1
|
Xu WB, Kotheeranurak V, Zhang HL, Feng JY, Liu JW, Chen CM, Lin GX, Rui G. Identification of the circRNA–miRNA–mRNA regulatory network in osteoarthritis using bioinformatics analysis. Front Genet 2022; 13:994163. [PMID: 36186471 PMCID: PMC9523487 DOI: 10.3389/fgene.2022.994163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Osteoarthritis (OA) is a degenerative joint disease that seriously affects the quality of people. Unfortunately, the pathogenesis of OA has not been fully known. Therefore, this study aimed to construct a ceRNA regulatory network related to OA to explore the pathogenesis of OA.Methods: Differentially expressed circRNAs (DEcircRNAs), microRNAs (DEmiRNAs), and mRNAs (DEmRNAs) were obtained from the Gene Expression Omnibus microarray data (GSE175959, GSE105027, and GSE169077). The miRNA response elements and target mRNAs were identified using bioinformatics approaches. Additionally, a circRNA–miRNA–mRNA network was established using Cytoscape version 3.8.0. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of mRNAs in the network were conducted to explore the possible mechanisms underlying OA development. Protein–protein interaction (PPI) analysis was performed to determine the hub genes. Based on the hub genes, a sub network was constructed using Cytoscape 3.8.0 version. Finally, connectivity map (CMap) and drug–gene interaction database (DGIdb) analyses were performed to identify the potential therapeutic targets for OA.Results: Altogether, five DEcircRNAs, 89 DEmiRNAs, and 345 DEmRNAs were identified. Moreover, a circRNA–miRNA–mRNA network was established using three circRNAs, seven miRNAs, and 37 mRNAs. GO and KEGG analyses demonstrated that the mRNAs in the network could be related to the occurrence and development of OA. PPI analysis was performed and six key genes, namely serpin family H member 1 [SERPINH1], collagen type VIII alpha 2 chain [COL8A2], collagen type XV alpha 1 chain [COL15A1], collagen type VI alpha 3 chain [COL6A3], collagen type V alpha 1 chain [COL5A1], and collagen type XI alpha 1 chain [COL11A1], were identified. Furthermore, a circRNA–miRNA–hub gene subnetwork was established in accordance with two circRNAs (hsa_circ_0075320 and hsa_circ_0051428), two miRNAs (hsa-miR-6124 and hsa-miR-1207-5p), and six hub genes (COL11A1, SERPINH1, COL6A3, COL5A1, COL8A2, and COL15A1). Finally, three chemicals (noscapine, diazepam, and TG100-115) based on CMap analysis and two drugs (collagenase Clostridium histolyticum and ocriplasmin) based on DGIdb were discovered as potential treatment options for OA.Conclusion: This study presents novel perspectives on the pathogenesis and treatment of OA based on circRNA-related competitive endogenous RNA regulatory networks.
Collapse
Affiliation(s)
- Wen-Bin Xu
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Vit Kotheeranurak
- Department of Orthopedics, Faculty of Medicine, Chulalongkorn University, and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Center of Excellence in Biomechanics and Innovative Spine Surgery, Chulalongkorn University, Bangkok, Thailand
| | - Huang-Lin Zhang
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Jin-Yi Feng
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jing-Wei Liu
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chien-Min Chen
- Division of Neurosurgery, Department of Surgery, Changhua Christian Hospital, Changhua, Taiwan
- Department of Leisure Industry Management, National Chin-Yi University of Technology, Taichung, Taiwan
- School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- *Correspondence: Chien-Min Chen, ; Guang-Xun Lin, ; Gang Rui,
| | - Guang-Xun Lin
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Chien-Min Chen, ; Guang-Xun Lin, ; Gang Rui,
| | - Gang Rui
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Chien-Min Chen, ; Guang-Xun Lin, ; Gang Rui,
| |
Collapse
|
2
|
Zhang R, Hou Z, Liao K, Yu C, Jing R, Tu C. Expression Profile and Bioinformatics Analysis of Circular RNAs in Patients with Vitiligo. Pharmgenomics Pers Med 2022; 15:785-796. [PMID: 36092681 PMCID: PMC9451056 DOI: 10.2147/pgpm.s371107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Rongxin Zhang
- Institute of Integrative Medicine, Dalian Medical University, Dalian, 116044, People’s Republic of China
- Department of Dermatology, The Second Hospital of Dalian Medical University, Dalian, 116027, People’s Republic of China
| | - Zhao Hou
- Department of Dermatology, The Second Hospital of Dalian Medical University, Dalian, 116027, People’s Republic of China
| | - Kexin Liao
- Department of Dermatology, The Second Hospital of Dalian Medical University, Dalian, 116027, People’s Republic of China
| | - Chao Yu
- Department of Dermatology, The Second Hospital of Dalian Medical University, Dalian, 116027, People’s Republic of China
| | - Rongrong Jing
- Institute of Integrative Medicine, Dalian Medical University, Dalian, 116044, People’s Republic of China
- Department of Dermatology, The Second Hospital of Dalian Medical University, Dalian, 116027, People’s Republic of China
| | - Caixia Tu
- Institute of Integrative Medicine, Dalian Medical University, Dalian, 116044, People’s Republic of China
- Department of Dermatology, The Second Hospital of Dalian Medical University, Dalian, 116027, People’s Republic of China
- Correspondence: Caixia Tu, Department of Dermatology, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116027, People’s Republic of China, Tel +8617709872288, Fax +86 411 84672130, Email
| |
Collapse
|
3
|
Hsa_circ_0000479/Hsa-miR-149-5p/RIG-I, IL-6 Axis: A Potential Novel Pathway to Regulate Immune Response against COVID-19. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:2762582. [PMID: 36081604 PMCID: PMC9448594 DOI: 10.1155/2022/2762582] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/12/2022] [Accepted: 08/08/2022] [Indexed: 12/27/2022]
Abstract
Background. COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global pandemic and mortality of people around the world. Some circular RNAs (circRNAs), one of the new types of noncoding RNAs (ncRNAs), act as competing endogenous RNAs (ceRNAs) and compete with mRNAs for shared miRNAs, to regulate gene expression. In the present study, we aimed to evaluate the expression and roles of hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 in COVID-19 infection. Materials and Methods. After extraction of total RNA from peripheral blood mononuclear cells (PBMC) of 50 patients with symptomatic COVID-19, 50 patients with nonsymptomatic COVID-19, and 50 normal controls, cDNA synthesis was performed. Online in silico tools were applied to evaluate the interaction between the genes in the hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis, and its role in COVID-19-related pathways. Quantification of the expression of these genes and confirmation of their interaction was done using the quantitative real-time PCR (qRT-PCR) technique. Results. The expression levels of hsa_circ_0000479, RIG-I, and IL-6 were increased in COVID-19 patients compared to healthy controls, while hsa-miR-149-5p expression was decreased. Moreover, there was a significant negative correlation between hsa-miR-149-5p and hsa_circ_0000479, RIG-I, IL-6 expressions, and also a positive expression correlation between hsa_circ_0000479 and IL-6, RIG-I. Then, bioinformatics tools revealed the role of hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis in PI3K-AKT and STAT3 signaling pathways. Conclusion. Upregulation of hsa_circ_0000479, RIG-I, and IL-6, and downregulation of hsa-miR-149-5p, along with correlation studies, indicate that hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis could play a role in regulating the immune response against SARS-CoV-2. However, more studies are needed in this area.
