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Lou W, Xiao S, Lin K. Identification of a hypoxia-suppressed lncRNA RAMP2-AS1 in breast cancer. Noncoding RNA Res 2024; 9:782-795. [PMID: 38590436 PMCID: PMC10999373 DOI: 10.1016/j.ncrna.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/08/2024] [Accepted: 02/06/2024] [Indexed: 04/10/2024] Open
Abstract
Hypoxia is a critical feature of solid tumors and exerts crucial roles in cancers, including breast cancer. However, the detailed relationship between lncRNA-miRNA-mRNA triple network and hypoxia in breast cancer is still indistinct. In this study, a series of in silico analyses and online databases or tools were employed to establish a hypoxia-related lncRNA-miRNA-mRNA network in breast cancer based on competing endogenous RNA mechanism at single-cell resolution. RAMP2-AS1 was, eventually, identified as the most potential lncRNA, which was significantly negatively associated with hypoxia in breast cancer. Compared with normal controls, RAMP2-AS1 was markedly downregulated in breast cancer. Moreover, survival analysis revealed favorable prognostic values of RAMP2-AS1 in total or in specific clinicopathological breast cancer patients. Next, miR-660-5p, miR-2277-5p and miR-1301-3p, upregulated and possessed poor prognostic values in breast cancer, were identified as three potential downstream miRNAs of RAMP2-AS1. Then, the most potential downstream hypoxia-related genes (ATM and MYH11) of RAMP2-AS1/miRNA axis in breast cancer were screened out. Intriguingly, in vitro experiments confirmed that RAMP2-AS1 was a hypoxia-suppressed lncRNA and miR-660-5p/ATM was a potential downstream axis of RAMP2-AS1 in breast cancer. Collectively, our current data elucidated a key hypoxia-suppressed lncRNA RAMP2-AS1 and its possible miRNA-mRNA regulatory mechanism in breast cancer.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Shuyuan Xiao
- Department of Anesthesiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Kuailu Lin
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325015, China
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2
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Singh RR, Mondal I, Janjua T, Popat A, Kulshreshtha R. Engineered smart materials for RNA based molecular therapy to treat Glioblastoma. Bioact Mater 2024; 33:396-423. [PMID: 38059120 PMCID: PMC10696434 DOI: 10.1016/j.bioactmat.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/19/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Glioblastoma (GBM) is an aggressive malignancy of the central nervous system (CNS) that remains incurable despite the multitude of improvements in cancer therapeutics. The conventional chemo and radiotherapy post-surgery have only been able to improve the prognosis slightly; however, the development of resistance and/or tumor recurrence is almost inevitable. There is a pressing need for adjuvant molecular therapies that can successfully and efficiently block tumor progression. During the last few decades, non-coding RNAs (ncRNAs) have emerged as key players in regulating various hallmarks of cancer including that of GBM. The levels of many ncRNAs are dysregulated in cancer, and ectopic modulation of their levels by delivering antagonists or overexpression constructs could serve as an attractive option for cancer therapy. The therapeutic potential of several types of ncRNAs, including miRNAs, lncRNAs, and circRNAs, has been validated in both in vitro and in vivo models of GBM. However, the delivery of these RNA-based therapeutics is highly challenging, especially to the tumors of the brain as the blood-brain barrier (BBB) poses as a major obstacle, among others. Also, since RNA is extremely fragile in nature, careful considerations must be met while designing a delivery agent. In this review we have shed light on how ncRNA therapy can overcome the limitations of its predecessor conventional therapy with an emphasis on smart nanomaterials that can aide in the safe and targeted delivery of nucleic acids to treat GBM. Additionally, critical gaps that currently exist for successful transition from viral to non-viral vector delivery systems have been identified. Finally, we have provided a perspective on the future directions, potential pathways, and target areas for achieving rapid clinical translation of, RNA-based macromolecular therapy to advance the effective treatment of GBM and other related diseases.
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Affiliation(s)
- Ravi Raj Singh
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
- School of Pharmacy, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Queensland –IIT Delhi Academy of Research (UQIDAR)
| | - Indranil Mondal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Taskeen Janjua
- School of Pharmacy, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Amirali Popat
- School of Pharmacy, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Functional Materials and Catalysis, Faculty of Chemistry, University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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3
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Hazra R, Utama R, Naik P, Dobin A, Spector DL. Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA sequencing datasets. Stem Cell Reports 2023; 18:2056-2070. [PMID: 37922916 PMCID: PMC10679778 DOI: 10.1016/j.stemcr.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023] Open
Abstract
Glioblastoma multiforme (GBM) is an aggressive, heterogeneous brain tumor in which glioblastoma stem cells (GSCs) are known culprits of therapy resistance. Long non-coding RNAs (lncRNAs) have been shown to play a critical role in both cancer and normal biology. A few studies have suggested that aberrant expression of lncRNAs is associated with GSCs. However, a comprehensive single-cell analysis of the GSC-associated lncRNA transcriptome has not been carried out. Here, we analyzed recently published single-cell RNA sequencing datasets of adult GBM tumors, GBM organoids, GSC-enriched GBM tumors, and developing human brain samples to identify lncRNAs highly expressed in GSCs. We further revealed that the GSC-specific lncRNAs GIHCG and LINC01563 promote proliferation, migration, and stemness in the GSC population. Together, this study identified a panel of uncharacterized GSC-enriched lncRNAs and set the stage for future in-depth studies to examine their role in GBM pathology and their potential as biomarkers and/or therapeutic targets in GBM.
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Affiliation(s)
- Rasmani Hazra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Payal Naik
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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4
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Hazra R, Utama R, Naik P, Dobin A, Spector DL. Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA-sequencing datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524887. [PMID: 36711961 PMCID: PMC9882256 DOI: 10.1101/2023.01.20.524887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Glioblastoma multiforme (GBM) is an aggressive, heterogeneous grade IV brain tumor. Glioblastoma stem cells (GSCs) initiate the tumor and are known culprits of therapy resistance. Mounting evidence has demonstrated a regulatory role of long non-coding RNAs (lncRNAs) in various biological processes, including pluripotency, differentiation, and tumorigenesis. A few studies have suggested that aberrant expression of lncRNAs is associated with GSCs. However, a comprehensive single-cell analysis of the GSC-associated lncRNA transcriptome has not been carried out. Here, we analyzed recently published single-cell RNA-sequencing datasets of adult human GBM tumors, GBM organoids, GSC-enriched GBM tumors, and developing human brains to identify lncRNAs highly expressed in GBM. To categorize GSC populations in the GBM tumors, we used the GSC marker genes SOX2, PROM1, FUT4, and L1CAM. We found three major GSC population clusters: radial glia, oligodendrocyte progenitor cells, and neurons. We found 10â€"100 lncRNAs significantly enriched in different GSC populations. We also validated the level of expression and localization of several GSC-enriched lncRNAs using qRT-PCR, single-molecule RNA FISH, and sub-cellular fractionation. We found that the radial glia GSC-enriched lncRNA PANTR1 is highly expressed in GSC lines and is localized to both the cytoplasmic and nuclear fractions. In contrast, the neuronal GSC-enriched lncRNAs LINC01563 and MALAT1 are highly enriched in the nuclear fraction of GSCs. Together, this study identified a panel of uncharacterized GSC-specific lncRNAs. These findings set the stage for future in-depth studies to examine their role in GBM pathology and their potential as biomarkers and/or therapeutic targets in GBM.
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Mukherjee S, Kundu U, Desai D, Pillai PP. Particulate Matters Affecting lncRNA Dysregulation and Glioblastoma Invasiveness: In Silico Applications and Current Insights. J Mol Neurosci 2022; 72:2188-2206. [PMID: 36370303 DOI: 10.1007/s12031-022-02069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/14/2022] [Indexed: 11/15/2022]
Abstract
With a reported rise in global air pollution, more than 50% of the population remains exposed to toxic air pollutants in the form of particulate matters (PMs). PMs, from various sources and of varying sizes, have a significant impact on health as long-time exposure to them has seen a correlation with various health hazards and have also been determined to be carcinogenic. In addition to disrupting known cellular pathways, PMs have also been associated with lncRNA dysregulation-a factor that increases predisposition towards the onset or progression of cancer. lncRNA dysregulation is further seen to mediate glioblastoma multiforme (GBM) progression. The vast array of information regarding cancer types including GBM and its various precursors can easily be obtained via innovative in silico approaches in the form of databases such as GEO and TCGA; however, a need to obtain selective and specific information correlating anthropogenic factors and disease progression-in the case of GBM-can serve as a critical tool to filter down and target specific PMs and lncRNAs responsible for regulating key cancer hallmarks in glioblastoma. The current review article proposes an in silico approach in the form of a database that reviews current updates on correlation of PMs with lncRNA dysregulation leading to GBM progression.
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Affiliation(s)
- Swagatama Mukherjee
- Division of Neurobiology, Department of Zoology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Uma Kundu
- Division of Neurobiology, Department of Zoology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Dhwani Desai
- Integrated Microbiome Resource, Department of Pharmacology and Marine Microbial Genomics and Biogeochemistry lab, Department of Biology, Dalhousie University, Halifix, Canada
| | - Prakash P Pillai
- Division of Neurobiology, Department of Zoology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390 002, Gujarat, India.
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Emam O, Wasfey EF, Hamdy NM. Notch-associated lncRNAs profiling circuiting epigenetic modification in colorectal cancer. Cancer Cell Int 2022; 22:316. [PMID: 36229883 PMCID: PMC9558410 DOI: 10.1186/s12935-022-02736-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/28/2022] [Indexed: 11/15/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most prevalent digestive cancers, ranking the 2nd cause of cancer-related fatality worldwide. The worldwide burden of CRC is predicted to rise by 60% by 2030. Environmental factors drive, first, inflammation and hence, cancer incidence increase. Main The Notch-signaling system is an evolutionarily conserved cascade, has role in the biological normal developmental processes as well as malignancies. Long non-coding RNAs (LncRNAs) have become major contributors in the advancement of cancer by serving as signal pathways regulators. They can control gene expression through post-translational changes, interactions with micro-RNAs or down-stream effector proteins. Recent emerging evidence has emphasized the role of lncRNAs in controlling Notch-signaling activity, regulating development of several cancers including CRC. Conclusion Notch-associated lncRNAs might be useful prognostic biomarkers or promising potential therapeutic targets for CRC treatment. Therefore, here-in we will focus on the role of “Notch-associated lncRNAs in CRC” highlighting “the impact of Notch-associated lncRNAs as player for cancer induction and/or progression.” Graphical Abstract ![]()
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Affiliation(s)
| | - Eman F Wasfey
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt.
