101
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Perez de Acha O, Rossi M, Gorospe M. Circular RNAs in Blood Malignancies. Front Mol Biosci 2020; 7:109. [PMID: 32676504 PMCID: PMC7333357 DOI: 10.3389/fmolb.2020.00109] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/08/2020] [Indexed: 12/30/2022] Open
Abstract
Circular (circ)RNAs influence a wide range of biological processes at least in part by interacting with proteins and microRNAs. CircRNAs expressed in the hematopoietic compartment have been increasingly recognized as modulators of physiological and pathological features of hematopoetic stem cell (HSC)-derived populations. In particular, several circRNAs were found to enhance or suppress tumor progression in blood malignancies such as leukemias and lymphomas. Moreover, numerous circRNAs have been proposed to help confer resistance to the conventional treatments used in hematopoietic cancers. Here, we review the most important circRNAs described thus far in acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), lymphomas, and multiple myeloma (MM). We discuss the usefulness of circRNAs as diagnostic and prognostic markers and their potential value as therapeutic targets.
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Affiliation(s)
- Olivia Perez de Acha
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, United States
| | - Martina Rossi
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, United States
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, United States
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102
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Das D, Das A, Sahu M, Mishra SS, Khan S, Bejugam PR, Rout PK, Das A, Bano S, Mishra GP, Raghav SK, Dixit A, Panda AC. Identification and Characterization of Circular Intronic RNAs Derived from Insulin Gene. Int J Mol Sci 2020; 21:ijms21124302. [PMID: 32560282 PMCID: PMC7352490 DOI: 10.3390/ijms21124302] [Citation(s) in RCA: 9] [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: 04/21/2020] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 01/09/2023] Open
Abstract
Circular RNAs (circRNAs) are a large family of noncoding RNAs that have emerged as novel regulators of gene expression. However, little is known about the function of circRNAs in pancreatic β-cells. Here, transcriptomic analysis of mice pancreatic islet RNA-sequencing data identified 77 differentially expressed circRNAs between mice fed with a normal diet and a high-fat diet. Surprisingly, multiple circRNAs were derived from the intron 2 of the preproinsulin 2 (Ins2) gene and are termed as circular intronic (ci)-Ins2. The expression of ci-Ins2 transcripts in mouse pancreatic islets, and βTC6 cells were confirmed by reverse transcription PCR, DNA sequencing, and RNase R treatment experiments. The level of ci-Ins2 was altered in βTC6 cells upon exposure to elevated levels of palmitate and glucose. Computational analysis predicted the interaction of several RNA-binding proteins with ci-Ins2 and their flanking region, suggesting their role in the ci-Ins2 function or biogenesis. Additionally, bioinformatics analysis predicted the association of several microRNAs with ci-Ins2. Gene ontology and pathway analysis of genes targeted by miRNAs associated with ci-Ins2 suggested the regulation of several key biological processes. Together, our findings indicate that differential expression of circRNAs, especially ci-Ins2 transcripts, may regulate β-cell function and may play a critical role in the development of diabetes.
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Affiliation(s)
- Debojyoti Das
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Aniruddha Das
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Mousumi Sahu
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
| | - Smruti Sambhav Mishra
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
| | - Shaheerah Khan
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
| | - Pruthvi R. Bejugam
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
| | - Pranita K. Rout
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
| | - Arundhati Das
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Shehnaz Bano
- National Center for Cell Sciences (NCCS), Pune, Maharashtra 411007, India;
| | - Gyan Prakash Mishra
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
| | - Sunil K. Raghav
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
| | - Anshuman Dixit
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
| | - Amaresh C. Panda
- Institute of Life Sciences (ILS), Nalco Square, Bhubaneswar, Odisha 751023, India; (D.D.); (A.D.); (M.S.); (S.S.M.); (S.K.); (P.R.B.); (P.K.R.); (A.D.); (G.P.M.); (S.K.R.); (A.D.)
- Correspondence: ; Tel.: +91-674-230-43-14
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103
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Bravo JI, Nozownik S, Danthi PS, Benayoun BA. Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation. Development 2020; 147:dev175786. [PMID: 32527937 PMCID: PMC10680986 DOI: 10.1242/dev.175786] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.
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Affiliation(s)
- Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Séverine Nozownik
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Magistère européen de Génétique, Université Paris Diderot-Paris 7, Paris 75014, France
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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104
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Tu C, He J, Qi L, Ren X, Zhang C, Duan Z, Yang K, Wang W, Lu Q, Li Z. Emerging landscape of circular RNAs as biomarkers and pivotal regulators in osteosarcoma. J Cell Physiol 2020; 235:9037-9058. [PMID: 32452026 DOI: 10.1002/jcp.29754] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/18/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
Osteosarcoma represents the most prevailing primary bone tumor and the third most common cancer in children and adolescents worldwide. Among noncoding RNAs, circular RNAs (circRNAs) refer to a unique class in the shape of a covalently closed continuous loop with neither 5' caps nor 3'-polyadenylated tails, which are generated through back-splicing. Recently, with the development of whole-genome and transcriptome sequencing technologies, a growing number of circRNAs have been found aberrantly expressed in multiple diseases, including osteosarcoma. circRNA are capable of various biological functions including miRNA sponge, mediating alternatives, regulating genes at posttranscriptional levels, and interacting with proteins, indicating a pivotal role of circRNA in cancer initiation, progression, chemoresistance, and immune response. Moreover, circRNAs have been thrust into the spotlight as potential biomarkers and therapeutic targets in osteosarcoma. Herein, we briefly summarize the origin and biogenesis of circRNA with current knowledge of circRNA in tumorigenesis of osteosarcoma, aiming to elucidate the specific role and clinical implication of circRNAs in osteosarcoma.
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Affiliation(s)
- Chao Tu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jieyu He
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaolei Ren
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chenghao Zhang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhixi Duan
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kexin Yang
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiong Lu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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105
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Lin Y, Huang G, Jin H, Jian Z. Circular RNA Gprc5a Promotes HCC Progression by Activating YAP1/TEAD1 Signalling Pathway by Sponging miR-1283. Onco Targets Ther 2020; 13:4509-4521. [PMID: 32547082 PMCID: PMC7247601 DOI: 10.2147/ott.s240261] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/18/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Circular RNA (circRNA) plays a critical role in tumorigenesis and tumor progression. Many studies indicate that circRNA Gprc5a is significantly upregulated and functions as an oncogene in a variety of cancers. However, the molecular mechanism of circGprc5a in liver cancer remains unclear. METHODS qRT-PCR was used to measure the expression levels of circGprc5a, miR-1283, YAP1 and TEAD1 mRNA in hepatocellular carcinoma (HCC) tissues or cells. YAP1 and TEAD1 protein levels were detected by Western blot. CCK-8 assay, cell colony formation, BrdU incorporation and Annexin V-FITC/PI assays were performed to analyze the effects of circGprc5a and miR-1283 on cell proliferation and apoptosis. The relationship between circGprc5a, miR-1283, YAP1 and TEAD1 was analyzed using bioinformatic analysis and luciferase. The tumor changes in mice were detected by in vivo experiments. RESULTS CircGprc5a was highly expressed in liver cancer, and closely related poor survival of patients with liver cancer. Knockout of circGprc5a inhibited proliferation of HCC and induced apoptosis. CircGprc5a activated the YAP1/TEAD1 signaling pathway by acting as a sponge for miR-1283. Furthermore, overexpression of miR-1283 abolished the promotion of circGprc5a on HCC cells. Therefore, miR-1283 expression correlated negatively with circGprc5a expression yet positively with the expression of YAP1/TEAD1 in liver cancer. CONCLUSION CircGprc5a promoted the development of HCC by inhibiting the expression of miR-1283 and activating the YAP1/TEAD1 signaling pathway.
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Affiliation(s)
- Ye Lin
- Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou510080, People’s Republic of China
| | - Guanqun Huang
- Department of General Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou510700, People’s Republic of China
| | - Haosheng Jin
- Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou510080, People’s Republic of China
| | - Zhixiang Jian
- Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou510080, People’s Republic of China
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106
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Mumtaz PT, Taban Q, Dar MA, Mir S, Haq ZU, Zargar SM, Shah RA, Ahmad SM. Deep Insights in Circular RNAs: from biogenesis to therapeutics. Biol Proced Online 2020; 22:10. [PMID: 32467674 PMCID: PMC7227217 DOI: 10.1186/s12575-020-00122-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract Circular RNAs (circRNAs) have emerged as a universal novel class of eukaryotic non-coding RNA (ncRNA) molecules and are becoming a new research hotspot in RNA biology. They form a covalent loop without 5′ cap and 3′ tail, unlike their linear counterparts. Endogenous circRNAs in mammalian cells are abundantly conserved and discovered so far. In the biogenesis of circRNAs exonic, intronic, reverse complementary sequences or RNA-binding proteins (RBPs) play a very important role. Interestingly, the majority of them are highly conserved, stable, resistant to RNase R and show developmental-stage/tissue-specific expression. CircRNAs play multifunctional roles as microRNA (miRNA) sponges, regulators of transcription and post-transcription, parental gene expression and translation of proteins in various diseased conditions. Growing evidence shows that circRNAs play an important role in neurological disorders, atherosclerotic vascular disease, and cancer and potentially serve as diagnostic or predictive biomarkers due to its abundance in various biological samples. Here, we review the biogenesis, properties, functions, and impact of circRNAs on various diseases. Graphical Abstract ![]()
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Affiliation(s)
- Peerzada Tajamul Mumtaz
- 1Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-e- Kashmir University of Agricultural Sciences and Technology, Kashmir, 19006 India.,2Department of Biochemistry, School of Life Sciences Jaipur National University, Jaipur, India
| | - Qamar Taban
- 1Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-e- Kashmir University of Agricultural Sciences and Technology, Kashmir, 19006 India.,3Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Mashooq Ahmad Dar
- 1Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-e- Kashmir University of Agricultural Sciences and Technology, Kashmir, 19006 India
| | - Shabir Mir
- Division of Animal Breeding and Genetics, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, Srinagar, India
| | - Zulfkar Ul Haq
- Division of Livestock Production and Management, SKUAST-K, Srinagar, India
| | - Sajad Majeed Zargar
- 1Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-e- Kashmir University of Agricultural Sciences and Technology, Kashmir, 19006 India.,6Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, J&K 190025 India
| | - Riaz Ahmad Shah
- 1Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-e- Kashmir University of Agricultural Sciences and Technology, Kashmir, 19006 India
| | - Syed Mudasir Ahmad
- 1Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-e- Kashmir University of Agricultural Sciences and Technology, Kashmir, 19006 India
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107
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The expanding regulatory mechanisms and cellular functions of circular RNAs. Nat Rev Mol Cell Biol 2020; 21:475-490. [PMID: 32366901 DOI: 10.1038/s41580-020-0243-y] [Citation(s) in RCA: 812] [Impact Index Per Article: 203.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
Many protein-coding genes in higher eukaryotes can produce circular RNAs (circRNAs) through back-splicing of exons. CircRNAs differ from mRNAs in their production, structure and turnover and thereby have unique cellular functions and potential biomedical applications. In this Review, I discuss recent progress in our understanding of the biogenesis of circRNAs and the regulation of their abundance and of their biological functions, including in transcription and splicing, sequestering or scaffolding of macromolecules to interfere with microRNA activities or signalling pathways, and serving as templates for translation. I further discuss the emerging roles of circRNAs in regulating immune responses and cell proliferation, and the possibilities of applying circRNA technologies in biomedical research.