Collapse
|
4
|
Zhang Y, Yang Y, Ju H, He X, Sun P, Tian Y, Yang P, Song XX, Yu T, Jiang Z. Comprehensive profile of circRNAs in formaldehyde induced heart development. Food Chem Toxicol 2022; 162:112899. [PMID: 35231573 DOI: 10.1016/j.fct.2022.112899] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/17/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) are a novel type of long non-coding RNAs that can regulate gene expression in heart development and heart disease. However, the expression pattern of circRNAs in congenital heart disease (CHD) induced by formaldehyde exposure is still unknown. We detected circRNAs expression profiles in heart tissue taken from six neonatal rat pups with formaldehyde exposure group and normal group using RNA-sequencing. Results revealed that a total of 54 circRNAs were dysregulated in the formaldehyde exposure group compared to the normal group. Among them, 31 were upregulated and 23 were downregulated (fold change = 2.0, p < 0.0 5). The qRT-qPCR results showed that expressions of 12:628708|632694, 18:77477060|77520779, 5:167486001|167526275 were significantly upregulated, while that of 7:41167312|4116775 and 20:50659751|5068786 were notably downregulated; the expression pattern was consistent with the RNA sequencing data. Bioinformatics analysis shows that the pathogenesis of formaldehyde exposure-induced CHD may involve Hippo-YAP pathway、Notch signaling pathway and other pathways. A key miRNA (rno-miR-665) was identified by constructing a circRNA-miRNA-mRNA co-expression network. In summary, the study illustrated that circRNAs differentially expressed in fetal heart tissues during formaldehyde exposure has potential biological functions and may be a biomarker or therapeutic target for CHD.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, People's Republic of China
| | - Yanyan Yang
- Department of Immunology, Basic Medicine School, Qingdao University, No. 308 Ningxia Road, Qingdao, 266071, People's Republic of China
| | - Hui Ju
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Road No. 16 Jiangsu, Qingdao, 266000, Shandong, People's Republic of China
| | - Xiangqin He
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, People's Republic of China
| | - Pin Sun
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, People's Republic of China
| | - Yu Tian
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, People's Republic of China
| | - Panyu Yang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, People's Republic of China
| | - Xiao-Xia Song
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, People's Republic of China
| | - Tao Yu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, People's Republic of China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Road No. 38 Dengzhou, Qingdao, 266021, People's Republic of China.
| | - Zhirong Jiang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, People's Republic of China.
| |
Collapse
|
5
|
Feng Y, Huang W, Paul C, Liu X, Sadayappan S, Wang Y, Pauklin S. Mitochondrial nucleoid in cardiac homeostasis: bidirectional signaling of mitochondria and nucleus in cardiac diseases. Basic Res Cardiol 2021; 116:49. [PMID: 34392401 PMCID: PMC8364536 DOI: 10.1007/s00395-021-00889-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/20/2021] [Indexed: 01/11/2023]
Abstract
Metabolic function and energy production in eukaryotic cells are regulated by mitochondria, which have been recognized as the intracellular 'powerhouses' of eukaryotic cells for their regulation of cellular homeostasis. Mitochondrial function is important not only in normal developmental and physiological processes, but also in a variety of human pathologies, including cardiac diseases. An emerging topic in the field of cardiovascular medicine is the implication of mitochondrial nucleoid for metabolic reprogramming. This review describes the linear/3D architecture of the mitochondrial nucleoid (e.g., highly organized protein-DNA structure of nucleoid) and how it is regulated by a variety of factors, such as noncoding RNA and its associated R-loop, for metabolic reprogramming in cardiac diseases. In addition, we highlight many of the presently unsolved questions regarding cardiac metabolism in terms of bidirectional signaling of mitochondrial nucleoid and 3D chromatin structure in the nucleus. In particular, we explore novel techniques to dissect the 3D structure of mitochondrial nucleoid and propose new insights into the mitochondrial retrograde signaling, and how it regulates the nuclear (3D) chromatin structures in mitochondrial diseases.
Collapse
Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford, OX3 7LD, UK
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA
| | - Christian Paul
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA
| | - Xingguo Liu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Sakthivel Sadayappan
- Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford, OX3 7LD, UK.
| |
Collapse
|
6
|
Qu F, Wang L, Wang C, Yu L, Zhao K, Zhong H. Circular RNA circ_0006168 enhances Taxol resistance in esophageal squamous cell carcinoma by regulating miR-194-5p/JMJD1C axis. Cancer Cell Int 2021; 21:273. [PMID: 34022910 PMCID: PMC8141117 DOI: 10.1186/s12935-021-01984-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/13/2021] [Indexed: 12/24/2022] Open
Abstract
Background Chemoresistance is one of the major obstacles for cancer therapy in the clinic. Circular RNAs (circRNAs) are involved in the pathogenesis of esophageal squamous cell carcinoma (ESCC) and chemoresistance. This study aimed to explore the role and molecular mechanism of circ_0006168 in Taxol resistance of ESCC. Methods The expression levels of circ_0006168, microRNA-194-5p (miR-194-5p) and jumonji domain containing 1C (JMJD1C) were measured by quantitative real-time polymerase chain reaction (qRT-PCR) or western blot. The half-inhibition concentration (IC50) value of Taxol was evaluated by Cell Counting Kit-8 (CCK-8) assay. Cell proliferation was evaluated by CCK-8 and colony formation assays. Cell migration and invasion were detected by transwell assay. Cell apoptosis was determined by flow cytometry. The interaction between miR-194-5p and circ_0006168 or JMJD1C was predicted by bioinformatics analysis (Circinteractome and TargetScan) and verified by dual-luciferase reporter and RNA Immunoprecipitation (RIP) and RNA pull-down assays. The mice xenograft model was established to investigate the roles of circ_0006168 in vivo. Results Circ_0006168 and JMJD1C were upregulated and miR-194-5p was downregulated in ESCC tissues, ESCC cells, and Taxol-resistant cells. Functionally, knockdown of circ_0006168 or JMJD1C increased Taxol sensitivity of ESCC in vitro via inhibiting cell proliferation, migration and invasion, and promoting apoptosis. Moreover, circ_0006168 could directly bind to miR-194-5p and JMJD1C was verified as a direct target of miR-194-5p. Mechanically, circ_0006168 was a sponge of miR-194-5p to regulate JMJD1C expression in ESCC cells. Furthermore, JMJD1C overexpression reversed the promotive effect of circ_0006168 knockdown on Taxol sensitivity. Besides, circ_0006168 silence suppressed tumor growth in vivo. Conclusion Circ_0006168 facilitated Taxol resistance in ESCC by regulating miR-194-5p/JMJD1C axis, providing a promising therapeutic target for ESCC chemotherapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01984-y.