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7
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Tooth Formation as Experimental Model to Study Chemotherapy on Tissue Development: Effect of a Specific Dose of Temozolomide/Veliparib. Genes (Basel) 2022; 13:genes13071198. [PMID: 35885982 PMCID: PMC9322384 DOI: 10.3390/genes13071198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Chemotherapy treatment of cancer in children can influence formation of normal tissues, leading to irreversible changes in their structure and function. Tooth formation is susceptible to several types of chemotherapy that induce irreversible changes in the structure of enamel, dentin and dental root morphology. These changes can make the teeth more prone to fracture or to caries when they have erupted. Recent studies report successful treatment of brain tumors with the alkylating drug temozolomide (TMZ) in combination with veliparib (VLP) in a glioblastoma in vivo mouse model. Whether these drugs also affect tooth formation is unknown. Aim: In this study the effect of TMZ/VLP on incisor formation was investigated in tissue sections of jaws from mice and compared with mice not treated with these drugs. Materials and method: The following aspects were studied using immunohistochemistry of specific protein markers including: (1) proliferation (by protein expression of proliferation marker Ki67) (2) a protein involved in paracellular ion transport (expression of tight junction (TJ) protein claudin-1) and (3) in transcellular passage of ions across the dental epithelium (expression of Na+, K+ 2Cl- cotransporter/NKCC1). Results: Chemotherapy with TMZ/VLP strongly reduced immunostaining for claudin-1 in distal parts of maturation ameloblasts. No gross changes were found in the treated mice, either in cell proliferation in the dental epithelium at the cervical loop or in the immunostaining pattern for NKCC1 in (non-ameloblastic) dental epithelium. The salivary glands in the treated mice contained strongly reduced immunostaining for NKCC1 in the basolateral membranes of acinar cells. Discussion/Conclusions: Based on the reduction of claudin-1 immunostaining in ameloblasts, TMZ/VLP may potentially influence forming enamel by changes in the structure of TJs structures in maturation ameloblasts, structures that are crucial for the selective passage of ions through the intercellular space between neighboring ameloblasts. The strongly reduced basolateral NKCC1 staining seen in fully-grown salivary glands of TMZ/VLP-treated mice suggests that TMZ/VLF could also influence ion transport in adult saliva by the salivary gland epithelium. This may cause treated children to be more susceptible to caries.
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8
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Yang X, Liu R. Long non-coding RNA HCG18 promotes gastric cancer progression by regulating miRNA-146a-5p/tumor necrosis factor receptor-associated factor 6 axis. Bioengineered 2022; 13:6781-6793. [PMID: 35240920 PMCID: PMC8973972 DOI: 10.1080/21655979.2022.2034565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although long non-coding RNAs (lncRNAs) have been demonstrated to be dysregulated in gastric cancer (GC), the function of lncRNA HCG18 (HCG18) in GC is elusive. Therefore, the study was designed to evaluate the underlying mechanism of HCG18 in GC. HCG18 and microRNA 146a-5p (miR-146a-5p) levels in GC were evaluated by RT-qPCR. The effects of miR-146a-5p and HCG18 on GC cell function were examined using Transwell assay, colony formation, and CCK-8 assays. Tumor necrosis factor receptor-associated factor 6 (TRAF6) and p65 expression levels were detected by Western blot. HCG18 and miR-146a-5p target genes were identified using luciferase reporter and bioinformatics assays. HCG18 expression was increased in GC. HCG18 overexpression significantly increased GC cell proliferation, invasion, and migration. Furthermore, HCG18 overexpression inhibited miR-146a-5p and upregulated TRAF6 and p65 expression. Finally, miR-146a-5p/TRAF6 was found to be involved in the role of HCG18 in GC progression in vivo. Altogether, HCG18 promotes GC progression via the miR-146a-5p/TRAF6 axis and could be a GC treatment target.
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Affiliation(s)
- Xianwu Yang
- Department of Gastroenterology, Shijiazhuang People's Hospital, Shijiazhuang City, P. R. China
| | - Run Liu
- Department of Gastroenterology, Shijiazhuang People's Hospital, Shijiazhuang City, P. R. China
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9
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Yang M, Zhang Y, Zhou Y, Zhao T, Li Z, Yue H, Piao Z. Analysis of the expression profiles of long noncoding RNAs and messenger RNAs in tongue squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2022; 134:230-239. [PMID: 35725960 DOI: 10.1016/j.oooo.2022.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/22/2021] [Accepted: 01/04/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Long noncoding RNAs (lncRNAs) are involved in the progression of tongue squamous cell carcinoma (TSCC). Therefore, it is necessary to comprehensively investigate the role of lncRNAs in TSCC. STUDY DESIGN In this study, RNA sequencing was performed to examine the expression profiles of lncRNAs and messenger RNAs (mRNAs) of patients with TSCC. The expression of selected lncRNAs in TSCC and paired adjacent tissues as well as in cell lines was validated via quantitative real-time polymerase chain reaction (qRT-PCR). The cell function of lncRNA iodothyronine deiodinase 2 antisense RNA 1 (DIO2-AS1) overexpression was assessed through 5-(3-carboxymethoxyphenyl)-2-(4.5-dimethyl-thiazoly)-3-(4-sulfophenyl) tetrazolium inner salt and Transwell assays. RESULTS A total of 342 lncRNAs and 6392 mRNAs were differentially expressed in TSCC tissues compared with paired adjacent tissues. qRT-PCR revealed the increased expression of AC093818.1 and reduced expression of CYP4F35P and DIO2-AS1 in TSCC. Furthermore, DIO2-AS1 overexpression inhibited Cal-27 cell proliferation, migration, and invasion. CONCLUSIONS We provide evidence that DIO2-AS1 is involved in TSCC progression. This study provides a direction for subsequent research.
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Affiliation(s)
- Mi Yang
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou 510182, Guangdong, China
| | - Yumin Zhang
- Department of Pediatric Stomatology, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou 510182, Guangdong, China
| | - Yang Zhou
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou 510182, Guangdong, China
| | - Tianyu Zhao
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou 510182, Guangdong, China
| | - Zhicong Li
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou 510182, Guangdong, China
| | - Haiqiong Yue
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou 510182, Guangdong, China
| | - Zhengguo Piao
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou 510182, Guangdong, China.
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Zhao N, Zhang J, Zhao L, Fu X, Zhao Q, Chao M, Cao H, Jiao Y, Hu Y, Chen C, Wang L, Wang H. Long Noncoding RNA NONHSAT079852.2 Contributes to GBM Recurrence by Functioning as a ceRNA for has-mir-10401-3p to Facilitate HSPA1A Upregulation. Front Oncol 2021; 11:636632. [PMID: 34307121 PMCID: PMC8297974 DOI: 10.3389/fonc.2021.636632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common brain malignancy and major cause of high mortality in patients with GBM, and its high recurrence rate is its most prominent feature. However, the pathobiological mechanisms involved in recurrent GBM remain largely unknown. Here, whole-transcriptome sequencing (RNA-sequencing, RNA-Seq) was used in characterizing the expression profile of recurrent GBM, and the aim was to identify crucial biomarkers that contribute to GBM relapse. Differentially expressed RNAs in three recurrent GBM tissues compared with three primary GBM tissues were identified through RNA-Seq. The function and mechanism of a candidate long noncoding RNA (lncRNA) in the progression and recurrence of GBM were elucidated by performing comprehensive bioinformatics analyses, such as functional enrichment analysis, protein-protein interaction prediction, and lncRNA-miRNA-mRNA regulatory network construction, and a series of in vitro assays. As the most significantly upregulated gene identified in recurrent GBM, HSPA1A is mainly related to antigen presentation and the MAPK signaling pathway, as indicated by functional enrichment analysis. HSPA1A was predicted as the target gene of the lncRNA NONHSAT079852.2. qRT-PCR revealed that NONHSAT079852.2 was significantly elevated in recurrent GBM relative to that in primary GBM, and high NONHSAT079852.2 expression was associated with the poor overall survival rates of patients with GBM. The knockdown of NONHSAT079852.2 successfully induced tumor cell apoptosis, inhibited the proliferation, migration, invasion and the expression level of HSPA1A in glioma cells. NONHSAT079852.2 was identified to be a sponge for hsa-miR-10401-3p through luciferase reporter assay. Moreover, HSPA1A was targeted and regulated by hsa-miR-10401-3p. Collectively, the results suggested that NONHSAT079852.2 acts as a sponge of hsa-mir-10401-3p and thereby enhances HSPA1A expression, promotes tumor cell proliferation and invasion, and leads to the progression and recurrence of GBM. This study will provide new insight into the regulatory mechanisms of NONHSAT079852.2-mediated competing endogenous RNA in the pathogenesis of recurrent GBM and evidence of the potential of lncRNAs as diagnostic biomarkers or potential therapeutic targets.