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108
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Huang W, Yang Y, Wu J, Niu Y, Yao Y, Zhang J, Huang X, Liang S, Chen R, Chen S, Guo L. Circular RNA cESRP1 sensitises small cell lung cancer cells to chemotherapy by sponging miR-93-5p to inhibit TGF-β signalling. Cell Death Differ 2020; 27:1709-1727. [PMID: 31728016 PMCID: PMC7206039 DOI: 10.1038/s41418-019-0455-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) are novel RNA molecules that play important roles in chemoresistance in different cancers, including breast and gastric cancers. However, whether circRNAs are involved in the response to chemotherapy in small cell lung cancer (SCLC) remains largely unknown. In this study, we observed that cESRP1 (circular RNA epithelial splicing regulatory protein-1) expression was significantly downregulated in the chemoresistant cells compared with the parental chemosensitive cells. cESRP1 enhanced drug sensitivity by repressing miR-93-5p in SCLC. Cytoplasmic cESRP1 could directly bind to miR-93-5p and inhibit the posttranscriptional repression mediated by miR-93-5p, thereby upregulating the expression of the miR-93-5p downstream targets Smad7/p21(CDKN1A) and forming a negative feedback loop to regulate transforming growth factor-β (TGF-β) mediated epithelial-mesenchymal transition. Furthermore, cESRP1 overexpression and TGF-β pathway inhibition both altered tumour responsiveness to chemotherapy in an acquired chemoresistant patient-derived xenograft model. Importantly, cESRP1 expression was downregulated in SCLC patient tissues and was associated with survival. Our findings reveal, for the first time, that cESRP1 plays crucial a role in SCLC chemosensitivity by sponging miR-93-5p to inhibit the TGF-β pathway, suggesting that cESRP1 may serve as a valuable prognostic biomarker and a potential therapeutic target in SCLC patients.
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Affiliation(s)
- Weimei Huang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yunchu Yang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jingfang Wu
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuchun Niu
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Oncology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Yao Yao
- Department of Pathology, Peking University Third Hospital, Beijing, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoxian Huang
- Clinical Laboratory, Gushang Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shumei Liang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Rui Chen
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Size Chen
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China.
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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109
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Van Der Steen N, Lyu Y, Hitzler AK, Becker AC, Seiler J, Diederichs S. The Circular RNA Landscape of Non-Small Cell Lung Cancer Cells. Cancers (Basel) 2020; 12:E1091. [PMID: 32353949 PMCID: PMC7281449 DOI: 10.3390/cancers12051091] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
The class of circular RNA (circRNA) is characterized by head-to-tail bonds between exons formed by backsplicing. Here, we provide a resource of circRNA expression in a comprehensive panel of 60 lung cancer and non-transformed cell lines (FL3C dataset). RNA sequencing after depletion of ribosomal RNA quantified the expression of circRNA and linear RNA. We detected 148,811 circular RNAs quantified by 2.8 million backsplicing reads originating from 12,251 genes. The number of identified circRNAs was markedly higher using rRNA depletion compared to public polyA-enriched RNA-seq datasets. CircRNAs almost never started in the first exon nor ended in the last exon and started more frequently in earlier exons. Most circRNAs showed high cell line specificity and correlated positively with their linear RNA counterpart. Known cancer genes produced more circRNAs than non-cancer genes. Subsets of circRNAs correlated with cell proliferation, histological subtype or genotype. CircTNFRSF21 was translated crossing the backsplice site in two different reading frames. Overexpression of circPVT1, circERBB2, circHIPK3, circCCNB1, circSMAD2, circTNFRSF21 and circKIF5B significantly increased colony formation. In conclusion, our data provide a comprehensive map of circRNA expression in lung cancer cells and global patterns of circRNA production as a useful resource for future research into lung cancer circRNAs.
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Affiliation(s)
- Nele Van Der Steen
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Yanhong Lyu
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Anne K Hitzler
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Andrea C Becker
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Jeanette Seiler
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106 Freiburg, Germany
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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110
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A Circular RNA from the MDM2 Locus Controls Cell Cycle Progression by Suppressing p53 Levels. Mol Cell Biol 2020; 40:MCB.00473-19. [PMID: 32041821 DOI: 10.1128/mcb.00473-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs produced by a noncanonical form of alternative splicing called back-splicing. To investigate a potential role of circRNAs in the p53 pathway, we analyzed RNA sequencing (RNA-seq) data from colorectal cancer cell lines (HCT116, RKO, and SW48) that were untreated or treated with a DNA-damaging agent. Surprisingly, unlike the strong p53-dependent induction of hundreds of p53-induced mRNAs upon DNA damage, only a few circRNAs were upregulated from p53-induced genes. circ-MDM2, an annotated circRNA from the MDM2 locus, was one of the handful of circRNAs that originated from a p53-induced gene. Given the central role of MDM2 in suppressing p53 protein levels and p53 activity, we investigated the function of circ-MDM2 Knocking down circ-MDM2 with small interfering RNAs (siRNAs) that targeted circ-MDM2 did not alter MDM2 mRNA or MDM2 protein levels but resulted in increased basal p53 levels and growth defects in vitro and in vivo Consistent with these results, transcriptome profiling showed increased expression of several direct p53 targets, reduced retinoblastoma protein (Rb) phosphorylation, and defects in G1-S progression upon silencing circ-MDM2 Our results on the initial characterization of circ-MDM2 identify a new player from the MDM2 locus that suppresses p53 levels and cell cycle progression.
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111
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Yan M, Gao H, Lv Z, Liu Y, Zhao S, Gong W, Liu W. Circular RNA PVT1 promotes metastasis via regulating of miR-526b/FOXC2 signals in OS cells. J Cell Mol Med 2020; 24:5593-5604. [PMID: 32249539 PMCID: PMC7214167 DOI: 10.1111/jcmm.15215] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022] Open
Abstract
As a class of covalently closed non-coding RNAs, circular RNAs (circRNAs) are key regulators in various malignancies including osteosarcoma (OS). In the present study, we found that circular RNA PVT1 (circPVT1) was up-regulated in OS and correlated with poor prognosis of patients with OS. Functionally, we showed that knockdown of circPVT1 suppressed OS cells metastasis. In addition, we found that (forkhead box C2) FOXC2 was a downstream gene in circPVT1-mediated metastasis in OS cells. We demonstrated that circPVT1 promoted OS cells metastasis via post-transcriptionally regulating of FOXC2. Furthermore, we revealed that microRNA 526b (miR-526b) was a key bridge which connected circPVT1 and FOXC2. We showed that miR-526b was down-regulated in OS tissue and cell lines. Through a transwell assay, we found that miR-526b suppressed OS cells metastasis by targeting of FOXC2. We also showed that miR-526b targeted circPVT1 via similar mircoRNA response elements (MREs) as it did for FOXC2. Finally, we proved that circPVT1 decoyed miR-526b to promote FOXC2-mediated metastasis in OS cells. In brief, our current study demonstrated that circPVT1, functioning as an oncogene, promotes OS cells metastasis via regulation of FOXC2 by acting as a ceRNA of miR-526b. CircPVT1/miR-526b/FOXC2 axis might be a novel target in molecular treatment of OS.
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Affiliation(s)
- Ming Yan
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun, P.R.China
| | - Hang Gao
- Department of Bone and Joint Surgery, The First Hospital of Jilin University, Changchun, P.R.China
| | - Zhenshan Lv
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun, P.R.China
| | - Ying Liu
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun, P.R.China
| | - Song Zhao
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun, P.R.China
| | - Weiquan Gong
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun, P.R.China
| | - Wei Liu
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun, P.R.China
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Das A, Das A, Das D, Abdelmohsen K, Panda AC. Circular RNAs in myogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194372. [PMID: 30946990 PMCID: PMC6773529 DOI: 10.1016/j.bbagrm.2019.02.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/09/2019] [Accepted: 02/21/2019] [Indexed: 01/08/2023]
Abstract
Skeletal muscles have an immense ability to regenerate from the muscle stem cells called satellite cells. The process of skeletal muscle regeneration is called myogenesis, which starts with activation of quiescent satellite cells immediately after muscle injury followed by proliferation and fusion of myoblasts into myotubes. Myogenesis is orchestrated through the expression of a specific set of genes which, at each step regulated by complex gene regulatory networks. Besides the well-established roles of transcription factors, increasing evidence demonstrated that circular (circ)RNAs modulate gene expression during myogenesis and are involved in muscle-related diseases. Here we review the recent findings of circRNAs involved in myogenesis.
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Affiliation(s)
- Arundhati Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Aniruddha Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Debojyoti Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, USA
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India.
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Ghetti M, Vannini I, Storlazzi CT, Martinelli G, Simonetti G. Linear and circular PVT1 in hematological malignancies and immune response: two faces of the same coin. Mol Cancer 2020; 19:69. [PMID: 32228602 PMCID: PMC7104523 DOI: 10.1186/s12943-020-01187-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
Non coding RNAs (ncRNAs) have emerged as regulators of human carcinogenesis by affecting the expression of key tumor suppressor genes and oncogenes. They are divided into short and long ncRNAs, according to their length. Circular RNAs (circRNAs) are included in the second group and were recently discovered as being originated by back-splicing, joining either single or multiple exons, or exons with retained introns. The human Plasmacytoma Variant Translocation 1 (PVT1) gene maps on the long arm of chromosome 8 (8q24) and encodes for 52 ncRNAs variants, including 26 linear and 26 circular isoforms, and 6 microRNAs. PVT1 genomic locus is 54 Kb downstream to MYC and several interactions have been described among these two genes, including a feedback regulatory mechanism. MYC-independent functions of PVT1/circPVT1 have been also reported, especially in the regulation of immune responses. We here review and discuss the role of both PVT1 and circPVT1 in the hematopoietic system. No information is currently available concerning their transforming ability in hematopoietic cells. However, present literature supports their cooperation with a more aggressive and/or undifferentiated cell phenotype, thus contributing to cancer progression. PVT1/circPVT1 upregulation through genomic amplification or rearrangements and/or increased transcription, provides a proliferative advantage to malignant cells in acute myeloid leukemia, acute promyelocytic leukemia, Burkitt lymphoma, multiple myeloma (linear PVT1) and acute lymphoblastic leukemia (circPVT1). In addition, PVT1 and circPVT1 regulate immune responses: the overexpression of the linear form in myeloid derived suppressor cells induced immune tolerance in preclinical tumor models and circPVT1 showed immunosuppressive properties in myeloid and lymphoid cell subsets. Overall, these recent data on PVT1 and circPVT1 functions in hematological malignancies and immune responses reflect two faces of the same coin: involvement in cancer progression by promoting a more aggressive phenotype of malignant cells and negative regulation of the immune system as a novel potential therapy-resistance mechanism.