Collapse
Affiliation(s)
- Fanyong Qu
- Department of Radiation Oncology, Yantai Affiliated Hospital of Binzhou Medical University, No. 717, Jinbu Street, Mu ping District, Yantai, Shandong, 264100, China.
| | - Lina Wang
- Department of Oncology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, 264100, China
| | - Caiyan Wang
- Department of Gastroenterology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, 264100, China
| | - Lingxia Yu
- Department of Oncology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, 264100, China
| | - Kaikai Zhao
- Department of Radiation Oncology, Yantai Affiliated Hospital of Binzhou Medical University, No. 717, Jinbu Street, Mu ping District, Yantai, Shandong, 264100, China
| | - Hao Zhong
- Department of Radiation Oncology, Yantai Affiliated Hospital of Binzhou Medical University, No. 717, Jinbu Street, Mu ping District, Yantai, Shandong, 264100, China
| |
Collapse
|
7
|
Chen P, Li C, Huang H, Liang L, Zhang J, Li Q, Wang Q, Zhang S, Zeng K, Zhang X, Liang J. Circular RNA profiles and the potential involvement of down-expression of hsa_circ_0001360 in cutaneous squamous cell carcinogenesis. FEBS Open Bio 2021; 11:1209-1222. [PMID: 33569895 PMCID: PMC8016141 DOI: 10.1002/2211-5463.13114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 12/27/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) act as sponges of noncoding RNAs and have been implicated in many pathophysiological processes, including tumor development and progression. However, their roles in cutaneous squamous cell carcinoma (cSCC) are not yet well understood. This study aimed to identify differentially expressed circRNAs and their potential functions in cutaneous squamous cell carcinogenesis. The expression profiles of circRNAs in three paired cSCC and adjacent nontumorous tissues were detected with RNA sequencing and bioinformatics analysis. The candidate circRNAs were validated by PCR, Sanger sequencing and quantitative RT‐PCR in another five matched samples. The biological functions of circRNAs in SCL‐1 cells were assessed using circRNA silencing and overexpression, 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium inner salt (MTS), flow cytometry, transwell and colony formation assays. In addition, the circRNA–miRNA–mRNA interaction networks were predicted by bioinformatics. In summary, 1115 circRNAs, including 457 up‐regulated and 658 down‐regulated circRNAs (fold change ≥ 2 and P < 0.05), were differentially expressed in cSCC compared with adjacent nontumorous tissues. Of four selected circRNAs, two circRNAs (hsa_circ_0000932 and hsa_circ_0001360) were confirmed to be significantly decreased in cSCC using PCR, Sanger sequencing and quantitative RT‐PCR. Furthermore, hsa_circ_0001360 silencing was found to result in a significant increase of the proliferation, migration and invasion but a significant decrease of apoptosis in SCL‐1 cells in vitro, whereas hsa_circ_0001360 overexpression showed the opposite regulatory effects. hsa_circ_0001360 was predicted to interact with five miRNAs and their corresponding genes. In conclusion, circRNA dysregulation may play a critical role in carcinogenesis of cSCC, and hsa_circ_0001360 may have potential as a biomarker for cSCC.
Collapse
Affiliation(s)
- Pingjiao Chen
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Changxing Li
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Liuping Liang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jing Zhang
- Institute of Dermatology, Guangzhou Medical University, China.,Department of Dermatology, Guangzhou Institute of Dermatology, China
| | - Qian Li
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qi Wang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sanquan Zhang
- Institute of Dermatology, Guangzhou Medical University, China.,Department of Dermatology, Guangzhou Institute of Dermatology, China
| | - Kang Zeng
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xibao Zhang
- Institute of Dermatology, Guangzhou Medical University, China.,Department of Dermatology, Guangzhou Institute of Dermatology, China
| | - Jingyao Liang
- Institute of Dermatology, Guangzhou Medical University, China.,Department of Dermatology, Guangzhou Institute of Dermatology, China
| |
Collapse
|
8
|
Vidal AF. Read-through circular RNAs reveal the plasticity of RNA processing mechanisms in human cells. RNA Biol 2020; 17:1823-1826. [PMID: 32783578 PMCID: PMC7714478 DOI: 10.1080/15476286.2020.1805233] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 01/22/2023] Open
Abstract
In the human genome, there are several genes whose primary transcripts are both canonically and non-canonically spliced to generate mRNAs and RNA circles, respectively. These RNA circles are a novel class of long non-coding RNAs that became known as circular RNAs (circRNAs). Recently, a new type of circRNA was discovered and called read-through circRNAs (rt-circRNAs). They are hybrid circles that include coding exons from two adjacent and similarly oriented genes. The function of rt-circRNAs, as well as the impact of read-through transcription in our transcriptome, remains to be elucidated. Although we have just begun to scratch it, here I discussed some insights that these fascinating circRNAs are already giving us about the plasticity of RNA processing in our cells.
Collapse
Affiliation(s)
- Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Brazil
- Graduate Program of Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| |
Collapse
|
9
|
Bao H, Zhou Q, Li Q, Niu M, Chen S, Yang P, Liu Z, Xia L. Differentially expressed circular RNAs in a murine asthma model. Mol Med Rep 2020; 22:5412-5422. [PMID: 33173985 PMCID: PMC7647044 DOI: 10.3892/mmr.2020.11617] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/25/2020] [Indexed: 01/14/2023] Open
Abstract
Allergic asthma is one of the most common allergic diseases; however, the mechanisms underlying its development have yet to be fully elucidated. Although allergic diseases are inheritable, genetic variance alone cannot explain the notable increase in the prevalence of allergic diseases over a short period of time in recent decades. Recently, research focus has been shifting to epigenetic factors, such as non-coding RNAs. Circular RNAs (circRNAs) are involved in the pathogenesis of various diseases. The aim of the present study was to further elucidate the etiology of allergic asthma by analyzing aberrantly expressed circRNAs in a murine asthma model. A mouse model of house dust mite allergen-induced asthma was established, and the qualified libraries were sequenced using next-generation sequencing. The expression levels of circRNAs were validated by reverse transcription-quantitative PCR (RT-qPCR) analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for biological pathway classification and enrichment analysis of the aberrantly expressed circRNAs. In addition, the interaction network of the differentially expressed circRNAs and microRNAs (miRNAs) was constructed using Cytoscape. By next-generation sequencing, a total of 150 circRNAs were revealed to be upregulated and 130 were downregulated in the murine asthma model group compared with in the control group. GO and KEGG analyses demonstrated that the differentially expressed circRNAs were mainly involved in processes such as ‘autoimmune disease’, ‘cell adhesion molecules (CAMs)’ and ‘endocytosis’, among others. The expression levels of six circRNAs, namely three upregulated (circ_0000909, circ_0000629 and circ_0000455) and three downregulated (circ_0001454, circ_0000723 and circ_0001389) circRNAs, were validated by RT-qPCR. In conclusion, the analyses suggested that circRNAs performed critical functions via endocytosis (such as macrophage endocytosis), cell adhesion molecules and lipid metabolism in allergic asthma. The interaction network revealed that certain miRNAs that may serve a role in asthma could be regulated by the differentially expressed circRNAs.
Collapse
Affiliation(s)
- Hui Bao
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Qiuyan Zhou
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Qiuju Li
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Mengmeng Niu
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Sanfeng Chen
- Department of Internal Medicine, Aged Care Hospital of Hangzhou, Hangzhou, Zhejiang 310015, P.R. China
| | - Pingchang Yang
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Zhigang Liu
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Lixin Xia
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| |
Collapse
|
10
|
Guerra BS, Lima J, Araujo B, Torres LB, Santos J, Machado D, Cunha E, Serrato JA, de Souza JS, Martins JV, Scalabrin EE, Herai RH. Biogenesis of circular RNAs and their role in cellular and molecular phenotypes of neurological disorders. Semin Cell Dev Biol 2020; 114:1-10. [PMID: 32893132 DOI: 10.1016/j.semcdb.2020.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 01/04/2023]
Abstract
Circular RNA (circRNA) is an unusual class of RNA-like structures composed by exonic and/or intronic sequences that are regulated by the backsplicing mechanism and by the spliceosome-mediated machinery. These circular transcripts tend to accumulate during aging in several human tissues, especially in the mammalian brain, and their expression is correlated with the occurrence of several human pathologies, including a broad spectrum of neurological disorders. Previous findings have also shown that circRNAs are significantly present in the neuronal tissue and are up-regulated during neurogenesis, with a significant number been derived from neural genes, suggesting these circular molecules are involved in the cellular and molecular phenotype of our brain. However, the complete biogenesis, the many types of circRNA molecules, and their involvement with neuronal phenotype and with the occurrence of pathologies are still a challenging avenue for researchers. In this updated review, we discuss the current findings of the biogenesis and the diversity of cirRNAs and their molecular involvement in neurological tissue phenotype. We also discuss how some circRNAs can act as sponge molecules, regulating the activity of microRNA expression over gene translation. Finally, we also show the correlation of altered circRNA expression in neurological disorders.