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Affiliation(s)
- Ningning Zhao
- College of Life Sciences, Northwest University, Xian, China
| | - Jiajie Zhang
- College of Life Sciences, Northwest University, Xian, China
| | - Lili Zhao
- College of Life Sciences, Northwest University, Xian, China
| | - Xiaoni Fu
- College of Life Sciences, Northwest University, Xian, China
| | - Qian Zhao
- College of Life Sciences, Northwest University, Xian, China
| | - Min Chao
- Department of Neurosurgery, Tangdu Hospital of Air Force Medical University, Xian, China
| | - Haiyan Cao
- Department of Neurosurgery, Tangdu Hospital of Air Force Medical University, Xian, China
| | - Yang Jiao
- Department of Neurosurgery, Tangdu Hospital of Air Force Medical University, Xian, China
| | - Yaqin Hu
- Department of Neurosurgery, Tangdu Hospital of Air Force Medical University, Xian, China
| | - Chao Chen
- College of Life Sciences, Northwest University, Xian, China
| | - Liang Wang
- Department of Neurosurgery, Tangdu Hospital of Air Force Medical University, Xian, China
| | - Huijuan Wang
- College of Life Sciences, Northwest University, Xian, China
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Wang Y, Shan A, Zhou Z, Li W, Xie L, Du B, Lei B. LncRNA TCONS_00004099-derived microRNA regulates oncogenesis through PTPRF in gliomas. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1023. [PMID: 34277823 PMCID: PMC8267291 DOI: 10.21037/atm-21-2442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/17/2021] [Indexed: 01/25/2023]
Abstract
Background Glioblastoma is the most common and aggressive primary tumor in the central nervous system (CNS). Patients with glioblastomas have poor prognosis due to its aggressive clinical behavior and resistance to the chemotherapeutic agent temozolomide (TMZ). Aberrant long non-coding RNAs (lncRNAs) are involved in glioma progression and its regulatory mechanisms. Analysis of sequencing data identified a new lncRNA, named lncRNA TCONS_00004099, which could derive a new microRNA and was highly expressed in glioma. Methods To elucidate the role of lncRNA TCONS_00004099 in gliomas, Quantitative Real-time PCR (qPCR) was used to assess the differential expression of lncRNA TCONS_00004099 and its related miRNA in glioma tissues, normal brain tissues, glioma cell lines (U87 and U251 cells), and a normal human embryonic brain cell line (HEB). Cell Counting Kit-8 (CCK8) assays to assess cell proliferation, flow cytometry assays examining apoptosis and the cell cycle, colony formation assays, wound healing assay, transwell assays, and zebrafish xenograft models were performed to further clarify the effects of the lncRNA and the related miRNA. Finally, Western blots were carried out to verify the mechanisms related to PTPRF (Protein Tyrosine Phosphatase Receptor Type F). Results LncRNA TCONS_00004099 was significantly increased in glioma tissues and glioma cell lines. A novel miRNA (miRNA TCONS_00004099) derived from the lncRNA was identified by qPCR. Knockdown of this lncRNA suppressed cell proliferation, migration, invasion and enhanced TMZ-induced apoptosis in U87 and U251 cell lines in vitro and in vivo. The miRNA mimics or inhibitor of miRNA TCONS_00004099 was used to reverse the effects of knockdown or overexpression of lncRNA TCONS_00004099, respectively. Western Blot analyses verified that PTPRF is one of the downstream targets of lncRNA TCONS_00004099. Conclusions These results demonstrated that lncRNA TCONS_00004099 promoted malignant behaviors in gliomas, including proliferation, metastasis, and anti-apoptosis. The effect of lncRNA TCONS_00004099 was mediated through miRNA TCONS_00004099 and its target PTPRF. Thus, the lncRNA TCONS_00004099/miRNA/PTPRF axis may be a potential therapeutic target for gliomas.
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Affiliation(s)
- Yuhao Wang
- Nosocomial Infection Control Center, People's Hospital of Shenzhen Baoan District, Shenzhen, China
| | - Aijun Shan
- Department of Emergency, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Zhiwei Zhou
- Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Faculty of Health Sciences, University of Macau, Macau, China
| | - Wenpeng Li
- Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lin Xie
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bo Du
- Department of Emergency, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Bingxi Lei
- Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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12
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Hassani B, Taheri M, Asgari Y, Zekri A, Sattari A, Ghafouri-Fard S, Pouresmaeili F. Expression Analysis of Long Non-Coding RNAs Related With FOXM1, GATA3, FOXA1 and ESR1 in Breast Tissues. Front Oncol 2021; 11:671418. [PMID: 34094972 PMCID: PMC8171254 DOI: 10.3389/fonc.2021.671418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common neoplasm among females. Estrogen receptor (ESR) signaling has a prominent impact in the pathogenesis of breast cancer. Among the transcription factors associated with ESR signaling, FOXM1, GATA3, FOXA1 and ESR1 have been suggested as a candidate in the pathogenesis of this neoplasm. In the current project, we have designed an in silico approach to find long non-coding RNAs (lncRNAs) that regulate these transcription factors. Then, we used clinical samples to carry out validation of our in silico findings. Our systems biology method led to the identification of APTR, AC144450.1, linc00663, ZNF337.AS1, and RAMP2.AS1 lncRNAs. Subsequently, we assessed the expression of these genes in breast cancer tissues compared with the adjacent non-cancerous tissues (ANCTs). Expression of GATA3 was significantly higher in breast cancer tissues compared with ANCTs (Ratio of mean expressions (RME) = 4.99, P value = 3.12E−04). Moreover, expression levels of APTR, AC144450.1, and ZNF337.AS1 were elevated in breast cancer tissues compared with control tissues (RME = 2.27, P value = 5.40E−03; Ratio of mean expressions = 615.95, P value = 7.39E−19 and RME = 1.78, P value = 3.40E−02, respectively). On the other hand, the expression of RAMP2.AS1 was lower in breast cancer tissues than controls (RME = 0.31, P value = 1.87E−03). Expression levels of FOXA1, ESR1, and FOXM1 and linc00663 were not significantly different between the two sets of samples. Expression of GATA3 was significantly associated with stage (P value = 4.77E−02). Moreover, expressions of FOXA1 and RAMP2.AS1 were associated with the mitotic rate (P values = 2.18E−02 and 1.77E−02, respectively). Finally, expressions of FOXM1 and ZNF337.AS1 were associated with breastfeeding duration (P values = 3.88E−02 and 4.33E−02, respectively). Based on the area under receiver operating characteristics curves, AC144450.1 had the optimal diagnostic power in differentiating between cancerous and non-cancerous tissues (AUC = 0.95, Sensitivity = 0.90, Specificity = 0.96). The combination of expression levels of all genes slightly increased the diagnostic power (AUC = 0.96). While there were several significant pairwise correlations between expression levels of genes in non-tumoral tissues, the most robust correlation was identified between linc00663 and RAMP2.AS1 (r = 0.61, P value = 3.08E−8). In the breast cancer tissues, the strongest correlations were reported between FOXM1/ZNF337.AS1 and FOXM1/RAMP2.AS1 pairs (r = 0.51, P value = 4.79E−5 and r = 0.51, P value = 6.39E−5, respectively). The current investigation suggests future assessment of the functional role of APTR, AC144450.1 and ZNF337.AS1 in the development of breast neoplasms.
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Affiliation(s)
- Bita Hassani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yazdan Asgari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zekri
- Department of Medical Genetics and Molecular biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Sattari
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Lim LJ, Ling LH, Neo YP, Chung AY, Goh BK, Chow PK, Chan CY, Cheow PC, Lee SY, Lim TK, Chong SS, Ooi LLPJ, Lee CG. Highly deregulated lncRNA LOC is associated with overall worse prognosis in Hepatocellular Carcinoma patients. J Cancer 2021; 12:3098-3113. [PMID: 33976720 PMCID: PMC8100808 DOI: 10.7150/jca.56340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/16/2021] [Indexed: 12/24/2022] Open
Abstract
Although numerous long non-coding RNAs (lncRNAs) were reported to be deregulated in Hepatocellular Carcinoma (HCC), experimentally characterized, and/or associated with patient's clinical characteristics, there is, thus far, minimal concerted research strategy to identify deregulated lncRNAs that modulate prognosis of HCC patients. Here, we present a novel strategy where we identify lncRNAs, which are not only de-regulated in HCC patients, but are also associated with pertinent clinical characteristics, potentially contributing to the prognosis of HCC patients. LOC101926913 (LOC) was further characterized because it is the most highly differentially expressed amongst those that are associated with the most number of clinical features (tumor-stage, vascular and tumor invasion and poorer overall survival). Experimental gain- and loss-of-function manipulation of LOC in liver cell-lines highlight LOC as a potential onco-lncRNA promoting cell proliferation, anchorage independent growth and invasion. LOC expression in cells up-regulated genes involved in GTPase-activities and downregulated genes associated with cellular detoxification, oxygen- and drug-transport. Hence, LOC may represent a novel therapeutic target, modulating prognosis of HCC patients through up-regulating GTPase-activities and down-regulating detoxification, oxygen- and drug-transport. This strategy may thus be useful for the identification of clinically relevant lncRNAs as potential biomarkers/targets that modulate prognosis in other cancers as well.
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Affiliation(s)
- Lee Jin Lim
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lay Hiang Ling
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yu Pei Neo
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-NUS Medical School, Singapore
| | - Alexander Y.F. Chung
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Brian K.P. Goh
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Pierce K.H. Chow
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
- Duke-NUS Medical School, Singapore
- Dept of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Chung Yip Chan
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Peng Chung Cheow
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Ser Yee Lee
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Tony K.H. Lim
- Dept of Pathology, Singapore General Hospital, Singapore
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - London L. P. J. Ooi
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
- Duke-NUS Medical School, Singapore
- Dept of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Caroline G. Lee
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-NUS Medical School, Singapore
- Div of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
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14
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Mahinfar P, Baradaran B, Davoudian S, Vahidian F, Cho WCS, Mansoori B. Long Non-Coding RNAs in Multidrug Resistance of Glioblastoma. Genes (Basel) 2021; 12:455. [PMID: 33806782 PMCID: PMC8004794 DOI: 10.3390/genes12030455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma, also known as glioblastoma multiforme, is the most aggressive brain tumor in adults. Despite the huge advance in developing novel therapeutic strategies for patients with glioblastoma, the appearance of multidrug resistance (MDR) against the common chemotherapeutic agents, including temozolomide, is considered as one of the important causes for the failure of glioblastoma treatment. On the other hand, recent studies have demonstrated the critical roles of long non-coding RNAs (lncRNAs), particularly in the development of MDR in glioblastoma. Therefore, this article aimed to review lncRNA's contribution to the regulation of MDR and elucidate the underlying mechanisms in glioblastoma, which will open up new lines of inquiry in the treatment of glioblastoma.
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Affiliation(s)
- Parvaneh Mahinfar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166/15731, Iran; (P.M.); (B.B.); (F.V.)
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166/15731, Iran; (P.M.); (B.B.); (F.V.)
| | - Sadaf Davoudian
- Humanitas Clinical and Research Center—IRCCS, 20089 Milan, Italy;
| | - Fatemeh Vahidian
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166/15731, Iran; (P.M.); (B.B.); (F.V.)
| | | | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166/15731, Iran; (P.M.); (B.B.); (F.V.)