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Affiliation(s)
- Martina Ghetti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Ivan Vannini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy.
| | | | - Giovanni Martinelli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
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Wang Z, Wei P, Wei D, Cao S, Liu H, Chen L, Han X, Zhao X, Liu C, Li G, Yang J, Pan X, Lei D. Effect of up-regulation of circMATR3 on the proliferation, metastasis, progression and survival of hypopharyngeal carcinoma. J Cell Mol Med 2020; 24:4687-4697. [PMID: 32166857 PMCID: PMC7176838 DOI: 10.1111/jcmm.15134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 12/12/2022] Open
Abstract
Increasing number of circular RNAs (circRNAs) have been reported to play important role in gene regulation, carcinogenesis and pathogenesis in various cancers. However, the biological functions and underlying molecular mechanisms of circRNAs in hypopharyngeal squamous cell carcinoma (HSCC) remain elusive. Thus, secondary circRNA‐seq profiling was performed to identify the differentially expressed circRNAs between HSCC tissues and adjacent normal tissues, and the expression level of circMATR3 (derived from human gene matrin3 (MATR3), has_circRNA_0008922) was confirmed by qRT‐PCR. Proliferation of HSCC cells was detected by cell counting kit‐8 (CCK8) assay, apoptosis and the cell cycle were analysed by flow cytometry, and the migration and invasion of HSCC cells was determined by transwell assay. Bioinformatics analysis was conducted to predict possible pathways and potential miRNA targets of circMATR3. We found that circMATR3 was up‐regulated in HSCC tissues, and abundant circMATR3 expression was markedly correlated with late T classification, advanced clinical stage, greater lymph node metastasis, and poor prognosis. Furthermore, knock‐down of circMATR3 significantly inhibited proliferation, migration and invasion of HSCC cells, whereas silencing of circMATR3 induced cell apoptosis. Our analysis predicted that circMATR3 may participate in cancer‐related pathways by serving as miRNA sponges. In conclusion, our findings first identified the oncogenic roles of circMATR3 in promoting the progression of HSCC and demonstrated that circMATR3 may be a novel prognostic marker and therapeutic target for HSCC.
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Affiliation(s)
- Zhanwang Wang
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dongmin Wei
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
| | - Shengda Cao
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
| | - Heng Liu
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
| | - Long Chen
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
| | - Xiao Han
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
| | - Xiaoyan Zhao
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
| | - Chuan Liu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianming Yang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Anhui Medical University, Hefei, China
| | - Xinliang Pan
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
| | - Dapeng Lei
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Key Laboratory of Otolaryngology, NHFPC (Shandong University), Shandong, China
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Guo SS, Li BX, Zou DB, Yang SJ, Sheng LX, Ouyang GF, Mu QT, Huang H. Tip of the iceberg: roles of circRNAs in hematological malignancies. Am J Cancer Res 2020; 10:367-382. [PMID: 32195014 PMCID: PMC7061755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023] Open
Abstract
Circular RNAs (circRNAs) are a new class of covalently closed RNA molecules whose 3'- and 5'-ends are linked by a back-splicing event. Emerging evidence has shown that circRNAs play a vital role in the occurrence and development of many diseases and are promising biomarkers and therapeutic targets. However, knowledge of circRNAs in hematological malignancies is limited. In this review, the biogenesis, categories, characteristics, and functions of circRNAs are summarized, especially the roles of circRNAs in hematopoiesis and hematological malignancies.
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Affiliation(s)
- Shan-Shan Guo
- Ningbo Hospital, School of Medicine, Zhejiang UniversityNingbo, Zhejiang, PR China
| | - Bi-Xia Li
- Ningbo University School of MedicineNingbo, Zhejiang, PR China
| | - Duo-Bing Zou
- Laboratory of Stem Cell Transplantation, Ningbo Hospital, School of Medicine, Zhejiang UniversityNingbo, Zhejiang, PR China
| | - Shu-Jun Yang
- Laboratory of Stem Cell Transplantation, Ningbo Hospital, School of Medicine, Zhejiang UniversityNingbo, Zhejiang, PR China
- Department of Hematology, Ningbo Hospital, School of Medicine, Zhejiang UniversityNingbo, Zhejiang, PR China
| | - Li-Xia Sheng
- Department of Hematology, Ningbo Hospital, School of Medicine, Zhejiang UniversityNingbo, Zhejiang, PR China
| | - Gui-Fang Ouyang
- Department of Hematology, Ningbo Hospital, School of Medicine, Zhejiang UniversityNingbo, Zhejiang, PR China
| | - Qi-Tian Mu
- Laboratory of Stem Cell Transplantation, Ningbo Hospital, School of Medicine, Zhejiang UniversityNingbo, Zhejiang, PR China
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, PR China
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116
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Guria A, Sharma P, Natesan S, Pandi G. Circular RNAs-The Road Less Traveled. Front Mol Biosci 2020; 6:146. [PMID: 31998746 PMCID: PMC6965350 DOI: 10.3389/fmolb.2019.00146] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs are the most recent addition in the non-coding RNA family, which has started to gain recognition after a decade of obscurity. The first couple of reports that emerged at the beginning of this decade and the amount of evidence that has accumulated thereafter has, however, encouraged RNA researchers to navigate further in the quest for the exploration of circular RNAs. The joining of 5′ and 3′ ends of RNA molecules through backsplicing forms circular RNAs during co-transcriptional or post-transcriptional processes. These molecules are capable of effectively sponging microRNAs, thereby regulating the cellular processes, as evidenced by numerous animal and plant systems. Preliminary studies have shown that circular RNA has an imperative role in transcriptional regulation and protein translation, and it also has significant therapeutic potential. The high stability of circular RNA is rendered by its closed ends; they are nevertheless prone to degradation by circulating endonucleases in serum or exosomes or by microRNA-mediated cleavage due to their high complementarity. However, the identification of circular RNAs involves diverse methodologies and the delineation of its possible role and mechanism in the regulation of cellular and molecular architecture has provided a new direction for the continuous research into circular RNA. In this review, we discuss the possible mechanism of circular RNA biogenesis, its structure, properties, degradation, and the growing amount of evidence regarding the detection methods and its role in animal and plant systems.
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Affiliation(s)
- Ashirbad Guria
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Priyanka Sharma
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Sankar Natesan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Gopal Pandi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
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Xiao Q, Luo J, Dai J. Computational Prediction of Human Disease- Associated circRNAs Based on Manifold Regularization Learning Framework. IEEE J Biomed Health Inform 2019; 23:2661-2669. [DOI: 10.1109/jbhi.2019.2891779] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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118
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Jin K, Wang S, Zhang Y, Xia M, Mo Y, Li X, Li G, Zeng Z, Xiong W, He Y. Long non-coding RNA PVT1 interacts with MYC and its downstream molecules to synergistically promote tumorigenesis. Cell Mol Life Sci 2019; 76:4275-4289. [PMID: 31309249 PMCID: PMC6803569 DOI: 10.1007/s00018-019-03222-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/22/2019] [Accepted: 07/05/2019] [Indexed: 02/06/2023]
Abstract
Numerous studies have shown that non-coding RNAs play crucial roles in the development and progression of various tumor cells. Plasmacytoma variant translocation 1 (PVT1) mainly encodes a long non-coding RNA (lncRNA) and is located on chromosome 8q24.21, which constitutes a fragile site for genetic aberrations. PVT1 is well-known for its interaction with its neighbor MYC, which is a qualified oncogene that plays a vital role in tumorigenesis. In the past several decades, increasing attention has been paid to the interaction mechanism between PVT1 and MYC, which will benefit the clinical treatment and prognosis of patients. In this review, we summarize the coamplification of PVT1 and MYC in cancer, the positive feedback mechanism, and the latest promoter competition mechanism of PVT1 and MYC, as well as how PVT1 participates in the downstream signaling pathway of c-Myc by regulating key molecules. We also briefly describe the treatment prospects and research directions of PVT1 and MYC.
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Affiliation(s)
- Ke Jin
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shufei Wang
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yazhuo Zhang
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Mengfang Xia
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yongzhen Mo
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yi He
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.
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Harper KL, Mcdonnell E, Whitehouse A. CircRNAs: From anonymity to novel regulators of gene expression in cancer (Review). Int J Oncol 2019; 55:1183-1193. [PMID: 31661122 DOI: 10.3892/ijo.2019.4904] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/31/2019] [Indexed: 12/27/2022] Open
Abstract
Circular RNAs (circRNAs) are a group of non‑coding RNAs, formed mostly through a unique backsplicing mechanism. Originally proposed to be a by‑product from errors in splicing, recent studies have shown they exhibit a range of roles in regulating gene expression, including sponging of microRNAs (miRNAs), interactions with RNA‑binding proteins and regulation of transcription. Though research is still in its infancy, evidence suggests circRNA levels are tightly regulated in the cell, reinforced by dysregulated circRNAs levels being implicated in a range of diseases, including cancer and viral infection. There is growing interest in circRNAs playing specific roles in cancers, either oncogenic or as tumour suppressors, with particular focus on their potential as novel biomarkers. This review will provide an overview of circRNA biogenesis and regulation, and their potential roles in the cell, with a focus on their dysregulation in cancer.