Collapse
Affiliation(s)
- B S Guerra
- Experimental Multiuser Laboratory, Graduate Program in Health Sciences (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil
| | - J Lima
- Department of Biotechnology, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil; Immunology Department, Biomedical Science Institute, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Bhs Araujo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, SP, Brazil
| | - L B Torres
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Jcc Santos
- Neuroscience laboratory, Department of Neurology and Neurosurgery, Federal University of São Paulo - UNIFESP/EPM, São Paulo, SP, 04039-002, Brazil
| | - Djs Machado
- Department of Biotechnology, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil
| | - Ebb Cunha
- Experimental Multiuser Laboratory, Graduate Program in Health Sciences (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil; Division of Genetic Research, AnaclinGENE, Genetics Laboratory, Curitiba, PR, Brazil
| | - J A Serrato
- Department of Biotechnology, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil
| | - J S de Souza
- Departamento de Medicina, Laboratório de Endocrinologia e Medicina Translacional, Universidade Federal de São Paulo, UNIFESP/EPM, Rua Pedro de Toledo, 669 - 11 andar, São Paulo, SP, 04039-032, Brazil; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - J V Martins
- Graduate Program in Informatics (PPGia), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, Brazil
| | - E E Scalabrin
- Graduate Program in Informatics (PPGia), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, Brazil
| | - R H Herai
- Experimental Multiuser Laboratory, Graduate Program in Health Sciences (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil; Scientific Department, Lico Kaesemodel Institute (ILK), Curitiba, PR, Brazil.
| |
Collapse
|
11
|
Han S, Kuang M, Sun C, Wang H, Wang D, Liu Q. Circular RNA hsa_circ_0076690 acts as a prognostic biomarker in osteoporosis and regulates osteogenic differentiation of hBMSCs via sponging miR-152. Aging (Albany NY) 2020; 12:15011-15020. [PMID: 32717724 PMCID: PMC7425508 DOI: 10.18632/aging.103560] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/04/2020] [Indexed: 05/15/2023]
Abstract
OBJECTIVE Osteoporosis is the most common skeletal disease world-wide. The aim of this study is to identify potential circRNA biomarkers for osteoporosis diagnosis and treatment, as well as their roles in regulating osteogenic differentiation. RESULTS Hsa_circ_0076690 expression was significantly decreased in osteoporosis patients compared to control and showed an acceptable diagnostic value in clinical samples. Subsequently, hsa_circ_0076690 was identified to act as a sponge of miR-152. The expression of hsa_circ_0076690 was gradually increased during osteogenic differentiation while miR-152 showed a decreased expression trend. Moreover, osteogenic differentiation was promoted by hsa_circ_0076690 over-expression and remain unchanged by miR-152/hsa_circ_0076690 co-overexpression. CONCLUSIONS In conclusion, our study revealed that hsa_circ_0076690 may act as a potential diagnostic biomarker for osteoporosis patients and hsa_circ_0076690 could regulate osteogenic differentiation of hBMSCs via sponging miR-152. MATERIALS AND METHODS A total of 114 participants were enrolled in this study with ethics approvals. CircRNAs were identified by means of RNA-sequencing and qRT-PCR experiment. The clinical significance was measured by ROC curve analysis. Target relationship was validated by luciferase reporter assay. The osteogenic-associated biomarkers and ALP activity were detected by western blots.
Collapse
Affiliation(s)
- Shijie Han
- Department of Orthopedics, The Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, PR China
| | - Mingjie Kuang
- Department of Orthopedics, The Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, PR China
| | - Chao Sun
- Department of Orthopedics, The Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, PR China
| | - Haifeng Wang
- Department of Orthopedics, The Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, PR China
| | - Dachuan Wang
- Department of Orthopedics, The Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, PR China
| | - Qian Liu
- Department of Pain, Qilu Hospital of Shandong University, Jinan 250012, Sahndong, PR China
| |
Collapse
|
12
|
Cavalcante GC, Magalhães L, Ribeiro-dos-Santos Â, Vidal AF. Mitochondrial Epigenetics: Non-Coding RNAs as a Novel Layer of Complexity. Int J Mol Sci 2020; 21:E1838. [PMID: 32155913 PMCID: PMC7084767 DOI: 10.3390/ijms21051838] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/29/2020] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are organelles responsible for several functions involved in cellular balance, including energy generation and apoptosis. For decades now, it has been well-known that mitochondria have their own genetic material (mitochondrial DNA), which is different from nuclear DNA in many ways. More recently, studies indicated that, much like nuclear DNA, mitochondrial DNA is regulated by epigenetic factors, particularly DNA methylation and non-coding RNAs (ncRNAs). This field is now called mitoepigenetics. Additionally, it has also been established that nucleus and mitochondria are constantly communicating to each other to regulate different cellular pathways. However, little is known about the mechanisms underlying mitoepigenetics and nuclei-mitochondria communication, and also about the involvement of the ncRNAs in mitochondrial functions and related diseases. In this context, this review presents the state-of-the-art knowledge, focusing on ncRNAs as new players in mitoepigenetic regulation and discussing future perspectives of these fields.
Collapse
Affiliation(s)
- Giovanna C. Cavalcante
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Researches, Federal University of Pará, Rua dos Mundurucus, 4487, 66073-005 Belém, PA, Brazil
| | - Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| |
Collapse
|
13
|
Jiang X, Ning Q. Circular RNAs as novel regulators, biomarkers and potential therapies in fibrosis. Epigenomics 2019; 11:1107-1116. [DOI: 10.2217/epi-2019-0001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Fibrosis is the excess deposition of extracellular matrix components which ultimately leads to the disruption of organ architecture and loss of function. Circular RNAs (circRNAs) are a newly discovered type of long noncoding RNAs with single-stranded covalently closed loops. It is known that circRNAs are novel regulators of gene expression via various ways, including miRNA sponge, protein sponge, regulation of transcription and post transcription. Recently, a growing body of evidence suggests that circular RNAs are also involved in tissue fibrosis in several organs. In this review, we summarized current studies of circular RNAs in fibrosis and hopefully aid in better understanding the molecular mechanism of fibrosis and provide a basis to explore new therapeutic targets of fibrosis.
