1
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Zhang W, Wei C, Wang L. Identification of Key lncRNAs, circRNAs, and mRNAs in Osteoarthritis via Bioinformatics Analysis. Mol Biotechnol 2024; 66:1660-1672. [PMID: 37382793 DOI: 10.1007/s12033-023-00790-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/09/2023] [Indexed: 06/30/2023]
Abstract
Osteoarthritis (OA) is a common degenerative joint disorder that adversely affects the quality of life of patients. Identification of novel diagnostic biomarkers is pivotal for the early detection and prevention of OA. Dataset GSE185059 was selected from Gene Expression Omnibus database to obtain differentially expressed lncRNAs (DE-lncRNAs), mRNAs (DE-mRNAs), and circRNAs (DE-circRNAs) between OA and normal samples. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as protein-protein interaction (PPI) network construction of DE-mRNAs were conducted. Hub genes were identified from PPI networks and validated by RT-qPCR. starBase database was utilized for predicting miRNAs binding with hub genes, selected DE-lncRNAs and DE-circRNAs, respectively. The competing endogenous RNA (ceRNA) networks were constructed. A total of 818 DE-mRNAs, 191 DE-lncRNAs, and 2053 DE-circRNAs were identified. The DE-mRNAs were significantly enriched in several inflammation-related GO terms and KEGG pathways such as positive regulation of cell-cell adhesion, TNF-alpha signaling pathway and NF-kappa B signaling pathway. Thirteen hub genes were identified, which were CFTR, GART, SMAD2, NCK1, TJP1, UBE2D1, EFTUD2, PRKACB, IL10, SNRPG, CHD4, RPS24, and SRSF6. OA-related DE-lncRNA/circRNA-miRNA-hub gene networks were constructed. We identified 13 hub genes and constructed the ceRNA networks related to OA, providing a theoretical basis for further research.
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Affiliation(s)
- Wenjing Zhang
- Department of Rheumatic Immunity, Changzhi People's Hospital, No. 502, Changxing Middle Road, Luzhou District, Changzhi, 046099, Shanxi, China
| | - Chun Wei
- Department of Rheumatic Immunity, Changzhi People's Hospital, No. 502, Changxing Middle Road, Luzhou District, Changzhi, 046099, Shanxi, China
| | - Ling Wang
- Department of Rheumatic Immunity, Changzhi People's Hospital, No. 502, Changxing Middle Road, Luzhou District, Changzhi, 046099, Shanxi, China.
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2
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Nopora A, Weidle UH. CircRNAs as New Therapeutic Entities and Tools for Target Identification in Acute Myeloid Leukemia. Cancer Genomics Proteomics 2024; 21:118-136. [PMID: 38423599 PMCID: PMC10905271 DOI: 10.21873/cgp.20434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 03/02/2024] Open
Abstract
Acute myeloid leukemia (AML) is a genetically extremely heterogeneous disease. Drug resistance after induction therapy is a very frequent event resulting in poor medium survival times. Therefore, the identification of new targets and treatment modalities is a medical high priority issue. We addressed our attention to circular RNAs (circRNAs), which can act as oncogenes or tumor suppressors in AML. We searched the literature (PubMed) and identified eight up-regulated and two down-regulated circ-RNAs with activity in preclinical in vivo models. In addition, we identified twenty-two up-regulated and four down-regulated circRNAs with activity in preclinical in vitro systems, but pending in vivo activity. Up-regulated RNAs are potential targets for si- or shRNA-based approaches, and down-regulated circRNAs can be reconstituted by replacement therapy to achieve a therapeutic benefit in preclinical systems. The up-regulated targets can be tackled with small molecules, antibody-based entities, or other modes of intervention. For down-regulated targets, up-regulators must be identified. The ranking of the identified circRNAs with respect to therapy of AML will depend on further target validation experiments.