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Affiliation(s)
- Katherine L Harper
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Euan Mcdonnell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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120
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Zhong R, Chen Z, Mo T, Li Z, Zhang P. Potential Role of circPVT1 as a proliferative factor and treatment target in esophageal carcinoma. Cancer Cell Int 2019; 19:267. [PMID: 31636510 PMCID: PMC6794789 DOI: 10.1186/s12935-019-0985-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/30/2019] [Indexed: 01/01/2023] Open
Abstract
Background Many circRNAs have been reported to play important roles in cancer development and have the potential to serve as a novel class of biomarkers for clinical diagnosis. However, the role of circRNAs in esophageal carcinoma (EC) remains unclear. In the current study, we investigated the potential role of circPVT1 in esophageal carcinoma. Methods Quantitative real-time PCR was performed to detect circPVT1 levels. CircPVT1-specific siRNA or plasmids were used to knock down or overexpression the target RNA. Hoechst Staining was implemented to evaluate the ratio of cell apoptosis. Transwell migration assays were carried out to study the effects of circPVT1 on esophageal squamous cell carcinoma cell invasion. RegRNA 2.0 was used for bioinformatics analysis. The expression levels of Pax-4, Pax-6, PPARα and PPAR-γ were assessed using Western blot. Results In the present study, we demonstrated a significant up-regulation of circPVT1 levels in EC tissues and cancer cell lines. The levels of circPVT1 decreased significantly when the cells were maintained to over-confluence. These results suggested a potential role for circPVT1 in cell proliferation. In addition, overexpressing circPVT1 in TE-10 cell promoted invasive ability of cancer cell. In contrast, siRNA knockdown of circPVT1 inhibited this phenomenon, leading to increased apoptosis levels of TE-10 cell. What’s more, miR-4663 had the effect of inhibiting tumor growth by downregulated Paxs and upregulated PPARs. Whereas, after the addition of circPVT1, this effect no longer worked, suggesting that circPVT1 may affect the malignancy of the tumor by affecting miRNA and regulating the levels of Paxs and PPARs. Conclusions Collectively, our study reveals a critical role for circPVT1 in esophageal carcinoma, which may provide new insights of this circRNA as a biomarker for the diagnosis and treatment target of EC.
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Affiliation(s)
- Rongrong Zhong
- 1Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, 300052 People's Republic of China.,Tianjin Geriatrics Institute, Tianjin, 300052 People's Republic of China
| | - Zhuozhi Chen
- 3The School of Life Science, Tianjin University, Tianjin, 300072 People's Republic of China
| | - Ting Mo
- 1Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, 300052 People's Republic of China.,Tianjin Geriatrics Institute, Tianjin, 300052 People's Republic of China
| | - Zimo Li
- 4The School of Graduate, Tianjin Medical University, Tianjin, 300072 People's Republic of China
| | - Peng Zhang
- 5Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin, 300052 People's Republic of China
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Zhu Y, Liu Y, Xiao B, Cai H, Liu M, Ma L, Yin H, Wang F. The circular RNA PVT1/miR-203/HOXD3 pathway promotes the progression of human hepatocellular carcinoma. Biol Open 2019; 8:bio.043687. [PMID: 31551242 PMCID: PMC6777361 DOI: 10.1242/bio.043687] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Accumulating evidence suggests that circular RNAs (circRNAs) play important roles in various physiological and pathological processes. In the present study, we explored the role of circRNA PVT1 in hepatocellular carcinoma (HCC). qRT-PCR was performed to detect the relative expression of circPVT1 in HCC tissues and cell lines. The oncogenic roles of circPVT1 in HCC were evaluated by cell counting kit-8 (CCK-8) assay, ethynyl deoxyuridine (EdU) incorporation assays, transwell assays, flow cytometry and in vivo xenograft growth. Furthermore, bioinformatics, luciferase reporter assays and rescue experiments were conducted to determine the underlying mechanism of circPVT1 in HCC. Enhanced circPVT1 expression was detected in HCC tissues, which was closely associated with poor prognosis of patients with HCC. Knockdown of circPVT1 decreased the proliferation and migration ability of HCC cell lines in vitro Conversely, upregulation of circPVT1 improved the growth and migration in HCC cells. Mechanistically, we found that circPVT1 could bind directly to miR-203 and contributed to the initiation and progression of HCC by regulating miR-203/homebox D3 (HOXD3) pathway. In conclusion, our study reveals that circPVT1 participates in the progression of HCC through the miR-203/homeobox D3 (HOXD3) pathway and might represent a potential therapeutic target for HCC treatment.
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Affiliation(s)
- Yiqing Zhu
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Yan Liu
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Bang Xiao
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Hui Cai
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Meng Liu
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Liye Ma
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Huirong Yin
- Center of Reproductive Medicine, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Fang Wang
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China .,Department of Clinical Genetics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
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122
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Mei M, Wang Y, Li Z, Zhang M. Role of circular RNA in hematological malignancies. Oncol Lett 2019; 18:4385-4392. [PMID: 31611947 PMCID: PMC6781753 DOI: 10.3892/ol.2019.10836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/13/2019] [Indexed: 12/18/2022] Open
Abstract
Compared with linear RNA, circular RNAs (circRNAs) form a covalently closed circular continuous loop and are highly conserved, stable and tissue-specific. In recent years, circRNAs received considerable attention in the diagnosis, classification, treatment and prognosis of hematological tumors. circRNAs function as microRNA sponges and competitive endogenous RNAs that play an essential role in the translation, regulation and interaction of proteins. The present review discussed the fundamental properties and functions of circRNAs and the latest advancements in the context of circRNAs in the clinical research of hematological malignancies, namely acute and chronic myeloid leukemia, and chronic lymphocytic leukemia. circRNAs show potential in the diagnosis and prognosis of various diseases and can be used as therapeutic targets and biomarkers for disease.
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Affiliation(s)
- Mei Mei
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yingjun Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Zhaoming Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Mingzhi Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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123
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Pandey PR, Munk R, Kundu G, De S, Abdelmohsen K, Gorospe M. Methods for analysis of circular RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1566. [PMID: 31489773 DOI: 10.1002/wrna.1566] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/11/2019] [Accepted: 08/13/2019] [Indexed: 12/26/2022]
Abstract
Eukaryotic cells express a myriad of circular RNAs (circRNAs), many of them displaying tissue-specific expression patterns. They arise from linear precursor RNAs in which 5' and 3' ends become covalently ligated. Given these features, biochemical and computational approaches traditionally used to study linear RNA must be adapted for analysis of circular RNAs. Such circRNA-specific methodologies are allowing the systematic identification of circRNAs and the analysis of their biological functions. Here, we review the resources and molecular methods currently utilized to quantify circRNAs, visualize their distribution, identify interacting partners, and elucidate their function. We discuss the challenges of analyzing circRNAs and propose alternative approaches for studying this unique class of transcripts. This article is characterized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Methods > RNA Analyses in vitro and In Silico RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Gautam Kundu
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
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124
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Peng H, Qin C, Zhang C, Su J, Xiao Q, Xiao Y, Xiao K, Liu Q. circCPA4 acts as a prognostic factor and regulates the proliferation and metastasis of glioma. J Cell Mol Med 2019; 23:6658-6665. [PMID: 31424161 PMCID: PMC6787466 DOI: 10.1111/jcmm.14541] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/09/2019] [Accepted: 06/15/2019] [Indexed: 12/27/2022] Open
Abstract
Circular RNAs (circRNAs) are reported to play vital roles in tumour process and might be potential prognostic biomarkers and therapeutic targets for tumours. But the expression and function of circRNAs in glioma remain unclear. Here, we performed circRNA microarray analysis of glioma tissues and matched normal brain tissue samples to explore the circRNA profile in glioma. GO analysis, KEGG and Reactom pathway analysis of linear mRNA transcripts corresponding to circRNAs were performed to study the involved biological process and pathways. The clinical significance of the selected circRNA was investigated by Kaplan‐Meier survival analysis. Relevant biological function, such as cell proliferation and metastasis, was detected in vitro and in vivo. And possible mechanism of the regulatory function of the selected circRNA in glioma was explored. We found that circCPA4 (hsa_circ_0082374) up‐regulated the most in glioma tissues and high levels of circCPA4 were positively related to poor outcome of glioma. And knockdown of circCPA4 suppresses cell proliferation and metastasis in glioma. Moreover, circCPA4 interacts with let‐7 and serves as a sponge for let‐7. Through the competitive endogenous RNA (ceRNA) mechanism, circCPA4 sponges let‐7 to regulate the expression of CPA4 and glioma progression. The circCPA4/let‐7/CPA4 axis regulates glioma progression by ceRNA mechanism, and circCPA4 could be a novel prognostic biomarker and target for glioma treatment.
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Affiliation(s)
- Hao Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Chaoying Qin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Chao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jun Su
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qun Xiao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yao Xiao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Kai Xiao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
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125
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Rolling Circle cDNA Synthesis Uncovers Circular RNA Splice Variants. Int J Mol Sci 2019; 20:ijms20163988. [PMID: 31426285 PMCID: PMC6721031 DOI: 10.3390/ijms20163988] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 11/17/2022] Open
Abstract
High-throughput RNA sequencing and novel bioinformatic pipelines have identified thousands of circular (circ)RNAs containing backsplice junction sequences. However, circRNAs generated from multiple exons may contain different combinations of exons and/or introns arising from alternative splicing, while the backsplice junction sequence is the same. To be able to identify circRNA splice variants, we developed a method termed circRNA-Rolling Circle Amplification (circRNA-RCA). This method detects full-length circRNA sequences by performing reverse transcription (RT) in the absence of RNase H activity, followed by polymerase chain reaction (PCR) amplification of full-length circRNAs using a forward primer spanning the backsplice junction sequence and a reverse primer exactly upstream of the forward primer. By sequencing the PCR products, circRNA splice variants bearing the same backsplice junctions, which were otherwise only predicted computationally, could be experimentally validated. The splice variants were further predicted to associate with different subsets of target RNA-binding proteins and microRNAs, supporting the notion that different circRNA splice variants can have different biological impacts. In sum, the circRNA-RCA method allows the accurate identification of full-length circRNA sequences, offering unique insight into their individual function.
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126
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Kong Y, Yang L, Wei W, Lyu N, Zou Y, Gao G, Ou X, Xie X, Tang H. CircPLK1 sponges miR-296-5p to facilitate triple-negative breast cancer progression. Epigenomics 2019; 11:1163-1176. [PMID: 31337246 DOI: 10.2217/epi-2019-0093] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To investigate the role of circRNAs in triple-negative breast cancer (TNBC) and the underlying mechanisms. Materials & methods: We performed circRNA microarrays to explore the expression profiles of TNBC cell lines. Experiments in vitro and in vivo were conducted to explore the effects of circPLK1 on tumor proliferation and metastasis as well as the interaction between circPLK1, miR-296-5p and PLK1 in TNBC. Results & conclusion: CircPLK1 was significantly upregulated in TNBC and associated with poor survivals. CircPLK1 knockdown inhibited cell growth and invasion in vitro as well as tumor occurrence and metastasis in vivo. CircPLK1-miR-296-5p-PLK1 axis regulates tumor progression by ceRNA mechanism in TNBC, indicating that circPLK1 may serve as a prognostic factor and novel therapeutic target for TNBC.