Collapse
Affiliation(s)
- Xiaoying Jiang
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, PR China
| | - Qilan Ning
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, PR China
| |
Collapse
|
14
|
Wu J, Zhou Q, Niu Y, Chen J, Zhu Y, Ye S, Xi Y, Wang F, Qiu H, Bu S. Aberrant expression of serum circANRIL and hsa_circ_0123996 in children with Kawasaki disease. J Clin Lab Anal 2019; 33:e22874. [PMID: 30843267 PMCID: PMC6595332 DOI: 10.1002/jcla.22874] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/27/2018] [Accepted: 02/10/2019] [Indexed: 12/19/2022] Open
Abstract
Background Kawasaki disease is a childhood systemic vasculitis that causes coronary artery abnormalities. The etiology remains unknown and there are no specific diagnostic tests. Circular non‐coding RNAs are a special class of endogenous RNAs that display some characteristics of an ideal biomarker. However, few studies have examined the expression of circRNAs in the serum of Kawasaki disease (KD) patients. The aim of this study was to identify circRNAs in the serum that can serve as potential biomarkers for KD diagnosis. Methods The cases were children diagnosed with KD (n = 56). The controls comprised healthy children (n = 56). Blood was collected from the patients before and after intravenous immunoglobulin therapy, and from the healthy controls. Levels of circANRIL and hsa_circ_0123996 in the serum were measured by quantitative reverse transcription PCR. Then, the potential relationship between serum circRNA levels and patients’ biochemical parameter levels was investigated. Receiver operating characteristic curves were constructed for evaluating the diagnostic value of these circRNAs. Results The serum levels of circANRIL were lower in patients with KD before therapy than in the controls, but became higher in the patients after therapy than before therapy. The serum levels of hsa_circ_0123996 were higher in patients with KD before therapy than in healthy controls. Conclusion Our study indicated that the circANRIL and hsa_circ_0123996 levels in the serum of patients with KD were significantly different from those in healthy individuals. circANRIL and hsa_circ_0123996 may become potential biomarkers for early KD diagnosis.
Collapse
Affiliation(s)
- Junhua Wu
- The Ningbo Women and Children's Hospital, Ningbo, China
| | - Qianqin Zhou
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| | - Yadan Niu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| | - Jiayi Chen
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| | - Yingchao Zhu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| | - Shazhou Ye
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| | - Yang Xi
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| | - Fuyan Wang
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| | - Haiyan Qiu
- The Ningbo Women and Children's Hospital, Ningbo, China
| | - Shizhong Bu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| |
Collapse
|
15
|
Zhang G, Diao S, Zhang T, Chen D, He C, Zhang J. Identification and characterization of circular RNAs during the sea buckthorn fruit development. RNA Biol 2019; 16:354-361. [PMID: 30681395 DOI: 10.1080/15476286.2019.1574162] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
As a rising star of noncoding RNA, circular RNAs (circRNAs) have a covalently closed loop structure, which formed by 3'-5' ligation during splicing. A few circRNAs were identified and thought to be transcriptional noise due to cognitive defect over the past 40 years. Recently, with the development of high-throughput RNA sequencing techniques and specific algorithms for circRNA detection and quantification, plenty of potential circRNAs were identified in many species which play important roles in various biological processes. However, researches on circRNAs in fruit ripening process were lacking. Here, we totally identified 2616 circRNAs in sea buckthorn fruit development process, which uniformly distributed in sea buckthorn chromosome. Among them, 1721 (65.8%) circRNAs were arising from the exons of their host genes, 252 circRNAs were identified as the differentially expressed circRNAs (DEcircRNAs) between three different development stages, and 181 (71.8%) DEcircRNAs had sequence similarity with 235 identified circRNAs from five know plant species. Functional annotation revealed that host genes of DEcircRNAs were predicted to be involved in carotenoid biosynthesis, lipid synthesis and plant hormone signal transduction. Additionally, 53 DEcircRNAs were predicted as the corresponding nine miRNAs sponges in sea buckthorn. Divergent reverse-transcription PCR and RT-qPCR were used for validate the differential expression and back-splicing sites of six DEcircRNAs. These results revealed the role of circRNAs in sea buckthorn fruit ripening process and promoted the noncoding RNA researches in plants.
Collapse
Affiliation(s)
- Guoyun Zhang
- a State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration , Research Institute of Forestry, Chinese Academy of Forestry , Beijing , China
| | - Songfeng Diao
- a State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration , Research Institute of Forestry, Chinese Academy of Forestry , Beijing , China.,b Non-timber Forestry Research and Development Center, Chinese Academy of Forestry , Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Forestry Administration , Zhengzhou , China
| | - Tong Zhang
- a State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration , Research Institute of Forestry, Chinese Academy of Forestry , Beijing , China
| | - Daoguo Chen
- a State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration , Research Institute of Forestry, Chinese Academy of Forestry , Beijing , China
| | - Caiyun He
- a State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration , Research Institute of Forestry, Chinese Academy of Forestry , Beijing , China
| | - Jianguo Zhang
- a State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration , Research Institute of Forestry, Chinese Academy of Forestry , Beijing , China.,c Collaborative Innovation Center of Sustainable Forestry in Southern China , Nanjing Forestry University , Nanjing , China
| |
Collapse
|
16
|
Sharma D, Sehgal P, Hariprakash J, Sivasubbu S, Scaria V. Methods for Annotation and Validation of Circular RNAs from RNAseq Data. Methods Mol Biol 2019; 1912:55-76. [PMID: 30635890 DOI: 10.1007/978-1-4939-8982-9_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Circular RNAs are an emerging class of transcript isoforms created by unique back splicing of exons to form a closed covalent circular structure. While initially considered as product of aberrant splicing, recent evidence suggests unique functions and conservation across evolution. While circular RNAs could be largely attributed to have little or no potential to encode for proteins, recent evidence points to at least a small subset of circular RNAs which encode for peptides. Circular RNAs are also increasingly shown to be biomarkers for a number of diseases including neurological disorders and cancer. The advent of deep sequencing has enabled large-scale identification of circular RNAs in human and other genomes. A number of computational approaches have come up in recent years to query circular RNAs on a genome-wide scale from RNA-seq data. In this chapter, we describe the application and methodology of identifying circular RNAs using three popular computational tools: FindCirc, Segemehl, and CIRI along with approaches for experimental validation of the unique splice junctions.
Collapse
Affiliation(s)
- Disha Sharma
- G.N. Ramachandran Knowledge Center for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Paras Sehgal
- Academy of Scientific and Innovative Research (AcSIR), CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Judith Hariprakash
- G.N. Ramachandran Knowledge Center for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sridhar Sivasubbu
- Academy of Scientific and Innovative Research (AcSIR), CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Vinod Scaria
- G.N. Ramachandran Knowledge Center for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.
| |
Collapse
|
17
|
Qu S, Hao X, Song W, Niu K, Yang X, Zhang X, Shang R, Wang Q, Li H, Liu Z. Circular RNA circRHOT1 is upregulated and promotes cell proliferation and invasion in pancreatic cancer. Epigenomics 2019; 11:53-63. [PMID: 30444423 DOI: 10.2217/epi-2018-0051] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We aimed to identify the roles of circRHOT1 in pancreatic cancer. Materials & methods: The circRHOT1 was acquired from our previous study followed by quantitative real-time PCR and fluorescence in situ hybridization validation in pancreatic cancer. We used siRNA and shRNA to explore the function of circRHOT1 in pancreatic cancer cells. Bioinformatic analyses were applied to study the potential mechanism of circRHOT1. Results: The circRHOT1 was upregulated in pancreatic cancer and predominantly located in the cytoplasm. Reducing the circRHOT1 expression may inhibit the pancreatic cancer cell proliferation, invasion and migration. The circRHOT1 may play a role in pancreatic cancer through binding miR-26b, miR-125a, miR-330 and miR-382 to regulate multiple tumor-associated pathways. Conclusion: This study demonstrated that circRHOT1 may serve as an oncogenic circRNA that promotes tumor progression.