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, 5230 Odense, Denmark
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15
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Yu HC, Huang KY, Lu MC, Huang Tseng HY, Liu SQ, Lai NS, Huang HB. Down-Regulation of LOC645166 in T Cells of Ankylosing Spondylitis Patients Promotes the NF-κB Signaling via Decreasingly Blocking Recruitment of the IKK Complex to K63-Linked Polyubiquitin Chains. Front Immunol 2021; 12:591706. [PMID: 33717069 PMCID: PMC7946993 DOI: 10.3389/fimmu.2021.591706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/11/2021] [Indexed: 01/01/2023] Open
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory disease that mainly affects the spine. AS is highly associated with the expression of HLA-B27. Up to 95% AS patients are HLA-B27-positive. However, only 1%-2% of the HLA-B27-positive carriers suffer from AS, implying that other factors may also govern the development of AS. Long non-coding RNAs (lncRNAs) can regulate the immune response via their binding proteins. In the present study, we have identified that the levels of lncRNA, LOC645166, in T cells of AS patients were reduced. Overexpression of LOC645166 in Jurkat cells down-regulated the IL-23p19 expression and suppressed the JAK2/STAT3 signaling in response to stimulation by phorbol 12-myristate 13-acetate. Suppression of STAT3 activation by LOC645166 was also observed when Jurkat cells or T cells of AS patient were treated with anti-CD3/CD28 antibodies. In order to explore the role of LOC645166 in the pathogenesis of AS, RNA pull-down assay plus proteomic approach and western blotting were performed and identified that LOC645166 prefers binding the K63-linked polyubiquitin chains. LOC645166 can suppress recruitment of the IKK complex to K63-linked polyubiquitin chains and diminish IKK2 activation, leading to down-regulation of NF-κB activation. Down-regulation of LOC645166 expression in T cells of AS patients up-regulates NF-kB activation via decreasingly impeding recruitment of the IKK complex to K63-linked polyubiquitin chains, allowing AS patients to exhibit more sensitivity to stimulation by the proinflammatory cytokines or by TLR ligands.
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Affiliation(s)
- Hui-Chun Yu
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Kuang-Yung Huang
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Ming-Chi Lu
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Hsien-Yu Huang Tseng
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Su-Qin Liu
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Ning-Sheng Lai
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Hsien-Bin Huang
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
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16
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Rezaei O, Tamizkar KH, Sharifi G, Taheri M, Ghafouri-Fard S. Emerging Role of Long Non-Coding RNAs in the Pathobiology of Glioblastoma. Front Oncol 2021; 10:625884. [PMID: 33634032 PMCID: PMC7901982 DOI: 10.3389/fonc.2020.625884] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma is the utmost aggressive diffuse kind of glioma which is originated from astrocytes, neural stem cells or progenitors. This malignant tumor has a poor survival rate. A number of genetic aberrations and somatic mutations have been associated with this kind of cancer. In recent times, the impact of long non-coding RNAs (lncRNAs) in glioblastoma has been underscored by several investigations. Up-regulation of a number of oncogenic lncRNAs such as H19, MALAT1, SNHGs, MIAT, UCA, HIF1A-AS2 and XIST in addition to down-regulation of other tumor suppressor lncRNAs namely GAS5, RNCR3 and NBAT1 indicate the role of these lncRNAs in the pathogenesis of glioblastoma. Several in vitro and a number of in vivo studies have demonstrated the contribution of these transcripts in the regulation of cell proliferation and apoptosis, cell survival, invasion and metastasis of glioblastoma cells. Moreover, some lncRNAs such as SBF2-AS1 are involved in conferring resistance to temozolomide. Finally, few circularRNAs have been identified that influence the evolution of glioblastoma. In this paper, we discuss the impacts of lncRNAs in the pathogenesis of glioblastoma, their applications as markers and their implications in the therapeutic responses in this kind of cancer.
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Affiliation(s)
- Omidvar Rezaei
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Guive Sharifi
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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17
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Katsushima K, Jallo G, Eberhart CG, Perera RJ. Long non-coding RNAs in brain tumors. NAR Cancer 2021; 3:zcaa041. [PMID: 34316694 PMCID: PMC8210177 DOI: 10.1093/narcan/zcaa041] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/09/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been found to be central players in the epigenetic, transcriptional and post-transcriptional regulation of gene expression. There is an accumulation of evidence on newly discovered lncRNAs, their molecular interactions and their roles in the development and progression of human brain tumors. LncRNAs can have either tumor suppressive or oncogenic functions in different brain cancers, making them attractive therapeutic targets and biomarkers for personalized therapy and precision diagnostics. Here, we summarize the current state of knowledge of the lncRNAs that have been implicated in brain cancer pathogenesis, particularly in gliomas and medulloblastomas. We discuss their epigenetic regulation as well as the prospects of using lncRNAs as diagnostic biomarkers and therapeutic targets in patients with brain tumors.
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Affiliation(s)
- Keisuke Katsushima
- Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans St., Baltimore, MD 21231, USA
| | - George Jallo
- Johns Hopkins All Children's Hospital, 600 5th St. South, St Petersburg, FL 33701, USA
| | - Charles G Eberhart
- Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans St., Baltimore, MD 21231, USA
| | - Ranjan J Perera
- Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans St., Baltimore, MD 21231, USA
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18
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FAM225B Is a Prognostic lncRNA for Patients with Recurrent Glioblastoma. DISEASE MARKERS 2020; 2020:8888085. [PMID: 33299501 PMCID: PMC7704151 DOI: 10.1155/2020/8888085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 12/22/2022]
Abstract
Objective The overall survival of patients with recurrent glioblastoma (rGBM) is quite different, so clinical outcome prediction is necessary to guide personalized clinical treatment for patients with rGBM. The expression level of lncRNA FAM225B was analyzed to determine its prognostic value in rGBMs. Methods We collected 109 samples of Chinese Glioma Genome Atlas (CGGA) RNA sequencing dataset and divided into training set and validation set. Then, we analyzed the expression of FAM225B, clinical characteristics, and overall survival (OS) information. Kaplan-Meier survival analysis was used to estimate the OS distributions. The prognostic value of FAM225B in rGBMs was tested by univariate and multivariate Cox regression analyses. Moreover, we analyzed the biological processes and signaling pathways of FAM225B. Results We found that FAM225B was upregulated in rGBMs (P = 0.0009). The expression of FAM225B increased with the grades of gliomas (P < 0.0001). The OS of rGBMs in the low-expression group was significantly longer than that in the high-expression group (P = 0.0041). Similar result was found in the training set (P = 0.0340) and verified in the validation set (P = 0.0292). In multivariate Cox regression analysis, FAM225B was identified to be an independent prognostic factor for rGBMs (P = 0.003). Biological process and KEGG pathway analyses implied FAM225B mainly played a functional role on transcription, regulation of transcription, cell migration, focal adhesion, etc. Conclusions FAM225B is expected to be as a new prognostic biomarker for the identification of rGBM patients with poor outcome. And our study provided a potential therapeutic target for rGBMs.
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19
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Song Z, Zhang Y, Chen Z, Zhang B. Identification of key genes in lung adenocarcinoma based on a competing endogenous RNA network. Oncol Lett 2020; 21:60. [PMID: 33281971 PMCID: PMC7709547 DOI: 10.3892/ol.2020.12322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 09/30/2020] [Indexed: 12/25/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most commonly diagnosed type of lung cancer and exhibits a high morbidity. The present study aimed to investigate the long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) mechanisms in LUAD. The receptor activity modifying protein 2-antisense RNA 1 (RAMP2-AS1) was identified using GSE113852 and GSE130779 datasets downloaded from the Gene Expression Omnibus database, and the downregulation of RAMP2-AS1 was the most significant in LUAD. In addition, microRNA (miR)-296-5p was identified to bind to RAMP2-AS1 via bioinformatics analysis. Subsequently, CD44, cyclin D3 (CCND3), neurocalcin δ (NCALD), microtubule actin crosslinking factor 1 (MACF1) and potassium channel tetramerization domain containing 15 were obtained by intersecting the predicted target genes of miR-296-5p and 368 differentially expressed mRNAs in LUAD. According to the Gene Expression Profiling Interactive Analysis and UALCAN databases, these five mRNAs were downregulated in LUAD, and their expression levels were positively correlated with those of RAMP2-AS1. CD44, CCND3, NCALD and MACF1 were selected as key mRNAs in LUAD based on prognostic analyses. Furthermore, functional enrichment analyses were performed and an interaction network was constructed to reveal the functions of the RAMP2-AS1-associated ceRNA in LUAD. The results indicated that the functions were mainly enriched in generic transcription pathways, cyclin D-associated events in G1 and epithelial stromal transformation. Reverse transcription-quantitative PCR assays revealed that RAMP2-AS1, CD44, CCND3, NCALD and MACF1 expression was lower in tumor tissues than in normal tissues, while miR-296-5p expression was higher in tumor tissues compared with in normal tissues. The association between RAMP2-AS1 and MACF1 was further confirmed using in vitro experiments. Overall, the present results indicated that RAMP2-AS1, miR-296-5p, CD44, CCND3, NCALD and MACF1 may be involved in LUAD progression and may therefore serve as potential biomarkers and provide a theoretical basis for the study of the pathogenesis of LUAD.
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Affiliation(s)
- Zikun Song
- Department of Intensive Care Medicine, The People's Second Hospital of Liaocheng, Linqing, Shandong 252601, P.R. China
| | - Yinjiang Zhang
- School of Pharmacy, Minzu University of China, Beijing 100081, P.R. China
| | - Zheren Chen
- Department of Oncology, Renmin Hospital of Shishou, Jingzhou, Hubei 434400, P.R. China
| | - Bicheng Zhang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430070, P.R. China
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20
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Non-coding RNAs in Brain Tumors, the Contribution of lncRNAs, circRNAs, and snoRNAs to Cancer Development-Their Diagnostic and Therapeutic Potential. Int J Mol Sci 2020; 21:ijms21197001. [PMID: 32977537 PMCID: PMC7582339 DOI: 10.3390/ijms21197001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 12/17/2022] Open
Abstract
Brain tumors are one of the most frightening ailments that afflict human beings worldwide. They are among the most lethal of all adult and pediatric solid tumors. The unique cell-intrinsic and microenvironmental properties of neural tissues are some of the most critical obstacles that researchers face in the diagnosis and treatment of brain tumors. Intensifying the search for potential new molecular markers in order to develop new effective treatments for patients might resolve this issue. Recently, the world of non-coding RNAs (ncRNAs) has become a field of intensive research since the discovery of their essential impact on carcinogenesis. Some of the most promising diagnostic and therapeutic regulatory RNAs are long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and small nucleolar RNAs (snoRNAs). Many recent reports indicate the important role of these molecules in brain tumor development, as well as their implications in metastasis. In the following review, we summarize the current state of knowledge about regulatory RNAs, namely lncRNA, circRNAs, and snoRNAs, and their impact on the development of brain tumors in children and adults with particular emphasis on malignant primary brain tumors-gliomas and medulloblastomas (MB). We also provide an overview of how these different ncRNAs may act as biomarkers in these tumors and we present their potential clinical implications.