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Affiliation(s)
- Yanan Kong
- Department of Breast Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
| | - Lu Yang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
| | - Weidong Wei
- Department of Breast Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
| | - Ning Lyu
- Department of Minimally Invasive Interventional Radiology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
| | - Yutian Zou
- Department of Breast Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
| | - Guanfeng Gao
- Department of Breast Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
| | - Xueqi Ou
- Department of Breast Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
| | - Xiaoming Xie
- Department of Breast Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
| | - Hailin Tang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine; Address: 651 East Dongfeng Road, Guangzhou, PR China
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127
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Zhao T, Zheng Y, Hao D, Jin X, Luo Q, Guo Y, Li D, Xi W, Xu Y, Chen Y, Gao Z, Zhang Y. Blood circRNAs as biomarkers for the diagnosis of community-acquired pneumonia. J Cell Biochem 2019; 120:16483-16494. [PMID: 31286543 DOI: 10.1002/jcb.28863] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/13/2019] [Accepted: 02/21/2019] [Indexed: 01/01/2023]
Abstract
Circular RNAs (circRNAs) have been reported as effective diagnostic and therapeutic biomarkers in many diseases, but the potential of using this easy-to-monitor and highly stable materials for diagnosing Community-acquired pneumonia (CAP) remains unexplored. Here, aiming to identify potential CAP-related circRNAs in peripheral blood and seeking to deepen the understanding of how circRNA-miRNA-mRNA regulatory networks may contribute to CAP, we applied microarrays profiling analysis and identified 8296 differentially expressed (DE) circRNAs between patients with CAP (n = 6) and healthy controls (n = 6). Subsequently, we validated the accumulation trends for the top 100 DE circRNAs based on qPCR in an independent validation cohort (30 patients vs 30 controls), and ultimately identified a panel of four circRNAs that perform extremely well as sensitive and specific biomarkers for diagnosing CAP: hsa_circ_0018429 (area under the curve [AUC] = 0.8216), hsa_circ_0026579 (AUC = 0.7733), hsa_circ_0125357 (AUC = 0.7730), and hsa_circ_0099188 (AUC = 0.6978); combined as a panel (AUC = 0.8776). In addition, hsa_circ_0026579 exhibited good performance in differentiating viral from bacterial or mixed infection, with an AUC of 0.863. We also identified 10 miRNAs that most likely to interact with these four circRNAs, and then predicted 205 mRNA target genes. The KEGG pathway enrichment analysis suggested highly plausible functional implications related to inflammation and to virus-infection-related signaling pathways (such as HTLV-1 infection and hepatitis B infection). Thus, we generated a genetic network of potential CAP-related regulatory interactions that should inform future hypothesis-driven research into the causes and potential treatment of this widespread and frequently fatal disease.
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Affiliation(s)
- Tian Zhao
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - YaLi Zheng
- Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - DengZai Hao
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Xuesong Jin
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - QiongZhen Luo
- Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - YaTao Guo
- Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - DaiXi Li
- Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Wen Xi
- Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yu Xu
- Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - YuSheng Chen
- Department of Pulmonary and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, China
| | - ZhanCheng Gao
- Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yan Zhang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
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128
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Lin YC, Lee YC, Chang KL, Hsiao KY. Analysis of common targets for circular RNAs. BMC Bioinformatics 2019; 20:372. [PMID: 31266442 PMCID: PMC6607602 DOI: 10.1186/s12859-019-2966-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
Background The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typically overwhelming due to the synergistic complexity caused by two factors ─ the binding of multiple miRNAs to a circRNA and the existence of multiple targets for each miRNA. Analysis of common targets (ACT) was designed to facilitate the identification of potential circRNA targets. Results We demonstrated the feasibility of the proposed feature/measurement to assess which genes are more likely to be regulated by circRNAs with given sequences by calculating the level of co-regulation by multiple miRNAs. The web service is made freely available at http://lab-x-omics.nchu.edu.tw/ACT_Server. Conclusions ACT allows users to identify potential circRNA-regulated genes and their associated pathways for further investigation. Electronic supplementary material The online version of this article (10.1186/s12859-019-2966-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ya-Chi Lin
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227, Taiwan.,Department of Biotechnology, Asia University, Taichung, 41354, Taiwan
| | - Yueh-Chun Lee
- Department of Radiation Oncology, Chung Shan Medical University Hospital, Taichung, 40201, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, 40201, Taiwan
| | - Kai-Li Chang
- Department of Physiology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Kuei-Yang Hsiao
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan. .,Program in Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan. .,Rong Hsing Research Center for Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan. .,Bachelor Program of Biotechnology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227, Taiwan.
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129
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Bach DH, Lee SK, Sood AK. Circular RNAs in Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 16:118-129. [PMID: 30861414 PMCID: PMC6411617 DOI: 10.1016/j.omtn.2019.02.005] [Citation(s) in RCA: 306] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded closed RNA molecules that are formed by precursor mRNA back-splicing or skipping events of thousands of genes in eukaryotes as covalently closed continuous loops. High-throughput sequencing and bioinformatics approaches have uncovered the broad expression of circRNAs across species. Their high stability, abundance, and evolutionary conservation among species points to their distinct properties and diverse cellular functions as efficient microRNAs and protein sponges; they also play important roles in modulating transcription and splicing. Additionally, most circRNAs are aberrantly expressed in pathological conditions and in a tissue-specific manner such as development and progression of cancer. Herein, we highlight the characteristics, functions, and mechanisms of action of circRNAs in cancer; we also provide an overview of recent progress in the circRNA field and future application of circRNAs as cancer biomarkers and novel therapeutic targets.
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Affiliation(s)
- Duc-Hiep Bach
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Korea; Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sang Kook Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Korea.
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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130
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Uludag H, Ubeda A, Ansari A. At the Intersection of Biomaterials and Gene Therapy: Progress in Non-viral Delivery of Nucleic Acids. Front Bioeng Biotechnol 2019; 7:131. [PMID: 31214586 PMCID: PMC6558074 DOI: 10.3389/fbioe.2019.00131] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/15/2019] [Indexed: 12/11/2022] Open
Abstract
Biomaterials play a critical role in technologies intended to deliver therapeutic agents in clinical settings. Recent explosion of our understanding of how cells utilize nucleic acids has garnered excitement to develop a range of older (e.g., antisense oligonucleotides, plasmid DNA and transposons) and emerging (e.g., short interfering RNA, messenger RNA and non-coding RNAs) nucleic acid agents for therapy of a wide range of diseases. This review will summarize biomaterials-centered advances to undertake effective utilization of nucleic acids for therapeutic purposes. We first review various types of nucleic acids and their unique abilities to deliver a range of clinical outcomes. Using recent advances in T-cell based therapy as a case in point, we summarize various possibilities for utilizing biomaterials to make an impact in this exciting therapeutic intervention technology, with the belief that this modality will serve as a therapeutic paradigm for other types of cellular therapies in the near future. We subsequently focus on contributions of biomaterials in emerging nucleic acid technologies, specifically focusing on the design of intelligent nanoparticles, deployment of mRNA as an alternative to plasmid DNA, long-acting (integrating) expression systems, and in vitro/in vivo expansion of engineered T-cells. We articulate the role of biomaterials in these emerging nucleic acid technologies in order to enhance the clinical impact of nucleic acids in the near future.
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Affiliation(s)
- Hasan Uludag
- Department of Chemical and Materinals Engineering, University of Alberta, Edmonton, AB, Canada
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Anyeld Ubeda
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Aysha Ansari
- Department of Chemical and Materinals Engineering, University of Alberta, Edmonton, AB, Canada
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131
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Adhikary J, Chakraborty S, Dalal S, Basu S, Dey A, Ghosh A. Circular PVT1: an oncogenic non-coding RNA with emerging clinical importance. J Clin Pathol 2019; 72:513-519. [PMID: 31154423 DOI: 10.1136/jclinpath-2019-205891] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
The importance of circular RNAs (circRNAs) in pathological processes like cancer is evident. Among the circRNAs, recent studies have brought circPVT1 under focus as the most potent oncogenic non-coding RNA. Recent studies on various aspects of circPVT1, including its biogenesis, molecular alteration and its probable role in oncogenesis, have been conducted for research and clinical interest. In this review, a first attempt has been made to summarise the available data on circPVT1 from PubMed and other relevant databases with special emphasis on its role in development, progression and prognosis of various malignant conditions. CircPVT1 is derived from the same genetic locus encoding for long non-coding RNA lncPVT1; however, existing literature suggested circPVT1 and lncPVT1 are transcripted independently by different promoters. The interaction between circRNA and microRNA has been highlighted in majority of the few malignancies in which circPVT1 was studied. Besides its importance in diagnostic and prognostic procedures, circPVT1 seemed to have huge therapeutic potential as evident from differential drug response of cancer cell line as well as primary tumors depending on expression level of the candidate. circPVT1 in cancer therapeutics might be promising as a biomarker to make the existing treatment protocol more effective and also as potential target for designing novel therapeutic intervention.
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Affiliation(s)
- Jayashree Adhikary
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | | | - Subhamita Dalal
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | | | - Abhijit Dey
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | - Amlan Ghosh
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
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132
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de Fraipont F, Gazzeri S, Cho WC, Eymin B. Circular RNAs and RNA Splice Variants as Biomarkers for Prognosis and Therapeutic Response in the Liquid Biopsies of Lung Cancer Patients. Front Genet 2019; 10:390. [PMID: 31134126 PMCID: PMC6514155 DOI: 10.3389/fgene.2019.00390] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/10/2019] [Indexed: 01/08/2023] Open
Abstract
Lung cancer, including non-small cell lung carcinoma (NSCLC), is the most frequently diagnosed cancer. It is also the leading cause of cancer-related mortality worldwide because of its late diagnosis and its resistance to therapies. Therefore, the identification of biomarkers for early diagnosis, prognosis, and monitoring of therapeutic response is urgently needed. Liquid biopsies, especially blood, are considered as promising tools to detect and quantify circulating cancer biomarkers. Cell-free circulating tumor DNA has been extensively studied. Recently, the possibility to detect and quantify RNAs in tumor biopsies, notably circulating cell-free RNAs, has gained great attention. RNA alternative splicing contributes to the proteome diversity through the biogenesis of several mRNA splice variants from the same pre-mRNA. Circular RNA (circRNA) is a new class of RNAs resulting from pre-mRNA back splicing. Owing to the development of high-throughput transcriptomic analyses, numerous RNA splice variants and, more recently, circRNAs have been identified and found to be differentially expressed in tumor patients compared to healthy controls. The contribution of some of these RNA splice variants and circRNAs to tumor progression, dissemination, or drug response has been clearly demonstrated in preclinical models. In this review, we discuss the potential of circRNAs and mRNA splice variants as candidate biomarkers for the prognosis and the therapeutic response of NSCLC in liquid biopsies.