Collapse
Affiliation(s)
- Shibin Qu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Xiaokun Hao
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
- Department of General Surgery, 141 Hospital, Xi'an, PR China
| | - Wenjie Song
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Kunwei Niu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Xisheng Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Xuan Zhang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Runze Shang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Quancheng Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Haimin Li
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Zhengcai Liu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| |
Collapse
|
18
|
Xiong DD, Dang YW, Lin P, Wen DY, He RQ, Luo DZ, Feng ZB, Chen G. A circRNA-miRNA-mRNA network identification for exploring underlying pathogenesis and therapy strategy of hepatocellular carcinoma. J Transl Med 2018; 16:220. [PMID: 30092792 PMCID: PMC6085698 DOI: 10.1186/s12967-018-1593-5] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) have received increasing attention in human tumor research. However, there are still a large number of unknown circRNAs that need to be deciphered. The aim of this study is to unearth novel circRNAs as well as their action mechanisms in hepatocellular carcinoma (HCC). METHODS A combinative strategy of big data mining, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and computational biology was employed to dig HCC-related circRNAs and to explore their potential action mechanisms. A connectivity map (CMap) analysis was conducted to identify potential therapeutic agents for HCC. RESULTS Six differently expressed circRNAs were obtained from three Gene Expression Omnibus microarray datasets (GSE78520, GSE94508 and GSE97332) using the RobustRankAggreg method. Following the RT-qPCR corroboration, three circRNAs (hsa_circRNA_102166, hsa_circRNA_100291 and hsa_circRNA_104515) were selected for further analysis. miRNA response elements of the three circRNAs were predicted. Five circRNA-miRNA interactions including two circRNAs (hsa_circRNA_104515 and hsa_circRNA_100291) and five miRNAs (hsa-miR-1303, hsa-miR-142-5p, hsa-miR-877-5p, hsa-miR-583 and hsa-miR-1276) were identified. Then, 1424 target genes of the above five miRNAs and 3278 differently expressed genes (DEGs) on HCC were collected. By intersecting the miRNA target genes and the DEGs, we acquired 172 overlapped genes. A protein-protein interaction network based on the 172 genes was established, with seven hubgenes (JUN, MYCN, AR, ESR1, FOXO1, IGF1 and CD34) determined from the network. The Gene Oncology, Kyoto Encyclopedia of Genes and Genomes and Reactome enrichment analyses revealed that the seven hubgenes were linked with some cancer-related biological functions and pathways. Additionally, three bioactive chemicals (decitabine, BW-B70C and gefitinib) based on the seven hubgenes were identified as therapeutic options for HCC by the CMap analysis. CONCLUSIONS Our study provides a novel insight into the pathogenesis and therapy of HCC from the circRNA-miRNA-mRNA network view.
Collapse
Affiliation(s)
- Dan-dan Xiong
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi Zhuang Autonomous Region People’s Republic of China
| | - Yi-wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi Zhuang Autonomous Region People’s Republic of China
| | - Peng Lin
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi Zhuang Autonomous Region People’s Republic of China
| | - Dong-yue Wen
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi Zhuang Autonomous Region People’s Republic of China
| | - Rong-quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi Zhuang Autonomous Region People’s Republic of China
| | - Dian-zhong Luo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi Zhuang Autonomous Region People’s Republic of China
| | - Zhen-bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi Zhuang Autonomous Region People’s Republic of China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi Zhuang Autonomous Region People’s Republic of China
| |
Collapse
|
19
|
Zhu P, Ge N, Liu D, Yang F, Zhang K, Guo J, Liu X, Wang S, Wang G, Sun S. Preliminary investigation of the function of hsa_circ_0006215 in pancreatic cancer. Oncol Lett 2018; 16:603-611. [PMID: 29930719 DOI: 10.3892/ol.2018.8652] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/07/2018] [Indexed: 02/07/2023] Open
Abstract
The incidence of pancreatic cancer is increasing annually in Asia as a whole. Pancreatic cancer ranks sixth in terms of incidence of all malignant tumors. Circular RNA (circRNA) is a type of non-coding RNA which forms a covalently closed continuous loop. CircRNA is extensively expressed in the cytoplasm, and is markedly conservative and stable. MicroRNA (miR)-378a-3p and human (hsa)_circ_0006215 were detected using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in tissue and cells. Western blot analysis detected the SERPINA4 and hsa_circ_0006215 expression in tissue. A Cell Counting Kit-8 assay was used to determine cell stability. Flow cytometry was used to determine the cell apoptotic rate. Transwell assays were used to determine cell migration. hsa_circ_0006215 was identified as a significantly upregulated circRNA. RT-qPCR results verified that, in 30 samples of pancreatic cancer tissue and paracancerous tissue, hsa_circ_0006215 expression was increased in pancreatic cancer tissue, miR-378a-3p expression was decreased in pancreatic cancer tissue, and SERPINA4 expression was increased in pancreatic cancer tissue (P<0.05). Using bioinformatics database and bioinformatics analysis, the interaction network of hsa_circ_0006215 indicated that this circRNA was most likely to regulate the expression of miR-378a-3p. Further interaction analysis revealed that the SERPINA4 gene was a regulatory target gene most likely to have an influence. The present study identified the effects of hsa_circ_0006215, miR-378a-3p and SERPINA4 signaling pathways in pancreatic cancer cells.
Collapse
Affiliation(s)
- Ping Zhu
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Nan Ge
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Dongyan Liu
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Fan Yang
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Kai Zhang
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Jintao Guo
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xiang Liu
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Sheng Wang
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Guoxin Wang
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Siyu Sun
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| |
Collapse
|
20
|
Liang J, Wu X, Sun S, Chen P, Liang X, Wang J, Ruan J, Zhang S, Zhang X. Circular RNA expression profile analysis of severe acne by RNA-Seq and bioinformatics. J Eur Acad Dermatol Venereol 2018; 32:1986-1992. [PMID: 29573483 DOI: 10.1111/jdv.14948] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/01/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND Acne is a common chronic skin disease with a multifactorial aetiology and pathogenesis. Recently, circular RNAs (circRNAs) have been identified as a key factor in regulating gene expression through circRNA-miRNA-mRNA networks in many biological processes and human diseases. However, the circRNAs expression in patients with acne is still unknown. OBJECTIVE To investigate circRNA expression profile in severe acne. METHODS The expression profile of circRNAs in three paired lesional skin and adjacent non-lesional skin in severe acne was detected by high-throughput RNA sequencing technology and bioinformatics analysis. The candidate circRNAs were validated by PCR, Sanger sequencing and qRT-PCR in the separate group (n = 4). The circRNA-miRNA-mRNA interaction networks were predicted. RESULTS A total of 538 circRNAs including 271 up- and 267 downregulated circRNAs were differentially expressed in lesional skin compared with adjacent non-lesional skin in severe acne. Gene Ontology and KEGG pathway enrichment analyses revealed that the aberrantly expressed circRNAs were primarily involved in inflammatory, metabolism and immune responses. Five candidate circRNAs (circRNA_0084927, circRNA_0001073, circRNA_0005941, circRNA_0086376 and circRNA_0018168) were validated to have significant decrease in severe acne by PCR, Sanger sequencing and qRT-PCR, in agreement with the results from RNA-Seq data analysis. The five identified circRNAs were predicted to interact with 213 miRNAs and regulated target gene expression. CONCLUSION This study firstly showed that circRNAs were differentially expressed in severe acne and suggested that circRNAs could be used as a potential biomarker for the drug targets of acne.