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21
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Balaji E V, Kumar N, Satarker S, Nampoothiri M. Zinc as a plausible epigenetic modulator of glioblastoma multiforme. Eur J Pharmacol 2020; 887:173549. [PMID: 32926916 DOI: 10.1016/j.ejphar.2020.173549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 01/04/2023]
Abstract
Glioblastoma Multiforme (GBM) is an aggressive brain tumor (WHO grade 4 astrocytoma) with unknown causes and is associated with a reduced life expectancy. The available treatment options namely radiotherapy, surgery and chemotherapy have failed to improve life expectancy. Out of the various therapeutic approaches, epigenetic therapy is one of the most studied. Epigenetic therapy is involved in the effective treatment of GBM by inhibiting DNA methyltransferase, histone deacetylation and non-coding RNA. It also promotes the expression of the tumor suppressor gene and is involved in the suppression of the oncogene. Various targets are being studied to implement proper epigenetic regulation to control GBM effectively. Zinc is one of the micronutrients which is considered to maintain epigenetic regulation by promoting the proper DNA folding, protecting genetic material from the oxidative damage and controlling the enzyme activation involved in the epigenetic regulation. Here, we are discussing the importance of zinc in regulating the epigenetic modifications and assessing its role in glioblastoma research. The discussion also highlights the importance of artificial intelligence using epigenetics for envisaging the glioma progression, diagnosis and its management.
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Affiliation(s)
- Vignesh Balaji E
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Nitesh Kumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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22
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Li A, Mallik S, Luo H, Jia P, Lee DF, Zhao Z. H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:180-191. [PMID: 32585626 PMCID: PMC7321791 DOI: 10.1016/j.omtn.2020.05.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/17/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs (lncRNAs) have recently been found to be important in gene regulation. lncRNA H19 has been reported to play an oncogenic role in many human cancers. Its specific regulatory role is still elusive. In this study, we developed a novel analytic approach by integrating the synergistic regulation among lncRNAs (e.g., H19), transcription factors (TFs), target genes, and microRNAs (miRNAs) and then applied it to the pan-cancer expression datasets from The Cancer Genome Atlas (TCGA). Using linear regression models, we identified 88 H19-TF-gene co-regulatory triplets, in which 93% of the TF-gene pairs were related to cancer, indicating that our approach was effective to identify disease-related lncRNA-TF-gene co-regulation mechanisms. lncRNAs can function as miRNA sponges. Our further experiments found that H19 might regulate SP1-TGFBR2 through let-7b and miR-200b, ETS1-TGFBR2 through miR-29a and miR-200b, and STAT3-KLF11 through miR-17 in breast cancer cell lines. Our work suggests that miRNA-mediated lncRNA-TF-gene co-regulation is complicated yet important in cancer.
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Affiliation(s)
- Aimin Li
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi 710048, China; Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Haidan Luo
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dung-Fang Lee
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.
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Su D, Ji Z, Xue P, Guo S, Jia Q, Sun H. Long-Noncoding RNA FGD5-AS1 Enhances the Viability, Migration, and Invasion of Glioblastoma Cells by Regulating the miR-103a-3p/TPD52 Axis. Cancer Manag Res 2020; 12:6317-6329. [PMID: 32848452 PMCID: PMC7425657 DOI: 10.2147/cmar.s253467] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/08/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose This study was designed to explore the functional role of FYVE, RhoGEF, and PH domain containing 5 antisense RNA 1 (FGD5-AS1) and the underlying regulatory mechanism in the progression of glioblastoma (GBM). Materials and Methods FGD5-AS1 expression was analyzed in The Cancer Genome Atlas (TCGA), and then detected in GBM tissues and cells by quantitative reverse-transcription polymerase chain reaction. Viability, migration, and invasion of GBM cells were assessed using the MTT, wound healing, and transwell assays, respectively. StarBase/TargetScan analysis and dual-luciferase reporter gene (DLR) assay were performed to investigate the relationship between FGD5-AS1/tumor protein D52 (TPD52) and miR-103a-3p. A xenograft tumor model was established to evaluate the role of FGD5-AS1 in GBM tumorigenesis in vivo. Results FGD5-AS1 was overexpressed in GBM tissues and cells, and silencing of FGD5-AS1 expression resulted in the inhibition of the viability, migration, and invasion of GBM cells. miR-130-3p was a target of FGD5-AS1, and its expression was negatively regulated by FGD5-AS1. Silencing miR-103a-3p expression resulted in the abrogation of the inhibitory effects of si-FGD5-AS1 on the viability, migration, and invasion of GBM cells. TPD52 was a target of miR-103a-3p and suppressed the antitumor effects of FGD5-AS1 silencing on GBM cells. In addition, FGD5-AS1 silencing inhibited the growth of xenograft tumors in vivo by modulating the miR-103a-3p/TPD52 axis. Conclusion Silencing of FGD5-AS1 inhibited the viability, migration, and invasion of GBM cells by regulating the miR-103a-3p/TPD52 axis.
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Affiliation(s)
- Daoqing Su
- Department of Neurosurgery, Liaocheng People's Hospital and Liaocheng Brain Hospital, Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng City, Shandong Province, People's Republic of China
| | - Zhengang Ji
- Department of Neurosurgery, Liaocheng People's Hospital and Liaocheng Brain Hospital, Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng City, Shandong Province, People's Republic of China
| | - Pengfei Xue
- Department of Neurosurgery, Liaocheng People's Hospital and Liaocheng Brain Hospital, Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng City, Shandong Province, People's Republic of China
| | - Shengfu Guo
- Department of Neurosurgery, Liaocheng People's Hospital and Liaocheng Brain Hospital, Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng City, Shandong Province, People's Republic of China
| | - Qingbin Jia
- Department of Neurosurgery, Liaocheng People's Hospital and Liaocheng Brain Hospital, Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng City, Shandong Province, People's Republic of China
| | - Hanyu Sun
- Department of Neurosurgery, Liaocheng People's Hospital and Liaocheng Brain Hospital, Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng City, Shandong Province, People's Republic of China
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24
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Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients. Sci Rep 2020; 10:11124. [PMID: 32636408 PMCID: PMC7341759 DOI: 10.1038/s41598-020-67742-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/12/2020] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are often aberrantly expressed in Hepatocellular Carcinoma (HCC). We hypothesize that lncRNAs modulate HCC prognoses through differential deregulation of key lncRNAs affecting important gene network in key cancer pathways associated with pertinent clinical phenotype. Here, we present a novel approach integrating lncRNA-mRNA expression profiles with clinical characteristics to identify lncRNA signatures in clinically-relevant co-expression lncRNA-mRNA networks residing in pertinent cancer pathways. Notably one network, associated with poorer prognosis, comprises five up-regulated lncRNAs significantly correlated (|Pearson Correlation Coefficient|≥ 0.9) with 91 up-regulated genes in the cell-cycle and Rho-GTPase pathways. All 5 lncRNAs and 85/91 (93.4%) of the correlated genes were significantly associated with higher tumor-grade while 3/5 lncRNAs were also associated with no tumor capsule. Interestingly, 2/5 lncRNAs that are correlated with numerous genes in this oncogenic network were experimentally shown to up-regulate genes involved in cell-cycle and transcriptional regulation. Another network comprising 4 down-regulated lncRNAs and 8 down-regulated metallothionein-family genes are significantly associated with tumor invasion. The identification of these key lncRNAs signatures that deregulate important network of genes in key cancer pathways associated with pertinent clinical phenotype may facilitate the design of novel therapeutic strategies targeting these 'master' regulators for better patient outcome.
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25
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Chen L, Wang G, Xu Z, Lin K, Mu S, Pan Y, Shan M. Overexpression of LncRNA PSMG3-AS1 Distinguishes Glioblastomas from Sarcoidosis. J Mol Neurosci 2020; 70:2015-2019. [PMID: 32529538 DOI: 10.1007/s12031-020-01605-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/19/2020] [Indexed: 11/24/2022]
Abstract
In clinical practices, glioblastomas (GBM) in some cases can be misdiagnosed as sarcoidosis. This study aimed to develop a biomarker to distinguish GBM from sarcoidosis. In this study, we found that PSMG3-AS1 was upregulated in plasma of GBM patients in comparison with that in sarcoidosis patients and healthy controls. Receiver operating characteristic (ROC) curve analysis showed that upregulation of PSMG3-AS1 effectively separated GBM patients from sarcoidosis patients and healthy controls. In GBM cells, overexpression of PSMG3-AS1 led to downregulated miR-34a and increased methylation of miR-34a gene. In addition, overexpression of PSMG3-AS1 reduced the inhibitory effects of miR-34a on GBM cell proliferation. In conclusion, overexpression of PSMG3-AS1 distinguishes GBM patients from patients with sarcoidosis, and PSMG3-AS1 may promote GBM cell proliferation by downregulating miR-34a through methylation.