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Affiliation(s)
- Florence de Fraipont
- INSERM U1209, CNRS UMR5309, Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
- Grenoble Hospital, La Tronche, France
| | - Sylvie Gazzeri
- INSERM U1209, CNRS UMR5309, Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Beatrice Eymin
- INSERM U1209, CNRS UMR5309, Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
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133
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Lai RW, Lu R, Danthi PS, Bravo JI, Goumba A, Sampathkumar NK, Benayoun BA. Multi-level remodeling of transcriptional landscapes in aging and longevity. BMB Rep 2019. [PMID: 30526773 PMCID: PMC6386224 DOI: 10.5483/bmbrep.2019.52.1.296] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and gene expression has been observed to be deregulated with aging. In this review, we discuss the current knowledge on the transcriptional alterations that have been described to occur with age in metazoans. First, we discuss age-related transcriptional changes in protein-coding genes, the expected functional impact of such changes, and how known pro-longevity interventions impact these changes. Second, we discuss the changes and impact of emerging aspects of transcription in aging, including age-related changes in splicing, lncRNAs and circRNAs. Third, we discuss the changes and potential impact of transcription of transposable elements with aging. Fourth, we highlight small ncRNAs and their potential impact on the regulation of aging phenotypes. Understanding the aging transcriptome will be key to identify important regulatory targets, and ultimately slow-down or reverse aging and extend healthy lifespan in humans.
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Affiliation(s)
- Rochelle W Lai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexandre Goumba
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089; USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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134
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Tao L, Yang L, Tian P, Guo X, Chen Y. Knockdown of circPVT1 inhibits progression of papillary thyroid carcinoma by sponging miR-126. RSC Adv 2019; 9:13316-13324. [PMID: 35520785 PMCID: PMC9066352 DOI: 10.1039/c9ra01820d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 04/24/2019] [Indexed: 02/03/2023] Open
Abstract
Background: Papillary thyroid carcinoma (PTC) is the most common thyroid cancer. Recent studies have reported that circular RNAs (circRNAs) play essential roles in human cancers, including PTC. However, the roles of circRNA plasmacytoma variant translocation 1 (PVT1) in PTC progression and its potential mechanism remain largely unknown. Methods: The expressions of circPVT1 and microRNA-126 (miR-126) were measured in PTC tissues and cells by quantitative real-time polymerase chain reaction (qRT-PCR). Cell viability, apoptosis, migration and invasion were detected in PTC cells by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT), flow cytometry, Western blot or trans-well assays, respectively. The interaction between circPVT1 and miR-126 was explored by bioinformatics analysis, luciferase activity assay and RNA immunoprecipitation. A mouse xenograft model was established to investigate the role of circPVT1 in PTC progression in vivo. Results: High expression of circPVT1 was shown in PTC tissues and cells and was associated with poor outcomes of patients. Knockdown of circPVT1 suppressed viability, migration and invasion but induced apoptosis in PTC cells. miR-126 was bound to circPVT1 and reduced in PTC tissues and cells. Moreover, inhibition of miR-126 reversed the regulatory effect of the circPVT1 interference on viability, apoptosis, migration and invasion in PTC cells. Besides, circPVT1 knockdown attenuated tumor growth via up-regulating miR-126 in vivo. Conclusion: CircPVT1 knockdown inhibited PTC progression by sponging miR-126. This may indicate circPVT1 as a novel target for treatment of PTC. Papillary thyroid carcinoma (PTC) is the most common thyroid cancer. Recent studies have reported that circular RNAs (circRNAs) play essential roles in human cancers, including PTC.![]()
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Affiliation(s)
- Ling Tao
- Institute of Inspection Technology, Xinyang Vocational and Technical College, Key Laboratory of Geriatric Diseases of Xinyang Xinyang 464000 China
| | - Li Yang
- Institute of Inspection Technology, Xinyang Vocational and Technical College, Key Laboratory of Geriatric Diseases of Xinyang Xinyang 464000 China
| | - Ping Tian
- Institute of Inspection Technology, Xinyang Vocational and Technical College, Key Laboratory of Geriatric Diseases of Xinyang Xinyang 464000 China
| | - Xiangyang Guo
- Department of Endocrinology, Xinyang Central Hospital Xinyang 464000 China
| | - Yanping Chen
- Department of Laboratory, Qingdao Women and Children's Hospital No. 6 Tongfu Road, Shibei District Qingdao 266000 China +86-0532-68661155
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135
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Abstract
Cancer is a serious health issue in the world due to a large body of cancer-related human deaths, and there is no current treatment available to efficiently treat the disease as the tumor is often diagnosed at a serious stage. Moreover, Cancer cells are often resistant to chemotherapy, radiotherapy, and molecular-targeted therapy. Upon further knowledge of mechanisms of tumorigenesis, aggressiveness, metastasis, and resistance to treatments, it is necessary to detect the disease at an earlier stage and for a better response to therapy. The hippo pathway possesses the unique capacity to lead to tumorigenesis. Mutations and altered expression of its core components (MST1/2, LATS1/2, YAP and TAZ) promote the migration, invasion, malignancy of cancer cells. The biological significance and deregulation of it have received a large body of interests in the past few years. Further understanding of hippo pathway will be responsible for cancer treatment. In this review, we try to discover the function of hippo pathway in different diversity of cancers, and discuss how Hippo pathway contributes to other cellular signaling pathways. Also, we try to describe how microRNAs, circRNAs, and ZNFs regulate hippo pathway in the process of cancer. It is necessary to find new therapy strategies for cancer.
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Affiliation(s)
- Yanyan Han
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
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136
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Wang H, Feng C, Wang M, Yang S, Wei F. Circular RNAs: Diversity of Functions and a Regulatory Nova in Oral Medicine: A Pilot Review. Cell Transplant 2019; 28:819-830. [PMID: 30945569 PMCID: PMC6719493 DOI: 10.1177/0963689719837917] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Oral diseases, such as cancers, inflammation, loss of bone/tooth/soft tissues, are serious threats to human health since some can cause systemic disease and effective treatments are limited. Thus, discovering promising biomarkers for physiological and pathological processes in oral medicine, and identifying novel targets for therapy have become a most critical issue. Recently, circular RNAs (circRNAs), which were once thought to be a class of non-coding RNAs (ncRNAs), are found to be of coding potential. CircRNAs are highly present in the cytoplasm of eukaryotic cells and are key elements in the physiological and biological processes of various pathological conditions, and are also reflected in oral development and progress. Previous studies have indicated that circRNAs are involved in the initiation and development of different types of diseases and tissues (e.g., cancers, cardiovascular diseases, neural development, growth and development, wood healing, liver regeneration). Moreover, growing evidence demonstrates that circRNAs play vital roles in oral cancers and osteogenic differentiation of periodontal ligament stem cells (PDLSCs). Here, we focus on the biological characteristics of circRNAs, beginning with an overview of previous studies on the functional roles of circRNAs as diagnostic biomarkers and therapeutic targets in oral medicine. We hope this will give us a promising new comprehension of the underlying mechanisms occurring during related biological and pathological progress, and contribute to the development of effective diagnostic biomarkers and therapeutic targets for oral diseases.
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Affiliation(s)
- Hong Wang
- 1 Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China.,2 Department of Orthodontics, School of Stomatology, Shandong University, Jinan, People's Republic of China.,* Both authors contributed equally
| | - Cheng Feng
- 3 Jinan Hospital of Traditional Chinese Medicine, Jinan, People's Republic of China.,* Both authors contributed equally
| | - Meng Wang
- 1 Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China.,2 Department of Orthodontics, School of Stomatology, Shandong University, Jinan, People's Republic of China
| | - Shuangyan Yang
- 1 Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China.,2 Department of Orthodontics, School of Stomatology, Shandong University, Jinan, People's Republic of China
| | - Fulan Wei
- 1 Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China.,2 Department of Orthodontics, School of Stomatology, Shandong University, Jinan, People's Republic of China
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137
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Sekar S, Liang WS. Circular RNA expression and function in the brain. Noncoding RNA Res 2019; 4:23-29. [PMID: 30891534 PMCID: PMC6404376 DOI: 10.1016/j.ncrna.2019.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/04/2019] [Indexed: 01/16/2023] Open
Abstract
Within the last decade, active research on circular RNAs (circRNAs) has dramatically improved our understanding of the expression and function of these non-coding RNAs. While several mechanisms for circRNA function have been proposed, including sequestration of microRNAs and regulation of cellular proteins, studies provide evidence that circRNAs can regulate transcription and may also serve as biomarkers. Due to the heterogeneous nature of the brain, and the dynamic transcriptional mechanisms that support neurobiological pathways, the influence of circRNAs is potentially extensive. Understanding how circRNAs contribute to key neurological pathways will fill gaps in our understanding of brain function and provide valuable insight into novel therapeutic approaches to treat neurological diseases. Here, we review recent research on circRNA expression in the brain, describe the proposed functions of circRNAs, and evaluate the role of circRNAs in neurological diseases.
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138
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Cai H, Li Y, Niringiyumukiza JD, Su P, Xiang W. Circular RNA involvement in aging: An emerging player with great potential. Mech Ageing Dev 2019; 178:16-24. [DOI: 10.1016/j.mad.2018.11.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/25/2018] [Accepted: 11/30/2018] [Indexed: 12/17/2022]
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139
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Tang H, Huang X, Wang J, Yang L, Kong Y, Gao G, Zhang L, Chen ZS, Xie X. circKIF4A acts as a prognostic factor and mediator to regulate the progression of triple-negative breast cancer. Mol Cancer 2019; 18:23. [PMID: 30744636 PMCID: PMC6369546 DOI: 10.1186/s12943-019-0946-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/20/2019] [Indexed: 12/15/2022] Open
Abstract
Background Increasing studies has found that circular RNAs (circRNAs) play vital roles in cancer progression. But the expression profile and function of circRNAs in triple-negative breast cancer (TNBC) are unclear. Methods We used a circRNA microarray to explore the circRNA expression profile of TNBC. The expression of the top upregulated circRNA, circKIF4A, was confirmed by qRT-PCR in breast cancer cell lines and tissues. Kaplan-Meier survival analysis was conducted to analyze the clinical impact of circKIF4A on TNBC. A series of experiments was performed to explore the functions of circKIF4A in TNBC progression, such as cell proliferation and migration. We investigated the regulatory effect of circKIF4A on miRNA and its target genes to explore the potential regulatory mechanisms of circKIF4A in TNBC. Results qRT-PCR analyses verified that circKIF4A was significantly upregulated and positively associated with poorer survival of TNBC. The inhibition of circKIF4A suppressed cell proliferation and migration in TNBC. Luciferase reporter assay and RNA immunoprecipitation assay revealed that circKIF4A and KIF4A could bind to miR-375 and that circKIF4A regulated the expression of KIF4A via sponging miR-375. Conclusions The circKIF4A-miR-375-KIF4A axis regulates TNBC progression via the competitive endogenous RNA (ceRNA) mechanism. circKIF4A may therefore serve as a prognostic biomarker and therapeutic target for TNBC. Electronic supplementary material The online version of this article (10.1186/s12943-019-0946-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hailin Tang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, China
| | - Xiaojia Huang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, China
| | - Jin Wang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, China
| | - Lu Yang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, China
| | - Yanan Kong
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, China
| | - Guanfeng Gao
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, China
| | - Lijuan Zhang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York, 11439, USA.
| | - Xiaoming Xie
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, China.