Collapse
Affiliation(s)
- J Liang
- Institute of Dermatology, Guangzhou Medical University, Guangzhou, China.,Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, China
| | - X Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - S Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - P Chen
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - X Liang
- Institute of Dermatology, Guangzhou Medical University, Guangzhou, China.,Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, China
| | - J Wang
- Institute of Dermatology, Guangzhou Medical University, Guangzhou, China.,Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, China
| | - J Ruan
- Department of Dermatology, Jinan University Medical School Affiliated Hospital of Dongguan, Dongguan, China
| | - S Zhang
- Institute of Dermatology, Guangzhou Medical University, Guangzhou, China.,Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, China
| | - X Zhang
- Institute of Dermatology, Guangzhou Medical University, Guangzhou, China.,Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, China
| |
Collapse
|
21
|
Lei W, Feng T, Fang X, Yu Y, Yang J, Zhao ZA, Liu J, Shen Z, Deng W, Hu S. Signature of circular RNAs in human induced pluripotent stem cells and derived cardiomyocytes. Stem Cell Res Ther 2018. [PMID: 29523209 PMCID: PMC5845222 DOI: 10.1186/s13287-018-0793-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Circular RNAs (circRNAs) are regarded as a novel class of noncoding RNA regulators. Although a number of circRNAs have been identified by bioinformatics analysis of RNA-seq data, tissue and disease-specific circRNAs are still to be uncovered to promote their application in basic research and clinical practice. The purpose of this study was to explore the circRNA profiles in human induced pluripotent stem cells (hiPSCs) and hiPSC-derived cardiomyocytes (hiPSC-CMs), and to identify cardiac or disease-specific circRNAs. Methods hiPSCs were generated from fibroblasts, and then further differentiated to hiPSC-CMs by modulating WNT signaling in RPMI+B27 medium. Following high-throughput RNA sequencing, circRNAs were extracted and quantified by a combined strategy known as CIRCexplorer. Integrative analysis was performed to illuminate the correlation between circRNAs and their parental linear isoforms. Cardiac and disease-specific expression of circRNAs was confirmed by quantitative reverse-transcription PCR. Results In this study, a total of 5602 circRNAs were identified in hiPSCs and hiPSC-CMs. Our data indicated, for the first time, more enriched expression of circRNAs in differentiated cardiomyocytes than in undifferentiated hiPSCs. In addition to the host gene-dependent expression, our integrative analysis also identified a number of circRNAs showing host gene-independent expression in hiPSCs and hiPSC-CMs. CircRNAs including circSLC8A1, circCACNA1D, circSPHKAP and circALPK2 showed cardiac-selective expression during cardiac differentiation and human heart-specific enrichment in fetal tissues. Furthermore, circSLC8A1 abnormally increased in heart tissues from patients suffering from dilated cardiomyopathy. Conclusions CircRNAs are highly enriched in hiPSC-differentiated CMs, and cardiac-specific circRNAs such as circSLC8A1, circCACNA1D, circSPHKAP and circALPK2 may serve as biomarkers of CMs. Detection of the excessive expression of circSLC8A1 provides a potential approach for pathological status indication of heart disease. Electronic supplementary material The online version of this article (10.1186/s13287-018-0793-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wei Lei
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China.,Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China
| | - Tingting Feng
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China.,Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China
| | - Xing Fang
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China.,Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China
| | - You Yu
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China.,Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China
| | - Junjie Yang
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China.,Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China
| | - Zhen-Ao Zhao
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China.,Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China
| | - Junwei Liu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhenya Shen
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China. .,Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China.
| | - Wenbo Deng
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Shijun Hu
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China. .,Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China.
| |
Collapse
|
22
|
Zhang M, Xin Y. Circular RNAs: a new frontier for cancer diagnosis and therapy. J Hematol Oncol 2018; 11:21. [PMID: 29433541 PMCID: PMC5809913 DOI: 10.1186/s13045-018-0569-5] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/06/2018] [Indexed: 01/17/2023] Open
Abstract
In recent years, circular RNAs (circRNAs) have attracted considerable attention because they play a significant role in many fields of cancer biology. Additionally, it has become increasingly clear that circRNAs have the potential to make contributions to the successful application of individualized cancer medicine. This brief review introduces circRNAs by describing their potential as a biomarker and therapeutic target and discussing the possible strategies to target them. This review also presents the challenges that are encountered by circRNAs for their definitive entry into clinical practice. Clearly, our understanding of circRNAs helps to add a new dimension to the molecular structure of cancer and will provide many new opportunities for cancer treatment.
Collapse
Affiliation(s)
- Miaoci Zhang
- Laboratory of Gastrointestinal Onco-Pathology, Cancer Institute & General Surgery Institute, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, Liaoning Province, 110001, China
| | - Yan Xin
- Laboratory of Gastrointestinal Onco-Pathology, Cancer Institute & General Surgery Institute, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, Liaoning Province, 110001, China.
| |
Collapse
|
23
|
Yang F, Zhu P, Guo J, Liu X, Wang S, Wang G, Liu W, Wang S, Ge N. Circular RNAs in thoracic diseases. J Thorac Dis 2017; 9:5382-5389. [PMID: 29312749 DOI: 10.21037/jtd.2017.10.143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs with continuous, covalently closed circular structures. Investigators have shown previously that circRNAs are regulators of gene expression in mammals. These tissue-specific transcripts are produced primarily by exonic or intronic sequences of housekeeping genes. Several biosynthetic models have been proposed for circRNAs, and consensus is lacking. CircRNAs are widely expressed in the cytoplasm and highly conserved, what is more, unlike other noncoding RNAs, circRNAs are relatively stable. These properties suggest special roles of circRNAs, such as microRNA (miRNA) sponges, regulators of selective splicing, or even protein-coding sequences. The expression of circRNAs is associated with many pathologic conditions; therefore, circRNAs may have utility as biomarker for the diagnosis or prediction of diseases. Authors previously have demonstrated that circRNAs can regulate the expression of a variety of disease-related miRNAs. The circRNA-miRNA-target gene interaction network regulates several pathways that inhibit or promote the occurrence of certain diseases. Based on their potential clinical relevance, circRNAs are a crucial topic of disease prevention and treatment research. Herein, we review current research regarding circRNAs and explore their potential clinical applications for thoracic diseases diagnosis and treatment.
Collapse
Affiliation(s)
- Fan Yang
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Ping Zhu
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jintao Guo
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xiang Liu
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Sheng Wang
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Guoxin Wang
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Wen Liu
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Shupeng Wang
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Nan Ge
- Endoscopy Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
| |
Collapse
|
24
|
Vidal AF, Ribeiro-Dos-Santos AM, Vinasco-Sandoval T, Magalhães L, Pinto P, Anaissi AKM, Demachki S, de Assumpção PP, Dos Santos SEB, Ribeiro-Dos-Santos Â. The comprehensive expression analysis of circular RNAs in gastric cancer and its association with field cancerization. Sci Rep 2017; 7:14551. [PMID: 29109417 PMCID: PMC5673933 DOI: 10.1038/s41598-017-15061-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/18/2017] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs comprise a new class of long noncoding RNAs characterized by their 5' and 3' ends covalently joined. Previous studies have demonstrated that some circular RNAs act as microRNA sponges, and are associated with cellular proliferation in cancer. We were the first to analyze the global expression of circular RNAs in samples of patients without gastric cancer, gastric cancer, and matched tumor-adjacent gastric tissue. Among the samples, we identified 736 previously annotated circular RNAs by RNA-Seq. The tumor-adjacent tissue presented the higher abundance of circular RNAs and could not be considered as a normal tissue, reinforcing the notion of field effect in gastric cancer. We identified five differentially expressed circular RNAs that may be potential biomarkers of this type of cancer. We also predicted candidate microRNAs targets of the highest expressed circular RNAs in gastric tissues and found five miRNAs. Overall, our results support the hypothesis of circular RNAs representing a novel factor in the dynamic epigenetic network of gene regulation, which involves the microRNAs, its mRNAs targets, and the circular RNAs-derived genes. Further studies are needed to elucidate the roles and the functional relevance of the circular RNAs in human diseases.