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Affiliation(s)
- Adam Nopora
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | - Ulrich H Weidle
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
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3
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Zhou Q, Shu X, Chai Y, Liu W, Li Z, Xi Y. The non-coding competing endogenous RNAs in acute myeloid leukemia: biological and clinical implications. Biomed Pharmacother 2023; 163:114807. [PMID: 37150037 DOI: 10.1016/j.biopha.2023.114807] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematologic carcinoma that has seen a considerable improvement in patient prognosis because of genetic diagnostics and molecularly-targeted therapies. Nevertheless, recurrence and drug resistance remain significant obstacles to leukemia treatment. It is critical to investigate the underlying molecular mechanisms and find solutions. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), circular RNAs, long non-coding RNAs, and pseudogenes, have been found to be crucial components in driving cancer. The competing endogenous RNA (ceRNA) mechanism has expanded the complexity of miRNA-mediated gene regulation. A great deal of literature has shown that ncRNAs are essential to the biological functions of the ceRNA network (ceRNET). NcRNAs can compete for the same miRNA response elements to influence miRNA-target RNA interactions. Recent evidence suggests that ceRNA might be a potential biomarker and therapeutic strategy. So far, however, there have been no comprehensive studies on ceRNET about AML. What is not yet clear is the clinical application of ceRNA in AML. This study attempts to summarize the development of research on the related ceRNAs in AML and the roles of ncRNAs in ceRNET. We also briefly describe the mechanisms of ceRNA and ceRNET. What's more significant is that we explore the clinical value of ceRNAs to provide accurate diagnostic and prognostic biomarkers as well as therapeutic targets. Finally, limitations and prospects are considered.
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Affiliation(s)
- Qi Zhou
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Xiaojun Shu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Vascular Surgery, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yihong Chai
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Wenling Liu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Zijian Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yaming Xi
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.
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Identification of Circular RNA Circ_0003256 as a Novel Player in Pediatric Acute Myeloid Leukemia. J Pediatr Hematol Oncol 2023; 45:29-37. [PMID: 36598961 DOI: 10.1097/mph.0000000000002372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/26/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Aberrant expression of circular RNAs (circRNAs) is tightly associated with the pathogenesis of human cancers, including pediatric acute myeloid leukemia (AML). In this report, we sought to define the precise action of circ_0003256 in the pathogenesis of pediatric AML. MATERIALS AND METHODS Circ_0003256, microRNA (miR)-582-3p, and protein kinase cAMP-activated catalytic subunit beta (PRKACB) were quantified by quantitative real-time polymerase chain reaction and Western blot. Cell proliferation, cycle distribution, and apoptosis were estimated by MTT, 5-ethynyl-2'-deoxyuridine, and flow cytometry assays, respectively. Direct relationships among circ_0003256, miR-582-3p, and PRKACB were verified by a dual-luciferase reporter and RNA pull-down assays. RESULTS Our data indicated that circ_0003256 was highly expressed in pediatric AML patients and cells. Suppression of circ_0003256 hindered cell proliferation and promoted apoptosis in THP-1 and MV4-11 cells. Mechanistically, circ_0003256 contained functional binding sites for miR-582-3p, and circ_0003256 suppression influenced cell behaviors by upregulating miR-582-3p. MiR-582-3p directly targeted and inhibited PRKACB and the inhibition of PRKACB phenocopied miR-582-3p overexpression in regulating cell functional behaviors. Moreover, circ_0003256 involved the posttranscriptional regulation of PRKACB through miR-582-3p. CONCLUSION Our findings identify that suppression of circ_0003256 impedes the malignant behaviors of pediatric AML cells by regulating PRKACB expression by competing for shared miR-582-3p.
