNA pools obtained through ribosomal fractionation and compared the RNA content with nuclear and (non-ribosome bound) cytosolic RNA pools. Results The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Conclusions Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes.
Collapse
|
188
|
Kim D, Song J, Han J, Kim Y, Chun CH, Jin EJ. Two non-coding RNAs, MicroRNA-101 and HOTTIP contribute cartilage integrity by epigenetic and homeotic regulation of integrin-α1. Cell Signal 2013; 25:2878-87. [PMID: 24018042 DOI: 10.1016/j.cellsig.2013.08.034] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/31/2013] [Indexed: 12/18/2022]
Abstract
Non-coding RNAs have been less studied in cartilage development and destruction regulated by sophisticated molecular events despite their considerable theranostic potential. In this study, we identified significant down-regulation of mR-101 and up-regulation of lncRNA, HOTTIP in the processes of endochondral ossification and osteoarthritic progression. In wing mesenchymal cells, up-expression of miR-101 by TGF-β3 treatment is targeting DNMT-3B and thereby altered the methylation of integrin-α1 addressed as a positive regulator of endochondral ossification in this study. In like manner, down-regulation of miR-101 also coordinately up-regulated DNMT-3B, down-regulated integrin-α1, and resulted in cartilage destruction. In an OA animal model, introduction of lentiviruses that encoded miR-101 or integrin-α1 successfully reduced cartilage destruction. In like manner, long non-coding RNA (lncRNA), HOTTIP, a known regulator for HoxA genes, was highly up-regulated and concurrent down-regulation of HoxA13 displayed the suppression of integrin-α1 in OA chondrocytes. In conclusion, two non-coding RNAs, miR-101 and HOTTIP regulate cartilage development and destruction by modulating integrin-α1 either epigenetically by DNMT-3B or transcriptionally by HoxA13 and data further suggest that these non-coding RNAs could be a potent predictive biomarker for OA as well as a therapeutic target for preventing cartilage-related diseases.
Collapse
Affiliation(s)
- Dongkyun Kim
- Department of Biological Sciences, College of Natural Sciences, Wonkwang University, Iksan, Chunbuk 570-749, Republic of Korea
| | | | | | | | | | | |
Collapse
|
189
|
Hombach S, Kretz M. The non-coding skin: Exploring the roles of long non-coding RNAs in epidermal homeostasis and disease. Bioessays 2013; 35:1093-100. [DOI: 10.1002/bies.201300068] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sonja Hombach
- Institute of Biochemistry, Genetics and Microbiology; University of Regensburg; Regensburg Germany
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology; University of Regensburg; Regensburg Germany
| |
Collapse
|
190
|
Abstract
The human genome encodes several thousand long non-protein coding transcripts>200 nucleotides in length, a subset of which were shown to play important roles in regulation of gene expression. We recently identified TINCR, a lncRNA required for induction of key differentiation genes in epidermal tissue, including genes mutated in human skin diseases characterized by disrupted epidermal barrier formation. High-throughput analyses of TINCR RNA- and protein-interactomes revealed TINCR interaction with differentiation mRNAs as well as the Staufen1 protein. TINCR, together with Staufen1, seems to stabilize a subset of mRNAs required for epidermal differentiation. Here, we discuss the emerging roles of Staufen1 and TINCR in the regulation of mammalian cell differentiation mediated by interaction with target mRNAs. We consider a role for TINCR as an epithelial-specific guide for targeting the Staufen1 protein to specific mRNAs, reflecting the increasing complexity of gene regulatory processes in mammalian cells and tissue.
Collapse
Affiliation(s)
- Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology; University of Regensburg; Regensburg, Germany
| |
Collapse
|
191
|
Tang JY, Lee JC, Chang YT, Hou MF, Huang HW, Liaw CC, Chang HW. Long noncoding RNAs-related diseases, cancers, and drugs. ScientificWorldJournal 2013; 2013:943539. [PMID: 23843741 PMCID: PMC3690748 DOI: 10.1155/2013/943539] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/20/2013] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNA (lncRNA) function is described in terms of related gene expressions, diseases, and cancers as well as their polymorphisms. Potential modulators of lncRNA function, including clinical drugs, natural products, and derivatives, are discussed, and bioinformatic resources are summarized. The improving knowledge of the lncRNA regulatory network has implications not only in gene expression, diseases, and cancers, but also in the development of lncRNA-based pharmacology.
Collapse
Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jin-Ching Lee
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yung-Ting Chang
- Doctor Degree Program in Marine Biotechnology, National Sun Yat-sen University/Academia Sinica, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Hurng-Wern Huang
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chih-Chuang Liaw
- Doctor Degree Program in Marine Biotechnology, National Sun Yat-sen University/Academia Sinica, Kaohsiung, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| |
Collapse
|