Collapse
Affiliation(s)
- Amanda Ferreira Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Pablo Pinto
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Ana K M Anaissi
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - Samia Demachki
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | | | - Sidney Emanuel Batista Dos Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará, Brazil.
- Center of Oncology Research, Federal University of Pará, Belém, Pará, Brazil.
| |
Collapse
|
25
|
Fang Y, Ma M, Wang J, Liu X, Wang Y. Circular RNAs play an important role in late-stage gastric cancer: Circular RNA expression profiles and bioinformatics analyses. Tumour Biol 2017. [PMID: 28639908 DOI: 10.1177/1010428317705850] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Gastric cancer is one of the most common tumors of the digestive system. Here, analysis of the expression profiles of circular RNAs in advanced gastric adenocarcinoma and adjacent normal mucosa tissues revealed differential expression of 306 circular RNAs, among which 273 were predicted to exert regulatory effects on target microRNAs. The downstream pathway networks of circular RNA-microRNA were mapped and the node genes were identified. In particular, we found that the expression of hsa_circ_0058246 was elevated in tumor specimens of patients with poor clinical outcomes. Our collective findings indicate that circular RNAs play a critical role in gastric cancer tumorigenesis. Data from this study provide a new perspective on the molecular pathways underlying metastasis and recurrence of gastric cancer and highlight potential therapeutic targets that may contribute to more effective diagnosis and treatment of the disease.
Collapse
Affiliation(s)
- Yantian Fang
- Department of Gastric Cancer and Soft Tissue Sarcomas, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Minzhe Ma
- Department of Gastric Cancer and Soft Tissue Sarcomas, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jiangli Wang
- Department of Gastric Cancer and Soft Tissue Sarcomas, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaowen Liu
- Department of Gastric Cancer and Soft Tissue Sarcomas, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yanong Wang
- Department of Gastric Cancer and Soft Tissue Sarcomas, Fudan University Shanghai Cancer Center, Shanghai, China
| |
Collapse
|
26
|
Meng YB, He X, Huang YF, Wu QN, Zhou YC, Hao DJ. Long Noncoding RNA CRNDE Promotes Multiple Myeloma Cell Growth by Suppressing miR-451. Oncol Res 2017; 25:1207-1214. [PMID: 28276319 PMCID: PMC7841033 DOI: 10.3727/096504017x14886679715637] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
It has been determined that long noncoding RNAs (lncRNAs) are identified as a potential regulatory factor in multiple tumors as well as multiple myeloma (MM). However, the role of colorectal neoplasia differentially expressed (CRNDE) in the pathogenesis of MM remains unclear. In this study, we found that the CRNDE expression level, in MM samples and cell lines, is higher than that in the control detected by real-time qPCR, which is also closely related to tumor progression and poor survival in MM patients. Knockdown of CRNDE significantly inhibits the proliferative vitality of MM cells (U266 and RPMI-8226), induces cell cycle arrest in the G0/G1 phase, and promotes apoptosis. After being transfected with siRNA, miR-451 expression observably increases. Bioinformatics analysis and luciferase assay reveal the interaction by complementary bonding between CRNDE and miR-451. Pearson’s correlation shows that CRNDE is negatively correlated to miR-451 expression in human MM samples. Subsequently, miR-451 inhibitor rescues the inhibited tumorigenesis induced by CRNDE knockdown. Our study illustrates that lncRNA CRNDE induces the proliferation and antiapoptosis capability of MM by acting as a ceRNA or molecular sponge via negatively targeting miR-451, which could act as a novel diagnostic marker and therapeutic target for MM.
Collapse
|
27
|
Escudero-Hernández C, Martínez-Abad B, Ruipérez V, Garrote JA, Arranz E. New IL-15 receptor-α splicing variants identified in intestinal epithelial Caco-2 cells. Innate Immun 2016; 23:44-53. [PMID: 27794069 DOI: 10.1177/1753425916674263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
IL-15 is a pleiotropic cytokine related to IL-2 which acts at a broader level than its counterpart. It is presented through its specific high-affinity receptor, IL-15Rα. Both cytokine and receptor are tightly regulated at multiple levels and are widely distributed. Thus, deregulation of their expression leads to an inflammatory immune response. Variants of splicing of IL-15Rα have been described in immune and barrier cells; however, their presence has not been focused on intestinal epithelial cells. In this study, we describe five new alternative variants of splicing of IL-15Rα in Caco-2 cells. Four of them were expressed into proteins inside Caco-2 cells, but these were unable to bind IL-15 or to follow the secretory pathway. However, the expression of mRNA itself might be relevant to diseases such as celiac disease, inflammatory bowel disease or colorectal cancer.
Collapse
Affiliation(s)
- Celia Escudero-Hernández
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain
| | - Beatriz Martínez-Abad
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain
| | - Violeta Ruipérez
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain
| | - José A Garrote
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain.,2 Laboratory of Molecular Genetics, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Eduardo Arranz
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain
| |
Collapse
|
28
|
Cao D, Ding Q, Yu W, Gao M, Wang Y. Long noncoding RNA SPRY4-IT1 promotes malignant development of colorectal cancer by targeting epithelial-mesenchymal transition. Onco Targets Ther 2016; 9:5417-25. [PMID: 27621655 PMCID: PMC5012848 DOI: 10.2147/ott.s111794] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The clinical significance and biological functions of long noncoding RNA SPRY4 intronic transcript 1 (SPRY4-IT1) in colorectal cancer (CRC) remain largely unclear. Herein, we are the first to report that the SPRY4-IT1 was significantly upregulated in CRC tissues, serum, and cells. Higher SPRY4-IT1 expression was markedly associated with advanced Tumor Node Metastasis (TNM) stage in a cohort of 84 CRC patients. Multivariate analyses indicated that SPRY4-IT1 expression could be useful as an independent predictor for overall survival. Further in vitro experiments revealed that knockdown of SPRY4-IT1 inhibited the proliferation, migration, and invasion of CRC cells and induced cell cycle arrestment. Moreover, we confirmed that the expression of epithelial–mesenchymal transition-related genes was modulated through alteration of SPRY4-IT1 expression. These results suggest that SPRY4-IT1, as an oncogenic regulator, may serve as a candidate prognostic marker and potential target for CRC therapies.
Collapse
Affiliation(s)
- Dong Cao
- Department of General Surgery, The People's Hospital of Putuo, Zhoushan
| | - Qiong Ding
- Department of General Surgery, The People's Hospital of Putuo, Zhoushan
| | - Wubin Yu
- Department of General Surgery, The People's Hospital of Putuo, Zhoushan
| | - Ming Gao
- Department of General Surgery, The People's Hospital of Putuo, Zhoushan
| | - Yilian Wang
- Department of Cardiology, The Second People's Hospital of Lianyungang, Xinpu, People's Republic of China
| |
Collapse
|