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Affiliation(s)
- Liusheng Chen
- 75th Army Military Medical Research Center, Dali, Yunnan Province, 671003, People's Republic of China
| | - Guanliang Wang
- Department of Traditional Chinese Medical Rehabilitation, 75th Army Military Hospital, Dali, Yunnan Province, 671003, People's Republic of China.
| | - Zihui Xu
- Department of Traditional Chinese Medicine, Second Affiliated Hospital of Army Military Medical University, Chongqing City, 400037, People's Republic of China
| | - Kailong Lin
- Department of Traditional Chinese Medical Rehabilitation, 75th Army Military Hospital, Dali, Yunnan Province, 671003, People's Republic of China
| | - Sen Mu
- 75th Army Military Medical Research Center, Dali, Yunnan Province, 671003, People's Republic of China
| | - Yicheng Pan
- Department of Traditional Chinese Medical Rehabilitation, 75th Army Military Hospital, Dali, Yunnan Province, 671003, People's Republic of China
| | - Mengya Shan
- Department of Traditional Chinese Medicine, Second Affiliated Hospital of Army Military Medical University, Chongqing City, 400037, People's Republic of China
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DeOcesano-Pereira C, Machado RAC, Chudzinski-Tavassi AM, Sogayar MC. Emerging Roles and Potential Applications of Non-Coding RNAs in Glioblastoma. Int J Mol Sci 2020; 21:E2611. [PMID: 32283739 PMCID: PMC7178171 DOI: 10.3390/ijms21072611] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a diversity of RNA species, which do not have the potential to encode proteins. Non-coding RNAs include two classes of RNAs, namely: short regulatory ncRNAs and long non-coding RNAs (lncRNAs). The short regulatory RNAs, containing up to 200 nucleotides, include small RNAs, such as microRNAs (miRNA), short interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs). The lncRNAs include long antisense RNAs and long intergenic RNAs (lincRNAs). Non-coding RNAs have been implicated as master regulators of several biological processes, their expression being strictly regulated under physiological conditions. In recent years, particularly in the last decade, substantial effort has been made to investigate the function of ncRNAs in several human diseases, including cancer. Glioblastoma is the most common and aggressive type of brain cancer in adults, with deregulated expression of small and long ncRNAs having been implicated in onset, progression, invasiveness, and recurrence of this tumor. The aim of this review is to guide the reader through important aspects of miRNA and lncRNA biology, focusing on the molecular mechanism associated with the progression of this highly malignant cancer type.
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Affiliation(s)
- Carlos DeOcesano-Pereira
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, 1500 Vital Brazil Avenue, São Paulo 05503-900 SP, Brazil; (C.D.-P.); (A.M.C.-T.)
| | - Raquel A. C. Machado
- Department of Life Science and Medicine, University of Luxembourg, Campus Belval, Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg;
| | - Ana Marisa Chudzinski-Tavassi
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, 1500 Vital Brazil Avenue, São Paulo 05503-900 SP, Brazil; (C.D.-P.); (A.M.C.-T.)
| | - Mari Cleide Sogayar
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo 05508-000, Brazil
- Cell and Molecular Therapy Center (NUCEL), School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
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Interaction of Long Noncoding RNAs and Notch Signaling: Implications for Tissue Homeostasis Loss. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1227:107-129. [PMID: 32072502 DOI: 10.1007/978-3-030-36422-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Notch signaling is a crucial pathway involved in cellular development, progression, and differentiation. Deregulation of Notch signaling pathway commonly impacts tissue homeostasis, being highly associated with proliferative disorders. The long noncoding RNAs (lncRNAs), which are transcripts with more than 200 nucleotides that do not code for proteins, were already described as Notch signaling pathway-interacting molecules. Many of them act as important transcriptional and posttranscriptional regulators, affecting gene expression and targeting other regulatory molecules, such as miRNAs. Due to their strong impact on function and gene expression of Notch-related molecules, lncRNAs influence susceptibility to cancer and other diseases, and can be regarded as potential biomarkers and therapeutic targets. Along this chapter, we summarize the cross talk between the Notch signaling pathway and their most important modulating lncRNAs, as well as the pathological consequences of these interactions, in different tissues.
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Hua X, Wang YY, Jia P, Xiong Q, Hu Y, Chang Y, Lai S, Xu Y, Zhao Z, Song J. Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression. BMC Med 2020; 18:2. [PMID: 31902369 PMCID: PMC6943904 DOI: 10.1186/s12916-019-1469-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/19/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Heart failure (HF) has been recognized as a global pandemic with a high rate of hospitalization, morbidity, and mortality. Although numerous advances have been made, its representative molecular signatures remain largely unknown, especially the role of genes in HF progression. The aim of the present prospective follow-up study was to reveal potential biomarkers associated with the progression of heart failure. METHODS We generated multi-level transcriptomic data from a cohort of left ventricular heart tissue collected from 21 HF patients and 9 healthy donors. By using Masson staining to calculate the fibrosis percentage for each sample, we applied lasso regression model to identify the genes associated with fibrosis as well as progression. The genes were further validated by immunohistochemistry (IHC) staining in the same cohort and qRT-PCR using another independent cohort (20 HF and 9 healthy donors). Enzyme-linked immunosorbent assay (ELISA) was used to measure the plasma level in a validation cohort (139 HF patients) for predicting HF progression. RESULTS Based on the multi-level transcriptomic data, we examined differentially expressed genes [mRNAs, microRNAs, and long non-coding RNAs (lncRNAs)] in the study cohort. The follow-up functional annotation and regulatory network analyses revealed their potential roles in regulating extracellular matrix. We further identified several genes that were associated with fibrosis. By using the survival time before transplantation, COL1A1 was identified as a potential biomarker for HF progression and its upregulation was confirmed by both IHC and qRT-PCR. Furthermore, COL1A1 content ≥ 256.5 ng/ml in plasma was found to be associated with poor survival within 1 year of heart transplantation from heart failure [hazard ratio (HR) 7.4, 95% confidence interval (CI) 3.5 to 15.8, Log-rank p value < 1.0 × 10- 4]. CONCLUSIONS Our results suggested that COL1A1 might be a plasma biomarker of HF and associated with HF progression, especially to predict the 1-year survival from HF onset to transplantation.
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Affiliation(s)
- Xiumeng Hua
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China
| | - Yin-Ying Wang
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX, 77030, USA
| | - Qing Xiong
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX, 77030, USA
| | - Yiqing Hu
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China
| | - Yuan Chang
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China
| | - Songqing Lai
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China
| | - Yong Xu
- Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St, Houston, TX, 77030, USA. .,Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Avenue, Nashville, TN, 37203, USA.
| | - Jiangping Song
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China.
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Chen R, Xin G, Zhang X. Long non-coding RNA HCP5 serves as a ceRNA sponging miR-17-5p and miR-27a/b to regulate the pathogenesis of childhood obesity via the MAPK signaling pathway. J Pediatr Endocrinol Metab 2019; 32:1327-1339. [PMID: 31622249 DOI: 10.1515/jpem-2018-0432] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/30/2019] [Indexed: 12/13/2022]
Abstract
Background This study aimed to investigate the completing endogenous RNA (ceRNA) network involved in childhood obesity. Methods The microarray dataset GSE9624 was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed long non-coding RNAs (lncRNAs) (DELs) and messenger RNAs (DEMs) were isolated between the childhood obesity and non-obesity tissue samples. Then, Gene Ontology (GO) functional and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of isolated DEMs were performed. DELs and DEMs targeted miRNAs were predicted to construct a ceRNA regulatory network. Finally, critical lncRNAs were validated in another dataset. Results A total of 1257 differentially expressed RNAs were screened, including 28 lncRNAs and 1229 mRNAs. In addition, these RNAs were mainly involved in defense response, cell cycle, mitogen-activated protein kinase (MAPK) signaling pathway, apoptosis, etc. Three lncRNAs (human leukocyte antigen complex 5 [HCP5], long intergenic non-protein coding RNA 839 [LINC00839] and receptor activity modifying protein 2 [RAMP2-AS1]) and two related miRNAs (hsa-miR-17-5p and hsa-miR-27a/b-3p) were identified as key RNAs in childhood obesity. Specifically, lncRNA HCP5 interacted with miR-17-5p and miR-27a/b to regulate nemo-like kinase (NLK) and Ras-related protein 2 (RRAS2) via the MAPK signaling pathway. Finally, four genes (RRAS2, NLK, bcl2/adenovirus E1B protein-interacting protein 3 [BNIP3] and phorbol-12-myristate-13-acetate-induced protein 1 [PMAIP1]) targeted by miRNAs were predicted as critical genes and might be novel diagnostic biomarkers of childhood obesity. Conclusions lncRNA HCP5 could serve as a ceRNA sponging miR-17-5p and miR-27a/b to regulate the pathogenesis of childhood obesity via NLK and RRAS2 in the MAPK signaling pathway.
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Affiliation(s)
- Rui Chen
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Guangda Xin
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xiaofei Zhang
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun, China
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Bai J, Xu J, Zhao J, Zhang R. lncRNA SNHG1 cooperated with miR-497/miR-195-5p to modify epithelial-mesenchymal transition underlying colorectal cancer exacerbation. J Cell Physiol 2019; 235:1453-1468. [PMID: 31276207 DOI: 10.1002/jcp.29065] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022]
Abstract
Our study was intended to provide evidence for whether long noncoding RNA (lncRNA) SNHG1 would accelerate the epithelial-mesenchymal transition (EMT) course intrinsic in colorectal cancer (CRC) by sponging downstream miR-497-5p and miR-195-5p. We altogether collected 338 pairs of CRC and noncancerous tissues, and meanwhile purchased five CRC cell lines (i.e., SW480, HCT116, Lovo, CaCO-2, and HT29) and human embryo intestinal mucosal tissue-sourced cell line (i.e., CCC-HIE-2). The CRC cells as mentioned above were appraised regarding their potencies in proliferation, migration, and invasion, after being transfected with pcDNA3.1-SNHG1, si-SNHG1, miR-195-5p mimic/inhibitor, and miR-497-5p mimic/inhibitor. Eventually, we depended on reverse transcription-polymerase chain reaction to assess SNHG1, miR-497-5p, and miR-195-5p expressions, and the protein levels of EMT-specific molecules were determined on the strength of western blotting. It seemed that there was a high potential for highly expressed SNHG1 and lowly expressed miR-497/miR-195 to symbolize CRC patients' unfavorable prognosis (p < .05). Concurrently, CRC cells were detected with higher SNHG1 expression and lower miR-497/miR-195 expression than CCC-HIE-2 cells (p < .05). In addition, the EMT process of CRC cells was facilitated markedly against the contexts of overexpressed SNHG1 and underexpressed miR-497-5p/miR-195-5p. Intriguingly, the strength of miR-195-5p collaborating with miR-497-5p in affecting the activity of CRC cells seemed to overweigh that of miR-497/miR-195-5p alone. Besides, both miR-195-5p and miR-497-5p were subjected to in vivo and in vitro modification of SNHG1 (p < .05). Conclusively, application of lncRNA SNHG1 for treating CRC might be promising, given its dual modulation of miR-497 and miR-195 underlying CRC pathogenesis.