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140
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Chen Z, Zuo X, Pu L, Zhang Y, Han G, Zhang L, Wu J, Wang X. circLARP4 induces cellular senescence through regulating miR-761/RUNX3/p53/p21 signaling in hepatocellular carcinoma. Cancer Sci 2019; 110:568-581. [PMID: 30520539 PMCID: PMC6361555 DOI: 10.1111/cas.13901] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/22/2018] [Accepted: 11/25/2018] [Indexed: 12/31/2022] Open
Abstract
Circular RNAs (circRNAs), a novel class of non-coding RNAs, have emerged as indispensable modulators in human malignancies. Aberrant cellular senescence is a phenotype observed in various cancers. The association of circRNAs with cellular senescence in tumors is yet to determined. Here, we investigated the role of circLARP4 in cellular senescence and cell proliferation in hepatocellular carcinoma (HCC). Downregulated circLARP4 level was observed in HCC tissues and cell lines. Low expression level of circLARP4 independently predicted poor survival outcome. Gain-of-function and loss-of-function assays demonstrated that circLARP4 suppressed HCC cell proliferation, mediated cell cycle arrest and induced senescence in vitro. Levels of p53 and p21, 2 key regulatory molecules in cellular senescence, were increased in circLARP4-overexpressed HCC cells and decreased in circLARP4-silenced HCC cells. In vivo experiments further confirmed the tumor-suppressing activity of circLARP4. Further mechanistic studies showed that circLARP4 dampened HCC progression by sponging miR-761, thereby promoting the expression level of RUNX3 and activating the downstream p53/p21 signaling. Our study revealed the role of circLARP4/miR-761/RUNX3/p53/p21 signaling in HCC progression, providing a potential survival predictor and therapeutic candidate for HCC.
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Affiliation(s)
- Zhiqiang Chen
- Hepatobiliary CenterThe First Affiliated Hospital of Nanjing Medical UniversityKey Laboratory of Liver TransplantationChinese Academy of Medical SciencesNHC Key Laboratory of Living Donor Liver TransplantationNanjingChina
| | - Xueliang Zuo
- Hepatobiliary CenterThe First Affiliated Hospital of Nanjing Medical UniversityKey Laboratory of Liver TransplantationChinese Academy of Medical SciencesNHC Key Laboratory of Living Donor Liver TransplantationNanjingChina
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalYijishan Hospital of Wannan Medical CollegeWuhuChina
| | - Liyong Pu
- Hepatobiliary CenterThe First Affiliated Hospital of Nanjing Medical UniversityKey Laboratory of Liver TransplantationChinese Academy of Medical SciencesNHC Key Laboratory of Living Donor Liver TransplantationNanjingChina
| | - Yao Zhang
- Hepatobiliary CenterThe First Affiliated Hospital of Nanjing Medical UniversityKey Laboratory of Liver TransplantationChinese Academy of Medical SciencesNHC Key Laboratory of Living Donor Liver TransplantationNanjingChina
| | - Guoyong Han
- Hepatobiliary CenterThe First Affiliated Hospital of Nanjing Medical UniversityKey Laboratory of Liver TransplantationChinese Academy of Medical SciencesNHC Key Laboratory of Living Donor Liver TransplantationNanjingChina
| | - Long Zhang
- Hepatobiliary CenterThe First Affiliated Hospital of Nanjing Medical UniversityKey Laboratory of Liver TransplantationChinese Academy of Medical SciencesNHC Key Laboratory of Living Donor Liver TransplantationNanjingChina
| | - Jindao Wu
- Hepatobiliary CenterThe First Affiliated Hospital of Nanjing Medical UniversityKey Laboratory of Liver TransplantationChinese Academy of Medical SciencesNHC Key Laboratory of Living Donor Liver TransplantationNanjingChina
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Xuehao Wang
- Hepatobiliary CenterThe First Affiliated Hospital of Nanjing Medical UniversityKey Laboratory of Liver TransplantationChinese Academy of Medical SciencesNHC Key Laboratory of Living Donor Liver TransplantationNanjingChina
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141
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Lai RW, Lu R, Danthi PS, Bravo JI, Goumba A, Sampathkumar NK, Benayoun BA. Multi-level remodeling of transcriptional landscapes in aging and longevity. BMB Rep 2019; 52:86-108. [PMID: 30526773 PMCID: PMC6386224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Indexed: 07/15/2024] Open
Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and gene expression has been observed to be deregulated with aging. In this review, we discuss the current knowledge on the transcriptional alterations that have been described to occur with age in metazoans. First, we discuss age-related transcriptional changes in protein-coding genes, the expected functional impact of such changes, and how known pro-longevity interventions impact these changes. Second, we discuss the changes and impact of emerging aspects of transcription in aging, including age-related changes in splicing, lncRNAs and circRNAs. Third, we discuss the changes and potential impact of transcription of transposable elements with aging. Fourth, we highlight small ncRNAs and their potential impact on the regulation of aging phenotypes. Understanding the aging transcriptome will be key to identify important regulatory targets, and ultimately slow-down or reverse aging and extend healthy lifespan in humans. [BMB Reports 2019; 52(1): 86-108].
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Affiliation(s)
| | | | - Prakroothi S. Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089,
USA
| | - Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089,
USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089,
USA
| | - Alexandre Goumba
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089,
USA
| | | | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089,
USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089,
USA
- USC Stem Cell Initiative, Los Angeles, CA 90089,
USA
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142
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Gao D, Qi X, Zhang X, Fang K, Guo Z, Li L. hsa_circRNA_0006528 as a competing endogenous RNA promotes human breast cancer progression by sponging miR-7-5p and activating the MAPK/ERK signaling pathway. Mol Carcinog 2018; 58:554-564. [PMID: 30520151 DOI: 10.1002/mc.22950] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 11/25/2018] [Accepted: 11/27/2018] [Indexed: 12/14/2022]
Abstract
Emerging research has indicated that circular RNAs (circRNAs), a novel class of non-coding RNAs, play a vital role in human tumorigenesis and progression. Our previous results suggested that hsa_circ_0006528 (circ_0006528), a circRNA with an unknown function, mediates adriamycin resistance in human breast cancer cells. However, the role of circ_0006528 in breast cancer progression remains unknown. Here, we investigated the probable involvement of circ_0006528 in breast cancer. We analyzed a cohort of 97 patients and found that circ_0006528 expression was significantly upregulated in human breast cancer tissues compared with that in adjacent non-tumorous tissues and was significantly associated with advanced tumor-node-metastasis (TNM) stage and poor prognosis. In addition, we found that in breast cancer cells, circ_0006528 could promote DNA synthesis and cell proliferation, invasion, and migration. Downregulating circ_0006528 induced G2 phase arrest and cell apoptosis. Further mechanistic studies revealed that circ_0006528 could sponge endogenous miR-7-5p and inhibit its activity. We also identified Raf1, which activates the MAPK/ERK signaling pathway, as a target of miR-7-5p and determined that circ_0006528 promotes breast cancer growth, invasion, and migration by promoting the expression of Raf1 and activates the MAPK/ERK pathway. Thus, this study provides the first evidence of the circ_0006528/miR-7-5p/Raf1/MEK/ERK regulatory network in the development of breast cancer and suggests that circ_0006528 is a potential therapeutic target and prognostic predictor for breast cancer.
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Affiliation(s)
- Danfeng Gao
- Oncology Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Xiaowei Qi
- Department of Pathology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Xiufen Zhang
- Oncology Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Kai Fang
- Oncology Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Zijian Guo
- Department of Oncological Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Lihua Li
- Oncology Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
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143
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MicroRNAs as Diagnostic and Prognostic Biomarkers in Ischemic Stroke-A Comprehensive Review and Bioinformatic Analysis. Cells 2018; 7:cells7120249. [PMID: 30563269 PMCID: PMC6316722 DOI: 10.3390/cells7120249] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/01/2018] [Accepted: 12/02/2018] [Indexed: 12/14/2022] Open
Abstract
Stroke is the second-most common cause of death worldwide. The pathophysiology of ischemic stroke (IS) is related to inflammation, atherosclerosis, blood coagulation, and platelet activation. MicroRNAs (miRNAs) play important roles in physiological and pathological processes of neurodegenerative diseases and progression of certain neurological diseases, such as IS. Several different miRNAs, and their target genes, are recognized to be involved in the pathophysiology of IS. The capacity of miRNAs to simultaneously regulate several target genes underlies their unique value as diagnostic and prognostic markers in IS. In this review, we focus on the role of miRNAs as diagnostic and prognostic biomarkers in IS. We discuss the most common and reliable detection methods available and promising tests currently under development. We also present original results from bioinformatic analyses of published results, identifying the ten most significant genes (HMGB1, YWHAZ, PIK3R1, STAT3, MAPK1, CBX5, CAPZB, THBS1, TNFRSF10B, RCOR1) associated with inflammation, blood coagulation, and platelet activation and targeted by miRNAs in IS. Additionally, we created miRNA-gene target interaction networks based on Gene Ontology (GO) information derived from publicly available databases. Among our most interesting findings, miR-19a-3p is the most widely modulated miRNA across all selected ontologies and might be proposed as novel biomarker in IS to be tested in future studies.
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144
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Xiao M, Feng Y, Liu C, Zhang Z. Prognostic values of long noncoding RNA PVT1 in various carcinomas: An updated systematic review and meta-analysis. Cell Prolif 2018; 51:e12519. [PMID: 30252166 PMCID: PMC6528925 DOI: 10.1111/cpr.12519] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 07/08/2018] [Accepted: 07/10/2018] [Indexed: 12/14/2022] Open
Abstract
Cancers have been a worldwide health problem with a high mortality rate, but ideal biomarkers are not available to effectively screen and diagnose patients. Currently, an increasing number of long noncoding RNAs have been reported to be abnormally expressed in human carcinomas and play a vital role in tumourigenesis. Plasmacytoma variant translocation 1 (PVT1) is upregulated in various carcinomas, and its overexpression is associated with poor survival in cancer patients. We conduct an updated meta-analysis to determine its potential in prognosis for tumours. In total, 14 studies comprising 2435 patients were enrolled according to Reporting Recommendations for Tumour Marker Prognostic Studies guidelines. High PVT1 expression indicated poor overall survival (hazard ratio [HR] = 1.98, 95% confidence interval [CI]: 1.62-2.42, P < 0.00001) and disease-free survival (HR = 1.63, 95% CI: 1.45-1.84, P < 0.00001). Additionally, increased PVT1 expression was positively associated with lymphatic node metastasis (odd ratio [OR] = 2.87, 95% CI: 1.66-4.96, P = 0.0002), distant metastasis (OR = 2.47, 95% CI: 1.74-3.50, P < 0.00001), advanced tumour-node-metastasis stages (OR = 2.59, 95% CI: 1.38-4.88, P = 0.003). New findings highlight that PVT1 acts as competing RNA to microRNAs to protect mRNAs from miRNAs repression. Therefore, we also discuss PVT1-related microRNAs and their interaction in tumourigenesis. In conclusion, PVT1 may be a potential biomarker of poor prognosis for patients with different cancer types.