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Du J, Jia F, Wang L. Advances in the Study of circRNAs in Hematological Malignancies. Front Oncol 2022; 12:900374. [PMID: 35795049 PMCID: PMC9250989 DOI: 10.3389/fonc.2022.900374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/23/2022] [Indexed: 11/26/2022] Open
Abstract
Circular RNAs (circRNAs) are non–protein-coding RNAs that have a circular structure and do not possess a 5` cap or 3` poly-A tail. Their structure is more stable than that of linear RNAs, and they are difficult to deform via hydrolysis. Advancements in measurement technology such as RNA sequencing have enabled the detection of circRNAs in various eukaryotes in both in vitro and in vivo studies. The main function of circRNAs involves sponging of microRNAs (MiRNAs) and interaction with proteins associated with physiological and pathological processes, while some circRNAs are involved in translation. circRNAs act as tumor suppressors or oncogenes during the development of many tumors and are emerging as new diagnostic and prognostic biomarkers. They also affect resistance to certain chemotherapy drugs such as imatinib. The objective of this review is to investigate the expression and clinical significance of circRNAs in hematological malignancies. We will also explore the effect of circRNAs on proliferation and apoptosis in hematological malignancy cells and their possible use as biomarkers or targets to determine prognoses. The current literature indicates that circRNAs may provide new therapeutic strategies for patients with hematologic malignancies.
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Affiliation(s)
- Jingyi Du
- School of Clinical Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Central Laboratory, Linyi People’s Hospital, Linyi, China
| | - Feiyu Jia
- Department of Education and Teaching, Linyi People’s Hospital, Linyi, China
- *Correspondence: Lijuan Wang, ; Feiyu Jia,
| | - Lijuan Wang
- Central Laboratory, Linyi People’s Hospital, Linyi, China
- Linyi Key Laboratory of Tumor Biology, Linyi, China
- *Correspondence: Lijuan Wang, ; Feiyu Jia,
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Ye Q, Li N, Zhou K, Liao C. Homo sapiens circular RNA 0003602 (Hsa_circ_0003602) accelerates the tumorigenicity of acute myeloid leukemia by modulating miR-502-5p/IGF1R axis. Mol Cell Biochem 2022; 477:635-644. [PMID: 34988853 DOI: 10.1007/s11010-021-04277-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022]
Abstract
Acute myeloid leukemia (AML) has become a worldwide malignant cancer. We intended to investigate the critical roles and mechanism underlying homo sapiens circular RNA 0003602 (hsa_circ_0003602) in AML progression, especially in tumor cell proliferation, migration, invasion, and apoptosis. Real-time PCR was applied to identify the differential expression of hsa_circ_0003602 and miR-502-5p in AML bone marrow tissues and cell lines. In addition, western blot analysis was employed to determine the levels insulin-like growth factor 1 receptor (IGF1R) protein. The biological behaviors were assessed by CCK-8 cell viability assay, flow cytometry assay for apoptosis detection, and Transwell migration and invasion assay. The relationships between target miRNA and downstream mRNA were investigated by bioinformatics, luciferase reporter assay, and biotin-labeled RNA pull-down assay. Hsa_circ_0003602 was upregulated and predicted poor survival in AML. Knockdown of hsa_circ_0003602 in AML cell lines induced the inhibition of proliferation, migration, and invasion and caused apoptosis. Hsa_circ_0003602 sequestered miR-502-5p by functioning as a competitive endogenous RNA (ceRNA), thereby regulating IGF1R expression. Hsa_circ_0003602 acted as a tumor promoter in AML via miR-502-5p/IGF1R axis. Our study provides evidence that hsa_circ_0003602, miR-502-5p, and IGF1R might form a regulatory axis to affect the carcinogenicity of AML cells and provide potential targets for the treatment of AML.
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MESH Headings
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- HL-60 Cells
- Humans
- K562 Cells
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Receptor, IGF Type 1/genetics
- Receptor, IGF Type 1/metabolism
- Signal Transduction
- THP-1 Cells
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Affiliation(s)
- Qidong Ye
- Department of Pediatrics, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, No. 59 Liuting Street, Ningbo, 315000, Zhejiang Province, People's Republic of China.