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Affiliation(s)
- Jinghui Bai
- Department of Internal Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Insititute, Shenyang, Liaoning, China
| | - Jian Xu
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Insititute, Shenyang, Liaoning, China
| | - Jian Zhao
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Insititute, Shenyang, Liaoning, China
| | - Rui Zhang
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Insititute, Shenyang, Liaoning, China
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Dornelles-Wawruk H, Soledad Heredia R, de Paula-Junior MR, Cardoso MTO, Bonadio RS, Dos Reis BF, Pic-Taylor A, de Oliveira SF, Mazzeu JF. A Balanced Reciprocal Translocation t(2;9)(p25;q13) Disrupting the LINC00299 Gene in a Patient with Intellectual Disability. Mol Syndromol 2019; 10:234-238. [PMID: 31602198 DOI: 10.1159/000500397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) are a class of noncoding RNAs implicated in several biological processes. LincRNA 299 (LINC00299) maps to 2p25.1 and its function is still unknown. However, this gene has been proposed as a candidate for intellectual disability (ID) in a patient with a balanced translocation where the breakpoint disrupted its ORF. Here, we describe a new case of LINC00299 disruption associated with ID. The individual, a 42-year-old woman, was referred to the clinical geneticist because of her son who had severe syndromic ID. G-banding and chromosomal microarray analysis were performed. Karyotyping of the boy revealed an extranumerary derivative chromosome identified as an unbalanced translocation between chromosomes 2 and 9 of maternal origin. The mother's karyotype showed a balanced translocation 46,XX,t(2;9)(p25;q13). Chromosomal microarray indicated a disruption of LINC00299. These data corroborate the role of LINC00299 as a causative gene for ID and broadens the spectrum of LINC00299-related phenotypes.
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Affiliation(s)
| | - Romina Soledad Heredia
- Hospital de Apoio de Brasília, Secretaria de Estado de Saúde do Distrito Federal, Brasilia, Brazil.,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasilia, Brazil
| | | | | | - Raphael S Bonadio
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Bianca F Dos Reis
- Hospital de Apoio de Brasília, Secretaria de Estado de Saúde do Distrito Federal, Brasilia, Brazil
| | - Aline Pic-Taylor
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Silviene F de Oliveira
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Juliana F Mazzeu
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasilia, Brazil.,Faculdade de Medicina, Universidade de Brasília, Brasilia, Brazil
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Yang S, Shergalis A, Lu D, Kyani A, Liu Z, Ljungman M, Neamati N. Design, Synthesis, and Biological Evaluation of Novel Allosteric Protein Disulfide Isomerase Inhibitors. J Med Chem 2019; 62:3447-3474. [PMID: 30759340 DOI: 10.1021/acs.jmedchem.8b01951] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein disulfide isomerase (PDI) is responsible for nascent protein folding in the endoplasmic reticulum (ER) and is critical for glioblastoma survival. To improve the potency of lead PDI inhibitor BAP2 (( E)-3-(3-(4-hydroxyphenyl)-3-oxoprop-1-en-1-yl)benzonitrile), we designed and synthesized 67 analogues. We determined that PDI inhibition relied on the A ring hydroxyl group of the chalcone scaffold and cLogP increase in the sulfonamide chain improved potency. Docking studies revealed that BAP2 and analogues bind to His256 in the b' domain of PDI, and mutation of His256 to Ala abolishes BAP2 analogue activity. BAP2 and optimized analogue 59 have modest thiol reactivity; however, we propose that PDI inhibition by BAP2 analogues depends on the b' domain. Importantly, analogues inhibit glioblastoma cell growth, induce ER stress, increase expression of G2M checkpoint proteins, and reduce expression of DNA repair proteins. Cumulatively, our results support inhibition of PDI as a novel strategy to treat glioblastoma.
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Affiliation(s)
- Suhui Yang
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Andrea Shergalis
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Dan Lu
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Anahita Kyani
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Ziwei Liu
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Mats Ljungman
- Department of Radiation Oncology Rogel Cancer Center , University of Michigan Medical School and Rogel Cancer Center, School of Public Health , Ann Arbor , Michigan 48109 , United States
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
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Oskooei VK, Ghafouri-Fard S. Are long non-coding RNAs involved in the interaction circuit between estrogen receptor and vitamin D receptor? Meta Gene 2019. [DOI: 10.1016/j.mgene.2018.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Do H, Kim W. Roles of Oncogenic Long Non-coding RNAs in Cancer Development. Genomics Inform 2018; 16:e18. [PMID: 30602079 PMCID: PMC6440676 DOI: 10.5808/gi.2018.16.4.e18] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/29/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are classified as RNAs that are longer than 200 nucleotides and cannot be translated into protein. Several studies have demonstrated that lncRNAs are directly or indirectly involved in a variety of biological processes and in the regulation of gene expression. In addition, lncRNAs have important roles in many diseases including cancer. It has been shown that abnormal expression of lncRNAs is observed in several human solid tumors. Several studies have shown that many lncRNAs can function as oncogenes in cancer development through the induction of cell cycle progression, cell proliferation and invasion, anti-apoptosis, and metastasis. Oncogenic lncRNAs have the potential to become promising biomarkers and might be potent prognostic targets in cancer therapy. However, the biological and molecular mechanisms of lncRNA involvement in tumorigenesis have not yet been fully elucidated. This review summarizes studies on the regulatory and functional roles of oncogenic lncRNAs in the development and progression of various types of cancer.
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Affiliation(s)
- Hyunhee Do
- Department of Biology Education, Korea National University of Education, Cheongju 28173, Korea
| | - Wanyeon Kim
- Department of Biology Education, Korea National University of Education, Cheongju 28173, Korea
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Li J, Zhu Y, Wang H, Ji X. Targeting Long Noncoding RNA in Glioma: A Pathway Perspective. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:431-441. [PMID: 30388617 PMCID: PMC6202792 DOI: 10.1016/j.omtn.2018.09.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/15/2018] [Accepted: 09/26/2018] [Indexed: 02/09/2023]
Abstract
Long noncoding RNAs (lncRNAs) participate extensively in biological processes of various cancers. The majority of these transcripts are uniquely expressed in differentiated tissues or specific cancer types. lncRNAs are aberrantly expressed in gliomas and exert diverse functions. In this article, we provided an overview of how lncRNAs regulate cellular processes in glioma, enumerated the lncRNAs that may act as glioma biomarkers, and showed their potential clinical implications.
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Affiliation(s)
- Junyang Li
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
| | - Yihao Zhu
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
| | - Handong Wang
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China.
| | - Xiangjun Ji
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
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Dong Z, Cui H. Epigenetic modulation of metabolism in glioblastoma. Semin Cancer Biol 2018; 57:45-51. [PMID: 30205139 DOI: 10.1016/j.semcancer.2018.09.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/06/2018] [Indexed: 12/15/2022]
Abstract
Epigenetic and metabolic alterations incancer cells are highly associated. Glioblastoma multiforme (GBM) is a complicated pathological process with dysregulated methylation and histone modifications. Metabolic modulation of epigenetics in gliomas was previously summarized. However, epigenetic modulation is also important in metabolic decision. Recently, there has been a tremendous increase in understanding of DNA methylation, chromatin modulation, and non-coding RNAs in the regulation of cell metabolism, especially glycolytic metabolism in GBM. In this review, we summarize DNA methylation, histone alteration, and non-coding RNA mediated epigenetic modulation of metabolism in GBM and discuss the future research directions in this area and its applications in GBM treatment.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Biology, Southwest University, Beibei, Chongqing, China; Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing, China; Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Biology, Southwest University, Beibei, Chongqing, China; Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing, China; Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing, China.
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Harris M, Svensson F, Kopanitsa L, Ladds G, Bailey D. Emerging patents in the therapeutic areas of glioma and glioblastoma. Expert Opin Ther Pat 2018; 28:573-590. [DOI: 10.1080/13543776.2018.1494155] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Matthew Harris
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Fredrik Svensson
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cambridge CB4 0WS, UK
| | - Liliya Kopanitsa
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cambridge CB4 0WS, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - David Bailey
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cambridge CB4 0WS, UK
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Zhou Y, Dai W, Wang H, Pan H, Wang Q. Long non-coding RNA CASP5 promotes the malignant phenotypes of human glioblastoma multiforme. Biochem Biophys Res Commun 2018; 500:966-972. [PMID: 29715460 DOI: 10.1016/j.bbrc.2018.04.217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been demonstrated to be intensively involved in the development of various carcinomas, including glioblastoma multiforme (GBM). However, only a few of them have been well characterized. LncRNA CASP5 have been found to be up-regulated in GBM tissues compared with normal tissues in a microarray-based lncRNA profiling study. In the present study, we further explored the biological role of lncRNA CASP5 in GBM. METHODS We examined the expression level of lncRNA CASP5 in GBM tissues as well as GBM cell lines. CCK-8 assay, flow cytometric analysis, western blotting, orthotopic GBM model as well as transwell assay were performed to investigate the biological role of CASP5. RESULTS We observed that lncRNA CASP5 was highly expressed in GBM tissues and cell lines. Knockdown of CASP5 greatly inhibited GBM proliferation and resulted in G1 cell cycle arrest along with higher apoptosis ratios in vitro and in vivo, while overexpression led to the opposite phenomenon. Furthermore, the migration and invasion ability of GBM cells were significantly decreased after CASP5 down-regulation, while increased migration and invasion can be observed after CASP5 up-regulation. CONCLUSION We demonstrate for the first time the potential oncogenic role of lncRNA CASP5 which may be helpful for identifying novel therapeutic targets in GBM.
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Affiliation(s)
- Yali Zhou
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210002, China
| | - Wei Dai
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing Medical University, Nanjing, 210002, China
| | - Handong Wang
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210002, China.
| | - Hao Pan
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210002, China
| | - Qiang Wang
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210002, China
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39
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Prognostic and clinicopathological significance of long non-coding RNA in glioma. Neurosurg Rev 2018; 43:1-8. [DOI: 10.1007/s10143-018-0965-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/20/2018] [Accepted: 03/07/2018] [Indexed: 02/06/2023]
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Reicher A, Foßelteder J, Kwong LN, Pichler M. Crosstalk between the Notch signaling pathway and long non-coding RNAs. Cancer Lett 2018; 420:91-96. [PMID: 29409809 DOI: 10.1016/j.canlet.2018.01.070] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/18/2018] [Accepted: 01/26/2018] [Indexed: 01/17/2023]
Abstract
The Notch signaling pathway has a key role in cellular development and is involved in initiation and progression of cancer by fundamentally influencing cellular processes such as differentiation, proliferation or migration. The pathway is regulated on many stages, generating diverse outcomes depending on cellular context or signaling dose. Recent studies suggest that long non-coding RNAs (lncRNAs), a class of non-coding RNAs deregulated in many cancers, are involved in regulating the Notch pathway activity by modulating the expression of receptors or ligands on transcriptional or posttranscriptional levels. LncRNAs are also downstream targets of Notch signaling and some of these Notch-induced lncRNAs have been reported to be inducers of its oncogenic effects. This cross-talk between Notch signaling and lncRNAs makes those molecules potential biomarkers for Notch signaling activity and interesting therapeutic RNA-based targets in the future.