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Affiliation(s)
- Meizhu Xiao
- Department of Obstetrics and GynecologyBeijing Chaoyang HospitalCapital Medical UniversityBeijingChina
| | - Ying Feng
- Department of Obstetrics and GynecologyBeijing Chaoyang HospitalCapital Medical UniversityBeijingChina
| | - Chongdong Liu
- Department of Obstetrics and GynecologyBeijing Chaoyang HospitalCapital Medical UniversityBeijingChina
| | - Zhenyu Zhang
- Department of Obstetrics and GynecologyBeijing Chaoyang HospitalCapital Medical UniversityBeijingChina
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145
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He X, Su W, Zhou Y, Ge X, Zhou J, Ou C. CircPVT1: a bridge linking Hippo pathway and human cancers. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:S91. [PMID: 30740412 DOI: 10.21037/atm.2018.11.06] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaoyun He
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Endocrinology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Weiping Su
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaolu Ge
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
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146
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Pandey PR, Rout PK, Das A, Gorospe M, Panda AC. RPAD (RNase R treatment, polyadenylation, and poly(A)+ RNA depletion) method to isolate highly pure circular RNA. Methods 2018; 155:41-48. [PMID: 30391514 DOI: 10.1016/j.ymeth.2018.10.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 01/17/2023] Open
Abstract
Recent developments in high-throughput RNA sequencing methods coupled with innovative bioinformatic tools have uncovered thousands of circular (circ)RNAs. CircRNAs have emerged as a vast and novel class of regulatory RNAs with potential to modulate gene expression by acting as sponges for microRNAs (miRNAs) and RNA-binding proteins (RBPs). The biochemical enrichment of circRNAs by exoribonuclease treatment or by depletion of polyadenylated RNAs coupled with deep-sequencing is widely used for the systematic identification of circRNAs. Although these methods enrich circRNAs substantially, they do not eliminate efficiently non-polyadenylated and highly-structured RNAs. Here, we describe a method we termed RPAD, based on initial RNase R treatment followed by Polyadenylation and poly(A)+ RNA Depletion. These joint interventions drastically depleted linear RNAs leading to isolation of highly pure circRNAs from total RNA pools. By facilitating the isolation of highly pure circRNAs, RPAD enables the elucidation of circRNA biogenesis, sequence, and function.
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Affiliation(s)
- Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, MD, USA
| | | | - Aniruddha Das
- Institute of Life Sciences, Bhubaneswar, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, MD, USA.
| | - Amaresh C Panda
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, MD, USA; Institute of Life Sciences, Bhubaneswar, India.
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PWCDA: Path Weighted Method for Predicting circRNA-Disease Associations. Int J Mol Sci 2018; 19:ijms19113410. [PMID: 30384427 PMCID: PMC6274797 DOI: 10.3390/ijms19113410] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
CircRNAs have particular biological structure and have proven to play important roles in diseases. It is time-consuming and costly to identify circRNA-disease associations by biological experiments. Therefore, it is appealing to develop computational methods for predicting circRNA-disease associations. In this study, we propose a new computational path weighted method for predicting circRNA-disease associations. Firstly, we calculate the functional similarity scores of diseases based on disease-related gene annotations and the semantic similarity scores of circRNAs based on circRNA-related gene ontology, respectively. To address missing similarity scores of diseases and circRNAs, we calculate the Gaussian Interaction Profile (GIP) kernel similarity scores for diseases and circRNAs, respectively, based on the circRNA-disease associations downloaded from circR2Disease database (http://bioinfo.snnu.edu.cn/CircR2Disease/). Then, we integrate disease functional similarity scores and circRNA semantic similarity scores with their related GIP kernel similarity scores to construct a heterogeneous network made up of three sub-networks: disease similarity network, circRNA similarity network and circRNA-disease association network. Finally, we compute an association score for each circRNA-disease pair based on paths connecting them in the heterogeneous network to determine whether this circRNA-disease pair is associated. We adopt leave one out cross validation (LOOCV) and five-fold cross validations to evaluate the performance of our proposed method. In addition, three common diseases, Breast Cancer, Gastric Cancer and Colorectal Cancer, are used for case studies. Experimental results illustrate the reliability and usefulness of our computational method in terms of different validation measures, which indicates PWCDA can effectively predict potential circRNA-disease associations.
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148
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Wang L, Tong X, Zhou Z, Wang S, Lei Z, Zhang T, Liu Z, Zeng Y, Li C, Zhao J, Su Z, Zhang C, Liu X, Xu G, Zhang HT. Circular RNA hsa_circ_0008305 (circPTK2) inhibits TGF-β-induced epithelial-mesenchymal transition and metastasis by controlling TIF1γ in non-small cell lung cancer. Mol Cancer 2018; 17:140. [PMID: 30261900 PMCID: PMC6161470 DOI: 10.1186/s12943-018-0889-7] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND TGF-β promotes tumor invasion and metastasis through inducing epithelial-mesenchymal transition (EMT) in non-small cell lung cancer (NSCLC). Circular RNAs (circRNAs) are recognized as functional non-coding RNAs involved in human cancers. However, whether and how circRNAs contribute to TGF-β-induced EMT and metastasis in NSCLC remain vague. Here, we investigated the regulation and function of Circular RNA hsa_circ_0008305 (circPTK2) in TGF-β-induced EMT and tumor metastasis, as well as a link between circPTK2 and transcriptional intermediary factor 1 γ (TIF1γ) in NSCLC. METHODS Circular RNAs were determined by human circRNA Array analysis, real-time quantitative reverse transcriptase PCR and northern blot. Luciferase reporter, RNA-binding protein immunoprecipitation (RIP), RNA pull-down and fluorescence in situ hybridization (FISH) assays were employed to test the interaction between circPTK2 and miR-429/miR-200b-3p. Ectopic overexpression and siRNA-mediated knockdown of circPTK2, TGF-β-induced EMT, Transwell migration and invasion in vitro, and in vivo experiment of metastasis were used to evaluate the function of circPTK2. Transcription and prognosis analyses were done in public databases. RESULTS CircPTK2 and TIF1γ were significantly down-regulated in NSCLC cells undergoing EMT induced by TGF-β. CircPTK2 overexpression augmented TIF1γ expression, inhibited TGF-β-induced EMT and NSCLC cell invasion, whereas circPTK2 knockdown had the opposite effects. CircPTK2 functions as a sponge of miR-429/miR-200b-3p, and miR-429/miR-200b-3p promote TGF-β-induced EMT and NSCLC cell invasion by targeting TIF1γ. CircPTK2 overexpression inhibited the invasion-promoting phenotype of endogenous miR-429/miR-200b-3p in NSCLC cells in response to TGF-β. CircPTK2 overexpression significantly decreased the expression of Snail, an important downstream transcriptional activator of TGF-β/Smad signaling. In an in vivo experiment of metastasis, circPTK2 overexpression suppressed NSCLC cell metastasis. Moreover, circPTK2 expression was dramatically down-regulated and positively correlated with TIF1γ expression in human NSCLC tissues. Especially, circPTK2 was significantly lower in metastatic NSCLC tissues than non-metastatic counterparts. CONCLUSION Our findings show that circPTK2 (hsa_circ_0008305) inhibits TGF-β-induced EMT and metastasis by controlling TIF1γ in NSCLC, revealing a novel mechanism by which circRNA regulates TGF-β-induced EMT and tumor metastasis, and suggesting that circPTK2 overexpression could provide a therapeutic strategy for advanced NSCLC.
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Affiliation(s)
- Longqiang Wang
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
| | - Xin Tong
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
| | - Zhengyu Zhou
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
- Laboratory Animal Center, Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Shengjie Wang
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
- Department of Basic Medicine, Kangda College of Nanjing Medical University, Lianyungang, 222000 China
| | - Zhe Lei
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
| | - Tianze Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150086 Heilongjiang China
| | - Zeyi Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, 215006 Jiangsu China
| | - Yuanyuan Zeng
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, 215006 Jiangsu China
| | - Chang Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, 215006 Jiangsu China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, 215006 Jiangsu China
| | - Zhiyue Su
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
| | - Cuijuan Zhang
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
| | - Xia Liu
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
| | - Guangquan Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150086 Heilongjiang China
| | - Hong-Tao Zhang
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, 199 Ren’ai Road, Suzhou, 215123 Jiangsu China
- Suzhou Key Laboratory for Molecular Cancer Genetics, Suzhou, 215123 Jiangsu China
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149
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Ding J, Zhou W, Li X, Sun M, Ding J, Zhu Q. Tandem DNAzyme for double digestion: a new tool for circRNA suppression. Biol Chem 2018; 400:247-253. [DOI: 10.1515/hsz-2018-0232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/29/2018] [Indexed: 01/08/2023]
Abstract
Abstract
Circular RNA (circRNA) play a crucial role in many biological processes and have been proved as potential biomarkers and therapeutic targets in many diseases. Manipulation of their expression is a critical task. In this study, we developed a new strategy for circRNA suppression with DNAzyme. Data showed single-digestion DNAzymes cleaved circRNA efficiently in vitro but not in cell culture. However, tandem DNAzymes for double digestion showed higher cleavage efficacy both in vitro and in cell culture. Functional study demonstrated that double-digestion DNAzymes suppressed the miRNA sponge function of circRNA and changed the proliferation and migration rates of HCC cells.
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Affiliation(s)
- Junyao Ding
- Xiangya School of Pharmaceutical Sciences in Central South University, 172 Tongzipo Road , Yuelu District, Changsha 410013, Hunan , China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences in Central South University, 172 Tongzipo Road , Yuelu District, Changsha 410013, Hunan , China
| | - Xiaojing Li
- Xiangya School of Pharmaceutical Sciences in Central South University, 172 Tongzipo Road , Yuelu District, Changsha 410013, Hunan , China
| | - Meng Sun
- Xiangya School of Pharmaceutical Sciences in Central South University, 172 Tongzipo Road , Yuelu District, Changsha 410013, Hunan , China
| | - Jingsong Ding
- Xiangya School of Pharmaceutical Sciences in Central South University, 172 Tongzipo Road , Yuelu District, Changsha 410013, Hunan , China
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, 172 Tongzipo Road , Yuelu District, Changsha 410013, Hunan , China
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150
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The emerging landscape of circular RNA in cardiovascular diseases. J Mol Cell Cardiol 2018; 122:134-139. [DOI: 10.1016/j.yjmcc.2018.08.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 06/30/2018] [Accepted: 08/13/2018] [Indexed: 12/22/2022]
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