| | - Nan Li
- Department of Pediatrics, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, No. 59 Liuting Street, Ningbo, 315000, Zhejiang Province, People's Republic of China
| | - Kai Zhou
- Department of Pediatrics, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, No. 59 Liuting Street, Ningbo, 315000, Zhejiang Province, People's Republic of China
| | - Cong Liao
- Department of Pediatrics, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, No. 59 Liuting Street, Ningbo, 315000, Zhejiang Province, People's Republic of China
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Zhang M, Bai X, Zeng X, Liu J, Liu F, Zhang Z. circRNA-miRNA-mRNA in breast cancer. Clin Chim Acta 2021; 523:120-130. [PMID: 34537217 DOI: 10.1016/j.cca.2021.09.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022]
Abstract
Among cancers, breast cancer has the highest incidence rate among women and poses a tremendous threat to women's health. Messenger RNA (mRNA), microRNA (miRNA) and circular RNA (circRNA) play vital roles in the progression of breast cancer through a variety of biological effects and mechanisms. Recently, the regulatory network formed by circRNAs, miRNAs and mRNAs has piqued attention and garnered interest. CircRNAs bind to miRNAs through a regulatory mechanism in which endogenous RNAs compete to indirectly regulate the expression of mRNA corresponding to downstream target genes of miRNAs, contributing to the progression of breast cancer. The circRNA-miRNA-mRNA axis may be a marker for the early diagnosis and prognosis of breast cancer and a potential breast cancer treatment target, providing unlimited possibilities for the development of breast cancer biomarkers and therapeutic strategies. This article reviews recent research progress on the circRNA-miRNA-mRNA axis as a regulatory network of competing endogenous RNAs in breast cancer. Herein, we focus on the mechanism and function of the circRNA-miRNA-mRNA axis in the occurrence and metastasis of breast cancer, and resistance to chemotherapy.
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Affiliation(s)
- Meilan Zhang
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang 421001, China
| | - Xue Bai
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang 421001, China
| | - Xuemei Zeng
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang 421001, China
| | - Jiangrong Liu
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang 421001, China
| | - Feng Liu
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang 421001, China
| | - Zhiwei Zhang
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang 421001, China
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Shang Z, Ming X, Wu J, Xiao Y. Downregulation of circ_0012152 inhibits proliferation and induces apoptosis in acute myeloid leukemia cells through the miR-625-5p/SOX12 axis. Hematol Oncol 2021; 39:539-548. [PMID: 34097310 DOI: 10.1002/hon.2895] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/18/2021] [Accepted: 05/31/2021] [Indexed: 12/18/2022]
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous disease featured by a clonal proliferation derived from primitive hematopoietic stem/progenitor cells. Circular RNAs (circRNAs) have been identified as crucial regulators in the progression of various cancers, including AML. However, the molecular mechanism of AML is still not definite. This study aimed to explore the influences of circ_0012152 on cell development in AML cells and the underlying regulatory mechanism. The expression of circ_0012152, microRNA-625-5p (miR-625-5p) and sex-determining region Y-related high mobility group box 12 (SOX12) was detected by quantitative real-time polymerase chain reaction. The proliferation of AML cells was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay for cell viability, 5-ethynyl-2'-deoxyuridine incorporation assay for DNA biosynthesis and flow cytometry for cell cycle distribution, respectively. The death of AML cells was detected by flow cytometry. The protein expression was assessed by Western blot assay. Dual-luciferase reporter and RNA immunoprecipitation assays were carried out to examine the relationships among circ_0012152, miR-625-5p and SOX12. The expression of circ_0012152 was increased in AML tissues and cells and circ_0012152 knockdown suppressed proliferation and promoted death in AML cells. Further exploration revealed that circ_0012152 inhibited miR-625-5p expression and downregulation of miR-625-5p overturned the effects of circ_0012152 knockdown on proliferation and death in AML cells. Moreover, miR-625-5p targeted SOX12 and circ_0012152 facilitated the expression of SOX12 by relieving miR-625-5p-mediated inhibitory effect on SOX12 in AML cells. Circ_0012152 knockdown suppressed cell proliferation and promoted death by targeting SOX12 mediated by miR-625-5p in AML cells.
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Affiliation(s)
- Zhen Shang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Ming
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaying Wu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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