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Affiliation(s)
- Andreas Reicher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria; Research Unit of Non-Coding RNA and Genome Editing in Cancer, Medical University of Graz, 8036 Graz, Austria; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Johannes Foßelteder
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria; Research Unit of Non-Coding RNA and Genome Editing in Cancer, Medical University of Graz, 8036 Graz, Austria
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria; Research Unit of Non-Coding RNA and Genome Editing in Cancer, Medical University of Graz, 8036 Graz, Austria; Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Merrick BA, Chang JS, Phadke DP, Bostrom MA, Shah RR, Wang X, Gordon O, Wright GM. HAfTs are novel lncRNA transcripts from aflatoxin exposure. PLoS One 2018; 13:e0190992. [PMID: 29351317 PMCID: PMC5774710 DOI: 10.1371/journal.pone.0190992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
The transcriptome can reveal insights into precancer biology. We recently conducted RNA-Seq analysis on liver RNA from male rats exposed to the carcinogen, aflatoxin B1 (AFB1), for 90 days prior to liver tumor onset. Among >1,000 differentially expressed transcripts, several novel, unannotated Cufflinks-assembled transcripts, or HAfTs (Hepatic Aflatoxin Transcripts) were found. We hypothesized PCR-cloning and RACE (rapid amplification of cDNA ends) could further HAfT identification. Sanger data was obtained for 6 transcripts by PCR and 16 transcripts by 5’- and 3’-RACE. BLAST alignments showed, with two exceptions, HAfT transcripts were lncRNAs, >200nt without apparent long open reading frames. Six rat HAfT transcripts were classified as ‘novel’ without RefSeq annotation. Sequence alignment and genomic synteny showed each rat lncRNA had a homologous locus in the mouse genome and over half had homologous loci in the human genome, including at least two loci (and possibly three others) that were previously unannotated. While HAfT functions are not yet clear, coregulatory roles may be possible from their adjacent orientation to known coding genes with altered expression that include 8 HAfT-gene pairs. For example, a unique rat HAfT, homologous to Pvt1, was adjacent to known genes controlling cell proliferation. Additionally, PCR and RACE Sanger sequencing showed many alternative splice variants and refinements of exon sequences compared to Cufflinks assembled transcripts and gene prediction algorithms. Presence of multiple splice variants and short tandem repeats found in some HAfTs may be consequential for secondary structure, transcriptional regulation, and function. In summary, we report novel, differentially expressed lncRNAs after exposure to the genotoxicant, AFB1, prior to neoplastic lesions. Complete cloning and sequencing of such transcripts could pave the way for a new set of sensitive and early prediction markers for chemical hepatocarcinogens.
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Affiliation(s)
- B. Alex Merrick
- Biomolecular Screening Branch, Division National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| | - Justin S. Chang
- Biomolecular Screening Branch, Division National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Dhiral P. Phadke
- Sciome, LLC, Research Triangle Park, North Carolina, United States of America
| | - Meredith A. Bostrom
- Genomics Laboratory, David H. Murdock Research Institute, Kannapolis, North Carolina, United State of America
| | - Ruchir R. Shah
- Sciome, LLC, Research Triangle Park, North Carolina, United States of America
| | - Xinguo Wang
- Genomics Laboratory, David H. Murdock Research Institute, Kannapolis, North Carolina, United State of America
| | - Oksana Gordon
- Genomics Laboratory, David H. Murdock Research Institute, Kannapolis, North Carolina, United State of America
| | - Garron M. Wright
- Genomics Laboratory, David H. Murdock Research Institute, Kannapolis, North Carolina, United State of America
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Alaei S, Sadeghi B, Najafi A, Masoudi-Nejad A. LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma. Genomics 2018; 111:76-89. [PMID: 29317304 DOI: 10.1016/j.ygeno.2018.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/05/2018] [Accepted: 01/05/2018] [Indexed: 12/19/2022]
Abstract
Many experimental and computational studies have identified key protein coding genes in initiation and progression of esophageal squamous cell carcinoma (ESCC). However, the number of researches that tried to reveal the role of long non-coding RNAs (lncRNAs) in ESCC has been limited. LncRNAs are one of the important regulators of cancers which are transcribed dominantly in the genome and in various conditions. The main goal of this study was to use a systems biology approach to predict novel lncRNAs as well as protein coding genes associated with ESCC and assess their prognostic values. By using microarray expression data for mRNAs and lncRNAs from a large number of ESCC patients, we utilized "Weighted Gene Co-expression Network Analysis" (WGCNA) method to make a big coding-non-coding gene co-expression network, and discovered important functional modules. Gene set enrichment and pathway analysis revealed major biological processes and pathways involved in these modules. After selecting some protein coding genes involved in biological processes and pathways related to cancer, we used "LncTar", a computational tool to predict potential interactions between these genes and lncRNAs. By combining interaction results with Pearson correlations, we introduced some novel lncRNAs with putative key regulatory roles in the network. Survival analysis with Kaplan-Meier estimator and Log-rank test statistic confirmed that most of the introduced genes are associated with poor prognosis in ESCC. Overall, our study reveals novel protein coding genes and lncRNAs associated with ESCC, along with their predicted interactions. Based on the promising results of survival analysis, these genes can be used as good estimators of patients' survival, or even can be analyzed further as new potential signatures or targets for the therapy of ESCC disease.
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Affiliation(s)
- Shervin Alaei
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Balal Sadeghi
- Food Hygiene and Public Health Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Zhu S, Fu W, Zhang L, Fu K, Hu J, Jia W, Liu G. LINC00473 antagonizes the tumour suppressor miR-195 to mediate the pathogenesis of Wilms tumour via IKKα. Cell Prolif 2017; 51. [PMID: 29159834 DOI: 10.1111/cpr.12416] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/26/2017] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES Although dramatic improvements of overall survival has achieved in patients with favourable histology Wilms tumour, disease recurrence is still the main cause of cancer-related death in childhood. Long non-coding RNAs (lncRNAs) as oncogenes or tumour suppressors are dysregulated during carcinogenesis. However, the role of lncRNAs in the pathogenesis of Wilms tumour is unknown. Here, an lncRNA LINC00473 signature that functioned as oncogene was identified in Wilms tumour. METHODS Wilms tumour (n = 15) and relative normal tissues were collected. The LINC00473 expression and function in Wilms tumour was determined. The LncRNA-miRNA network of LINC00473 was analysed in vitro and vivo. RESULTS We uncovered that the expression of LINC00473 was elevated in tumour tissues than that in relative normal tissues. Higher LINC00473 levels correlated to higher stage and unfavourable histology Wilms tumour. Mechanistically, knockdown of LINC00473 inhibited cell vitality and induced Bcl-2-dependent apoptosis and G1/S arrest via CDK2 and cyclin D1. Moreover, LINC00473 harboured binding sites for miR-195 and limited miR-195 availability in a dose-dependent manner. Forced expression of miR-195 impaired tumour survival and metastasis, which, however, could be restored by LINC00473. Furthermore, IKKα was the downstream of LINC00473/miR-195 signals and could be directly targeted by miR-195 to participate LINC00473-induced tumour progression. Loss-of-function of LINC00473 in vivo effectively promoted the regression of Wilms tumour via miR-195/IKKα-mediated growth inhibition. CONCLUSION LINC00473 as an oncogene is up-regulated to participate into the molecular pathogenesis of Wilms tumour via miR-195/IKKα.
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Affiliation(s)
- Shibo Zhu
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wen Fu
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liyu Zhang
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Kai Fu
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jinhua Hu
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei Jia
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Guochang Liu
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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Li Y, Wang Z, Nair A, Song W, Yang P, Zhang X, Sun Z. Comprehensive Profiling of lincRNAs in Lung Adenocarcinoma of Never Smokers Reveals Their Roles in Cancer Development and Prognosis. Genes (Basel) 2017; 8:genes8110321. [PMID: 29137177 PMCID: PMC5704234 DOI: 10.3390/genes8110321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/28/2017] [Accepted: 11/06/2017] [Indexed: 01/08/2023] Open
Abstract
Long intergenic non-coding RNA (lincRNA) is a family of gene transcripts, the functions of which are largely unknown. Although cigarette smoking is the main cause for lung cancer, lung cancer in non-smokers is a separate entity and its underlying cause is little known. Growing evidence suggests lincRNAs play a significant role in cancer development and progression; however, such data is lacking for lung cancer in non-smokers, or those who have never smoked. This study conducted comprehensive profiling of lincRNAs from RNA sequencing (RNA-seq) data of non-smoker patients with lung adenocarcinoma. Both known and novel lincRNAs distinctly segregated tumors from normal tissues. Approximately one third of lincRNAs were differentially expressed between tumors and normal samples and most of them were coordinated with their putative protein gene targets. More importantly, lincRNAs defined two clusters of tumors that were associated with tumor aggressiveness and patient survival. We identified a subset of lincRNAs that were differentially expressed and also associated with patient survival. Very high concordance (R2 = 0.9) was observed for the differentially expressed lincRNAs in the Cancer Genome Atlas (TCGA) validation set of 85 transcriptomes and the lincRNAs associated with survival from the discovery set were similarly predictive in the validation set. These lincRNAs warrant further investigation as potential diagnostic and prognostic markers.
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Affiliation(s)
- Ying Li
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
- Department of Pulmonary Medicine, People's Hospital of Henan Province, Zhengzhou 450003, China.
| | - Zheng Wang
- Department of Pulmonary Medicine, People's Hospital of Henan Province, Zhengzhou 450003, China.
| | - Asha Nair
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
| | - Wei Song
- Department of Pulmonary Medicine, People's Hospital of Henan Province, Zhengzhou 450003, China.
| | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
| | - Xiaoju Zhang
- Department of Pulmonary Medicine, People's Hospital of Henan Province, Zhengzhou 450003, China.
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
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